Index

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

a - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList.ViewSetupPrecursor

a - Variable in class net.preibisch.mvrecon.fiji.ImgLib2Temp.ValuePair

a - Variable in class net.preibisch.mvrecon.fiji.ImgLib2Temp.ValueTriple

a - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.PairError

a - Variable in class net.preibisch.mvrecon.headless.definedataset.StackList.ViewSetupPrecursor

A - Variable in class net.preibisch.legacy.registration.bead.laplace.DoGMaximum

absolute() - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Sets each component of this tuple to its absolute value.

absolute() - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Sets each component of this tuple to its absolute value.

absolute() - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Sets each component of this tuple to its absolute value.

absolute() - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Sets each component of this tuple to its absolute value.

absolute() - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Sets each component of this tuple to its absolute value.

absolute(Tuple3d) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Sets each component of the tuple parameter to its absolute value and places the modified values into this tuple.

absolute(Tuple3f) - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Sets each component of the tuple parameter to its absolute value and places the modified values into this tuple.

absolute(Tuple3i) - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Sets each component of the tuple parameter to its absolute value and places the modified values into this tuple.

absolute(Tuple4d) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Sets each component of the tuple parameter to its absolute value and places the modified values into this tuple.

absolute(Tuple4f) - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Sets each component of the tuple parameter to its absolute value and places the modified values into this tuple.

absoluteDownsampling - Variable in class net.preibisch.mvrecon.process.n5api.N5ApiTools.MultiResolutionLevelInfo

absoluteDownsamplingDouble() - Method in class net.preibisch.mvrecon.process.n5api.N5ApiTools.MultiResolutionLevelInfo

absoluteDownsamplingInt() - Method in class net.preibisch.mvrecon.process.n5api.N5ApiTools.MultiResolutionLevelInfo

absoluteThreshold - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters

AbstractDetection<T> - Class in net.preibisch.legacy.registration.detection

AbstractDetection(int, double[]) - Constructor for class net.preibisch.legacy.registration.detection.AbstractDetection

AbstractDetection(int, double[], double) - Constructor for class net.preibisch.legacy.registration.detection.AbstractDetection

AbstractImgFactoryImgLoader - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

AbstractImgFactoryImgLoader() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AbstractImgFactoryImgLoader

AbstractImgLoader - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

AbstractImgLoader() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AbstractImgLoader

AbstractPointDescriptor<P,F> - Class in net.preibisch.mvrecon.process.pointcloud.pointdescriptor

AbstractPointDescriptor(P, ArrayList<P>, SimilarityMeasure, Matcher) - Constructor for class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.AbstractPointDescriptor

AbstractTransformedImgRandomAccess<T> - Class in net.preibisch.mvrecon.process.fusion.transformed

AbstractTransformedImgRandomAccess(RandomAccessibleInterval<T>, InterpolatorFactory<FloatType, RandomAccessible<FloatType>>, boolean, float, FloatType, long[]) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedImgRandomAccess

AbstractTransformedImgRandomAccessible<T> - Class in net.preibisch.mvrecon.process.fusion.transformed

AbstractTransformedImgRandomAccessible(RandomAccessibleInterval<T>, boolean, float, FloatType, Interval) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedImgRandomAccessible

AbstractTransformedIntervalRandomAccess - Class in net.preibisch.mvrecon.process.fusion.transformed

AbstractTransformedIntervalRandomAccess(Interval, InterpolatorFactory<FloatType, RandomAccessible<FloatType>>, FloatType, long[]) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccess

AbstractTransformedIntervalRandomAccessible - Class in net.preibisch.mvrecon.process.fusion.transformed

AbstractTransformedIntervalRandomAccessible(Interval, FloatType, Interval) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccessible

accept(File, String) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.SimView.DirectoryFilter

accept(RandomAccessibleInterval<UnsignedShortType>) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.smartspim.LazySmartSpimLoader

accept(RandomAccessibleInterval<T>) - Method in class net.preibisch.mvrecon.process.downsampling.lazy.LazyDownsample2x

accept(RandomAccessibleInterval<T>) - Method in class net.preibisch.mvrecon.process.downsampling.lazy.LazyHalfPixelDownsample2x

accept(RandomAccessibleInterval<T>) - Method in class net.preibisch.mvrecon.process.fusion.lazy.LazyAffineFusion

accept(RandomAccessibleInterval<T>) - Method in class net.preibisch.mvrecon.process.fusion.lazy.LazyNonRigidFusion

accept(RandomAccessibleInterval<T>) - Method in class net.preibisch.mvrecon.process.interestpointdetection.methods.lazygauss.LazyGauss

accept(RandomAccessibleInterval<T>) - Method in class net.preibisch.mvrecon.process.interestpointdetection.methods.lazygauss.LazyWeightedGauss

accurateCUDA - Variable in class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGParameters

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.plugin.apply.BigDataViewerTransformationWindow.ApplyButtonListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.plugin.apply.BigDataViewerTransformationWindow.CancelButtonListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.FinishedButtonListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.statistics.GraphFrame

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.statistics.SelectTimepointEntry

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.plugin.util.MouseOverPopUpStateChanger

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.plugin.util.PluginHelper.ChooseDirectoryListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.plugin.util.PluginHelper.ChooseXmlFileListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.ToggleDialogActionBrightness

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.AnalyzeErrorPopup.MyActionListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.ApplyTransformationPopup.MyActionListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BDVPopup.MyActionListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BoundingBoxPopup.MyActionListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.DeconvolutionPopup.MyActionListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.DetectInterestPointsPopup.MyActionListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.DisplayFusedImagesPopup.DisplayVirtualFused

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.DisplayRawImagesPopup.MyActionListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.FusionPopup.MyActionListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.IntensityAdjustmentPopup.MyActionListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.InterestPointsExplorerPopup.MyActionListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.LazyBDVPopup.MyActionListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.MaxProjectPopup.MyActionListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.MissingViewsPopup.MarkMissingListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.MissingViewsPopup.MarkMissingRemoveMetadataListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.MissingViewsPopup.MarkPresentListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.QualityPopup.MyActionListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.RegisterInterestPointsPopup.MyActionListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.RegistrationExplorerPopup.MyActionListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.RemoveDetectionsPopup.CreateFromCorrespondencesListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.RemoveDetectionsPopup.HistogramListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.RemoveDetectionsPopup.InteractiveListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.RemoveDetectionsPopup.RelativeDistanceHistogramListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.RemoveDetectionsPopup.RelativeThinOutListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.RemoveDetectionsPopup.ThinOutListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.RemoveTransformationPopup.MyActionListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.ReorientSamplePopup.MyActionListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.ResavePopup.MyActionListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.SpecifyCalibrationPopup.MyActionListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.VisualizeDetectionsPopup.MyActionListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.VisualizeNonRigid.MyActionListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.process.interestpointremoval.InteractiveProjections.FinishedButtonListener

actionPerformed(ActionEvent) - Method in class net.preibisch.mvrecon.process.interestpointremoval.InteractiveProjections.RemoveInsideROIButtonListener

ACTIVE_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.XmlIoFlatfieldCorrectedWrappedImgLoader

add(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Adds a scalar to each component of this matrix.

add(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Adds a scalar to each component of this matrix.

add(double, Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Adds a scalar to each component of the matrix m1 and places the result into this.

add(double, Matrix4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Adds a scalar to each component of the matrix m1 and places the result into this.

add(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Adds a scalar to each component of this matrix.

add(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Adds a scalar to each component of this matrix.

add(float, Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Adds a scalar to each component of the matrix m1 and places the result into this.

add(float, Matrix4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Adds a scalar to each component of the matrix m1 and places the result into this.

add(Point, Point) - Static method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test.TestPointDescriptor

add(ViewDescription) - Method in class net.preibisch.mvrecon.fiji.plugin.apply.ModelLink

add(NumericAffineModel3D) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

add(NumericAffineTransform3D) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

add(Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Sets the value of this matrix to the sum of itself and matrix m1.

add(Matrix3d, Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Sets the value of this matrix to the matrix sum of matrices m1 and m2.

add(Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Sets the value of this matrix to the matrix sum of itself and matrix m1.

add(Matrix3f, Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Sets the value of this matrix to the matrix sum of matrices m1 and m2.

add(Matrix4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the value of this matrix to sum of itself and matrix m1.

add(Matrix4d, Matrix4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the value of this matrix to the matrix sum of matrices m1 and m2.

add(Matrix4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the value of this matrix to the sum of itself and matrix m1.

add(Matrix4f, Matrix4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the value of this matrix to the matrix sum of matrices m1 and m2.

add(Transform3D) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Adds this transform to transform t1 and places the result into this: this = this + t1.

add(Transform3D, Transform3D) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Adds transforms t1 and t2 and places the result into this transform.

add(Tuple3d) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Sets the value of this tuple to the sum of itself and t1.

add(Tuple3d, Tuple3d) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Sets the value of this tuple to the sum of tuples t1 and t2.

add(Tuple3f) - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Sets the value of this tuple to the vector sum of itself and tuple t1.

add(Tuple3f, Tuple3f) - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Sets the value of this tuple to the vector sum of tuples t1 and t2.

add(Tuple3i) - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Sets the value of this tuple to the sum of itself and t1.

add(Tuple3i, Tuple3i) - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Sets the value of this tuple to the sum of tuples t1 and t2.

add(Tuple4d) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Sets the value of this tuple to the sum of itself and tuple t1.

add(Tuple4d, Tuple4d) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Sets the value of this tuple to the tuple sum of tuples t1 and t2.

add(Tuple4f) - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Sets the value of this tuple to the sum of itself and t1.

add(Tuple4f, Tuple4f) - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Sets the value of this tuple to the sum of tuples t1 and t2.

ADD_ALL - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.GroupParameters.InterestpointGroupingType

addAddtionalParameters(GenericDialog) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGaussianGUI

addAddtionalParameters(GenericDialog) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

addAdvancedPoints(ArrayList<Point>, ArrayList<Point>) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test.TestPointDescriptor

addAndFixTiles(Collection<ViewId>, HashMap<ViewId, Tile<M>>, Collection<ViewId>, Collection<? extends Group<ViewId>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.global.GlobalOpt

addAppleA() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

addBoundingBox(BoundingBox) - Method in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBoxes

addButton(String, ActionListener) - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

addCheckbox(String) - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

Add a checkbox to the XML-loading dialog.

addColorMode() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

addColorMode() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorerPanel

addCompression(GenericDialog, boolean) - Static method in class net.preibisch.mvrecon.fiji.plugin.util.PluginHelper

addCorrespondences(List<PointMatchGeneric<I>>, List<Integer>, ViewId, ViewId, String, String, InterestPoints, InterestPoints) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.MatcherPairwiseTools

addCorrespondences(List<PointMatchGeneric<I>>, ViewId, ViewId, String, String, InterestPoints, InterestPoints) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.MatcherPairwiseTools

addCorrespondencesFromGroups(Collection<? extends Pair<?, P>>, Map<V, ViewInterestPointLists>, Map<V, HashMap<String, List<CorrespondingInterestPoints>>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.MatcherPairwiseTools

addCredits(GenericDialog) - Static method in class net.preibisch.mvrecon.fiji.plugin.util.GUIHelper

addCurrentViewerTransform(ViewerPanel) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough

addDimension(RealRandomAccessible<T>) - Static method in class util.RealViews

Add a dimension to a RealRandomAccessible.

addEqualLabels(int, int) - Method in class net.preibisch.legacy.registration.threshold.ConnectedComponent

addFilter(Class<? extends Entity>, List<? extends Entity>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedTableModel

addFilter(Class<? extends Entity>, List<? extends Entity>) - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.ISpimDataTableModel

addFilter(Class<? extends Entity>, List<? extends Entity>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MissingViewsTableModelDecorator

addFilter(Class<? extends Entity>, List<? extends Entity>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MultiViewTableModelDecorator

addGroupingFactor(Class<? extends Entity>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedTableModel

addGroupingFactor(Class<? extends Entity>) - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.ISpimDataTableModel

addGroupingFactor(Class<? extends Entity>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MissingViewsTableModelDecorator

addGroupingFactor(Class<? extends Entity>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MultiViewTableModelDecorator

addHelp() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

addHelpListener(JTable) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointExplorerPanel

addHistoryNavigation() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

addHyperLink(GenericDialog, String, String) - Static method in class net.preibisch.mvrecon.fiji.plugin.util.GUIHelper

addHyperLinkListener(MultiLineLabel, String) - Static method in class net.preibisch.mvrecon.fiji.plugin.util.GUIHelper

addIntensityAdjustments(ViewId, AffineModel1D) - Method in class net.preibisch.mvrecon.fiji.spimdata.intensityadjust.IntensityAdjustments

addInterestPointList(String, InterestPoints) - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.ViewInterestPointLists

addInterestPoints(HashMap<ViewId, List<InterestPoint>>, DoGParameters) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoG

addInterestPoints(SpimData2, String, HashMap<ViewId, List<InterestPoint>>) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.InterestPointTools

Add interest points.

addInterestPoints(SpimData2, String, HashMap<ViewId, List<InterestPoint>>, String) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.InterestPointTools

Add interest points.

additionalSmoothBlending - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

additionalSmoothBlending - Static variable in class net.preibisch.mvrecon.process.deconvolution.MultiViewDeconvolution

addLabel(int) - Method in class net.preibisch.legacy.registration.threshold.ConnectedComponent

addListener(SelectedViewDescriptionListener<AS>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorer

addListener(SelectedViewDescriptionListener<AS>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

addListeners() - Method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.BoundingBoxGUI.ManageListeners

addListeners(GenericDialog, Choice, Label, Label) - Method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.ModifyDefinedBoundingBoxGUI

addListeners(GenericDialog, Choice, MyMultiLineLabel, ArrayList<MultiViewDatasetDefinition>) - Method in class net.preibisch.mvrecon.fiji.plugin.Define_Multi_View_Dataset

addListeners(GenericDialog, TextField, Label, Label) - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

addListeners(GenericDialog, Vector<?>, Label, long[]) - Method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.MinFilterThresholdBoundingBoxGUI

addMaxIntensityShortcut() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

Adjust the max-intensity (white point) of BDV sources by ±10% per press: [ / ] – lower / raise the max of the currently visible sources { / } – lower / raise the max of all sources (including inactive ones) Lowering the max brightens the image; raising it darkens it.

addMessage(GenericDialog, String[], Font, Color) - Static method in class net.preibisch.mvrecon.fiji.plugin.util.MyMultiLineLabel

addMessageAsJLabel(String, GenericDialog) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition

addMessageAsJLabel(String, GenericDialog, Font) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition

addMessageAsJLabel(String, GenericDialog, Font, Color) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition

addNatMethBeadsPaper(GenericDialog) - Static method in class net.preibisch.mvrecon.fiji.plugin.util.GUIHelper

addNatMethBeadsPaper(GenericDialog, String) - Static method in class net.preibisch.mvrecon.fiji.plugin.util.GUIHelper

addNeighboursShortcut() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

'n'/'N' opens the ViewNeighboursWindow on first press (and applies); subsequent presses re-apply with the window's current params.

addNotify() - Method in class net.preibisch.mvrecon.fiji.plugin.util.MyMultiLineLabel

addOverlapShortcut() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

'o'/'O' opens the ViewOverlapWindow on first press (and applies); subsequent presses toggle expand ↔ collapse.

addPointMatches(Link<Group<? extends ViewId>>, Tile<M>, Tile<M>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.strong.ImageCorrelationPointMatchCreator

addPopupMenu(JTable) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

addPopupMenu(JTable) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointExplorerPanel

addPopupMenu(JTable) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationExplorerPanel

addPopupMenu(JTable) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorerPanel

addPSF(ViewId, PointSpreadFunction) - Method in class net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions.PointSpreadFunctions

addQuery(GenericDialog) - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.NonRigidParametersGUI

addQuery(GenericDialog) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGaussianGUI

addQuery(GenericDialog) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.CenterOfMassGUI

addQuery(GenericDialog) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.FRGLDMGUI

addQuery(GenericDialog) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.GeometricHashingGUI

addQuery(GenericDialog) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.IterativeClosestPointGUI

addQuery(GenericDialog) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.LoadCorrespondencesGUI

addQuery(GenericDialog) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.PairwiseGUI

addQuery(GenericDialog) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.RGLDMGUI

addQuery(GenericDialog) - Method in interface net.preibisch.mvrecon.fiji.plugin.util.GenericDialogAppender

addRansacQuery(GenericDialog) - Static method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.PairwiseGUI

Adds the standard RANSAC parameters to a dialog: allowed error, minimal number of inliers, number of iterations, multi-consensus, and an "Advanced_RANSAC_options" checkbox (maxTrust / inlier ratio / filter-RANSAC).

addReCenterShortcut() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

addRightClickSaveAs() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

addSaveAsDirectoryField(GenericDialogPlus, String, String, int) - Static method in class net.preibisch.mvrecon.fiji.plugin.util.PluginHelper

addSaveAsFileField(GenericDialogPlus, String, String, int) - Static method in class net.preibisch.mvrecon.fiji.plugin.util.PluginHelper

addScreenshot() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

addScrollBars(Object) - Static method in class net.preibisch.mvrecon.fiji.plugin.util.GUIHelper

A copy of Curtis's method https://github.com/openmicroscopy/bioformats/blob/v4.4.8/components/loci-plugins/src/loci/plugins/util/WindowTools.java#L72

addSelected(List<T>, Collection<T>) - Method in class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.MatchIndices

addSelectionDialog() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

addSimpleParametersToDialog(GenericDialog) - Static method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters

addSimplePoints(ArrayList<Point>, ArrayList<Point>) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test.TestPointDescriptor

addSortingFactor(Class<? extends Entity>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedTableModel

addSortingFactor(Class<? extends Entity>) - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.ISpimDataTableModel

addSortingFactor(Class<? extends Entity>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MissingViewsTableModelDecorator

addSortingFactor(Class<? extends Entity>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MultiViewTableModelDecorator

addTableModelListener(TableModelListener) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MissingViewsTableModelDecorator

addTableModelListener(TableModelListener) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MultiViewTableModelDecorator

addViewSetupIdShortcut() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

addWebsite(GenericDialog) - Static method in class net.preibisch.mvrecon.fiji.plugin.util.GUIHelper

addWebsite(GenericDialog, String) - Static method in class net.preibisch.mvrecon.fiji.plugin.util.GUIHelper

adjustAllTransforms(Collection<? extends ViewId>, Map<ViewId, ? extends ViewRegistration>, double, double) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.TransformVirtual

Collects all ViewRegistrations, updates them, and potentially adds anisotropy and downsampling transformations

adjustAllTransforms(Map<ViewId, ? extends AffineTransform3D>, double, double) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.TransformVirtual

Updates existing transformations with anisotropy and downsampling transformations

adjustBlending - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

adjustBlending(BasicViewDescription<?>, float[], float[], AffineTransform3D) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

Compute how much blending in the input has to be done so the target values blending and border are achieved in the fused image

adjustBlending(Dimensions, String, float[], float[], AffineTransform3D) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

adjustContentBased(BasicViewDescription<?>, double[], double[], double[], double) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

Compute how much sigma in the input has to be applied so the target values of sigma1 and 2 are achieved in the fused image

AdjustInput - Class in net.preibisch.mvrecon.process.deconvolution.normalization

AdjustInput() - Constructor for class net.preibisch.mvrecon.process.deconvolution.normalization.AdjustInput

adjustIntensities - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

adjustIntensities - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

adjustIntensities() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

adjustIntensities() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

adjustmentValueChanged(AdjustmentEvent) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.SigmaListener

adjustmentValueChanged(AdjustmentEvent) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.ThresholdListener

advancedParameters() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.NonRigidParametersGUI

advancedRegistrationParameters(BasicRegistrationParameters, List<TimePoint>, SpimData2, List<ViewId>) - Method in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

AdvancedRegistrationParameters - Class in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters

AdvancedRegistrationParameters() - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.AdvancedRegistrationParameters

AFFINE - Static variable in class net.preibisch.mvrecon.vecmath.Transform3D

An affine matrix can translate, rotate, reflect, scale anisotropically, and shear.

affineModel1dToXml(ViewId, AffineModel1D) - Method in class net.preibisch.mvrecon.fiji.spimdata.intensityadjust.XmlIoIntensityAdjustments

AffineTransform3DAdapter() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough.AffineTransform3DAdapter

affineTransformsEqual(AffineTransform3D, AffineTransform3D) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

aggregateStatistics(List<? extends SplitResult>) - Method in class net.preibisch.mvrecon.process.splitting.SplitDistributeEvenly

aggregateStatistics(List<? extends SplitResult>) - Method in class net.preibisch.mvrecon.process.splitting.SplitOctTree

aggregateStatistics(List<? extends SplitResult>) - Method in interface net.preibisch.mvrecon.process.splitting.SplitView

Aggregate statistics from multiple split results into a summary string.

ALL - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoG.ValueChange

ALL - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.BasicRegistrationParameters.InterestPointOverlapType

ALL_AGAINST_ALL - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.BasicRegistrationParameters.OverlapType

ALL_TO_ALL - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.BasicRegistrationParameters.RegistrationType

ALL_TO_ALL_WITH_RANGE - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.BasicRegistrationParameters.RegistrationType

AllAgainstAllOverlap<V> - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap

AllAgainstAllOverlap(int) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap.AllAgainstAllOverlap

AllAnglesInOneFile - Enum constant in enum class net.preibisch.mvrecon.headless.definedataset.StackListParameters.AngleOption

allAttributeInstances - Variable in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

AllChannelsInOneFile - Enum constant in enum class net.preibisch.mvrecon.headless.definedataset.StackListParameters.ChannelOption

AllenOMEZarrLoader - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

AllenOMEZarrLoader(URI, StorageFormat, AbstractSequenceDescription<?, ?, ?>, Map<ViewId, AllenOMEZarrLoader.OMEZARREntry>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AllenOMEZarrLoader

AllenOMEZarrLoader.OMEZARREntry - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

AllenOMEZarrProperties - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

AllenOMEZarrProperties(AbstractSequenceDescription<?, ?, ?>, Map<ViewId, AllenOMEZarrLoader.OMEZARREntry>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AllenOMEZarrProperties

AllIlluminationsInOneFile - Enum constant in enum class net.preibisch.mvrecon.headless.definedataset.StackListParameters.IlluminationOption

allImageSizesEqual() - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

AllInRange<V> - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.range

AllInRange() - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.range.AllInRange

allowModifyDimensions() - Method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.AutomaticReorientationBoundingBoxGUI

allowModifyDimensions() - Method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.BDVBoundingBoxGUI

allowModifyDimensions() - Method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.BoundingBoxGUI

allowModifyDimensions() - Method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.MaximumBoundingBoxGUI

allowModifyDimensions() - Method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.MinFilterThresholdBoundingBoxGUI

allowModifyDimensions() - Method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.ModifyDefinedBoundingBoxGUI

allPairs(List<? extends V>, Collection<? extends Group<V>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.AllToAll

allPairs(List<? extends V>, Collection<? extends Group<V>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.IndividualTimepoints

allPairs(List<? extends V>, Collection<? extends Group<V>>, RangeComparator<V>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.AllToAllRange

AllTilesInOneFile - Enum constant in enum class net.preibisch.mvrecon.headless.definedataset.StackListParameters.TileOption

AllTimePointsInOneFile - Enum constant in enum class net.preibisch.mvrecon.headless.definedataset.StackListParameters.TimePointOption

allToAll(List<? extends V>, Collection<V>, Collection<? extends Collection<V>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.PairwiseStrategyTools

AllToAll<V> - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation

AllToAll(List<V>, Set<Group<V>>) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.AllToAll

AllToAllGUI - Class in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global

AllToAllGUI() - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.AllToAllGUI

allToAllRange(List<? extends V>, Collection<V>, Collection<? extends Collection<V>>, RangeComparator<V>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.PairwiseStrategyTools

AllToAllRange<V,R> - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation

AllToAllRange(List<V>, Set<Group<V>>, R) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.AllToAllRange

allViews(Group<? extends V>, Group<? extends V>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.MatcherPairwiseTools

allVoxelSizesTheSame(FileListViewDetectionState) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListViewDetectionState

alpha - Variable in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidParameters

alternating - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.grid.RegularTranformHelpers.GridPreset

alternating - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.grid.RegularTranformHelpers.RegularTranslationParameters

ALWAYS - Enum constant in enum class net.preibisch.mvrecon.fiji.spimdata.explorer.viewneighbours.ViewNeighboursWindow.ResetPolicy

ALWAYS - Enum constant in enum class net.preibisch.mvrecon.fiji.spimdata.explorer.viewneighbours.ViewOverlapWindow.ResetPolicy

AMPLITUDE_DIR_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoDHMImgLoader

AMPLITUDE_ID_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoDHMImgLoader

Analyze_Errors - Class in net.preibisch.mvrecon.fiji.plugin

Fiji menu entry for "Analyze Alignment Errors".

Analyze_Errors() - Constructor for class net.preibisch.mvrecon.fiji.plugin.Analyze_Errors

AnalyzeErrorPopup - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

AnalyzeErrorPopup() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.AnalyzeErrorPopup

AnalyzeErrorPopup.MyActionListener - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

AnalyzeErrorsResultsWindow - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror

Sortable results browser for AnalyzeErrorsUtil.

AnalyzeErrorsResultsWindow(SpimData2, ArrayList<AnalyzeErrorsUtil.PairError>, AnalyzeErrorsUtil.Parameters, ViewSetupExplorerPanel<?>, Collection<? extends ViewId>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsResultsWindow

AnalyzeErrorsResultsWindow.BdvResetPolicy - Enum Class in net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror

Controls when row clicks recentre BDV.

AnalyzeErrorsUtil - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror

AnalyzeErrorsUtil.GroupPairResult - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror

Aggregated error statistics for one (groupA, groupB) bucket.

AnalyzeErrorsUtil.Mode - Enum Class in net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror

Display mode for AnalyzeErrorsResultsWindow.

AnalyzeErrorsUtil.PairError - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror

Per-(viewA, viewB) error result returned by AnalyzeErrorsUtil.getErrors(net.preibisch.mvrecon.fiji.spimdata.SpimData2, java.util.List<mpicbg.spim.data.sequence.ViewId>, java.util.Map<java.lang.String, java.lang.Double>).

AnalyzeErrorsUtil.Parameters - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror

Bundle of dialog choices returned by AnalyzeErrorsUtil.getParametersExtended(net.preibisch.mvrecon.fiji.spimdata.SpimData2, java.util.List<mpicbg.spim.data.sequence.ViewId>).

AnalyzeErrorsUtil.SingleGroupError - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror

Per-group aggregate of errors and connected groups (Single-view mode, grouped).

AnalyzeErrorsUtil.SingleViewError - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror

Per-view aggregate of errors and connections (Single-view mode, ungrouped).

analyzeMaximum(RandomAccess<FloatType>, float, int, int, int, float, float, float, RejectStatistics, ArrayList<DoGMaximum>) - Static method in class net.preibisch.legacy.registration.bead.laplace.LaPlaceFunctions

angle - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.AngleInfo

angle - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.TileOrAngleInfo

angle - Variable in class net.preibisch.mvrecon.vecmath.AxisAngle4d

The angle of rotation in radians.

angle - Variable in class net.preibisch.mvrecon.vecmath.AxisAngle4f

The angle of rotation in radians.

angle(Vector3d) - Method in class net.preibisch.mvrecon.vecmath.Vector3d

Returns the angle in radians between this vector and the vector parameter; the return value is constrained to the range [0,PI].

angle(Vector3f) - Method in class net.preibisch.mvrecon.vecmath.Vector3f

Returns the angle in radians between this vector and the vector parameter; the return value is constrained to the range [0,PI].

angle(Vector4d) - Method in class net.preibisch.mvrecon.vecmath.Vector4d

Returns the (4-space) angle in radians between this vector and the vector parameter; the return value is constrained to the range [0,PI].

angle(Vector4f) - Method in class net.preibisch.mvrecon.vecmath.Vector4f

Returns the (4-space) angle in radians between this vector and the vector parameter; the return value is constrained to the range [0,PI].

ANGLE_PATTERN - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData

ANGLE_PATTERN - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

angleChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

AngleInfo() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.AngleInfo

angleNameList - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

angleNameList - Variable in class net.preibisch.mvrecon.headless.definedataset.StackList.ViewSetupPrecursor

angleNames - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

angleNames - Variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

angles - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

angles - Variable in class net.preibisch.mvrecon.headless.definedataset.DefineDataSetParameters

angles - Variable in class net.preibisch.mvrecon.headless.definedataset.StackListParameters

angles() - Method in class net.preibisch.mvrecon.fiji.plugin.apply.ModelLink

angles() - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

ANISOTROPY_CHOICES - Static variable in class net.preibisch.mvrecon.process.splitting.SplitOctTree

anyGroupingSelected() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.Parameters

appendName(URI, String) - Static method in class util.URITools

apply() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.viewneighbours.ViewNeighboursWindow

Compute the connected views for the explorer's current selection using the window's configured label, drive the explorer selection to selection ∪ connected, and paint per-source category colours in BDV.

apply() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.viewneighbours.ViewOverlapWindow

Run the geometric-overlap query against the panel's selection (or lastActual when re-applying), filter the universe by the attribute checkboxes, and paint per-source category colours in BDV.

apply(double) - Method in class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.FastAffineModel1D

apply(double) - Method in class net.preibisch.mvrecon.process.fusion.intensityadjust.IntensityAdjuster

apply(double[]) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.FixedModel

apply(double[]) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantAffineModel3D

apply(double[]) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantFixedModel

apply(double[]) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel2D

apply(double[]) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel3D

apply(double[]) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantSimilarityModel3D

apply(CoordinateTransform) - Method in class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.PointMatch1D

Apply_Transformation - Class in net.preibisch.mvrecon.fiji.plugin

Apply_Transformation() - Constructor for class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

applyAngles(LoadParseQueryXML) - Method in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

applyAxis - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

applyAxis - Variable in class net.preibisch.mvrecon.headless.definedataset.DefineDataSetParameters

applyAxis - Variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

applyAxis() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

applyAxis() - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

applyAxis() - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

applyAxis(SpimData) - Static method in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

applyAxisGrouped(SpimData) - Static method in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

applyAxisGrouped(SpimData, boolean) - Static method in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

ApplyButtonListener(Frame, BigDataViewer) - Constructor for class net.preibisch.mvrecon.fiji.plugin.apply.BigDataViewerTransformationWindow.ApplyButtonListener

applyCal(Specify_Calibration.Cal, SpimData, List<ViewId>) - Static method in class net.preibisch.mvrecon.fiji.plugin.Specify_Calibration

applyCategoryColors(BasicBDVPopup, Map<Integer, ARGBType>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVColors

Walk the BDV's active sources and override each one's ConverterSetup colour from colorBySetupId.

applyChannels(LoadParseQueryXML) - Method in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

applyFast(CoordinateTransform) - Method in class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.Point1D

applyHard(ArrayList<Cursor<FloatType>>, double) - Static method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccess

applyIllums(LoadParseQueryXML) - Method in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

applyInPlace(double[]) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.FixedModel

applyInPlace(double[]) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantAffineModel3D

applyInPlace(double[]) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantFixedModel

applyInPlace(double[]) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel2D

applyInPlace(double[]) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel3D

applyInPlace(double[]) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantSimilarityModel3D

applyInPlace(AbstractAffineModel3D<?>, Point3d) - Static method in class net.preibisch.legacy.mpicbg.Java3d

applyInPlace(AbstractAffineModel3D<?>, Point3d, double[]) - Static method in class net.preibisch.legacy.mpicbg.Java3d

applyInverseInPlace(AbstractAffineModel3D<?>, Point3d) - Static method in class net.preibisch.legacy.mpicbg.Java3d

applyInverseInPlace(AbstractAffineModel3D<?>, Point3d, double[]) - Static method in class net.preibisch.legacy.mpicbg.Java3d

applyModels(SpimData, double, int, Map<ViewDescription, ImgLib2Temp.Pair<double[], String>>) - Method in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

ApplyParameters - Class in net.preibisch.mvrecon.fiji.plugin.apply

ApplyParameters() - Constructor for class net.preibisch.mvrecon.fiji.plugin.apply.ApplyParameters

applySmooth(ArrayList<Cursor<FloatType>>, double, float, float) - Static method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccess

applyTiles(LoadParseQueryXML) - Method in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

applyTimepoints(LoadParseQueryXML) - Method in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

applyTo - Variable in class net.preibisch.mvrecon.fiji.plugin.apply.ApplyParameters

applyToChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

applyToSpimData(AS, List<? extends Group<? extends BasicViewDescription<?>>>, RegularTranformHelpers.RegularTranslationParameters, boolean) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.grid.RegularTranformHelpers

applyTransform(ArrayList<Point>) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test.TestPointDescriptor

applyTransformation(Collection<InterestPoint>, AffineTransform3D) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

applyTransformation(HashMap<String, Collection<InterestPoint>>, AffineTransform3D) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

ApplyTransformationPopup - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

ApplyTransformationPopup() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.ApplyTransformationPopup

ApplyTransformationPopup.MyActionListener - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

APPROX_AVG - Enum constant in enum class net.preibisch.mvrecon.process.deconvolution.init.PsiInit.PsiInitType

approximateEntropy(RandomAccessibleInterval<FloatType>, ImgFactory<ComplexFloatType>, double[], double[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.ContentBasedFFTRealRandomAccessible

approximateLowerBound(double[]) - Static method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxMaximal

approximateUpperBound(double[]) - Static method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxMaximal

areListsEqual(List<String>, List<String>) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM

argb(int, int, int) - Static method in class util.ColorStream

arrayImg(BlockSupplier<T>, Interval) - Static method in class util.BlockSupplierUtils

ArrayImg - Enum constant in enum class net.preibisch.mvrecon.headless.definedataset.StackListParameters.Container

ASK - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters.PreAlign

askForFixedViews(Subset<ViewId>, Set<ViewId>, String) - Method in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

askForReferenceView(Subset<ViewId>, String) - Method in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

askForRegistrations(GenericDialog) - Method in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

askUserForParameters(boolean, GlobalOptimizationParameters.PreAlign) - Static method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters

askUserForSimpleParameters() - Static method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters

askWhenMoreThan - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.RemoveTransformationPopup

askWhenMoreThan - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.ResavePopup

assembleAllCorrespondingPoints(ViewId, InterestPoints, Collection<? extends CorrespondingInterestPoints>, Collection<? extends ViewId>, Map<? extends ViewId, ? extends ViewInterestPointLists>) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidTools

assembleAngles(List<Angle>) - Method in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

assembleChannels(List<Channel>) - Method in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

assembleDataTypes(AbstractSpimData<?>, Collection<Integer>) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

assembleDefaultPattern() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

assembleDefaultPattern(int, int, int, int, int) - Static method in class net.preibisch.mvrecon.headless.definedataset.StackList

assembleDimensions(Collection<? extends ViewId>, Map<ViewId, ? extends BasicViewDescription<?>>) - Static method in class net.preibisch.mvrecon.process.fusion.lazy.LazyFusionTools

assembleDimensions(Collection<? extends ViewId>, SpimData) - Static method in class net.preibisch.mvrecon.process.fusion.lazy.LazyFusionTools

assembleDimensions(SpimData, Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

assembleIllums(List<Illumination>) - Method in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

assembleInputData(SpimData2, TimePoint, Channel, List<ViewId>) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

assembleIPsForNonRigid(Map<ViewId, ViewInterestPointLists>, Collection<? extends ViewId>, List<String>) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidTools

assembleJobs(long[], int[]) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

assembleJobs(long[], int[], int[]) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

assembleJobs(ViewId, long[], int[]) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

assembleJobs(ViewId, long[], int[], int[]) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

assembleJobs(ViewId, N5ApiTools.MultiResolutionLevelInfo) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

assembleJobs(ViewId, N5ApiTools.MultiResolutionLevelInfo, int[]) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

assembleJobs(N5ApiTools.MultiResolutionLevelInfo) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

assembleJobs(N5ApiTools.MultiResolutionLevelInfo, int[]) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

assemblePSFs(ArrayList<ViewId>, HashMap<ViewId, PointSpreadFunction>) - Static method in class net.preibisch.mvrecon.fiji.plugin.PSF_Assign

assembleRegistrationNames(SpimData, List<ViewId>) - Static method in class net.preibisch.mvrecon.fiji.plugin.util.GUIHelper

assembleTiles(List<Tile>) - Method in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

assembleTimepoints(List<TimePoint>) - Method in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

assembleTimepoints(TimePoints) - Static method in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

assembleViews(Set<Tile<?>>, HashMap<ViewId, ? extends Tile<?>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.global.GlobalOptTwoRound

assembleViewSetups(SpimData, Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

assembleViewsToUse(SpimData2, Collection<? extends ViewId>, boolean) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidTools

assign(SpimData2, Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.fiji.plugin.PSF_Assign

assign(SpimData2, Collection<? extends ViewId>, String, boolean) - Static method in class net.preibisch.mvrecon.fiji.plugin.PSF_Assign

assignGlobalValues() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData

assigns global metadata

assignLoggingDescriptions(Pair<?, ?>, PairwiseResult<?>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.MatcherPairwiseTools

assignPointMatches(HashMap<ViewId, Tile<M>>, ArrayList<Group<ViewId>>, Collection<ViewId>) - Method in interface net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.PointMatchCreator

assign pointmatches for all views that this object knows and that are present in tileMap.keySet(), which comes from getAllViews() plus what is in the group definition of the globalopt called last

assignPointMatches(HashMap<ViewId, Tile<M>>, ArrayList<Group<ViewId>>, Collection<ViewId>) - Method in class net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.strong.ImageCorrelationPointMatchCreator

assignPointMatches(HashMap<ViewId, Tile<M>>, ArrayList<Group<ViewId>>, Collection<ViewId>) - Method in class net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.strong.InterestPointMatchCreator

assignPointMatches(HashMap<ViewId, Tile<M>>, ArrayList<Group<ViewId>>, Collection<ViewId>) - Method in class net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.weak.MetaDataWeakLinkCreator

assignPointMatches(List<LinkedInterestPoint<P>>, List<LinkedInterestPoint<P>>) - Method in interface net.preibisch.mvrecon.process.pointcloud.icp.PointMatchIdentification

assignPointMatches(List<LinkedInterestPoint<P>>, List<LinkedInterestPoint<P>>) - Method in class net.preibisch.mvrecon.process.pointcloud.icp.SimplePointMatchIdentification

assignTypeChoices - Static variable in class net.preibisch.mvrecon.fiji.plugin.PSF_Assign

assignViewsToTiles(M, List<ViewId>, List<Group<ViewId>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.global.GlobalOpt

assignWeights(HashMap<ViewId, Tile<M>>, ArrayList<Group<ViewId>>, Collection<ViewId>) - Method in interface net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.PointMatchCreator

By default all weights are 1, if wanted one can adjust them here, otherwise simply return.

assignWeights(HashMap<ViewId, Tile<M>>, ArrayList<Group<ViewId>>, Collection<ViewId>) - Method in class net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.strong.ImageCorrelationPointMatchCreator

assignWeights(HashMap<ViewId, Tile<M>>, ArrayList<Group<ViewId>>, Collection<ViewId>) - Method in class net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.strong.InterestPointMatchCreator

assignWeights(HashMap<ViewId, Tile<M>>, ArrayList<Group<ViewId>>, Collection<ViewId>) - Method in class net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.weak.MetaDataWeakLinkCreator

assignWeights(List<? extends Pair<? extends Pair<ViewId, ViewId>, ? extends PairwiseResult<?>>>, ArrayList<Group<ViewId>>, HashMap<ViewId, Tile<M>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.strong.InterestPointMatchCreator

attributeChoice - Variable in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

attributeChoiceList - Static variable in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

attributeInstancesToProcess - Variable in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

attributes - Variable in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

AutomaticReorientationBoundingBoxGUI - Class in net.preibisch.mvrecon.fiji.plugin.boundingbox

AutomaticReorientationBoundingBoxGUI(SpimData2, List<ViewId>) - Constructor for class net.preibisch.mvrecon.fiji.plugin.boundingbox.AutomaticReorientationBoundingBoxGUI

availableDownsamplings(AbstractSpimData<?>, ViewId) - Static method in class net.preibisch.mvrecon.process.downsampling.DownsampleTools

average(SpimData2, Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.fiji.plugin.PSF_Average

average(SpimData2, Collection<? extends ViewId>, int, boolean) - Static method in class net.preibisch.mvrecon.fiji.plugin.PSF_Average

averagePSF(SpimData2, Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.fiji.plugin.PSF_Average

averageTransformedPSF(SpimData2, Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.fiji.plugin.PSF_View

averageTransforms(Collection<? extends AffineGet>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

averageVectors(Collection<double[]>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

averagingChoices - Static variable in class net.preibisch.mvrecon.fiji.plugin.PSF_Average

avg - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.GroupPairResult

avg - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.SingleGroupError

avg - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.SingleViewError

AVG - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI.FusionType

AVG - Enum constant in enum class net.preibisch.mvrecon.process.deconvolution.init.PsiInit.PsiInitType

AVG - Enum constant in enum class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval.Fusion

AVG_BLEND - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI.FusionType

AVG_BLEND_CONTENT - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI.FusionType

AVG_CONTENT - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI.FusionType

avgAnisoF - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

avgAnisoF - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

avgDepth - Variable in class net.preibisch.mvrecon.process.splitting.SplitOctTree.OctTreeSplitResult

avgDetections - Variable in class net.preibisch.mvrecon.process.splitting.SplitOctTree.OctTreeSplitResult

avgError - Variable in class net.preibisch.legacy.registration.bead.error.GlobalErrorStatisticsImpl

avgLocalError - Variable in class net.preibisch.legacy.registration.bead.error.GlobalErrorStatisticsImpl

avgMaxSets - Variable in class net.preibisch.mvrecon.process.splitting.SplitOctTree.OctTreeSplitResult

avgOutlierPercent - Variable in class net.preibisch.mvrecon.process.splitting.SplitOctTree.OctTreeSplitResult

ax - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.LocalCoordinateSystemPointDescriptor

ax - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.TranslationInvariantLocalCoordinateSystemPointDescriptor

axesChoice - Variable in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

axis - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.AngleInfo

axis - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.TileOrAngleInfo

AxisAngle4d - Class in net.preibisch.mvrecon.vecmath

A four-element axis angle represented by double-precision floating point x,y,z,angle components.

AxisAngle4d() - Constructor for class net.preibisch.mvrecon.vecmath.AxisAngle4d

Constructs and initializes an AxisAngle4d to (0,0,1,0).

AxisAngle4d(double[]) - Constructor for class net.preibisch.mvrecon.vecmath.AxisAngle4d

Constructs and initializes an AxisAngle4d from the components contained in the array.

AxisAngle4d(double, double, double, double) - Constructor for class net.preibisch.mvrecon.vecmath.AxisAngle4d

Constructs and initializes an AxisAngle4d from the specified x, y, z, and angle.

AxisAngle4d(AxisAngle4d) - Constructor for class net.preibisch.mvrecon.vecmath.AxisAngle4d

Constructs and initializes an AxisAngle4d from the specified AxisAngle4d.

AxisAngle4d(AxisAngle4f) - Constructor for class net.preibisch.mvrecon.vecmath.AxisAngle4d

Constructs and initializes an AxisAngle4d from the specified AxisAngle4f.

AxisAngle4d(Vector3d, double) - Constructor for class net.preibisch.mvrecon.vecmath.AxisAngle4d

Constructs and initializes an AxisAngle4d from the specified axis and angle.

AxisAngle4f - Class in net.preibisch.mvrecon.vecmath

A four-element axis angle represented by single-precision floating point x,y,z,angle components.

AxisAngle4f() - Constructor for class net.preibisch.mvrecon.vecmath.AxisAngle4f

Constructs and initializes an AxisAngle4f to (0,0,1,0).

AxisAngle4f(float[]) - Constructor for class net.preibisch.mvrecon.vecmath.AxisAngle4f

Constructs and initializes an AxisAngle4f from the array of length 4.

AxisAngle4f(float, float, float, float) - Constructor for class net.preibisch.mvrecon.vecmath.AxisAngle4f

Constructs and initializes a AxisAngle4f from the specified xyzw coordinates.

AxisAngle4f(AxisAngle4d) - Constructor for class net.preibisch.mvrecon.vecmath.AxisAngle4f

Constructs and initializes an AxisAngle4f from the specified AxisAngle4d.

AxisAngle4f(AxisAngle4f) - Constructor for class net.preibisch.mvrecon.vecmath.AxisAngle4f

Constructs and initializes an AxisAngle4f from the specified AxisAngle4f.

AxisAngle4f(Vector3f, float) - Constructor for class net.preibisch.mvrecon.vecmath.AxisAngle4f

Constructs and initializes an AxisAngle4f from the specified axis and angle.

ay - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.TranslationInvariantLocalCoordinateSystemPointDescriptor

az - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.TranslationInvariantLocalCoordinateSystemPointDescriptor

B

b - Variable in class net.preibisch.mvrecon.fiji.ImgLib2Temp.ValuePair

b - Variable in class net.preibisch.mvrecon.fiji.ImgLib2Temp.ValueTriple

b - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.PairError

B - Variable in class net.preibisch.legacy.registration.bead.laplace.DoGMaximum

BakeManualTransformationPopup - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

BakeManualTransformationPopup() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BakeManualTransformationPopup

baseN5 - Static variable in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

BasicBDVPopup - Interface in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

basicRegistrationParameters(List<TimePoint>, int, SpimData2, List<ViewId>) - Method in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

BasicRegistrationParameters - Class in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters

BasicRegistrationParameters() - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.BasicRegistrationParameters

BasicRegistrationParameters.InterestPointOverlapType - Enum Class in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters

BasicRegistrationParameters.OverlapType - Enum Class in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters

BasicRegistrationParameters.RegistrationType - Enum Class in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters

batchCalculateFireNumber(File, File, FRC.ThresholdMethod, ResultsTable, boolean) - Method in class net.preibisch.mvrecon.process.quality.FRC

Convenience function to batch calculate the FRC by going though file on two separate directories.

bck(int) - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccess

bck(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccess

bck(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccess

bck(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessFirstWins

bck(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessMax

bck(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessNoWeights

bck(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridAccess

bck(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGridRandomAccess

bck(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputGeneralRandomAccess

bck(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccess2d

bck(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccess

bck(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccess

bck(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.InterpolatingNonRigidRasteredRandomAccess

bck(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.NonRigidRasteredRandomAccess

bck(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.TransformedRasteredRandomAccess

bck(int) - Method in class util.StackingRealRandomAccessible.StackingRealRandomAccess

bdv - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BDVPopup

bdv - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.LazyBDVPopup

BDVBoundingBoxGUI - Class in net.preibisch.mvrecon.fiji.plugin.boundingbox

BDVBoundingBoxGUI(SpimData2, List<ViewId>) - Constructor for class net.preibisch.mvrecon.fiji.plugin.boundingbox.BDVBoundingBoxGUI

BDVChecker(BigDataViewer, Label, Label, Label) - Constructor for class net.preibisch.mvrecon.fiji.plugin.apply.BigDataViewerTransformationWindow.BDVChecker

BDVColors - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.bdv

Shared category-colour utilities for explorer-driven BDV highlights.

BDVFlyThrough - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.bdv

BDVFlyThrough() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough

BDVFlyThrough.AffineTransform3DAdapter - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.bdv

BDVFlyThrough.MyTarget - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.bdv

bdvPopup() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.ExplorerWindow

bdvPopup() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

BDVPopup - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

BDVPopup() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BDVPopup

BDVPopup.MyActionListener - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

bdvRunning() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BasicBDVPopup

bdvRunning() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BDVPopup

bdvRunning() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.LazyBDVPopup

BDVSourceNaming - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

Source-name utilities used by both BDVPopup (eager) and LazyBDVPopup so they label sources identically as "VS: <viewSetupId> TP: <timepointId>".

BDVSourceNaming() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BDVSourceNaming

BDVTools - Class in util

Utility methods for BigDataViewer operations.

BDVTools() - Constructor for class util.BDVTools

BDVUtils - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.bdv

BDVUtils() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVUtils

beginAttempt() - Method in class net.preibisch.mvrecon.process.export.RetryTracker

Call this before each retry cycle.

BigDataViewerTransformationWindow - Class in net.preibisch.mvrecon.fiji.plugin.apply

BigDataViewerTransformationWindow(BigDataViewer) - Constructor for class net.preibisch.mvrecon.fiji.plugin.apply.BigDataViewerTransformationWindow

BigDataViewerTransformationWindow.ApplyButtonListener - Class in net.preibisch.mvrecon.fiji.plugin.apply

BigDataViewerTransformationWindow.BDVChecker - Class in net.preibisch.mvrecon.fiji.plugin.apply

BigDataViewerTransformationWindow.CancelButtonListener - Class in net.preibisch.mvrecon.fiji.plugin.apply

binData(List<Double>, double, double, int) - Static method in class net.preibisch.mvrecon.process.interestpointremoval.histogram.Histogram

BioformatsReaderSetupHook - Interface in net.preibisch.mvrecon.fiji.spimdata.imgloaders.util

BioformatsReaderUtils - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders.util

BioformatsReaderUtils() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.util.BioformatsReaderUtils

BITS_PER_SAMPLE - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

BITS_PER_SAMPLE - Static variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

blendingBorder - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

BlendingFunction3D<D,F> - Class in net.preibisch.mvrecon.process.fusion.blk.tps

blendingRange - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

BlendingRealRandomAccess - Class in net.preibisch.mvrecon.process.fusion.transformed.weights

BlendingRealRandomAccess(Interval, float[], float[]) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccess

RealRandomAccess that computes a blending function for a certain Interval

BlendingRealRandomAccessible - Class in net.preibisch.mvrecon.process.fusion.transformed.weights

RealRandomAccess that computed cosine-blending for a certain interval

BlendingRealRandomAccessible(Interval, float[], float[]) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccessible

RealRandomAccess that computes a blending function for a certain Interval

BlendingRealRandomAccessible(Interval, int[], int[]) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccessible

BlkAffineFusion - Class in net.preibisch.mvrecon.process.fusion.blk

BlkAffineFusion() - Constructor for class net.preibisch.mvrecon.process.fusion.blk.BlkAffineFusion

BlkThinPlateSplineFusion - Class in net.preibisch.mvrecon.process.fusion.blk

BlkThinPlateSplineFusion() - Constructor for class net.preibisch.mvrecon.process.fusion.blk.BlkThinPlateSplineFusion

Block - Class in net.preibisch.mvrecon.process.cuda

Block(ExecutorService, long[], long[], long[], long[], long[], boolean) - Constructor for class net.preibisch.mvrecon.process.cuda.Block

blockContainsContent(Block, RandomAccessibleInterval<FloatType>, ExecutorService) - Static method in class net.preibisch.mvrecon.process.deconvolution.DeconView

blockFactory - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

BlockGenerator<T> - Interface in net.preibisch.mvrecon.process.cuda

BlockGeneratorFixedSizePrecise - Class in net.preibisch.mvrecon.process.cuda

BlockGeneratorFixedSizePrecise(long[]) - Constructor for class net.preibisch.mvrecon.process.cuda.BlockGeneratorFixedSizePrecise

BlockGeneratorFixedSizePrecise(ExecutorService, long[]) - Constructor for class net.preibisch.mvrecon.process.cuda.BlockGeneratorFixedSizePrecise

BlockGeneratorVariableSizePrecise - Class in net.preibisch.mvrecon.process.cuda

This BlockGenerator cares that the overlap within the image is accounted for and that an outofbounds strategy is taken into account.

BlockGeneratorVariableSizePrecise(long[]) - Constructor for class net.preibisch.mvrecon.process.cuda.BlockGeneratorVariableSizePrecise

BlockGeneratorVariableSizePrecise(ExecutorService, long[]) - Constructor for class net.preibisch.mvrecon.process.cuda.BlockGeneratorVariableSizePrecise

BlockGeneratorVariableSizeSimple - Class in net.preibisch.mvrecon.process.cuda

This BlockGenerator only cares that the overlap within the image is accounted for, not about an outofbounds strategy.

BlockGeneratorVariableSizeSimple(long[]) - Constructor for class net.preibisch.mvrecon.process.cuda.BlockGeneratorVariableSizeSimple

BlockGeneratorVariableSizeSimple(ExecutorService, long[]) - Constructor for class net.preibisch.mvrecon.process.cuda.BlockGeneratorVariableSizeSimple

blocksChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

blocksize() - Method in class net.preibisch.mvrecon.process.export.DisplayImage

blocksize() - Method in class net.preibisch.mvrecon.process.export.ExportLarge2DTIFF

blocksize() - Method in class net.preibisch.mvrecon.process.export.ExportN5Api

blocksize() - Method in interface net.preibisch.mvrecon.process.export.ImgExport

specify the desired 3d blocksize used for the Lazy instances

blocksize() - Method in class net.preibisch.mvrecon.process.export.OpenSeaDragon

blocksize() - Method in class net.preibisch.mvrecon.process.export.Save3dTIFF

blockSize - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

blockSize - Static variable in class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2

blockSize - Variable in class net.preibisch.mvrecon.process.n5api.N5ApiTools.MultiResolutionLevelInfo

blockSizeFactor - Variable in class net.preibisch.mvrecon.fiji.plugin.resave.ParametersResaveN5Api

blockSizeIndex - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

BlockSorter - Class in net.preibisch.mvrecon.process.cuda

We need to sort blocks in a way so consecutive ones are not influenced by their predecessors

BlockSorter() - Constructor for class net.preibisch.mvrecon.process.cuda.BlockSorter

BlockSupplierUtils - Class in util

BlockSupplierUtils() - Constructor for class util.BlockSupplierUtils

Bool - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping

Bool(boolean) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Bool

bottomM - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.Parameters

boundingBox - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

boundingBox - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

boundingBox - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

boundingBox - Variable in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccessible

BoundingBox - Class in net.preibisch.mvrecon.fiji.spimdata.boundingbox

BoundingBox(int[], int[]) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox

BoundingBox(String, int[], int[]) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox

BoundingBox(Interval) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox

BOUNDINGBOX_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.XmlKeysBoundingBox

BOUNDINGBOX_TAG_MAX - Static variable in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.XmlKeysBoundingBox

BOUNDINGBOX_TAG_MIN - Static variable in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.XmlKeysBoundingBox

BOUNDINGBOX_TAG_NAME - Static variable in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.XmlKeysBoundingBox

BoundingBoxBigDataViewer - Class in net.preibisch.mvrecon.process.boundingbox

BoundingBoxBigDataViewer(SpimData, Collection<ViewId>) - Constructor for class net.preibisch.mvrecon.process.boundingbox.BoundingBoxBigDataViewer

BoundingBoxes - Class in net.preibisch.mvrecon.fiji.spimdata.boundingbox

BoundingBoxes() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBoxes

BoundingBoxes(Collection<BoundingBox>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBoxes

BOUNDINGBOXES_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.XmlKeysBoundingBox

BoundingBoxEstimation - Interface in net.preibisch.mvrecon.process.boundingbox

BoundingBoxGUI - Class in net.preibisch.mvrecon.fiji.plugin.boundingbox

BoundingBoxGUI(SpimData2, List<ViewId>) - Constructor for class net.preibisch.mvrecon.fiji.plugin.boundingbox.BoundingBoxGUI

BoundingBoxGUI(SpimData2, List<ViewId>, BoundingBox) - Constructor for class net.preibisch.mvrecon.fiji.plugin.boundingbox.BoundingBoxGUI

BoundingBoxGUI.ManageListeners - Class in net.preibisch.mvrecon.fiji.plugin.boundingbox

BoundingBoxMaximal - Class in net.preibisch.mvrecon.process.boundingbox

BoundingBoxMaximal(Collection<? extends ViewId>, HashMap<? extends ViewId, Dimensions>, HashMap<? extends ViewId, AffineTransform3D>) - Constructor for class net.preibisch.mvrecon.process.boundingbox.BoundingBoxMaximal

BoundingBoxMaximal(Collection<? extends ViewId>, AbstractSpimData<? extends AbstractSequenceDescription<?, ?, ? extends ImgLoader>>) - Constructor for class net.preibisch.mvrecon.process.boundingbox.BoundingBoxMaximal

BoundingBoxMaximalGroupOverlap<V> - Class in net.preibisch.mvrecon.process.boundingbox

BoundingBoxMaximalGroupOverlap(Collection<? extends Iterable<V>>, AbstractSpimData<?>) - Constructor for class net.preibisch.mvrecon.process.boundingbox.BoundingBoxMaximalGroupOverlap

BoundingBoxMaximalGroupOverlap(Collection<? extends Iterable<V>>, AbstractSequenceDescription<? extends BasicViewSetup, ?, ?>, ViewRegistrations) - Constructor for class net.preibisch.mvrecon.process.boundingbox.BoundingBoxMaximalGroupOverlap

BoundingBoxMinFilterThreshold - Class in net.preibisch.mvrecon.process.boundingbox

BoundingBoxMinFilterThreshold(SpimData2, ExecutorService, Collection<? extends ViewId>, ImgFactory<FloatType>, double, int, boolean, int) - Constructor for class net.preibisch.mvrecon.process.boundingbox.BoundingBoxMinFilterThreshold

boundingBoxOffset - Variable in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccessible

BoundingBoxPopup - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

BoundingBoxPopup() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BoundingBoxPopup

BoundingBoxPopup.MyActionListener - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

BoundingBoxReorientation - Class in net.preibisch.mvrecon.process.boundingbox

BoundingBoxReorientation(SpimData2, ArrayList<RealLocalizable>, double, boolean, List<ViewId>) - Constructor for class net.preibisch.mvrecon.process.boundingbox.BoundingBoxReorientation

BoundingBoxReorientation(SpimData2, List<ViewId>, String, boolean, double, boolean, List<ViewId>) - Constructor for class net.preibisch.mvrecon.process.boundingbox.BoundingBoxReorientation

BoundingBoxReorientation(SpimData2, List<ViewId>, HashMap<ViewId, ? extends Collection<? extends RealLocalizable>>, double, boolean, List<ViewId>) - Constructor for class net.preibisch.mvrecon.process.boundingbox.BoundingBoxReorientation

BoundingBoxTools - Class in net.preibisch.mvrecon.process.boundingbox

BoundingBoxTools() - Constructor for class net.preibisch.mvrecon.process.boundingbox.BoundingBoxTools

boundingBoxToXml(BoundingBox) - Method in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.XmlIoBoundingBoxes

BRIGHTIMG_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.XmlIoFlatfieldCorrectedWrappedImgLoader

brightnessChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

bs - Static variable in class util.ColorStream

buildDefaultFilePattern() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData

buildEntityList(String, List<? extends Entity>, boolean) - Static method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

buildLocalCoordinateSystem(ArrayList<LinkedPoint<P>>) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.TranslationInvariantLocalCoordinateSystemPointDescriptor

buildLocalCoordinateSystem(ArrayList<LinkedPoint<P>>, boolean) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.LocalCoordinateSystemPointDescriptor

buildPatternParser(String) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData

buildTimepointList(List<TimePoint>, boolean) - Static method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

builFilePattern(String) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData

buttonText - Variable in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

bx - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.LocalCoordinateSystemPointDescriptor

bx - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.TranslationInvariantLocalCoordinateSystemPointDescriptor

by - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.LocalCoordinateSystemPointDescriptor

by - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.TranslationInvariantLocalCoordinateSystemPointDescriptor

BY_SUM_OF_SAMPLES - Enum constant in enum class net.preibisch.mvrecon.imglib2.st.filter.GaussianFilterFactory.WeightType

BY_SUM_OF_WEIGHTS - Enum constant in enum class net.preibisch.mvrecon.imglib2.st.filter.GaussianFilterFactory.WeightType

bytesPerImage - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader.IFDData

bytesPerImage - Variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader.IFDData

bytesPerPixel() - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

bz - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.TranslationInvariantLocalCoordinateSystemPointDescriptor

C

c - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList.ViewSetupPrecursor

c - Variable in class net.preibisch.mvrecon.fiji.ImgLib2Temp.ValueTriple

c - Variable in class net.preibisch.mvrecon.headless.definedataset.StackList.ViewSetupPrecursor

cache - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationExplorerPanel

CACHE_GROUP - Static variable in class net.preibisch.mvrecon.process.fusion.blk.DisplacementFieldN5Tools

cacheBlockSize - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

CACHED - Enum constant in enum class net.preibisch.mvrecon.process.fusion.FusionTools.ImgDataType

CACHED_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.XmlIoFlatfieldCorrectedWrappedImgLoader

cacheImages() - Method in class net.preibisch.mvrecon.process.deconvolution.util.ProcessInputImages

cacheImages(int, int) - Method in class net.preibisch.mvrecon.process.deconvolution.util.ProcessInputImages

cacheMaxNumBlocks - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

cacheNormalizedWeights() - Method in class net.preibisch.mvrecon.process.deconvolution.util.ProcessInputImages

cacheNormalizedWeights(int, int) - Method in class net.preibisch.mvrecon.process.deconvolution.util.ProcessInputImages

cacheRandomAccessibleInterval(Collection<Group<V>>, int, int, HashMap<Group<V>, RandomAccessibleInterval<FloatType>>) - Static method in class net.preibisch.mvrecon.process.deconvolution.util.ProcessInputImages

cacheRandomAccessibleInterval(RandomAccessibleInterval<T>, long, T, int...) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

cacheRandomAccessibleInterval(RandomAccessibleInterval<T>, T, int...) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

cacheTypeInputImg - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

cacheTypeWeights - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

cacheUnnormalizedWeights() - Method in class net.preibisch.mvrecon.process.deconvolution.util.ProcessInputImages

cacheUnnormalizedWeights(int, int) - Method in class net.preibisch.mvrecon.process.deconvolution.util.ProcessInputImages

Cal(double[], String) - Constructor for class net.preibisch.mvrecon.fiji.plugin.Specify_Calibration.Cal

calculateFireNumber(double[][], FRC.ThresholdMethod) - Method in class net.preibisch.mvrecon.process.quality.FRC

Utility function that calculates the Fourier Image Resolution (FIRE) number using the provided FRC curve data.

calculateFireNumber(ImageProcessor, ImageProcessor, FRC.ThresholdMethod) - Method in class net.preibisch.mvrecon.process.quality.FRC

Utility function that calculates the Fourier Image Resolution (FIRE) number using the provided images.

calculateFrcCurve(ImageProcessor, ImageProcessor) - Method in class net.preibisch.mvrecon.process.quality.FRC

Calculate the Fourier Ring Correlation curve for two images.

calculateHash(ViewRegistration, ViewRegistration) - Static method in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.PairwiseStitchingResult

get a very simple hash of two ViewRegistrations

calculateThresholdCurve(double[][], FRC.ThresholdMethod) - Method in class net.preibisch.mvrecon.process.quality.FRC

Calculate the curve representing the minimum correlation required to distinguish two images for each resolution in the input FRC curve.

Calibrateable - Interface in net.preibisch.mvrecon.process.export

CalibratedImg<T> - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

CalibratedImg(Img<T>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.CalibratedImg

CalibratedImg(Img<T>, double, double, double) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.CalibratedImg

Calibration - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

Calibration() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.StackList.Calibration

Calibration() - Constructor for class net.preibisch.mvrecon.headless.definedataset.StackList.Calibration

Calibration(double, double, double) - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.StackList.Calibration

Calibration(double, double, double) - Constructor for class net.preibisch.mvrecon.headless.definedataset.StackList.Calibration

Calibration(double, double, double, String) - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.StackList.Calibration

Calibration(double, double, double, String) - Constructor for class net.preibisch.mvrecon.headless.definedataset.StackList.Calibration

Calibration(int, int, int, double, double, double) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.Calibration

calibration1 - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

calibration2 - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

calibrationChoice1 - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

calibrationChoice2 - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

calibrations - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

call() - Method in class net.preibisch.mvrecon.headless.definedataset.Rewrite_LuxendoXML

call() - Method in class net.preibisch.mvrecon.process.deconvolution.init.PsiInitAvgApproxThread

call() - Method in class net.preibisch.mvrecon.process.deconvolution.init.PsiInitAvgPreciseThread

call() - Method in class net.preibisch.mvrecon.process.deconvolution.init.PsiInitBlurredFusedThread

calUnit - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList.Calibration

calUnit - Variable in class net.preibisch.mvrecon.headless.definedataset.StackList.Calibration

calUnit() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

calUnit() - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

calUnit() - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

calX - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList.Calibration

calX - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

calX - Variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

calX - Variable in class net.preibisch.mvrecon.headless.definedataset.StackList.Calibration

calX() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

calX() - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

calX() - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

calY - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList.Calibration

calY - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

calY - Variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

calY - Variable in class net.preibisch.mvrecon.headless.definedataset.StackList.Calibration

calY() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

calY() - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

calY() - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

calZ - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList.Calibration

calZ - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

calZ - Variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

calZ - Variable in class net.preibisch.mvrecon.headless.definedataset.StackList.Calibration

calZ() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

calZ() - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

calZ() - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

CAM_PATTERN - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData

CancelButtonListener(Frame, BigDataViewer) - Constructor for class net.preibisch.mvrecon.fiji.plugin.apply.BigDataViewerTransformationWindow.CancelButtonListener

canDoNumDimension(int) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.FixedModel

canDoNumDimension(int) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantAffineModel3D

canDoNumDimension(int) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantFixedModel

canDoNumDimension(int) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantModel

The TranslationInvariantModel can tell which dimensions it supports.

canDoNumDimension(int) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel2D

canDoNumDimension(int) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel3D

canDoNumDimension(int) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantSimilarityModel3D

canLoadTileLocationFromMeta() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

canLoadTileLocationFromMeta() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListImageJ

canLoadTileLocationFromMeta() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListLOCI

capacity() - Method in class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.FlattenedMatches

capacity() - Method in class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.MatchIndices

ceilScaled(double[], double) - Static method in class util.Grid

cellDim - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

cellDim - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.DisplayFusedImagesPopup

cellDim - Static variable in class net.preibisch.mvrecon.process.deconvolution.MultiViewDeconvolution

CellImg - Enum constant in enum class net.preibisch.mvrecon.headless.definedataset.StackListParameters.Container

cellImgBoundedCache(BlockSupplier<T>, long[], int[], int) - Static method in class util.BlockSupplierUtils

center - Variable in class net.preibisch.legacy.registration.threshold.ComponentProperties

CenterOfMassGUI - Class in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise

Center of mass GUI

CenterOfMassGUI() - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.CenterOfMassGUI

CenterOfMassPairwise<I> - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.centerofmass

CenterOfMassPairwise(CenterOfMassParameters) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.centerofmass.CenterOfMassPairwise

CenterOfMassParameters - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.centerofmass

Center of Mass (Avg/Median) implementation

CenterOfMassParameters(int) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.centerofmass.CenterOfMassParameters

centerType - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.CenterOfMassGUI

centerType - Variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.centerofmass.CenterOfMassParameters

centerWindow(Window) - Static method in class net.preibisch.mvrecon.process.interestpointremoval.histogram.Histogram

channel() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.FileMapEntry

CHANNEL_PATTERN - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData

CHANNEL_PATTERN - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

channelChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

channelCount - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.TileOrAngleInfo

channelIndex(Group<? extends ViewDescription>, ArrayList<Channel>) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

ChannelInfo() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.ChannelInfo

channelName(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

channelName(int) - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

channelNameList - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

channelNameList - Variable in class net.preibisch.mvrecon.headless.definedataset.StackList.ViewSetupPrecursor

channelNames - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

channelNames - Variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

ChannelOrIlluminationInfo() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.ChannelOrIlluminationInfo

channels - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM.SmartSPIMMetaData

channels - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

channels - Variable in class net.preibisch.mvrecon.headless.definedataset.DefineDataSetParameters

channels - Variable in class net.preibisch.mvrecon.headless.definedataset.StackListParameters

channels() - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

channels(List<? extends Group<? extends ViewDescription>>) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

CHANNELS_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoSmartSPIMImgLoader

channelsGrouped() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.ExplorerWindow

channelsGrouped() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorerPanel

chartMouseClicked(ChartMouseEvent) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.statistics.MouseListenerTimelapse

chartMouseClicked(ChartMouseEvent) - Method in class net.preibisch.mvrecon.process.interestpointremoval.histogram.MouseListenerValue

chartMouseMoved(ChartMouseEvent) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.statistics.MouseListenerTimelapse

chartMouseMoved(ChartMouseEvent) - Method in class net.preibisch.mvrecon.process.interestpointremoval.histogram.MouseListenerValue

checkAndRemoveZeroVolume(SpimData2, IL) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyFileMapImgLoaderLOCI

checkAndRemoveZeroVolume(SpimData2, IL, boolean) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyFileMapImgLoaderLOCI

check if views in spimData contain zero-valued planes at the end of the z-axis.

checkBoxResult - Variable in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

checkBoxText - Variable in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

checkIntegrity(File) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.DHMMetaData

checkMaximaXTree(ArrayList<DoGMaximum>, float) - Static method in class net.preibisch.legacy.registration.bead.laplace.LaPlaceFunctions

checkMultipleTimepoints(Map<Integer, List<Pair<Integer, Integer>>>) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil

checkMultiplicity(Map<T, List<S>>) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil

checkPath(String) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoaderLOCI

ChooseDirectoryListener(TextField) - Constructor for class net.preibisch.mvrecon.fiji.plugin.util.PluginHelper.ChooseDirectoryListener

ChooseXmlFileListener(TextField) - Constructor for class net.preibisch.mvrecon.fiji.plugin.util.PluginHelper.ChooseXmlFileListener

clamp(double, double) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Clamps this tuple to the range [low, high].

clamp(double, double) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Clamps this tuple to the range [low, high].

clamp(double, double, Tuple3d) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Clamps the tuple parameter to the range [low, high] and places the values into this tuple.

clamp(double, double, Tuple4d) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Clamps the tuple parameter to the range [low, high] and places the values into this tuple.

clamp(float, float) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

clamp(float, float) - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Clamps this tuple to the range [low, high].

clamp(float, float) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

clamp(float, float) - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Clamps this tuple to the range [low, high].

clamp(float, float, Tuple3d) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

clamp(float, float, Tuple3f) - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Clamps the tuple parameter to the range [low, high] and places the values into this tuple.

clamp(float, float, Tuple4d) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

clamp(float, float, Tuple4f) - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Clamps the tuple parameter to the range [low, high] and places the values into this tuple.

clamp(int, int) - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Clamps this tuple to the range [low, high].

clamp(int, int, Tuple3i) - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Clamps the tuple parameter to the range [low, high] and places the values into this tuple.

clampMax(double) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Clamps the maximum value of this tuple to the max parameter.

clampMax(double) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Clamps the maximum value of this tuple to the max parameter.

clampMax(double, Tuple3d) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Clamps the maximum value of the tuple parameter to the max parameter and places the values into this tuple.

clampMax(double, Tuple4d) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Clamps the maximum value of the tuple parameter to the max parameter and places the values into this tuple.

clampMax(float) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

clampMax(float) - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Clamps the maximum value of this tuple to the max parameter.

clampMax(float) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

clampMax(float) - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Clamps the maximum value of this tuple to the max parameter.

clampMax(float, Tuple3d) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

clampMax(float, Tuple3f) - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Clamps the maximum value of the tuple parameter to the max parameter and places the values into this tuple.

clampMax(float, Tuple4d) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

clampMax(float, Tuple4f) - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Clamps the maximum value of the tuple parameter to the max parameter and places the values into this tuple.

clampMax(int) - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Clamps the maximum value of this tuple to the max parameter.

clampMax(int, Tuple3i) - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Clamps the maximum value of the tuple parameter to the max parameter and places the values into this tuple.

clampMin(double) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Clamps the minimum value of this tuple to the min parameter.

clampMin(double) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Clamps the minimum value of this tuple to the min parameter.

clampMin(double, Tuple3d) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Clamps the minimum value of the tuple parameter to the min parameter and places the values into this tuple.

clampMin(double, Tuple4d) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Clamps the minimum value of the tuple parameter to the min parameter and places the values into this tuple.

clampMin(float) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

clampMin(float) - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Clamps the minimum value of this tuple to the min parameter.

clampMin(float) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

clampMin(float) - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Clamps the minimum value of this tuple to the min parameter.

clampMin(float, Tuple3d) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

clampMin(float, Tuple3f) - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Clamps the minimum value of the tuple parameter to the min parameter and places the values into this tuple.

clampMin(float, Tuple4d) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

clampMin(float, Tuple4f) - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Clamps the minimum value of the tuple parameter to the min parameter and places the values into this tuple.

clampMin(int) - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Clamps the minimum value of this tuple to the min parameter.

clampMin(int, Tuple3i) - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Clamps the minimum value of the tuple parameter to the min parameter and places the values into this tuple.

cleanupViewSetupIdOverlay() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

clear() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough.MyTarget

clearAllViewerTransform() - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough

clearCorrespondences(Collection<V>, Map<V, ViewInterestPointLists>, Map<V, HashMap<String, Double>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.MatcherPairwiseTools

clearCorrespondences(Map<V, ? extends Map<String, ? extends InterestPoints>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.MatcherPairwiseTools

clearFilters() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedTableModel

clearFilters() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.ISpimDataTableModel

clearFilters() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MissingViewsTableModelDecorator

clearFilters() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MultiViewTableModelDecorator

clearGroupingCheckboxes() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

Update UI checkboxes when grouping is programmatically cleared.

clearGroupingCheckboxes() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorerPanel

clearGroupingFactors() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedTableModel

clearGroupingFactors() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.ISpimDataTableModel

clearGroupingFactors() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MissingViewsTableModelDecorator

clearGroupingFactors() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MultiViewTableModelDecorator

clearSortingFactors() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedTableModel

clearSortingFactors() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.ISpimDataTableModel

clearSortingFactors() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MissingViewsTableModelDecorator

clearSortingFactors() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MultiViewTableModelDecorator

clone() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoint

clone() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.GroupedInterestPoint

clone() - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4d

Creates a new object of the same class as this object.

clone() - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4f

Creates a new object of the same class as this object.

clone() - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Creates a new object of the same class as this object.

clone() - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Creates a new object of the same class as this object.

clone() - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Creates a new object of the same class as this object.

clone() - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Creates a new object of the same class as this object.

clone() - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Creates a new object of the same class as this object.

clone() - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Creates a new object of the same class as this object.

clone() - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Creates a new object of the same class as this object.

clone() - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Creates a new object of the same class as this object.

clone() - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Creates a new object of the same class as this object.

close() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

close() - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

close(Frame) - Method in class net.preibisch.mvrecon.process.interestpointremoval.InteractiveProjections

close(Frame, BigDataViewer) - Method in class net.preibisch.mvrecon.fiji.plugin.apply.BigDataViewerTransformationWindow

closeBDV() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BasicBDVPopup

closeBDV() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BDVPopup

closeBDV() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.LazyBDVPopup

CLOSEST_PIXEL_WINS - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI.FusionType

closestLargerLongDivisableBy(long, long) - Static method in class net.preibisch.mvrecon.process.splitting.SplitDistributeEvenly

closestLongDivisableBy(long, long) - Static method in class net.preibisch.mvrecon.process.splitting.SplitDistributeEvenly

closestSmallerLongDivisableBy(long, long) - Static method in class net.preibisch.mvrecon.process.splitting.SplitDistributeEvenly

cloudThreads - Static variable in class util.URITools

coefficientMatches() - Method in class net.preibisch.mvrecon.process.fusion.intensity.ViewPairCoefficientMatches

Coefficients - Class in net.preibisch.mvrecon.process.fusion.intensity

Holds flattened coefficient array and dimensions.

Coefficients(double[][], int...) - Constructor for class net.preibisch.mvrecon.process.fusion.intensity.Coefficients

collapse() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.viewneighbours.ViewNeighboursWindow

Drive selection back to lastActual and reset BDV colours of the previously highlighted views.

collapse() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.viewneighbours.ViewOverlapWindow

collect(int, List<? extends Pair<? extends Pair<ViewId, ViewId>, ? extends PairwiseResult<?>>>) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.statistics.RegistrationStatistics

collectImageSizes(AbstractSpimData<?>) - Static method in class net.preibisch.mvrecon.process.splitting.SplittingTools

collectInterestPointData(SpimData2, boolean) - Static method in class net.preibisch.mvrecon.fiji.spimdata.XmlIoSpimData2

Collect all modified interest points as serializable InterestPointData objects.

collectNumericPrefixes(Iterable<String>) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.patterndetector.NumericalFilenamePatternDetector

color - Variable in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

Color3f - Class in net.preibisch.mvrecon.vecmath

A three-element color value represented by single precision floating point x,y,z values.

Color3f() - Constructor for class net.preibisch.mvrecon.vecmath.Color3f

Constructs and initializes a Color3f to (0.0, 0.0, 0.0).

Color3f(float[]) - Constructor for class net.preibisch.mvrecon.vecmath.Color3f

Constructs and initializes a Color3f from the array of length 3.

Color3f(float, float, float) - Constructor for class net.preibisch.mvrecon.vecmath.Color3f

Constructs and initializes a Color3f from the three xyz values.

Color3f(Color) - Constructor for class net.preibisch.mvrecon.vecmath.Color3f

Constructs and initializes a Color3f from the specified AWT Color object.

Color3f(Color3f) - Constructor for class net.preibisch.mvrecon.vecmath.Color3f

Constructs and initializes a Color3f from the specified Color3f.

Color3f(Tuple3d) - Constructor for class net.preibisch.mvrecon.vecmath.Color3f

Constructs and initializes a Color3f from the specified Tuple3d.

Color3f(Tuple3f) - Constructor for class net.preibisch.mvrecon.vecmath.Color3f

Constructs and initializes a Color3f from the specified Tuple3f.

colorByFactors(BigDataViewer, AbstractSpimData<?>, Set<Class<? extends Entity>>, long) - Static method in class util.BDVTools

Colors sources based on grouping factors (Tile, Illumination, etc.).

colorMode - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

colorMode() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.ExplorerWindow

colorMode() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

colorSourcesBatch(BigDataViewer, long) - Static method in class util.BDVTools

Colors sources sequentially using the proper ConverterSetups API.

ColorStream - Class in util

Generate a stream of `random' saturated RGB colors with all colors being maximally distinct from each other.

ColorStream() - Constructor for class util.ColorStream

combineBy(List<V>, Set<Class<? extends Entity>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

Combining means to combine all views that share everything except what they are grouped after, e.g. channel (for example used to group GFP, RFP, DAPI for a Tile) v1: angle 0, channel 0 v2: angle 1, channel 0 v3: angle 1, channel 1 combine by channel: [v1], [v2 v3]

combineOrSplitBy(List<V>, Set<Class<? extends Entity>>, boolean) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

Combining means to combine all views that share everything except what they are grouped after, e.g. channel (for example used to group GFP, RFP, DAPI for a Tile) Split means the opposite in some way, make a group for every instance of an attribute, e.g. channel (for example group everthing that is GFP and everything that it RFP) v1: angle 0, channel 0 v2: angle 1, channel 0 v3: angle 1, channel 1 combine by channel: [v1], [v2 v3] split by channel: [v1 v2], [v3]

CombineWeightsMulRandomAccess - Class in net.preibisch.mvrecon.process.fusion.transformed.weightcombination

CombineWeightsMulRandomAccess(int, List<? extends RandomAccessible<FloatType>>) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsMulRandomAccess

CombineWeightsRandomAccess - Class in net.preibisch.mvrecon.process.fusion.transformed.weightcombination

CombineWeightsRandomAccess(int, List<? extends RandomAccessible<FloatType>>) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccess

CombineWeightsRandomAccessibleInterval - Class in net.preibisch.mvrecon.process.fusion.transformed.weightcombination

CombineWeightsRandomAccessibleInterval(Interval, List<? extends RandomAccessible<FloatType>>, CombineWeightsRandomAccessibleInterval.CombineType) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccessibleInterval

Combines N randomaccessibles in a defined interval by multiplication or average

CombineWeightsRandomAccessibleInterval(Interval, RandomAccessible<FloatType>, RandomAccessible<FloatType>, CombineWeightsRandomAccessibleInterval.CombineType) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccessibleInterval

Combines two randomaccessibles in a defined interval by multiplication or average

CombineWeightsRandomAccessibleInterval.CombineType - Enum Class in net.preibisch.mvrecon.process.fusion.transformed.weightcombination

CombineWeightsSumRandomAccess - Class in net.preibisch.mvrecon.process.fusion.transformed.weightcombination

CombineWeightsSumRandomAccess(int, List<? extends RandomAccessible<FloatType>>) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsSumRandomAccess

COMMENTS_HEADER - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

COMMENTS_HEADER - Static variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

COMMENTS_OFFSET_HEADER - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

COMMENTS_OFFSET_HEADER - Static variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

commonSize(List<Img<T>>) - Static method in class net.preibisch.mvrecon.process.psf.PSFCombination

Returns the bounding box so that all images can fit in there or null if input is null or input.size is 0

commonStrings(List<String>, List<String>) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.DHMMetaData

comparator - Variable in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

compareTo(RegistrationStatistics) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.statistics.RegistrationStatistics

compareTo(BoundingBox) - Method in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox

compareTo(CorrespondingInterestPoints) - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.CorrespondingInterestPoints

compareTo(CUDADevice) - Method in class net.preibisch.mvrecon.process.cuda.CUDADevice

ComponentProperties - Class in net.preibisch.legacy.registration.threshold

ComponentProperties() - Constructor for class net.preibisch.legacy.registration.threshold.ComponentProperties

compress - Variable in class net.preibisch.mvrecon.fiji.plugin.resave.Resave_TIFF.ParametersResaveAsTIFF

compress() - Method in class net.preibisch.mvrecon.fiji.plugin.resave.Resave_TIFF.ParametersResaveAsTIFF

compression - Variable in class net.preibisch.mvrecon.fiji.plugin.resave.ParametersResaveN5Api

compressionDescriptionsString - Static variable in class net.preibisch.mvrecon.fiji.plugin.util.PluginHelper

compressionsColors - Static variable in class net.preibisch.mvrecon.fiji.plugin.util.PluginHelper

compressionsString - Static variable in class net.preibisch.mvrecon.fiji.plugin.util.PluginHelper

computation - Variable in class net.preibisch.legacy.registration.bead.SegmentationBenchmark

computationOnChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

computationOnChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGaussianGUI

computeAverageCalibration(Iterable<? extends BasicViewDescription<?>>, ViewRegistrations) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

computeAverageImage(Collection<? extends RandomAccessibleInterval<T>>, ImgFactory<T>, boolean) - Static method in class net.preibisch.mvrecon.process.psf.PSFCombination

compute the average psf in original calibration and after applying the transformations

ComputeBlockMulThread - Interface in net.preibisch.mvrecon.process.deconvolution.iteration.mul

Executes one Lucy-Richardson iteration on one specifc block.

ComputeBlockMulThreadAbstract - Class in net.preibisch.mvrecon.process.deconvolution.iteration.mul

ComputeBlockMulThreadAbstract(float, int, int[], int) - Constructor for class net.preibisch.mvrecon.process.deconvolution.iteration.mul.ComputeBlockMulThreadAbstract

Instantiate a block thread

ComputeBlockMulThreadAbstract(ImgFactory<FloatType>, int, float, int[], int) - Constructor for class net.preibisch.mvrecon.process.deconvolution.iteration.mul.ComputeBlockMulThreadAbstract

Instantiate a block thread

ComputeBlockMulThreadCPU - Class in net.preibisch.mvrecon.process.deconvolution.iteration.mul

ComputeBlockMulThreadCPU(ExecutorService, int, float, float, int, int[], ImgFactory<FloatType>) - Constructor for class net.preibisch.mvrecon.process.deconvolution.iteration.mul.ComputeBlockMulThreadCPU

ComputeBlockMulThreadCPUFactory - Class in net.preibisch.mvrecon.process.deconvolution.iteration.mul

ComputeBlockMulThreadCPUFactory(ExecutorService, int, float, float, int[], ImgFactory<FloatType>) - Constructor for class net.preibisch.mvrecon.process.deconvolution.iteration.mul.ComputeBlockMulThreadCPUFactory

ComputeBlockMulThreadCPUFactory(ExecutorService, int, float, int[], ImgFactory<FloatType>) - Constructor for class net.preibisch.mvrecon.process.deconvolution.iteration.mul.ComputeBlockMulThreadCPUFactory

ComputeBlockSeqThread - Interface in net.preibisch.mvrecon.process.deconvolution.iteration.sequential

Executes one Lucy-Richardson iteration on one specifc block.

ComputeBlockSeqThreadAbstract - Class in net.preibisch.mvrecon.process.deconvolution.iteration.sequential

ComputeBlockSeqThreadAbstract(float, int[], int) - Constructor for class net.preibisch.mvrecon.process.deconvolution.iteration.sequential.ComputeBlockSeqThreadAbstract

Instantiate a block thread

ComputeBlockSeqThreadAbstract(ImgFactory<FloatType>, float, int[], int) - Constructor for class net.preibisch.mvrecon.process.deconvolution.iteration.sequential.ComputeBlockSeqThreadAbstract

Instantiate a block thread

ComputeBlockSeqThreadCPU - Class in net.preibisch.mvrecon.process.deconvolution.iteration.sequential

ComputeBlockSeqThreadCPU(ExecutorService, float, float, int, int[], ImgFactory<FloatType>) - Constructor for class net.preibisch.mvrecon.process.deconvolution.iteration.sequential.ComputeBlockSeqThreadCPU

ComputeBlockSeqThreadCPUFactory - Class in net.preibisch.mvrecon.process.deconvolution.iteration.sequential

ComputeBlockSeqThreadCPUFactory(ExecutorService, float, float, int[], ImgFactory<FloatType>) - Constructor for class net.preibisch.mvrecon.process.deconvolution.iteration.sequential.ComputeBlockSeqThreadCPUFactory

ComputeBlockSeqThreadCPUFactory(ExecutorService, float, int[], ImgFactory<FloatType>) - Constructor for class net.preibisch.mvrecon.process.deconvolution.iteration.sequential.ComputeBlockSeqThreadCPUFactory

ComputeBlockSeqThreadCUDA - Class in net.preibisch.mvrecon.process.deconvolution.iteration.sequential

ComputeBlockSeqThreadCUDA(ExecutorService, float, float, int, int[], CUDAFourierConvolution, CUDADevice) - Constructor for class net.preibisch.mvrecon.process.deconvolution.iteration.sequential.ComputeBlockSeqThreadCUDA

ComputeBlockSeqThreadCUDAFactory - Class in net.preibisch.mvrecon.process.deconvolution.iteration.sequential

ComputeBlockSeqThreadCUDAFactory(ExecutorService, float, float, int[], CUDAFourierConvolution, HashMap<Integer, CUDADevice>) - Constructor for class net.preibisch.mvrecon.process.deconvolution.iteration.sequential.ComputeBlockSeqThreadCUDAFactory

computeBlocksizeFactor() - Method in class net.preibisch.mvrecon.process.export.ExportN5Api

ComputeBlockThread - Interface in net.preibisch.mvrecon.process.deconvolution.iteration

Executes one Lucy-Richardson iteration on one specifc block.

ComputeBlockThread.IterationStatistics - Class in net.preibisch.mvrecon.process.deconvolution.iteration

ComputeBlockThreadAbstract - Class in net.preibisch.mvrecon.process.deconvolution.iteration

ComputeBlockThreadAbstract(ImgFactory<FloatType>, float, int[], int) - Constructor for class net.preibisch.mvrecon.process.deconvolution.iteration.ComputeBlockThreadAbstract

Instantiate a block thread

ComputeBlockThreadFactory<C> - Interface in net.preibisch.mvrecon.process.deconvolution.iteration

computeBoundingBox(Img<T>, double, int[], int[]) - Static method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxMinFilterThreshold

computeCalibration(BasicViewDescription<?>, ViewRegistrations) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

computeConvolution(Img<ComplexFloatType>, Img<ComplexFloatType>, RandomAccessibleInterval<R>, boolean, ExecutorService) - Static method in class util.FFTConvolution

computeCrossViewNailDonations(SplitViewerImgLoader, Map<Integer, List<Integer>>, Map<ViewId, ViewRegistration>, Collection<? extends ViewId>, double, double, ViewInterestPoints, String, int, double, int, int[], int[], Consumer<SplitImgLoaderThinPlateSplineFusion.LandmarkRecord>) - Static method in class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion

Compute cross-view nail donations across all underlying views in one pass.

computeDerivativeVector3(RandomAccess<FloatType>) - Static method in class net.preibisch.legacy.registration.bead.laplace.LaPlaceFunctions

computeDoG(RandomAccessible<T>, RandomAccessible<T>, Interval, double, double, int, boolean, boolean, double, double, int[], ExecutorService, CUDASeparableConvolution, CUDADevice, boolean, double) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2

computeDoG(RandomAccessible<T>, RandomAccessible<T>, Interval, double, double, int, boolean, boolean, double, double, ExecutorService) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2

computeEigenDecomposition(double[]) - Static method in class net.preibisch.legacy.registration.bead.laplace.LaPlaceFunctions

computeExponentialKernel(ArrayImg<FloatType, ?>, int) - Static method in class net.preibisch.mvrecon.process.deconvolution.DeconViewPSF

computeFactory - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

computeFinalValues(long, long, RandomAccessibleInterval<FloatType>, RandomAccessibleInterval<FloatType>, RandomAccessibleInterval<FloatType>, double, float, float, double[]) - Static method in class net.preibisch.mvrecon.process.deconvolution.iteration.mul.DeconvolutionMethods

computeFinalValues(long, long, RandomAccessibleInterval<FloatType>, RandomAccessibleInterval<FloatType>, RandomAccessibleInterval<FloatType>, double, float, float, double[]) - Static method in class net.preibisch.mvrecon.process.deconvolution.iteration.sequential.DeconvolutionMethods

computeFinalValuesMul(long, long, RandomAccessibleInterval<FloatType>, List<? extends RandomAccessibleInterval<FloatType>>, List<? extends RandomAccessibleInterval<FloatType>>, double, float, float, double[]) - Static method in class net.preibisch.mvrecon.process.deconvolution.iteration.mul.DeconvolutionMethods

computeFinalValuesMul(long, long, RandomAccessibleInterval<FloatType>, List<? extends RandomAccessibleInterval<FloatType>>, List<? extends RandomAccessibleInterval<FloatType>>, double, float, float, double[]) - Static method in class net.preibisch.mvrecon.process.deconvolution.iteration.sequential.DeconvolutionMethods

computeFRC(ViewId, BasicImgLoader, int, int, boolean) - Static method in class net.preibisch.mvrecon.process.quality.FRCTools

computeFRC(RandomAccessible<FloatType>, Point, int) - Static method in class net.preibisch.mvrecon.process.quality.FRCRealRandomAccessible

computeGaussCUDA(RandomAccessibleInterval<FloatType>, double[], CUDASeparableConvolution, CUDADevice, boolean, double) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2

computeGaussLocalization(ArrayList<SimplePeak>, RandomAccessibleInterval<FloatType>, double, boolean, boolean, float, boolean) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.Localization

computeGrids(Collection<? extends ViewId>, HashMap<? extends ViewId, ? extends Collection<? extends NonrigidIP>>, long[], double, Interval, boolean, ExecutorService) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidTools

computeGroupPairs(SpimData2, ArrayList<AnalyzeErrorsUtil.PairError>, AnalyzeErrorsUtil.Parameters) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil

Bucket per-pair errors into per-group-pair buckets using Group.combineBy(java.util.List<V>, java.util.Set<java.lang.Class<? extends mpicbg.spim.data.generic.base.Entity>>) (collapse semantics — same as ViewSetupExplorer / Interest_Point_Registration grouping).

computeHessianMatrix3x3(RandomAccess<FloatType>) - Static method in class net.preibisch.legacy.registration.bead.laplace.LaPlaceFunctions

computeImgFFT(Interval, RandomAccessible<R>, ImgFactory<ComplexFloatType>, ExecutorService) - Static method in class util.FFTConvolution

computeIntensityAdjustment(AbstractSpimData<?>, List<? extends ViewId>, M, Interval, double, int, Map<? extends ViewId, AffineModel1D>) - Static method in class net.preibisch.mvrecon.process.fusion.intensityadjust.IntensityAdjustmentTools

computeInvertedKernel(ArrayImg<FloatType, ?>) - Static method in class net.preibisch.mvrecon.process.deconvolution.DeconViewPSF

computeK(int) - Static method in class net.preibisch.legacy.registration.bead.laplace.LaPlaceFunctions

computeKernelFFT(Interval, long[], long[], boolean, RandomAccessible<R>, ImgFactory<ComplexFloatType>, ExecutorService) - Static method in class util.FFTConvolution

computeKWeight(float) - Static method in class net.preibisch.legacy.registration.bead.laplace.LaPlaceFunctions

computeLazyMinFilter(Img<T>, int) - Static method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxMinFilterThreshold

By lazy I mean I was lazy to use a second image, one could of course implement it on a n-d line by line basis @TODO

computeMapBackModel(Dimensions, AffineTransform3D, AbstractModel<?>, Model<?>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

computeMatching(ArrayList<LocalCoordinateSystemPointDescriptor<I>>, KNearestNeighborSearchOnKDTree<LocalCoordinateSystemPointDescriptor<I>>, ArrayList<PointMatchGeneric<I>>, double, double) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.geometrichashing.GeometricHasher

computeMatching(ArrayList<TranslationInvariantLocalCoordinateSystemPointDescriptor<I>>, KNearestNeighborSearchOnKDTree<TranslationInvariantLocalCoordinateSystemPointDescriptor<I>>, ArrayList<PointMatchGeneric<I>>, double) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.fastrgldm.FRGLDMMatcher

computeMaxAverageTransformedPSF(Collection<? extends RandomAccessibleInterval<T>>, ImgFactory<T>) - Static method in class net.preibisch.mvrecon.process.psf.PSFCombination

computeMaxBoundingBoxDimensions(Collection<ViewId>, HashMap<ViewId, Dimensions>, HashMap<ViewId, AffineTransform3D>, double[], double[]) - Static method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxMaximal

computeMaxDimTransformedPSF(Collection<? extends Interval>) - Static method in class net.preibisch.mvrecon.process.psf.PSFCombination

computeMaxProjection(RandomAccessibleInterval<S>, ImgFactory<S>, int, boolean) - Static method in class net.preibisch.mvrecon.process.psf.PSFCombination

computeMaxProjectionPSF(Img<T>) - Static method in class net.preibisch.mvrecon.process.psf.PSFCombination

computeMinDimTransformedPSF(Collection<? extends Interval>) - Static method in class net.preibisch.mvrecon.process.psf.PSFCombination

computeModels(M, boolean, PointMatchCreator, ConvergenceStrategy, Collection<ViewId>, Collection<Group<ViewId>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.global.GlobalOpt

computeModels(M, boolean, PointMatchCreator, IterativeConvergenceStrategy, LinkRemovalStrategy, Collection<ViewId>, Collection<Group<ViewId>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.global.GlobalOptIterative

computeModels(M, boolean, PointMatchCreator, IterativeConvergenceStrategy, LinkRemovalStrategy, Collection<Pair<Group<ViewId>, Group<ViewId>>>, Collection<ViewId>, Collection<Group<ViewId>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.global.GlobalOptIterative

computeModels(M, boolean, PointMatchCreator, IterativeConvergenceStrategy, LinkRemovalStrategy, Collection<Pair<Group<ViewId>, Group<ViewId>>>, WeakLinkFactory, ConvergenceStrategy, Collection<ViewId>, Collection<Group<ViewId>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.global.GlobalOptTwoRound

computeModels(M, boolean, PointMatchCreator, IterativeConvergenceStrategy, LinkRemovalStrategy, WeakLinkFactory, ConvergenceStrategy, Collection<ViewId>, Collection<Group<ViewId>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.global.GlobalOptTwoRound

computeNumBlocksDim(long, long, double, int, String) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2

computeOnIndex - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

computeOutlierRatio(List<OctTreeSplitCriterion.SplitCorrespondence>) - Static method in class net.preibisch.mvrecon.process.splitting.ConsensusSetCriterion

Compute the aggregate outlier ratio across all view pairs.

computePairs(List<Pair<V, V>>, Map<V, ? extends Map<String, ? extends Collection<I>>>, MatcherPairwise<I>, boolean, ExecutorService) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.MatcherPairwiseTools

computePairs(List<Pair<V, V>>, Map<V, HashMap<String, Collection<I>>>, MatcherPairwise<I>, boolean) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.MatcherPairwiseTools

computePD(int, int, int) - Static method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.SubsetMatcher

computePDRecursive(int, int, int) - Static method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.SubsetMatcher

Computes recursively how to create different PointDescriptors of the same Point when some tolerance is allowed, e.g. there are outliers which should be identified.

computeProjection(Img<S>, int, boolean) - Static method in class net.preibisch.mvrecon.process.psf.PSFCombination

Get projection along the smallest dimension (which is usually the rotation axis)

computeQuadraticLocalization(ArrayList<SimplePeak>, RandomAccessible<FloatType>, Interval, boolean, boolean, float, boolean, ExecutorService) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.Localization

computeQuotient(long, long, RandomAccessibleInterval<FloatType>, RandomAccessibleInterval<FloatType>) - Static method in class net.preibisch.mvrecon.process.deconvolution.iteration.mul.DeconvolutionMethods

One thread of a method to compute the quotient between two images of the multiview deconvolution

computeQuotient(long, long, RandomAccessibleInterval<FloatType>, RandomAccessibleInterval<FloatType>) - Static method in class net.preibisch.mvrecon.process.deconvolution.iteration.sequential.DeconvolutionMethods

One thread of a method to compute the quotient between two images of the multiview deconvolution

computeRANSAC(ArrayList<PointMatchGeneric<I>>, ArrayList<PointMatchGeneric<I>>, ArrayList<Integer>, Model<?>, double, double, int, int, boolean, double, boolean) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac.RANSAC

computeReferencePoints(Collection<ViewId>, ArrayList<HashSet<CorrespondingIP>>) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidTools

computeRelativeDownsampling(int[][], int) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

computeRelativeFRC(RandomAccessible<FloatType>, Point, int, int) - Static method in class net.preibisch.mvrecon.process.quality.FRCRealRandomAccessible

computeScrollbarPositionFromValue(double, double, double, int) - Static method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.HelperFunctions

computeSigma(int, float, float) - Static method in class net.preibisch.legacy.registration.bead.laplace.LaPlaceFunctions

computeSigma2(double, int) - Static method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.HelperFunctions

computeSigmaDiff(float[], float) - Static method in class net.preibisch.legacy.registration.bead.laplace.LaPlaceFunctions

computeSigmas(float, int) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2

computeSingleGroupErrors(SpimData2, ArrayList<AnalyzeErrorsUtil.PairError>, AnalyzeErrorsUtil.Parameters) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil

Aggregate AnalyzeErrorsUtil.PairErrors into one AnalyzeErrorsUtil.SingleGroupError per group that participates in at least one group-pair under the supplied grouping AnalyzeErrorsUtil.Parameters.

computeSingleViewErrors(ArrayList<AnalyzeErrorsUtil.PairError>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil

Aggregate AnalyzeErrorsUtil.PairErrors into one AnalyzeErrorsUtil.SingleViewError per view that appears in at least one pair.

computeTiles(M, boolean, PointMatchCreator, ConvergenceStrategy, Collection<ViewId>, Collection<Group<ViewId>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.global.GlobalOpt

computeTiles(M, boolean, PointMatchCreator, IterativeConvergenceStrategy, LinkRemovalStrategy, Collection<Pair<Group<ViewId>, Group<ViewId>>>, Collection<ViewId>, Collection<Group<ViewId>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.global.GlobalOptIterative

computeTiles(M, boolean, PointMatchCreator, IterativeConvergenceStrategy, LinkRemovalStrategy, Collection<Pair<Group<ViewId>, Group<ViewId>>>, WeakLinkFactory, ConvergenceStrategy, Collection<ViewId>, Collection<Group<ViewId>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.global.GlobalOptTwoRound

computeValueFromScrollbarPosition(int, double, double, int) - Static method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.HelperFunctions

concatenateBoundingBoxOffset(DisplacementFields.TransformedDisplacementField<D>, Interval) - Static method in class net.preibisch.mvrecon.process.fusion.blk.BlkThinPlateSplineFusion

configureAnonymous(N5Factory, String) - Static method in class util.S3Tools

Configure the factory's S3 client with anonymous credentials and an optional region.

configureRegion(N5Factory, String) - Static method in class util.S3Tools

Configure the factory's S3 client to use the given region (credentialed path).

CONGRUENT - Static variable in class net.preibisch.mvrecon.vecmath.Transform3D

This is an angle and length preserving matrix, meaning that it can translate, rotate, and reflect about an axis, and scale by an amount that is uniform in all directions.

conjugate() - Method in class net.preibisch.mvrecon.vecmath.Quat4d

Negate the value of of each of this quaternion's x,y,z coordinates in place.

conjugate() - Method in class net.preibisch.mvrecon.vecmath.Quat4f

Sets the value of this quaternion to the conjugate of itself.

conjugate(Quat4d) - Method in class net.preibisch.mvrecon.vecmath.Quat4d

Sets the value of this quaternion to the conjugate of quaternion q1.

conjugate(Quat4f) - Method in class net.preibisch.mvrecon.vecmath.Quat4f

Sets the value of this quaternion to the conjugate of quaternion q1.

ConnectedComponent - Class in net.preibisch.legacy.registration.threshold

ConnectedComponent() - Constructor for class net.preibisch.legacy.registration.threshold.ConnectedComponent

connectedFor(SpimData2, Collection<? extends ViewId>, Collection<? extends ViewId>, Map<String, Double>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.ViewNeighbors

Per-click connectivity query.

connectedGroups - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.SingleGroupError

connectedTo(ViewId, SpimData2, Collection<? extends ViewId>, Map<String, Double>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.ViewNeighbors

Convenience: connected set for a single view (returns empty set if v not in universe).

connectedViews - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.SingleViewError

connectedViews(SpimData2, Collection<? extends ViewId>, Map<String, Double>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.ViewNeighbors

For each view in universe, return the set of other views in universe that share at least one same-label correspondence with it.

ConsensusSetCriterion - Class in net.preibisch.mvrecon.process.splitting

Criterion based on multi-consensus RANSAC sets.

ConsensusSetCriterion(SpimData2, Set<String>, int, ConsensusSetCriterion.ToleranceMode, double) - Constructor for class net.preibisch.mvrecon.process.splitting.ConsensusSetCriterion

Constructor.

ConsensusSetCriterion.ToleranceMode - Enum Class in net.preibisch.mvrecon.process.splitting

consensusSetId - Variable in class net.preibisch.mvrecon.process.splitting.OctTreeSplitCriterion.SplitCorrespondence

Consensus set ID (-1 for single-consensus mode)

container - Variable in class net.preibisch.mvrecon.headless.definedataset.StackListParameters

contains(String) - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.ViewInterestPointLists

contains(String, String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.util.GUIHelper

contains(V) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

containsAdjustments(IntensityAdjustments, Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.process.fusion.intensityadjust.IntensityAdjustmentTools

containsAny(String, String...) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition

containsBoth(V, V, Collection<? extends Group<V>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

ContentBased - Class in net.preibisch.mvrecon.process.fusion.blk

ContentBased() - Constructor for class net.preibisch.mvrecon.process.fusion.blk.ContentBased

ContentBasedFFTRealRandomAccessible<T> - Class in net.preibisch.mvrecon.process.fusion.transformed.weights

Computes the content-based fusion on a given image

ContentBasedFFTRealRandomAccessible(RandomAccessibleInterval<T>, ImgFactory<ComplexFloatType>, double[], double[]) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.weights.ContentBasedFFTRealRandomAccessible

ContentBasedRealRandomAccessible - Class in net.preibisch.mvrecon.process.fusion.transformed.weights

ContentBasedRealRandomAccessible(RandomAccessibleInterval<T>, double[], double[], int[], float) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.weights.ContentBasedRealRandomAccessible

controlPointDistance - Variable in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidParameters

ConvergenceStrategy - Class in net.preibisch.mvrecon.process.interestpointregistration.global.convergence

ConvergenceStrategy(double) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.global.convergence.ConvergenceStrategy

ConvergenceStrategy(double, int, int) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.global.convergence.ConvergenceStrategy

convert(SpimData) - Static method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

convert(FloatType, FloatType) - Method in class net.preibisch.mvrecon.process.fusion.intensityadjust.IntensityAdjuster

convertChoices - Static variable in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5

convertInput(RandomAccessibleInterval<T>) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

convertIntegerList(List<Integer>) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

convertToOutputType(BlockSupplier<FloatType>, Converter<FloatType, T>, T) - Static method in class net.preibisch.mvrecon.process.fusion.blk.BlkAffineFusion

convertVirtual(RandomAccessible<T>) - Static method in class util.ImgLib2Tools

convertVirtualRAI(RandomAccessibleInterval<T>) - Static method in class util.ImgLib2Tools

convolution3DfftCUDA(float[], int[], float[], int[], int) - Method in interface net.preibisch.mvrecon.process.cuda.CUDAFourierConvolution

convolution3DfftCUDAInPlace(float[], int[], float[], int[], int) - Method in interface net.preibisch.mvrecon.process.cuda.CUDAFourierConvolution

convolutionCPU(float[], float[], float[], float[], int, int, int, int, int, int, int, float) - Method in interface net.preibisch.mvrecon.process.cuda.CUDASeparableConvolution

convolve() - Method in class util.FFTConvolution

convolve(RandomAccessible<R>, Interval, RandomAccessible<R>, Interval, RandomAccessibleInterval<R>, ImgFactory<ComplexFloatType>, int) - Static method in class util.FFTConvolution

convolve_127(float[], float[], float[], float[], int, int, int, boolean, boolean, boolean, int, float, int) - Method in interface net.preibisch.mvrecon.process.cuda.CUDASeparableConvolution

convolve_15(float[], float[], float[], float[], int, int, int, boolean, boolean, boolean, int, float, int) - Method in interface net.preibisch.mvrecon.process.cuda.CUDASeparableConvolution

convolve_31(float[], float[], float[], float[], int, int, int, boolean, boolean, boolean, int, float, int) - Method in interface net.preibisch.mvrecon.process.cuda.CUDASeparableConvolution

convolve_63(float[], float[], float[], float[], int, int, int, boolean, boolean, boolean, int, float, int) - Method in interface net.preibisch.mvrecon.process.cuda.CUDASeparableConvolution

convolve_7(float[], float[], float[], float[], int, int, int, boolean, boolean, boolean, int, float, int) - Method in interface net.preibisch.mvrecon.process.cuda.CUDASeparableConvolution

convolve1(RandomAccessibleInterval<FloatType>, ArrayImg<FloatType, ?>, ArrayImg<FloatType, ?>) - Method in class net.preibisch.mvrecon.process.deconvolution.iteration.sequential.ComputeBlockSeqThreadCUDA

convolve1(RandomAccessibleInterval<FloatType>, Img<FloatType>, Img<ComplexFloatType>, Img<FloatType>) - Method in class net.preibisch.mvrecon.process.deconvolution.iteration.mul.ComputeBlockMulThreadCPU

convolve1(RandomAccessibleInterval<FloatType>, Img<FloatType>, Img<ComplexFloatType>, Img<FloatType>) - Method in class net.preibisch.mvrecon.process.deconvolution.iteration.sequential.ComputeBlockSeqThreadCPU

convolve2(ArrayImg<FloatType, ?>, ArrayImg<FloatType, ?>, ArrayImg<FloatType, ?>) - Method in class net.preibisch.mvrecon.process.deconvolution.iteration.sequential.ComputeBlockSeqThreadCUDA

convolve2(RandomAccessibleInterval<FloatType>, Img<FloatType>, Img<ComplexFloatType>, Img<FloatType>) - Method in class net.preibisch.mvrecon.process.deconvolution.iteration.mul.ComputeBlockMulThreadCPU

convolve2(RandomAccessibleInterval<FloatType>, Img<FloatType>, Img<ComplexFloatType>, Img<FloatType>) - Method in class net.preibisch.mvrecon.process.deconvolution.iteration.sequential.ComputeBlockSeqThreadCPU

copy() - Method in class net.preibisch.mvrecon.imglib2.st.render.FilteredMaxDistanceSearchOnKDTree

copy() - Method in interface net.preibisch.mvrecon.imglib2.st.render.IntegratingNeighborSearch

Create a copy.

copy() - Method in class net.preibisch.mvrecon.imglib2.st.render.IntegratingNeighborSearchInterpolator

copy() - Method in class net.preibisch.mvrecon.imglib2.st.render.NearestNeighborMaxDistanceSearchOnKDTree

copy() - Method in class net.preibisch.mvrecon.imglib2.st.render.util.SimpleSampler

copy() - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccess

copy() - Method in class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.FastAffineModel1D

copy() - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccess

copy() - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessFirstWins

copy() - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessMax

copy() - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessNoWeights

copy() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.CorrespondingIP

copy() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.DistanceVisualizingRandomAccess

copy() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridAccess

copy() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

copy() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

copy() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGridRandomAccess

copy() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.InterpolatingNonRigidRandomAccess

copy() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidRandomAccess

copy() - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputGeneralRandomAccess

copy() - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccess

copy() - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccess2d

copy() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccess

copy() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccess

copy() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.InterpolatingNonRigidRasteredRandomAccess

copy() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.NonRigidRasteredRandomAccess

copy() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.TransformedRasteredRandomAccess

copy() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.FixedModel

copy() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantAffineModel3D

copy() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantFixedModel

copy() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel2D

copy() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel3D

copy() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantSimilarityModel3D

copy() - Method in class util.StackingRealRandomAccessible.StackingRealRandomAccess

copy(RandomAccessible<? extends T>, RandomAccessibleInterval<T>) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2

copy(RandomAccessible<T>, RandomAccessibleInterval<S>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.FileMapImgLoaderLOCI2

Deprecated.

Use RealTypeConverters.copyFromTo(RandomAccessible, RandomAccessibleInterval).

copy(KeyValueAccess, String, String) - Static method in class util.URITools

copyBlock(RandomAccessible<FloatType>, RandomAccessibleInterval<FloatType>) - Method in class net.preibisch.mvrecon.process.cuda.Block

copyFactory - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

copyFile(File, File) - Static method in class util.URITools

copyImages() - Method in class net.preibisch.mvrecon.process.deconvolution.util.ProcessInputImages

copyImages(ImgFactory<FloatType>) - Method in class net.preibisch.mvrecon.process.deconvolution.util.ProcessInputImages

copyImg(long, long, RandomAccessibleInterval<T>, RandomAccessibleInterval<T>) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

copyImg(RandomAccessibleInterval<T>, ImgFactory<T>, T, ExecutorService) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

copyImg(RandomAccessibleInterval<T>, ImgFactory<T>, T, ExecutorService, boolean) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

copyImg(RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, ExecutorService) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

copyImg(RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, ExecutorService, boolean) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

copyImgNoTranslation(RandomAccessibleInterval<T>, ImgFactory<T>, T, ExecutorService) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

copyImgNoTranslation(RandomAccessibleInterval<T>, ImgFactory<T>, T, ExecutorService, boolean) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

copyIPs(List<CorrespondingIP>) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidTools

copyIPs(Set<CorrespondingIP>) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidTools

copyNormalizedWeights() - Method in class net.preibisch.mvrecon.process.deconvolution.util.ProcessInputImages

copyNormalizedWeights(ImgFactory<FloatType>) - Method in class net.preibisch.mvrecon.process.deconvolution.util.ProcessInputImages

copyOf(FlattenedMatches, int) - Static method in class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.FlattenedMatches

copyRandomAccess() - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccess

copyRandomAccess() - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccess

copyRandomAccess() - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessFirstWins

copyRandomAccess() - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessMax

copyRandomAccess() - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessNoWeights

copyRandomAccess() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.DistanceVisualizingRandomAccess

copyRandomAccess() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.InterpolatingNonRigidRandomAccess

copyRandomAccess() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidRandomAccess

copyRandomAccess() - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputGeneralRandomAccess

copyRandomAccess() - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccess

copyRandomAccess() - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccess2d

copyRandomAccess() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsMulRandomAccess

copyRandomAccess() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccess

copyRandomAccess() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsSumRandomAccess

copyRandomAccess() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.InterpolatingNonRigidRasteredRandomAccess

copyRandomAccess() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.NonRigidRasteredRandomAccess

copyRandomAccess() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.TransformedRasteredRandomAccess

copyRandomAccessibleInterval(Collection<Group<V>>, ExecutorService, ImgFactory<FloatType>, HashMap<Group<V>, RandomAccessibleInterval<FloatType>>) - Static method in class net.preibisch.mvrecon.process.deconvolution.util.ProcessInputImages

copyRealRandomAccess() - Method in class net.preibisch.mvrecon.imglib2.st.render.IntegratingNeighborSearchInterpolator

copyRealRandomAccess() - Method in class util.StackingRealRandomAccessible.StackingRealRandomAccess

copySelected(double[], double[]) - Method in class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.MatchIndices

copySelected(FlattenedMatches, FlattenedMatches) - Method in class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.MatchIndices

copySelection() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationExplorerPanel

copyUnnormalizedWeights() - Method in class net.preibisch.mvrecon.process.deconvolution.util.ProcessInputImages

copyUnnormalizedWeights(ImgFactory<FloatType>) - Method in class net.preibisch.mvrecon.process.deconvolution.util.ProcessInputImages

coreStringToDouble(Object) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.NumberUtils

coreStringToInt(Object) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.NumberUtils

coreStringToLong(Object) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.NumberUtils

corners(BasicViewSetup, ViewRegistration) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap.ParallelepipedOverlap

The 8 world-space corners of the unit voxel cube [0..d-1]^3 transformed by the view's registration affine.

corners(Dimensions, AffineTransform3D) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap.ParallelepipedOverlap

CORR - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.Split_Views.InterestPointAdding

corrDataset() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

corrDataset(String) - Static method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

correctForDownsampling(List<InterestPoint>, AffineTransform3D) - Static method in class net.preibisch.mvrecon.process.downsampling.DownsampleTools

CorrespondenceExtraction<T> - Interface in net.preibisch.legacy.registration.detection.descriptor

correspondences - Variable in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5.InterestPointData

CorrespondenceTools - Class in net.preibisch.mvrecon.fiji.spimdata.interestpoints

Utility methods for managing interest point correspondences.

CorrespondenceTools() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.interestpoints.CorrespondenceTools

CorrespondingInterestPoints - Class in net.preibisch.mvrecon.fiji.spimdata.interestpoints

Defines a pair of corresponding interest points

CorrespondingInterestPoints(int, int, int, String, int) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.interestpoints.CorrespondingInterestPoints

CorrespondingInterestPoints(int, int, int, String, int, int) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.interestpoints.CorrespondingInterestPoints

CorrespondingInterestPoints(int, ViewId, String, int) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.interestpoints.CorrespondingInterestPoints

CorrespondingInterestPoints(int, ViewId, String, int, int) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.interestpoints.CorrespondingInterestPoints

CorrespondingInterestPoints(CorrespondingInterestPoints) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.interestpoints.CorrespondingInterestPoints

CorrespondingIP - Class in net.preibisch.mvrecon.process.fusion.transformed.nonrigid

CorrespondingIP(InterestPoint, ViewId, InterestPoint, ViewId) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.CorrespondingIP

correspondingLabel - Variable in class net.preibisch.mvrecon.process.interestpointremoval.CreateFromCorrespondencesParameters

corrViewKey - Variable in class net.preibisch.mvrecon.process.splitting.OctTreeSplitCriterion.SplitCorrespondence

Key identifying the corresponding view: "timepointId_setupId"

cos - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel2D

count - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.GroupPairResult

count - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader.IFDEntry

count - Variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader.IFDEntry

COUNT - Enum constant in enum class net.preibisch.mvrecon.process.splitting.ConsensusSetCriterion.ToleranceMode

countAfter() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.InterestPointGrouping

countAvgErrors - Variable in class net.preibisch.legacy.registration.bead.error.GlobalErrorStatisticsImpl

countBefore() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.InterestPointGrouping

create() - Method in class net.preibisch.mvrecon.imglib2.st.filter.DensityFilterFactory

create() - Method in interface net.preibisch.mvrecon.imglib2.st.filter.FilterFactory

create() - Method in class net.preibisch.mvrecon.imglib2.st.filter.GaussianFilterFactory

create() - Method in class net.preibisch.mvrecon.imglib2.st.filter.MeanFilterFactory

create() - Method in class net.preibisch.mvrecon.imglib2.st.filter.MedianFilterFactory

create(int) - Method in interface net.preibisch.mvrecon.process.deconvolution.iteration.ComputeBlockThreadFactory

create(int) - Method in class net.preibisch.mvrecon.process.deconvolution.iteration.mul.ComputeBlockMulThreadCPUFactory

create(int) - Method in class net.preibisch.mvrecon.process.deconvolution.iteration.sequential.ComputeBlockSeqThreadCPUFactory

create(int) - Method in class net.preibisch.mvrecon.process.deconvolution.iteration.sequential.ComputeBlockSeqThreadCUDAFactory

create(long[], int[]) - Static method in class util.Grid

create(long[], int[], int[]) - Static method in class util.Grid

create(HashMap<ViewId, Tile<M>>) - Method in class net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.weak.MetaDataWeakLinkFactory

create(HashMap<ViewId, Tile<M>>) - Method in interface net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.weak.WeakLinkFactory

create(RandomAccessibleInterval<R>, RandomAccessibleInterval<S>, RandomAccessibleInterval<T>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.FlatFieldCorrectedRandomAccessibleIntervals

create(RandomAccessibleInterval<R>, RandomAccessibleInterval<S>, RandomAccessibleInterval<T>, O) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.FlatFieldCorrectedRandomAccessibleIntervals

create(RandomAccessibleInterval<T>, double[], double[], float) - Static method in class net.preibisch.mvrecon.process.fusion.blk.ContentBased

create(SpimData2, Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.fiji.plugin.CreateFromCorresponding_Detections

create(IntegratingNeighborSearch<T>) - Method in class net.preibisch.mvrecon.imglib2.st.render.IntegratingNeighborSearchInterpolatorFactory

create(IntegratingNeighborSearch<T>, RealInterval) - Method in class net.preibisch.mvrecon.imglib2.st.render.IntegratingNeighborSearchInterpolatorFactory

createAndInitImgLoader(String, File, SequenceDescription) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

createAndInitImgLoader(String, File, SequenceDescription) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListImageJ

createAndInitImgLoader(String, File, SequenceDescription) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListLOCI

createAnisotropicBoundingBox(Interval, double) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

Creates an anisotropic bounding box by floor/ceil to include all data and provides the affine transformation to scale it to global coordinates

createArray(int) - Method in class net.preibisch.legacy.registration.detection.Detection

createArray(int) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test.PointNode

createBDV(AbstractSpimData<?>, URI) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BDVPopup

createBDV(ExplorerWindow<?>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BDVPopup

createBDVPath(String, int, StorageFormat) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

createBDVPath(ViewId, int, StorageFormat) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

createCandidates(AbstractPointDescriptor<?, ?>, AbstractPointDescriptor<?, ?>) - Method in interface net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.Matcher

createCandidates(AbstractPointDescriptor<?, ?>, AbstractPointDescriptor<?, ?>) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.SimpleMatcher

createCandidates(AbstractPointDescriptor<?, ?>, AbstractPointDescriptor<?, ?>) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.SubsetMatcher

createChart(IntervalXYDataset, String, String) - Method in class net.preibisch.mvrecon.process.interestpointremoval.histogram.Histogram

createDataset(String) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.DHM

createDataset(String) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition

createDataset(String) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.LightSheetZ1

createDataset(String) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.MicroManager

createDataset(String) - Method in interface net.preibisch.mvrecon.fiji.datasetmanager.MultiViewDatasetDefinition

This method is supposed to (interactively, ideally ImageJ-macroscriptable) query all necessary data from the user to build up a SpimData object and save it as an XML file.

createDataset(String) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.OMEZARR

createDataset(String) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.SimView

createDataset(String) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM

createDataset(String) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

createDataset(String, DefineDataSetParameters) - Static method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1

createDataset(String, DefineDataSetParameters) - Static method in class net.preibisch.mvrecon.headless.definedataset.MicroManager

createDataset(String, StackListParameters) - Static method in class net.preibisch.mvrecon.headless.definedataset.StackListImageJ

createDataset(String, StackListParameters) - Static method in class net.preibisch.mvrecon.headless.definedataset.StackListLOCI

createDataset(List<Double>, int, String) - Method in class net.preibisch.mvrecon.process.interestpointremoval.histogram.Histogram

createDownsampledBDVPath(String, int, StorageFormat) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

createDownsampledBoundingBox(Interval, double) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

Creates a downsampled bounding box by rounding and provides the affine transformation to scale it to global coordinates, which also corrects for the fact that the fused image is ZEROMIN (TODO: change that)

createEmptyDataset(N5Writer, String, Interval, double[], int[], D, Compression) - Static method in class net.preibisch.mvrecon.process.fusion.blk.DisplacementFieldN5Tools

Backward-compatible overload: no correspondence-label / min annotation (treated as "no correspondence midpoints used") and no corner anchors.

createEmptyDataset(N5Writer, String, Interval, double[], int[], D, Compression, String, int) - Static method in class net.preibisch.mvrecon.process.fusion.blk.DisplacementFieldN5Tools

Backward-compatible overload: correspondence label + min, no corner anchors.

createEmptyDataset(N5Writer, String, Interval, double[], int[], D, Compression, String, int, boolean, double) - Static method in class net.preibisch.mvrecon.process.fusion.blk.DisplacementFieldN5Tools

Backward-compatible overload: corner anchors with N=2 (corners only).

createEmptyDataset(N5Writer, String, Interval, double[], int[], D, Compression, String, int, boolean, double, int) - Static method in class net.preibisch.mvrecon.process.fusion.blk.DisplacementFieldN5Tools

Backward-compatible overload: no per-split schedule.

createEmptyDataset(N5Writer, String, Interval, double[], int[], D, Compression, String, int, boolean, double, int, int[], int[]) - Static method in class net.preibisch.mvrecon.process.fusion.blk.DisplacementFieldN5Tools

Pre-create an empty dfield dataset (4D, shape (n, gridX, gridY, gridZ)) with the right block size, datatype, compression, and attributes.

createExecutorService() - Static method in class net.preibisch.mvrecon.process.deconvolution.DeconViews

createExecutorService() - Static method in class util.FFTConvolution

Utility function to create an ExecutorService Number of threads utilized matches available processors in runtime.

createExecutorService(int) - Static method in class util.FFTConvolution

Utility function to create an ExecutorService

createFailedBlocksMap(Collection<T>) - Method in class net.preibisch.mvrecon.process.export.RetryTracker

Create the map of all blocks, from which we then remove each one that succeeded piece by piece

createFilter(IterableRealInterval<S>) - Method in interface net.preibisch.mvrecon.imglib2.st.filter.FilterFactory

createFilter(IterableRealInterval<S>) - Method in class net.preibisch.mvrecon.imglib2.st.filter.RadiusSearchFilterFactory

createFilter(KDTree<S>) - Method in class net.preibisch.mvrecon.imglib2.st.filter.GaussianFilterFactory

createFilter(KDTree<S>) - Method in class net.preibisch.mvrecon.imglib2.st.filter.MeanFilterFactory

createFilter(KDTree<S>) - Method in class net.preibisch.mvrecon.imglib2.st.filter.RadiusSearchFilterFactory

createFilter(KDTree<T>) - Method in class net.preibisch.mvrecon.imglib2.st.filter.DensityFilterFactory

createFilter(KDTree<T>) - Method in class net.preibisch.mvrecon.imglib2.st.filter.MedianFilterFactory

createFixedExecutorService() - Static method in class net.preibisch.mvrecon.Threads

createFixedExecutorService(int) - Static method in class net.preibisch.mvrecon.Threads

createFlexibleExecutorService() - Static method in class net.preibisch.mvrecon.Threads

createFlexibleExecutorService(int) - Static method in class net.preibisch.mvrecon.Threads

createFor(SpimData2, Collection<? extends ViewId>, CreateFromCorrespondencesParameters) - Static method in class net.preibisch.mvrecon.process.interestpointremoval.CreateInterestPointsFromCorrespondences

CreateFromCorrespondencesListener() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.RemoveDetectionsPopup.CreateFromCorrespondencesListener

CreateFromCorrespondencesParameters - Class in net.preibisch.mvrecon.process.interestpointremoval

CreateFromCorrespondencesParameters() - Constructor for class net.preibisch.mvrecon.process.interestpointremoval.CreateFromCorrespondencesParameters

CreateFromCorresponding_Detections - Class in net.preibisch.mvrecon.fiji.plugin

CreateFromCorresponding_Detections() - Constructor for class net.preibisch.mvrecon.fiji.plugin.CreateFromCorresponding_Detections

createGroupsForAllViews(Set<V>, Set<Group<V>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.Subset

Create a Set of groups that contains all views, with |group| >= 1.

createHyperlinkLabel(String, URI) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.SimpleHyperlinkPopup

createImageReaderWithSetupHooks() - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.util.BioformatsReaderUtils

createImg(CellGrid, Cache<Long, Cell<?>>, T, Set<AccessFlags>) - Static method in class util.Lazy

createImg(Interval, int[], T, Set<AccessFlags>, CellLoader<T>) - Static method in class util.Lazy

createImgLoader(File, String, int, int, int, int, int, AbstractSequenceDescription<?, ?, ?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoStackImgLoader

createImgLoader(File, String, int, int, int, int, int, AbstractSequenceDescription<?, ?, ?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoStackImgLoaderIJ

createImgLoader(File, String, int, int, int, int, int, AbstractSequenceDescription<?, ?, ?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoStackImgLoaderLOCI

createImgLoaderElement(XmlIoBasicImgLoader<L>, BasicImgLoader, File) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.XmlIoSplitViewerImgLoader

CreateInterestPointsFromCorrespondences - Class in net.preibisch.mvrecon.process.interestpointremoval

CreateInterestPointsFromCorrespondences() - Constructor for class net.preibisch.mvrecon.process.interestpointremoval.CreateInterestPointsFromCorrespondences

createLinearIntensityMapOperator(T, int, Coefficients, Dimensions, ClampType) - Static method in class net.preibisch.mvrecon.process.fusion.intensity.FastLinearIntensityMap

Create a UnaryBlockOperator to apply an interpolated linear intensity map to blocks of the standard ImgLib2 RealTypes.

createLocalCoordinateSystemPointDescriptors(KDTree<I>, Collection<I>, int) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.fastrgldm.FRGLDMMatcher

createLocalCoordinateSystemPointDescriptors(KDTree<I>, Collection<I>, int, boolean) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.geometrichashing.GeometricHasher

createLocalCoordinateSystemPointDescriptors(KDTree<VirtualPointNode<P>>, ArrayList<VirtualPointNode<P>>, int, boolean) - Static method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test.TestPointDescriptor

createMissingViews() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

createModelPointDescriptors(KDTree<VirtualPointNode<P>>, ArrayList<VirtualPointNode<P>>, int, TranslationInvariantModel<?>, Matcher, SimilarityMeasure) - Static method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test.TestPointDescriptor

createMonotoneCubicSpline(List<? extends RealLocalizable>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.MonotoneCubicSpline

createMonotoneCubicSpline(List<Double>, List<? extends RealLocalizable>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.MonotoneCubicSpline

createMultiResolutionAffine(BasicImgLoader, Map<ViewId, AffineTransform3D>, Map<ViewId, ? extends BasicViewDescription<?>>, Collection<? extends ViewId>, FusionGUI.FusionType, int, Interval, Map<? extends ViewId, AffineModel1D>, int, int, int) - Static method in class net.preibisch.mvrecon.fiji.plugin.interactive.MultiResolutionTools

createMultiResolutionAffine(SpimData2, Collection<? extends ViewId>, Interval, int, int, int) - Static method in class net.preibisch.mvrecon.fiji.plugin.interactive.MultiResolutionTools

createMultiResolutionNonRigid(BasicImgLoader, Map<ViewId, AffineTransform3D>, Map<ViewId, ViewInterestPointLists>, Map<ViewId, ? extends BasicViewDescription<?>>, Collection<? extends ViewId>, Collection<? extends ViewId>, ArrayList<String>, FusionGUI.FusionType, boolean, long, double, int, Interval, Map<? extends ViewId, AffineModel1D>, ExecutorService, int, int, int) - Static method in class net.preibisch.mvrecon.fiji.plugin.interactive.MultiResolutionTools

createMultiResolutionNonRigid(SpimData2, Collection<? extends ViewId>, Collection<? extends ViewId>, ArrayList<String>, long, Interval, ExecutorService, int, int, int) - Static method in class net.preibisch.mvrecon.fiji.plugin.interactive.MultiResolutionTools

createMultiResolutionNonRigid(SpimData2, Collection<? extends ViewId>, Collection<? extends ViewId>, ArrayList<String>, FusionGUI.FusionType, boolean, long, double, int, Interval, Map<? extends ViewId, AffineModel1D>, ExecutorService, int, int, int) - Static method in class net.preibisch.mvrecon.fiji.plugin.interactive.MultiResolutionTools

createN5datasetPath(int, int, String) - Static method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

createN5PropertiesInstance() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AllenOMEZarrLoader

createN5URIfromXMLURI(URI) - Static method in class net.preibisch.mvrecon.fiji.plugin.resave.ParametersResaveN5Api

createNewPartitionFile(File) - Static method in class net.preibisch.mvrecon.fiji.plugin.util.PluginHelper

createNewSpimDataForFusion(StorageFormat, URI, URI, Map<ViewId, AllenOMEZarrLoader.OMEZARREntry>, ArrayList<ViewSetup>, ArrayList<TimePoint>) - Static method in class net.preibisch.mvrecon.process.n5api.SpimData2Tools

createNonRigidVirtualImages(BasicImgLoader, Map<ViewId, ? extends BasicViewDescription<?>>, Collection<? extends ViewId>, Map<ViewId, AffineTransform3D>, HashMap<ViewId, ModelGrid>, Interval, FusionGUI.FusionType, boolean, int, Map<? extends ViewId, AffineModel1D>, int) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidTools

createOffsets(Interval, int[]) - Static method in class util.Grid

createOMEXMLMetadata(IFormatReader) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyLightSheetZ1ImgLoader

createOMEXMLMetadata(IFormatReader) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoaderLOCI

createOMEZarrMetadata(int, String, String, double[], String, int, Function<Integer, String>, Function<Integer, AffineTransform3D>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.OMEZarrAttributes

createOMEZARRURIfromXMLURI(URI) - Static method in class net.preibisch.mvrecon.fiji.plugin.resave.ParametersResaveN5Api

createProposedMipMaps(int[][], int[][], Collection<Integer>) - Static method in class net.preibisch.mvrecon.fiji.plugin.resave.ParametersResaveN5Api

createPsiInitialization() - Method in class net.preibisch.mvrecon.process.deconvolution.init.PsiInitAvgApproxFactory

createPsiInitialization() - Method in class net.preibisch.mvrecon.process.deconvolution.init.PsiInitAvgPreciseFactory

createPsiInitialization() - Method in class net.preibisch.mvrecon.process.deconvolution.init.PsiInitBlurredFusedFactory

createPsiInitialization() - Method in interface net.preibisch.mvrecon.process.deconvolution.init.PsiInitFactory

createPsiInitialization() - Method in class net.preibisch.mvrecon.process.deconvolution.init.PsiInitFromFileFactory

createPsiInitialization() - Method in class net.preibisch.mvrecon.process.deconvolution.init.PsiInitFromRAIFactory

createRenderResult() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough.MyTarget

createSequenceDescription(String, String, String, String, String, StackList.Calibration) - Static method in class net.preibisch.mvrecon.headless.definedataset.StackList

Create sequence description for StackList.

createSequenceDescription(LightSheetZ1MetaData, File) - Static method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1

Create sequence description for LightSheetZ1MetaData.

createSequenceDescription(MultipageTiffReader, File) - Static method in class net.preibisch.mvrecon.headless.definedataset.MicroManager

Create sequence description for MultipageTiffReader.

createSimplePointDescriptors(KDTree<I>, List<I>, int, Matcher, SimilarityMeasure) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm.RGLDMMatcher

createSourceAndConverter(RandomAccessibleInterval<ARGBType>) - Static method in class net.preibisch.mvrecon.process.export.ExportLarge2DTIFF

createTimePoints() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

createTimePoints(DHMMetaData) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.DHM

createTimePoints(SimViewMetaData) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.SimView

createTimePoints(SmartSPIM.SmartSPIMMetaData) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM

createTimePoints(MultipageTiffReader) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.MicroManager

createTimePoints(LightSheetZ1MetaData) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.LightSheetZ1

createVariable() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

createVariable() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

createViewRegistrations(Map<ViewId, ViewDescription>, double) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.DatasetCreationUtils

Assembles the ViewRegistration object consisting of a list of ViewRegistrations for all ViewDescriptions that are present

createViewRegistrations(Map<ViewId, ViewDescription>, double) - Static method in class net.preibisch.mvrecon.headless.definedataset.DefineDataSet

Assembles the ViewRegistration object consisting of a list of ViewRegistrations for all ViewDescriptions that are present

createViewSetups() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

createViewSetups(DHMMetaData) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.DHM

createViewSetups(SimViewMetaData) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.SimView

createViewSetups(SmartSPIM.SmartSPIMMetaData, double) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM

createViewSetups(MultipageTiffReader) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.MicroManager

createViewSetups(LightSheetZ1MetaData) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.LightSheetZ1

createVirtualNodeList(ArrayList<P>) - Static method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test.TestPointDescriptor

createVolatileRAIs(List<Pair<RandomAccessibleInterval<FloatType>, AffineTransform3D>>) - Static method in class net.preibisch.mvrecon.fiji.plugin.interactive.MultiResolutionTools

createVolatileRAIs(List<Pair<RandomAccessibleInterval<FloatType>, AffineTransform3D>>, long, int[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.interactive.MultiResolutionTools

createXMLObject(SpimData2, List<ViewId>, Generic_Resave_HDF5.ParametersResaveHDF5, ProgressWriter, boolean) - Static method in class net.preibisch.mvrecon.fiji.plugin.resave.Resave_HDF5

createXMLObject(SpimData2, List<ViewId>, Resave_TIFF.ParametersResaveAsTIFF) - Static method in class net.preibisch.mvrecon.fiji.plugin.resave.Resave_TIFF

CRITERION_NAME - Static variable in class net.preibisch.mvrecon.process.splitting.ConsensusSetCriterion

CRITERION_NAME - Static variable in class net.preibisch.mvrecon.process.splitting.CrossViewCorrespondenceCriterion

CRITERION_NAMES - Static variable in class net.preibisch.mvrecon.process.splitting.SplitOctTree

criterionSatisfiedPercent - Variable in class net.preibisch.mvrecon.process.splitting.SplitOctTree.OctTreeSplitResult

cross(Vector3d, Vector3d) - Method in class net.preibisch.mvrecon.vecmath.Vector3d

Sets this vector to the vector cross product of vectors v1 and v2.

cross(Vector3f, Vector3f) - Method in class net.preibisch.mvrecon.vecmath.Vector3f

Sets this vector to be the vector cross product of vectors v1 and v2.

CrossCorrelationPairwiseQualityMeasure(double) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.PairwiseStitchingResult.CrossCorrelationPairwiseQualityMeasure

CrossViewCorrespondenceCriterion - Class in net.preibisch.mvrecon.process.splitting

Criterion that counts cross-view corresponding interest points within a region.

CrossViewCorrespondenceCriterion(SpimData2, Set<String>, int) - Constructor for class net.preibisch.mvrecon.process.splitting.CrossViewCorrespondenceCriterion

Constructor.

cubeFor(RealInterval) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

cuda - Variable in class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGParameters

CUDADevice - Class in net.preibisch.mvrecon.process.cuda

CUDADevice(int, String, long, long, int, int) - Constructor for class net.preibisch.mvrecon.process.cuda.CUDADevice

CUDAFourierConvolution - Interface in net.preibisch.mvrecon.process.cuda

CUDASeparableConvolution - Interface in net.preibisch.mvrecon.process.cuda

Interface to load the native library for separable convolution using CUDA/CPU (https://github.com/StephanPreibisch/SeparableConvolutionCUDALib)

CUDASeparableConvolutionFunctions - Class in net.preibisch.mvrecon.process.cuda

Executes gaussian convolution using the native CUDA implementation (https://github.com/StephanPreibisch/SeparableConvolutionCUDALib)

CUDASeparableConvolutionFunctions(CUDASeparableConvolution, int) - Constructor for class net.preibisch.mvrecon.process.cuda.CUDASeparableConvolutionFunctions

CUDASeparableConvolutionFunctions.OutOfBounds - Enum Class in net.preibisch.mvrecon.process.cuda

CUDAStandardFunctions - Interface in net.preibisch.mvrecon.process.cuda

CUDATools - Class in net.preibisch.mvrecon.process.cuda

CUDATools() - Constructor for class net.preibisch.mvrecon.process.cuda.CUDATools

currentInstance - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

currentPanel - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Detection

cx - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.LocalCoordinateSystemPointDescriptor

cx - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.TranslationInvariantLocalCoordinateSystemPointDescriptor

cy - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.LocalCoordinateSystemPointDescriptor

cy - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.TranslationInvariantLocalCoordinateSystemPointDescriptor

cz - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.LocalCoordinateSystemPointDescriptor

cz - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.TranslationInvariantLocalCoordinateSystemPointDescriptor

CZIReaderSetupHook - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders.util

CZITileOrAngleRefiner - Class in net.preibisch.mvrecon.fiji.datasetmanager.metadatarefinement

CZITileOrAngleRefiner() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.metadatarefinement.CZITileOrAngleRefiner

D

DARKIMG_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.XmlIoFlatfieldCorrectedWrappedImgLoader

data - Variable in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

data - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

Data_Explorer - Class in net.preibisch.mvrecon.fiji.plugin

Data_Explorer() - Constructor for class net.preibisch.mvrecon.fiji.plugin.Data_Explorer

dataAccess - Variable in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

dataAccess - Variable in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

dataset - Variable in class net.preibisch.mvrecon.process.n5api.N5ApiTools.MultiResolutionLevelInfo

DatasetCreationUtils - Class in net.preibisch.mvrecon.fiji.datasetmanager

DatasetCreationUtils() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.DatasetCreationUtils

datasetMatches(N5Reader, String, Interval, double[]) - Static method in class net.preibisch.mvrecon.process.fusion.blk.DisplacementFieldN5Tools

Backward-compatible overload: no correspondence-label / anchor checks.

datasetMatches(N5Reader, String, Interval, double[], String, int) - Static method in class net.preibisch.mvrecon.process.fusion.blk.DisplacementFieldN5Tools

Backward-compatible overload: correspondence-label + min check, no anchor check.

datasetMatches(N5Reader, String, Interval, double[], String, int, boolean, double) - Static method in class net.preibisch.mvrecon.process.fusion.blk.DisplacementFieldN5Tools

Backward-compatible overload: corner anchors with N=2 (corners only).

datasetMatches(N5Reader, String, Interval, double[], String, int, boolean, double, int) - Static method in class net.preibisch.mvrecon.process.fusion.blk.DisplacementFieldN5Tools

Backward-compatible overload: no per-split schedule.

datasetMatches(N5Reader, String, Interval, double[], String, int, boolean, double, int, int[], int[]) - Static method in class net.preibisch.mvrecon.process.fusion.blk.DisplacementFieldN5Tools

Check whether a dfield dataset already exists at the given path with the expected spacing, offset (= bbox.min), correspondence label/min, and corner-anchor config.

datasetPath(ViewId) - Static method in class net.preibisch.mvrecon.process.fusion.blk.DisplacementFieldN5Tools

Canonical N5/Zarr dataset path for the displacement field of a given underlying view.

dataType - Variable in class net.preibisch.mvrecon.process.n5api.N5ApiTools.MultiResolutionLevelInfo

debugInterval - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

debugMissingInterestPoints - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

When true, prints individual warnings for each view missing interest points.

debugMode - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

debugShowFiles() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

decide(RandomAccessibleInterval<?>, int[], int, int[], int[]) - Method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.LoopBack2d

decIndex() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

decIndex() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

decIndex(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

decIndex(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

DeconView - Class in net.preibisch.mvrecon.process.deconvolution

One view for the multiview deconvolution, contains image, weight, and PSFs

DeconView(ExecutorService, RandomAccessibleInterval<FloatType>, ArrayImg<FloatType, ?>) - Constructor for class net.preibisch.mvrecon.process.deconvolution.DeconView

DeconView(ExecutorService, RandomAccessibleInterval<FloatType>, RandomAccessibleInterval<FloatType>, ArrayImg<FloatType, ?>) - Constructor for class net.preibisch.mvrecon.process.deconvolution.DeconView

DeconView(ExecutorService, RandomAccessibleInterval<FloatType>, RandomAccessibleInterval<FloatType>, ArrayImg<FloatType, ?>, int[]) - Constructor for class net.preibisch.mvrecon.process.deconvolution.DeconView

DeconView(ExecutorService, RandomAccessibleInterval<FloatType>, RandomAccessibleInterval<FloatType>, ArrayImg<FloatType, ?>, DeconViewPSF.PSFTYPE, int[], boolean) - Constructor for class net.preibisch.mvrecon.process.deconvolution.DeconView

DeconView(ExecutorService, RandomAccessibleInterval<FloatType>, RandomAccessibleInterval<FloatType>, ArrayImg<FloatType, ?>, DeconViewPSF.PSFTYPE, int[], int, boolean) - Constructor for class net.preibisch.mvrecon.process.deconvolution.DeconView

DeconViewPSF - Class in net.preibisch.mvrecon.process.deconvolution

Handles the PSF for a specific view for the deconvolution

DeconViewPSF(ArrayImg<FloatType, ?>) - Constructor for class net.preibisch.mvrecon.process.deconvolution.DeconViewPSF

DeconViewPSF(ArrayImg<FloatType, ?>, DeconViewPSF.PSFTYPE) - Constructor for class net.preibisch.mvrecon.process.deconvolution.DeconViewPSF

DeconViewPSF.PSFTYPE - Enum Class in net.preibisch.mvrecon.process.deconvolution

DeconViews - Class in net.preibisch.mvrecon.process.deconvolution

DeconViews(Collection<DeconView>, ExecutorService) - Constructor for class net.preibisch.mvrecon.process.deconvolution.DeconViews

DeconvolutionGUI - Class in net.preibisch.mvrecon.fiji.plugin.fusion

DeconvolutionGUI(SpimData2, List<ViewId>, ExecutorService) - Constructor for class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

DeconvolutionMethods - Class in net.preibisch.mvrecon.process.deconvolution.iteration.mul

DeconvolutionMethods - Class in net.preibisch.mvrecon.process.deconvolution.iteration.sequential

DeconvolutionMethods() - Constructor for class net.preibisch.mvrecon.process.deconvolution.iteration.mul.DeconvolutionMethods

DeconvolutionMethods() - Constructor for class net.preibisch.mvrecon.process.deconvolution.iteration.sequential.DeconvolutionMethods

DeconvolutionPopup - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

DeconvolutionPopup() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.DeconvolutionPopup

DeconvolutionPopup.MyActionListener - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

deconvolve(SpimData2, List<ViewId>) - Static method in class net.preibisch.mvrecon.fiji.plugin.Image_Deconvolution

deconvolve(SpimData2, List<ViewId>, ExecutorService) - Static method in class net.preibisch.mvrecon.fiji.plugin.Image_Deconvolution

defaulCalUnit - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.DHM

defaulCalX - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.DHM

defaulCalY - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.DHM

defaulCalZ - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.DHM

DEFAULT_RADIUS - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.InterestPointGroupingMinDistance

defaultAbsoluteError - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters

defaultAdditional - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.NonRigidParametersGUI

defaultAdditionalInterestPoints - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.NonRigidParametersGUI

defaultAdditionalIPs - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.NonRigidParametersGUI

defaultAdditionalSigmaX - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

defaultAdditionalSigmaY - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

defaultAdditionalSigmaZ - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

defaultAdditionalSmoothBlending - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultAdjustBlending - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultAdjustIntensities - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultAdjustIntensities - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

defaultAdvanced - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.NonRigidParametersGUI

defaultAdvancedBlockSize - Static variable in class net.preibisch.mvrecon.process.export.ExportN5Api

defaultAdvancedRANSAC - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.PairwiseGUI

defaultAffine - Static variable in class net.preibisch.mvrecon.fiji.plugin.Intensity_Adjustment

defaultAffineExpansion - Static variable in class net.preibisch.mvrecon.process.fusion.lazy.LazyFusionTools

defaultAlgorithm - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Detection

defaultAlgorithm - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

defaultAlpha - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.NonRigidParametersGUI

defaultAngle - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultAngleChoice - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackListImageJ

defaultAngleChoice - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackListLOCI

defaultAngleChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.Display_View

defaultAngleChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultAngleIndex - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultAngleIndices - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultAngles - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

defaultAngleString - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultAnisotropyChoice - Static variable in class net.preibisch.mvrecon.process.splitting.SplitOctTree

defaultApplyRotAxis - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.LightSheetZ1

defaultApplyRotAxis - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.MicroManager

defaultApplyTo - Static variable in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

defaultAssignIlluminations - Static variable in class net.preibisch.mvrecon.fiji.plugin.Split_Views

defaultAssignType - Static variable in class net.preibisch.mvrecon.fiji.plugin.PSF_Assign

defaultAttributeChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

defaultAttributeEntityIndex - Static variable in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

defaultAttributePatternString - Static variable in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

defaultAttributeSelectedEntities - Static variable in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

defaultAveraging - Static variable in class net.preibisch.mvrecon.fiji.plugin.PSF_Average

defaultAxis - Static variable in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

defaultBackgroundIntensity - Static variable in class net.preibisch.mvrecon.fiji.plugin.boundingbox.MinFilterThresholdBoundingBoxGUI

defaultBasePath - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.OMEZARR.MultipleOMEZARRListChooser

defaultBB - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultBB - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

defaultBB - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

defaultBDV - Static variable in class net.preibisch.mvrecon.process.export.ExportN5Api

defaultBdvResetPolicy - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsResultsWindow

defaultBlendingBorder - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultBlendingBorder - Static variable in class net.preibisch.mvrecon.process.deconvolution.MultiViewDeconvolution

defaultBlendingBorder - Static variable in class net.preibisch.mvrecon.process.fusion.FusionTools

defaultBlendingRange - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultBlendingRange - Static variable in class net.preibisch.mvrecon.process.deconvolution.MultiViewDeconvolution

defaultBlendingRange - Static variable in class net.preibisch.mvrecon.process.fusion.FusionTools

defaultBlockSize - Static variable in class net.preibisch.mvrecon.fiji.plugin.resave.ParametersResaveN5Api

defaultBlockSize - Static variable in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

defaultBlockSize - Static variable in class net.preibisch.mvrecon.process.deconvolution.DeconView

defaultBlockSize2d - Static variable in class net.preibisch.mvrecon.process.fusion.lazy.LazyFusionTools

defaultBlockSize3d - Static variable in class net.preibisch.mvrecon.process.fusion.lazy.LazyFusionTools

defaultBlocksizeFactorX_H5 - Static variable in class net.preibisch.mvrecon.process.export.ExportN5Api

defaultBlocksizeFactorX_N5 - Static variable in class net.preibisch.mvrecon.process.export.ExportN5Api

defaultBlocksizeFactorY_H5 - Static variable in class net.preibisch.mvrecon.process.export.ExportN5Api

defaultBlocksizeFactorY_N5 - Static variable in class net.preibisch.mvrecon.process.export.ExportN5Api

defaultBlocksizeFactorZ_H5 - Static variable in class net.preibisch.mvrecon.process.export.ExportN5Api

defaultBlocksizeFactorZ_N5 - Static variable in class net.preibisch.mvrecon.process.export.ExportN5Api

defaultBlockSizeIndex - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultBlocksizePrecomputeX - Static variable in class net.preibisch.mvrecon.process.export.DisplayImage

defaultBlocksizePrecomputeY - Static variable in class net.preibisch.mvrecon.process.export.DisplayImage

defaultBlocksizePrecomputeZ - Static variable in class net.preibisch.mvrecon.process.export.DisplayImage

defaultBlocksizeVirtualX - Static variable in class net.preibisch.mvrecon.process.export.DisplayImage

defaultBlocksizeVirtualY - Static variable in class net.preibisch.mvrecon.process.export.DisplayImage

defaultBlocksizeVirtualZ - Static variable in class net.preibisch.mvrecon.process.export.DisplayImage

defaultBlockSizeX - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultBlocksizeX_H5 - Static variable in class net.preibisch.mvrecon.process.export.ExportN5Api

defaultBlocksizeX_N5 - Static variable in class net.preibisch.mvrecon.process.export.ExportN5Api

defaultBlockSizeXY - Static variable in class net.preibisch.mvrecon.fiji.plugin.resave.ParametersResaveN5Api

defaultBlockSizeY - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultBlocksizeY_H5 - Static variable in class net.preibisch.mvrecon.process.export.ExportN5Api

defaultBlocksizeY_N5 - Static variable in class net.preibisch.mvrecon.process.export.ExportN5Api

defaultBlockSizeZ - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultBlocksizeZ_H5 - Static variable in class net.preibisch.mvrecon.process.export.ExportN5Api

defaultBlocksizeZ_N5 - Static variable in class net.preibisch.mvrecon.process.export.ExportN5Api

defaultBottomMBest - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil

defaultBoundingBox - Static variable in class net.preibisch.mvrecon.fiji.plugin.boundingbox.ModifyDefinedBoundingBoxGUI

defaultBoundingBoxAlgorithm - Static variable in class net.preibisch.mvrecon.fiji.plugin.Define_Bounding_Box

defaultBoxes - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough

defaultBrightness - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

defaultCache - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.DisplayFusedImagesPopup

defaultCacheBlockSize - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultCacheMaxNumBlocks - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultCalibration1 - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

defaultCalibration2 - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

defaultCenterChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.CenterOfMassGUI

defaultCenterChoice - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.centerofmass.CenterOfMassParameters

defaultChannel - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultChannelChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.Display_View

defaultChannelChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultChannelChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.Split_Views

defaultChannelFrom - Static variable in class net.preibisch.mvrecon.fiji.plugin.PSF_Assign

defaultChannelIndex - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultChannelIndices - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultChannelleChoice - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackListImageJ

defaultChannelleChoice - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackListLOCI

defaultChannels - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

defaultChannelString - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultChannelTo - Static variable in class net.preibisch.mvrecon.fiji.plugin.PSF_Assign

defaultChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultChoice - Static variable in class net.preibisch.mvrecon.process.export.DisplayImage

defaultChoiceB - Static variable in class net.preibisch.mvrecon.process.export.ExportLarge2DTIFF

defaultChoiceB - Static variable in class net.preibisch.mvrecon.process.export.OpenSeaDragon

defaultChoiceG - Static variable in class net.preibisch.mvrecon.process.export.ExportLarge2DTIFF

defaultChoiceG - Static variable in class net.preibisch.mvrecon.process.export.OpenSeaDragon

defaultChoiceR - Static variable in class net.preibisch.mvrecon.process.export.ExportLarge2DTIFF

defaultChoiceR - Static variable in class net.preibisch.mvrecon.process.export.OpenSeaDragon

defaultColumnClassesMV() - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedTableModel

defaultColumnClassesStitching() - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedTableModel

defaultCompress - Static variable in class net.preibisch.mvrecon.fiji.plugin.resave.Resave_TIFF

defaultCompression - Static variable in class net.preibisch.mvrecon.fiji.plugin.util.PluginHelper

defaultCompression - Static variable in class net.preibisch.mvrecon.process.export.ExportLarge2DTIFF

defaultComputationChoiceIndex - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGaussianGUI

defaultComputeOnIndex - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultConfirmFiles - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM

defaultContentBasedSigma1 - Static variable in class net.preibisch.mvrecon.process.fusion.blk.ContentBased

defaultContentBasedSigma1 - Static variable in class net.preibisch.mvrecon.process.fusion.FusionTools

defaultContentBasedSigma2 - Static variable in class net.preibisch.mvrecon.process.fusion.blk.ContentBased

defaultContentBasedSigma2 - Static variable in class net.preibisch.mvrecon.process.fusion.FusionTools

defaultControlPointDistance - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.NonRigidParametersGUI

defaultConvertChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5

defaultCorresponding - Static variable in class net.preibisch.mvrecon.fiji.plugin.PSF_Extract

defaultCriterionChoice - Static variable in class net.preibisch.mvrecon.process.splitting.SplitOctTree

defaultCutoffThresholdMax - Static variable in class net.preibisch.mvrecon.fiji.plugin.ThinOut_Detections

defaultCutoffThresholdMin - Static variable in class net.preibisch.mvrecon.fiji.plugin.ThinOut_Detections

defaultData() - Static method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.statistics.TimeLapseDisplay

defaultDataset - Static variable in class net.preibisch.mvrecon.process.export.OpenSeaDragon

defaultDatasetDef - Static variable in class net.preibisch.mvrecon.fiji.plugin.Define_Multi_View_Dataset

defaultDatasetName - Static variable in class net.preibisch.mvrecon.process.export.ExportN5Api

defaultDebugInterval - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultDebugMode - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultDefineAnisotropy - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Detection

defaultDefineAs - Static variable in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

defaultDefineMinMax - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

defaultDegrees - Static variable in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

defaultDensity - Static variable in class net.preibisch.mvrecon.fiji.plugin.Split_Views

defaultDetections - Static variable in class net.preibisch.mvrecon.fiji.plugin.boundingbox.AutomaticReorientationBoundingBoxGUI

defaultDetections - Static variable in class net.preibisch.mvrecon.fiji.plugin.Visualize_Detections

defaultDir - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.DHM

defaultDir - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.OMEZARR

defaultDir - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.SimView

defaultDir - Static variable in class net.preibisch.mvrecon.headless.definedataset.ResaveImaris

defaultDirectory - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.OMEZARR

defaultDirectory - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

defaultDirectory - Static variable in class net.preibisch.mvrecon.process.cuda.NativeLibraryTools

defaultDiscardedObjectSize - Static variable in class net.preibisch.mvrecon.fiji.plugin.boundingbox.MinFilterThresholdBoundingBoxGUI

defaultDisplacementFieldSpacing - Static variable in class net.preibisch.mvrecon.process.fusion.blk.BlkThinPlateSplineFusion

defaultDisplay - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.VisualizeNonRigid

defaultDisplayChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.PSF_View

defaultDisplayInput - Static variable in class net.preibisch.mvrecon.fiji.plugin.Visualize_Detections

defaultDisplaySegmentationImage - Static variable in class net.preibisch.mvrecon.fiji.plugin.boundingbox.MinFilterThresholdBoundingBoxGUI

defaultDownsample - Static variable in class net.preibisch.mvrecon.fiji.plugin.Visualize_Detections

defaultDownsampleXYIndex - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

defaultDownsampleZIndex - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

defaultDownsampling - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultDownsampling - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

defaultDownsampling - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

defaultDownsampling - Static variable in class net.preibisch.mvrecon.fiji.plugin.Intensity_Adjustment

defaultDownsamplingAutomatic - Static variable in class net.preibisch.mvrecon.fiji.plugin.boundingbox.MinFilterThresholdBoundingBoxGUI

defaultError - Static variable in class net.preibisch.mvrecon.fiji.plugin.Split_Views

defaultExclusionRadiusIP - Static variable in class net.preibisch.mvrecon.fiji.plugin.Split_Views

defaultExpertGrouping - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters

defaultFakeLabel() - Static method in class net.preibisch.mvrecon.process.splitting.SplittingTools

defaultFFTSize - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

defaultFile - Static variable in class net.preibisch.mvrecon.headless.definedataset.ResaveImaris

defaultFileNamePattern - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

defaultFindMax - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGaussianGUI

defaultFindMin - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGaussianGUI

defaultFirst - Static variable in class net.preibisch.mvrecon.fiji.plugin.Switch_Attributes

defaultFirstFile - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.LightSheetZ1

defaultFirstFile - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.MicroManager

defaultFixBioformats - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.LightSheetZ1

defaultFixedViews - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

defaultFixViews - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

DefaultFlatfieldCorrectionWrappedImgLoader - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield

DefaultFlatfieldCorrectionWrappedImgLoader(ImgLoader) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.DefaultFlatfieldCorrectionWrappedImgLoader

DefaultFlatfieldCorrectionWrappedImgLoader(ImgLoader, boolean) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.DefaultFlatfieldCorrectionWrappedImgLoader

defaultFN - Static variable in class net.preibisch.mvrecon.process.export.Save3dTIFF

defaultFormat - Static variable in class net.preibisch.mvrecon.fiji.plugin.resave.ParametersResaveN5Api

defaultFormat - Static variable in class net.preibisch.mvrecon.process.export.OpenSeaDragon

defaultFRCStepSize - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

defaultFuseFrom - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

defaultFuseTo - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

defaultFusionType - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

defaultFusionType - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.DisplayFusedImagesPopup

defaultGlobalOpt - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters

defaultGlobalOptError - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.LoadCorrespondencesGUI

defaultGroupAngles - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil

defaultGroupChannels - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

defaultGroupChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

defaultGroupIllums - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultGroupIllums - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Detection

defaultGroupIllums - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

defaultGroupTiles - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultGroupTiles - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Detection

defaultGroupTiles - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

defaultGroupTimePoints - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

defaultIdentityRegularization - Static variable in class net.preibisch.mvrecon.fiji.plugin.Intensity_Adjustment

defaultIllum - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultIllumChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultIlluminationChoice - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackListImageJ

defaultIlluminationChoice - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackListLOCI

defaultIlluminationChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.Display_View

defaultIlluminations - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

defaultIllumIndex - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultIllumIndices - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultIllumString - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultImageSigmaX - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

defaultImageSigmaY - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

defaultImageSigmaZ - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

defaultImgExportAlgorithm - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultImgExportAlgorithm - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

defaultImgExportAlgorithm - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

defaultImgType - Static variable in class net.preibisch.mvrecon.fiji.plugin.Display_View

defaultImgX - Static variable in class net.preibisch.mvrecon.process.splitting.SplitDistributeEvenly

defaultImgY - Static variable in class net.preibisch.mvrecon.process.splitting.SplitDistributeEvenly

defaultImgZ - Static variable in class net.preibisch.mvrecon.process.splitting.SplitDistributeEvenly

defaultInput - Static variable in class net.preibisch.mvrecon.headless.definedataset.Rewrite_LuxendoXML

defaultInputImgCacheType - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultInterestpointOverlapType - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

defaultInterpolation - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

defaultInterpolation - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.DisplayFusedImagesPopup

defaultIntervalExpansion - Static variable in class net.preibisch.mvrecon.process.fusion.blk.BlkThinPlateSplineFusion

defaultIPChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.Split_Views

defaultIPDistance - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

defaultIPGrouping - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

defaultItem - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.SimView

defaultJSON - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough

defaultLabel - Static variable in class net.preibisch.mvrecon.fiji.plugin.CreateFromCorresponding_Detections

defaultLabel - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.NonRigidParametersGUI

defaultLabel - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Detection

defaultLabel - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

defaultLabel - Static variable in class net.preibisch.mvrecon.fiji.plugin.PSF_Extract

defaultLabel - Static variable in class net.preibisch.mvrecon.fiji.plugin.ThinOut_Detections

defaultLabel - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.RemoveDetectionsPopup

defaultLabelChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

defaultLabelChoices - Static variable in class net.preibisch.mvrecon.process.splitting.ConsensusSetCriterion

defaultLabelChoices - Static variable in class net.preibisch.mvrecon.process.splitting.CrossViewCorrespondenceCriterion

defaultLabelWeights - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

defaultLambda - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultLambda - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.TransformationModelGUI

defaultLimitDetections - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Detection

defaultLimitSearchRadius - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm.RGLDMParameters

defaultLittleEndian - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.SimView

defaultLoadChoice - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition

defaultLocalization - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

defaultLocations - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.OMEZARR.MultipleOMEZARRListChooser

defaultManuallyAssignViewId - Static variable in class net.preibisch.mvrecon.process.export.ExportN5Api

defaultMapBack - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

defaultMatchAcrossLabels - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

defaultMax - Static variable in class net.preibisch.mvrecon.fiji.plugin.boundingbox.BoundingBoxGUI

defaultMax - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

defaultMax - Static variable in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5

defaultMax - Static variable in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxBigDataViewer

defaultMaxCorrespondences - Static variable in class net.preibisch.mvrecon.process.splitting.CrossViewCorrespondenceCriterion

defaultMaxDetections - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

defaultMaxDetectionsTypeIndex - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

defaultMaxEpsionRANSAC - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.icp.IterativeClosestPointParameters

defaultMaxError - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters

defaultMaxInliers - Static variable in class net.preibisch.mvrecon.fiji.plugin.Intensity_Adjustment

defaultMaxIntensity - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

defaultMaxIntensity - Static variable in class net.preibisch.mvrecon.process.export.DisplayImage

defaultMaxIterations - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters

defaultMaxPlateauWidth - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters

defaultMaxPoints - Static variable in class net.preibisch.mvrecon.fiji.plugin.Split_Views

defaultMetadataFile - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM

defaultMethod - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough

defaultMethodChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.Split_Views

defaultMiddleK - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil

defaultMin - Static variable in class net.preibisch.mvrecon.fiji.plugin.boundingbox.BoundingBoxGUI

defaultMin - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

defaultMin - Static variable in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5

defaultMin - Static variable in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxBigDataViewer

defaultMinCorrespondences - Static variable in class net.preibisch.mvrecon.process.splitting.ConsensusSetCriterion

defaultMinInlierRatio - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.icp.IterativeClosestPointParameters

defaultMinIntensity - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

defaultMinIntensity - Static variable in class net.preibisch.mvrecon.process.export.DisplayImage

defaultMinNumMatches - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.LoadCorrespondencesGUI

defaultMinNumMatches - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.PairwiseGUI

defaultMinNumPoints - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.icp.IterativeClosestPointParameters

defaultMinPoints - Static variable in class net.preibisch.mvrecon.fiji.plugin.Split_Views

defaultMinSplitLevels - Static variable in class net.preibisch.mvrecon.process.splitting.SplitOctTree

defaultMinTileSize - Static variable in class net.preibisch.mvrecon.process.splitting.SplitOctTree

defaultMode - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil

defaultModel - Static variable in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

defaultModel - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.FRGLDMGUI

defaultModel - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.GeometricHashingGUI

defaultModel - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.IterativeClosestPointGUI

defaultModel - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.LoadCorrespondencesGUI

defaultModel - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.RGLDMGUI

defaultModels - Static variable in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

defaultModifyCal - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.LightSheetZ1

defaultModifyCal - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.MicroManager

defaultModifyCal - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.SimView

defaultModifyStackSize - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.SimView

defaultMul - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultMultiConsensus - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.PairwiseGUI

defaultMultiRes - Static variable in class net.preibisch.mvrecon.process.export.ExportN5Api

defaultName - Static variable in class net.preibisch.mvrecon.fiji.plugin.Define_Bounding_Box

defaultNewLabel - Static variable in class net.preibisch.mvrecon.fiji.plugin.CreateFromCorresponding_Detections

defaultNewLabel - Static variable in class net.preibisch.mvrecon.fiji.plugin.ThinOut_Detections

defaultNewLabel - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.RemoveDetectionsPopup

defaultNonRigidAcrossTime - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.NonRigidParametersGUI

defaultNonrigidExpansion - Static variable in class net.preibisch.mvrecon.process.fusion.lazy.LazyFusionTools

defaultNumDirs - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.OMEZARR.MultipleOMEZARRListChooser

defaultNumIterations - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultNumIterationsRANSAC - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.icp.IterativeClosestPointParameters

defaultNumThreads - Static variable in class net.preibisch.mvrecon.fiji.plugin.resave.ParametersResaveN5Api

defaultNumTransformations - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultOmeZarrDim - Static variable in class net.preibisch.mvrecon.process.export.ExportN5Api

defaultOmeZarrOneContainer - Static variable in class net.preibisch.mvrecon.process.export.ExportN5Api

defaultOpenAll - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.DHM

defaultOptimize - Static variable in class net.preibisch.mvrecon.process.splitting.SplitDistributeEvenly

defaultOption - Static variable in class net.preibisch.mvrecon.process.export.ExportN5Api

defaultOsemSpeedup - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultOverlapExpansion(double) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidTools

defaultOverlapType - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

defaultOverlapX - Static variable in class net.preibisch.mvrecon.process.splitting.SplitDistributeEvenly

defaultOverlapY - Static variable in class net.preibisch.mvrecon.process.splitting.SplitDistributeEvenly

defaultOverlapZ - Static variable in class net.preibisch.mvrecon.process.splitting.SplitDistributeEvenly

defaultPath - Static variable in class net.preibisch.mvrecon.fiji.plugin.resave.Resave_TIFF

defaultPath - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough

defaultPath - Static variable in class net.preibisch.mvrecon.process.export.ExportLarge2DTIFF

defaultPath - Static variable in class net.preibisch.mvrecon.process.export.OpenSeaDragon

defaultPath - Static variable in class net.preibisch.mvrecon.process.export.Save3dTIFF

defaultPathURI - Static variable in class net.preibisch.mvrecon.process.export.ExportN5Api

defaultPercent - Static variable in class net.preibisch.mvrecon.fiji.plugin.boundingbox.AutomaticReorientationBoundingBoxGUI

defaultPixelType - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

defaultPrealign - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters

defaultPreciseAvgMax - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultPreserveAnisotropy - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

defaultPreserveAnisotropy - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

defaultPrintAll - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil

defaultPSF - Static variable in class net.preibisch.mvrecon.fiji.plugin.PSF_Assign

defaultPSFPath - Static variable in class net.preibisch.mvrecon.fiji.plugin.PSF_Assign

defaultPSFSizeX - Static variable in class net.preibisch.mvrecon.fiji.plugin.PSF_Extract

defaultPSFSizeY - Static variable in class net.preibisch.mvrecon.fiji.plugin.PSF_Extract

defaultPSFSizeZ - Static variable in class net.preibisch.mvrecon.fiji.plugin.PSF_Extract

defaultPSFType - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultPsiCopyBlockSize - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultPsiInit - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultPsiStartFile - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultQueryPath - Static variable in class net.preibisch.mvrecon.fiji.plugin.Define_Multi_View_Dataset

defaultRange - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

defaultRANSACIterationChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.PairwiseGUI

defaultReferenceTimepointIndex - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

defaultReferenceView - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

defaultRegistrationType - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

defaultRegularizationModelIndex - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.TransformationModelGUI

defaultRegularize - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.FRGLDMGUI

defaultRegularize - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.GeometricHashingGUI

defaultRegularize - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.IterativeClosestPointGUI

defaultRegularize - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.LoadCorrespondencesGUI

defaultRegularize - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.RGLDMGUI

defaultRelativeError - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters

defaultRelativeLabel - Static variable in class net.preibisch.mvrecon.fiji.plugin.RelativeThinOut_Detections

defaultRemoveKeep - Static variable in class net.preibisch.mvrecon.fiji.plugin.ThinOut_Detections

defaultRemoveMinIntensity - Static variable in class net.preibisch.mvrecon.fiji.plugin.PSF_Extract

defaultReorientate - Static variable in class net.preibisch.mvrecon.fiji.plugin.boundingbox.AutomaticReorientationBoundingBoxGUI

defaultResetPolicy - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.viewneighbours.ViewNeighboursWindow

defaultResetPolicy - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.viewneighbours.ViewOverlapWindow

defaultResultChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.Split_Views

defaultRotAxis - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.LightSheetZ1

defaultRotAxis - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.MicroManager

defaultSameFixedViews - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

defaultSameMinMax - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

defaultSameModelAngles - Static variable in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

defaultSameModelChannels - Static variable in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

defaultSameModelIlluminations - Static variable in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

defaultSameModelTiles - Static variable in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

defaultSameModelTimePoints - Static variable in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

defaultSameReferenceView - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

defaultSaveOnTheFly - Static variable in class net.preibisch.mvrecon.fiji.plugin.Split_Views

defaultScale - Static variable in class net.preibisch.mvrecon.process.fusion.blk.ContentBased

defaultScale - Static variable in class net.preibisch.mvrecon.process.fusion.transformed.weights.ContentBasedRealRandomAccessible

defaultScalebar - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough

defaultSearchRadius - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm.RGLDMParameters

defaultSecond - Static variable in class net.preibisch.mvrecon.fiji.plugin.Switch_Attributes

defaultSelectedAngleIndex - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultSelectedChannelIndex - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultSelectedIllumIndex - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultSelectedTileIndex - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultSelectedTimePointIndex - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultSetMinMax - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Detection

defaultShowDistanceMap - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.NonRigidParametersGUI

defaultShowStatistics - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

defaultSigma - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGaussianGUI

defaultSigma - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough

defaultSimple - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters

defaultSplittingType - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultSplittingType - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

defaultSplittingType - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

defaultTestEmptyBlocks - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultThreshold - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGaussianGUI

defaultTile - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultTileChoice - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackListImageJ

defaultTileChoice - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackListLOCI

defaultTileChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.Display_View

defaultTileChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultTileIndex - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultTileIndices - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultTileOverlap - Static variable in class net.preibisch.mvrecon.process.export.OpenSeaDragon

defaultTiles - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

defaultTileSize - Static variable in class net.preibisch.mvrecon.process.export.OpenSeaDragon

defaultTileString - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultTimePoint - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultTimepointChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.Display_View

defaultTimePointChoice - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackListImageJ

defaultTimePointChoice - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackListLOCI

defaultTimePointFrom - Static variable in class net.preibisch.mvrecon.fiji.plugin.PSF_Assign

defaultTimePointIndex - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultTimePointIndices - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultTimepoints - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

defaultTimePointString - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultToleranceMode - Static variable in class net.preibisch.mvrecon.process.splitting.ConsensusSetCriterion

defaultToleranceValue - Static variable in class net.preibisch.mvrecon.process.splitting.ConsensusSetCriterion

defaultTopNWorst - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil

defaultTPChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultTpId - Static variable in class net.preibisch.mvrecon.process.export.ExportN5Api

defaultTransformationChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

defaultTranslationRegularization - Static variable in class net.preibisch.mvrecon.fiji.plugin.Intensity_Adjustment

defaultType - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.SimView

defaultURIListChoice - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.OMEZARR

defaultUseAllViews - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil

defaultUseGPUMem - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGaussianGUI

defaultUseMinMaxForAll - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

defaultUseRANSAC - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.icp.IterativeClosestPointParameters

defaultUseRelativeFRC - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

defaultUseSharding - Static variable in class net.preibisch.mvrecon.fiji.plugin.resave.ParametersResaveN5Api

defaultUseSharding - Static variable in class net.preibisch.mvrecon.process.export.ExportN5Api

defaultUseTikhonovRegularization - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultUseXMLPath - Static variable in class net.preibisch.mvrecon.process.export.Save3dTIFF

defaultViewChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

defaultVirtual - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition

defaultVSId - Static variable in class net.preibisch.mvrecon.process.export.ExportN5Api

defaultWeightCacheType - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

defaultWidth - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough

defaultXMLName - Static variable in class net.preibisch.mvrecon.fiji.plugin.Define_Multi_View_Dataset

defaultXMLOutURI - Static variable in class net.preibisch.mvrecon.process.export.ExportN5Api

defaultXMLURI - Static variable in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

defaultZarrChoice - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.OMEZARR

Define_Bounding_Box - Class in net.preibisch.mvrecon.fiji.plugin

Define_Bounding_Box() - Constructor for class net.preibisch.mvrecon.fiji.plugin.Define_Bounding_Box

Define_Multi_View_Dataset - Class in net.preibisch.mvrecon.fiji.plugin

Define_Multi_View_Dataset() - Constructor for class net.preibisch.mvrecon.fiji.plugin.Define_Multi_View_Dataset

defineAs - Variable in class net.preibisch.mvrecon.fiji.plugin.apply.ApplyParameters

defineAsChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

defineBoundingBox(SpimData2, List<ViewId>) - Method in class net.preibisch.mvrecon.fiji.plugin.Define_Bounding_Box

defineBoundingBox(SpimData2, List<ViewId>, String, boolean) - Method in class net.preibisch.mvrecon.fiji.plugin.Define_Bounding_Box

defineDataset(boolean) - Method in class net.preibisch.mvrecon.fiji.plugin.Define_Multi_View_Dataset

DefineDataSet - Class in net.preibisch.mvrecon.headless.definedataset

General class for LightSheetZ1 and MicroManager

DefineDataSet() - Constructor for class net.preibisch.mvrecon.headless.definedataset.DefineDataSet

DefineDataSetParameters - Class in net.preibisch.mvrecon.headless.definedataset

DefineDataSet Parameters class

DefineDataSetParameters() - Constructor for class net.preibisch.mvrecon.headless.definedataset.DefineDataSetParameters

DefineDataSetParameters.RotationAxis - Enum Class in net.preibisch.mvrecon.headless.definedataset

defineMinMax - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

defineMinMax(double[]) - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

defineNewDataset - Variable in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

definePairs() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.PairwiseSetup

Given a list of views and their grouping, identify all pairs that need to be compared

definePairsAbstract() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.AllToAllRange

definePairsAbstract() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.PairwiseSetup

abstract method called by the public definePairs method

delete - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointExplorerPanel

delete() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointExplorerPanel

delete() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationExplorerPanel

deleteCorrespondingInterestPoints() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoints

deleteCorrespondingInterestPoints() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

deleteInterestPoints() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoints

deleteInterestPoints() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

deleteLastViewerTransform() - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough

DensityFilter<T> - Class in net.preibisch.mvrecon.imglib2.st.filter

Visualizes the density at a certain location given the radius

DensityFilter(RadiusNeighborSearch<T>, double) - Constructor for class net.preibisch.mvrecon.imglib2.st.filter.DensityFilter

DensityFilterFactory<T> - Class in net.preibisch.mvrecon.imglib2.st.filter

DensityFilterFactory(T, double) - Constructor for class net.preibisch.mvrecon.imglib2.st.filter.DensityFilterFactory

depth() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

depth() - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

derivativeVector - Variable in class net.preibisch.legacy.registration.bead.laplace.DoGMaximum

description() - Method in class net.preibisch.mvrecon.process.splitting.ConsensusSetCriterion

description() - Method in class net.preibisch.mvrecon.process.splitting.CrossViewCorrespondenceCriterion

description() - Method in interface net.preibisch.mvrecon.process.splitting.OctTreeSplitCriterion

description() - Method in class net.preibisch.mvrecon.process.splitting.SplitDistributeEvenly

description() - Method in interface net.preibisch.mvrecon.process.splitting.SplitInterval

description() - Method in class net.preibisch.mvrecon.process.splitting.SplitOctTree

description() - Method in interface net.preibisch.mvrecon.process.splitting.SplitView

descriptorDistance(F) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.AbstractPointDescriptor

Matches two AbstractPointDescriptors of the same kind yielding a similarity value, the lower the better (0 means identical)

descriptorDistance(LocalCoordinateSystemPointDescriptor<P>) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.LocalCoordinateSystemPointDescriptor

descriptorDistance(TranslationInvariantLocalCoordinateSystemPointDescriptor<P>) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.TranslationInvariantLocalCoordinateSystemPointDescriptor

deserialize(JsonElement, Type, JsonDeserializationContext) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough.AffineTransform3DAdapter

det(double[]) - Static method in class net.preibisch.legacy.registration.bead.laplace.LaPlaceFunctions

DetectChromaticAbberation - Class in net.preibisch.mvrecon.process.chromaticabberation

DetectChromaticAbberation() - Constructor for class net.preibisch.mvrecon.process.chromaticabberation.DetectChromaticAbberation

detectDimensionsInFile(File, Map<FileMapEntry, Pair<Dimensions, VoxelDimensions>>, ImageReader) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil

detectInterestPoints(SpimData2, Collection<? extends ViewId>) - Method in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Detection

detectInterestPoints(SpimData2, Collection<? extends ViewId>, String, boolean) - Method in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Detection

DetectInterestPointsPopup - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

DetectInterestPointsPopup() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.DetectInterestPointsPopup

DetectInterestPointsPopup.MyActionListener - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

Detection - Class in net.preibisch.legacy.registration.detection

Detection(int, double[]) - Constructor for class net.preibisch.legacy.registration.detection.Detection

Detection(int, double[], double) - Constructor for class net.preibisch.legacy.registration.detection.Detection

detectionId - Variable in class net.preibisch.mvrecon.process.splitting.OctTreeSplitCriterion.SplitCorrespondence

Detection ID (for counting unique detections)

detections - Variable in class net.preibisch.mvrecon.fiji.plugin.Visualize_Detections.Params

detectionsChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.Visualize_Detections

detectNumericPatterns(Iterable<String>) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.patterndetector.NumericalFilenamePatternDetector

detectPatterns(List<String>) - Method in interface net.preibisch.mvrecon.fiji.datasetmanager.patterndetector.FilenamePatternDetector

detectPatterns(List<String>) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.patterndetector.NumericalFilenamePatternDetector

detectS3Region(URI) - Static method in class util.URITools

Attempts to detect the AWS region of an S3 bucket without any credentials.

detectSubsets() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.PairwiseSetup

Given a list of pairs of views that need to be compared, find subsets that are not overlapping

detectSubsets() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.ReferenceTimepoint

Given a list of pairs of views that need to be compared, find subsets that are not overlapping

detectSubsets(List<V>, List<Pair<V, V>>, Set<Group<V>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.PairwiseSetup

Given a list of views, pairs of views that need to be compared, and groups - find subsets that are not overlapping

detectViewsInFile(File, Map<File, Map<Class<? extends Entity>, FileListDatasetDefinitionUtil.CheckResult>>, FileListViewDetectionState, List<String>, ImageReader) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil

detectViewsInFiles(List<File>, FileListViewDetectionState) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil

determinant() - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Computes the determinant of this matrix.

determinant() - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Computes the determinant of this matrix.

determinant() - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Computes the determinant of this matrix.

determinant() - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Computes the determinate of this matrix.

determinant() - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Calculates and returns the determinant of this transform.

determineInputBitDepth(Iterable<? extends ViewDescription>, SpimData2) - Static method in class net.preibisch.mvrecon.fiji.plugin.Image_Fusion

determineInputBitDepth(Group<ViewDescription>, SpimData2, RandomAccessibleInterval<FloatType>) - Static method in class net.preibisch.mvrecon.fiji.plugin.Image_Fusion

determineOptimalBoundingBox() - Method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxReorientation

determineSizeSimple() - Method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxReorientation

deviceChoice - Static variable in class net.preibisch.mvrecon.process.cuda.CUDATools

0 ... n == index for i'th CUDA device

deviceCUDA - Variable in class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGParameters

DHM - Class in net.preibisch.mvrecon.fiji.datasetmanager

DHM() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.DHM

DHMImgLoader - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

DHMImgLoader(File, String, String, String, List<String>, List<String>, String, int, int, AbstractSequenceDescription<?, ?, ?>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.DHMImgLoader

DHMMetaData - Class in net.preibisch.mvrecon.fiji.datasetmanager

DHMMetaData(File, double, double, double, String, boolean) - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.DHMMetaData

dialogName() - Method in class net.preibisch.mvrecon.fiji.plugin.apply.ModelLink

DifferenceOfGaussianGUI - Class in net.preibisch.mvrecon.fiji.plugin.interestpointdetection

DifferenceOfGaussianGUI(SpimData2, List<ViewId>) - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGaussianGUI

DifferenceOfGUI - Class in net.preibisch.mvrecon.fiji.plugin.interestpointdetection

DifferenceOfGUI(SpimData2, List<ViewId>) - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

differenceThreshold - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.geometrichashing.GeometricHashingParameters

differenceThreshold - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm.RGLDMParameters

dimension(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox

dimension(int) - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccessibleInterval

dimension(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval

dimension(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGrid

dimension(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccessibleInterval

dimensionChoiceAnglesFalse - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

dimensionChoiceAnglesTrue - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

dimensionChoiceChannelsFalse - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

dimensionChoiceChannelsTrue - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

dimensionChoiceIlluminationsFalse - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

dimensionChoiceIlluminationsTrue - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

dimensionChoiceTilesFalse - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

dimensionChoiceTilesTrue - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

dimensionChoiceTimePointsFalse - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

dimensionChoiceTimePointsTrue - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

dimensionOrder - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.grid.RegularTranformHelpers.GridPreset

dimensionOrder - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.grid.RegularTranformHelpers.RegularTranslationParameters

dimensions - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM.SmartSPIMMetaData

dimensions - Variable in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxMaximal

dimensions - Variable in class net.preibisch.mvrecon.process.n5api.N5ApiTools.MultiResolutionLevelInfo

dimensions(long[]) - Method in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox

dimensions(long[]) - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccessibleInterval

dimensions(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval

dimensions(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGrid

dimensions(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccessibleInterval

dir - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM.SmartSPIMMetaData

directory - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

directory - Variable in class net.preibisch.mvrecon.headless.definedataset.StackListParameters

DIRECTORY_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.XmlIOFileMapImgLoaderLOCI2

DIRECTORY_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoFileListImgLoaderLOCI

DIRECTORY_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoLightSheetZ1ImgLoader

DIRECTORY_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoMicroManagerImgLoader

DIRECTORY_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoSimViewImgLoader

DIRECTORY_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoStackImgLoader

DirectoryFilter() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.SimView.DirectoryFilter

DirectoryFilter(String) - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.SimView.DirectoryFilter

disableGroupingIfActive() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

DisplacementFieldN5Tools - Class in net.preibisch.mvrecon.process.fusion.blk

Static helpers to persist displacement fields to an N5/Zarr container and reload them as in-memory ArrayImgs.

display(RandomAccessibleInterval<FloatType>, FusionTools.ImgDataType) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

display(RandomAccessibleInterval<FloatType>, FusionTools.ImgDataType, double, double, int[], int) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

display(RandomAccessibleInterval<FloatType>, FusionTools.ImgDataType, int[], int) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

display(SpimData2, Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.fiji.plugin.PSF_View

display(SpimData2, Collection<? extends ViewId>, int) - Static method in class net.preibisch.mvrecon.fiji.plugin.PSF_View

DISPLAY_SETTINGS_HEADER - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

DISPLAY_SETTINGS_HEADER - Static variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

DISPLAY_SETTINGS_OFFSET_HEADER - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

DISPLAY_SETTINGS_OFFSET_HEADER - Static variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

Display_View - Class in net.preibisch.mvrecon.fiji.plugin

Display_View() - Constructor for class net.preibisch.mvrecon.fiji.plugin.Display_View

displayBoundingBoxes(GenericDialog, List<BoundingBox>) - Static method in class net.preibisch.mvrecon.fiji.plugin.util.GUIHelper

displayCached(RandomAccessibleInterval<FloatType>) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

displayCached(RandomAccessibleInterval<FloatType>, double, double) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

displayCached(RandomAccessibleInterval<FloatType>, double, double, int[], int) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

displayCached(RandomAccessibleInterval<FloatType>, int[], int) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

displayChoices - Static variable in class net.preibisch.mvrecon.fiji.plugin.PSF_View

displayCopy(RandomAccessibleInterval<FloatType>) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

displayCopy(RandomAccessibleInterval<FloatType>, double, double) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

DisplayFusedImagesPopup - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

DisplayFusedImagesPopup() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.DisplayFusedImagesPopup

DisplayFusedImagesPopup.DisplayVirtualFused - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

DisplayImage - Class in net.preibisch.mvrecon.process.export

DisplayImage() - Constructor for class net.preibisch.mvrecon.process.export.DisplayImage

DisplayImage(boolean) - Constructor for class net.preibisch.mvrecon.process.export.DisplayImage

displayInput - Variable in class net.preibisch.mvrecon.fiji.plugin.Visualize_Detections.Params

DisplayRawImagesPopup - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

DisplayRawImagesPopup() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.DisplayRawImagesPopup

DisplayRawImagesPopup.MyActionListener - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

displayRegistrationNames(GenericDialog, HashMap<String, Integer>) - Static method in class net.preibisch.mvrecon.fiji.plugin.util.GUIHelper

displayStringToDouble(Object) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.NumberUtils

displayStringToInt(Object) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.NumberUtils

displayStringToLong(Object) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.NumberUtils

DisplayVirtualFused(SpimData, ArrayList<ViewId>, Interval, double) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.DisplayFusedImagesPopup.DisplayVirtualFused

displayVirtually(RandomAccessibleInterval<FloatType>) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

displayVirtually(RandomAccessibleInterval<FloatType>, double, double) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

dispose() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoG

disposeViewerWindow(BigDataViewer) - Static method in class net.preibisch.mvrecon.fiji.plugin.apply.BigDataViewerTransformationWindow

distance - Variable in class net.preibisch.legacy.registration.detection.AbstractDetection

distance(Point3d) - Method in class net.preibisch.mvrecon.vecmath.Point3d

Returns the distance between this point and point p1.

distance(Point3f) - Method in class net.preibisch.mvrecon.vecmath.Point3f

Computes the distance between this point and point p1.

distance(Point4d) - Method in class net.preibisch.mvrecon.vecmath.Point4d

Returns the distance between this point and point p1.

distance(Point4f) - Method in class net.preibisch.mvrecon.vecmath.Point4f

Computes the distance between this point and point p1.

DistanceHistogram - Class in net.preibisch.mvrecon.process.interestpointremoval

DistanceHistogram() - Constructor for class net.preibisch.mvrecon.process.interestpointremoval.DistanceHistogram

distanceL1(Point3d) - Method in class net.preibisch.mvrecon.vecmath.Point3d

Computes the L-1 (Manhattan) distance between this point and point p1.

distanceL1(Point3f) - Method in class net.preibisch.mvrecon.vecmath.Point3f

Computes the L-1 (Manhattan) distance between this point and point p1.

distanceL1(Point4d) - Method in class net.preibisch.mvrecon.vecmath.Point4d

Computes the L-1 (Manhattan) distance between this point and point p1.

distanceL1(Point4f) - Method in class net.preibisch.mvrecon.vecmath.Point4f

Computes the L-1 (Manhattan) distance between this point and point p1.

distanceLinf(Point3d) - Method in class net.preibisch.mvrecon.vecmath.Point3d

Computes the L-infinite distance between this point and point p1.

distanceLinf(Point3f) - Method in class net.preibisch.mvrecon.vecmath.Point3f

Computes the L-infinite distance between this point and point p1.

distanceLinf(Point4d) - Method in class net.preibisch.mvrecon.vecmath.Point4d

Computes the L-infinite distance between this point and point p1.

distanceLinf(Point4f) - Method in class net.preibisch.mvrecon.vecmath.Point4f

Computes the L-infinite distance between this point and point p1.

distanceSquared(Point3d) - Method in class net.preibisch.mvrecon.vecmath.Point3d

Returns the square of the distance between this point and point p1.

distanceSquared(Point3f) - Method in class net.preibisch.mvrecon.vecmath.Point3f

Computes the square of the distance between this point and point p1.

distanceSquared(Point4d) - Method in class net.preibisch.mvrecon.vecmath.Point4d

Returns the square of the distance between this point and point p1.

distanceSquared(Point4f) - Method in class net.preibisch.mvrecon.vecmath.Point4f

Computes the square of the distance between this point and point p1.

distanceTo(PointNode) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test.PointNode

distanceTo(T) - Method in class net.preibisch.legacy.registration.detection.AbstractDetection

DistanceVisualizingRandomAccess - Class in net.preibisch.mvrecon.process.fusion.transformed.nonrigid

Virtually transforms any RandomAccessibleInterval<RealType> into a RandomAccess<FloatType> using an AffineTransformation and Linear Interpolation.

DistanceVisualizingRandomAccess(Interval, ModelGrid, AffineTransform3D, InterpolatorFactory<FloatType, RandomAccessible<FloatType>>, FloatType, long[]) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.DistanceVisualizingRandomAccess

DistanceVisualizingRandomAccessible - Class in net.preibisch.mvrecon.process.fusion.transformed.nonrigid

DistanceVisualizingRandomAccessible(Interval, ModelGrid, AffineTransform3D, FloatType, Interval) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.DistanceVisualizingRandomAccessible

distinctLabels - Variable in class net.preibisch.legacy.registration.threshold.ConnectedComponent

distributeGridFRC(RandomAccessibleInterval<FloatType>, double, int, int, boolean, int, ExecutorService) - Static method in class net.preibisch.mvrecon.process.quality.FRCTools

distributeSquaresXY(Interval, long, double) - Static method in class net.preibisch.mvrecon.process.quality.FRCTools

div(NumericAffineModel3D) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

div(NumericAffineTransform3D) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

divideIntoBlocks(long[], long[]) - Method in interface net.preibisch.mvrecon.process.cuda.BlockGenerator

Divides an image into blocks

divideIntoBlocks(long[], long[]) - Method in class net.preibisch.mvrecon.process.cuda.BlockGeneratorFixedSizePrecise

Divides an image into blocks

divideIntoBlocks(long[], long[]) - Method in class net.preibisch.mvrecon.process.cuda.BlockGeneratorVariableSizePrecise

Divides an image into blocks

divideIntoBlocks(long[], long[]) - Method in class net.preibisch.mvrecon.process.cuda.BlockGeneratorVariableSizeSimple

Divides an image into blocks

divideIntoPortions(long) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

DO_NOT_GROUP - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.GroupParameters.InterestpointGroupingType

DoG - Class in net.preibisch.mvrecon.process.interestpointdetection.methods.dog

DoG(DoGParameters) - Constructor for class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoG

dogDetection(RandomAccessible<FloatType>, Interval) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoG

dogDetection(RandomAccessibleInterval<FloatType>) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoG

DoGImgLib2 - Class in net.preibisch.mvrecon.process.interestpointdetection.methods.dog

DoGImgLib2() - Constructor for class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2

DoGImgLib2.SpecialPoint - Enum Class in net.preibisch.mvrecon.process.interestpointdetection.methods.dog

DoGMaximum - Class in net.preibisch.legacy.registration.bead.laplace

DoGMaximum(int, int, int, int) - Constructor for class net.preibisch.legacy.registration.bead.laplace.DoGMaximum

DoGParameters - Class in net.preibisch.mvrecon.process.interestpointdetection.methods.dog

DoGParameters() - Constructor for class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGParameters

DoGParameters(Collection<ViewDescription>, ImgLoader, double, double) - Constructor for class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGParameters

DoGParameters(Collection<ViewDescription>, ImgLoader, double, int) - Constructor for class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGParameters

DoGWindow - Class in net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive

DoGWindow(InteractiveDoG) - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.DoGWindow

DonatedNail(double[], double[], ViewId) - Constructor for class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion.DonatedNail

donorViewId - Variable in class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion.DonatedNail

donorViewId - Variable in class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion.LandmarkRecord

doPlot(double[][], double[][], FRC.ThresholdMethod, double, String) - Method in class net.preibisch.mvrecon.process.quality.FRC

Simple method to plot the data using {ij.gui.Plot #Plot}

dot(Vector3d) - Method in class net.preibisch.mvrecon.vecmath.Vector3d

Returns the dot product of this vector and vector v1.

dot(Vector3f) - Method in class net.preibisch.mvrecon.vecmath.Vector3f

Computes the dot product of this vector and vector v1.

dot(Vector4d) - Method in class net.preibisch.mvrecon.vecmath.Vector4d

Returns the dot product of this vector and vector v1.

dot(Vector4f) - Method in class net.preibisch.mvrecon.vecmath.Vector4f

returns the dot product of this vector and v1

doubleStringCoreToDisplay(Object) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.NumberUtils

doubleStringDisplayToCore(Object) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.NumberUtils

doubleToCoreString(double) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.NumberUtils

doubleToDisplayString(double) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.NumberUtils

downsample - Variable in class net.preibisch.mvrecon.fiji.plugin.Visualize_Detections.Params

downsample(RandomAccessibleInterval<T>, long[]) - Static method in class net.preibisch.mvrecon.process.downsampling.Downsample

Downsample - Class in net.preibisch.mvrecon.process.downsampling

Downsample() - Constructor for class net.preibisch.mvrecon.process.downsampling.Downsample

downsampleChoiceXY - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

downsampleChoiceZ - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

downsampleFactor(int, int, VoxelDimensions) - Static method in class net.preibisch.mvrecon.process.downsampling.DownsampleTools

downsampleHDF5(RandomAccessibleInterval<T>, int[]) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.MultiResolutionFlatfieldCorrectionWrappedImgLoader

downsampling code form WriteSequenceToHdf5, distilled into one method

DownsampleTools - Class in net.preibisch.mvrecon.process.downsampling

DownsampleTools() - Constructor for class net.preibisch.mvrecon.process.downsampling.DownsampleTools

downsampleXY - Variable in class net.preibisch.mvrecon.process.interestpointdetection.methods.InterestPointParameters

downsampleXYIndex - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

downsampleZ - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

downsampleZ - Variable in class net.preibisch.mvrecon.process.interestpointdetection.methods.InterestPointParameters

downsampling - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

downsampling - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

downsampling - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

drawOverlays(Graphics) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointOverlay

drawOverlays(Graphics) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupIdOverlay

drawProjectedInterestPoints(ImagePlus, Collection<InterestPoint>, int) - Static method in class net.preibisch.mvrecon.process.interestpointremoval.InteractiveProjections

drawRealLocalizable(Collection<L>, ImagePlus, double, Color, boolean) - Static method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.HelperFunctions

ds - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

ds - Static variable in class net.preibisch.mvrecon.process.downsampling.DownsampleTools

dt - Variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.geometrichashing.GeometricHashingParameters

dt - Variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm.RGLDMParameters

duplicate() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoint

duplicate() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.GroupedInterestPoint

duplicate(ViewTransform) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationExplorerPanel

Duplicate_Transformation - Class in net.preibisch.mvrecon.fiji.plugin

Duplicate_Transformation() - Constructor for class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

duplicateTransformations(int, ViewId, ViewId, SpimData2) - Method in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

duplicateTypeOnSameNativeImg() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

duplicateTypeOnSameNativeImg() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

duplicationChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

E

EFFICIENT_BAYESIAN - Enum constant in enum class net.preibisch.mvrecon.process.deconvolution.DeconViewPSF.PSFTYPE

eigenValues - Variable in class net.preibisch.legacy.registration.bead.laplace.DoGMaximum

eigenVectors - Variable in class net.preibisch.legacy.registration.bead.laplace.DoGMaximum

elements - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedTableModel

elements() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedTableModel

elements(boolean) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedTableModel

EmptyEntity - Class in net.preibisch.mvrecon.fiji.spimdata

EmptyEntity(int, String) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.EmptyEntity

enableNonRigid - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.NonRigidParametersGUI

entitiesPerAttribute() - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

entropyRRA() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.ContentBasedRealRandomAccessible

epsilonEquals(AxisAngle4d, double) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4d

Returns true if the L-infinite distance between this axis-angle and axis-angle a1 is less than or equal to the epsilon parameter, otherwise returns false.

epsilonEquals(AxisAngle4f, float) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4f

Returns true if the L-infinite distance between this axis-angle and axis-angle a1 is less than or equal to the epsilon parameter, otherwise returns false.

epsilonEquals(Matrix3d, double) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Returns true if the L-infinite distance between this matrix and matrix m1 is less than or equal to the epsilon parameter, otherwise returns false.

epsilonEquals(Matrix3f, float) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Returns true if the L-infinite distance between this matrix and matrix m1 is less than or equal to the epsilon parameter, otherwise returns false.

epsilonEquals(Matrix4d, double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Returns true if the L-infinite distance between this matrix and matrix m1 is less than or equal to the epsilon parameter, otherwise returns false.

epsilonEquals(Matrix4d, float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Deprecated.

Use epsilonEquals(Matrix4d,double) instead

epsilonEquals(Matrix4f, float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Returns true if the L-infinite distance between this matrix and matrix m1 is less than or equal to the epsilon parameter, otherwise returns false.

epsilonEquals(Transform3D, double) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Returns true if the L-infinite distance between this matrix and matrix m1 is less than or equal to the epsilon parameter, otherwise returns false.

epsilonEquals(Tuple3d, double) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Returns true if the L-infinite distance between this tuple and tuple t1 is less than or equal to the epsilon parameter, otherwise returns false.

epsilonEquals(Tuple3f, float) - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Returns true if the L-infinite distance between this tuple and tuple t1 is less than or equal to the epsilon parameter, otherwise returns false.

epsilonEquals(Tuple4d, double) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Returns true if the L-infinite distance between this tuple and tuple t1 is less than or equal to the epsilon parameter, otherwise returns false.

epsilonEquals(Tuple4f, float) - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Returns true if the L-infinite distance between this tuple and tuple t1 is less than or equal to the epsilon parameter, otherwise returns false.

equalCalibration(VoxelDimensions, VoxelDimensions) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListViewDetectionState

equalizeLabels(Img<IntType>) - Method in class net.preibisch.legacy.registration.threshold.ConnectedComponent

equals(Object) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.AngleInfo

equals(Object) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.ChannelInfo

equals(Object) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.TileInfo

equals(Object) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList.ViewSetupPrecursor

equals(Object) - Method in class net.preibisch.mvrecon.fiji.plugin.Specify_Calibration.Cal

equals(Object) - Method in class net.preibisch.mvrecon.fiji.spimdata.EmptyEntity

Two Entitys are equal if they have the same and the same tag as both are unknown types of entities.

equals(Object) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.FileMapEntry

equals(Object) - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoint

equals(Object) - Method in class net.preibisch.mvrecon.headless.definedataset.StackList.ViewSetupPrecursor

equals(Object) - Method in class net.preibisch.mvrecon.process.fusion.intensity.IntensityCorrection.SerializableRealInterval

equals(Object) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.CorrespondingIP

equals(Object) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

equals(Object) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.GroupedInterestPoint

equals(Object) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4d

Returns true if the Object o1 is of type AxisAngle4d and all of the data members of o1 are equal to the corresponding data members in this AxisAngle4d.

equals(Object) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4f

Returns true if the Object o1 is of type AxisAngle4f and all of the data members of o1 are equal to the corresponding data members in this AxisAngle4f.

equals(Object) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Returns true if the Object t1 is of type Matrix3d and all of the data members of t1 are equal to the corresponding data members in this Matrix3d.

equals(Object) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Returns true if the Object o1 is of type Matrix3f and all of the data members of o1 are equal to the corresponding data members in this Matrix3f.

equals(Object) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Returns true if the Object t1 is of type Matrix4d and all of the data members of t1 are equal to the corresponding data members in this Matrix4d.

equals(Object) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Returns true if the Object t1 is of type Matrix4f and all of the data members of t1 are equal to the corresponding data members in this Matrix4f.

equals(Object) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Returns true if the Object o1 is of type Transform3D and all of the data members of o1 are equal to the corresponding data members in this Transform3D.

equals(Object) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Returns true if the Object t1 is of type Tuple3d and all of the data members of t1 are equal to the corresponding data members in this Tuple3d.

equals(Object) - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Returns true if the Object t1 is of type Tuple3f and all of the data members of t1 are equal to the corresponding data members in this Tuple3f.

equals(Object) - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Returns true if the Object t1 is of type Tuple3i and all of the data members of t1 are equal to the corresponding data members in this Tuple3i.

equals(Object) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Returns true if the Object t1 is of type Tuple4d and all of the data members of t1 are equal to the corresponding data members in this Tuple4d.

equals(Object) - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Returns true if the Object t1 is of type Tuple4f and all of the data members of t1 are equal to the corresponding data members in this Tuple4f.

equals(AbstractDetection<?>) - Method in class net.preibisch.legacy.registration.detection.AbstractDetection

equals(AxisAngle4d) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4d

Returns true if all of the data members of AxisAngle4d a1 are equal to the corresponding data members in this AxisAngle4d.

equals(AxisAngle4f) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4f

Returns true if all of the data members of AxisAngle4f a1 are equal to the corresponding data members in this AxisAngle4f.

equals(Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Returns true if all of the data members of Matrix3d m1 are equal to the corresponding data members in this Matrix3d.

equals(Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Returns true if all of the data members of Matrix3f m1 are equal to the corresponding data members in this Matrix3f.

equals(Matrix4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Returns true if all of the data members of Matrix4d m1 are equal to the corresponding data members in this Matrix4d.

equals(Matrix4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Returns true if all of the data members of Matrix4f m1 are equal to the corresponding data members in this Matrix4f.

equals(Transform3D) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Returns true if all of the data members of transform t1 are equal to the corresponding data members in this Transform3D.

equals(Tuple3d) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Returns true if all of the data members of Tuple3d t1 are equal to the corresponding data members in this Tuple3d.

equals(Tuple3f) - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Returns true if the Object t1 is of type Tuple3f and all of the data members of t1 are equal to the corresponding data members in this Tuple3f.

equals(Tuple4d) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Returns true if all of the data members of Tuple4d t1 are equal to the corresponding data members in this Tuple4d.

equals(Tuple4f) - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Returns true if all of the data members of Tuple4f t1 are equal to the corresponding data members in this Tuple4f.

err - Variable in class net.preibisch.mvrecon.fiji.plugin.resave.ProgressWriterIJ

err() - Method in class net.preibisch.mvrecon.fiji.plugin.resave.ProgressWriterIJ

error - Static variable in class net.preibisch.mvrecon.fiji.plugin.util.GUIHelper

errorMsg1 - Static variable in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

errorPx - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.PairError

estimate(String) - Method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxBigDataViewer

estimate(String) - Method in interface net.preibisch.mvrecon.process.boundingbox.BoundingBoxEstimation

estimate(String) - Method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxMaximal

estimate(String) - Method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxMaximalGroupOverlap

estimate(String) - Method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxMinFilterThreshold

estimate(String) - Method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxReorientation

estimateAnisotropy(SpimData, List<ViewId>) - Static method in class net.preibisch.mvrecon.process.fusion.lazy.LazyFusionTools

estimateBounds(RealInterval, AffineGet) - Static method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxMaximalGroupOverlap

Calculate the boundary interval of an interval after it has been transformed by transform.

estimateFRC(SpimData2, List<ViewId>) - Static method in class net.preibisch.mvrecon.fiji.plugin.Image_Quality

estimateIntialModel(List<PointMatchGeneric<LinkedInterestPoint<P>>>, Model<?>) - Method in class net.preibisch.mvrecon.process.pointcloud.icp.ICP

Estimates an initial Model based on some given PointMatches.

estimateMultiResPyramid(Dimensions, double) - Static method in class net.preibisch.mvrecon.process.export.ExportN5Api

EVratioA - Variable in class net.preibisch.legacy.registration.bead.laplace.DoGMaximum

EVratioB - Variable in class net.preibisch.legacy.registration.bead.laplace.DoGMaximum

EVratioC - Variable in class net.preibisch.legacy.registration.bead.laplace.DoGMaximum

exceptionIds - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

execTasks(ArrayList<Callable<Void>>, int, String) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

execTasks(ArrayList<Callable<Void>>, ExecutorService, String) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

expandAccumulatedViewInfos(Map<Class<? extends Entity>, List<Integer>>, FilenamePatternDetector, FileListViewDetectionState) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil

expandMapIndexed(Map<T, List<FileMapEntry>>, boolean) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil

expandMapSingleFromFile(Map<T, List<FileMapEntry>>, FilenamePatternDetector, List<Integer>) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil

expandMapSingleFromFileGroupedFormat(Map<T, List<FileMapEntry>>, FilenamePatternDetector, List<Integer>, Map<String, Pair<File, Integer>>) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil

expandTimePointMapIndexed(Map<T, List<FileMapEntry>>) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil

explorer - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

explorer() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

ExplorerWindow<AS> - Interface in net.preibisch.mvrecon.fiji.spimdata.explorer

ExplorerWindowSetable - Interface in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

export(RandomAccessibleInterval<FloatType>, DeconvolutionGUI, ImgExport, Group<ViewDescription>) - Static method in class net.preibisch.mvrecon.fiji.plugin.Image_Deconvolution

export(RandomAccessibleInterval<T>, ExecutorService, T, QualityGUI, ImgExport, Group<ViewDescription>, double[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.Image_Quality

exportImage(BlockSupplier<T>, Interval, double, double, String, Group<? extends ViewDescription>) - Method in class net.preibisch.mvrecon.process.export.DisplayImage

exportImage(BlockSupplier<T>, Interval, double, double, String, Group<? extends ViewDescription>) - Method in class net.preibisch.mvrecon.process.export.ExportLarge2DTIFF

exportImage(BlockSupplier<T>, Interval, double, double, String, Group<? extends ViewDescription>) - Method in class net.preibisch.mvrecon.process.export.ExportN5Api

exportImage(BlockSupplier<T>, Interval, double, double, String, Group<? extends ViewDescription>) - Method in interface net.preibisch.mvrecon.process.export.ImgExport

Exports the image using a predefined min/max

exportImage(BlockSupplier<T>, Interval, double, double, String, Group<? extends ViewDescription>) - Method in class net.preibisch.mvrecon.process.export.OpenSeaDragon

exportImage(BlockSupplier<T>, Interval, double, double, String, Group<? extends ViewDescription>) - Method in class net.preibisch.mvrecon.process.export.Save3dTIFF

ExportLarge2DTIFF - Class in net.preibisch.mvrecon.process.export

ExportLarge2DTIFF() - Constructor for class net.preibisch.mvrecon.process.export.ExportLarge2DTIFF

ExportN5Api - Class in net.preibisch.mvrecon.process.export

ExportN5Api() - Constructor for class net.preibisch.mvrecon.process.export.ExportN5Api

exportOptions() - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

EXTEND_BORDER_PIXELS - Enum constant in enum class net.preibisch.mvrecon.process.cuda.CUDASeparableConvolutionFunctions.OutOfBounds

extendInput(RandomAccessible<T>) - Static method in class net.preibisch.mvrecon.process.fusion.blk.BlkAffineFusion

EXTENSION_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoDHMImgLoader

extract(SpimData2, Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.fiji.plugin.PSF_Extract

extract(SpimData2, Collection<? extends ViewId>, String, boolean) - Static method in class net.preibisch.mvrecon.fiji.plugin.PSF_Extract

extract3DVolume(RandomAccessibleInterval<T>) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AllenOMEZarrLoader.OMEZARREntry

extractCorrespondenceCandidates(ArrayList<I>, ArrayList<I>, double, int, double) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.geometrichashing.GeometricHasher

extractCorrespondenceCandidates(ArrayList<I>, ArrayList<I>, int, double) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.fastrgldm.FRGLDMMatcher

extractCorrespondenceCandidates(ArrayList<T>, ArrayList<T>, double, double, boolean) - Method in interface net.preibisch.legacy.registration.detection.descriptor.CorrespondenceExtraction

extractCorrespondenceCandidates(List<I>, List<I>, int, int, double, double, boolean, double) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm.RGLDMMatcher

extractFullResSeries(IFormatReader, int) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil

extractPoints(String, boolean, boolean, List<ViewId>, SpimData2) - Static method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxReorientation

Gets point locations in local or global coordinates

extractPoints(HashMap<ViewId, ? extends Collection<? extends RealLocalizable>>, List<ViewId>, SpimData2) - Static method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxReorientation

extractPSFLocal(RealRandomAccessible<T>, Collection<RealLocalizable>, RandomAccessibleInterval<T>) - Static method in class net.preibisch.mvrecon.process.psf.PSFExtraction

Extracts the PSF by summing up the local neighborhood of locations (most likely RANSAC correspondences)

extractPSFMultiThreaded(RealRandomAccessible<T>, Collection<RealLocalizable>, RandomAccessibleInterval<T>) - Static method in class net.preibisch.mvrecon.process.psf.PSFExtraction

F

f - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

failWith(PairwiseResult<I>, String, String, Exception) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.icp.IterativeClosestPointPairwise

FALSE - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters.PreAlign

FastAffineModel1D - Class in net.preibisch.mvrecon.process.fusion.intensity.mpicbg

FastAffineModel1D() - Constructor for class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.FastAffineModel1D

fastFilterRansac(FlattenedMatches, int, double, double, int, double) - Method in class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.FastAffineModel1D

Estimate a AffineModel1D from a set with many outliers by first filtering the worst outliers with RANSAC and filter potential outliers by robust iterative regression.

FastLinearIntensityMap - Class in net.preibisch.mvrecon.process.fusion.intensity

FastLinearIntensityMap() - Constructor for class net.preibisch.mvrecon.process.fusion.intensity.FastLinearIntensityMap

FFTConvolution<R> - Class in util

Computes the convolution of an image with an arbitrary kernel.

FFTConvolution(Img<R>, Img<R>) - Constructor for class util.FFTConvolution

Compute a Fourier space based convolution in-place (img will be replaced by the convolved result).

FFTConvolution(Img<R>, Img<R>, ExecutorService) - Constructor for class util.FFTConvolution

Compute a Fourier space based convolution in-place (img will be replaced by the convolved result).

FFTConvolution(Img<R>, Img<R>, RandomAccessibleInterval<R>) - Constructor for class util.FFTConvolution

Compute a Fourier space based convolution The image will be extended by mirroring with single boundary, the kernel will be zero-padded.

FFTConvolution(Img<R>, Img<R>, RandomAccessibleInterval<R>, ExecutorService) - Constructor for class util.FFTConvolution

Compute a Fourier space based convolution The image will be extended by mirroring with single boundary, the kernel will be zero-padded.

FFTConvolution(RandomAccessible<R>, Interval, RandomAccessible<R>, Interval, ImgFactory<ComplexFloatType>) - Constructor for class util.FFTConvolution

Compute a Fourier space based convolution in-place (img will be replaced by the convolved result).

FFTConvolution(RandomAccessible<R>, Interval, RandomAccessible<R>, Interval, ImgFactory<ComplexFloatType>, ExecutorService) - Constructor for class util.FFTConvolution

Compute a Fourier space based convolution in-place (img will be replaced by the convolved result).

FFTConvolution(RandomAccessible<R>, Interval, RandomAccessible<R>, Interval, RandomAccessibleInterval<R>, ImgFactory<ComplexFloatType>) - Constructor for class util.FFTConvolution

Compute a Fourier space based convolution.

FFTConvolution(RandomAccessible<R>, Interval, RandomAccessible<R>, Interval, RandomAccessibleInterval<R>, ImgFactory<ComplexFloatType>, ExecutorService) - Constructor for class util.FFTConvolution

Compute a Fourier space based convolution.

FFTConvolution(RandomAccessibleInterval<R>, RandomAccessibleInterval<R>, ImgFactory<ComplexFloatType>) - Constructor for class util.FFTConvolution

Compute a Fourier space based convolution in-place (img will be replaced by the convolved result).

FFTConvolution(RandomAccessibleInterval<R>, RandomAccessibleInterval<R>, ImgFactory<ComplexFloatType>, ExecutorService) - Constructor for class util.FFTConvolution

Compute a Fourier space based convolution in-place (img will be replaced by the convolved result).

FFTConvolution(RandomAccessibleInterval<R>, RandomAccessibleInterval<R>, RandomAccessibleInterval<R>, ImgFactory<ComplexFloatType>) - Constructor for class util.FFTConvolution

Compute a Fourier space based convolution The image will be extended by mirroring with single boundary, the kernel will be zero-padded.

FFTConvolution(RandomAccessibleInterval<R>, RandomAccessibleInterval<R>, RandomAccessibleInterval<R>, ImgFactory<ComplexFloatType>, ExecutorService) - Constructor for class util.FFTConvolution

Compute a Fourier space based convolution The image will be extended by mirroring with single boundary, the kernel will be zero-padded.

fftImgFactory() - Method in class util.FFTConvolution

fftSize - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

file() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.FileMapEntry

FILE_MAPPING_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.XmlIOFileMapImgLoaderLOCI2

FILE_MAPPING_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoFileListImgLoaderLOCI

FILE_PATTERN_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoStackImgLoader

FileListDatasetDefinition - Class in net.preibisch.mvrecon.fiji.datasetmanager

FileListDatasetDefinition() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition

FileListDatasetDefinition.FileListChooser - Interface in net.preibisch.mvrecon.fiji.datasetmanager

FileListDatasetDefinition.SimpleDirectoryFileListChooser - Class in net.preibisch.mvrecon.fiji.datasetmanager

FileListDatasetDefinition.WildcardFileListChooser - Class in net.preibisch.mvrecon.fiji.datasetmanager

FileListDatasetDefinitionUtil - Class in net.preibisch.mvrecon.fiji.datasetmanager

FileListDatasetDefinitionUtil() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil

FileListDatasetDefinitionUtil.AngleInfo - Class in net.preibisch.mvrecon.fiji.datasetmanager

FileListDatasetDefinitionUtil.ChannelInfo - Class in net.preibisch.mvrecon.fiji.datasetmanager

FileListDatasetDefinitionUtil.ChannelOrIlluminationInfo - Class in net.preibisch.mvrecon.fiji.datasetmanager

FileListDatasetDefinitionUtil.CheckResult - Enum Class in net.preibisch.mvrecon.fiji.datasetmanager

FileListDatasetDefinitionUtil.TileInfo - Class in net.preibisch.mvrecon.fiji.datasetmanager

FileListDatasetDefinitionUtil.TileOrAngleInfo - Class in net.preibisch.mvrecon.fiji.datasetmanager

FileListViewDetectionState - Class in net.preibisch.mvrecon.fiji.datasetmanager

FileListViewDetectionState() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.FileListViewDetectionState

fileMap - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.LazyLoadingFlatFieldCorrectionMap

FileMapEntry - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2

FileMapEntry(File, int, int) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.FileMapEntry

FileMapGettable - Interface in net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2

FileMapImgLoaderLOCI - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

FileMapImgLoaderLOCI(Map<? extends ViewId, FileMapEntry>, AbstractSequenceDescription<?, ?, ?>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.FileMapImgLoaderLOCI

FileMapImgLoaderLOCI(Map<? extends ViewId, FileMapEntry>, AbstractSequenceDescription<?, ?, ?>, boolean) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.FileMapImgLoaderLOCI

FileMapImgLoaderLOCI2 - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2

FileMapImgLoaderLOCI2(Map<? extends ViewId, FileMapEntry>, AbstractSequenceDescription<?, ?, ?>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.FileMapImgLoaderLOCI2

FileMapImgLoaderLOCI2(Map<? extends ViewId, FileMapEntry>, AbstractSequenceDescription<?, ?, ?>, boolean) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.FileMapImgLoaderLOCI2

FileMapImgLoaderLOCI2.FileMapSetupImgLoaderLOCI2<T> - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2

FileMapSetupImgLoaderLOCI2(int) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.FileMapImgLoaderLOCI2.FileMapSetupImgLoaderLOCI2

fileNamePattern - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

fileNamePattern - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoader

FilenamePatternDetector - Interface in net.preibisch.mvrecon.fiji.datasetmanager.patterndetector

filePattern - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData

FILEPATTERN_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoSimViewImgLoader

files() - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

FILES_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.XmlIOFileMapImgLoaderLOCI2

FILES_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoFileListImgLoaderLOCI

filter(IterableRealInterval<S>, C, FilterFactory<S, T>) - Static method in class net.preibisch.mvrecon.imglib2.st.filter.Filters

filter(IterableRealInterval<S>, RandomAccessibleInterval<T>, FilterFactory<S, T>) - Static method in class net.preibisch.mvrecon.imglib2.st.filter.Filters

filter(IterableRealInterval<S>, FilterFactory<S, T>) - Static method in class net.preibisch.mvrecon.imglib2.st.filter.Filters

filter(RealLocalizable, T) - Method in class net.preibisch.mvrecon.imglib2.st.filter.DensityFilter

filter(RealLocalizable, T) - Method in interface net.preibisch.mvrecon.imglib2.st.filter.Filter

filter(RealLocalizable, T) - Method in class net.preibisch.mvrecon.imglib2.st.filter.GaussianFilter

filter(RealLocalizable, T) - Method in class net.preibisch.mvrecon.imglib2.st.filter.MeanFilter

filter(RealLocalizable, T) - Method in class net.preibisch.mvrecon.imglib2.st.filter.MedianFilter

filter(FlattenedMatches, Collection<PointMatch>) - Method in class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.RansacRegressionReduceFilter

Filter<T> - Interface in net.preibisch.mvrecon.imglib2.st.filter

filter_ransac - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac.RANSACParameters

filterBlocksForContent(List<List<Block>>, RandomAccessibleInterval<FloatType>, ExecutorService) - Static method in class net.preibisch.mvrecon.process.deconvolution.DeconView

FilteredAndGroupedExplorer<AS> - Class in net.preibisch.mvrecon.fiji.spimdata.explorer

FilteredAndGroupedExplorer() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorer

FilteredAndGroupedExplorerPanel<AS> - Class in net.preibisch.mvrecon.fiji.spimdata.explorer

FilteredAndGroupedExplorerPanel(FilteredAndGroupedExplorer<AS>, AS, URI, XmlIoSpimData2) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

FilteredAndGroupedTableModel<AS> - Class in net.preibisch.mvrecon.fiji.spimdata.explorer

FilteredAndGroupedTableModel(ExplorerWindow<AS>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedTableModel

FilteredMaxDistanceSearchOnKDTree<S,T> - Class in net.preibisch.mvrecon.imglib2.st.render

FilteredMaxDistanceSearchOnKDTree(KDTree<S>, RadiusSearchFilterFactory<S, T>) - Constructor for class net.preibisch.mvrecon.imglib2.st.render.FilteredMaxDistanceSearchOnKDTree

filteredViewIdsCurrentTimepoint(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

FilterFactory<S,T> - Interface in net.preibisch.mvrecon.imglib2.st.filter

filterForOverlappingInterestPoints(Map<ViewId, HashMap<String, Collection<InterestPoint>>>, Collection<? extends Group<ViewId>>, Map<ViewId, ViewRegistration>, Map<ViewId, ViewDescription>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

filterForOverlappingInterestPoints(Map<ViewId, HashMap<String, Collection<InterestPoint>>>, Collection<? extends Group<ViewId>>, Map<ViewId, ViewRegistration>, Map<ViewId, ViewDescription>, int) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

filterGroupsForMissingViews(AbstractSpimData<?>, Collection<Group<V>>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

Removes Views in Groups that are missing, and entire groups if no views are left

filterMissingViews(Set<? extends V>) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

filterMissingViews(AbstractSpimData<?>, Collection<V>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

Removes all missing views from the list, be careful, it modifies the collection!

filterMissingViews(AbstractSequenceDescription<?, ?, ?>, Collection<V>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

Removes all missing views from the list, be careful, it modifies the collection!

filterMissingViews(Group<V>, Set<? extends V>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

filterPeaks(ArrayList<RefinedPeak<Point>>, double) - Static method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.HelperFunctions

filterPeaks(ArrayList<RefinedPeak<Point>>, Rectangle, double) - Static method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.HelperFunctions

filterPresentViews(Set<V>, List<V>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.Subset

Checks which fixed views are present in the views list and puts them into a HashMap

filterRansac - Variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac.RANSACParameters

filterRemainingViewIdsAndLabels(List<ViewId>, Map<ViewId, HashMap<String, Double>>, Map<ViewId, ViewInterestPointLists>) - Method in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

Filters - Class in net.preibisch.mvrecon.imglib2.st.filter

Filters() - Constructor for class net.preibisch.mvrecon.imglib2.st.filter.Filters

FILTERS_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoSmartSPIMImgLoader

finalize() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyLightSheetZ1ImgLoader

finalize() - Method in class net.preibisch.mvrecon.process.cuda.Block

WARNING: this method may never get invoked, unless the garbage collector processes this instance; what is likely to happen is that the native memory consumed by the ExecutorService is never released.

findCalibrations(AbstractSpimData<? extends AbstractSequenceDescription<?, ?, ?>>, List<ViewId>) - Static method in class net.preibisch.mvrecon.fiji.plugin.Specify_Calibration

findCorrespondingDescriptors(ArrayList<D>, ArrayList<D>, double, double, boolean, double) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm.RGLDMMatcher

findFirstPresentViewId(SpimData2, int) - Static method in class net.preibisch.mvrecon.process.splitting.SplittingTools

findGroup(Tile<?>, HashMap<ViewId, ? extends Tile<?>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.global.linkremoval.MaxErrorLinkRemoval

findGroupsAssociatedWithSubset(HashSet<V>, Set<Group<V>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.PairwiseSetup

findInterestPoints(TimePoint) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGaussianGUI

findInterestPoints(TimePoint) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.InterestPointDetectionGUI

findInterestPoints(RandomAccessibleInterval<T>, double, double, boolean, boolean, double, double, ExecutorService) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoG

findInterestPoints(DoGParameters) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoG

findLowestResolutionLevel(MultiResolutionImgLoader, ViewId) - Static method in class net.preibisch.mvrecon.process.downsampling.DownsampleTools

findMax - Variable in class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGParameters

findMaxima - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoGParams

findMin - Variable in class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGParameters

findMinima - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoGParams

findMinStepSize(AbstractSpimData<?>) - Static method in class net.preibisch.mvrecon.process.splitting.SplittingTools

findNumPresent(HashMap<String, Integer>, List<? extends ViewId>, String) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

findPeaks(RandomAccessibleInterval<FloatType>, RandomAccessibleInterval<FloatType>, float, ExecutorService) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2

findRange(SpimData2, List<ViewId>, int[], int[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.BoundingBoxGUI

findUniqueInterestPoints(Collection<CorrespondingIP>) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidTools

findUniqueInterestPoints(Map<ViewId, Collection<CorrespondingIP>>) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidTools

finish() - Method in class net.preibisch.mvrecon.process.export.DisplayImage

finish() - Method in class net.preibisch.mvrecon.process.export.ExportLarge2DTIFF

finish() - Method in class net.preibisch.mvrecon.process.export.ExportN5Api

finish() - Method in interface net.preibisch.mvrecon.process.export.ImgExport

Called last when the fusion is finished (e.g. to write the XML)

finish() - Method in class net.preibisch.mvrecon.process.export.OpenSeaDragon

finish() - Method in class net.preibisch.mvrecon.process.export.Save3dTIFF

finish(RandomAccessibleInterval<FloatType>, RandomAccessibleInterval<T>, Converter<FloatType, T>, T) - Static method in class net.preibisch.mvrecon.process.fusion.lazy.LazyAffineFusion

FinishedButtonListener - Class in net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive

FinishedButtonListener(Frame, boolean) - Constructor for class net.preibisch.mvrecon.process.interestpointremoval.InteractiveProjections.FinishedButtonListener

FinishedButtonListener(InteractiveDoG, boolean) - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.FinishedButtonListener

finishFiles() - Method in class net.preibisch.legacy.mpicbg.SketchTikZFileObject

FIRST_WINS - Enum constant in enum class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval.Fusion

firstSelectedVD - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

firstSelectedVD() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.ExplorerWindow

firstSelectedVD() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

fit(Collection<P>) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.FixedModel

fit(Collection<P>) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantAffineModel3D

fit(Collection<P>) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantFixedModel

fit(Collection<P>) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel2D

Closed form weighted least squares solution as described by \citet{SchaeferAl06} and implemented by Johannes Schindelin.

fit(Collection<P>) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel3D

fit(Collection<P>) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantSimilarityModel3D

fit(FlattenedMatches) - Method in class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.FastAffineModel1D

fitAffineTransform(double[][], double[][]) - Static method in class net.preibisch.mvrecon.process.fusion.blk.BlkThinPlateSplineFusion

Fit an affine that approximates the TPS mapping from source to target landmarks.

fitMatches(ArrayList<PointMatch>) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.AbstractPointDescriptor

Computes a fit between this these PointMatches, this method is called by the Matcher

fitMatches(ArrayList<PointMatch>) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.LocalCoordinateSystemPointDescriptor

Not necessary as the main matching method is overwritten

fitMatches(ArrayList<PointMatch>) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.ModelPointDescriptor

fitMatches(ArrayList<PointMatch>) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.SimplePointDescriptor

fitMatches(ArrayList<PointMatch>) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.TranslationInvariantLocalCoordinateSystemPointDescriptor

Not necessary as the main matching method is overwritten

fitsIntoArrayImg(long, long, long) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyMicroManagerImgLoader

fixBioformats(SpimData2, File, LightSheetZ1MetaData) - Static method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

FIXED_1_OVER_7 - Enum constant in enum class net.preibisch.mvrecon.process.quality.FRC.ThresholdMethod

fixedGridFRC(RandomAccessibleInterval<FloatType>, int, int, int, boolean, int, ExecutorService) - Static method in class net.preibisch.mvrecon.process.quality.FRCTools

fixedGridXY(Interval, long) - Static method in class net.preibisch.mvrecon.process.quality.FRCTools

FixedModel - Class in net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model

This model just applies some other TranslationInvariantModel without computing anything.

FixedModel(double, double, double, double, double, double, double, double, double, double, double, double) - Constructor for class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.FixedModel

fixedViews - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.FixMapBackParameters

fixMapBackParameters(SequenceDescription, PairwiseSetup<ViewId>, int, int, BasicRegistrationParameters.RegistrationType) - Method in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

FixMapBackParameters - Class in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters

FixMapBackParameters() - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.FixMapBackParameters

fixSizeIfNecessary(RandomAccessibleInterval<T>, Dimensions, ViewId) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.SimViewSetupImgLoader

fixViews(HashSet<V>, List<Pair<V, V>>, Set<Group<V>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.Subset

fixViews(List<V>) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.Subset

Fix an additional list of views (removes pairs from subsets and sets list of fixed views)

fixViewsChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.FixMapBackParameters

fixViewsInAllSubsets(List<V>) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.PairwiseSetup

Fix an additional list of views (removes them from pairs and subsets)

fixViewsIndex - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.AdvancedRegistrationParameters

FLATFIELD_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.XmlIoFlatfieldCorrectedWrappedImgLoader

FlatFieldCorrectedRandomAccessibleInterval<O,T,S,R> - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield

FlatFieldCorrectedRandomAccessibleInterval(O, RandomAccessibleInterval<T>, RandomAccessibleInterval<S>, RandomAccessibleInterval<R>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.FlatFieldCorrectedRandomAccessibleInterval

FlatFieldCorrectedRandomAccessibleIntervals - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield

FlatFieldCorrectedRandomAccessibleIntervals() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.FlatFieldCorrectedRandomAccessibleIntervals

FlatFieldCorrectionPopup - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

FlatFieldCorrectionPopup() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.FlatFieldCorrectionPopup

FlatfieldCorrectionWrappedImgLoader<IL> - Interface in net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield

FLATFIELDS_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.XmlIoFlatfieldCorrectedWrappedImgLoader

FlattenedMatches - Class in net.preibisch.mvrecon.process.fusion.intensity.mpicbg

FlattenedMatches(int, int) - Constructor for class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.FlattenedMatches

FlattenedMatches(Collection<P>) - Constructor for class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.FlattenedMatches

flip() - Method in class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.FlattenedMatches

flipQ(Collection<PointMatch>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.QualityPointMatch

floorScaled(double[], double) - Static method in class util.Grid

fluorophore - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.ChannelInfo

fluorophore - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.ChannelOrIlluminationInfo

folderFor(URI, Pair<Integer, Integer>, long, long) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM.SmartSPIMMetaData

folderFor(Pair<Integer, Integer>, long, long) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM.SmartSPIMMetaData

forEachAbstractSpimSource(Collection<? extends SourceAndConverter<?>>, BiConsumer<? super SourceAndConverter<?>, ? super AbstractSpimSource<?>>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVUtils

forEachTransformedSource(Collection<? extends SourceAndConverter<?>>, BiConsumer<? super SourceAndConverter<?>, ? super TransformedSource<?>>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVUtils

forGridBlocks(String, int) - Static method in class net.preibisch.mvrecon.process.export.RetryTracker

Convenience constructor for grid blocks with default settings

format - Variable in class net.preibisch.mvrecon.fiji.plugin.resave.ParametersResaveN5Api

formatEntry(String, int, int) - Static method in class net.preibisch.mvrecon.fiji.plugin.Define_Multi_View_Dataset

frame - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorer

frame() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointExplorer

frame() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationExplorer

FrameListener - Class in net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive

FrameListener(InteractiveDoG) - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.FrameListener

FRC - Class in net.preibisch.mvrecon.process.quality

Compute the Fourier Ring Correlation, a measure of the resolution of a microscopy image.

FRC() - Constructor for class net.preibisch.mvrecon.process.quality.FRC

FRC.ThresholdMethod - Enum Class in net.preibisch.mvrecon.process.quality

FRCRealRandomAccessible<T> - Class in net.preibisch.mvrecon.process.quality

Computes the fourier ring correlation at specific positions and interpolates between all points

FRCRealRandomAccessible(RandomAccessibleInterval<T>, List<Point>, int, boolean, ExecutorService) - Constructor for class net.preibisch.mvrecon.process.quality.FRCRealRandomAccessible

frcStepSize - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

FRCTools - Class in net.preibisch.mvrecon.process.quality

FRCTools() - Constructor for class net.preibisch.mvrecon.process.quality.FRCTools

FRGLDMGUI - Class in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise

Fast Redundant Geometric Local Descriptor Matching (RGLDM)

FRGLDMGUI() - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.FRGLDMGUI

FRGLDMMatcher<I> - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.fastrgldm

FRGLDMMatcher() - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.fastrgldm.FRGLDMMatcher

FRGLDMPairwise<I> - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.fastrgldm

FRGLDMPairwise(RANSACParameters, FRGLDMParameters) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.fastrgldm.FRGLDMPairwise

FRGLDMParameters - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.fastrgldm

FRGLDMParameters(Model<?>) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.fastrgldm.FRGLDMParameters

FRGLDMParameters(Model<?>, double, int) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.fastrgldm.FRGLDMParameters

from(ViewId, String, InterestPointsN5) - Static method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5.InterestPointData

Extract data from an InterestPointsN5 object by direct reference (zero-copy).

FROM_FILE - Enum constant in enum class net.preibisch.mvrecon.process.deconvolution.init.PsiInit.PsiInitType

FROM_RAI - Enum constant in enum class net.preibisch.mvrecon.process.deconvolution.init.PsiInit.PsiInitType

fromSemicolonSeparatedString(String) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoDHMImgLoader

fromURI(URI) - Static method in class util.URITools

fromXml(Element) - Method in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.XmlIoBoundingBoxes

fromXml(Element) - Method in class net.preibisch.mvrecon.fiji.spimdata.intensityadjust.XmlIoIntensityAdjustments

fromXml(Element) - Method in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.XmlIoStitchingResults

fromXml(Element, File, AbstractSequenceDescription<?, ?, ?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.XmlIOFileMapImgLoaderLOCI2

fromXml(Element, File, AbstractSequenceDescription<?, ?, ?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.XmlIoFlatfieldCorrectedWrappedImgLoader

fromXml(Element, File, AbstractSequenceDescription<?, ?, ?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.XmlIoSplitImgLoader

fromXml(Element, File, AbstractSequenceDescription<?, ?, ?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.XmlIoSplitMultiResolutionImgLoader

fromXml(Element, File, AbstractSequenceDescription<?, ?, ?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.XmlIoSplitViewerImgLoader

fromXml(Element, File, AbstractSequenceDescription<?, ?, ?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoAllenOMEZarrLoader

fromXml(Element, File, AbstractSequenceDescription<?, ?, ?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoDHMImgLoader

fromXml(Element, File, AbstractSequenceDescription<?, ?, ?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoFileListImgLoaderLOCI

fromXml(Element, File, AbstractSequenceDescription<?, ?, ?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoLightSheetZ1ImgLoader

fromXml(Element, File, AbstractSequenceDescription<?, ?, ?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoMicroManagerImgLoader

fromXml(Element, File, AbstractSequenceDescription<?, ?, ?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoSimViewImgLoader

fromXml(Element, File, AbstractSequenceDescription<?, ?, ?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoSmartSPIMImgLoader

fromXml(Element, File, AbstractSequenceDescription<?, ?, ?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoStackImgLoader

fromXml(Element, URI) - Method in class net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions.XmlIoPointSpreadFunctions

fromXml(Element, URI) - Method in class net.preibisch.mvrecon.fiji.spimdata.XmlIoSpimData2

fromXml(Element, URI, Map<ViewId, ViewDescription>) - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.XmlIoViewInterestPoints

fromXml(Element, URI, AbstractSequenceDescription<?, ?, ?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.XmlIOFileMapImgLoaderLOCI2

fromXml(Element, URI, AbstractSequenceDescription<?, ?, ?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.XmlIoSplitImgLoader

fromXml(Element, URI, AbstractSequenceDescription<?, ?, ?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.XmlIoSplitMultiResolutionImgLoader

fromXml(Element, URI, AbstractSequenceDescription<?, ?, ?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.XmlIoSplitViewerImgLoader

fromXml(Element, URI, AbstractSequenceDescription<?, ?, ?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoAllenOMEZarrLoader

fromXml(Element, URI, AbstractSequenceDescription<?, ?, ?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoSmartSPIMImgLoader

frustum(double, double, double, double, double, double) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Creates a perspective projection transform that mimics a standard, camera-based, view-model.

fuse(SpimData2, List<ViewId>) - Static method in class net.preibisch.mvrecon.fiji.plugin.Image_Fusion

FUSED_BLURRED - Enum constant in enum class net.preibisch.mvrecon.process.deconvolution.init.PsiInit.PsiInitType

FusedNonZeroRandomAccess - Class in net.preibisch.mvrecon.process.deconvolution.util

FusedNonZeroRandomAccess(int, List<? extends RandomAccessible<FloatType>>, List<? extends RandomAccessible<FloatType>>) - Constructor for class net.preibisch.mvrecon.process.deconvolution.util.FusedNonZeroRandomAccess

FusedNonZeroRandomAccessibleInterval - Class in net.preibisch.mvrecon.process.deconvolution.util

FusedNonZeroRandomAccessibleInterval(Interval, List<? extends RandomAccessible<FloatType>>, List<? extends RandomAccessible<FloatType>>) - Constructor for class net.preibisch.mvrecon.process.deconvolution.util.FusedNonZeroRandomAccessibleInterval

FusedRandomAccess - Class in net.preibisch.mvrecon.process.fusion.transformed

FusedRandomAccess(int, List<? extends RandomAccessible<FloatType>>, List<? extends RandomAccessible<FloatType>>) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccess

FusedRandomAccessFirstWins - Class in net.preibisch.mvrecon.process.fusion.transformed

FusedRandomAccessFirstWins(int, List<? extends RandomAccessible<FloatType>>, List<? extends RandomAccessible<FloatType>>) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessFirstWins

FusedRandomAccessibleInterval - Class in net.preibisch.mvrecon.process.fusion.transformed

FusedRandomAccessibleInterval(Interval, FusedRandomAccessibleInterval.Fusion, List<? extends RandomAccessible<FloatType>>) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval

FusedRandomAccessibleInterval(Interval, FusedRandomAccessibleInterval.Fusion, List<? extends RandomAccessible<FloatType>>, List<? extends RandomAccessible<FloatType>>) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval

FusedRandomAccessibleInterval.Fusion - Enum Class in net.preibisch.mvrecon.process.fusion.transformed

FusedRandomAccessMax - Class in net.preibisch.mvrecon.process.fusion.transformed

FusedRandomAccessMax(int, List<? extends RandomAccessible<FloatType>>) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessMax

FusedRandomAccessNoWeights - Class in net.preibisch.mvrecon.process.fusion.transformed

FusedRandomAccessNoWeights(int, List<? extends RandomAccessible<FloatType>>) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessNoWeights

fuseFrom - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

fuseGroups() - Method in class net.preibisch.mvrecon.process.deconvolution.util.ProcessInputImages

fuseGroups(AbstractSpimData<?>, HashMap<Group<V>, RandomAccessibleInterval<FloatType>>, HashMap<Group<V>, RandomAccessibleInterval<FloatType>>, HashMap<V, AffineTransform3D>, Collection<Group<V>>, Interval, double, float[], float[], float[], float[], Map<? extends ViewId, AffineModel1D>) - Static method in class net.preibisch.mvrecon.process.deconvolution.util.ProcessInputImages

fuseRAIs(Collection<Pair<RandomAccessibleInterval<FloatType>, AffineTransform3D>>, double, Interval, int) - Static method in class net.preibisch.mvrecon.process.quality.FRCTools

fuseTo - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

fuseVirtual(AbstractSpimData<?>, Collection<? extends ViewId>, FusionGUI.FusionType, int, Interval, Map<? extends ViewId, AffineModel1D>) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

fuseVirtual(AbstractSpimData<?>, Collection<? extends ViewId>, FusionGUI.FusionType, Interval) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

Virtually fuses views

fuseVirtual(AbstractSpimData<?>, Collection<? extends ViewId>, FusionGUI.FusionType, Interval, Map<? extends ViewId, AffineModel1D>) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

Virtually fuses views

fuseVirtual(AbstractSpimData<? extends AbstractSequenceDescription<?, ?, ? extends ImgLoader>>, Collection<? extends ViewId>, FusionGUI.FusionType) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

Virtually fuses views using a maximal bounding box around all views

fuseVirtual(BasicImgLoader, Map<ViewId, ? extends AffineTransform3D>, Map<ViewId, ? extends BasicViewDescription<?>>, Collection<? extends ViewId>, FusionGUI.FusionType, int, Interval, Map<? extends ViewId, AffineModel1D>) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

fuseVirtual(BasicImgLoader, Map<ViewId, ? extends AffineTransform3D>, Map<ViewId, ? extends BasicViewDescription<?>>, Collection<? extends ViewId>, FusionGUI.FusionType, Interval) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

Virtually fuses views

fuseVirtual(SpimData2, Collection<? extends ViewId>, FusionGUI.FusionType, boolean) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

Virtually fuses views using a maximal bounding box around all views

fuseVirtualInterpolatedNonRigid(BasicImgLoader, Map<ViewId, AffineTransform3D>, Map<ViewId, ViewInterestPointLists>, Map<ViewId, ? extends BasicViewDescription<?>>, Collection<? extends ViewId>, Collection<? extends ViewId>, ArrayList<String>, FusionGUI.FusionType, boolean, long[], double, boolean, int, Interval, Map<? extends ViewId, AffineModel1D>, ExecutorService) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidTools

fuseVirtualInterpolatedNonRigid(SpimData2, Collection<? extends ViewId>, Collection<? extends ViewId>, ArrayList<String>, FusionGUI.FusionType, boolean, long[], double, boolean, int, Interval, Map<? extends ViewId, AffineModel1D>, ExecutorService) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidTools

fusion - Variable in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval

FusionExportInterface - Interface in net.preibisch.mvrecon.fiji.plugin.fusion

FusionGUI - Class in net.preibisch.mvrecon.fiji.plugin.fusion

FusionGUI(SpimData2, List<ViewId>) - Constructor for class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

FusionGUI.FusionType - Enum Class in net.preibisch.mvrecon.fiji.plugin.fusion

FusionPopup - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

FusionPopup() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.FusionPopup

FusionPopup.MyActionListener - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

FusionTools - Class in net.preibisch.mvrecon.process.fusion

FusionTools() - Constructor for class net.preibisch.mvrecon.process.fusion.FusionTools

FusionTools.ImgDataType - Enum Class in net.preibisch.mvrecon.process.fusion

fusionType - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

fusionTypes - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

fwd(int) - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccess

fwd(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccess

fwd(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccess

fwd(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessFirstWins

fwd(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessMax

fwd(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessNoWeights

fwd(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridAccess

fwd(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGridRandomAccess

fwd(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputGeneralRandomAccess

fwd(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccess2d

fwd(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccess

fwd(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccess

fwd(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.InterpolatingNonRigidRasteredRandomAccess

fwd(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.NonRigidRasteredRandomAccess

fwd(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.TransformedRasteredRandomAccess

fwd(int) - Method in class util.StackingRealRandomAccessible.StackingRealRandomAccess

G

gauss(float[], int[], double) - Method in class net.preibisch.mvrecon.process.cuda.CUDASeparableConvolutionFunctions

Compute Gaussian convolution with and extend-border-pixels outofbounds strategy

gauss(float[], int[], double[]) - Method in class net.preibisch.mvrecon.process.cuda.CUDASeparableConvolutionFunctions

Compute Gaussian convolution with and extend-border-pixels outofbounds strategy

gauss(float[], int[], double[], CUDASeparableConvolutionFunctions.OutOfBounds, float) - Method in class net.preibisch.mvrecon.process.cuda.CUDASeparableConvolutionFunctions

Compute Gaussian convolution

gauss(float[], int[], double[], CUDASeparableConvolutionFunctions.OutOfBounds, float, CUDASeparableConvolution, int) - Static method in class net.preibisch.mvrecon.process.cuda.CUDASeparableConvolutionFunctions

Compute Gaussian convolution

gauss(float[], int[], double, CUDASeparableConvolutionFunctions.OutOfBounds, float) - Method in class net.preibisch.mvrecon.process.cuda.CUDASeparableConvolutionFunctions

Compute Gaussian convolution

gauss(float[], int[], double, CUDASeparableConvolutionFunctions.OutOfBounds, float, CUDASeparableConvolution, int) - Static method in class net.preibisch.mvrecon.process.cuda.CUDASeparableConvolutionFunctions

Compute Gaussian convolution

gauss(float[], int[], float[]) - Method in class net.preibisch.mvrecon.process.cuda.CUDASeparableConvolutionFunctions

GaussianFilter<S,T> - Class in net.preibisch.mvrecon.imglib2.st.filter

GaussianFilter(RadiusNeighborSearch<S>, T, double, double, GaussianFilterFactory.WeightType) - Constructor for class net.preibisch.mvrecon.imglib2.st.filter.GaussianFilter

GaussianFilterFactory<S,T> - Class in net.preibisch.mvrecon.imglib2.st.filter

GaussianFilterFactory(T, double, double, GaussianFilterFactory.WeightType) - Constructor for class net.preibisch.mvrecon.imglib2.st.filter.GaussianFilterFactory

GaussianFilterFactory(T, double, GaussianFilterFactory.WeightType) - Constructor for class net.preibisch.mvrecon.imglib2.st.filter.GaussianFilterFactory

GaussianFilterFactory.WeightType - Enum Class in net.preibisch.mvrecon.imglib2.st.filter

gd - Variable in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

generateLabel(int, int, int, int) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

generateLabel(int, int, int, int) - Static method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

generateOverlappingPairs(List<V>, Collection<? extends Group<V>>) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap.SimpleBoundingBoxOverlap

Generate overlapping pairs directly without creating all n^2 pairs first.

generateRegularGrid(RegularTranformHelpers.RegularTranslationParameters, Dimensions) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.grid.RegularTranformHelpers

Generic_Resave_HDF5 - Class in net.preibisch.mvrecon.fiji.plugin.resave

Generic_Resave_HDF5() - Constructor for class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5

Generic_Resave_HDF5.LoopBack2d - Class in net.preibisch.mvrecon.fiji.plugin.resave

Generic_Resave_HDF5.ParametersResaveHDF5 - Class in net.preibisch.mvrecon.fiji.plugin.resave

GenericDialogAppender - Interface in net.preibisch.mvrecon.fiji.plugin.util

GenericLoadParseQueryXML<AS,S,V,D,L,X> - Class in net.preibisch.mvrecon.fiji.plugin.queryXML

Interface for interactive parsing of spimdata XMLs

GenericLoadParseQueryXML(X) - Constructor for class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

GeometricHasher<I> - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.geometrichashing

Class that actually computes the geometric hashing

GeometricHasher() - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.geometrichashing.GeometricHasher

GeometricHashingGUI - Class in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise

GeometricHashingGUI() - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.GeometricHashingGUI

GeometricHashingPairwise<I> - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.geometrichashing

GeometricHashingPairwise(RANSACParameters, GeometricHashingParameters) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.geometrichashing.GeometricHashingPairwise

GeometricHashingParameters - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.geometrichashing

GeometricHashingParameters(Model<?>) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.geometrichashing.GeometricHashingParameters

GeometricHashingParameters(Model<?>, double, double, int) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.geometrichashing.GeometricHashingParameters

get() - Method in class net.preibisch.mvrecon.imglib2.st.render.IntegratingNeighborSearchInterpolator

get() - Method in class net.preibisch.mvrecon.imglib2.st.render.util.SimpleSampler

get() - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccess

get() - Method in class net.preibisch.mvrecon.process.deconvolution.util.FusedNonZeroRandomAccess

get() - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccess

get() - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessFirstWins

get() - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessMax

get() - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessNoWeights

get() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.DistanceVisualizingRandomAccess

get() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridAccess

get() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGridRandomAccess

get() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.InterpolatingNonRigidRandomAccess

get() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidRandomAccess

get() - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputGeneralRandomAccess

get() - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccess

get() - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccess2d

get() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsMulRandomAccess

get() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsSumRandomAccess

get() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccess

get() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.InterpolatingNonRigidRasteredRandomAccess

get() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.NonRigidRasteredRandomAccess

get() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.TransformedRasteredRandomAccess

get() - Method in class net.preibisch.mvrecon.vecmath.Color3f

Returns a new AWT color object initialized with the r,g,b values of this Color3f object.

get() - Method in class util.StackingRealRandomAccessible.StackingRealRandomAccess

get(double[]) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4d

Gets the value of this axis angle and places it into the array a of length four in x,y,z,angle order.

get(double[]) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Places the values of this transform into the double precision array of length 16.

get(double[]) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Copies the x,y,z coordinates of this tuple into the array t of length 3.

get(double[]) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Gets the value of this tuple and places it into the array t of length four in x,y,z,w order.

get(float[]) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4f

Copies the value of this axis-angle into the array a.

get(float[]) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Places the values of this transform into the single precision array of length 16.

get(float[]) - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Gets the value of this tuple and copies the values into t.

get(float[]) - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Copies the values of this tuple into the array t.

get(int) - Method in class net.preibisch.legacy.registration.detection.AbstractDetection

get(int) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test.PointNode

get(int[]) - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Copies the values of this tuple into the array t.

get(long) - Static method in class util.ColorStream

get(Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Performs an SVD normalization of this matrix in order to acquire the normalized rotational component; the values are placed into the Matrix3d parameter.

get(Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Performs an SVD normalization of this matrix in order to acquire the normalized rotational component; the values are placed into the Matrix3d parameter.

get(Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Places the normalized rotational component of this transform into the 3x3 matrix argument.

get(Matrix3d, Vector3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Performs an SVD normalization of this matrix to calculate the rotation as a 3x3 matrix, the translation, and the scale.

get(Matrix3d, Vector3d) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Places the normalized rotational component of this transform into the matrix parameter; place the translational component into the vector parameter.

get(Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Performs an SVD normalization of this matrix in order to acquire the normalized rotational component; the values are placed into the Matrix3f parameter.

get(Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Performs an SVD normalization of this matrix in order to acquire the normalized rotational component; the values are placed into the Matrix3f parameter.

get(Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Places the normalized rotational component of this transform into the 3x3 matrix argument.

get(Matrix3f, Vector3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Performs an SVD normalization of this matrix to calculate the rotation as a 3x3 matrix, the translation, and the scale.

get(Matrix3f, Vector3d) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Places the normalized rotational component of this transform into the matrix parameter; place the translational component into the vector parameter.

get(Matrix3f, Vector3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Performs an SVD normalization of this matrix to calculate the rotation as a 3x3 matrix, the translation, and the scale.

get(Matrix3f, Vector3f) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Places the normalized rotational component of this transform into the matrix parameter; place the translational component into the vector parameter.

get(Matrix4d) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Places the values of this transform into the double precision matrix argument.

get(Matrix4f) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Places the values of this transform into the single precision matrix argument.

get(Quat4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Performs an SVD normalization of q1 matrix in order to acquire the normalized rotational component; the values are placed into the Quat4d parameter.

get(Quat4d) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Places the quaternion equivalent of the normalized rotational component of this transform into the quaternion parameter.

get(Quat4d, Vector3d) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Places the quaternion equivalent of the normalized rotational component of this transform into the quaternion parameter; places the translational component into the Vector parameter.

get(Quat4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Performs an SVD normalization of this matrix in order to acquire the normalized rotational component; the values are placed into the Quat4f parameter.

get(Quat4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Performs an SVD normalization of this matrix in order to acquire the normalized rotational component; the values are placed into the Quat4f parameter.

get(Quat4f) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Places the quaternion equivalent of the normalized rotational component of this transform into the quaternion parameter.

get(Quat4f, Vector3d) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Places the quaternion equivalent of the normalized rotational component of this transform into the quaternion parameter; places the translational component into the Vector parameter.

get(Quat4f, Vector3f) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Places the quaternion equivalent of the normalized rotational component of this transform into the quaternion parameter; places the translational component into the Vector parameter.

get(Tuple3d) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Copies the x,y,z coordinates of this tuple into the tuple t.

get(Tuple3f) - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Gets the value of this tuple and copies the values into t.

get(Tuple3i) - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Copies the values of this tuple into the tuple t.

get(Tuple4d) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Gets the value of this tuple and places it into the Tuple4d argument of length four in x,y,z,w order.

get(Tuple4f) - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Copies the values of this tuple into the tuple t.

get(Vector3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Retrieves the translational components of this matrix.

get(Vector3d) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Retrieves the translational components of this transform.

get(Vector3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Retrieves the translational components of this matrix.

get(Vector3f) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Retrieves the translational components of this transform.

getA() - Method in interface net.preibisch.mvrecon.fiji.ImgLib2Temp.Pair

getA() - Method in interface net.preibisch.mvrecon.fiji.ImgLib2Temp.Triple

getA() - Method in class net.preibisch.mvrecon.fiji.ImgLib2Temp.ValuePair

getA() - Method in class net.preibisch.mvrecon.fiji.ImgLib2Temp.ValueTriple

getAbsoluteLocalAlignmentError() - Method in interface net.preibisch.legacy.registration.bead.error.GlobalErrorStatistics

getAbsoluteLocalAlignmentError() - Method in class net.preibisch.legacy.registration.bead.error.GlobalErrorStatisticsImpl

getAccumulateMap(Class<? extends Entity>) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListViewDetectionState

getAdditionalSmoothBlending() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getAffineModel3D(Transform3D) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

getAffineTransform(Affine3D<?>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

getAlignmentErrorCount() - Method in interface net.preibisch.legacy.registration.bead.error.GlobalErrorStatistics

getAlignmentErrorCount() - Method in class net.preibisch.legacy.registration.bead.error.GlobalErrorStatisticsImpl

getAllAccesses() - Method in class net.preibisch.mvrecon.process.deconvolution.util.FusedNonZeroRandomAccessibleInterval

getAllAnglesForChannelTimepointSorted(SpimData, Collection<? extends ViewId>, Channel, TimePoint) - Static method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

getAllAnglesSorted(SpimData, Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

getAllBoundingBoxes(SpimData2, Collection<ViewId>, boolean) - Static method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxTools

getAllChannelsSorted(SpimData, Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

getAllCorrespondingInterestPointMap(ViewInterestPoints, Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.InterestPointTools

getAllIlluminationsForChannelTimepointSorted(SpimData, Collection<? extends ViewId>, Channel, TimePoint) - Static method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

getAllIlluminationsSorted(SpimData, Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

getAllInstancesOfEntitySorted(AbstractSpimData<?>, Collection<? extends ViewId>, Class<E>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

getAllInterestPointLabels(HashMap<String, Integer>, List<? extends ViewId>) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.InterestPointTools

getAllInterestPointLabels(SpimData2, List<? extends ViewId>) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.InterestPointTools

Goes through all Views and checks all available labels for interest point detection

getAllInterestPointMap(ViewInterestPoints, Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.InterestPointTools

getAllInterestPoints(Collection<? extends V>, Map<V, ViewRegistration>, Map<V, ViewInterestPointLists>, Map<V, HashMap<String, Double>>, boolean) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

getAllInterestPoints(Collection<? extends V>, Map<V, ViewRegistration>, Map<V, ViewInterestPointLists>, Map<V, HashMap<String, Double>>, boolean, int) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

getAllPairwiseResultsForViewId(Set<ViewId>) - Method in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.StitchingResults

getAllTilesSorted(SpimData, Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

getAllTimePointsSorted(Collection<? extends ViewDescription>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

getAllTimePointsSorted(SpimData, Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

getAllTimePointsSortedUnchecked(Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

getAllTimePointsSortedWithoutPresenceCheck(Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

getAllTransformedInterestPoints(Collection<? extends V>, Map<V, ViewRegistration>, Map<V, ViewInterestPointLists>, Map<V, HashMap<String, Double>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

getAllViewDescriptionsSorted(SpimData, List<? extends ViewId>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

getAllViewIdsForChannelSorted(SpimData, Collection<? extends ViewId>, Channel) - Static method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

getAllViewIdsForChannelTimePointSorted(SpimData, Collection<? extends ViewId>, Channel, TimePoint) - Static method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

getAllViewIdsForTimePointSorted(SpimData, Collection<? extends ViewId>, TimePoint) - Static method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

getAllViewIdsSorted(SpimData, List<? extends ViewSetup>, List<? extends TimePoint>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

getAllViews() - Method in interface net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.PointMatchCreator

getAllViews() - Method in class net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.strong.ImageCorrelationPointMatchCreator

getAllViews() - Method in class net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.strong.InterestPointMatchCreator

getAllViews() - Method in class net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.weak.WeakLinkPointMatchCreator

getAllViewSetups(Collection<? extends ViewDescription>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

getAllViewSetupsSorted(SpimData, Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

getAlpha() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGrid

getAlpha() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidParameters

getAlpha() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidRandomAccess

getAlpha() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidRandomAccessible

getAlpha() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.NonRigidRasteredRandomAccess

getAlpha() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.NonRigidRasteredRandomAccessible

getAmbigousMatches() - Method in class net.preibisch.mvrecon.process.pointcloud.icp.ICP

Returns the ArrayList of ambigous PointMatches indentified in the last ICP iteration, or null if no iteration has been computed yet.

getAmbiguousAngleTile() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListViewDetectionState

getAmbiguousIllumChannel() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListViewDetectionState

getAmpChannelId() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.DHMMetaData

getAmpChannelId() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.DHMImgLoader

getAmpChannelId() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyDHMImgLoader

getAmplitudeDir() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.DHMMetaData

getAmplitudeDir() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.DHMImgLoader

getAmplitudeDir() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyDHMImgLoader

getAngle() - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4d

Get the axis angle, in radians.
An axis angle is a rotation angle about the vector (x,y,z).

getAngle() - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4f

Get the axis angle, in radians.
An axis angle is a rotation angle about the vector (x,y,z).

getAngle(AbstractSequenceDescription<?, ?, ?>, ViewId) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyFileMapImgLoaderLOCI

getAngle(AbstractSequenceDescription<?, ?, ?>, ViewId) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyLightSheetZ1ImgLoader

getAngle(BasicViewDescription<?>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyFileMapImgLoaderLOCI

getAngle(BasicViewDescription<?>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyLightSheetZ1ImgLoader

getAngleInt(String) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData

getAngleMap() - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

getAngleName(List<Angle>) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

getAnglesToProcess() - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.LoadParseQueryXML

getAngleString(int) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData

getAnisotropy() - Method in class net.preibisch.mvrecon.process.splitting.SplitOctTree

getAnisotropyFactor() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getAnisotropyFactor() - Method in interface net.preibisch.mvrecon.fiji.plugin.fusion.FusionExportInterface

getAnisotropyFactor() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

getAnisotropyFactor() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

getAnyBDVPopup() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

Returns the first registered popup that implements BasicBDVPopup, regardless of whether a BDV is currently open.

getAtBase(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

getAtBase(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

getAttributes(AS, Comparator<String>) - Static method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

getAutoNormalize() - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Returns the state of auto-normalization.

getAverageAlignmentError() - Method in interface net.preibisch.legacy.registration.bead.error.GlobalErrorStatistics

getAverageAlignmentError() - Method in class net.preibisch.legacy.registration.bead.error.GlobalErrorStatisticsImpl

getAverageAnisotropyFactor(SequenceDescription, Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

getAverageAnisotropyFactor(SpimData, Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

getAverageError() - Method in class net.preibisch.mvrecon.process.pointcloud.icp.ICP

Returns the average error of the last ICP iteration, or -1 if no iteration has been computed yet.

getAverageLocalAlignmentError() - Method in interface net.preibisch.legacy.registration.bead.error.GlobalErrorStatistics

getAverageLocalAlignmentError() - Method in class net.preibisch.legacy.registration.bead.error.GlobalErrorStatisticsImpl

getAvg() - Method in interface net.preibisch.mvrecon.process.deconvolution.init.PsiInit

getAvg() - Method in class net.preibisch.mvrecon.process.deconvolution.init.PsiInitAvgApprox

getAvg() - Method in class net.preibisch.mvrecon.process.deconvolution.init.PsiInitAvgPrecise

getAvg() - Method in class net.preibisch.mvrecon.process.deconvolution.init.PsiInitBlurredFused

getAvg() - Method in class net.preibisch.mvrecon.process.deconvolution.init.PsiInitFromFile

getAvg() - Method in class net.preibisch.mvrecon.process.deconvolution.init.PsiInitFromRAI

getAvgCorrelation(Set<ViewId>) - Method in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.StitchingResults

getB() - Method in interface net.preibisch.mvrecon.fiji.ImgLib2Temp.Pair

getB() - Method in interface net.preibisch.mvrecon.fiji.ImgLib2Temp.Triple

getB() - Method in class net.preibisch.mvrecon.fiji.ImgLib2Temp.ValuePair

getB() - Method in class net.preibisch.mvrecon.fiji.ImgLib2Temp.ValueTriple

getBasePath() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoints

getBasePath() - Method in class net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions.PointSpreadFunction

getBasisPoint() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.AbstractPointDescriptor

The basis point for this descriptor

getBDV() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BasicBDVPopup

getBDV() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BDVPopup

getBDV() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.LazyBDVPopup

getBDV(AbstractSpimData<?>, Collection<ViewId>) - Static method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxBigDataViewer

getBDVSourceIndex(BasicViewSetup, AbstractSpimData<?>) - Static method in class util.BDVTools

Gets the BDV display index for a ViewSetup.

getBDVTimePointIndex(TimePoint, AbstractSpimData<?>) - Static method in class util.BDVTools

Gets the BDV display index for a TimePoint.

getBeads(Img<IntType>, Img<FloatType>, int, int, int, boolean, double) - Method in class net.preibisch.legacy.registration.threshold.ConnectedComponent

getBestPointMatchSet() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.AbstractPointDescriptor

The combination of descriptorpoints that yielded the best similarity in the last comparison

getBestType() - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Returns the least general type of this matrix; the order of generality from least to most is: ZERO, IDENTITY, SCALE/TRANSLATION, ORTHOGONAL, RIGID, CONGRUENT, AFFINE.

getBlendingAndGrouping() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getBlendingBorder() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getBlendingRange() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getBlockFactory() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getBlocks() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getBlockSize() - Method in class net.preibisch.mvrecon.process.cuda.Block

getBlockSize() - Method in class net.preibisch.mvrecon.process.deconvolution.DeconView

getBlockSize() - Method in interface net.preibisch.mvrecon.process.deconvolution.iteration.ComputeBlockThread

getBlockSize() - Method in class net.preibisch.mvrecon.process.deconvolution.iteration.ComputeBlockThreadAbstract

getBoundingBox() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getBoundingBox() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

getBoundingBox() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

getBoundingBox() - Method in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.PairwiseStitchingResult

getBoundingBox() - Method in class net.preibisch.mvrecon.process.deconvolution.util.ProcessInputImages

getBoundingBox() - Method in class net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.Link

getBoundingBox(float, float) - Static method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test.TestPointDescriptor

getBoundingBox(BasicViewSetup, ViewRegistration) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap.SimpleBoundingBoxOverlap

getBoundingBox(Dimensions, AffineTransform3D) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap.SimpleBoundingBoxOverlap

getBoundingBox(SpimData2, String) - Static method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxTools

Finds a bounding box by title in the SpimData2 bounding box collection.

getBoundingBox(SpimData2, List<ViewId>, String) - Static method in class net.preibisch.mvrecon.process.fusion.lazy.LazyFusionTools

getBoundingBox(V, Map<Integer, ? extends BasicViewSetup>, ViewRegistrations) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap.SimpleBoundingBoxOverlap

getBoundingBoxChoices(List<BoundingBox>) - Static method in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

getBoundingBoxChoices(List<BoundingBox>, boolean) - Static method in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

getBoundingBoxDescription(BoundingBox) - Static method in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox

getBoundingBoxes() - Method in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBoxes

getBoundingBoxes() - Method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

getBoundingBoxReal(BasicViewSetup, ViewRegistration) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap.SimpleBoundingBoxOverlap

getBoundingBoxReal(Dimensions, AffineTransform3D) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap.SimpleBoundingBoxOverlap

getBoundingBoxReal(V, Map<Integer, ? extends BasicViewSetup>, ViewRegistrations) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap.SimpleBoundingBoxOverlap

getBounds(AbstractSpimData<?>, ViewId) - Static method in class net.preibisch.mvrecon.process.fusion.intensity.IntensityCorrection

getBrightImg(ViewId) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.LazyLoadingFlatFieldCorrectionMap

getBytesPerPixel(IFormatReader) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.util.BioformatsReaderUtils

getC() - Method in interface net.preibisch.mvrecon.fiji.ImgLib2Temp.Triple

getC() - Method in class net.preibisch.mvrecon.fiji.ImgLib2Temp.ValueTriple

getCacheBlockSize() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getCacheControl() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitViewerImgLoader

getCacheMaxNumBlocks() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getCal() - Method in class net.preibisch.mvrecon.fiji.plugin.Specify_Calibration.Cal

getCallables(List<MatcherPairwiseTools.MatchingTask<V>>, Map<V, ? extends Map<String, ? extends Collection<I>>>, MatcherPairwise<I>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.MatcherPairwiseTools

getCalX() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.CalibratedImg

getCalX() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.Calibration

getCalY() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.CalibratedImg

getCalY() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.Calibration

getCalZ() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.CalibratedImg

getCalZ() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.Calibration

getCandidates() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.PairwiseResult

getCenterOfMass(Collection<ImgLib2Temp.Pair<Dimensions, AffineGet>>) - Static method in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

getCenterType() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.centerofmass.CenterOfMassParameters

getChannel(BasicViewDescription<?>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyFileMapImgLoaderLOCI

getChannel(BasicViewDescription<?>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyLightSheetZ1ImgLoader

getChannelsToProcess() - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.LoadParseQueryXML

getChartXLocation(Point, ChartPanel) - Static method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.statistics.MouseListenerTimelapse

getChartXLocation(Point, ChartPanel) - Static method in class net.preibisch.mvrecon.process.interestpointremoval.histogram.MouseListenerValue

getCoefficients(SplitViewerImgLoader, Map<Integer, List<Integer>>, Map<ViewId, ViewRegistration>, ViewId, double, double) - Static method in class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion

Backward-compatible overload — center landmarks only (no correspondence-based midpoint landmarks).

getCoefficients(SplitViewerImgLoader, Map<Integer, List<Integer>>, Map<ViewId, ViewRegistration>, ViewId, double, double, ViewInterestPoints, String, int) - Static method in class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion

Backward-compatible overload — correspondence midpoints but no corner anchors.

getCoefficients(SplitViewerImgLoader, Map<Integer, List<Integer>>, Map<ViewId, ViewRegistration>, ViewId, double, double, ViewInterestPoints, String, int, boolean, double) - Static method in class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion

Backward-compatible overload — corner anchors with N=2 (corners only).

getCoefficients(SplitViewerImgLoader, Map<Integer, List<Integer>>, Map<ViewId, ViewRegistration>, ViewId, double, double, ViewInterestPoints, String, int, boolean, double, int) - Static method in class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion

Backward-compatible overload — no landmark visitor.

getCoefficients(SplitViewerImgLoader, Map<Integer, List<Integer>>, Map<ViewId, ViewRegistration>, ViewId, double, double, ViewInterestPoints, String, int, boolean, double, int, int[], int[], Consumer<SplitImgLoaderThinPlateSplineFusion.LandmarkRecord>) - Static method in class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion

Backward-compatible overload — no donated nails.

getCoefficients(SplitViewerImgLoader, Map<Integer, List<Integer>>, Map<ViewId, ViewRegistration>, ViewId, double, double, ViewInterestPoints, String, int, boolean, double, int, int[], int[], Consumer<SplitImgLoaderThinPlateSplineFusion.LandmarkRecord>, List<SplitImgLoaderThinPlateSplineFusion.DonatedNail>) - Static method in class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion

Build TPS Landmarks for one underlying view U.

getCoefficients(SplitViewerImgLoader, Map<Integer, List<Integer>>, Map<ViewId, ViewRegistration>, ViewId, double, double, ViewInterestPoints, String, int, boolean, double, int, Consumer<SplitImgLoaderThinPlateSplineFusion.LandmarkRecord>) - Static method in class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion

Backward-compatible overload — visitor only, no per-split schedule, no donated nails.

getColoredHtmlFromPattern(String, boolean) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition

getColorN(long) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition

getColumn(int, double[]) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Copies the matrix values in the specified column into the array parameter.

getColumn(int, double[]) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Copies the matrix values in the specified column into the array parameter.

getColumn(int, float[]) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Copies the matrix values in the specified column into the array parameter.

getColumn(int, float[]) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Copies the matrix values in the specified column into the array parameter.

getColumn(int, Vector3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Copies the matrix values in the specified column into the vector parameter.

getColumn(int, Vector3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Copies the matrix values in the specified column into the vector parameter.

getColumn(int, Vector4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Copies the matrix values in the specified column into the vector parameter.

getColumn(int, Vector4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Copies the matrix values in the specified column into the vector parameter.

getColumnClass(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MissingViewsTableModelDecorator

getColumnClass(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MultiViewTableModelDecorator

getColumnCount() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedTableModel

getColumnCount() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

getColumnCount() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MissingViewsTableModelDecorator

getColumnCount() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MultiViewTableModelDecorator

getColumnCount() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationTableModel

getColumnName(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedTableModel

getColumnName(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

getColumnName(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MissingViewsTableModelDecorator

getColumnName(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MultiViewTableModelDecorator

getColumnName(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationTableModel

getComparator() - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

getComplexConjugate() - Method in class util.FFTConvolution

getComplexFFT(ImageProcessor) - Method in class net.preibisch.mvrecon.process.quality.FRC

Convert an image into a Fourier image with real and imaginary parts

getComputeBlockSize() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getComputeBlockThreadFactory() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getComputeDevice() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getComputeVersion() - Method in class net.preibisch.mvrecon.process.cuda.CUDADevice

getConsensusSetId() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.CorrespondingInterestPoints

getContentBasedImg() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.ContentBasedFFTRealRandomAccessible

getControlPointDistance() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidParameters

getConvertChoice() - Method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.ParametersResaveHDF5

getCopyFactory() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getCorrectIntersection(double[], FRC.ThresholdMethod) - Method in class net.preibisch.mvrecon.process.quality.FRC

Get the correction intersection representing the image resolution.

getCorrespodingLabel() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.CorrespondingInterestPoints

getCorrespondenceColorId(ViewId, int, int) - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointOverlay.InterestPointSource

getCorrespondenceColorId(ViewId, int, int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

getCorrespondingDetectionId() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.CorrespondingInterestPoints

getCorrespondingInterestPoints(V, Map<V, ViewRegistration>, Map<V, ViewInterestPointLists>, Map<V, String>, boolean) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

getCorrespondingInterestPointsCopy() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoints

getCorrespondingInterestPointsCopy() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

getCorrespondingLabel() - Method in class net.preibisch.mvrecon.process.interestpointremoval.CreateFromCorrespondencesParameters

getCorrespondingViewId() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.CorrespondingInterestPoints

getCorrIP() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.CorrespondingIP

getCorrL() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.CorrespondingIP

getCorrViewId() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.CorrespondingIP

getCorrW() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.CorrespondingIP

getCount() - Method in class net.preibisch.mvrecon.fiji.plugin.Specify_Calibration.Cal

getCriterion() - Method in class net.preibisch.mvrecon.process.splitting.SplitOctTree

getCUDAcomputeCapabilityMajorVersion(int) - Method in interface net.preibisch.mvrecon.process.cuda.CUDAStandardFunctions

getCUDAcomputeCapabilityMinorVersion(int) - Method in interface net.preibisch.mvrecon.process.cuda.CUDAStandardFunctions

getCUDACoordinates(int[]) - Static method in class net.preibisch.mvrecon.process.cuda.CUDATools

getCUDAKernels(double[], int[]) - Static method in class net.preibisch.mvrecon.process.cuda.CUDASeparableConvolutionFunctions

getCurrentViewDescription() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationTableModel

getCurrentViewDescriptions() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

getCZIFile() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyLightSheetZ1ImgLoader

getCZIFile() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LightSheetZ1ImgLoader

getDarkImg(ViewId) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.LazyLoadingFlatFieldCorrectionMap

getData() - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

getDatasetList() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.OMEZARR.MultipleOMEZARRListChooser

getDatasetList() - Method in interface net.preibisch.mvrecon.fiji.datasetmanager.OMEZARR.URIListChooser

getDatasetList() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.OMEZARR.WildcardDirectoryListChooser

getDatasetPath(N5Reader, int, int, int) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AllenOMEZarrProperties

getDataType(N5Reader, int) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AllenOMEZarrProperties

getDebug() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getDebugImage() - Method in class net.preibisch.mvrecon.process.deconvolution.MultiViewDeconvolution

getDebugInterval() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getDebugMode() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getDeconvolutionGrouping(Group<ViewDescription>) - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getDefaultFixedViews() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.AllToAllRange

getDefaultFixedViews() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.PairwiseSetup

Get a list of fixed views necessary for the specific strategy to work

getDefaultFixedViews() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.ReferenceTimepoint

getDefaultMultipleAngles() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

getDefaultMultipleAngles() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListImageJ

getDefaultMultipleAngles() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListLOCI

getDefaultMultipleChannels() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

getDefaultMultipleChannels() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListImageJ

getDefaultMultipleChannels() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListLOCI

getDefaultMultipleIlluminations() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

getDefaultMultipleIlluminations() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListImageJ

getDefaultMultipleIlluminations() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListLOCI

getDefaultMultipleTiles() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

getDefaultMultipleTiles() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListImageJ

getDefaultMultipleTiles() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListLOCI

getDefaultMultipleTimepoints() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

getDefaultMultipleTimepoints() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListImageJ

getDefaultMultipleTimepoints() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListLOCI

getDeflate() - Method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.ParametersResaveHDF5

getDepth() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.DHMMetaData

getDepth() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.Calibration

getDescription() - Method in interface net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition.FileListChooser

getDescription() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition.SimpleDirectoryFileListChooser

getDescription() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition.WildcardFileListChooser

getDescription() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.OMEZARR.MultipleOMEZARRListChooser

getDescription() - Method in interface net.preibisch.mvrecon.fiji.datasetmanager.OMEZARR.URIListChooser

getDescription() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.OMEZARR.WildcardDirectoryListChooser

getDescription() - Method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.AutomaticReorientationBoundingBoxGUI

getDescription() - Method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.BDVBoundingBoxGUI

getDescription() - Method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.BoundingBoxGUI

getDescription() - Method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.MaximumBoundingBoxGUI

getDescription() - Method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.MinFilterThresholdBoundingBoxGUI

getDescription() - Method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.ModifyDefinedBoundingBoxGUI

getDescription() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGaussianGUI

getDescription() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.InterestPointDetectionGUI

getDescription() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.CenterOfMassGUI

getDescription() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.FRGLDMGUI

getDescription() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.GeometricHashingGUI

getDescription() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.IterativeClosestPointGUI

getDescription() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.LoadCorrespondencesGUI

getDescription() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.PairwiseGUI

getDescription() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.RGLDMGUI

getDescription() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.TransformationModelGUI

getDescription() - Method in class net.preibisch.mvrecon.process.export.DisplayImage

getDescription() - Method in class net.preibisch.mvrecon.process.export.ExportLarge2DTIFF

getDescription() - Method in class net.preibisch.mvrecon.process.export.ExportN5Api

getDescription() - Method in interface net.preibisch.mvrecon.process.export.ImgExport

getDescription() - Method in class net.preibisch.mvrecon.process.export.OpenSeaDragon

getDescription() - Method in class net.preibisch.mvrecon.process.export.Save3dTIFF

getDescription() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.PairwiseResult

getDescription() - Method in enum class net.preibisch.mvrecon.process.splitting.ConsensusSetCriterion.ToleranceMode

getDescriptorPoint(int) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.AbstractPointDescriptor

Returns a certain nearest neighbor (relative to the basis point) of this AbstractPointDescriptor

getDetailMap() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListViewDetectionState

getDetectionId() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.CorrespondingInterestPoints

getDeterminantSign() - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Returns the sign of the determinant of this matrix; a return value of true indicates a non-negative determinant; a return value of false indicates a negative determinant.

getDeviceId() - Method in class net.preibisch.mvrecon.process.cuda.CUDADevice

getDeviceName() - Method in class net.preibisch.mvrecon.process.cuda.CUDADevice

getDifferenceThreshold() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.geometrichashing.GeometricHashingParameters

getDifferenceThreshold() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm.RGLDMParameters

getDiffSigma(float, float) - Static method in class net.preibisch.legacy.registration.bead.laplace.LaPlaceFunctions

getDimensionMap() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListViewDetectionState

getDimensionOrder(String) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.grid.RegularTranformHelpers

getDimensions(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox

getDimensions(Interval) - Static method in class net.preibisch.mvrecon.process.quality.FRCTools

getDimensions(N5Reader, int, int, int) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AllenOMEZarrProperties

getDir() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.DHMMetaData

getDirectoriesFromPattern(String) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.OMEZARR.WildcardDirectoryListChooser

getDistance() - Method in class net.preibisch.legacy.registration.detection.AbstractDetection

getDistance() - Method in class net.preibisch.mvrecon.imglib2.st.render.NearestNeighborMaxDistanceSearchOnKDTree

getDistance() - Method in class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.PointMatch1D

getDistance(Point) - Method in class net.preibisch.legacy.registration.detection.AbstractDetection

getDistanceFade() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointOverlay.InterestPointSource

getDistanceFade() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

getDistanceThreshold() - Method in class net.preibisch.mvrecon.process.pointcloud.icp.SimplePointMatchIdentification

getDistanceTo(DoGMaximum) - Method in class net.preibisch.legacy.registration.bead.laplace.DoGMaximum

Computes the distance between two DoG Maxima

getDouble(Hashtable<String, Object>, String) - Static method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

getDoublePosition(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoint

getDoublePosition(int) - Method in class net.preibisch.mvrecon.imglib2.st.render.util.SimpleRealLocalizable

getDoublePosition(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridAccess

getDoublePosition(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccess2d

getDoublePosition(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccess

getDoublePosition(int) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.LocalCoordinateSystemPointDescriptor

getDoublePosition(int) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test.VirtualPointNode

getDoublePosition(int) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.TranslationInvariantLocalCoordinateSystemPointDescriptor

getDoublePosition(int) - Method in class util.StackingRealRandomAccessible.StackingRealRandomAccess

getDownsampledBoundingBox() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getDownsampledBoundingBox() - Method in interface net.preibisch.mvrecon.fiji.plugin.fusion.FusionExportInterface

getDownsampledBoundingBox() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

getDownsampledBoundingBox() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

getDownsampledBoundingBox() - Method in class net.preibisch.mvrecon.process.deconvolution.util.ProcessInputImages

getDownsampledModels() - Method in class net.preibisch.mvrecon.process.deconvolution.util.ProcessInputImages

getDownsampling() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getDownsampling() - Method in interface net.preibisch.mvrecon.fiji.plugin.fusion.FusionExportInterface

getDownsampling() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

getDownsampling() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

getEffectiveSize() - Method in class net.preibisch.mvrecon.process.cuda.Block

getElement(int, int) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Retrieves the value at the specified row and column of the specified matrix.

getElement(int, int) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Retrieves the value at the specified row and column of this matrix.

getElement(int, int) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Retrieves the value at the specified row and column of this matrix.

getElement(int, int) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Retrieves the value at the specified row and column of this matrix.

getElements() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedTableModel

getElements() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.ISpimDataTableModel

getElements() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MissingViewsTableModelDecorator

getElements() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MultiViewTableModelDecorator

getEntitiesPerPixel() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

getEntitiesPerPixel() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

getEntityNamesOrIds(List<? extends Entity>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

getEntropy() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.ContentBasedRealRandomAccessible

getError() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.PairwiseResult

getErrors(Set<ViewId>) - Method in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.StitchingResults

getErrors(SpimData2, List<ViewId>, Map<String, Double>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil

Compute weighted error per (viewA, viewB) pair, returning the list sorted desc by error.

getExecutorService() - Method in class net.preibisch.mvrecon.process.deconvolution.DeconViews

getExperimentDir(File) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.SimView

getExt() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.DHMMetaData

getExt() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.DHMImgLoader

getExt() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyDHMImgLoader

getExtendedDescription() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.DHM

getExtendedDescription() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition

getExtendedDescription() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.LightSheetZ1

getExtendedDescription() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.MicroManager

getExtendedDescription() - Method in interface net.preibisch.mvrecon.fiji.datasetmanager.MultiViewDatasetDefinition

An explanation for the user what exactly this MultiViewDatasetDefinition supports and how it needs to be stored.

getExtendedDescription() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.OMEZARR

getExtendedDescription() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.SimView

getExtendedDescription() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM

getExtendedDescription() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListImageJ

getExtendedDescription() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListLOCI

getExtraSpaceFactor() - Method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxMinFilterThreshold

getFFTFactory(Img<? extends RealType<?>>) - Static method in class util.FFTConvolution

getFFTSize() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

getFile() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyMicroManagerImgLoader

getFile() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MicroManagerImgLoader

getFile() - Method in class net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions.PointSpreadFunction

getFile(ViewId) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoader

getFileList() - Method in interface net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition.FileListChooser

getFileList() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition.SimpleDirectoryFileListChooser

getFileList() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition.WildcardFileListChooser

getFileMap() - Method in interface net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.FileMapGettable

getFileMap() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.FileMapImgLoaderLOCI2

getFileMap() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.FileMapImgLoaderLOCI

getFileMap() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.LazyLoadingFlatFieldCorrectionMap

getFileMap() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyFileMapImgLoaderLOCI

getFileName(String) - Method in class net.preibisch.mvrecon.process.export.Save3dTIFF

getFileName(URI) - Static method in class util.URITools

getFileNameFor(int, int, int, int, int) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

getFileNamePattern() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoader

getFileNamePattern() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.StackImgLoader

getFileNamesFor(String, String, String, String, String, String, int, int, int, int, int, int, int, int, int, int) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData

getFileNamesFor(String, String, String, String, String, String, String, String, String, String, String, int, int, int, int, int) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

getFilesFromPattern(String, long) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition

getFilteredViewDescriptions(AbstractSequenceDescription<?, ?, ?>, Map<Class<? extends Entity>, List<? extends Entity>>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.SpimDataTools

getFilteredViewDescriptions(AbstractSequenceDescription<?, ?, ?>, Map<Class<? extends Entity>, List<? extends Entity>>, boolean) - Static method in class net.preibisch.mvrecon.fiji.spimdata.SpimDataTools

getFilterRansac() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac.RANSACParameters

getFilters() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedTableModel

getFilters() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.ISpimDataTableModel

getFilters() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MissingViewsTableModelDecorator

getFilters() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MultiViewTableModelDecorator

getFirst() - Method in class net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.Link

getFixedViews() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.Subset

getFlippedMatches() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.PairwiseResult

getFloatImage(int, boolean, ImgLoaderHint...) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.FileMapImgLoaderLOCI2.FileMapSetupImgLoaderLOCI2

getFloatImage(int, boolean, ImgLoaderHint...) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.SimViewSetupImgLoader

getFloatImage(int, boolean, ImgLoaderHint...) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.SmartSPIMSetupImgLoader

getFloatImage(int, boolean, ImgLoaderHint...) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitSetupImgLoader

getFloatImage(int, int, boolean, ImgLoaderHint...) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitMultiResolutionSetupImgLoader

getFloatImage(ViewId, boolean) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyDHMImgLoader

getFloatImage(ViewId, boolean) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyFileMapImgLoaderLOCI

getFloatImage(ViewId, boolean) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyLightSheetZ1ImgLoader

getFloatImage(ViewId, boolean) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyMicroManagerImgLoader

getFloatImage(ViewId, boolean) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoaderIJ

Get FloatType image normalized to the range [0,1].

getFloatImage(ViewId, boolean) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoaderLOCI

Get FloatType image normalized to the range [0,1].

getFloatKernelPadded(double[], int) - Static method in class net.preibisch.mvrecon.process.cuda.CUDASeparableConvolutionFunctions

getFloatPosition(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoint

getFloatPosition(int) - Method in class net.preibisch.mvrecon.imglib2.st.render.util.SimpleRealLocalizable

getFloatPosition(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridAccess

getFloatPosition(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccess2d

getFloatPosition(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccess

getFloatPosition(int) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.LocalCoordinateSystemPointDescriptor

getFloatPosition(int) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test.VirtualPointNode

getFloatPosition(int) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.TranslationInvariantLocalCoordinateSystemPointDescriptor

getFloatPosition(int) - Method in class util.StackingRealRandomAccessible.StackingRealRandomAccess

getFloatProcessor(RandomAccessible<FloatType>, int, int, int, int) - Static method in class net.preibisch.mvrecon.process.quality.FRCRealRandomAccessible

getFloatRAI(RandomAccessibleInterval<T>) - Static method in class net.preibisch.mvrecon.process.quality.FRCRealRandomAccessible

getFloatValue(byte[], int, boolean) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoaderLOCI

getFormat() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AllenOMEZarrLoader

getFrame() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.DoGWindow

getFrame() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorer

getFRCStepSize() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

getFreeDeviceMemory() - Method in class net.preibisch.mvrecon.process.cuda.CUDADevice

getFreeMemDeviceCUDA(int) - Method in interface net.preibisch.mvrecon.process.cuda.CUDAStandardFunctions

getFullDesc() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.PairwiseResult

getFusedZeroMinInterval(Interval) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

getFusion() - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval

getFusionGroups() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getFusionGroups() - Method in interface net.preibisch.mvrecon.fiji.plugin.fusion.FusionExportInterface

getFusionGroups() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

getFusionGroups() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

getFusionGroups(SpimData2, List<ViewId>, int) - Static method in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

getFusionMinMax(RandomAccessibleInterval<T>, double, double) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

getFusionType() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

getGenericDialog() - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

getGlobalOptimizationParametersForSelection(int, boolean) - Static method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters

getGlobalShifts() - Method in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.StitchingResults

getGroupedFormat() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListViewDetectionState

getGroupedImagePlusForInteractive(String) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

getGroupedPairs() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.Subset

Computes a list of grouped views that need to be compared, expressed as pairs.

getGroupingFactors() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedTableModel

getGroupingFactors() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.ISpimDataTableModel

getGroupingFactors() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MissingViewsTableModelDecorator

getGroupingFactors() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MultiViewTableModelDecorator

getGroups() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

getGroups() - Method in class net.preibisch.mvrecon.process.deconvolution.util.ProcessInputImages

getGroups() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.PairwiseSetup

getGroups() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.Subset

getGroups(SpimData2, List<? extends ViewId>, boolean, boolean, boolean, boolean) - Static method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.AdvancedRegistrationParameters

getGroups(SpimData2, List<ViewId>, boolean, boolean, boolean) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.AdvancedRegistrationParameters

getGroupSelection(String, String, List<Group<ViewDescription>>) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

getGroupsSorted(Collection<Group<V>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

getGroupUsageMap() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListViewDetectionState

getHash() - Method in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.PairwiseStitchingResult

getHashMap() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.ViewInterestPointLists

getHDF5File() - Method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.ParametersResaveHDF5

getHeight() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.DHMMetaData

getHeight() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough.MyTarget

getHeight() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.Calibration

getHeight() - Method in class net.preibisch.mvrecon.process.export.OpenSeaDragon.OpenSeaDragonImgLib2

getHelpHtml() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

getHelpHtml() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorerPanel

getHigherDimensionIndicies() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AllenOMEZarrLoader.OMEZARREntry

getHistogramTitle(Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.process.interestpointremoval.DistanceHistogram

getId() - Method in class net.preibisch.mvrecon.fiji.spimdata.EmptyEntity

Get the unique id of this entity.

getId() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoint

getId() - Method in interface net.preibisch.mvrecon.process.deconvolution.iteration.ComputeBlockThread

getId() - Method in class net.preibisch.mvrecon.process.deconvolution.iteration.ComputeBlockThreadAbstract

getId() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.AbstractPointDescriptor

Return the unique id of this descriptor

getID() - Method in class net.preibisch.legacy.registration.detection.AbstractDetection

getIdMap() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListViewDetectionState

getIJLogWindow() - Static method in class net.preibisch.mvrecon.fiji.plugin.util.MultiWindowLayoutHelper

get the ImageJ log window (if present)

getIllumination(BasicViewDescription<?>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyFileMapImgLoaderLOCI

getIllumination(BasicViewDescription<?>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyLightSheetZ1ImgLoader

getIlluminationsToProcess() - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.LoadParseQueryXML

getIllumName(List<Illumination>) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

getImage() - Method in class net.preibisch.mvrecon.process.deconvolution.DeconView

getImage(int, int, ImgLoaderHint...) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitMultiResolutionSetupImgLoader

getImage(int, int, ImgLoaderHint...) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitViewerSetupImgLoader

getImage(int, ImgLoaderHint...) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.FileMapImgLoaderLOCI2.FileMapSetupImgLoaderLOCI2

getImage(int, ImgLoaderHint...) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.SimViewSetupImgLoader

getImage(int, ImgLoaderHint...) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.SmartSPIMSetupImgLoader

getImage(int, ImgLoaderHint...) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitMultiResolutionSetupImgLoader

getImage(int, ImgLoaderHint...) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitSetupImgLoader

getImage(int, ImgLoaderHint...) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitViewerSetupImgLoader

getImage(ViewId) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyDHMImgLoader

getImage(ViewId) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyFileMapImgLoaderLOCI

getImage(ViewId) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyLightSheetZ1ImgLoader

getImage(ViewId) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyMicroManagerImgLoader

getImage(ViewId) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoaderIJ

Get UnsignedShortType un-normalized image.

getImage(ViewId) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoaderLOCI

Get UnsignedShortType un-normalized image.

getImage(T, ImgLoader, ViewId, boolean) - Static method in class net.preibisch.mvrecon.fiji.plugin.Max_Project

getImagePlusForInteractive(String) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

getImagePlusInstance(BlockSupplier<T>, Interval, int[], boolean, String, double, double, ExecutorService) - Static method in class net.preibisch.mvrecon.process.export.DisplayImage

getImagePlusInstance(RandomAccessibleInterval<T>, boolean, String, double, double, ExecutorService) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

getImages() - Method in class net.preibisch.mvrecon.process.deconvolution.util.ProcessInputImages

getImages() - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval

getImageSize(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.FileMapImgLoaderLOCI2.FileMapSetupImgLoaderLOCI2

getImageSize(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.SimViewSetupImgLoader

getImageSize(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.SmartSPIMSetupImgLoader

getImageSize(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitMultiResolutionSetupImgLoader

getImageSize(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitSetupImgLoader

getImageSize(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitViewerSetupImgLoader

getImageSize(int, int) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitMultiResolutionSetupImgLoader

getImageSize(int, int) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitViewerSetupImgLoader

getImageSize(ViewId) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AbstractImgLoader

getImageType() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AbstractImgLoader

getImageType() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.FileMapImgLoaderLOCI2.FileMapSetupImgLoaderLOCI2

getImageType() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.SimViewSetupImgLoader

getImageType() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.SmartSPIMSetupImgLoader

getImageType() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitMultiResolutionSetupImgLoader

getImageType() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitSetupImgLoader

getImageType() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitViewerSetupImgLoader

getImg() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.CalibratedImg

getImgFactory() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AbstractImgFactoryImgLoader

getImgFactory() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.FileMapImgLoaderLOCI

getImgFactory() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LightSheetZ1ImgLoader

getImgFactory() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.StackImgLoader

getImgSizeInt(Interval) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2

getIndexKeys() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

getIndexKeys() - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

getIndividualSets(List<ViewId>) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.AllToAllGUI

getIndividualSets(List<ViewId>) - Method in interface net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalGUI

getIndividualSets(List<ViewId>) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.IndividualTimepointGUI

getInliers() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.PairwiseResult

getInlierSetIds() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.PairwiseResult

getInputImgCacheType() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getInputXML() - Static method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5

getInsideValue(FloatType, RealRandomAccess<FloatType>, boolean, float) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedImgRandomAccess

getInstance() - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.util.CZIReaderSetupHook

getInstanceFromNameOrId(AbstractSequenceDescription<?, ?, ?>, Class<? extends Entity>, String) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

getInstancesOfAttribute(AbstractSequenceDescription<?, ?, ?>, Class<? extends Entity>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.SpimDataTools

getIntensity() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointValue

getIntensityAdjustments() - Method in class net.preibisch.mvrecon.fiji.spimdata.intensityadjust.IntensityAdjustments

getIntensityAdjustments() - Method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

getInterestPointList(String) - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.ViewInterestPointLists

getInterestPointMap() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.IPL

getInterestPointMap() - Method in class net.preibisch.mvrecon.process.interestpointremoval.InteractiveProjections

getInterestPoints(V, Map<V, ViewRegistration>, Map<V, ViewInterestPointLists>, Map<V, HashMap<String, Double>>, boolean) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

getInterestPoints(V, Map<V, ViewRegistration>, Map<V, ViewInterestPointLists>, Map<V, HashMap<String, Double>>, boolean, ConcurrentHashMap<String, ConcurrentLinkedQueue<V>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

getInterestPointsCopy() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoints

getInterestPointsCopy() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

getInterpolatedSource(int, int, Interpolation) - Method in class net.preibisch.mvrecon.fiji.plugin.interactive.MultiResolutionSource

getInterpolation() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

getIntersections(double[][], double[]) - Method in class net.preibisch.mvrecon.process.quality.FRC

Computes the crossing points of the FRC curve and the threshold curve.

getInterval() - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval

getIntervals() - Method in class net.preibisch.mvrecon.process.splitting.SplitResult

getIntPosition(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccess2d

getIntValue(byte[], int, boolean) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoaderLOCI

getInvariant(int) - Method in interface net.preibisch.mvrecon.fiji.datasetmanager.patterndetector.FilenamePatternDetector

getInvariant(int) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.patterndetector.NumericalFilenamePatternDetector

getInverseTransform() - Method in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.PairwiseStitchingResult

getIO() - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

getIP() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.CorrespondingIP

getIPL(Collection<IPL>, String) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidTools

getJARFile(boolean) - Static method in class net.preibisch.mvrecon.Version

getJSONFile() - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough

getKernel1() - Method in class net.preibisch.mvrecon.process.deconvolution.DeconViewPSF

getKernel1FFT() - Method in class net.preibisch.mvrecon.process.deconvolution.DeconViewPSF

getKernel2() - Method in class net.preibisch.mvrecon.process.deconvolution.DeconViewPSF

getKernel2FFT() - Method in class net.preibisch.mvrecon.process.deconvolution.DeconViewPSF

getKernelSize(double[]) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2

getKeyValueAccess(URI) - Static method in class util.URITools

A little hack to get a generic KeyValueAccess for a cloud store

getL() - Method in interface net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonrigidIP

getL() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.SimpleReferenceIP

getLabel() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.IPL

getLabel() - Method in class net.preibisch.mvrecon.process.interestpointremoval.ThinOutParameters

getLabel(SpimData2, List<ViewId>) - Static method in class net.preibisch.mvrecon.fiji.plugin.Show_Histogram

getLabelA() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.PairwiseResult

getLabelB() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.PairwiseResult

getLabels() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.NonRigidParametersGUI

getLabels() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidParameters

getLabels() - Method in class net.preibisch.mvrecon.process.splitting.ConsensusSetCriterion

getLabels() - Method in class net.preibisch.mvrecon.process.splitting.CrossViewCorrespondenceCriterion

getLabels() - Method in interface net.preibisch.mvrecon.process.splitting.OctTreeSplitCriterion

getLabels(SpimData2, List<ViewId>) - Static method in class net.preibisch.mvrecon.fiji.plugin.Show_Relative_Histogram

getLambda() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getLayoutAngles() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoader

getLayoutAngles() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.StackImgLoader

getLayoutChannels() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoader

getLayoutChannels() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.StackImgLoader

getLayoutIlluminations() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoader

getLayoutIlluminations() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.StackImgLoader

getLayoutTiles() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoader

getLayoutTiles() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.StackImgLoader

getLayoutTimePoints() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoader

getLayoutTimePoints() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.StackImgLoader

getLibraryExtensions() - Static method in class net.preibisch.mvrecon.process.cuda.NativeLibraryTools

getLines() - Method in class net.preibisch.mvrecon.fiji.plugin.util.MyMultiLineLabel

getLinkedObject() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.LinkedInterestPoint

getLinkedObject() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.LinkedPoint

getLinkQuality() - Method in class net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.Link

getListeners() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorer

getListeners() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

getListOfViewSetupIdsPresentInAllSubsets(List<Subset<ViewId>>) - Method in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

getLocalCoordinates(double[], double[], long[], long[], int) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridAccess

getLocalCoordinates(int) - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointOverlay.InterestPointSource

getLocalCoordinates(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

getLocalToGlobalTransform(ViewId, int, AffineTransform3D) - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointOverlay.InterestPointSource

getLocalToGlobalTransform(ViewId, int, AffineTransform3D) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

getLocations(long, long) - Static method in class net.preibisch.mvrecon.process.quality.FRCTools

getLongestPathPrefix(Collection<String>) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition

getLongPosition(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccess2d

getLoopSize() - Method in class net.preibisch.mvrecon.process.fusion.ImagePortion

getM00() - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Get the first matrix element in the first row.

getM00() - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Get the first matrix element in the first row.

getM00() - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Get the first matrix element in the first row.

getM00() - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Get the first matrix element in the first row.

getM01() - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Get the second matrix element in the first row.

getM01() - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Get the second matrix element in the first row.

getM01() - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Get the second matrix element in the first row.

getM01() - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Get the second matrix element in the first row.

getM02() - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Get the third matrix element in the first row.

getM02() - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Get the third matrix element in the first row.

getM02() - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Get the third matrix element in the first row.

getM02() - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Get the third matrix element in the first row.

getM03() - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Get the fourth element of the first row.

getM03() - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Get the fourth element of the first row.

getM10() - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Get first matrix element in the second row.

getM10() - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Get first matrix element in the second row.

getM10() - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Get first matrix element in the second row.

getM10() - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Get first matrix element in the second row.

getM11() - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Get second matrix element in the second row.

getM11() - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Get second matrix element in the second row.

getM11() - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Get second matrix element in the second row.

getM11() - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Get second matrix element in the second row.

getM12() - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Get the third matrix element in the second row.

getM12() - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Get the third matrix element in the second row.

getM12() - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Get the third matrix element in the second row.

getM12() - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Get the third matrix element in the second row.

getM13() - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Get the fourth element of the second row.

getM13() - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Get the fourth element of the second row.

getM20() - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Get the first matrix element in the third row.

getM20() - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Get the first matrix element in the third row.

getM20() - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Get the first matrix element in the third row.

getM20() - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Get the first matrix element in the third row.

getM21() - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Get the second matrix element in the third row.

getM21() - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Get the second matrix element in the third row.

getM21() - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Get the second matrix element in the third row.

getM21() - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Get the second matrix element in the third row.

getM22() - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Get the third matrix element in the third row .

getM22() - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Get the third matrix element in the third row .

getM22() - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Get the third matrix element in the third row.

getM22() - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Get the third matrix element in the third row.

getM23() - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Get the fourth element of the third row.

getM23() - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Get the fourth element of the third row.

getM30() - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Get the first element of the fourth row.

getM30() - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Get the first element of the fourth row.

getM31() - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Get the second element of the fourth row.

getM31() - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Get the second element of the fourth row.

getM32() - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Get the third element of the fourth row.

getM32() - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Get the third element of the fourth row.

getM33() - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Get the fourth element of the fourth row.

getM33() - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Get the fourth element of the fourth row.

getMajorComputeVersion() - Method in class net.preibisch.mvrecon.process.cuda.CUDADevice

getMatchingModel() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.CenterOfMassGUI

getMatchingModel() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.FRGLDMGUI

getMatchingModel() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.GeometricHashingGUI

getMatchingModel() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.IterativeClosestPointGUI

getMatchingModel() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.LoadCorrespondencesGUI

getMatchingModel() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.PairwiseGUI

getMatchingModel() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.RGLDMGUI

getMatrix3d(Matrix3d) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel3D

getMatrix4d(AffineModel3D) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

getMatrix4d(RigidModel3D) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

getMatrix4d(Matrix4d) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel3D

getMax() - Method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.ParametersResaveHDF5

getMax() - Method in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox

getMax() - Method in interface net.preibisch.mvrecon.process.deconvolution.init.PsiInit

getMax() - Method in class net.preibisch.mvrecon.process.deconvolution.init.PsiInitAvgApprox

getMax() - Method in class net.preibisch.mvrecon.process.deconvolution.init.PsiInitAvgPrecise

getMax() - Method in class net.preibisch.mvrecon.process.deconvolution.init.PsiInitBlurredFused

getMax() - Method in class net.preibisch.mvrecon.process.deconvolution.init.PsiInitFromFile

getMax() - Method in class net.preibisch.mvrecon.process.deconvolution.init.PsiInitFromRAI

getMax() - Method in class net.preibisch.mvrecon.process.deconvolution.util.FusedNonZeroRandomAccess

getMax() - Method in class net.preibisch.mvrecon.process.interestpointremoval.histogram.Histogram

getMax() - Method in class net.preibisch.mvrecon.process.interestpointremoval.ThinOutParameters

getMaxAlignmentError() - Method in interface net.preibisch.legacy.registration.bead.error.GlobalErrorStatistics

getMaxAlignmentError() - Method in class net.preibisch.legacy.registration.bead.error.GlobalErrorStatisticsImpl

getMaxCorrespondences() - Method in class net.preibisch.mvrecon.process.splitting.CrossViewCorrespondenceCriterion

getMaxDistance() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.icp.IterativeClosestPointParameters

getMaxEpsilon() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac.RANSACParameters

getMaxEpsilonRANSAC() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.icp.IterativeClosestPointParameters

getMaxError() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.CenterOfMassGUI

getMaxError() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.FRGLDMGUI

getMaxError() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.GeometricHashingGUI

getMaxError() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.IterativeClosestPointGUI

getMaxError() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.LoadCorrespondencesGUI

getMaxError() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.PairwiseGUI

getMaxError() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.RGLDMGUI

getMaxError() - Method in class net.preibisch.mvrecon.process.interestpointregistration.global.convergence.ConvergenceStrategy

getMaximalError() - Method in class net.preibisch.mvrecon.process.pointcloud.icp.ICP

Returns the maximum error of a PointMatch of the last ICP iteration, or -1 if no iteration has been computed yet.

getMaxIntensity() - Method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxMinFilterThreshold

getMaxIterations() - Method in class net.preibisch.mvrecon.process.interestpointregistration.global.convergence.ConvergenceStrategy

getMaxIterationsRANSAC() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.icp.IterativeClosestPointParameters

getMaxNonzero(IFormatReader) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyFileMapImgLoaderLOCI

getMaxNonzero(RandomAccessibleInterval<T>, int) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyFileMapImgLoaderLOCI

get the highest index in dimension dim where a hyperslice of img in that dimension contains nonzero values.

getMaxNumIterations() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.icp.IterativeClosestPointParameters

getMaxPlateauWidth() - Method in class net.preibisch.mvrecon.process.interestpointregistration.global.convergence.ConvergenceStrategy

getMaxTrust() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac.RANSACParameters

getMeanCorrected(RandomAccessibleInterval<P>, RandomAccessibleInterval<Q>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.FlatFieldCorrectedRandomAccessibleInterval

getMemDeviceCUDA(int) - Method in interface net.preibisch.mvrecon.process.cuda.CUDAStandardFunctions

getMin() - Method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.ParametersResaveHDF5

getMin() - Method in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox

getMin() - Method in class net.preibisch.mvrecon.process.interestpointremoval.histogram.Histogram

getMin() - Method in class net.preibisch.mvrecon.process.interestpointremoval.ThinOutParameters

getMinAlignmentError() - Method in interface net.preibisch.legacy.registration.bead.error.GlobalErrorStatistics

getMinAlignmentError() - Method in class net.preibisch.legacy.registration.bead.error.GlobalErrorStatisticsImpl

getMinBoundingInterval(Collection<Collection<Pair<RealInterval, AffineGet>>>) - Static method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxMaximalGroupOverlap

getMinBoundingIntervalSingle(Collection<Pair<RealInterval, AffineGet>>) - Static method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxMaximalGroupOverlap

getMinCorrespondences() - Method in class net.preibisch.mvrecon.process.splitting.ConsensusSetCriterion

getMinimumSize() - Method in class net.preibisch.mvrecon.fiji.plugin.util.MyMultiLineLabel

getMinInlierRatio() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.icp.IterativeClosestPointParameters

getMinInlierRatio() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac.RANSACParameters

getMinIntensity() - Method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxMinFilterThreshold

getMinMax(List<Double>) - Static method in class net.preibisch.mvrecon.process.interestpointremoval.histogram.Histogram

getMinMax(RandomAccessibleInterval<P>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.FlatFieldCorrectedRandomAccessibleInterval

getMinMaxNumChannelsIndexed(FileListViewDetectionState) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListViewDetectionState

getMinMaxNumSeriesIndexed(FileListViewDetectionState) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListViewDetectionState

getMinNumMatches() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac.RANSACParameters

getMinNumMatches() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.FixedModel

getMinNumMatches() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantAffineModel3D

getMinNumMatches() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantFixedModel

getMinNumMatches() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel2D

getMinNumMatches() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel3D

getMinNumMatches() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantSimilarityModel3D

getMinNumPoints() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.icp.IterativeClosestPointParameters

getMinorComputeVersion() - Method in class net.preibisch.mvrecon.process.cuda.CUDADevice

getMinRes(BasicViewDescription<?>) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

getMinSizeMultiplier() - Method in class net.preibisch.mvrecon.process.splitting.SplitOctTree

getMinSplitLevels() - Method in class net.preibisch.mvrecon.process.splitting.SplitOctTree

getMinStepSize() - Method in class net.preibisch.mvrecon.process.splitting.SplitOctTree

getMinValue() - Method in interface net.preibisch.mvrecon.process.deconvolution.iteration.ComputeBlockThread

getMinValue() - Method in class net.preibisch.mvrecon.process.deconvolution.iteration.ComputeBlockThreadAbstract

getMipmapManual() - Method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.ParametersResaveHDF5

getMipmapResolutions() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitMultiResolutionSetupImgLoader

getMipmapResolutions() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitViewerSetupImgLoader

getMipmapResolutions(N5Reader, int) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AllenOMEZarrProperties

getMipMapTransform(BasicImgLoader, ViewId, long[]) - Static method in class net.preibisch.mvrecon.process.downsampling.DownsampleTools

Returns the mipmap transform if you were to open that ViewId with this ImgLoader at the specified downsample factors

getMipmapTransforms() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitMultiResolutionSetupImgLoader

getMipmapTransforms() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitViewerSetupImgLoader

getModel() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.TransformationModelGUI

getModel() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

getModel() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.fastrgldm.FRGLDMParameters

getModel() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.geometrichashing.GeometricHashingParameters

getModel() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.icp.IterativeClosestPointParameters

getModel() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm.RGLDMParameters

getModel(AffineGet) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

getModelFromFile(File) - Static method in class net.preibisch.legacy.io.IOFunctions

getMultiplicityMap() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListViewDetectionState

getN5dataset() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

getName() - Method in class net.preibisch.mvrecon.fiji.plugin.interactive.MultiResolutionSource

getName() - Method in class net.preibisch.mvrecon.fiji.spimdata.EmptyEntity

getNameDeviceCUDA(int, byte[]) - Method in interface net.preibisch.mvrecon.process.cuda.CUDAStandardFunctions

getNameForFusionGroup(Group<ViewDescription>, int) - Static method in class net.preibisch.mvrecon.process.export.OpenSeaDragon

getNativeTypeFactory() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

getNativeTypeFactory() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

getNeighbors() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.SubsetMatcher

getNewExporterInstance() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getNewExporterInstance() - Method in interface net.preibisch.mvrecon.fiji.plugin.fusion.FusionExportInterface

getNewExporterInstance() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

getNewExporterInstance() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

getNewInstance() - Method in interface net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition.FileListChooser

getNewInstance() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition.SimpleDirectoryFileListChooser

getNewInstance() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition.WildcardFileListChooser

getNewInstance() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.OMEZARR.MultipleOMEZARRListChooser

getNewInstance() - Method in interface net.preibisch.mvrecon.fiji.datasetmanager.OMEZARR.URIListChooser

getNewInstance() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.OMEZARR.WildcardDirectoryListChooser

getNewLabel() - Method in class net.preibisch.mvrecon.process.interestpointremoval.CreateFromCorrespondencesParameters

getNewLabel() - Method in class net.preibisch.mvrecon.process.interestpointremoval.ThinOutParameters

getNonInterferingBlocks() - Method in class net.preibisch.mvrecon.process.deconvolution.DeconView

getNonRigidParameters() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getNonRigidParameters() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

getNormalizationFactor(ArrayList<PointMatch>, Object) - Method in interface net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.Matcher

Computes a normalization factor for the case that the different set of PointMatches are not comparable (for example number of neighbors used is not constant)

getNormalizationFactor(ArrayList<PointMatch>, Object) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.ModelPriorMatcher

getNormalizationFactor(ArrayList<PointMatch>, Object) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.ModelPriorSubsetMatcher

getNormalizationFactor(ArrayList<PointMatch>, Object) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.SimpleMatcher

getNormalizationFactor(ArrayList<PointMatch>, Object) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.SubsetMatcher

getNormalizedWeights() - Method in class net.preibisch.mvrecon.process.deconvolution.util.ProcessInputImages

getNumAmbigousMatches() - Method in class net.preibisch.mvrecon.process.pointcloud.icp.ICP

Returns the number of ambigous PointMatches indentified in the last ICP iteration, or -1 if no iteration has been computed yet.

getNumBlocks() - Method in class net.preibisch.mvrecon.process.deconvolution.DeconView

getNumCandidates() - Method in interface net.preibisch.legacy.registration.bead.error.GlobalErrorStatistics

getNumCandidates() - Method in class net.preibisch.legacy.registration.bead.error.GlobalErrorStatisticsImpl

getNumCombinations() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.SubsetMatcher

getNumCorrespondences() - Method in interface net.preibisch.legacy.registration.bead.error.GlobalErrorStatistics

getNumCorrespondences() - Method in class net.preibisch.legacy.registration.bead.error.GlobalErrorStatisticsImpl

getNumDetections() - Method in interface net.preibisch.legacy.registration.bead.error.GlobalErrorStatistics

getNumDetections() - Method in class net.preibisch.legacy.registration.bead.error.GlobalErrorStatisticsImpl

getNumDevicesCUDA() - Method in interface net.preibisch.mvrecon.process.cuda.CUDAStandardFunctions

getNumDimensions() - Method in class net.preibisch.legacy.registration.detection.AbstractDetection

getNumDimensions() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test.PointNode

getNumIterations() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getNumIterations() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac.RANSACParameters

getNumMatchings() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.SubsetMatcher

getNumMipmapLevels() - Method in class net.preibisch.mvrecon.fiji.plugin.interactive.MultiResolutionSource

getNumNeighbors() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.fastrgldm.FRGLDMParameters

getNumNeighbors() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm.RGLDMParameters

getNumNeighbors() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.SubsetMatcher

getNumPointMatches() - Method in class net.preibisch.mvrecon.process.pointcloud.icp.ICP

Returns the number of PointMatches of the last ICP iteration, or -1 if no iteration has been computed yet.

getNumPoints() - Method in class net.preibisch.mvrecon.process.fusion.tps.Landmarks

getNumThreads() - Method in class net.preibisch.mvrecon.process.deconvolution.DeconViews

getNumVariables() - Method in interface net.preibisch.mvrecon.fiji.datasetmanager.patterndetector.FilenamePatternDetector

getNumVariables() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.patterndetector.NumericalFilenamePatternDetector

getNumViews() - Method in interface net.preibisch.mvrecon.process.deconvolution.iteration.mul.ComputeBlockMulThread

getNumViews() - Method in class net.preibisch.mvrecon.process.deconvolution.iteration.mul.ComputeBlockMulThreadAbstract

getOccurences(Point, Point, List<PointMatchGeneric<P>>) - Static method in class net.preibisch.mvrecon.process.pointcloud.icp.ICP

Computes if one Point pair occurs more than once in a List of PointMatches

getOptimalTimePoint(ArrayList<RegistrationStatistics>) - Static method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.statistics.TimeLapseDisplay

Select a timepoint with minimal maxError and maximal minRatio

getOrCreateBrightImgDownsampled(ViewId, int[]) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.MultiResolutionFlatfieldCorrectionWrappedImgLoader

getOrCreateDarkImgDownsampled(ViewId, int[]) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.MultiResolutionFlatfieldCorrectionWrappedImgLoader

getOrderedNearestNeighboringPoints() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.AbstractPointDescriptor

getOSEMspeedup() - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccessibleInterval

getOSEMSpeedUp() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getOutput() - Method in class net.preibisch.legacy.mpicbg.SketchTikZFileObject

getOverlapDetection(SpimData) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.BasicRegistrationParameters

getOverlapInterval(V, V) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap.AllAgainstAllOverlap

getOverlapInterval(V, V) - Method in interface net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap.OverlapDetection

getOverlapInterval(V, V) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap.SimpleBoundingBoxOverlap

getPair() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.MatcherPairwiseTools.MatchingTask

getPairs() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.PairwiseSetup

getPairs() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.Subset

getPairwiseLinks() - Method in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.PairwiseLinkImpl

getPairwiseLinks() - Method in interface net.preibisch.mvrecon.fiji.spimdata.stitchingresults.PairwiseLinkInterface

getPairwiseLinks() - Method in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.StitchingResults

getPairwiseResults() - Method in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.StitchingResults

getPairwiseResultsForPair(Pair<Group<ViewId>, Group<ViewId>>) - Method in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.StitchingResults

getPanel() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorer

getPanel() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedTableModel

getPanel() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.ISpimDataTableModel

getPanel() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MissingViewsTableModelDecorator

getPanel() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MultiViewTableModelDecorator

getParameters() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGaussianGUI

getParameters() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.InterestPointDetectionGUI

getParameters() - Static method in class net.preibisch.mvrecon.fiji.plugin.resave.Resave_TIFF

getParameters() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoints

getParameters(ExportMipmapInfo, boolean, boolean) - Static method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5

getParameters(ExportMipmapInfo, boolean, String, boolean) - Static method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5

getParameters(ViewInterestPoints, List<? extends ViewId>, String) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

getParameters(SpimData2, List<ViewId>) - Static method in class net.preibisch.mvrecon.fiji.plugin.CreateFromCorresponding_Detections

getParameters(SpimData2, List<ViewId>) - Static method in class net.preibisch.mvrecon.fiji.plugin.RelativeThinOut_Detections

getParameters(SpimData2, List<ViewId>) - Static method in class net.preibisch.mvrecon.fiji.plugin.ThinOut_Detections

getParameters(SpimData2, List<ViewId>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil

Backwards-compatible wrapper that returns just the labels-and-weights map.

getParametersExtended(SpimData2, List<ViewId>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil

Extended dialog returning the full AnalyzeErrorsUtil.Parameters bundle (labels+weights, grouping, top/bottom caps).

getParamtersIJ(URI, URI, Collection<ViewSetup>, StorageFormat, boolean) - Static method in class net.preibisch.mvrecon.fiji.plugin.resave.ParametersResaveN5Api

getParamtersIJ(URI, Collection<ViewSetup>, StorageFormat, boolean) - Static method in class net.preibisch.mvrecon.fiji.plugin.resave.ParametersResaveN5Api

getParentURI(URI) - Static method in class util.URITools

getParentURINoEx(URI) - Static method in class util.URITools

getPartitions(AbstractSpimData<?>, Generic_Resave_HDF5.ParametersResaveHDF5) - Static method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5

getPath() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AllenOMEZarrLoader.OMEZARREntry

getPath() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoader

getPath() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.StackImgLoader

getPatternAsRegex() - Method in interface net.preibisch.mvrecon.fiji.datasetmanager.patterndetector.FilenamePatternDetector

getPatternAsRegex() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.patterndetector.NumericalFilenamePatternDetector

getPatternFile(FilenamePatternDetector, List<Integer>, List<Integer>, List<List<Integer>>) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil

getPerSetupExportMipmapInfo(AbstractSpimData<?>, Generic_Resave_HDF5.ParametersResaveHDF5) - Static method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5

getPhaseChannelId() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.DHMMetaData

getPhaseChannelId() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.DHMImgLoader

getPhaseChannelId() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyDHMImgLoader

getPhaseDir() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.DHMMetaData

getPhaseDir() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.DHMImgLoader

getPhaseDir() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyDHMImgLoader

getPixelSize() - Method in interface net.preibisch.mvrecon.process.export.Calibrateable

getPixelSize() - Method in class net.preibisch.mvrecon.process.export.DisplayImage

getPixelSize() - Method in class net.preibisch.mvrecon.process.export.ExportN5Api

getPixelSize() - Method in class net.preibisch.mvrecon.process.export.Save3dTIFF

getPixelType() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getPixelType() - Method in interface net.preibisch.mvrecon.fiji.plugin.fusion.FusionExportInterface

0 == "32-bit floating point", 1 == "16-bit unsigned integer"

getPixelType() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

getPixelType() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

getPixelType() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

getPixelType() - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

getPlaneSizeInBytes(IFormatReader) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.util.BioformatsReaderUtils

getPlaneThickness() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointOverlay.InterestPointSource

getPlaneThickness() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

getPoint() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test.VirtualPointNode

getPoint1() - Method in class net.preibisch.legacy.mpicbg.PointMatchGeneric

getPoint2() - Method in class net.preibisch.legacy.mpicbg.PointMatchGeneric

getPointMatches() - Method in class net.preibisch.mvrecon.process.pointcloud.icp.ICP

Return the List of PointMatches (target, reference) of the last ICP iteration

getPointMatchIdentification() - Method in class net.preibisch.mvrecon.process.pointcloud.icp.ICP

Returns the current PointMatchIdentification that is used to identfy corresponding points

getPoints(SpimData2, ViewId, String, boolean) - Static method in class net.preibisch.mvrecon.process.psf.PSFExtraction

getPointSizeScale() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointOverlay.InterestPointSource

getPointSizeScale() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

getPointSpreadFunctions() - Method in class net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions.PointSpreadFunctions

getPointSpreadFunctions() - Method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

getPosition() - Method in class net.preibisch.mvrecon.imglib2.st.render.NearestNeighborMaxDistanceSearchOnKDTree

getPotentialBleachers(List<ViewId>, Map<ViewId, RealInterval>) - Static method in class net.preibisch.mvrecon.process.fusion.intensity.IntensityCorrection

Given a list of ViewIds in the order they were acquired (such that views later in the list have been potentially bleached by earlier views), finds for each ViewId the potential "bleachers" (earlier views with overlapping bounds).

getPreferredSize() - Method in class net.preibisch.mvrecon.fiji.plugin.util.MyMultiLineLabel

getProgressWriter() - Static method in class net.preibisch.legacy.io.IOFunctions

getPSF() - Method in class net.preibisch.mvrecon.process.deconvolution.DeconView

getPSF() - Method in class net.preibisch.mvrecon.process.psf.PSFExtraction

getPSFCopy() - Method in class net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions.PointSpreadFunction

getPSFCopyArrayImg() - Method in class net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions.PointSpreadFunction

getPSFs() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getPSFType() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getPSI() - Method in class net.preibisch.mvrecon.process.deconvolution.MultiViewDeconvolution

getPsiBlockTmp() - Method in interface net.preibisch.mvrecon.process.deconvolution.iteration.ComputeBlockThread

contains the deconvolved image at the current iteration, copied into a block from outside (outofbounds is mirror)

getPsiBlockTmp() - Method in class net.preibisch.mvrecon.process.deconvolution.iteration.ComputeBlockThreadAbstract

contains the deconvolved image at the current iteration, copied into a block from outside (outofbounds is mirror)

getPsiCopyBlockSize() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getPSIDimensions() - Method in class net.preibisch.mvrecon.process.deconvolution.DeconViews

getPsiFactory() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getPsiFile() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getPsiInitFactory() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getQuality() - Method in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.PairwiseStitchingResult.CrossCorrelationPairwiseQualityMeasure

getQuality() - Method in interface net.preibisch.mvrecon.fiji.spimdata.stitchingresults.PairwiseStitchingResult.PairwiseQualityMeasure

getQuality() - Method in class net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.QualityPointMatch

getQualityList() - Method in class net.preibisch.mvrecon.process.quality.FRCRealRandomAccessible

getRadius() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.InterestPointGroupingMinDistance

getRandomAccessibleInterval() - Method in class net.preibisch.mvrecon.process.quality.FRCRealRandomAccessible

getRandomAccessibleInterval(int, double) - Method in class net.preibisch.mvrecon.process.quality.FRCRealRandomAccessible

getRangeRepresentation(Pair<Integer, Integer>) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition

getRatioOfDistance() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.fastrgldm.FRGLDMParameters

getRatioOfDistance() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.geometrichashing.GeometricHashingParameters

getRatioOfDistance() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm.RGLDMParameters

getReader() - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

getRealRandomAccessible() - Method in class net.preibisch.mvrecon.process.quality.FRCRealRandomAccessible

getRealSum() - Method in class net.preibisch.mvrecon.process.deconvolution.util.FusedNonZeroRandomAccess

getRedundancy() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.fastrgldm.FRGLDMParameters

getRedundancy() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.geometrichashing.GeometricHashingParameters

getRedundancy() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm.RGLDMParameters

getReferenceTimePoint() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.statistics.GraphFrame

getReferenceTimePoint() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.statistics.MouseListenerTimelapse

getReferenceTimepointId() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.range.ReferenceTimepointRange

getRelativeLabel() - Method in class net.preibisch.mvrecon.process.interestpointremoval.RelativeThinOutParameters

getRequiredNumNeighbors() - Method in interface net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.Matcher

getRequiredNumNeighbors() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.SimpleMatcher

getRequiredNumNeighbors() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.SubsetMatcher

getResolutions() - Method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.ParametersResaveHDF5

getResolutionS0(double[], double, double) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.OMEZarrAttributes

getReusableRenderResult() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough.MyTarget

getRigidModel3D(Transform3D) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

getRoatationFromMetadata(Angle) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.grid.RegularTranformHelpers

getRotation(Vector3d, Vector3d) - Static method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxReorientation

Computes a Transform3D that will rotate vector v0 into the direction of vector v1.

getRotationAxis(RigidModel3D) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

WARNING: This fails on older MACs, in this case remove: Check if Apple's out-dated Java 3D version 1.3 is installed in System/Library/Java/Extensions/ on your Mac.

getRotationScale(Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Gets the upper 3x3 values of this matrix and places them into the matrix m1.

getRotationScale(Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Gets the upper 3x3 values of this matrix and places them into the matrix m1.

getRotationScale(Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Gets the upper 3x3 values of this matrix and places them into the matrix m1.

getRotationScale(Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Gets the upper 3x3 values of this matrix and places them into the matrix m1.

getRotationScale(Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Gets the upper 3x3 values of this matrix and places them into the matrix m1.

getRow(int, double[]) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Copies the matrix values in the specified row into the array parameter.

getRow(int, double[]) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Copies the matrix values in the specified row into the array parameter.

getRow(int, float[]) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Copies the matrix values in the specified row into the array parameter.

getRow(int, float[]) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Copies the matrix values in the specified row into the array parameter.

getRow(int, Vector3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Copies the matrix values in the specified row into the vector parameter.

getRow(int, Vector3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Copies the matrix values in the specified row into the vector parameter.

getRow(int, Vector4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Copies the matrix values in the specified row into the vector parameter.

getRow(int, Vector4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Copies the matrix values in the specified row into the vector parameter.

getRowCount() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedTableModel

getRowCount() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

getRowCount() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MissingViewsTableModelDecorator

getRowCount() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MultiViewTableModelDecorator

getRowCount() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationTableModel

getSampler() - Method in class net.preibisch.mvrecon.imglib2.st.render.FilteredMaxDistanceSearchOnKDTree

getSampler() - Method in interface net.preibisch.mvrecon.imglib2.st.render.IntegratingNeighborSearch

Access the data of the nearest neighbor.

getSampler() - Method in class net.preibisch.mvrecon.imglib2.st.render.NearestNeighborMaxDistanceSearchOnKDTree

getScale() - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Performs an SVD normalization of this matrix to calculate and return the uniform scale factor.

getScale() - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Performs an SVD normalization of this matrix to calculate and return the uniform scale factor.

getScale() - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Performs an SVD normalization of this matrix to calculate and return the uniform scale factor.

getScale() - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Performs an SVD normalization of this matrix to calculate and return the uniform scale factor.

getScale() - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Returns the uniform scale factor of this matrix.

getScale(Vector3d) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Gets the possibly non-uniform scale components of the current transform and places them into the scale vector.

getScaling(Affine3D<?>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

getScaling(Affine3D<?>, double[]) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

getScaling(AffineGet) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

getScaling(AffineGet, double[]) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

getScaling(Transform3D) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

getScaling(Transform3D, double[]) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

getSecond() - Method in class net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.Link

getSelectedCol() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

getSelectedLabel(String[], int) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.InterestPointTools

getSelectedRow() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

getSelectedRows() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

getSelectedViews() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.selection.SelectionDialog

getSelectedViews(ExplorerWindow<?>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.ApplyTransformationPopup

getSelectedViews(ExplorerWindow<?>, boolean) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.ApplyTransformationPopup

getSelectionListener() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

getSelectionListener() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorerPanel

getSeqFile() - Method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.ParametersResaveHDF5

getSetupImgLoader(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.FileMapImgLoaderLOCI2

getSetupImgLoader(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.DefaultFlatfieldCorrectionWrappedImgLoader

getSetupImgLoader(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.MultiResolutionFlatfieldCorrectionWrappedImgLoader

getSetupImgLoader(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.SimViewImgLoader

getSetupImgLoader(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.SmartSPIMImgLoader

getSetupImgLoader(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitImgLoader

getSetupImgLoader(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitMultiResolutionImgLoader

getSetupImgLoader(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitViewerImgLoader

getSetupsPerPartition() - Method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.ParametersResaveHDF5

getShapeType(ViewId, int) - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointOverlay.InterestPointSource

getShapeType(ViewId, int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

getShortName(String) - Static method in class net.preibisch.legacy.io.IOFunctions

getShortValue(byte[], int, boolean) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoaderLOCI

getShortValueInt(byte[], int, boolean) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoaderLOCI

getSimilarity(ArrayList<PointMatch>) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.similarity.LinearDistance

getSimilarity(ArrayList<PointMatch>) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.similarity.ManhattanDistance

getSimilarity(ArrayList<PointMatch>) - Method in interface net.preibisch.mvrecon.process.pointcloud.pointdescriptor.similarity.SimilarityMeasure

getSimilarity(ArrayList<PointMatch>) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.similarity.SquareDistance

getSimilarityMeasure() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.AbstractPointDescriptor

getSimpleDialog(boolean) - Method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.BoundingBoxGUI

getSize(BasicViewSetup) - Static method in class net.preibisch.mvrecon.fiji.spimdata.ViewSetupUtils

getSizeOrLoad(BasicViewSetup, TimePoint, ImgLoader) - Static method in class net.preibisch.mvrecon.fiji.spimdata.ViewSetupUtils

getSmoothedCurve(double[][]) - Method in class net.preibisch.mvrecon.process.quality.FRC

Perform LOESS smoothing on the FRC curve

getSmoothedCurve(double[][], double, int) - Method in class net.preibisch.mvrecon.process.quality.FRC

Perform LOESS smoothing on the FRC curve.

getSource(int, int) - Method in class net.preibisch.mvrecon.fiji.plugin.interactive.MultiResolutionSource

getSourcePoints() - Method in class net.preibisch.mvrecon.process.fusion.tps.Landmarks

Get the source point coordinates.

getSourceTransform(int, int, AffineTransform3D) - Method in class net.preibisch.mvrecon.fiji.plugin.interactive.MultiResolutionSource

getSpecialColumn(ISpimDataTableModel.SpecialColumnType) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedTableModel

getSpecialColumn(ISpimDataTableModel.SpecialColumnType) - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.ISpimDataTableModel

getSpecialColumn(ISpimDataTableModel.SpecialColumnType) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MissingViewsTableModelDecorator

getSpecialColumn(ISpimDataTableModel.SpecialColumnType) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MultiViewTableModelDecorator

getSpimData() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getSpimData() - Method in interface net.preibisch.mvrecon.fiji.plugin.fusion.FusionExportInterface

getSpimData() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

getSpimData() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

getSpimData() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.ExplorerWindow

getSpimData() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorer

getSpimData() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

getSpimData() - Method in class net.preibisch.mvrecon.process.splitting.ConsensusSetCriterion

getSpimData() - Method in class net.preibisch.mvrecon.process.splitting.CrossViewCorrespondenceCriterion

getSpimData() - Method in interface net.preibisch.mvrecon.process.splitting.OctTreeSplitCriterion

getSpimDataDescription(AS, ArrayList<String>, ArrayList<HashSet<Integer>>, int) - Static method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

getSplit() - Method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.ParametersResaveHDF5

getSplittingType() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getSplittingType() - Method in interface net.preibisch.mvrecon.fiji.plugin.fusion.FusionExportInterface

0 == "Each timepoint & channel", 1 == "Each timepoint, channel & illumination", 2 == "All views together", 3 == "Each view"

getSplittingType() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

getSplittingType() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

getSquareDistance() - Method in class net.preibisch.mvrecon.imglib2.st.render.NearestNeighborMaxDistanceSearchOnKDTree

getSquareTaperedImage(ImageProcessor) - Method in class net.preibisch.mvrecon.process.quality.FRC

Applies a Tukey window function to the image and then pads it to the next square size power of two.

getStackDir() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.DHMMetaData

getStackDir() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.DHMImgLoader

getStackDir() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyDHMImgLoader

getStartPosition() - Method in class net.preibisch.mvrecon.process.fusion.ImagePortion

getState(int, int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

getStatistics() - Method in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

getStitchingResults() - Method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

getStringRepresentation() - Method in interface net.preibisch.mvrecon.fiji.datasetmanager.patterndetector.FilenamePatternDetector

getStringRepresentation() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.patterndetector.NumericalFilenamePatternDetector

getSubdivisions() - Method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.ParametersResaveHDF5

getSubsets() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.PairwiseSetup

getSubsetSize() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.SubsetMatcher

getSummaryMetadata() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

getSummaryMetadata() - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

getSupportedCompressions() - Static method in class net.preibisch.mvrecon.process.export.ExportLarge2DTIFF

getTable() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointExplorerPanel

getTable() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationExplorerPanel

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointExplorerPanel.MyRenderer

getTableModel() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

getTableModel() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointExplorerPanel

getTag() - Method in class net.preibisch.mvrecon.fiji.spimdata.EmptyEntity

getTargetPoints() - Method in class net.preibisch.mvrecon.process.fusion.tps.Landmarks

Get the target point coordinates.

getTargetW() - Method in interface net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonrigidIP

getTargetW() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.SimpleReferenceIP

getTasksList(List<Pair<V, V>>, Map<V, ? extends Map<String, ?>>, boolean) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.MatcherPairwiseTools

getTemplate() - Method in class net.preibisch.legacy.mpicbg.SketchTikZFileObject

getTile(BasicViewDescription<?>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyFileMapImgLoaderLOCI

getTile(BasicViewDescription<?>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyLightSheetZ1ImgLoader

getTilesToProcess() - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.LoadParseQueryXML

getTimepointInt(String) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData

getTimepoints() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.DHMMetaData

getTimepoints() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.DHMImgLoader

getTimepoints() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyDHMImgLoader

getTimepointsPerPartition() - Method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.ParametersResaveHDF5

getTimePointsToProcess() - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

getTimepointString(int) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData

getTimestampsAndZPlanes(boolean) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.DHMMetaData

Go through the directories and make sure all timestamps are present for all ampliude/phase-stacks

getTitle() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.DHM

getTitle() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition

getTitle() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.LightSheetZ1

getTitle() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.MicroManager

getTitle() - Method in interface net.preibisch.mvrecon.fiji.datasetmanager.MultiViewDatasetDefinition

Defines the title under which it will be displayed in the list of available multi-view dataset definitions

getTitle() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.OMEZARR

getTitle() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.SimView

getTitle() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM

getTitle() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListImageJ

getTitle() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListLOCI

getTitle() - Method in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox

getTitle() - Method in class net.preibisch.mvrecon.process.deconvolution.DeconView

getTitle(int, Group<ViewDescription>) - Static method in class net.preibisch.mvrecon.fiji.plugin.Image_Fusion

getToleranceMode() - Method in class net.preibisch.mvrecon.process.splitting.ConsensusSetCriterion

getToleranceValue() - Method in class net.preibisch.mvrecon.process.splitting.ConsensusSetCriterion

getTotalAttempts() - Method in class net.preibisch.mvrecon.process.export.RetryTracker

getTotalAvgQuality() - Method in class net.preibisch.mvrecon.process.quality.FRCRealRandomAccessible

getTotalDeviceMemory() - Method in class net.preibisch.mvrecon.process.cuda.CUDADevice

getTransform() - Method in class net.preibisch.mvrecon.fiji.plugin.apply.BigDataViewerTransformationWindow

getTransform() - Method in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.PairwiseStitchingResult

getTransform() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

getTransform() - Method in class net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.Link

getTransform(V, Map<V, ViewRegistration>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

getTransform3D(M) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

getTransform3D(Affine3D<?>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

getTransform3D(AffineGet) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

getTransformedCorrespondingInterestPoints(V, Map<V, ViewRegistration>, Map<V, ViewInterestPointLists>, Map<V, String>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

getTransformedNormalizedPSF(ArrayImg<T, ?>, AffineTransform3D) - Static method in class net.preibisch.mvrecon.process.psf.PSFExtraction

getTransformedNormalizedPSF(AffineTransform3D) - Method in class net.preibisch.mvrecon.process.psf.PSFExtraction

getType() - Method in class net.preibisch.mvrecon.fiji.plugin.interactive.MultiResolutionSource

getType() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.FlatFieldCorrectedRandomAccessibleInterval

getType() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.VirtuallyNormalizedRandomAccessibleInterval

getType() - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccessibleInterval

getType() - Method in class net.preibisch.mvrecon.process.fusion.blk.tps.BlendingFunction3D

getType() - Method in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccessible

getType() - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval

getType() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGrid

getType() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGrid

getType() - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputGeneralRandomAccessible

getType() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccessibleInterval

getType() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccessible

getType() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.ContentBasedFFTRealRandomAccessible

getType() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.ContentBasedRealRandomAccessible

getType() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.InterpolatingNonRigidRasteredRandomAccessible

getType() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.NonRigidRasteredRandomAccessible

getType() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.TransformedRasteredRandomAccessible

getType() - Method in class net.preibisch.mvrecon.process.quality.FRCRealRandomAccessible

getType() - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Returns the type of this matrix as an or'ed bitmask of of all of the type classifications to which it belongs.

getType() - Method in class util.StackingRealRandomAccessible

getUnderlyingImageLoader(SpimData2) - Static method in class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion

getUnderlyingImgLoader() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitImgLoader

getUnderlyingImgLoader() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitMultiResolutionImgLoader

getUnderlyingImgLoader() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitViewerImgLoader

getUnit() - Method in interface net.preibisch.mvrecon.process.export.Calibrateable

getUnit() - Method in class net.preibisch.mvrecon.process.export.DisplayImage

getUnit() - Method in class net.preibisch.mvrecon.process.export.ExportN5Api

getUnit() - Method in class net.preibisch.mvrecon.process.export.Save3dTIFF

getUnnormalizedWeights() - Method in class net.preibisch.mvrecon.process.deconvolution.util.ProcessInputImages

getUseRelativeFRC() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

getUseTikhonov() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getUseW() - Method in class net.preibisch.legacy.registration.detection.AbstractDetection

getV() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.GroupedInterestPoint

getValueAt(int, int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedTableModel

getValueAt(int, int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

getValueAt(int, int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MissingViewsTableModelDecorator

getValueAt(int, int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MultiViewTableModelDecorator

getValueAt(int, int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationTableModel

getValuesForVariable(int) - Method in interface net.preibisch.mvrecon.fiji.datasetmanager.patterndetector.FilenamePatternDetector

getValuesForVariable(int) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.patterndetector.NumericalFilenamePatternDetector

getVDComparator(Class<? extends Entity>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.SpimDataTools

get a Comparator to sort ViewDescriptions by the ID of the Attribute of class cl

getVDListComparator(Class<? extends Entity>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.SpimDataTools

get a Comparator of Lists of ViewDescriptions the first elements of the lists are compared by the ID of their Attribute of class cl (it is a good idea to sort the lists themselves first)

getVectorDiff(double[], double[]) - Static method in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.VectorUtil

getVectorLength(double[]) - Static method in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.VectorUtil

getVectorSum(double[], double[]) - Static method in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.VectorUtil

getVersion() - Static method in class net.preibisch.mvrecon.Version

getViewId() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.CorrespondingIP

getViewId(String) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

getViewId(SequenceDescription, TimePoint, Channel, Angle, Illumination, Tile) - Static method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

getViewIds() - Method in class net.preibisch.mvrecon.fiji.spimdata.GroupedViews

getViewIdsToProcess() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.InterestPointDetectionGUI

getViewIdToPath() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AllenOMEZarrLoader

getViewInterestPointLists(int, int) - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.ViewInterestPoints

getViewInterestPointLists(ViewId) - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.ViewInterestPoints

getViewInterestPoints() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

getViewInterestPoints() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.ViewInterestPoints

getViewInterestPoints() - Method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

getViewRegistrations() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationTableModel

getViews() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getViews() - Method in interface net.preibisch.mvrecon.fiji.plugin.fusion.FusionExportInterface

getViews() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

getViews() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

getViews() - Method in class net.preibisch.mvrecon.process.deconvolution.DeconViews

getViews() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

getViews() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.PairwiseSetup

getViewSelection(String, String) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

getViewSetup(List<? extends ViewSetup>, Channel, Angle, Illumination, Tile) - Static method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

getViewSetupsToProcess() - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

getViewsSorted(Collection<V>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

getVolatileImage(int, int, ImgLoaderHint...) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitViewerSetupImgLoader

getVolatileImageType() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitViewerSetupImgLoader

getVoxelDimensions() - Method in class net.preibisch.mvrecon.fiji.plugin.interactive.MultiResolutionSource

getVoxelSize(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.FileMapImgLoaderLOCI2.FileMapSetupImgLoaderLOCI2

getVoxelSize(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.SimViewSetupImgLoader

getVoxelSize(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.SmartSPIMSetupImgLoader

getVoxelSize(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitMultiResolutionSetupImgLoader

getVoxelSize(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitSetupImgLoader

getVoxelSize(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitViewerSetupImgLoader

getVoxelSize(BasicViewSetup) - Static method in class net.preibisch.mvrecon.fiji.spimdata.ViewSetupUtils

getVoxelSize(ViewId) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AbstractImgLoader

getVoxelSizeOrLoad(BasicViewSetup, TimePoint, ImgLoader) - Static method in class net.preibisch.mvrecon.fiji.spimdata.ViewSetupUtils

getW() - Method in interface net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonrigidIP

getW() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.SimpleReferenceIP

getW() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.Quaternion

getW() - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Get the w coordinate.

getW() - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Get the w coordinate.

getWasZGrouped() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListViewDetectionState

getWeight() - Method in class net.preibisch.legacy.registration.detection.AbstractDetection

getWeight() - Method in class net.preibisch.mvrecon.process.deconvolution.DeconView

getWeightCacheType() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

getWeights() - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval

getWeights() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccessibleInterval

getWidth() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.DHMMetaData

getWidth() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough.MyTarget

getWidth() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.Calibration

getWidth() - Method in class net.preibisch.mvrecon.process.export.OpenSeaDragon.OpenSeaDragonImgLib2

getWorldCoordinates(double[], int[], long[], long[], int) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGridRandomAccess

getWorldCoordinates(double[], Localizable, long[], long[], int) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGrid

getWrappedImgLoder() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.DefaultFlatfieldCorrectionWrappedImgLoader

getWrappedImgLoder() - Method in interface net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.FlatfieldCorrectionWrappedImgLoader

getWrappedImgLoder() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.MultiResolutionFlatfieldCorrectionWrappedImgLoader

getWrappedReferencePoints() - Method in class net.preibisch.mvrecon.process.pointcloud.icp.ICP

getWrappedTargetPoints() - Method in class net.preibisch.mvrecon.process.pointcloud.icp.ICP

getX() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.Quaternion

getX() - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4d

Get value of x coordinate.

getX() - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4f

Get value of x coordinate.

getX() - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Get the x coordinate.

getX() - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Get the x coordinate.

getX() - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Get the x coordinate.

getX() - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Get the x coordinate.

getX() - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Get the x coordinate.

getXDim(int) - Static method in class net.preibisch.mvrecon.process.interestpointremoval.InteractiveProjections

getXMLFileName() - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

getXMLLabel(URI) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorerPanel

getXMLPath() - Method in class net.preibisch.mvrecon.fiji.plugin.resave.Resave_TIFF.ParametersResaveAsTIFF

getXMLRepresentation() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoints

getXMLRepresentation() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

getXMLURI() - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

getY() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.Quaternion

getY() - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4d

Get value of y coordinate.

getY() - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4f

Get value of y coordinate.

getY() - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Get the y coordinate.

getY() - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Get the y coordinate.

getY() - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Get the y coordinate.

getY() - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Get the y coordinate.

getY() - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Get the y coordinate.

getYDim(int) - Static method in class net.preibisch.mvrecon.process.interestpointremoval.InteractiveProjections

getZ() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.Quaternion

getZ() - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4d

Get value of z coordinate.

getZ() - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4f

Get value of z coordinate.

getZ() - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Get the z coordinate.

getZ() - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Get the z coordinate.

getZ() - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Get the z coordinate.

getZ() - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Get the z coordinate.

getZ() - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Get the z coordinate.

getZPlanes() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.DHMMetaData

getZPlanes() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.DHMImgLoader

getZPlanes() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyDHMImgLoader

ghParams - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.GeometricHashingGUI

GLOB_SPECIAL_CHARS - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition

GlobalErrorStatistics - Interface in net.preibisch.legacy.registration.bead.error

GlobalErrorStatisticsImpl - Class in net.preibisch.legacy.registration.bead.error

GlobalErrorStatisticsImpl() - Constructor for class net.preibisch.legacy.registration.bead.error.GlobalErrorStatisticsImpl

GlobalGUI - Interface in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global

GlobalOpt - Class in net.preibisch.mvrecon.process.interestpointregistration.global

GlobalOpt() - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.global.GlobalOpt

globalOptError() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.CenterOfMassGUI

globalOptError() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.FRGLDMGUI

globalOptError() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.GeometricHashingGUI

globalOptError() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.IterativeClosestPointGUI

globalOptError() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.LoadCorrespondencesGUI

globalOptError() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.PairwiseGUI

globalOptError() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.RGLDMGUI

GlobalOptimizationParameters - Class in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global

GlobalOptimizationParameters() - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters

GlobalOptimizationParameters(double, double, GlobalOptimizationParameters.GlobalOptType, boolean, boolean) - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters

GlobalOptimizationParameters.GlobalOptType - Enum Class in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global

GlobalOptimizationParameters.PreAlign - Enum Class in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global

GlobalOptIterative - Class in net.preibisch.mvrecon.process.interestpointregistration.global

GlobalOptIterative() - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.global.GlobalOptIterative

globalOptMaxError - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.LoadCorrespondencesGUI

globalOptParams - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.AdvancedRegistrationParameters

GlobalOptTwoRound - Class in net.preibisch.mvrecon.process.interestpointregistration.global

GlobalOptTwoRound() - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.global.GlobalOptTwoRound

goBackToInitialTransform - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough

goldenRatio - Static variable in class util.ColorStream

good - Static variable in class net.preibisch.mvrecon.fiji.plugin.util.GUIHelper

goodMsg1 - Static variable in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

GraphFrame - Class in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.statistics

GraphFrame(TimePoints, JFreeChart, int, boolean, List<SelectTimepointEntry>, ArrayList<RegistrationStatistics>) - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.statistics.GraphFrame

GRAY - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVColors

greatestCommonDivisor(long, long) - Static method in class net.preibisch.mvrecon.process.splitting.SplittingTools

GREEN - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVColors

Grid - Class in util

gridBlockCount(Interval, double[], int[]) - Static method in class net.preibisch.mvrecon.process.fusion.blk.DisplacementFieldN5Tools

Compute the per-dim count of dfield blocks for the given bbox/spacing/blockSize.

gridBlockToViewId(long[][]) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

gridCell(long[], long[], int[]) - Static method in class util.Grid

gridMoveRequested - Variable in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

GridPreset(boolean[], boolean[], String) - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.grid.RegularTranformHelpers.GridPreset

gridToDatasetBdv(int, StorageFormat) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

gridToDatasetBdv(StorageFormat) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

group - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.SingleGroupError

group(Group<V>) - Method in interface net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Grouping

group(Group<V>) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.InterestPointGrouping

Group<V> - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping

Group() - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

Group(Collection<V>) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

Group(V) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

groupA - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.GroupPairResult

groupAngles - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.Parameters

groupB - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.GroupPairResult

groupByChannel(List<ViewId>, SequenceDescription) - Static method in class net.preibisch.mvrecon.fiji.spimdata.GroupedViews

groupByChannel(List<V>, AbstractSequenceDescription<?, ? extends BasicViewDescription<?>, ?>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

groupChannels - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.BasicRegistrationParameters

groupChannels - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.Parameters

GroupedInterestPoint<V> - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping

Single interest point, extends InterestPoint to remember where it came from for grouping

GroupedInterestPoint(V, int, double[]) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.GroupedInterestPoint

GroupedRowWindow - Interface in net.preibisch.mvrecon.fiji.spimdata.explorer

GroupedViews - Class in net.preibisch.mvrecon.fiji.spimdata

GroupedViews(List<ViewId>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.GroupedViews

A group of ViewIds that represents itself as the first ViewId

groupIlluminations - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.Parameters

groupIllums - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

groupIllums - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.BasicRegistrationParameters

groupIllums() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

groupIllumsCheckbox - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorerPanel

grouping - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.GroupParameters

Grouping<V,X> - Interface in net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping

groupingParameters(Collection<Subset<ViewId>>) - Method in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

GroupPairResult(Group<ViewDescription>, Group<ViewDescription>, int, int, double, double, double) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.GroupPairResult

GroupParameters - Class in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters

GroupParameters() - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.GroupParameters

GroupParameters.InterestpointGroupingType - Enum Class in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters

groups - Variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.PairwiseSetup

groupsSpanTimepoints(Set<Group<V>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.ReferenceTimepoint

Checks if groups exist than span multiple timepoints

groupTiles - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

groupTiles - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.BasicRegistrationParameters

groupTiles - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.Parameters

groupTiles() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

groupTilesCheckbox - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorerPanel

groupTimePoints - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.AdvancedRegistrationParameters

groupZPlanes(FileListViewDetectionState, FilenamePatternDetector, List<Integer>) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil

gs - Static variable in class util.ColorStream

GUIHelper - Class in net.preibisch.mvrecon.fiji.plugin.util

GUIHelper() - Constructor for class net.preibisch.mvrecon.fiji.plugin.util.GUIHelper

gvids(Collection<?>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

gvids(Group<?>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

gzipLevel - Static variable in class net.preibisch.mvrecon.fiji.plugin.util.PluginHelper

H

hadDetections() - Method in class net.preibisch.mvrecon.process.psf.PSFExtraction

HALF_BIT - Enum constant in enum class net.preibisch.mvrecon.process.quality.FRC.ThresholdMethod

hardWeights(float, double) - Static method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccess

hasCommonScale(Map<String, Pair<DatasetAttributes, Pair<VoxelDimensions, double[]>>>) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.OMEZARR

hasCorrespondences() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5.InterestPointData

hasGroups(Collection<? extends Subset<?>>) - Static method in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

hashCode() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.AngleInfo

hashCode() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.ChannelInfo

hashCode() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.TileInfo

hashCode() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList.ViewSetupPrecursor

hashCode() - Method in class net.preibisch.mvrecon.fiji.spimdata.EmptyEntity

hashCode() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.FileMapEntry

hashCode() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoint

hashCode() - Method in class net.preibisch.mvrecon.headless.definedataset.StackList.ViewSetupPrecursor

hashCode() - Method in class net.preibisch.mvrecon.process.fusion.intensity.IntensityCorrection.SerializableRealInterval

hashCode() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.CorrespondingIP

hashCode() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

hashCode() - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4d

Returns a hash code value based on the data values in this object.

hashCode() - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4f

Returns a hash code value based on the data values in this object.

hashCode() - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Returns a hash code value based on the data values in this object.

hashCode() - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Returns a hash code value based on the data values in this object.

hashCode() - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Returns a hash code value based on the data values in this object.

hashCode() - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Returns a hash code value based on the data values in this object.

hashCode() - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Returns a hash code value based on the data values in this object.

hashCode() - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Returns a hash code value based on the data values in this object.

hashCode() - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Returns a hash code value based on the data values in this object.

hashCode() - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Returns a hash code value based on the data values in this object.

hashCode() - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Returns a hash code value based on the data values in this object.

hashCode() - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Returns a hash code value based on the data values in this object.

hasInterestPoints() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5.InterestPointData

hasMinValue - Variable in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedImgRandomAccess

hasMinValue - Variable in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedImgRandomAccessible

hasModifiedCorrespondingInterestPoints() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoints

hasModifiedInterestPoints() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoints

hasMultipleAngles - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

hasMultipleChannels - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

hasMultipleIlluminations - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

hasMultipleTiles - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

hasMultipleTimePoints - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

headline - Static variable in class net.preibisch.mvrecon.fiji.plugin.util.GUIHelper

height() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

height() - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

HelperFunctions - Class in net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive

HelperFunctions() - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.HelperFunctions

hessianMatrix3x3 - Variable in class net.preibisch.legacy.registration.bead.laplace.DoGMaximum

hideMissingViewsCheckbox - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorerPanel

HIGHEST_VIEWID_WINS - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI.FusionType

Histogram - Class in net.preibisch.mvrecon.process.interestpointremoval.histogram

Histogram(List<Double>, int, String, String) - Constructor for class net.preibisch.mvrecon.process.interestpointremoval.histogram.Histogram

HistogramListener(SpimData2, ArrayList<ViewId>, String, int) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.RemoveDetectionsPopup.HistogramListener

I

i - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList.ViewSetupPrecursor

i - Variable in class net.preibisch.mvrecon.headless.definedataset.StackList.ViewSetupPrecursor

i - Variable in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccess

i - Variable in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessFirstWins

ICP<P> - Class in net.preibisch.mvrecon.process.pointcloud.icp

Implementation of the ICP, takes anything RealLocalizable and internally uses LinkedInterestPoint to compute the ICP

ICP(List<P>, List<P>, boolean, double, double, int) - Constructor for class net.preibisch.mvrecon.process.pointcloud.icp.ICP

Also instantiates a new ICP instance, but uses the SimplePointMatchIdentification to define corresponding points.

ICP(List<P>, List<P>, double, boolean, double, double, int) - Constructor for class net.preibisch.mvrecon.process.pointcloud.icp.ICP

Also instantiates a new ICP instance, but uses the SimplePointMatchIdentification to define corresponding points.

ICP(List<P>, List<P>, PointMatchIdentification<P>, boolean, double, double, int) - Constructor for class net.preibisch.mvrecon.process.pointcloud.icp.ICP

Instantiates a new ICP object with the List of target and reference points as well as the PointMatchIdentification interface that defines how corresponding points are identified.

id - Variable in class net.preibisch.legacy.registration.detection.AbstractDetection

id - Variable in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoint

identifyChannelPairs(SpimData2, List<V>) - Static method in class net.preibisch.mvrecon.process.chromaticabberation.DetectChromaticAbberation

identifySubsets(PairwiseSetup<ViewId>, OverlapDetection<ViewId>) - Method in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

identifyViewIdPairs(SpimData2, List<V>, Pair<Channel, Channel>) - Static method in class net.preibisch.mvrecon.process.chromaticabberation.DetectChromaticAbberation

IDENTITY - Static variable in class net.preibisch.mvrecon.vecmath.Transform3D

An identity matrix.

ids - Variable in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5.InterestPointData

IFDData() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader.IFDData

IFDData() - Constructor for class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader.IFDData

IFDEntry(char, char, long, long) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader.IFDEntry

IFDEntry(char, char, long, long) - Constructor for class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader.IFDEntry

ignoreMissingViews - Static variable in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxMaximal

ignoreScaling - Variable in class net.preibisch.mvrecon.fiji.plugin.apply.BigDataViewerTransformationWindow

illumChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

ILLUMINATION_PATTERN - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

illuminations - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

illuminations - Variable in class net.preibisch.mvrecon.headless.definedataset.DefineDataSetParameters

illuminations - Variable in class net.preibisch.mvrecon.headless.definedataset.StackListParameters

illuminations() - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

illuminationsNameList - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

illuminationsNameList - Variable in class net.preibisch.mvrecon.headless.definedataset.StackList.ViewSetupPrecursor

illumsGrouped() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.ExplorerWindow

illumsGrouped() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorerPanel

Image_Deconvolution - Class in net.preibisch.mvrecon.fiji.plugin

Plugin to fuse images using transformations from the SpimData object

Image_Deconvolution() - Constructor for class net.preibisch.mvrecon.fiji.plugin.Image_Deconvolution

IMAGE_DESCRIPTION - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

IMAGE_DESCRIPTION - Static variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

Image_Fusion - Class in net.preibisch.mvrecon.fiji.plugin

Plugin to fuse images using transformations from the SpimData object

Image_Fusion() - Constructor for class net.preibisch.mvrecon.fiji.plugin.Image_Fusion

Image_Quality - Class in net.preibisch.mvrecon.fiji.plugin

Plugin to fuse images using transformations from the SpimData object

Image_Quality() - Constructor for class net.preibisch.mvrecon.fiji.plugin.Image_Quality

IMAGE_SPLITTING_NAME - Static variable in class net.preibisch.mvrecon.process.splitting.SplittingTools

ImageCorrelationPointMatchCreator - Class in net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.strong

ImageCorrelationPointMatchCreator(Collection<? extends PairwiseStitchingResult<? extends ViewId>>) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.strong.ImageCorrelationPointMatchCreator

ImageCorrelationPointMatchCreator(Collection<? extends PairwiseStitchingResult<? extends ViewId>>, double) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.strong.ImageCorrelationPointMatchCreator

imageFiles - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.grid.RegularTranformHelpers

ImagePlusListener - Class in net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive

ImagePlusListener(InteractiveDoG) - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.ImagePlusListener

ImagePortion - Class in net.preibisch.mvrecon.process.fusion

ImagePortion(long, long) - Constructor for class net.preibisch.mvrecon.process.fusion.ImagePortion

images - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.grid.RegularTranformHelpers

imageSigmaX - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

imageSigmaX - Variable in class net.preibisch.mvrecon.process.interestpointdetection.methods.InterestPointParameters

imageSigmaY - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

imageSigmaY - Variable in class net.preibisch.mvrecon.process.interestpointdetection.methods.InterestPointParameters

imageSigmaZ - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

imageSigmaZ - Variable in class net.preibisch.mvrecon.process.interestpointdetection.methods.InterestPointParameters

imageSizes() - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

imaginaryEigenValues - Variable in class net.preibisch.legacy.registration.bead.laplace.RejectStatistics

img - Variable in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedImgRandomAccess

img - Variable in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedImgRandomAccessible

img - Variable in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

img - Variable in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

imgDataTypeChoice - Static variable in class net.preibisch.mvrecon.process.fusion.FusionTools

imgExport - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

imgExport - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

imgExport - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

ImgExport - Interface in net.preibisch.mvrecon.process.export

imgExportDescriptions - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

imgExportDescriptions - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

imgExportDescriptions - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

imgFactory1 - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AbstractImgFactoryImgLoader

imgFFT() - Method in class util.FFTConvolution

IMGLIB2CONTAINER_PATTERN_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoLightSheetZ1ImgLoader

IMGLIB2CONTAINER_PATTERN_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoMicroManagerImgLoader

ImgLib2Temp - Class in net.preibisch.mvrecon.fiji

ImgLib2Temp() - Constructor for class net.preibisch.mvrecon.fiji.ImgLib2Temp

ImgLib2Temp.Pair<A,B> - Interface in net.preibisch.mvrecon.fiji

ImgLib2Temp.Triple<A,B,C> - Interface in net.preibisch.mvrecon.fiji

ImgLib2Temp.ValuePair<A,B> - Class in net.preibisch.mvrecon.fiji

ImgLib2Temp.ValueTriple<A,B,C> - Class in net.preibisch.mvrecon.fiji

ImgLib2Tools - Class in util

ImgLib2Tools() - Constructor for class util.ImgLib2Tools

imgloader - Variable in class net.preibisch.mvrecon.process.interestpointdetection.methods.InterestPointParameters

imgMaxX - Variable in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccess

imgMaxY - Variable in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccess

imgMaxZ - Variable in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccess

imgMinX - Variable in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccess

imgMinY - Variable in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccess

imgMinZ - Variable in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccess

imgtype - Variable in class net.preibisch.mvrecon.fiji.plugin.Display_View

imgTypes - Static variable in class net.preibisch.mvrecon.fiji.plugin.Display_View

imp - Variable in class net.preibisch.mvrecon.process.interestpointremoval.InteractiveProjections

incIndex() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

incIndex() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

incIndex(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

incIndex(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

increaseCount() - Method in class net.preibisch.mvrecon.fiji.plugin.Specify_Calibration.Cal

increasing - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.grid.RegularTranformHelpers.GridPreset

increasing - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.grid.RegularTranformHelpers.RegularTranslationParameters

INDEPENDENT - Enum constant in enum class net.preibisch.mvrecon.process.deconvolution.DeconViewPSF.PSFTYPE

independentCopy() - Method in class net.preibisch.mvrecon.process.fusion.blk.tps.BlendingFunction3D

independentCopy() - Method in class net.preibisch.mvrecon.process.fusion.blk.tps.MaskingFunction3D

index - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.ChannelOrIlluminationInfo

index - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.TileOrAngleInfo

index - Static variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.AbstractPointDescriptor

index() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

index() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

INDEX_MAP_HEADER - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

INDEX_MAP_HEADER - Static variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

INDEX_MAP_OFFSET_HEADER - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

INDEX_MAP_OFFSET_HEADER - Static variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

indices() - Method in class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.MatchIndices

Get the internal index array.

IndividualTimepointGUI - Class in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global

IndividualTimepointGUI(SpimData2) - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.IndividualTimepointGUI

IndividualTimepoints - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation

IndividualTimepoints(List<ViewId>, Set<Group<ViewId>>) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.IndividualTimepoints

init() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoader

init(Converter<FloatType, T>, BasicImgLoader, Collection<? extends ViewId>, Map<ViewId, ? extends BasicViewDescription<?>>, Map<ViewId, Landmarks>, FusionGUI.FusionType, double, int, Comparator<ViewId>, Map<ViewId, Coefficients>, Interval, T, int[]) - Static method in class net.preibisch.mvrecon.process.fusion.blk.BlkThinPlateSplineFusion

TODO javadoc

init(Converter<FloatType, T>, BasicImgLoader, Collection<? extends ViewId>, Map<ViewId, ? extends AffineTransform3D>, Map<ViewId, ? extends BasicViewDescription<?>>, FusionGUI.FusionType, double, int, Map<ViewId, AffineModel1D>, Interval, T, int[]) - Static method in class net.preibisch.mvrecon.process.fusion.blk.BlkAffineFusion

TODO javadoc

init(Converter<FloatType, T>, BasicImgLoader, Collection<? extends ViewId>, Map<ViewId, ? extends AffineTransform3D>, Map<ViewId, ? extends BasicViewDescription<?>>, FusionGUI.FusionType, int, Map<ViewId, AffineModel1D>, Interval, T, int[]) - Static method in class net.preibisch.mvrecon.process.fusion.lazy.LazyAffineFusion

init(Converter<FloatType, T>, BasicImgLoader, Map<ViewId, AffineTransform3D>, Map<ViewId, ViewInterestPointLists>, Map<ViewId, ? extends BasicViewDescription<?>>, Collection<? extends ViewId>, Collection<? extends ViewId>, List<String>, FusionGUI.FusionType, boolean, long[], double, boolean, int, Map<? extends ViewId, AffineModel1D>, ExecutorService, Interval, T, int[]) - Static method in class net.preibisch.mvrecon.process.fusion.lazy.LazyNonRigidFusion

init(Converter<FloatType, T>, SplitViewerImgLoader, Collection<? extends ViewId>, Map<ViewId, ViewRegistration>, Map<ViewId, ? extends BasicViewDescription<?>>, FusionGUI.FusionType, int, double, int, Map<Integer, Integer>, Map<ViewId, Coefficients>, Interval, T, int[]) - Static method in class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion

Backward-compatible overload — center landmarks only (no correspondence-based midpoint landmarks).

init(Converter<FloatType, T>, SplitViewerImgLoader, Collection<? extends ViewId>, Map<ViewId, ViewRegistration>, Map<ViewId, ? extends BasicViewDescription<?>>, FusionGUI.FusionType, int, double, int, Map<Integer, Integer>, Map<ViewId, Coefficients>, Interval, T, int[], ViewInterestPoints, String, int) - Static method in class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion

Backward-compatible overload — correspondence midpoints, no corner anchors.

init(Converter<FloatType, T>, SplitViewerImgLoader, Collection<? extends ViewId>, Map<ViewId, ViewRegistration>, Map<ViewId, ? extends BasicViewDescription<?>>, FusionGUI.FusionType, int, double, int, Map<Integer, Integer>, Map<ViewId, Coefficients>, Interval, T, int[], ViewInterestPoints, String, int, boolean, double) - Static method in class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion

Backward-compatible overload — corner anchors with N=2 (corners only).

init(Converter<FloatType, T>, SplitViewerImgLoader, Collection<? extends ViewId>, Map<ViewId, ViewRegistration>, Map<ViewId, ? extends BasicViewDescription<?>>, FusionGUI.FusionType, int, double, int, Map<Integer, Integer>, Map<ViewId, Coefficients>, Interval, T, int[], ViewInterestPoints, String, int, boolean, double, int) - Static method in class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion

Backward-compatible overload — no landmark visitor.

init(Converter<FloatType, T>, SplitViewerImgLoader, Collection<? extends ViewId>, Map<ViewId, ViewRegistration>, Map<ViewId, ? extends BasicViewDescription<?>>, FusionGUI.FusionType, int, double, int, Map<Integer, Integer>, Map<ViewId, Coefficients>, Interval, T, int[], ViewInterestPoints, String, int, boolean, double, int, int[], int[], Consumer<SplitImgLoaderThinPlateSplineFusion.LandmarkRecord>) - Static method in class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion

init(Converter<FloatType, T>, SplitViewerImgLoader, Collection<? extends ViewId>, Map<ViewId, ViewRegistration>, Map<ViewId, ? extends BasicViewDescription<?>>, FusionGUI.FusionType, int, double, int, Map<Integer, Integer>, Map<ViewId, Coefficients>, Interval, T, int[], ViewInterestPoints, String, int, boolean, double, int, Consumer<SplitImgLoaderThinPlateSplineFusion.LandmarkRecord>) - Static method in class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion

Backward-compatible overload — visitor only, no per-split schedule.

init(RandomAccessible<T>, Interval, T, double[], int[]) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.methods.lazygauss.LazyGauss

init(RandomAccessible<T>, Interval, T, int[], int) - Static method in class net.preibisch.mvrecon.process.downsampling.lazy.LazyDownsample2x

init(RandomAccessible<T>, Interval, T, int[], int) - Static method in class net.preibisch.mvrecon.process.downsampling.lazy.LazyHalfPixelDownsample2x

init(RandomAccessible<T>, RandomAccessible<T>, Interval, T, double[], int[]) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.methods.lazygauss.LazyWeightedGauss

init(SmartSPIM.SmartSPIMMetaData, int, int, int) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.smartspim.LazySmartSpimLoader

init(DeconViews, int[]) - Method in class net.preibisch.mvrecon.process.deconvolution.DeconViewPSF

Init the PSF, once the Views object contains all views

initBrightness(double, double, ViewerFrame) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BDVPopup

set BDV brightness by sampling the mid z plane (and 1/4 and 3/4 if z is large enough ) of the currently selected source (typically the first source) and getting quantiles from intensity histogram (slightly modified version of InitializeViewerState.initBrightness)

initComponent() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

initComponent() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationExplorerPanel

initComponent() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorerPanel

initComponent(ViewInterestPoints) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointExplorerPanel

initGlobalOpt(M, PointMatchCreator, Collection<ViewId>, Collection<Group<ViewId>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.global.GlobalOpt

initInteractiveKit() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoG

Initialize the image kit - DoG and RANSAC windows to adjust the parameters

initLazy(Consumer<RandomAccessibleInterval<T>>, Interval, int[], T) - Static method in class net.preibisch.mvrecon.process.fusion.lazy.LazyFusionTools

initN5Writing - Static variable in class net.preibisch.mvrecon.fiji.spimdata.XmlIoSpimData2

initOutputFile(String, String) - Static method in class net.preibisch.legacy.mpicbg.SketchTikZFileObject

initPopups() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

initPopups() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorerPanel

initSetupViewIdName(AbstractSpimData<?>, BasicViewSetup, List<ConverterSetup>, List<SourceAndConverter<?>>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BDVSourceNaming

Mirrors BDV-core's private BigDataViewer.initSetupNumericType but uses BDVSourceNaming.viewIdSourceName(BasicViewSetup, AbstractSequenceDescription) for the source name.

initTransform(int, int, boolean, ViewerState) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BDVPopup

initTransform(ViewerPanel) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BDVPopup

initWasSuccessful() - Method in class net.preibisch.mvrecon.process.deconvolution.MultiViewDeconvolution

initWasSuccessful() - Method in class net.preibisch.mvrecon.process.deconvolution.MultiViewDeconvolutionMul

initWithIntensityCoefficients(Converter<FloatType, T>, BasicImgLoader, Collection<? extends ViewId>, Map<ViewId, ? extends AffineTransform3D>, Map<ViewId, ? extends BasicViewDescription<?>>, FusionGUI.FusionType, double, Map<Integer, Integer>, int, Map<ViewId, Coefficients>, Interval, T, int[]) - Static method in class net.preibisch.mvrecon.process.fusion.blk.BlkAffineFusion

initWithLoadedDfields(Converter<FloatType, T>, BasicImgLoader, Collection<? extends ViewId>, Map<ViewId, ? extends BasicViewDescription<?>>, Map<ViewId, AffineTransform3D>, Map<ViewId, Interval>, Map<ViewId, DisplacementFields.TransformedDisplacementField<D>>, FusionGUI.FusionType, double, int, Comparator<ViewId>, Map<ViewId, Coefficients>, Interval, T, int[]) - Static method in class net.preibisch.mvrecon.process.fusion.blk.BlkThinPlateSplineFusion

Entry point that accepts pre-sampled (un-offset) displacement fields instead of building them from landmarks.

initWithLoadedDfields(Converter<FloatType, T>, SplitViewerImgLoader, Collection<? extends ViewId>, Map<ViewId, ? extends BasicViewDescription<?>>, Map<ViewId, Interval>, Map<ViewId, DisplacementFields.TransformedDisplacementField<D>>, FusionGUI.FusionType, double, int, Map<Integer, Integer>, Map<ViewId, Coefficients>, Interval, T, int[], Map<ViewId, AffineTransform3D>) - Static method in class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion

Same as SplitImgLoaderThinPlateSplineFusion.init(net.imglib2.converter.Converter<net.imglib2.type.numeric.real.FloatType, T>, net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitViewerImgLoader, java.util.Collection<? extends mpicbg.spim.data.sequence.ViewId>, java.util.Map<mpicbg.spim.data.sequence.ViewId, mpicbg.spim.data.registration.ViewRegistration>, java.util.Map<mpicbg.spim.data.sequence.ViewId, ? extends mpicbg.spim.data.generic.sequence.BasicViewDescription<?>>, net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI.FusionType, int, double, int, java.util.Map<java.lang.Integer, java.lang.Integer>, java.util.Map<mpicbg.spim.data.sequence.ViewId, net.preibisch.mvrecon.process.fusion.intensity.Coefficients>, net.imglib2.Interval, T, int[]) but accepts pre-built per-underlying-view dfields and approximate affines (e.g. loaded from disk after a distributed Phase-1.5 materialization).

inlierRatioMax - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoG

inlierRatioMin - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoG

inputBytePerPixel(ViewId, SpimData2) - Static method in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

inRange(V, V) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.range.AllInRange

inRange(V, V) - Method in interface net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.range.RangeComparator

inRange(V, V) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.range.ReferenceTimepointRange

inRange(V, V) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.range.TimepointRange

instantiate(ViewId, boolean, Dimensions, List<ViewSetup>) - Method in interface net.preibisch.mvrecon.process.n5api.SpimData2Tools.InstantiateViewSetup

instantiate(ViewId, boolean, Dimensions, List<ViewSetup>) - Method in class net.preibisch.mvrecon.process.n5api.SpimData2Tools.InstantiateViewSetupBigStitcher

instantiate(ViewId, boolean, Dimensions, List<ViewSetup>) - Method in class net.preibisch.mvrecon.process.n5api.SpimData2Tools.InstantiateViewSetupBigStitcherSpark

instantiatefromXML(URI, String) - Static method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoints

instantiateImageReader() - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyLightSheetZ1ImgLoader

instantiateImg(long[], T) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoader

instantiateN5Reader(StorageFormat, URI) - Static method in class util.URITools

instantiateN5Writer(StorageFormat, URI) - Static method in class util.URITools

InstantiateViewSetupBigStitcher(int) - Constructor for class net.preibisch.mvrecon.process.n5api.SpimData2Tools.InstantiateViewSetupBigStitcher

InstantiateViewSetupBigStitcherSpark(String, String, String, String) - Constructor for class net.preibisch.mvrecon.process.n5api.SpimData2Tools.InstantiateViewSetupBigStitcherSpark

integral(double[][]) - Static method in class net.preibisch.mvrecon.process.quality.FRCRealRandomAccessible

IntegratingNeighborSearch<T> - Interface in net.preibisch.mvrecon.imglib2.st.render

Integrating Nearest-neighbor search in an Euclidean space.

IntegratingNeighborSearchInterpolator<T> - Class in net.preibisch.mvrecon.imglib2.st.render

IntegratingNeighborSearchInterpolator(IntegratingNeighborSearch<T>) - Constructor for class net.preibisch.mvrecon.imglib2.st.render.IntegratingNeighborSearchInterpolator

IntegratingNeighborSearchInterpolatorFactory<T> - Class in net.preibisch.mvrecon.imglib2.st.render

IntegratingNeighborSearchInterpolatorFactory() - Constructor for class net.preibisch.mvrecon.imglib2.st.render.IntegratingNeighborSearchInterpolatorFactory

intensity - Variable in class net.preibisch.legacy.segmentation.SimplePeak

Intensity_Adjustment - Class in net.preibisch.mvrecon.fiji.plugin

Intensity_Adjustment() - Constructor for class net.preibisch.mvrecon.fiji.plugin.Intensity_Adjustment

INTENSITYADJ_SETUP_ATTRIBUTE_NAME - Static variable in class net.preibisch.mvrecon.fiji.spimdata.intensityadjust.XmlKeysIntensityAdjustments

INTENSITYADJ_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.intensityadjust.XmlKeysIntensityAdjustments

INTENSITYADJ_TIMEPOINT_ATTRIBUTE_NAME - Static variable in class net.preibisch.mvrecon.fiji.spimdata.intensityadjust.XmlKeysIntensityAdjustments

INTENSITYADJ_VALUE_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.intensityadjust.XmlKeysIntensityAdjustments

IntensityAdjuster - Class in net.preibisch.mvrecon.process.fusion.intensityadjust

IntensityAdjuster(AffineModel1D) - Constructor for class net.preibisch.mvrecon.process.fusion.intensityadjust.IntensityAdjuster

intensityAdjustment(SpimData2, List<ViewId>) - Method in class net.preibisch.mvrecon.fiji.plugin.Intensity_Adjustment

intensityAdjustment(SpimData2, List<ViewId>, String, boolean) - Method in class net.preibisch.mvrecon.fiji.plugin.Intensity_Adjustment

IntensityAdjustmentPopup - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

IntensityAdjustmentPopup() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.IntensityAdjustmentPopup

IntensityAdjustmentPopup.MyActionListener - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

IntensityAdjustments - Class in net.preibisch.mvrecon.fiji.spimdata.intensityadjust

IntensityAdjustments() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.intensityadjust.IntensityAdjustments

IntensityAdjustments(HashMap<ViewId, AffineModel1D>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.intensityadjust.IntensityAdjustments

IntensityAdjustmentTools - Class in net.preibisch.mvrecon.process.fusion.intensityadjust

IntensityAdjustmentTools() - Constructor for class net.preibisch.mvrecon.process.fusion.intensityadjust.IntensityAdjustmentTools

IntensityCorrection - Class in net.preibisch.mvrecon.process.fusion.intensity

IntensityCorrection() - Constructor for class net.preibisch.mvrecon.process.fusion.intensity.IntensityCorrection

IntensityCorrection.SerializableRealInterval - Class in net.preibisch.mvrecon.process.fusion.intensity

InteractiveDoG - Class in net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive

InteractiveDoG(ImagePlus, InteractiveDoGParams) - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoG

InteractiveDoG(ImagePlus, InteractiveDoGParams, double, double) - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoG

Triggers the interactive radial symmetry plugin Single-channel imageplus, 2d or 3d or 4d

InteractiveDoG.ValueChange - Enum Class in net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive

InteractiveDoGParams - Class in net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive

InteractiveDoGParams() - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoGParams

InteractiveListener(int) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.RemoveDetectionsPopup.InteractiveListener

InteractiveProjections - Class in net.preibisch.mvrecon.process.interestpointremoval

InteractiveProjections(SpimData2, ViewDescription, String, String, int) - Constructor for class net.preibisch.mvrecon.process.interestpointremoval.InteractiveProjections

InteractiveProjections.FinishedButtonListener - Class in net.preibisch.mvrecon.process.interestpointremoval

InteractiveProjections.RemoveInsideROIButtonListener - Class in net.preibisch.mvrecon.process.interestpointremoval

INTEREST_POINT_COLUMN - Enum constant in enum class net.preibisch.mvrecon.fiji.spimdata.explorer.ISpimDataTableModel.SpecialColumnType

Interest_Point_Detection - Class in net.preibisch.mvrecon.fiji.plugin

Plugin to detect interest points, store them on disk, and link them into the XML Different plugins to detect interest points are supported, needs to implement the InterestPointDetectionGUI interface

Interest_Point_Detection() - Constructor for class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Detection

Interest_Point_Registration - Class in net.preibisch.mvrecon.fiji.plugin

Interest_Point_Registration() - Constructor for class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

InterestPoint - Class in net.preibisch.mvrecon.fiji.spimdata.interestpoints

Single interest point, extends mpicbg Point by an id

InterestPoint(int, double[]) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoint

InterestPointData(int, int, String, int[], double[][], ArrayList<CorrespondingInterestPoints>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5.InterestPointData

InterestPointDetectionGUI - Class in net.preibisch.mvrecon.fiji.plugin.interestpointdetection

InterestPointDetectionGUI(SpimData2, List<ViewId>) - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.InterestPointDetectionGUI

InterestPointExplorer<AS> - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint

InterestPointExplorer(URI, XmlIoSpimData2, FilteredAndGroupedExplorer<AS>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointExplorer

InterestPointExplorerPanel - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint

InterestPointExplorerPanel(ViewInterestPoints, FilteredAndGroupedExplorer<?>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointExplorerPanel

InterestPointExplorerPanel.MyRenderer - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint

InterestPointGrouping<V> - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping

Interface for grouping interest points from multiple views that are in one group

InterestPointGrouping(Map<V, HashMap<String, Collection<InterestPoint>>>) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.InterestPointGrouping

InterestPointGroupingAll<V> - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping

The simplest way to group interest points, just add them all (this will create problems in overlaps)

InterestPointGroupingAll(Map<V, HashMap<String, Collection<InterestPoint>>>) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.InterestPointGroupingAll

InterestPointGroupingMinDistance<V> - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping

The simplest way to group interest points, just add them all (this will create problems in overlaps)

InterestPointGroupingMinDistance(double, Map<V, HashMap<String, Collection<InterestPoint>>>) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.InterestPointGroupingMinDistance

InterestPointGroupingMinDistance(Map<V, HashMap<String, Collection<InterestPoint>>>) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.InterestPointGroupingMinDistance

InterestPointMatchCreator - Class in net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.strong

InterestPointMatchCreator(List<? extends Pair<? extends Pair<ViewId, ViewId>, ? extends PairwiseResult<?>>>, Map<ViewId, ? extends Map<String, Double>>) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.strong.InterestPointMatchCreator

interestpointOverlapChoices - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.BasicRegistrationParameters

interestPointOverlapType - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.BasicRegistrationParameters

InterestPointOverlay - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint

InterestPointOverlay(ViewerPanel, Collection<? extends InterestPointOverlay.InterestPointSource>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointOverlay

InterestPointOverlay.InterestPointSource - Interface in net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint

InterestPointParameters - Class in net.preibisch.mvrecon.process.interestpointdetection.methods

InterestPointParameters() - Constructor for class net.preibisch.mvrecon.process.interestpointdetection.methods.InterestPointParameters

InterestPointParameters(Collection<ViewDescription>, ImgLoader) - Constructor for class net.preibisch.mvrecon.process.interestpointdetection.methods.InterestPointParameters

InterestPoints - Class in net.preibisch.mvrecon.fiji.spimdata.interestpoints

A list of interest points for a certain label, can save and load from textfile as specified in the XML

InterestPoints(URI) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoints

InterestPointsExplorerPopup - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

InterestPointsExplorerPopup() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.InterestPointsExplorerPopup

InterestPointsExplorerPopup.MyActionListener - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

InterestPointsN5 - Class in net.preibisch.mvrecon.fiji.spimdata.interestpoints

InterestPointsN5(URI, String) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

InterestPointsN5.InterestPointData - Class in net.preibisch.mvrecon.fiji.spimdata.interestpoints

Serializable data container for interest points and correspondences.

InterestPointTableModel - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint

InterestPointTableModel(ViewInterestPoints, InterestPointExplorerPanel) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

InterestPointTools - Class in net.preibisch.mvrecon.process.interestpointdetection

The type Interest point tools.

InterestPointTools() - Constructor for class net.preibisch.mvrecon.process.interestpointdetection.InterestPointTools

InterestPointValue - Class in net.preibisch.mvrecon.fiji.spimdata.interestpoints

InterestPointValue(int, double[], double) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointValue

interleavedId(int, int) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

interleavedId(int, int) - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

interpolate(double[], int, int, double, double) - Static method in class util.ColorStream

interpolate(double, P) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.MonotoneCubicSpline

interpolate(Quat4d, double) - Method in class net.preibisch.mvrecon.vecmath.Quat4d

Performs a great circle interpolation between this quaternion and the quaternion parameter and places the result into this quaternion.

interpolate(Quat4d, Quat4d, double) - Method in class net.preibisch.mvrecon.vecmath.Quat4d

Performs a great circle interpolation between quaternion q1 and quaternion q2 and places the result into this quaternion.

interpolate(Quat4f, float) - Method in class net.preibisch.mvrecon.vecmath.Quat4f

Performs a great circle interpolation between this quaternion and the quaternion parameter and places the result into this quaternion.

interpolate(Quat4f, Quat4f, float) - Method in class net.preibisch.mvrecon.vecmath.Quat4f

Performs a great circle interpolation between quaternion q1 and quaternion q2 and places the result into this quaternion.

interpolate(Tuple3d, double) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Linearly interpolates between this tuple and tuple t1 and places the result into this tuple: this = (1-alpha)*this + alpha*t1.

interpolate(Tuple3d, float) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

interpolate(Tuple3d, Tuple3d, double) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Linearly interpolates between tuples t1 and t2 and places the result into this tuple: this = (1-alpha)*t1 + alpha*t2.

interpolate(Tuple3d, Tuple3d, float) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

interpolate(Tuple3f, float) - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Linearly interpolates between this tuple and tuple t1 and places the result into this tuple: this = (1-alpha)*this + alpha*t1.

interpolate(Tuple3f, Tuple3f, float) - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Linearly interpolates between tuples t1 and t2 and places the result into this tuple: this = (1-alpha)*t1 + alpha*t2.

interpolate(Tuple4d, double) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Linearly interpolates between this tuple and tuple t1 and places the result into this tuple: this = (1-alpha)*this + alpha*t1.

interpolate(Tuple4d, float) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

interpolate(Tuple4d, Tuple4d, double) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Linearly interpolates between tuples t1 and t2 and places the result into this tuple: this = (1-alpha)*t1 + alpha*t2.

interpolate(Tuple4d, Tuple4d, float) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

interpolate(Tuple4f, float) - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Linearly interpolates between this tuple and tuple t1 and places the result into this tuple: this = (1-alpha)*this + alpha*t1.

interpolate(Tuple4f, Tuple4f, float) - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Linearly interpolates between tuples t1 and t2 and places the result into this tuple: this = (1-alpha)*t1 + alpha*t2.

interpolateSteps - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough

interpolateTransforms(ArrayList<AffineTransform3D>, boolean, double, int) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough

InterpolatingNonRigidRandomAccess<T> - Class in net.preibisch.mvrecon.process.fusion.transformed.nonrigid

Virtually transforms any RandomAccessibleInterval<RealType> into a RandomAccess<FloatType> using an AffineTransformation and Linear Interpolation.

InterpolatingNonRigidRandomAccess(RandomAccessibleInterval<T>, ModelGrid, AffineModel3D, InterpolatorFactory<FloatType, RandomAccessible<FloatType>>, boolean, float, FloatType, long[]) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.InterpolatingNonRigidRandomAccess

InterpolatingNonRigidRandomAccessible<T> - Class in net.preibisch.mvrecon.process.fusion.transformed.nonrigid

InterpolatingNonRigidRandomAccessible(RandomAccessibleInterval<T>, ModelGrid, AffineModel3D, boolean, float, FloatType, Interval) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.InterpolatingNonRigidRandomAccessible

InterpolatingNonRigidRandomAccessible(RandomAccessibleInterval<T>, ModelGrid, AffineModel3D, Interval) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.InterpolatingNonRigidRandomAccessible

InterpolatingNonRigidRasteredRandomAccess<T> - Class in net.preibisch.mvrecon.process.fusion.transformed.weights

InterpolatingNonRigidRasteredRandomAccess(RealRandomAccessible<T>, T, ModelGrid, AffineModel3D, int[]) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.weights.InterpolatingNonRigidRasteredRandomAccess

InterpolatingNonRigidRasteredRandomAccessible<T> - Class in net.preibisch.mvrecon.process.fusion.transformed.weights

InterpolatingNonRigidRasteredRandomAccessible(RealRandomAccessible<T>, T, ModelGrid, AffineModel3D, long[]) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.weights.InterpolatingNonRigidRasteredRandomAccessible

interpolation - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

interpolationMethods - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough

interpolationTypes - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

interpolatorFactory - Variable in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccess

interpolatorFactory - Variable in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccessible

intersects(double[][], double[][]) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap.ParallelepipedOverlap

3-D SAT for two parallelepipeds given by their 8 world-space corners.

intersectsLinearInterpolation(double, double, double, long, long, long, long, long, long) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccess

interval - Variable in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccess

interval - Variable in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccessible

INTERVAL_TAG_MAX - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.XmlIoSplitViewerImgLoader

INTERVAL_TAG_MIN - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.XmlIoSplitViewerImgLoader

intStringCoreToDisplay(Object) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.NumberUtils

intStringDisplayToCore(Object) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.NumberUtils

intToCoreString(long) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.NumberUtils

intToDisplayString(int) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.NumberUtils

INVALID - Enum constant in enum class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2.SpecialPoint

inverse() - Method in class net.preibisch.mvrecon.vecmath.Quat4d

Sets the value of this quaternion to the quaternion inverse of itself.

inverse() - Method in class net.preibisch.mvrecon.vecmath.Quat4f

Sets the value of this quaternion to the quaternion inverse of itself.

inverse(Quat4d) - Method in class net.preibisch.mvrecon.vecmath.Quat4d

Sets the value of this quaternion to quaternion inverse of quaternion q1.

inverse(Quat4f) - Method in class net.preibisch.mvrecon.vecmath.Quat4f

Sets the value of this quaternion to quaternion inverse of quaternion q1.

inverseTransformedBoundingBox(ThinplateSplineTransform, Dimensions) - Static method in class net.preibisch.mvrecon.process.fusion.blk.BlkThinPlateSplineFusion

Get the bounding box in render coordinates of an image of the given dimension when back-projected through the inverse of the given transform from rendered to image coordinates.

invert() - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Inverts this matrix in place.

invert() - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Inverts this matrix in place.

invert() - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Inverts this matrix in place.

invert() - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Inverts this matrix in place.

invert() - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Inverts this transform in place.

invert(double[]) - Static method in class net.preibisch.legacy.registration.bead.laplace.LaPlaceFunctions

invert(Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Sets the value of this matrix to the matrix inverse of the passed matrix m1.

invert(Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Sets the value of this matrix to the matrix inverse of the passed matrix m1.

invert(Matrix4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the value of this matrix to the matrix inverse of the passed (user declared) matrix m1.

invert(Matrix4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the value of this matrix to the matrix inverse of the passed (user declared) matrix m1.

invert(Transform3D) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the value of this transform to the inverse of the passed Transform3D parameter.

invertMapSortValue(Map<T, List<FileMapEntry>>) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil

io - Variable in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

io - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

io() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

IOFunctions - Class in net.preibisch.legacy.io

IOFunctions() - Constructor for class net.preibisch.legacy.io.IOFunctions

Never instantiate this class, it contains only static methods

IP - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.Split_Views.InterestPointAdding

ipDataset() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

ipDataset(String) - Static method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

ipGroupChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.GroupParameters

IPL - Class in net.preibisch.mvrecon.process.fusion.transformed.nonrigid

IPL(String, Map<Integer, InterestPoint>) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.IPL

ipMap - Variable in class net.preibisch.mvrecon.process.interestpointremoval.InteractiveProjections

ir - Variable in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedImgRandomAccess

is2d(Collection<? extends BasicViewDescription<?>>) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

is2d(Collection<? extends ViewId>, Map<ViewId, ? extends BasicViewDescription<?>>) - Static method in class net.preibisch.mvrecon.process.fusion.blk.BlkAffineFusion

isActive() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.NonRigidParametersGUI

isActive() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.DefaultFlatfieldCorrectionWrappedImgLoader

isActive() - Method in interface net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.FlatfieldCorrectionWrappedImgLoader

isActive() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.MultiResolutionFlatfieldCorrectionWrappedImgLoader

isApproximatelyIdentity(Affine3D<?>, double) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

isCached() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.DefaultFlatfieldCorrectionWrappedImgLoader

isCached() - Method in interface net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.FlatfieldCorrectionWrappedImgLoader

isCached() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.MultiResolutionFlatfieldCorrectionWrappedImgLoader

isCellEditable(int, int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedTableModel

isCellEditable(int, int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

isCellEditable(int, int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MissingViewsTableModelDecorator

isCellEditable(int, int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MultiViewTableModelDecorator

isCellEditable(int, int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationTableModel

isCheckBoxSelected() - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

Result of the checkbox added via GenericLoadParseQueryXML.addCheckbox(String); false if none was added.

isContained(V, Collection<? extends Group<V>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

isConverged(TileConfiguration) - Method in class net.preibisch.mvrecon.process.interestpointregistration.global.convergence.IterativeConvergenceStrategy

isConverged(TileConfiguration) - Method in class net.preibisch.mvrecon.process.interestpointregistration.global.convergence.SimpleIterativeConvergenceStrategy

isCorrect(Point, Point) - Static method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test.TestPointDescriptor

isExpanded() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.viewneighbours.ViewNeighboursWindow

True iff this window is currently in an "expanded" state (the explorer's selection equals the last expanded set, which differs from the original anchor).

isExpanded() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.viewneighbours.ViewOverlapWindow

True iff this window is currently in an "expanded" state (the explorer's selection equals the last expanded set, which differs from the original anchor).

isFile(URI) - Static method in class util.URITools

isFilterMode() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointOverlay.InterestPointSource

isFilterMode() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

isFinished() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoG

isGC(URI) - Static method in class util.URITools

isHeadless() - Static method in class net.preibisch.mvrecon.fiji.plugin.util.PluginHelper

isHideMissingViews() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedTableModel

isImgLoaderVirtual() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

isImgLoaderVirtual() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

isImgLoaderVirtual() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

isImgLoaderVirtual(SpimData) - Static method in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

isInside(P, Rectangle) - Static method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.HelperFunctions

isKnownScheme(URI) - Static method in class util.URITools

isLeaf() - Method in class net.preibisch.legacy.registration.detection.AbstractDetection

isLeaf() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test.PointNode

isLittleEndian() - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

isLoaded() - Method in class net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions.PointSpreadFunction

isMac - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

isMax - Variable in class net.preibisch.legacy.segmentation.SimplePeak

isMin - Variable in class net.preibisch.legacy.segmentation.SimplePeak

isModified() - Method in class net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions.PointSpreadFunction

isMultiplicative() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

isMultiResolution() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

isMultiResolution() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

isMultiResolution() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

isMultiResolution(SpimData) - Static method in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

isNonezero(IterableInterval<T>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyFileMapImgLoaderLOCI

check whether any pixel in slice is nonzero.

isNonzero(byte[]) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyFileMapImgLoaderLOCI

ISpimDataTableModel<AS> - Interface in net.preibisch.mvrecon.fiji.spimdata.explorer

ISpimDataTableModel.SpecialColumnType - Enum Class in net.preibisch.mvrecon.fiji.spimdata.explorer

isPowerOfTwo(int) - Static method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

isPowerOfTwo(int[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

isPrecise() - Method in class net.preibisch.mvrecon.process.cuda.Block

isPresent(int) - Method in class net.preibisch.mvrecon.fiji.plugin.interactive.MultiResolutionSource

isRoiChanged(InteractiveDoG.ValueChange, Rectangle, boolean) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoG

isRunning - Variable in class net.preibisch.mvrecon.fiji.plugin.apply.BigDataViewerTransformationWindow

isRunning - Variable in class net.preibisch.mvrecon.process.interestpointremoval.InteractiveProjections

isRunning() - Method in class net.preibisch.mvrecon.fiji.plugin.apply.BigDataViewerTransformationWindow

isRunning() - Method in class net.preibisch.mvrecon.process.interestpointremoval.InteractiveProjections

isS3(URI) - Static method in class util.URITools

isSpecialPoint(Cursor<FloatType>, float) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2

isSplitDataset() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorerPanel

Detects if the dataset is a Split dataset (created by splitting large images into tiles)

isUsed - Variable in class net.preibisch.legacy.registration.detection.AbstractDetection

isUsed() - Method in class net.preibisch.legacy.registration.detection.AbstractDetection

isValidFilePattern() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData

isVisible() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupIdOverlay

isZSizeEqualInEveryFile(SpimData2, FileMapGettable) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyFileMapImgLoaderLOCI

for every file in the dataset file list check if the z-size is equal for every series.

iteration - Variable in class net.preibisch.legacy.registration.bead.laplace.DoGMaximum

IterationStatistics() - Constructor for class net.preibisch.mvrecon.process.deconvolution.iteration.ComputeBlockThread.IterationStatistics

IterativeClosestPointGUI - Class in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise

Iterative closest point implementation

IterativeClosestPointGUI() - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.IterativeClosestPointGUI

IterativeClosestPointPairwise<I> - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.icp

Iterative closest point implementation

IterativeClosestPointPairwise(IterativeClosestPointParameters) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.icp.IterativeClosestPointPairwise

IterativeClosestPointParameters - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.icp

IterativeClosestPointParameters(Model<?>) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.icp.IterativeClosestPointParameters

IterativeClosestPointParameters(Model<?>, double, int, boolean, double, double, int, int) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.icp.IterativeClosestPointParameters

IterativeClosestPointParameters(Model<?>, IterativeClosestPointParameters) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.icp.IterativeClosestPointParameters

IterativeConvergenceStrategy - Class in net.preibisch.mvrecon.process.interestpointregistration.global.convergence

IterativeConvergenceStrategy(double) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.global.convergence.IterativeConvergenceStrategy

IterativeConvergenceStrategy(double, int, int) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.global.convergence.IterativeConvergenceStrategy

iterator() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

iterator() - Static method in class util.ColorStream

itx - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel2D

ity - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel2D

J

Java3d - Class in net.preibisch.legacy.mpicbg

Java3d() - Constructor for class net.preibisch.legacy.mpicbg.Java3d

jumpToLastViewerTransform(ViewerPanel) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough

K

keep - Variable in class net.preibisch.mvrecon.process.interestpointremoval.ThinOutParameters

keepImgFFT() - Method in class util.FFTConvolution

keepRange() - Method in class net.preibisch.mvrecon.process.interestpointremoval.ThinOutParameters

keepRotation - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.grid.RegularTranformHelpers.RegularTranslationParameters

kernelFFT() - Method in class util.FFTConvolution

keyExtractor() - Method in class net.preibisch.mvrecon.process.export.RetryTracker

L

label - Variable in class net.preibisch.mvrecon.fiji.plugin.Visualize_Detections.Params

label - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointExplorerPanel

label - Variable in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5.InterestPointData

label - Variable in class net.preibisch.mvrecon.process.interestpointremoval.ThinOutParameters

label(HashMap<String, Integer>, int) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

labelA - Variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.MatcherPairwiseTools.MatchingTask

labelAndWeights - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.Parameters

labelB - Variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.MatcherPairwiseTools.MatchingTask

labelList - Variable in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidParameters

labelMap - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.BasicRegistrationParameters

LabelPopUp - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

LabelPopUp(String) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.LabelPopUp

lambda - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

LandmarkRecord(ViewId, String, double[], double[]) - Constructor for class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion.LandmarkRecord

LandmarkRecord(ViewId, ViewId, String, double[], double[]) - Constructor for class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion.LandmarkRecord

Landmarks - Class in net.preibisch.mvrecon.process.fusion.tps

Landmarks (corresponding source and target coordinates) that can be used to construct a ThinplateSplineTransform.

Landmarks(double[][], double[][]) - Constructor for class net.preibisch.mvrecon.process.fusion.tps.Landmarks

LaPlaceFunctions - Class in net.preibisch.legacy.registration.bead.laplace

LaPlaceFunctions() - Constructor for class net.preibisch.legacy.registration.bead.laplace.LaPlaceFunctions

laPlaceValue - Variable in class net.preibisch.legacy.registration.bead.laplace.DoGMaximum

largefont - Static variable in class net.preibisch.mvrecon.fiji.plugin.util.GUIHelper

largestatusfont - Static variable in class net.preibisch.mvrecon.fiji.plugin.util.GUIHelper

lastDisplayedFile - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

lastDisplayedFile - Static variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

lastExportPath - Static variable in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5

lastImageSize(long, long, long) - Static method in class net.preibisch.mvrecon.process.splitting.SplitDistributeEvenly

lastPresetIndex - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.grid.RegularTranformHelpers

lastSelectedVDs - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationExplorerPanel

lastURI() - Method in class net.preibisch.mvrecon.fiji.spimdata.XmlIoSpimData2

LAYOUT_ANGLE_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoStackImgLoader

LAYOUT_CHANNEL_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoStackImgLoader

LAYOUT_ILLUMINATION_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoStackImgLoader

LAYOUT_TILE_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoStackImgLoader

LAYOUT_TP_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoStackImgLoader

layoutAngles - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoader

layoutChannels - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoader

layoutIllum - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoader

layoutTiles - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoader

layoutTP - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoader

Lazy - Class in util

Convenience methods to create lazy evaluated cached cell images with ops or consumers.

LazyAffineFusion<T> - Class in net.preibisch.mvrecon.process.fusion.lazy

BigStitcher Affine Fusion in blocks

LazyAffineFusion(Converter<FloatType, T>, BasicImgLoader, Collection<? extends ViewId>, Map<ViewId, ? extends AffineTransform3D>, Map<ViewId, ? extends BasicViewDescription<?>>, FusionGUI.FusionType, int, Map<ViewId, AffineModel1D>, long[], T) - Constructor for class net.preibisch.mvrecon.process.fusion.lazy.LazyAffineFusion

Creates a consumer that will fill the requested RandomAccessibleInterval single-threaded

LazyBDVPopup - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

Opt-in alternative to BDVPopup that opens BigDataViewer with NO sources and then dynamically adds (and removes / hides) sources as the user selects views in the explorer.

LazyBDVPopup() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.LazyBDVPopup

LazyBDVPopup.MyActionListener - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

LazyDownsample2x<T> - Class in net.preibisch.mvrecon.process.downsampling.lazy

LazyDownsample2x(long[], RandomAccessible<T>, Interval, int, T) - Constructor for class net.preibisch.mvrecon.process.downsampling.lazy.LazyDownsample2x

LazyFusionTools - Class in net.preibisch.mvrecon.process.fusion.lazy

LazyFusionTools() - Constructor for class net.preibisch.mvrecon.process.fusion.lazy.LazyFusionTools

LazyGauss<T> - Class in net.preibisch.mvrecon.process.interestpointdetection.methods.lazygauss

Simple Gaussian filter Op

LazyGauss(long[], RandomAccessible<T>, T, double[]) - Constructor for class net.preibisch.mvrecon.process.interestpointdetection.methods.lazygauss.LazyGauss

LazyHalfPixelDownsample2x<T> - Class in net.preibisch.mvrecon.process.downsampling.lazy

LazyHalfPixelDownsample2x(long[], RandomAccessible<T>, Interval, int, T) - Constructor for class net.preibisch.mvrecon.process.downsampling.lazy.LazyHalfPixelDownsample2x

LazyLoadingFlatFieldCorrectionMap<IL> - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield

LazyLoadingFlatFieldCorrectionMap() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.LazyLoadingFlatFieldCorrectionMap

LazyNonRigidFusion<T> - Class in net.preibisch.mvrecon.process.fusion.lazy

LazyNonRigidFusion(Converter<FloatType, T>, BasicImgLoader, Map<ViewId, AffineTransform3D>, Map<ViewId, ViewInterestPointLists>, Map<ViewId, ? extends BasicViewDescription<?>>, Collection<? extends ViewId>, Collection<? extends ViewId>, List<String>, FusionGUI.FusionType, boolean, long[], double, boolean, int, Map<? extends ViewId, AffineModel1D>, ExecutorService, Interval, long[], T) - Constructor for class net.preibisch.mvrecon.process.fusion.lazy.LazyNonRigidFusion

LazySmartSpimLoader - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders.smartspim

LazySmartSpimLoader(SmartSPIM.SmartSPIMMetaData, int, int, int) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.smartspim.LazySmartSpimLoader

LazyWeightedGauss<T> - Class in net.preibisch.mvrecon.process.interestpointdetection.methods.lazygauss

Simple Gaussian filter Op

LazyWeightedGauss(long[], RandomAccessible<T>, RandomAccessible<T>, Interval, T, double[]) - Constructor for class net.preibisch.mvrecon.process.interestpointdetection.methods.lazygauss.LazyWeightedGauss

leadingZeros(String, int) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

leadingZeros(String, int) - Static method in class net.preibisch.mvrecon.headless.definedataset.StackList

leafCount - Variable in class net.preibisch.mvrecon.process.splitting.SplitOctTree.OctTreeSplitResult

LegacyDHMImgLoader - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

LegacyDHMImgLoader(File, String, String, String, List<String>, List<String>, String, int, int, AbstractSequenceDescription<?, ?, ?>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyDHMImgLoader

LegacyFileMapImgLoaderLOCI - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

LegacyFileMapImgLoaderLOCI(Map<? extends ViewId, FileMapEntry>, AbstractSequenceDescription<?, ?, ?>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyFileMapImgLoaderLOCI

LegacyFileMapImgLoaderLOCI(Map<? extends ViewId, FileMapEntry>, AbstractSequenceDescription<?, ?, ?>, boolean) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyFileMapImgLoaderLOCI

LegacyLightSheetZ1ImgLoader - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

LegacyLightSheetZ1ImgLoader(File, ImgFactory<? extends NativeType<?>>, AbstractSequenceDescription<?, ?, ?>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyLightSheetZ1ImgLoader

LegacyMicroManagerImgLoader - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

LegacyMicroManagerImgLoader(File, AbstractSequenceDescription<?, ?, ?>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyMicroManagerImgLoader

LegacyStackImgLoader - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

LegacyStackImgLoader(File, String, int, int, int, int, int, AbstractSequenceDescription<?, ?, ?>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoader

For a local initialization without the XML

LegacyStackImgLoaderIJ - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

LegacyStackImgLoaderIJ(File, String, int, int, int, int, int, AbstractSequenceDescription<?, ?, ?>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoaderIJ

LegacyStackImgLoaderLOCI - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

LegacyStackImgLoaderLOCI(File, String, int, int, int, int, int, AbstractSequenceDescription<?, ?, ?>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoaderLOCI

length() - Method in class net.preibisch.mvrecon.vecmath.Vector3d

Returns the length of this vector.

length() - Method in class net.preibisch.mvrecon.vecmath.Vector3f

Returns the length of this vector.

length() - Method in class net.preibisch.mvrecon.vecmath.Vector4d

Returns the length of this vector.

length() - Method in class net.preibisch.mvrecon.vecmath.Vector4f

Returns the length of this vector.

lengthSquared() - Method in class net.preibisch.mvrecon.vecmath.Vector3d

Returns the squared length of this vector.

lengthSquared() - Method in class net.preibisch.mvrecon.vecmath.Vector3f

Returns the squared length of this vector.

lengthSquared() - Method in class net.preibisch.mvrecon.vecmath.Vector4d

Returns the squared length of this vector.

lengthSquared() - Method in class net.preibisch.mvrecon.vecmath.Vector4f

Returns the squared length of this vector

LIGHTBLUE - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVColors

lightsheetThickness() - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

LightSheetZ1 - Class in net.preibisch.mvrecon.fiji.datasetmanager

LightSheetZ1 - Class in net.preibisch.mvrecon.headless.definedataset

DataSet definition for LightSheetZ1

LightSheetZ1() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.LightSheetZ1

LightSheetZ1() - Constructor for class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1

LightSheetZ1ImgLoader - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

LightSheetZ1ImgLoader(File, ImgFactory<? extends NativeType<?>>, AbstractSequenceDescription<?, ?, ?>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LightSheetZ1ImgLoader

LightSheetZ1MetaData - Class in net.preibisch.mvrecon.headless.definedataset

LightSheetZ1MetaData() - Constructor for class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

limitDetectionChoice - Static variable in class net.preibisch.mvrecon.process.interestpointdetection.InterestPointTools

limitDetections - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

limitDetections - Variable in class net.preibisch.mvrecon.process.interestpointdetection.methods.InterestPointParameters

limitList(int, int, List<InterestPoint>) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.InterestPointTools

limitSearchRadius - Variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm.RGLDMParameters

limitSearchRadius() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm.RGLDMParameters

line_ascent - Variable in class net.preibisch.mvrecon.fiji.plugin.util.MyMultiLineLabel

line_height - Variable in class net.preibisch.mvrecon.fiji.plugin.util.MyMultiLineLabel

line_widths - Variable in class net.preibisch.mvrecon.fiji.plugin.util.MyMultiLineLabel

LinearDistance - Class in net.preibisch.mvrecon.process.pointcloud.pointdescriptor.similarity

LinearDistance() - Constructor for class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.similarity.LinearDistance

linearIntensityMap(Coefficients, Dimensions) - Static method in class net.preibisch.mvrecon.process.fusion.intensity.FastLinearIntensityMap

Apply an interpolated linear intensity map to blocks of the standard ImgLib2 RealTypes.

lines - Variable in class net.preibisch.mvrecon.fiji.plugin.util.MyMultiLineLabel

Link<T> - Class in net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating

Link(T, T, RealInterval, AffineGet, double) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.Link

LinkedInterestPoint<P> - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise

LinkedInterestPoint(int, double[], P) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.LinkedInterestPoint

LinkedPoint<P> - Class in net.preibisch.mvrecon.process.pointcloud.pointdescriptor

LinkedPoint(double[], double[], P) - Constructor for class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.LinkedPoint

LinkedPoint(double[], P) - Constructor for class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.LinkedPoint

LinkRemovalStrategy - Interface in net.preibisch.mvrecon.process.interestpointregistration.global.linkremoval

listAllTimePoints(List<TimePoint>) - Static method in class net.preibisch.mvrecon.process.n5api.SpimData2Tools

listener - Variable in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

listeners - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

listIntersect(List<T>, List<T>) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil

LITTLEENDIAN_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoSimViewImgLoader

load() - Method in class net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions.PointSpreadFunction

load(URI) - Method in class net.preibisch.mvrecon.fiji.spimdata.XmlIoSpimData2

loadAllCalibrations() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

loadAllTileLocations() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

loadAndTestPSF(File) - Static method in class net.preibisch.mvrecon.fiji.plugin.PSF_Assign

loadCalibration(File) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

loadCalibration(File) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListImageJ

loadCalibration(File) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListLOCI

loadChoices - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition

loadCorrespondences() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoints

loadCorrespondences() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

loadCorrespondences(ViewId) - Method in class net.preibisch.mvrecon.process.splitting.ConsensusSetCriterion

Override to validate that correspondences have multi-consensus information.

loadCorrespondences(ViewId) - Method in interface net.preibisch.mvrecon.process.splitting.OctTreeSplitCriterion

Load all correspondences for a view.

LoadCorrespondencesGUI - Class in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise

LoadCorrespondencesGUI(SpimData2) - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.LoadCorrespondencesGUI

LoadCorrespondencesPairwise<I> - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.loadcorrespondences

LoadCorrespondencesPairwise(SpimData2, int) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.loadcorrespondences.LoadCorrespondencesPairwise

loadCorrespondencesV1(N5Reader, String) - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

Load correspondences in v1.x format (3xN array: detectionId_A, detectionId_B, metadataId) Sets consensusSetId to -1 for all correspondences (single-consensus mode)

loadCorrespondencesV2(N5Reader, String) - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

Load correspondences in v2.x format (4xN array: detectionId_A, detectionId_B, metadataId, consensusSetId) Reads consensusSetId from 4th column, decoding 0xFFFFFFFFFFFFFFFF as -1

loadDimensions(SpimData2, List<ViewSetup>) - Static method in class net.preibisch.mvrecon.fiji.plugin.resave.Resave_HDF5

loadFileIfNecessary(File) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.LazyLoadingFlatFieldCorrectionMap

loadFirstCalibration() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

loadGroupTransformPSFs(PointSpreadFunctions, ProcessInputImages<V>, boolean) - Static method in class net.preibisch.mvrecon.process.deconvolution.util.PSFPreparation

loadImage(URI, String) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM.SmartSPIMMetaData

loadImage(URI, Pair<Integer, Integer>, long, long, String) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM.SmartSPIMMetaData

loadImage(Pair<Integer, Integer>, long, long, String) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM.SmartSPIMMetaData

loadImageSize(int, int, int) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM.SmartSPIMMetaData

loadImageSize(SmartSPIM.SmartSPIMMetaData, int, int, int) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM.SmartSPIMMetaData

loadInterestPoints() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoints

loadInterestPoints() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

loadMetaData() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.DHMMetaData

loadMetaData(File) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoaderLOCI

loadMetaData(File) - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

loadMetaData(File, boolean) - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

loadMetaData(ViewId) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AbstractImgLoader

Loads only the metadata from the image, should call updateMetaDataCache( ... )

loadMetaData(ViewId) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyDHMImgLoader

loadMetaData(ViewId) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyFileMapImgLoaderLOCI

loadMetaData(ViewId) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyLightSheetZ1ImgLoader

loadMetaData(ViewId) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyMicroManagerImgLoader

loadMetaData(ViewId) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoaderIJ

loadMetaData(ViewId) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoaderLOCI

loadNativeLibrary(Class<L>) - Static method in class net.preibisch.mvrecon.process.cuda.NativeLibraryTools

loadNativeLibrary(String, Class<L>) - Static method in class net.preibisch.mvrecon.process.cuda.NativeLibraryTools

loadNativeLibrary(ArrayList<String>, File, Class<L>) - Static method in class net.preibisch.mvrecon.process.cuda.NativeLibraryTools

loadNativeLibrary(ArrayList<String>, Class<L>) - Static method in class net.preibisch.mvrecon.process.cuda.NativeLibraryTools

loadOMEZarr(N5Reader, String) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.OMEZarrAttributes

LoadParseQueryXML - Class in net.preibisch.mvrecon.fiji.plugin.queryXML

LoadParseQueryXML() - Constructor for class net.preibisch.mvrecon.fiji.plugin.queryXML.LoadParseQueryXML

loadSpimData(URI, XmlIoSpimData2) - Static method in class util.URITools

loadTileLocation(File, int) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoaderLOCI

loadTileLocationFromMetaData(File, int) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

loadTileLocationFromMetaData(File, int) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListImageJ

loadTileLocationFromMetaData(File, int) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListLOCI

loadTimepoints(File) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.DHMMetaData

loadViewerTransforms() - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough

loadViewerTransforms(File) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough

LocalCoordinateSystemPointDescriptor<P> - Class in net.preibisch.mvrecon.process.pointcloud.pointdescriptor

LocalCoordinateSystemPointDescriptor(P, ArrayList<P>, boolean) - Constructor for class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.LocalCoordinateSystemPointDescriptor

localization - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

localization - Variable in class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGParameters

0 = no subpixel localization 1 = quadratic fit

Localization - Class in net.preibisch.mvrecon.process.interestpointdetection

Localization() - Constructor for class net.preibisch.mvrecon.process.interestpointdetection.Localization

localizationChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

localize(double[]) - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoint

localize(double[]) - Method in class net.preibisch.mvrecon.imglib2.st.render.util.SimpleRealLocalizable

localize(double[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridAccess

localize(double[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccess2d

localize(double[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccess

localize(double[]) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.LocalCoordinateSystemPointDescriptor

localize(double[]) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test.VirtualPointNode

localize(double[]) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.TranslationInvariantLocalCoordinateSystemPointDescriptor

localize(double[]) - Method in class util.StackingRealRandomAccessible.StackingRealRandomAccess

localize(float[]) - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoint

localize(float[]) - Method in class net.preibisch.mvrecon.imglib2.st.render.util.SimpleRealLocalizable

localize(float[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridAccess

localize(float[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccess2d

localize(float[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccess

localize(float[]) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.LocalCoordinateSystemPointDescriptor

localize(float[]) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test.VirtualPointNode

localize(float[]) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.TranslationInvariantLocalCoordinateSystemPointDescriptor

localize(float[]) - Method in class util.StackingRealRandomAccessible.StackingRealRandomAccess

localize(int[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccess2d

localize(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccess2d

location - Variable in class net.preibisch.legacy.segmentation.SimplePeak

location - Variable in class net.preibisch.mvrecon.process.splitting.OctTreeSplitCriterion.SplitCorrespondence

Detection location in local coordinates (for spatial partitioning)

locations - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

locations - Variable in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5.InterestPointData

locationX - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.TileInfo

locationX - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.TileOrAngleInfo

locationY - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.TileInfo

locationY - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.TileOrAngleInfo

locationZ - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.TileInfo

locationZ - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.TileOrAngleInfo

longToCoreString(long) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.NumberUtils

longToDisplayString(long) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.NumberUtils

lookAt(Point3d, Point3d, Vector3d) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Helping function that specifies the position and orientation of a view matrix.

lookup - Variable in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.ViewInterestPointLists

LoopBack2d() - Constructor for class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.LoopBack2d

loopSize - Variable in class net.preibisch.mvrecon.process.fusion.ImagePortion

lowerThreshold - Variable in class net.preibisch.mvrecon.process.interestpointremoval.ThinOutParameters

LOWEST_VIEWID_WINS - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI.FusionType

lowestCommonMultiplier(long, long) - Static method in class net.preibisch.mvrecon.process.splitting.SplittingTools

M

m00 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.FixedModel

m00 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantAffineModel3D

m00 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantFixedModel

m00 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel3D

m00 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantSimilarityModel3D

m00 - Variable in class net.preibisch.mvrecon.vecmath.Matrix3d

The first matrix element in the first row.

m00 - Variable in class net.preibisch.mvrecon.vecmath.Matrix3f

The first matrix element in the first row.

m00 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4d

The first element of the first row.

m00 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4f

The first element of the first row.

m01 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.FixedModel

m01 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantAffineModel3D

m01 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantFixedModel

m01 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel3D

m01 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantSimilarityModel3D

m01 - Variable in class net.preibisch.mvrecon.vecmath.Matrix3d

The second matrix element in the first row.

m01 - Variable in class net.preibisch.mvrecon.vecmath.Matrix3f

The second matrix element in the first row.

m01 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4d

The second element of the first row.

m01 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4f

The second element of the first row.

m02 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.FixedModel

m02 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantAffineModel3D

m02 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantFixedModel

m02 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel3D

m02 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantSimilarityModel3D

m02 - Variable in class net.preibisch.mvrecon.vecmath.Matrix3d

The third matrix element in the first row.

m02 - Variable in class net.preibisch.mvrecon.vecmath.Matrix3f

The third matrix element in the first row.

m02 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4d

The third element of the first row.

m02 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4f

The third element of the first row.

m03 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.FixedModel

m03 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4d

The fourth element of the first row.

m03 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4f

The fourth element of the first row.

m10 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.FixedModel

m10 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantAffineModel3D

m10 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantFixedModel

m10 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel3D

m10 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantSimilarityModel3D

m10 - Variable in class net.preibisch.mvrecon.vecmath.Matrix3d

The first matrix element in the second row.

m10 - Variable in class net.preibisch.mvrecon.vecmath.Matrix3f

The first matrix element in the second row.

m10 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4d

The first element of the second row.

m10 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4f

The first element of the second row.

m11 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.FixedModel

m11 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantAffineModel3D

m11 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantFixedModel

m11 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel3D

m11 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantSimilarityModel3D

m11 - Variable in class net.preibisch.mvrecon.vecmath.Matrix3d

The second matrix element in the second row.

m11 - Variable in class net.preibisch.mvrecon.vecmath.Matrix3f

The second matrix element in the second row.

m11 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4d

The second element of the second row.

m11 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4f

The second element of the second row.

m12 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.FixedModel

m12 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantAffineModel3D

m12 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantFixedModel

m12 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel3D

m12 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantSimilarityModel3D

m12 - Variable in class net.preibisch.mvrecon.vecmath.Matrix3d

The third matrix element in the second row.

m12 - Variable in class net.preibisch.mvrecon.vecmath.Matrix3f

The third matrix element in the second row.

m12 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4d

The third element of the second row.

m12 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4f

The third element of the second row.

m13 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.FixedModel

m13 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4d

The fourth element of the second row.

m13 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4f

The fourth element of the second row.

m20 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.FixedModel

m20 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantAffineModel3D

m20 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantFixedModel

m20 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel3D

m20 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantSimilarityModel3D

m20 - Variable in class net.preibisch.mvrecon.vecmath.Matrix3d

The first matrix element in the third row.

m20 - Variable in class net.preibisch.mvrecon.vecmath.Matrix3f

The first matrix element in the third row.

m20 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4d

The first element of the third row.

m20 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4f

The first element of the third row.

m21 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.FixedModel

m21 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantAffineModel3D

m21 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantFixedModel

m21 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel3D

m21 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantSimilarityModel3D

m21 - Variable in class net.preibisch.mvrecon.vecmath.Matrix3d

The second matrix element in the third row.

m21 - Variable in class net.preibisch.mvrecon.vecmath.Matrix3f

The second matrix element in the third row.

m21 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4d

The second element of the third row.

m21 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4f

The second element of the third row.

m22 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.FixedModel

m22 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantAffineModel3D

m22 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantFixedModel

m22 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel3D

m22 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantSimilarityModel3D

m22 - Variable in class net.preibisch.mvrecon.vecmath.Matrix3d

The third matrix element in the third row.

m22 - Variable in class net.preibisch.mvrecon.vecmath.Matrix3f

The third matrix element in the third row.

m22 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4d

The third element of the third row.

m22 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4f

The third element of the third row.

m23 - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.FixedModel

m23 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4d

The fourth element of the third row.

m23 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4f

The fourth element of the third row.

m30 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4d

The first element of the fourth row.

m30 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4f

The first element of the fourth row.

m31 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4d

The second element of the fourth row.

m31 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4f

The second element of the fourth row.

m32 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4d

The third element of the fourth row.

m32 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4f

The third element of the fourth row.

m33 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4d

The fourth element of the fourth row.

m33 - Variable in class net.preibisch.mvrecon.vecmath.Matrix4f

The fourth element of the fourth row.

MAGENTA - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVColors

main(String[]) - Static method in class net.preibisch.legacy.io.ParsePattern

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.DHM

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.DHMMetaData

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.grid.RegularTranformHelpers

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.LightSheetZ1

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.MicroManager

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.OMEZARR

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.patterndetector.NumericalFilenamePatternDetector

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.SimView

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.Analyze_Errors

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.CreateFromCorresponding_Detections

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.Data_Explorer

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.Define_Bounding_Box

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.Define_Multi_View_Dataset

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.Display_View

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.Image_Deconvolution

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.Image_Fusion

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.Image_Quality

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.Intensity_Adjustment

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.interactive.MultiResolutionSource

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Detection

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoG

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.statistics.TimeLapseDisplay

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.PSF_Assign

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.queryXML.LoadParseQueryXML

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.RelativeThinOut_Detections

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.RemoveIntensity_Adjustment

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.resave.Resave_HDF5

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.resave.Resave_N5Api

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.resave.Resave_TIFF

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.Specify_Calibration

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.Split_Views

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.Switch_Attributes

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.ThinOut_Detections

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.util.MultiWindowLayoutHelper

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.Visualize_Detections

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.MonotoneCubicSpline

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AllenOMEZarrLoader

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.DefaultFlatfieldCorrectionWrappedImgLoader

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.LazyLoadingFlatFieldCorrectionMap

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.MultiResolutionFlatfieldCorrectionWrappedImgLoader

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.OMEZarrAttributes

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.smartspim.LazySmartSpimLoader

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.spimdata.SpimDataExample

main(String[]) - Static method in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.StitchingResults

main(String[]) - Static method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

main(String[]) - Static method in class net.preibisch.mvrecon.headless.definedataset.ResaveImaris

main(String...) - Static method in class net.preibisch.mvrecon.headless.definedataset.Rewrite_LuxendoXML

main(String[]) - Static method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxMaximalGroupOverlap

main(String[]) - Static method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxMinFilterThreshold

main(String[]) - Static method in class net.preibisch.mvrecon.process.cuda.Block

main(String[]) - Static method in class net.preibisch.mvrecon.process.cuda.BlockGeneratorVariableSizePrecise

main(String[]) - Static method in class net.preibisch.mvrecon.process.cuda.BlockGeneratorVariableSizeSimple

main(String[]) - Static method in class net.preibisch.mvrecon.process.cuda.NativeLibraryTools

main(String[]) - Static method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccessibleInterval

main(String[]) - Static method in class net.preibisch.mvrecon.process.downsampling.Downsample

main(String[]) - Static method in class net.preibisch.mvrecon.process.downsampling.lazy.LazyDownsample2x

main(String[]) - Static method in class net.preibisch.mvrecon.process.downsampling.lazy.LazyHalfPixelDownsample2x

main(String[]) - Static method in class net.preibisch.mvrecon.process.export.ExportLarge2DTIFF

main(String[]) - Static method in class net.preibisch.mvrecon.process.fusion.blk.ContentBased

main(String[]) - Static method in class net.preibisch.mvrecon.process.fusion.lazy.LazyAffineFusion

main(String[]) - Static method in class net.preibisch.mvrecon.process.fusion.lazy.LazyNonRigidFusion

main(String[]) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccess

main(String[]) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.weights.ContentBasedFFTRealRandomAccessible

main(String[]) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.weights.ContentBasedRealRandomAccessible

main(String[]) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2

main(String[]) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.methods.lazygauss.LazyGauss

main(String[]) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.methods.lazygauss.LazyWeightedGauss

main(String[]) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.global.GlobalOpt

main(String[]) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.strong.ImageCorrelationPointMatchCreator

main(String[]) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

main(String[]) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.PairwiseSetup

main(String[]) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.fastrgldm.FRGLDMMatcher

main(String[]) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.icp.IterativeClosestPointPairwise

main(String[]) - Static method in class net.preibisch.mvrecon.process.interestpointremoval.histogram.Histogram

main(String[]) - Static method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test.TestPointDescriptor

main(String[]) - Static method in class net.preibisch.mvrecon.process.splitting.SplitDistributeEvenly

main(String[]) - Static method in class net.preibisch.mvrecon.Threads

main(String[]) - Static method in class util.URITools

makeChoiceList(String) - Static method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

makeMarker(double) - Method in class net.preibisch.mvrecon.process.interestpointremoval.histogram.MouseListenerValue

makeMarker(int) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.statistics.MouseListenerTimelapse

makeSameSize(Img<T>, long[]) - Static method in class net.preibisch.mvrecon.process.psf.PSFCombination

Make image the same size as defined, center it

ManageDeconvolutionDialogListeners - Class in net.preibisch.mvrecon.fiji.plugin.fusion

ManageDeconvolutionDialogListeners(GenericDialog, Choice, TextField, Choice, Choice, Choice, Choice, Choice, Choice, Label, Label, DeconvolutionGUI) - Constructor for class net.preibisch.mvrecon.fiji.plugin.fusion.ManageDeconvolutionDialogListeners

ManageFusionDialogListeners - Class in net.preibisch.mvrecon.fiji.plugin.fusion

ManageFusionDialogListeners(GenericDialog, Choice, TextField, Choice, Choice, Checkbox, Choice, Label, Label, FusionGUI) - Constructor for class net.preibisch.mvrecon.fiji.plugin.fusion.ManageFusionDialogListeners

ManageListeners(GenericDialog, Vector<?>, Vector<?>, Label, Label) - Constructor for class net.preibisch.mvrecon.fiji.plugin.boundingbox.BoundingBoxGUI.ManageListeners

ManageQualityDialogListeners - Class in net.preibisch.mvrecon.fiji.plugin.fusion

ManageQualityDialogListeners(GenericDialog, Choice, TextField, Checkbox, Choice, Label, Label, QualityGUI) - Constructor for class net.preibisch.mvrecon.fiji.plugin.fusion.ManageQualityDialogListeners

ManhattanDistance - Class in net.preibisch.mvrecon.process.pointcloud.pointdescriptor.similarity

ManhattanDistance() - Constructor for class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.similarity.ManhattanDistance

manuallyDefinedMinMax() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

mapBackChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.FixMapBackParameters

mapBackIndex - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.AdvancedRegistrationParameters

mapBackViews - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.FixMapBackParameters

MAPPING_C_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.XmlIOFileMapImgLoaderLOCI2

MAPPING_C_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoFileListImgLoaderLOCI

MAPPING_FILE_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.XmlIOFileMapImgLoaderLOCI2

MAPPING_FILE_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoFileListImgLoaderLOCI

MAPPING_SERIES_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.XmlIOFileMapImgLoaderLOCI2

MAPPING_SERIES_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoFileListImgLoaderLOCI

MAPPING_TP_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.XmlIOFileMapImgLoaderLOCI2

MAPPING_TP_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoFileListImgLoaderLOCI

MAPPING_VS_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.XmlIOFileMapImgLoaderLOCI2

MAPPING_VS_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoFileListImgLoaderLOCI

mapTilesAndAnglesToSeries(List<FileListDatasetDefinitionUtil.TileOrAngleInfo>) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil

mapTimepointsChannelsAndIlluminations(List<Pair<Integer, List<FileListDatasetDefinitionUtil.ChannelOrIlluminationInfo>>>) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil

margin_height - Variable in class net.preibisch.mvrecon.fiji.plugin.util.MyMultiLineLabel

margin_width - Variable in class net.preibisch.mvrecon.fiji.plugin.util.MyMultiLineLabel

MarkMissingListener() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.MissingViewsPopup.MarkMissingListener

MarkMissingRemoveMetadataListener() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.MissingViewsPopup.MarkMissingRemoveMetadataListener

MarkPresentListener() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.MissingViewsPopup.MarkPresentListener

MaskingFunction3D<D,T,F,P> - Class in net.preibisch.mvrecon.process.fusion.blk.tps

MASTER_FILE_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoLightSheetZ1ImgLoader

MASTER_FILE_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoMicroManagerImgLoader

match(Collection<I>, Collection<I>, V, V, String, String) - Method in interface net.preibisch.mvrecon.process.interestpointregistration.pairwise.MatcherPairwise

Computes a pairwise matching between two lists of interestpoints.

match(Collection<I>, Collection<I>, V, V, String, String) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.centerofmass.CenterOfMassPairwise

match(Collection<I>, Collection<I>, V, V, String, String) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.fastrgldm.FRGLDMPairwise

match(Collection<I>, Collection<I>, V, V, String, String) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.geometrichashing.GeometricHashingPairwise

match(Collection<I>, Collection<I>, V, V, String, String) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.icp.IterativeClosestPointPairwise

match(Collection<I>, Collection<I>, V, V, String, String) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.loadcorrespondences.LoadCorrespondencesPairwise

match(Collection<I>, Collection<I>, V, V, String, String) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm.RGLDMPairwise

matchAcrossLabels - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.BasicRegistrationParameters

Matcher - Interface in net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher

MatcherPairwise<I> - Interface in net.preibisch.mvrecon.process.interestpointregistration.pairwise

MatcherPairwiseTools - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise

MatcherPairwiseTools() - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.MatcherPairwiseTools

MatcherPairwiseTools.MatchingTask<V> - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise

matchHistograms(AbstractSpimData<?>, ViewId, List<ViewId>, ViewId, List<ViewId>, UnbleachFunction, double, int[], double, double, int) - Static method in class net.preibisch.mvrecon.process.fusion.intensity.IntensityCorrection

matchHistograms(AbstractSpimData<?>, ViewId, ViewId, double, int[], double, double, int) - Static method in class net.preibisch.mvrecon.process.fusion.intensity.IntensityCorrection

MatchIndices - Class in net.preibisch.mvrecon.process.fusion.intensity.mpicbg

MatchIndices(int) - Constructor for class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.MatchIndices

MatchingTask(V, V, String, String) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.MatcherPairwiseTools.MatchingTask

matchRansac(AbstractSpimData<?>, ViewId, List<ViewId>, ViewId, List<ViewId>, UnbleachFunction, double, int[], double, double, int, int, double, double, int, double) - Static method in class net.preibisch.mvrecon.process.fusion.intensity.IntensityCorrection

matchRansac(AbstractSpimData<?>, ViewId, ViewId, double, int[], double, double, int, int, double, double, int, double) - Static method in class net.preibisch.mvrecon.process.fusion.intensity.IntensityCorrection

Matrix3d - Class in net.preibisch.mvrecon.vecmath

A double precision floating point 3 by 3 matrix.

Matrix3d() - Constructor for class net.preibisch.mvrecon.vecmath.Matrix3d

Constructs and initializes a Matrix3d to all zeros.

Matrix3d(double[]) - Constructor for class net.preibisch.mvrecon.vecmath.Matrix3d

Constructs and initializes a Matrix3d from the specified nine- element array.

Matrix3d(double, double, double, double, double, double, double, double, double) - Constructor for class net.preibisch.mvrecon.vecmath.Matrix3d

Constructs and initializes a Matrix3d from the specified nine values.

Matrix3d(Matrix3d) - Constructor for class net.preibisch.mvrecon.vecmath.Matrix3d

Constructs a new matrix with the same values as the Matrix3d parameter.

Matrix3d(Matrix3f) - Constructor for class net.preibisch.mvrecon.vecmath.Matrix3d

Constructs a new matrix with the same values as the Matrix3f parameter.

Matrix3f - Class in net.preibisch.mvrecon.vecmath

A single precision floating point 3 by 3 matrix.

Matrix3f() - Constructor for class net.preibisch.mvrecon.vecmath.Matrix3f

Constructs and initializes a Matrix3f to all zeros.

Matrix3f(float[]) - Constructor for class net.preibisch.mvrecon.vecmath.Matrix3f

Constructs and initializes a Matrix3f from the specified nine-element array. this.m00 =v[0], this.m01=v[1], etc.

Matrix3f(float, float, float, float, float, float, float, float, float) - Constructor for class net.preibisch.mvrecon.vecmath.Matrix3f

Constructs and initializes a Matrix3f from the specified nine values.

Matrix3f(Matrix3d) - Constructor for class net.preibisch.mvrecon.vecmath.Matrix3f

Constructs a new matrix with the same values as the Matrix3d parameter.

Matrix3f(Matrix3f) - Constructor for class net.preibisch.mvrecon.vecmath.Matrix3f

Constructs a new matrix with the same values as the Matrix3f parameter.

Matrix4d - Class in net.preibisch.mvrecon.vecmath

A double precision floating point 4 by 4 matrix.

Matrix4d() - Constructor for class net.preibisch.mvrecon.vecmath.Matrix4d

Constructs and initializes a Matrix4d to all zeros.

Matrix4d(double[]) - Constructor for class net.preibisch.mvrecon.vecmath.Matrix4d

Constructs and initializes a Matrix4d from the specified 16 element array. this.m00 =v[0], this.m01=v[1], etc.

Matrix4d(double, double, double, double, double, double, double, double, double, double, double, double, double, double, double, double) - Constructor for class net.preibisch.mvrecon.vecmath.Matrix4d

Constructs and initializes a Matrix4d from the specified 16 values.

Matrix4d(Matrix3d, Vector3d, double) - Constructor for class net.preibisch.mvrecon.vecmath.Matrix4d

Constructs and initializes a Matrix4f from the rotation matrix, translation, and scale values; the scale is applied only to the rotational components of the matrix (upper 3x3) and not to the translational components of the matrix.

Matrix4d(Matrix3f, Vector3d, double) - Constructor for class net.preibisch.mvrecon.vecmath.Matrix4d

Constructs and initializes a Matrix4d from the rotation matrix, translation, and scale values; the scale is applied only to the rotational components of the matrix (upper 3x3) and not to the translational components of the matrix.

Matrix4d(Matrix4d) - Constructor for class net.preibisch.mvrecon.vecmath.Matrix4d

Constructs a new matrix with the same values as the Matrix4d parameter.

Matrix4d(Matrix4f) - Constructor for class net.preibisch.mvrecon.vecmath.Matrix4d

Constructs a new matrix with the same values as the Matrix4f parameter.

Matrix4d(Quat4d, Vector3d, double) - Constructor for class net.preibisch.mvrecon.vecmath.Matrix4d

Constructs and initializes a Matrix4d from the quaternion, translation, and scale values; the scale is applied only to the rotational components of the matrix (upper 3x3) and not to the translational components.

Matrix4d(Quat4f, Vector3d, double) - Constructor for class net.preibisch.mvrecon.vecmath.Matrix4d

Constructs and initializes a Matrix4d from the quaternion, translation, and scale values; the scale is applied only to the rotational components of the matrix (upper 3x3) and not to the translational components.

Matrix4f - Class in net.preibisch.mvrecon.vecmath

A single precision floating point 4 by 4 matrix.

Matrix4f() - Constructor for class net.preibisch.mvrecon.vecmath.Matrix4f

Constructs and initializes a Matrix4f to all zeros.

Matrix4f(float[]) - Constructor for class net.preibisch.mvrecon.vecmath.Matrix4f

Constructs and initializes a Matrix4f from the specified 16 element array. this.m00 =v[0], this.m01=v[1], etc.

Matrix4f(float, float, float, float, float, float, float, float, float, float, float, float, float, float, float, float) - Constructor for class net.preibisch.mvrecon.vecmath.Matrix4f

Constructs and initializes a Matrix4f from the specified 16 values.

Matrix4f(Matrix3f, Vector3f, float) - Constructor for class net.preibisch.mvrecon.vecmath.Matrix4f

Constructs and initializes a Matrix4f from the rotation matrix, translation, and scale values; the scale is applied only to the rotational components of the matrix (upper 3x3) and not to the translational components of the matrix.

Matrix4f(Matrix4d) - Constructor for class net.preibisch.mvrecon.vecmath.Matrix4f

Constructs a new matrix with the same values as the Matrix4d parameter.

Matrix4f(Matrix4f) - Constructor for class net.preibisch.mvrecon.vecmath.Matrix4f

Constructs a new matrix with the same values as the Matrix4f parameter.

Matrix4f(Quat4f, Vector3f, float) - Constructor for class net.preibisch.mvrecon.vecmath.Matrix4f

Constructs and initializes a Matrix4f from the quaternion, translation, and scale values; the scale is applied only to the rotational components of the matrix (upper 3x3) and not to the translational components.

max - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

max - Variable in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox

max - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.GroupPairResult

max - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.SingleGroupError

max - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.SingleViewError

max - Variable in class net.preibisch.mvrecon.process.interestpointremoval.histogram.Histogram

max(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox

max(int) - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccessibleInterval

max(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval

max(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGrid

max(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccessibleInterval

max(long[]) - Method in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox

max(long[]) - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccessibleInterval

max(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval

max(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGrid

max(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccessibleInterval

max(long[], long[]) - Static method in class net.preibisch.mvrecon.process.cuda.Block

max(Positionable) - Method in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox

max(Positionable) - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccessibleInterval

max(Positionable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval

max(Positionable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGrid

max(Positionable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccessibleInterval

MAX - Enum constant in enum class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval.Fusion

MAX - Enum constant in enum class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2.SpecialPoint

max_epsilon - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac.RANSACParameters

MAX_INTENSITY - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI.FusionType

Max_Project - Class in net.preibisch.mvrecon.fiji.plugin

Max_Project() - Constructor for class net.preibisch.mvrecon.fiji.plugin.Max_Project

max_trust - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac.RANSACParameters

max_width - Variable in class net.preibisch.mvrecon.fiji.plugin.util.MyMultiLineLabel

maxBlock - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

maxBlock() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.ManageDeconvolutionDialogListeners

maxCacheSize - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

maxCacheSize - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.DisplayFusedImagesPopup

maxCacheSize - Static variable in class net.preibisch.mvrecon.process.deconvolution.MultiViewDeconvolution

maxChange - Variable in class net.preibisch.mvrecon.process.deconvolution.iteration.ComputeBlockThread.IterationStatistics

maxDepth - Variable in class net.preibisch.mvrecon.process.splitting.SplitOctTree.OctTreeSplitResult

maxDetections - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

maxDetections - Variable in class net.preibisch.mvrecon.process.interestpointdetection.methods.InterestPointParameters

maxDetections - Variable in class net.preibisch.mvrecon.process.splitting.SplitOctTree.OctTreeSplitResult

maxDetectionsTypeIndex - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

maxDetectionsTypeIndex - Variable in class net.preibisch.mvrecon.process.interestpointdetection.methods.InterestPointParameters

maxDiffRange - Static variable in class net.preibisch.mvrecon.process.deconvolution.MultiViewDeconvolution

maxDistance - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.icp.IterativeClosestPointParameters

maxDistance(Collection<? extends PointMatch>) - Static method in class net.preibisch.mvrecon.process.pointcloud.icp.ICP

maxEpsilon - Variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac.RANSACParameters

maxError - Variable in class net.preibisch.legacy.registration.bead.error.GlobalErrorStatisticsImpl

maxError - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters

MaxErrorLinkRemoval - Class in net.preibisch.mvrecon.process.interestpointregistration.global.linkremoval

MaxErrorLinkRemoval() - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.global.linkremoval.MaxErrorLinkRemoval

maxErrorMax - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoG

maxErrorMin - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoG

maximalBoundingBox(Collection<? extends ViewId>, HashMap<? extends ViewId, Dimensions>, HashMap<? extends ViewId, AffineTransform3D>, String) - Static method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxTools

maximalBoundingBox(SpimData2, Collection<V>, String) - Static method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxTools

MaximumBoundingBoxGUI - Class in net.preibisch.mvrecon.fiji.plugin.boundingbox

MaximumBoundingBoxGUI(SpimData2, List<ViewId>) - Constructor for class net.preibisch.mvrecon.fiji.plugin.boundingbox.MaximumBoundingBoxGUI

maxIntensity - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

maxIntensity - Variable in class net.preibisch.mvrecon.process.interestpointdetection.methods.InterestPointParameters

maxIntensity() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

maxIntervalSpread(List<ViewSetup>) - Method in class net.preibisch.mvrecon.process.splitting.SplitDistributeEvenly

maxIntervalSpread(List<ViewSetup>) - Method in interface net.preibisch.mvrecon.process.splitting.SplitInterval

maxIntervalSpread(List<ViewSetup>) - Method in class net.preibisch.mvrecon.process.splitting.SplitOctTree

maxIntervalSpread(List<ViewSetup>) - Method in interface net.preibisch.mvrecon.process.splitting.SplitView

Compute the maximum number of intervals any single view could produce.

maxIterations - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters

maxIterations - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.icp.IterativeClosestPointParameters

maxMaxSets - Variable in class net.preibisch.mvrecon.process.splitting.SplitOctTree.OctTreeSplitResult

maxNumGroups(SpimData2, List<ViewId>, DeconvolutionGUI, int) - Static method in class net.preibisch.mvrecon.fiji.plugin.fusion.ManageDeconvolutionDialogListeners

maxNumInputPixelsPerInputGroup(SpimData2, List<ViewId>, int) - Static method in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

maxPerPairCorrLog - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.PairwiseResult

Maximum number of per-pair "[…] >>> […]: Loaded N corresponding…" / "Not enough…" lines to print across one batch of pairwise tasks before per-pair output is suppressed.

maxPerPairLog - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.strong.InterestPointMatchCreator

Maximum number of per-pair "Connecting … <-> …" lines to print from InterestPointMatchCreator.assignPointMatches(java.util.HashMap<mpicbg.spim.data.sequence.ViewId, mpicbg.models.Tile<M>>, java.util.ArrayList<net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group<mpicbg.spim.data.sequence.ViewId>>, java.util.Collection<mpicbg.spim.data.sequence.ViewId>) before the per-pair output is suppressed.

maxPerViewTransformLog - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

Maximum number of per-view 'Transformation Models:' lines to print from TransformationTools.printAndSummarizeTransformations(java.lang.Iterable<? extends mpicbg.spim.data.sequence.ViewId>, java.util.Map<? extends mpicbg.spim.data.sequence.ViewId, ? extends mpicbg.models.Tile>) per call before output is suppressed.

maxPlateauWidth - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters

maxPrefix(List<String>) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.patterndetector.NumericalFilenamePatternDetector

maxProject(List<? extends ViewDescription>, ImgLoader, T) - Static method in class net.preibisch.mvrecon.fiji.plugin.Max_Project

maxProject(SpimData, List<? extends ViewId>, T) - Static method in class net.preibisch.mvrecon.fiji.plugin.Max_Project

MaxProjectPopup - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

MaxProjectPopup() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.MaxProjectPopup

MaxProjectPopup.MyActionListener - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

maxTransformedKernel(HashMap<ViewId, PointSpreadFunction>, ViewRegistrations) - Static method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

maxTrust - Variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac.RANSACParameters

maxX - Variable in class net.preibisch.legacy.registration.threshold.ComponentProperties

maxY - Variable in class net.preibisch.legacy.registration.threshold.ComponentProperties

maxZ - Variable in class net.preibisch.legacy.registration.threshold.ComponentProperties

mdLength - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader.IFDData

mdLength - Variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader.IFDData

mdOffset - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader.IFDData

mdOffset - Variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader.IFDData

meanDistance(Collection<? extends PointMatch>) - Static method in class net.preibisch.mvrecon.process.pointcloud.icp.ICP

MeanFilter<S,T> - Class in net.preibisch.mvrecon.imglib2.st.filter

MeanFilter(RadiusNeighborSearch<S>, double, T) - Constructor for class net.preibisch.mvrecon.imglib2.st.filter.MeanFilter

MeanFilterFactory<S,T> - Class in net.preibisch.mvrecon.imglib2.st.filter

MeanFilterFactory(T, double) - Constructor for class net.preibisch.mvrecon.imglib2.st.filter.MeanFilterFactory

measure() - Method in class net.preibisch.mvrecon.fiji.plugin.util.MyMultiLineLabel

MedianFilter<T> - Class in net.preibisch.mvrecon.imglib2.st.filter

MedianFilter(RadiusNeighborSearch<T>, double, T) - Constructor for class net.preibisch.mvrecon.imglib2.st.filter.MedianFilter

MedianFilterFactory<T> - Class in net.preibisch.mvrecon.imglib2.st.filter

MedianFilterFactory(T, double) - Constructor for class net.preibisch.mvrecon.imglib2.st.filter.MedianFilterFactory

mediumstatusfont - Static variable in class net.preibisch.mvrecon.fiji.plugin.util.GUIHelper

mediumstatusNonItalicfont - Static variable in class net.preibisch.mvrecon.fiji.plugin.util.GUIHelper

memberOf(V, Set<Group<V>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

Identifies all groups that a certain view is a member of

merge(Map<V, HashMap<String, Collection<InterestPoint>>>) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.InterestPointGrouping

merge(Map<V, HashMap<String, Collection<InterestPoint>>>) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.InterestPointGroupingAll

merge(Map<V, HashMap<String, Collection<InterestPoint>>>) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.InterestPointGroupingMinDistance

merge(Group<V>, Group<V>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

Merges two Groups of views

mergeAll(Map<V, HashMap<String, Collection<InterestPoint>>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.InterestPointGroupingAll

mergeAllOverlappingGroups(Collection<Group<V>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

Merges all overlapping groups into a new List, the input remains unchanged

mergeDistance - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.GroupParameters

mergeOverlapping(Group<V>, Group<V>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

Merges two Groups of views

mergeSets(ArrayList<HashSet<V>>, ArrayList<ArrayList<Pair<V, V>>>, int, int) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.PairwiseSetup

Merge two sets with indices i1, i2

mergeSets(ArrayList<HashSet<V>>, ArrayList<ArrayList<Pair<V, V>>>, Collection<Integer>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.PairwiseSetup

Merge N sets with indices Note: This method collects all views and pairs from the sets being merged, removes the old sets from vSets and pairSets, and adds the merged set at the END.

message1 - Variable in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

message2 - Variable in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

messagePaper - Static variable in class net.preibisch.mvrecon.fiji.plugin.util.GUIHelper

messageWebsite - Static variable in class net.preibisch.mvrecon.fiji.plugin.util.GUIHelper

metadataFile - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM.SmartSPIMMetaData

METADATAFILE_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoSmartSPIMImgLoader

MetaDataWeakLinkCreator<N> - Class in net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.weak

Uses the previous state as an approximate knowledge for the metadata of the acquisition.

MetaDataWeakLinkCreator(HashMap<ViewId, Tile<N>>, OverlapDetection<ViewId>, Map<ViewId, ViewRegistration>) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.weak.MetaDataWeakLinkCreator

MetaDataWeakLinkFactory - Class in net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.weak

MetaDataWeakLinkFactory(Map<ViewId, ViewRegistration>, OverlapDetection<ViewId>) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.weak.MetaDataWeakLinkFactory

method - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters

MicroManager - Class in net.preibisch.mvrecon.fiji.datasetmanager

MicroManager - Class in net.preibisch.mvrecon.headless.definedataset

DataSet definition for MicroManager

MicroManager() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.MicroManager

MicroManager() - Constructor for class net.preibisch.mvrecon.headless.definedataset.MicroManager

MicroManagerImgLoader - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

MicroManagerImgLoader(File, AbstractSequenceDescription<?, ?, ?>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MicroManagerImgLoader

middleK - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.Parameters

min - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

min - Variable in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox

min - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.GroupPairResult

min - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.SingleGroupError

min - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.SingleViewError

min - Variable in class net.preibisch.mvrecon.process.interestpointremoval.histogram.Histogram

min(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox

min(int) - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccessibleInterval

min(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval

min(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGrid

min(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccessibleInterval

min(long[]) - Method in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox

min(long[]) - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccessibleInterval

min(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval

min(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGrid

min(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccessibleInterval

min(Positionable) - Method in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox

min(Positionable) - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccessibleInterval

min(Positionable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval

min(Positionable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGrid

min(Positionable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccessibleInterval

MIN - Enum constant in enum class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2.SpecialPoint

min_inlier_ratio - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac.RANSACParameters

min_num_matches - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac.RANSACParameters

MIN_NUM_MATCHES - Static variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.FixedModel

MIN_NUM_MATCHES - Static variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantAffineModel3D

MIN_NUM_MATCHES - Static variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantFixedModel

MIN_NUM_MATCHES - Static variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel2D

MIN_NUM_MATCHES - Static variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel3D

MIN_NUM_MATCHES - Static variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantSimilarityModel3D

min_width - Variable in class net.preibisch.mvrecon.fiji.plugin.util.MyMultiLineLabel

minDepth - Variable in class net.preibisch.mvrecon.process.splitting.SplitOctTree.OctTreeSplitResult

minDetections - Variable in class net.preibisch.mvrecon.process.splitting.SplitOctTree.OctTreeSplitResult

minError - Variable in class net.preibisch.legacy.registration.bead.error.GlobalErrorStatisticsImpl

minEVratio - Variable in class net.preibisch.legacy.registration.bead.laplace.DoGMaximum

MinFilterThresholdBoundingBoxGUI - Class in net.preibisch.mvrecon.fiji.plugin.boundingbox

MinFilterThresholdBoundingBoxGUI(SpimData2, List<ViewId>) - Constructor for class net.preibisch.mvrecon.fiji.plugin.boundingbox.MinFilterThresholdBoundingBoxGUI

minInlierRatio - Variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac.RANSACParameters

minIntensity - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

minIntensity - Variable in class net.preibisch.mvrecon.process.interestpointdetection.methods.InterestPointParameters

minIntensity() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

minMax(RandomAccessibleInterval<T>) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

minMax(RandomAccessibleInterval<T>, ExecutorService) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

minMax(RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, ExecutorService) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2

MINMAX - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoG.ValueChange

minMaxApprox(RandomAccessibleInterval<T>) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

Deprecated.

minMaxApprox1(RandomAccessibleInterval<T>) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

minMaxApprox1(RandomAccessibleInterval<T>, int) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

minMaxApprox1(RandomAccessibleInterval<T>, Random, int) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

minMaxAvgApprox1(RandomAccessibleInterval<T>, Random, int) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

minMaxError - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.global.convergence.SimpleIterativeConvergenceStrategy

minMaxSets - Variable in class net.preibisch.mvrecon.process.splitting.SplitOctTree.OctTreeSplitResult

minNumMatches - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.LoadCorrespondencesGUI

minNumMatches - Variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac.RANSACParameters

minResolution - Variable in class net.preibisch.mvrecon.fiji.plugin.apply.ApplyParameters

minResolution(SequenceDescription, Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.DatasetCreationUtils

minSizeMultiplierFloor - Static variable in class net.preibisch.mvrecon.process.splitting.SplitOctTree

minValue - Static variable in class net.preibisch.mvrecon.process.deconvolution.MultiViewDeconvolution

minValue - Variable in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedImgRandomAccess

minValue - Variable in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedImgRandomAccessible

minValueImg - Static variable in class net.preibisch.mvrecon.process.deconvolution.MultiViewDeconvolution

minX - Variable in class net.preibisch.legacy.registration.threshold.ComponentProperties

minY - Variable in class net.preibisch.legacy.registration.threshold.ComponentProperties

minZ - Variable in class net.preibisch.legacy.registration.threshold.ComponentProperties

mipMapInfoToDownsamplings(Map<Integer, ExportMipmapInfo>) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

mirror(Img<T>, int, int) - Static method in class net.preibisch.mvrecon.process.deconvolution.util.Mirror

Mirror - Class in net.preibisch.mvrecon.process.deconvolution.util

Mirrors an n-dimensional image along an axis (one of the dimensions).

Mirror() - Constructor for class net.preibisch.mvrecon.process.deconvolution.util.Mirror

MissingViewsPopup - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

Submenu for managing missing views: mark as missing, mark as present, or mark as missing with metadata removal.

MissingViewsPopup() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.MissingViewsPopup

MissingViewsPopup.MarkMissingListener - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

Listener for "Mark Selected Views as Missing"

MissingViewsPopup.MarkMissingRemoveMetadataListener - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

Listener for "Mark as Missing and Remove Metadata"

MissingViewsPopup.MarkPresentListener - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

Listener for "Mark Selected Views as Present"

MissingViewsTableModelDecorator<AS> - Class in net.preibisch.mvrecon.fiji.spimdata.explorer

MissingViewsTableModelDecorator(ISpimDataTableModel<AS>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.MissingViewsTableModelDecorator

MM_METADATA - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

MM_METADATA - Static variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

mode - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.Parameters

model - Variable in class net.preibisch.mvrecon.fiji.plugin.apply.ApplyParameters

model - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.FRGLDMGUI

model - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.GeometricHashingGUI

model - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.IterativeClosestPointGUI

model - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.LoadCorrespondencesGUI

model - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.RGLDMGUI

model - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.FixMapBackParameters

model() - Method in class net.preibisch.mvrecon.fiji.plugin.apply.ModelLink

modelChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

modelChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.TransformationModelGUI

modelDescription() - Method in class net.preibisch.mvrecon.fiji.plugin.apply.ModelLink

ModelGrid - Class in net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid

ModelGrid(long[], Interval, Collection<? extends NonrigidIP>, double, boolean) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGrid

ModelGridAccess - Class in net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid

ModelGridAccess(RandomAccessibleInterval<NumericAffineModel3D>, long[], long[]) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridAccess

ModelGridTools - Class in net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid

ModelGridTools() - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridTools

ModelLink - Class in net.preibisch.mvrecon.fiji.plugin.apply

ModelLink(ViewDescription) - Constructor for class net.preibisch.mvrecon.fiji.plugin.apply.ModelLink

ModelPointDescriptor<P> - Class in net.preibisch.mvrecon.process.pointcloud.pointdescriptor

ModelPointDescriptor(P, ArrayList<P>, TranslationInvariantModel<?>, SimilarityMeasure, Matcher) - Constructor for class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.ModelPointDescriptor

Creates a ModelPointDescriptor that can perform matching using a Model For the computational process it only modifies the world coordinates of its own descriptorPoints, thus providing the opportunity for multi-threading.

ModelPriorMatcher - Class in net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher

This class does a simple matching but computes a normalizationFactor based a given model prior.

ModelPriorMatcher(int, RigidModel3D) - Constructor for class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.ModelPriorMatcher

ModelPriorSubsetMatcher - Class in net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher

ModelPriorSubsetMatcher(int, int, RigidModel3D) - Constructor for class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.ModelPriorSubsetMatcher

ModifyDefinedBoundingBoxGUI - Class in net.preibisch.mvrecon.fiji.plugin.boundingbox

ModifyDefinedBoundingBoxGUI(SpimData2, List<ViewId>) - Constructor for class net.preibisch.mvrecon.fiji.plugin.boundingbox.ModifyDefinedBoundingBoxGUI

modStep - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.ChannelOrIlluminationInfo

MonotoneCubicSpline - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.bdv

n-dimensional extension of the monotone cubic spline implementation by Leszek Wach: https://gist.github.com/lecho/7627739#file-splineinterpolation-java

mostPresentCal(Collection<Specify_Calibration.Cal>) - Static method in class net.preibisch.mvrecon.fiji.plugin.Specify_Calibration

mouseClicked(MouseEvent) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.ROIListener

mouseClicked(MouseEvent) - Method in class net.preibisch.mvrecon.fiji.plugin.util.MouseOverPopUpStateChanger

mouseEntered(MouseEvent) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.ROIListener

mouseEntered(MouseEvent) - Method in class net.preibisch.mvrecon.fiji.plugin.util.MouseOverPopUpStateChanger

mouseExited(MouseEvent) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.ROIListener

mouseExited(MouseEvent) - Method in class net.preibisch.mvrecon.fiji.plugin.util.MouseOverPopUpStateChanger

MouseListenerTimelapse - Class in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.statistics

MouseListenerValue - Class in net.preibisch.mvrecon.process.interestpointremoval.histogram

MouseOverPopUpStateChanger - Class in net.preibisch.mvrecon.fiji.plugin.util

MouseOverPopUpStateChanger(JMenuItem[], int, MouseOverPopUpStateChanger.StateChanger) - Constructor for class net.preibisch.mvrecon.fiji.plugin.util.MouseOverPopUpStateChanger

MouseOverPopUpStateChanger.StateChanger - Interface in net.preibisch.mvrecon.fiji.plugin.util

mousePressed(MouseEvent) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.ROIListener

mousePressed(MouseEvent) - Method in class net.preibisch.mvrecon.fiji.plugin.util.MouseOverPopUpStateChanger

mouseReleased(MouseEvent) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.ROIListener

mouseReleased(MouseEvent) - Method in class net.preibisch.mvrecon.fiji.plugin.util.MouseOverPopUpStateChanger

move(double[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridAccess

move(double[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccess

move(double[]) - Method in class util.StackingRealRandomAccessible.StackingRealRandomAccess

move(double, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridAccess

move(double, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccess

move(double, int) - Method in class util.StackingRealRandomAccessible.StackingRealRandomAccess

move(float[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridAccess

move(float[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccess

move(float[]) - Method in class util.StackingRealRandomAccessible.StackingRealRandomAccess

move(float, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridAccess

move(float, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccess

move(float, int) - Method in class util.StackingRealRandomAccessible.StackingRealRandomAccess

move(int[]) - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccess

move(int[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccess

move(int[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccess

move(int[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessFirstWins

move(int[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessMax

move(int[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessNoWeights

move(int[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridAccess

move(int[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGridRandomAccess

move(int[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputGeneralRandomAccess

move(int[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccess2d

move(int[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccess

move(int[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccess

move(int[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.InterpolatingNonRigidRasteredRandomAccess

move(int[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.NonRigidRasteredRandomAccess

move(int[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.TransformedRasteredRandomAccess

move(int[]) - Method in class util.StackingRealRandomAccessible.StackingRealRandomAccess

move(int, int) - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccess

move(int, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccess

move(int, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccess

move(int, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessFirstWins

move(int, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessMax

move(int, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessNoWeights

move(int, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridAccess

move(int, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGridRandomAccess

move(int, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputGeneralRandomAccess

move(int, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccess2d

move(int, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccess

move(int, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccess

move(int, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.InterpolatingNonRigidRasteredRandomAccess

move(int, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.NonRigidRasteredRandomAccess

move(int, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.TransformedRasteredRandomAccess

move(int, int) - Method in class util.StackingRealRandomAccessible.StackingRealRandomAccess

move(long[]) - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccess

move(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccess

move(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccess

move(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessFirstWins

move(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessMax

move(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessNoWeights

move(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridAccess

move(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGridRandomAccess

move(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputGeneralRandomAccess

move(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccess2d

move(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccess

move(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccess

move(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.InterpolatingNonRigidRasteredRandomAccess

move(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.NonRigidRasteredRandomAccess

move(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.TransformedRasteredRandomAccess

move(long[]) - Method in class util.StackingRealRandomAccessible.StackingRealRandomAccess

move(long, int) - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccess

move(long, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccess

move(long, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccess

move(long, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessFirstWins

move(long, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessMax

move(long, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessNoWeights

move(long, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridAccess

move(long, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGridRandomAccess

move(long, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputGeneralRandomAccess

move(long, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccess2d

move(long, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccess

move(long, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccess

move(long, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.InterpolatingNonRigidRasteredRandomAccess

move(long, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.NonRigidRasteredRandomAccess

move(long, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.TransformedRasteredRandomAccess

move(long, int) - Method in class util.StackingRealRandomAccessible.StackingRealRandomAccess

move(Localizable) - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccess

move(Localizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccess

move(Localizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccess

move(Localizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessFirstWins

move(Localizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessMax

move(Localizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessNoWeights

move(Localizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridAccess

move(Localizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGridRandomAccess

move(Localizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputGeneralRandomAccess

move(Localizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccess2d

move(Localizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccess

move(Localizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccess

move(Localizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.InterpolatingNonRigidRasteredRandomAccess

move(Localizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.NonRigidRasteredRandomAccess

move(Localizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.TransformedRasteredRandomAccess

move(Localizable) - Method in class util.StackingRealRandomAccessible.StackingRealRandomAccess

move(RealLocalizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridAccess

move(RealLocalizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccess

move(RealLocalizable) - Method in class util.StackingRealRandomAccessible.StackingRealRandomAccess

moveToScreenFraction(Component, double, double) - Static method in class net.preibisch.mvrecon.fiji.plugin.util.MultiWindowLayoutHelper

move a component (such as a JFrame Window) to x and y, expressed as fractions of the screen width and height of the screen the component is on.

mul - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

mul(double) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

mul(double) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

mul(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Multiplies each element of this matrix by a scalar.

mul(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Multiplies each element of this matrix by a scalar.

mul(double) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Multiplies each element of this transform by a scalar.

mul(double, Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Multiplies each element of matrix m1 by a scalar and places the result into this.

mul(double, Matrix4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Multiplies each element of matrix m1 by a scalar and places the result into this.

mul(double, Transform3D) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Multiplies each element of transform t1 by a scalar and places the result into this.

mul(float) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

mul(float) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

mul(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Multiplies each element of this matrix by a scalar.

mul(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Multiplies each element of this matrix by a scalar.

mul(float, Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Multiplies each element of matrix m1 by a scalar and places the result into this.

mul(float, Matrix4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Multiplies each element of matrix m1 by a scalar and places the result into this.

mul(NumericAffineModel3D) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

mul(NumericAffineTransform3D) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

mul(Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Sets the value of this matrix to the result of multiplying itself with matrix m1.

mul(Matrix3d, Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Sets the value of this matrix to the result of multiplying the two argument matrices together.

mul(Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Sets the value of this matrix to the result of multiplying itself with matrix m1.

mul(Matrix3f, Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Sets the value of this matrix to the result of multiplying the two argument matrices together.

mul(Matrix4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the value of this matrix to the result of multiplying itself with matrix m1.

mul(Matrix4d, Matrix4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the value of this matrix to the result of multiplying the two argument matrices together.

mul(Matrix4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the value of this matrix to the result of multiplying itself with matrix m1.

mul(Matrix4f, Matrix4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the value of this matrix to the result of multiplying the two argument matrices together.

mul(Quat4d) - Method in class net.preibisch.mvrecon.vecmath.Quat4d

Sets the value of this quaternion to the quaternion product of itself and q1 (this = this * q1).

mul(Quat4d, Quat4d) - Method in class net.preibisch.mvrecon.vecmath.Quat4d

Sets the value of this quaternion to the quaternion product of quaternions q1 and q2 (this = q1 * q2).

mul(Quat4f) - Method in class net.preibisch.mvrecon.vecmath.Quat4f

Sets the value of this quaternion to the quaternion product of itself and q1 (this = this * q1).

mul(Quat4f, Quat4f) - Method in class net.preibisch.mvrecon.vecmath.Quat4f

Sets the value of this quaternion to the quaternion product of quaternions q1 and q2 (this = q1 * q2).

mul(Transform3D) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the value of this transform to the result of multiplying itself with transform t1 (this = this * t1).

mul(Transform3D, Transform3D) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the value of this transform to the result of multiplying transform t1 by transform t2 (this = t1*t2).

MUL - Enum constant in enum class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccessibleInterval.CombineType

mulInverse(Quat4d) - Method in class net.preibisch.mvrecon.vecmath.Quat4d

Multiplies this quaternion by the inverse of quaternion q1 and places the value into this quaternion.

mulInverse(Quat4d, Quat4d) - Method in class net.preibisch.mvrecon.vecmath.Quat4d

Multiplies quaternion q1 by the inverse of quaternion q2 and places the value into this quaternion.

mulInverse(Quat4f) - Method in class net.preibisch.mvrecon.vecmath.Quat4f

Multiplies this quaternion by the inverse of quaternion q1 and places the value into this quaternion.

mulInverse(Quat4f, Quat4f) - Method in class net.preibisch.mvrecon.vecmath.Quat4f

Multiplies quaternion q1 by the inverse of quaternion q2 and places the value into this quaternion.

mulInverse(Transform3D) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Multiplies this transform by the inverse of transform t1.

mulInverse(Transform3D, Transform3D) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Multiplies transform t1 by the inverse of transform t2.

mulNormalize(Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Multiplies this matrix by matrix m1, does an SVD normalization of the result, and places the result back into this matrix this = SVDnorm(this*m1).

mulNormalize(Matrix3d, Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Multiplies matrix m1 by matrix m2, does an SVD normalization of the result, and places the result into this matrix this = SVDnorm(m1*m2).

mulNormalize(Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Multiplies this matrix by matrix m1, does an SVD normalization of the result, and places the result back into this matrix. this = SVDnorm(this*m1).

mulNormalize(Matrix3f, Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Multiplies matrix m1 by matrix m2, does an SVD normalization of the result, and places the result into this matrix. this = SVDnorm(m1*m2).

multi_consensus - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac.RANSACParameters

multiConsensus - Variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac.RANSACParameters

multiConsensus() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac.RANSACParameters

MultipageTiffReader - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

Adapted version from the MicroManager codebase that supports the new diSPIM related tags and multiple-file reading.

MultipageTiffReader - Class in net.preibisch.mvrecon.headless.definedataset

Adapted version from the MicroManager codebase that supports the new diSPIM related tags and multiple-file reading.

MultipageTiffReader(File) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

MultipageTiffReader(File) - Constructor for class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

MultipageTiffReader.IFDData - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

MultipageTiffReader.IFDData - Class in net.preibisch.mvrecon.headless.definedataset

MultipageTiffReader.IFDEntry - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

MultipageTiffReader.IFDEntry - Class in net.preibisch.mvrecon.headless.definedataset

MULTIPLE_INDEXED - Enum constant in enum class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.CheckResult

MUlTIPLE_NAMED - Enum constant in enum class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.CheckResult

multipleAngleOption - Variable in class net.preibisch.mvrecon.headless.definedataset.StackListParameters

multipleChannelOption - Variable in class net.preibisch.mvrecon.headless.definedataset.StackListParameters

multipleIlluminationOption - Variable in class net.preibisch.mvrecon.headless.definedataset.StackListParameters

multipleInterestPointsGUI(String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

MultipleOMEZARRListChooser() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.OMEZARR.MultipleOMEZARRListChooser

multipleTileOption - Variable in class net.preibisch.mvrecon.headless.definedataset.StackListParameters

multipleTimePointOption - Variable in class net.preibisch.mvrecon.headless.definedataset.StackListParameters

multiplyComplex(Img<ComplexFloatType>, Img<ComplexFloatType>) - Static method in class util.FFTConvolution

MultiResolutionFlatfieldCorrectionWrappedImgLoader - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield

MultiResolutionFlatfieldCorrectionWrappedImgLoader(MultiResolutionImgLoader) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.MultiResolutionFlatfieldCorrectionWrappedImgLoader

MultiResolutionFlatfieldCorrectionWrappedImgLoader(MultiResolutionImgLoader, boolean) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.MultiResolutionFlatfieldCorrectionWrappedImgLoader

MultiResolutionLevelInfo(String, long[], DataType, int[], int[], int[], int[]) - Constructor for class net.preibisch.mvrecon.process.n5api.N5ApiTools.MultiResolutionLevelInfo

MultiResolutionSource - Class in net.preibisch.mvrecon.fiji.plugin.interactive

MultiResolutionSource(ArrayList<Pair<RandomAccessibleInterval<VolatileFloatType>, AffineTransform3D>>, String) - Constructor for class net.preibisch.mvrecon.fiji.plugin.interactive.MultiResolutionSource

MultiResolutionTools - Class in net.preibisch.mvrecon.fiji.plugin.interactive

MultiResolutionTools() - Constructor for class net.preibisch.mvrecon.fiji.plugin.interactive.MultiResolutionTools

MultiViewDatasetDefinition - Interface in net.preibisch.mvrecon.fiji.datasetmanager

MultiViewDeconvolution<C> - Class in net.preibisch.mvrecon.process.deconvolution

MultiViewDeconvolution(DeconViews, int, PsiInitFactory, ComputeBlockThreadFactory<C>, ImgFactory<FloatType>) - Constructor for class net.preibisch.mvrecon.process.deconvolution.MultiViewDeconvolution

MultiViewDeconvolutionMul - Class in net.preibisch.mvrecon.process.deconvolution

MultiViewDeconvolutionMul(DeconViews, int, PsiInitFactory, ComputeBlockThreadFactory<ComputeBlockMulThread>, ImgFactory<FloatType>) - Constructor for class net.preibisch.mvrecon.process.deconvolution.MultiViewDeconvolutionMul

MultiViewDeconvolutionSeq - Class in net.preibisch.mvrecon.process.deconvolution

MultiViewDeconvolutionSeq(DeconViews, int, PsiInitFactory, ComputeBlockThreadFactory<ComputeBlockSeqThread>, ImgFactory<FloatType>) - Constructor for class net.preibisch.mvrecon.process.deconvolution.MultiViewDeconvolutionSeq

MultiViewTableModelDecorator<AS> - Class in net.preibisch.mvrecon.fiji.spimdata.explorer

MultiViewTableModelDecorator(ISpimDataTableModel<AS>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.MultiViewTableModelDecorator

MultiWindowLayoutHelper - Class in net.preibisch.mvrecon.fiji.plugin.util

MultiWindowLayoutHelper() - Constructor for class net.preibisch.mvrecon.fiji.plugin.util.MultiWindowLayoutHelper

mulTransposeBoth(Matrix3d, Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Multiplies the transpose of matrix m1 times the transpose of matrix m2, and places the result into this.

mulTransposeBoth(Matrix3f, Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Multiplies the transpose of matrix m1 times the transpose of matrix m2, and places the result into this.

mulTransposeBoth(Matrix4d, Matrix4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Multiplies the transpose of matrix m1 times the transpose of matrix m2, and places the result into this.

mulTransposeBoth(Matrix4f, Matrix4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Multiplies the transpose of matrix m1 times the transpose of matrix m2, and places the result into this.

mulTransposeBoth(Transform3D, Transform3D) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Multiplies the transpose of transform t1 by the transpose of transform t2 and places the result into this transform (this = transpose(t1) * transpose(t2)).

mulTransposeLeft(Matrix3d, Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Multiplies the transpose of matrix m1 times matrix m2, and places the result into this.

mulTransposeLeft(Matrix3f, Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Multiplies the transpose of matrix m1 times matrix m2, and places the result into this.

mulTransposeLeft(Matrix4d, Matrix4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Multiplies the transpose of matrix m1 times matrix m2, and places the result into this.

mulTransposeLeft(Matrix4f, Matrix4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Multiplies the transpose of matrix m1 times matrix m2, and places the result into this.

mulTransposeLeft(Transform3D, Transform3D) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Multiplies the transpose of transform t1 by transform t2 and places the result into this matrix (this = transpose(t1) * t2).

mulTransposeRight(Matrix3d, Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Multiplies matrix m1 times the transpose of matrix m2, and places the result into this.

mulTransposeRight(Matrix3f, Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Multiplies matrix m1 times the transpose of matrix m2, and places the result into this.

mulTransposeRight(Matrix4d, Matrix4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Multiplies matrix m1 times the transpose of matrix m2, and places the result into this.

mulTransposeRight(Matrix4f, Matrix4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Multiplies matrix m1 times the transpose of matrix m2, and places the result into this.

mulTransposeRight(Transform3D, Transform3D) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Multiplies transform t1 by the transpose of transform t2 and places the result into this transform (this = t1 * transpose(t2)).

MyActionListener() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.AnalyzeErrorPopup.MyActionListener

MyActionListener() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.ApplyTransformationPopup.MyActionListener

MyActionListener() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BDVPopup.MyActionListener

MyActionListener() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BoundingBoxPopup.MyActionListener

MyActionListener() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.DeconvolutionPopup.MyActionListener

MyActionListener() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.DetectInterestPointsPopup.MyActionListener

MyActionListener() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.FusionPopup.MyActionListener

MyActionListener() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.InterestPointsExplorerPopup.MyActionListener

MyActionListener() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.LazyBDVPopup.MyActionListener

MyActionListener() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.MaxProjectPopup.MyActionListener

MyActionListener() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.QualityPopup.MyActionListener

MyActionListener() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.RegisterInterestPointsPopup.MyActionListener

MyActionListener() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.RegistrationExplorerPopup.MyActionListener

MyActionListener() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.ReorientSamplePopup.MyActionListener

MyActionListener() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.SpecifyCalibrationPopup.MyActionListener

MyActionListener() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.VisualizeDetectionsPopup.MyActionListener

MyActionListener() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.VisualizeNonRigid.MyActionListener

MyActionListener(int) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.DisplayRawImagesPopup.MyActionListener

MyActionListener(int) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.IntensityAdjustmentPopup.MyActionListener

MyActionListener(int) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.RemoveTransformationPopup.MyActionListener

MyActionListener(int) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.ResavePopup.MyActionListener

MyMultiLineLabel - Class in net.preibisch.mvrecon.fiji.plugin.util

MyMultiLineLabel(GenericDialog, Panel, String[]) - Constructor for class net.preibisch.mvrecon.fiji.plugin.util.MyMultiLineLabel

MyMultiLineLabel(GenericDialog, Panel, String[], int) - Constructor for class net.preibisch.mvrecon.fiji.plugin.util.MyMultiLineLabel

MyRenderer() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointExplorerPanel.MyRenderer

MyTarget(int, int) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough.MyTarget

myURL - Static variable in class net.preibisch.mvrecon.fiji.plugin.util.GUIHelper

N

n - Variable in class net.preibisch.mvrecon.imglib2.st.render.FilteredMaxDistanceSearchOnKDTree

n - Variable in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccessible

N - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel3D

N - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantSimilarityModel3D

N5ApiTools - Class in net.preibisch.mvrecon.process.n5api

N5ApiTools() - Constructor for class net.preibisch.mvrecon.process.n5api.N5ApiTools

N5ApiTools.MultiResolutionLevelInfo - Class in net.preibisch.mvrecon.process.n5api

n5URI - Variable in class net.preibisch.mvrecon.fiji.plugin.resave.ParametersResaveN5Api

name - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.ChannelInfo

name - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.ChannelOrIlluminationInfo

nameForGroup(Group<ViewDescription>) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

NamePattern - Class in net.preibisch.mvrecon.fiji.spimdata

NamePattern() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.NamePattern

NativeLibraryTools - Class in net.preibisch.mvrecon.process.cuda

NativeLibraryTools() - Constructor for class net.preibisch.mvrecon.process.cuda.NativeLibraryTools

navigateHistoryBackward() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

navigateHistoryForward() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

nDimensions - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.grid.RegularTranformHelpers.RegularTranslationParameters

NearestNeighborMaxDistanceSearchOnKDTree<T> - Class in net.preibisch.mvrecon.imglib2.st.render

NearestNeighborMaxDistanceSearchOnKDTree(KDTree<T>, T, double) - Constructor for class net.preibisch.mvrecon.imglib2.st.render.NearestNeighborMaxDistanceSearchOnKDTree

negate() - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Negates the value of this matrix: this = -this.

negate() - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Negates the value of this matrix: this = -this.

negate() - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Negates the value of this matrix: this = -this.

negate() - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Negates the value of this matrix: this = -this.

negate() - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Negates the value of this tuple in place.

negate() - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Negates the value of this tuple in place.

negate() - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Negates the value of this tuple in place.

negate() - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Negates the value of this tuple in place.

negate() - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Negates the value of this tuple in place.

negate(Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Sets the value of this matrix equal to the negation of of the Matrix3d parameter.

negate(Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Sets the value of this matrix equal to the negation of of the Matrix3f parameter.

negate(Matrix4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the value of this matrix equal to the negation of of the Matrix4d parameter.

negate(Matrix4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the value of this matrix equal to the negation of of the Matrix4f parameter.

negate(Tuple3d) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Sets the value of this tuple to the negation of tuple t1.

negate(Tuple3f) - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Sets the value of this tuple to the negation of tuple t1.

negate(Tuple3i) - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Sets the value of this tuple to the negation of tuple t1.

negate(Tuple4d) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Sets the value of this tuple to the negation of tuple t1.

negate(Tuple4f) - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Sets the value of this tuple to the negation of tuple t1.

NEGATIVE_DETERMINANT - Static variable in class net.preibisch.mvrecon.vecmath.Transform3D

This matrix has a negative determinant; an orthogonal matrix with a positive determinant is a rotation matrix; an orthogonal matrix with a negative determinant is a reflection and rotation matrix.

net.preibisch.legacy.io - package net.preibisch.legacy.io

net.preibisch.legacy.mpicbg - package net.preibisch.legacy.mpicbg

net.preibisch.legacy.registration.bead - package net.preibisch.legacy.registration.bead

net.preibisch.legacy.registration.bead.error - package net.preibisch.legacy.registration.bead.error

net.preibisch.legacy.registration.bead.laplace - package net.preibisch.legacy.registration.bead.laplace

net.preibisch.legacy.registration.detection - package net.preibisch.legacy.registration.detection

net.preibisch.legacy.registration.detection.descriptor - package net.preibisch.legacy.registration.detection.descriptor

net.preibisch.legacy.registration.threshold - package net.preibisch.legacy.registration.threshold

net.preibisch.legacy.segmentation - package net.preibisch.legacy.segmentation

net.preibisch.mvrecon - package net.preibisch.mvrecon

net.preibisch.mvrecon.fiji - package net.preibisch.mvrecon.fiji

net.preibisch.mvrecon.fiji.datasetmanager - package net.preibisch.mvrecon.fiji.datasetmanager

net.preibisch.mvrecon.fiji.datasetmanager.grid - package net.preibisch.mvrecon.fiji.datasetmanager.grid

net.preibisch.mvrecon.fiji.datasetmanager.metadatarefinement - package net.preibisch.mvrecon.fiji.datasetmanager.metadatarefinement

net.preibisch.mvrecon.fiji.datasetmanager.patterndetector - package net.preibisch.mvrecon.fiji.datasetmanager.patterndetector

net.preibisch.mvrecon.fiji.plugin - package net.preibisch.mvrecon.fiji.plugin

net.preibisch.mvrecon.fiji.plugin.apply - package net.preibisch.mvrecon.fiji.plugin.apply

net.preibisch.mvrecon.fiji.plugin.boundingbox - package net.preibisch.mvrecon.fiji.plugin.boundingbox

net.preibisch.mvrecon.fiji.plugin.fusion - package net.preibisch.mvrecon.fiji.plugin.fusion

net.preibisch.mvrecon.fiji.plugin.interactive - package net.preibisch.mvrecon.fiji.plugin.interactive

net.preibisch.mvrecon.fiji.plugin.interestpointdetection - package net.preibisch.mvrecon.fiji.plugin.interestpointdetection

net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive - package net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive

net.preibisch.mvrecon.fiji.plugin.interestpointregistration - package net.preibisch.mvrecon.fiji.plugin.interestpointregistration

net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global - package net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global

net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise - package net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise

net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters - package net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters

net.preibisch.mvrecon.fiji.plugin.interestpointregistration.statistics - package net.preibisch.mvrecon.fiji.plugin.interestpointregistration.statistics

net.preibisch.mvrecon.fiji.plugin.queryXML - package net.preibisch.mvrecon.fiji.plugin.queryXML

net.preibisch.mvrecon.fiji.plugin.resave - package net.preibisch.mvrecon.fiji.plugin.resave

net.preibisch.mvrecon.fiji.plugin.util - package net.preibisch.mvrecon.fiji.plugin.util

net.preibisch.mvrecon.fiji.spimdata - package net.preibisch.mvrecon.fiji.spimdata

net.preibisch.mvrecon.fiji.spimdata.boundingbox - package net.preibisch.mvrecon.fiji.spimdata.boundingbox

net.preibisch.mvrecon.fiji.spimdata.explorer - package net.preibisch.mvrecon.fiji.spimdata.explorer

net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror - package net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror

net.preibisch.mvrecon.fiji.spimdata.explorer.bdv - package net.preibisch.mvrecon.fiji.spimdata.explorer.bdv

net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint - package net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint

net.preibisch.mvrecon.fiji.spimdata.explorer.popup - package net.preibisch.mvrecon.fiji.spimdata.explorer.popup

net.preibisch.mvrecon.fiji.spimdata.explorer.registration - package net.preibisch.mvrecon.fiji.spimdata.explorer.registration

net.preibisch.mvrecon.fiji.spimdata.explorer.selection - package net.preibisch.mvrecon.fiji.spimdata.explorer.selection

net.preibisch.mvrecon.fiji.spimdata.explorer.viewneighbours - package net.preibisch.mvrecon.fiji.spimdata.explorer.viewneighbours

net.preibisch.mvrecon.fiji.spimdata.imgloaders - package net.preibisch.mvrecon.fiji.spimdata.imgloaders

net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2 - package net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2

net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield - package net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield

net.preibisch.mvrecon.fiji.spimdata.imgloaders.smartspim - package net.preibisch.mvrecon.fiji.spimdata.imgloaders.smartspim

net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting - package net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting

net.preibisch.mvrecon.fiji.spimdata.imgloaders.util - package net.preibisch.mvrecon.fiji.spimdata.imgloaders.util

net.preibisch.mvrecon.fiji.spimdata.intensityadjust - package net.preibisch.mvrecon.fiji.spimdata.intensityadjust

net.preibisch.mvrecon.fiji.spimdata.interestpoints - package net.preibisch.mvrecon.fiji.spimdata.interestpoints

net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions - package net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions

net.preibisch.mvrecon.fiji.spimdata.stitchingresults - package net.preibisch.mvrecon.fiji.spimdata.stitchingresults

net.preibisch.mvrecon.headless.definedataset - package net.preibisch.mvrecon.headless.definedataset

net.preibisch.mvrecon.imglib2.st.filter - package net.preibisch.mvrecon.imglib2.st.filter

net.preibisch.mvrecon.imglib2.st.render - package net.preibisch.mvrecon.imglib2.st.render

net.preibisch.mvrecon.imglib2.st.render.util - package net.preibisch.mvrecon.imglib2.st.render.util

net.preibisch.mvrecon.process.boundingbox - package net.preibisch.mvrecon.process.boundingbox

net.preibisch.mvrecon.process.chromaticabberation - package net.preibisch.mvrecon.process.chromaticabberation

net.preibisch.mvrecon.process.cuda - package net.preibisch.mvrecon.process.cuda

net.preibisch.mvrecon.process.deconvolution - package net.preibisch.mvrecon.process.deconvolution

net.preibisch.mvrecon.process.deconvolution.init - package net.preibisch.mvrecon.process.deconvolution.init

net.preibisch.mvrecon.process.deconvolution.iteration - package net.preibisch.mvrecon.process.deconvolution.iteration

net.preibisch.mvrecon.process.deconvolution.iteration.mul - package net.preibisch.mvrecon.process.deconvolution.iteration.mul

net.preibisch.mvrecon.process.deconvolution.iteration.sequential - package net.preibisch.mvrecon.process.deconvolution.iteration.sequential

net.preibisch.mvrecon.process.deconvolution.normalization - package net.preibisch.mvrecon.process.deconvolution.normalization

net.preibisch.mvrecon.process.deconvolution.util - package net.preibisch.mvrecon.process.deconvolution.util

net.preibisch.mvrecon.process.downsampling - package net.preibisch.mvrecon.process.downsampling

net.preibisch.mvrecon.process.downsampling.lazy - package net.preibisch.mvrecon.process.downsampling.lazy

net.preibisch.mvrecon.process.export - package net.preibisch.mvrecon.process.export

net.preibisch.mvrecon.process.fusion - package net.preibisch.mvrecon.process.fusion

net.preibisch.mvrecon.process.fusion.blk - package net.preibisch.mvrecon.process.fusion.blk

net.preibisch.mvrecon.process.fusion.blk.tps - package net.preibisch.mvrecon.process.fusion.blk.tps

net.preibisch.mvrecon.process.fusion.intensity - package net.preibisch.mvrecon.process.fusion.intensity

net.preibisch.mvrecon.process.fusion.intensity.mpicbg - package net.preibisch.mvrecon.process.fusion.intensity.mpicbg

net.preibisch.mvrecon.process.fusion.intensityadjust - package net.preibisch.mvrecon.process.fusion.intensityadjust

net.preibisch.mvrecon.process.fusion.lazy - package net.preibisch.mvrecon.process.fusion.lazy

net.preibisch.mvrecon.process.fusion.tps - package net.preibisch.mvrecon.process.fusion.tps

net.preibisch.mvrecon.process.fusion.transformed - package net.preibisch.mvrecon.process.fusion.transformed

net.preibisch.mvrecon.process.fusion.transformed.nonrigid - package net.preibisch.mvrecon.process.fusion.transformed.nonrigid

net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid - package net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid

net.preibisch.mvrecon.process.fusion.transformed.weightcombination - package net.preibisch.mvrecon.process.fusion.transformed.weightcombination

net.preibisch.mvrecon.process.fusion.transformed.weights - package net.preibisch.mvrecon.process.fusion.transformed.weights

net.preibisch.mvrecon.process.interestpointdetection - package net.preibisch.mvrecon.process.interestpointdetection

net.preibisch.mvrecon.process.interestpointdetection.methods - package net.preibisch.mvrecon.process.interestpointdetection.methods

net.preibisch.mvrecon.process.interestpointdetection.methods.dog - package net.preibisch.mvrecon.process.interestpointdetection.methods.dog

net.preibisch.mvrecon.process.interestpointdetection.methods.lazygauss - package net.preibisch.mvrecon.process.interestpointdetection.methods.lazygauss

net.preibisch.mvrecon.process.interestpointregistration - package net.preibisch.mvrecon.process.interestpointregistration

net.preibisch.mvrecon.process.interestpointregistration.global - package net.preibisch.mvrecon.process.interestpointregistration.global

net.preibisch.mvrecon.process.interestpointregistration.global.convergence - package net.preibisch.mvrecon.process.interestpointregistration.global.convergence

net.preibisch.mvrecon.process.interestpointregistration.global.linkremoval - package net.preibisch.mvrecon.process.interestpointregistration.global.linkremoval

net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating - package net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating

net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.strong - package net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.strong

net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.weak - package net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.weak

net.preibisch.mvrecon.process.interestpointregistration.pairwise - package net.preibisch.mvrecon.process.interestpointregistration.pairwise

net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation - package net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation

net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping - package net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping

net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap - package net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap

net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.range - package net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.range

net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.centerofmass - package net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.centerofmass

net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.fastrgldm - package net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.fastrgldm

net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.geometrichashing - package net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.geometrichashing

net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.icp - package net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.icp

net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.loadcorrespondences - package net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.loadcorrespondences

net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac - package net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac

net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm - package net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm

net.preibisch.mvrecon.process.interestpointremoval - package net.preibisch.mvrecon.process.interestpointremoval

net.preibisch.mvrecon.process.interestpointremoval.histogram - package net.preibisch.mvrecon.process.interestpointremoval.histogram

net.preibisch.mvrecon.process.n5api - package net.preibisch.mvrecon.process.n5api

net.preibisch.mvrecon.process.pointcloud.icp - package net.preibisch.mvrecon.process.pointcloud.icp

net.preibisch.mvrecon.process.pointcloud.pointdescriptor - package net.preibisch.mvrecon.process.pointcloud.pointdescriptor

net.preibisch.mvrecon.process.pointcloud.pointdescriptor.exception - package net.preibisch.mvrecon.process.pointcloud.pointdescriptor.exception

net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher - package net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher

net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model - package net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model

net.preibisch.mvrecon.process.pointcloud.pointdescriptor.similarity - package net.preibisch.mvrecon.process.pointcloud.pointdescriptor.similarity

net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test - package net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test

net.preibisch.mvrecon.process.psf - package net.preibisch.mvrecon.process.psf

net.preibisch.mvrecon.process.quality - package net.preibisch.mvrecon.process.quality

net.preibisch.mvrecon.process.splitting - package net.preibisch.mvrecon.process.splitting

net.preibisch.mvrecon.vecmath - package net.preibisch.mvrecon.vecmath

neutral - Static variable in class net.preibisch.mvrecon.fiji.plugin.util.GUIHelper

neutralMsg1a - Static variable in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

neutralMsg1b - Static variable in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

NEVER - Enum constant in enum class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsResultsWindow.BdvResetPolicy

NEVER - Enum constant in enum class net.preibisch.mvrecon.fiji.spimdata.explorer.viewneighbours.ViewNeighboursWindow.ResetPolicy

NEVER - Enum constant in enum class net.preibisch.mvrecon.fiji.spimdata.explorer.viewneighbours.ViewOverlapWindow.ResetPolicy

NEW_VIEW_SELECTED - Enum constant in enum class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsResultsWindow.BdvResetPolicy

NEW_VIEW_SELECTED - Enum constant in enum class net.preibisch.mvrecon.fiji.spimdata.explorer.viewneighbours.ViewNeighboursWindow.ResetPolicy

NEW_VIEW_SELECTED - Enum constant in enum class net.preibisch.mvrecon.fiji.spimdata.explorer.viewneighbours.ViewOverlapWindow.ResetPolicy

new2oldSetupId - Variable in class net.preibisch.mvrecon.process.splitting.SplittingTools.SetupSplitResult

new2oldSetupId() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitViewerImgLoader

newInstance() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.DHM

newInstance() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition

newInstance() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.LightSheetZ1

newInstance() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.MicroManager

newInstance() - Method in interface net.preibisch.mvrecon.fiji.datasetmanager.MultiViewDatasetDefinition

newInstance() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.OMEZARR

newInstance() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.SimView

newInstance() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM

newInstance() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListImageJ

newInstance() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListLOCI

newInstance() - Method in class net.preibisch.mvrecon.process.export.DisplayImage

newInstance() - Method in class net.preibisch.mvrecon.process.export.ExportLarge2DTIFF

newInstance() - Method in class net.preibisch.mvrecon.process.export.ExportN5Api

newInstance() - Method in interface net.preibisch.mvrecon.process.export.ImgExport

newInstance() - Method in class net.preibisch.mvrecon.process.export.OpenSeaDragon

newInstance() - Method in class net.preibisch.mvrecon.process.export.Save3dTIFF

newInstance(int, double[]) - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoint

newInstance(int, double[]) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.GroupedInterestPoint

newInstance(int, double[]) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test.VirtualPointNode

newInstance(URI, ViewId, String) - Static method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoints

newInstance(SpimData2) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.CenterOfMassGUI

newInstance(SpimData2) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.FRGLDMGUI

newInstance(SpimData2) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.GeometricHashingGUI

newInstance(SpimData2) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.IterativeClosestPointGUI

newInstance(SpimData2) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.LoadCorrespondencesGUI

newInstance(SpimData2) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.PairwiseGUI

newInstance(SpimData2) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.RGLDMGUI

newInstance(SpimData2, List<ViewId>) - Method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.AutomaticReorientationBoundingBoxGUI

newInstance(SpimData2, List<ViewId>) - Method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.BDVBoundingBoxGUI

newInstance(SpimData2, List<ViewId>) - Method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.BoundingBoxGUI

newInstance(SpimData2, List<ViewId>) - Method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.MaximumBoundingBoxGUI

newInstance(SpimData2, List<ViewId>) - Method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.MinFilterThresholdBoundingBoxGUI

newInstance(SpimData2, List<ViewId>) - Method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.ModifyDefinedBoundingBoxGUI

newInstance(SpimData2, List<ViewId>) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGaussianGUI

newInstance(SpimData2, List<ViewId>) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.InterestPointDetectionGUI

newInterestpoints - Variable in class net.preibisch.mvrecon.process.splitting.SplittingTools.SetupSplitResult

newLabel - Variable in class net.preibisch.mvrecon.process.interestpointremoval.CreateFromCorrespondencesParameters

newLabel - Variable in class net.preibisch.mvrecon.process.interestpointremoval.ThinOutParameters

newMatrixEntry(ViewTransform, double, int) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationExplorerPanel

newName(ViewTransform, String) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationExplorerPanel

newRegistrations - Variable in class net.preibisch.mvrecon.process.splitting.SplittingTools.SetupSplitResult

newSetupId2Interval - Variable in class net.preibisch.mvrecon.process.splitting.SplittingTools.SetupSplitResult

newSetupId2Interval() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitViewerImgLoader

newSetupIds - Variable in class net.preibisch.mvrecon.process.splitting.SplittingTools.SetupSplitResult

newSetups - Variable in class net.preibisch.mvrecon.process.splitting.SplittingTools.SetupSplitResult

next() - Static method in class util.ColorStream

nextIFD - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader.IFDData

nextIFD - Variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader.IFDData

nextIFDOffsetLocation - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader.IFDData

nextIFDOffsetLocation - Variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader.IFDData

nextOverlappingGroup(List<Group<V>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

Identify the indices of the next overlapping groups ordered by size, or return null if none are overlapping

NikonND2TileOrAngleRefiner - Class in net.preibisch.mvrecon.fiji.datasetmanager.metadatarefinement

NikonND2TileOrAngleRefiner() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.metadatarefinement.NikonND2TileOrAngleRefiner

nn - Variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.fastrgldm.FRGLDMParameters

nn - Variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm.RGLDMParameters

NO_OPTIMIZATION - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters.GlobalOptType

noInverseOfHessianMatrix - Variable in class net.preibisch.legacy.registration.bead.laplace.RejectStatistics

noLocalization(ArrayList<SimplePeak>, boolean, boolean, boolean) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.Localization

noMsg2 - Static variable in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

NONE - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.Split_Views.InterestPointAdding

NONE - Enum constant in enum class net.preibisch.mvrecon.imglib2.st.filter.GaussianFilterFactory.WeightType

NONE - Enum constant in enum class net.preibisch.mvrecon.process.splitting.ConsensusSetCriterion.ToleranceMode

nonRigidAcrossTime - Variable in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidParameters

nonRigidAcrossTime() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidParameters

NonrigidIP - Interface in net.preibisch.mvrecon.process.fusion.transformed.nonrigid

NonRigidParameters - Class in net.preibisch.mvrecon.process.fusion.transformed.nonrigid

NonRigidParameters() - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidParameters

NonRigidParametersGUI - Class in net.preibisch.mvrecon.fiji.plugin.fusion

NonRigidParametersGUI(SpimData2, List<? extends ViewId>) - Constructor for class net.preibisch.mvrecon.fiji.plugin.fusion.NonRigidParametersGUI

NonRigidRandomAccess<T> - Class in net.preibisch.mvrecon.process.fusion.transformed.nonrigid

Virtually transforms any RandomAccessibleInterval<RealType> into a RandomAccess<FloatType> using an AffineTransformation and Linear Interpolation.

NonRigidRandomAccess(RandomAccessibleInterval<T>, Collection<? extends NonrigidIP>, double, AffineModel3D, InterpolatorFactory<FloatType, RandomAccessible<FloatType>>, boolean, float, FloatType, long[]) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidRandomAccess

NonRigidRandomAccessible<T> - Class in net.preibisch.mvrecon.process.fusion.transformed.nonrigid

NonRigidRandomAccessible(RandomAccessibleInterval<T>, Collection<? extends NonrigidIP>, double, AffineModel3D, boolean, float, FloatType, Interval) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidRandomAccessible

NonRigidRandomAccessible(RandomAccessibleInterval<T>, Collection<? extends NonrigidIP>, AffineModel3D, Interval) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidRandomAccessible

NonRigidRasteredRandomAccess<T> - Class in net.preibisch.mvrecon.process.fusion.transformed.weights

NonRigidRasteredRandomAccess(RealRandomAccessible<T>, T, Collection<? extends NonrigidIP>, double, AffineModel3D, int[]) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.weights.NonRigidRasteredRandomAccess

NonRigidRasteredRandomAccessible<T> - Class in net.preibisch.mvrecon.process.fusion.transformed.weights

NonRigidRasteredRandomAccessible(RealRandomAccessible<T>, T, Collection<? extends NonrigidIP>, double, AffineModel3D, long[]) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.weights.NonRigidRasteredRandomAccessible

NonRigidTools - Class in net.preibisch.mvrecon.process.fusion.transformed.nonrigid

NonRigidTools() - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidTools

NonRigidWeightTools - Class in net.preibisch.mvrecon.process.fusion.transformed.nonrigid

NonRigidWeightTools() - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidWeightTools

NonWastefulRealPoint - Class in net.preibisch.mvrecon.fiji.spimdata.interestpoints

NonWastefulRealPoint(double[], boolean) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.interestpoints.NonWastefulRealPoint

normalize - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.LocalCoordinateSystemPointDescriptor

normalize() - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Performs singular value decomposition normalization of this matrix.

normalize() - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Performs singular value decomposition normalization of this matrix.

normalize() - Method in class net.preibisch.mvrecon.vecmath.Quat4d

Normalizes the value of this quaternion in place.

normalize() - Method in class net.preibisch.mvrecon.vecmath.Quat4f

Normalizes the value of this quaternion in place.

normalize() - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Normalizes the rotational components (upper 3x3) of this matrix in place using a Singular Value Decomposition (SVD).

normalize() - Method in class net.preibisch.mvrecon.vecmath.Vector3d

Normalizes this vector in place.

normalize() - Method in class net.preibisch.mvrecon.vecmath.Vector3f

Normalizes this vector in place.

normalize() - Method in class net.preibisch.mvrecon.vecmath.Vector4d

Normalizes this vector in place.

normalize() - Method in class net.preibisch.mvrecon.vecmath.Vector4f

Normalizes this vector in place.

normalize(IterableInterval<T>) - Static method in class net.preibisch.mvrecon.process.psf.PSFExtraction

normalize(Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Perform singular value decomposition normalization of matrix m1 and place the normalized values into this.

normalize(Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Perform singular value decomposition normalization of matrix m1 and place the normalized values into this.

normalize(Quat4d) - Method in class net.preibisch.mvrecon.vecmath.Quat4d

Sets the value of this quaternion to the normalized value of quaternion q1.

normalize(Quat4f) - Method in class net.preibisch.mvrecon.vecmath.Quat4f

Sets the value of this quaternion to the normalized value of quaternion q1.

normalize(Transform3D) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Normalizes the rotational components (upper 3x3) of transform t1 using a Singular Value Decomposition (SVD), and places the result into this transform.

normalize(Vector3d) - Method in class net.preibisch.mvrecon.vecmath.Vector3d

Sets the value of this vector to the normalization of vector v1.

normalize(Vector3f) - Method in class net.preibisch.mvrecon.vecmath.Vector3f

Sets the value of this vector to the normalization of vector v1.

normalize(Vector4d) - Method in class net.preibisch.mvrecon.vecmath.Vector4d

Sets the value of this vector to the normalization of vector v1.

normalize(Vector4f) - Method in class net.preibisch.mvrecon.vecmath.Vector4f

Sets the value of this vector to the normalization of vector v1.

normalizeCP() - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Perform cross product normalization of this matrix.

normalizeCP() - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Perform cross product normalization of this matrix.

normalizeCP() - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Normalizes the rotational components (upper 3x3) of this transform in place using a Cross Product (CP) normalization.

normalizeCP(Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Perform cross product normalization of matrix m1 and place the normalized values into this.

normalizeCP(Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Perform cross product normalization of matrix m1 and place the normalized values into this.

normalizeCP(Transform3D) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Normalizes the rotational components (upper 3x3) of transform t1 using a Cross Product (CP) normalization, and places the result into this transform.

normalizeImage(RandomAccessibleInterval<FloatType>) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

Normalizes the image to the range [0...1]

normalizeImage(RandomAccessibleInterval<FloatType>, float, float) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

Normalizes the image to the range [0...1]

normalizeImage(RandomAccessibleInterval<FloatType>, float, float, ExecutorService) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

Normalizes the image to the range [0...1]

normalizeVirtual(RandomAccessible<T>, double, double) - Static method in class util.ImgLib2Tools

normalizeVirtualRAI(RandomAccessibleInterval<T>) - Static method in class util.ImgLib2Tools

normalizeVirtualRAI(RandomAccessibleInterval<T>, double, double) - Static method in class util.ImgLib2Tools

normalizeWeights() - Method in class net.preibisch.mvrecon.process.deconvolution.util.ProcessInputImages

normalizeWeights(double) - Method in class net.preibisch.mvrecon.process.deconvolution.util.ProcessInputImages

normalizeWeights(double, boolean, float, float) - Method in class net.preibisch.mvrecon.process.deconvolution.util.ProcessInputImages

normalizeWeights(HashMap<Group<V>, RandomAccessibleInterval<FloatType>>, List<Group<V>>, double, boolean, float, float) - Static method in class net.preibisch.mvrecon.process.deconvolution.util.ProcessInputImages

NormalizingRandomAccess<T> - Class in net.preibisch.mvrecon.process.deconvolution.normalization

NormalizingRandomAccess(int, ArrayList<RandomAccessibleInterval<FloatType>>, double, boolean, float, float, T) - Constructor for class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccess

NormalizingRandomAccessibleInterval<T> - Class in net.preibisch.mvrecon.process.deconvolution.normalization

NormalizingRandomAccessibleInterval(RandomAccessibleInterval<T>, int, ArrayList<RandomAccessibleInterval<FloatType>>, double, boolean, float, float, T) - Constructor for class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccessibleInterval

normToSum1(IterableInterval<FloatType>) - Static method in class net.preibisch.mvrecon.process.deconvolution.normalization.AdjustInput

Norms an image so that the sum over all pixels is 1.

noStableMaxima - Variable in class net.preibisch.legacy.registration.bead.laplace.RejectStatistics

NoSuitablePointsException - Exception Class in net.preibisch.mvrecon.process.pointcloud.pointdescriptor.exception

NoSuitablePointsException() - Constructor for exception class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.exception.NoSuitablePointsException

NoSuitablePointsException(Object, String) - Constructor for exception class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.exception.NoSuitablePointsException

NoSuitablePointsException(String) - Constructor for exception class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.exception.NoSuitablePointsException

notHighestValueInIdentityRadius - Variable in class net.preibisch.legacy.registration.bead.laplace.RejectStatistics

nrgui - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

nrgui - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

nSteps - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.grid.RegularTranformHelpers.RegularTranslationParameters

num_iterations - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac.RANSACParameters

num_lines - Variable in class net.preibisch.mvrecon.fiji.plugin.util.MyMultiLineLabel

numAngles() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

numAngles() - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

numAngles() - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

numBackups - Static variable in class net.preibisch.mvrecon.fiji.spimdata.XmlIoSpimData2

NumberUtils - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

NumberUtils() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.NumberUtils

numBlocks(int[]) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2

numCandidates - Variable in class net.preibisch.legacy.registration.bead.error.GlobalErrorStatisticsImpl

numCellCreatorThreads - Variable in class net.preibisch.mvrecon.fiji.plugin.resave.ParametersResaveN5Api

numChannels() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

numChannels() - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

numChannels() - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

numChannelsAndAngles() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

numChannelsAndAngles() - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

numConsensusSetsBetweenVisible(ViewInterestPoints, List<? extends ViewId>, String) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

numContributingPixels() - Method in class net.preibisch.mvrecon.process.deconvolution.util.FusedNonZeroRandomAccess

numCorr - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.GroupPairResult

numCorr - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.PairError

numCorr - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.SingleGroupError

numCorr - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.SingleViewError

numCorrespondences - Variable in class net.preibisch.legacy.registration.bead.error.GlobalErrorStatisticsImpl

numCorrespondences(ViewInterestPoints, List<? extends ViewId>, String) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

numCorresponding(ViewInterestPoints, List<? extends ViewId>, String) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

numCorrespondingBetweenVisible(ViewInterestPoints, List<? extends ViewId>, String) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

numDetections - Variable in class net.preibisch.legacy.registration.bead.error.GlobalErrorStatisticsImpl

numDetections(ViewInterestPoints, List<? extends ViewId>, String) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

numDigitsAngles - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData.Pattern

numDigitsAngles - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

numDigitsAngles - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoader

numDigitsCams - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData.Pattern

numDigitsChannels - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData.Pattern

numDigitsChannels - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

numDigitsChannels - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoader

numDigitsIlluminations - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

numDigitsIlluminations - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoader

numDigitsPlanes - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData.Pattern

numDigitsTiles - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

numDigitsTiles - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoader

numDigitsTimepoints - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData.Pattern

numDigitsTimepoints - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

numDigitsTimepoints - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoader

numDimensions - Variable in class util.StackingRealRandomAccessible

numDimensions() - Method in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox

numDimensions() - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoint

numDimensions() - Method in class net.preibisch.mvrecon.imglib2.st.render.FilteredMaxDistanceSearchOnKDTree

numDimensions() - Method in class net.preibisch.mvrecon.imglib2.st.render.util.SimpleRealLocalizable

numDimensions() - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccessibleInterval

numDimensions() - Method in class net.preibisch.mvrecon.process.fusion.intensity.IntensityCorrection.SerializableRealInterval

numDimensions() - Method in class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.FlattenedMatches

numDimensions() - Method in class net.preibisch.mvrecon.process.fusion.tps.Landmarks

numDimensions() - Method in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccessible

numDimensions() - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval

numDimensions() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGrid

numDimensions() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridAccess

numDimensions() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGrid

numDimensions() - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputGeneralRandomAccessible

numDimensions() - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccess2d

numDimensions() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccessibleInterval

numDimensions() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccess

numDimensions() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccessible

numDimensions() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.ContentBasedFFTRealRandomAccessible

numDimensions() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.ContentBasedRealRandomAccessible

numDimensions() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.InterpolatingNonRigidRasteredRandomAccessible

numDimensions() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.NonRigidRasteredRandomAccessible

numDimensions() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.TransformedRasteredRandomAccessible

numDimensions() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.AbstractPointDescriptor

Dimensionality of the Points of this AbstractPointDescriptor

numDimensions() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.LocalCoordinateSystemPointDescriptor

numDimensions() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test.VirtualPointNode

numDimensions() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.TranslationInvariantLocalCoordinateSystemPointDescriptor

numDimensions() - Method in class net.preibisch.mvrecon.process.quality.FRCRealRandomAccessible

numDimensions() - Method in class util.StackingRealRandomAccessible

numDimensions() - Method in class util.StackingRealRandomAccessible.StackingRealRandomAccess

NumericAffineModel3D - Class in net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid

NumericAffineModel3D() - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

NumericAffineModel3D(AffineModel3D) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

NumericAffineModel3D(NativeImg<?, ? extends DoubleAccess>) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

NumericAffineModel3D(NumericAffineModel3D) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

NumericAffineTransform3D - Class in net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid

NumericAffineTransform3D() - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

NumericAffineTransform3D(NativeImg<?, ? extends DoubleAccess>) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

NumericAffineTransform3D(AffineTransform3D) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

NumericAffineTransform3D(NumericAffineTransform3D) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

NumericalFilenamePatternDetector - Class in net.preibisch.mvrecon.fiji.datasetmanager.patterndetector

NumericalFilenamePatternDetector() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.patterndetector.NumericalFilenamePatternDetector

numIlluminations() - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

numImages - Variable in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccess

numIntervals - Variable in class net.preibisch.mvrecon.process.splitting.SplitResult

numIterations - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

numIterations - Variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac.RANSACParameters

numMipmapLevels() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitMultiResolutionSetupImgLoader

numMipmapLevels() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitViewerSetupImgLoader

numNeighbors - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm.RGLDMParameters

numNeighbors() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.AbstractPointDescriptor

The number of neighbors used for this descriptor

numParallelBlocks() - Method in interface net.preibisch.mvrecon.process.deconvolution.iteration.ComputeBlockThreadFactory

numParallelBlocks() - Method in class net.preibisch.mvrecon.process.deconvolution.iteration.mul.ComputeBlockMulThreadCPUFactory

numParallelBlocks() - Method in class net.preibisch.mvrecon.process.deconvolution.iteration.sequential.ComputeBlockSeqThreadCPUFactory

numParallelBlocks() - Method in class net.preibisch.mvrecon.process.deconvolution.iteration.sequential.ComputeBlockSeqThreadCUDAFactory

numPixels(long[], double) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

numPixels(long[], long[], double) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

numPixels(Dimensions, boolean, double[]) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2

numPixels(Interval, double) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

numPositions() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

numPositions() - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

numThreads() - Static method in class net.preibisch.mvrecon.Threads

numTiles() - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

numTimepoints() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

numTimepoints() - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

numTimepoints() - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

O

objective() - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

OctTreeSplitCriterion - Interface in net.preibisch.mvrecon.process.splitting

Generic criterion interface for deciding whether to continue splitting an octant in the oct-tree splitting algorithm.

OctTreeSplitCriterion.SplitCorrespondence - Class in net.preibisch.mvrecon.process.splitting

Lightweight structure for correspondence data during splitting.

OctTreeSplitResult(ArrayList<Interval>, SplitOctTree.SplitStatsAccumulator) - Constructor for class net.preibisch.mvrecon.process.splitting.SplitOctTree.OctTreeSplitResult

of(D, Dimensions, float[], float[]) - Static method in class net.preibisch.mvrecon.process.fusion.blk.tps.BlendingFunction3D

Blending weights are 0 <= w <= 1.

of(D, T, Dimensions, float[]) - Static method in class net.preibisch.mvrecon.process.fusion.blk.tps.MaskingFunction3D

Weights are w=0 for the outermost border pixels of interval.

offsetX - Variable in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccess

offsetX - Variable in class net.preibisch.mvrecon.process.fusion.transformed.weights.InterpolatingNonRigidRasteredRandomAccess

offsetX - Variable in class net.preibisch.mvrecon.process.fusion.transformed.weights.NonRigidRasteredRandomAccess

offsetY - Variable in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccess

offsetY - Variable in class net.preibisch.mvrecon.process.fusion.transformed.weights.InterpolatingNonRigidRasteredRandomAccess

offsetY - Variable in class net.preibisch.mvrecon.process.fusion.transformed.weights.NonRigidRasteredRandomAccess

offsetZ - Variable in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccess

offsetZ - Variable in class net.preibisch.mvrecon.process.fusion.transformed.weights.InterpolatingNonRigidRasteredRandomAccess

offsetZ - Variable in class net.preibisch.mvrecon.process.fusion.transformed.weights.NonRigidRasteredRandomAccess

old2newSetupId(Map<Integer, Integer>) - Static method in class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion

OLDSETUP_NAME - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.XmlIoSplitViewerImgLoader

oldSetupId - Variable in class net.preibisch.mvrecon.process.splitting.SplittingTools.SetupSplitResult

OMEZARR - Class in net.preibisch.mvrecon.fiji.datasetmanager

OMEZARR() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.OMEZARR

OMEZARR.MultipleOMEZARRListChooser - Class in net.preibisch.mvrecon.fiji.datasetmanager

OMEZARR.URIListChooser - Interface in net.preibisch.mvrecon.fiji.datasetmanager

OMEZARR.WildcardDirectoryListChooser - Class in net.preibisch.mvrecon.fiji.datasetmanager

OMEZarrAttributes - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

OMEZarrAttributes() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.OMEZarrAttributes

OMEZARREntry(String, int[]) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AllenOMEZarrLoader.OMEZARREntry

ONE_ROUND_ITERATIVE - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters.GlobalOptType

ONE_ROUND_SIMPLE - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters.GlobalOptType

OneAngle - Enum constant in enum class net.preibisch.mvrecon.headless.definedataset.StackListParameters.AngleOption

OneChannel - Enum constant in enum class net.preibisch.mvrecon.headless.definedataset.StackListParameters.ChannelOption

OneFilePerAngle - Enum constant in enum class net.preibisch.mvrecon.headless.definedataset.StackListParameters.AngleOption

OneFilePerChannel - Enum constant in enum class net.preibisch.mvrecon.headless.definedataset.StackListParameters.ChannelOption

OneFilePerIllumination - Enum constant in enum class net.preibisch.mvrecon.headless.definedataset.StackListParameters.IlluminationOption

OneFilePerTile - Enum constant in enum class net.preibisch.mvrecon.headless.definedataset.StackListParameters.TileOption

OneFilePerTimePoint - Enum constant in enum class net.preibisch.mvrecon.headless.definedataset.StackListParameters.TimePointOption

OneIllumination - Enum constant in enum class net.preibisch.mvrecon.headless.definedataset.StackListParameters.IlluminationOption

oneSetContainsBoth(V, V, Collection<? extends Collection<V>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.PairwiseStrategyTools

OneTile - Enum constant in enum class net.preibisch.mvrecon.headless.definedataset.StackListParameters.TileOption

OneTimePoint - Enum constant in enum class net.preibisch.mvrecon.headless.definedataset.StackListParameters.TimePointOption

open(File) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoaderIJ

open(String, ImgFactory<FloatType>) - Static method in class net.preibisch.mvrecon.fiji.plugin.util.OpenImg

openAndDownsample(BasicImgLoader, ViewId, long[], boolean) - Static method in class net.preibisch.mvrecon.process.downsampling.DownsampleTools

Opens the image at a specified downsampling level (e.g. 4,4,1).

openAs32Bit(File) - Static method in class net.preibisch.legacy.io.IOFunctions

openAs32Bit(File, ImgFactory<FloatType>) - Static method in class net.preibisch.legacy.io.IOFunctions

openAs32BitArrayImg(File) - Static method in class net.preibisch.legacy.io.IOFunctions

openAtLowestLevel(ImgLoader, ViewId) - Static method in class net.preibisch.mvrecon.process.downsampling.DownsampleTools

openAtLowestLevel(ImgLoader, ViewId, AffineTransform3D) - Static method in class net.preibisch.mvrecon.process.downsampling.DownsampleTools

openBDV(ExplorerWindow<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.LazyBDVPopup

Open BDV in lazy mode for panel's data, if not already open.

openCZI(T, ViewId) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyLightSheetZ1ImgLoader

openDownsampled(BasicImgLoader, ViewId, AffineTransform3D) - Static method in class net.preibisch.mvrecon.process.downsampling.DownsampleTools

Opens the image at an appropriate resolution for the provided transformation and concatenates an extra transform

openDownsampled(BasicImgLoader, ViewId, AffineTransform3D, double[]) - Static method in class net.preibisch.mvrecon.process.downsampling.DownsampleTools

Opens the image at an appropriate resolution for the provided transformation and concatenates an extra transform

openDownsampled2(BasicImgLoader, ViewId, AffineTransform3D, double[]) - Static method in class net.preibisch.mvrecon.process.downsampling.DownsampleTools

Opens the image at an appropriate resolution for the provided transformation and concatenates an extra transform

openFileRead(File) - Static method in class net.preibisch.legacy.io.TextFileAccess

openFileRead(String) - Static method in class net.preibisch.legacy.io.TextFileAccess

openFileReadCloudReader(KeyValueAccess, URI) - Static method in class util.URITools

openFileReadCloudStream(KeyValueAccess, URI) - Static method in class util.URITools

openFileReadEx(File) - Static method in class net.preibisch.legacy.io.TextFileAccess

openFileReadEx(String) - Static method in class net.preibisch.legacy.io.TextFileAccess

openFiles - Variable in class net.preibisch.legacy.registration.bead.SegmentationBenchmark

openFileWrite(File) - Static method in class net.preibisch.legacy.io.TextFileAccess

openFileWrite(String) - Static method in class net.preibisch.legacy.io.TextFileAccess

openFileWriteCloudStream(KeyValueAccess, URI) - Static method in class util.URITools

openFileWriteCloudWriter(KeyValueAccess, URI) - Static method in class util.URITools

openFileWriteEx(File) - Static method in class net.preibisch.legacy.io.TextFileAccess

openFileWriteEx(String) - Static method in class net.preibisch.legacy.io.TextFileAccess

openImg(T, ViewId) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyFileMapImgLoaderLOCI

OpenImg - Class in net.preibisch.mvrecon.fiji.plugin.util

OpenImg() - Constructor for class net.preibisch.mvrecon.fiji.plugin.util.OpenImg

openLOCI(File, T, ViewId) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoaderLOCI

OpenSeaDragon - Class in net.preibisch.mvrecon.process.export

OpenSeaDragon() - Constructor for class net.preibisch.mvrecon.process.export.OpenSeaDragon

OpenSeaDragon.OpenSeaDragonImgLib2 - Class in net.preibisch.mvrecon.process.export

OpenSeaDragonImgLib2(BlockSupplier<UnsignedByteType>, BlockSupplier<UnsignedByteType>, BlockSupplier<UnsignedByteType>, Interval) - Constructor for class net.preibisch.mvrecon.process.export.OpenSeaDragon.OpenSeaDragonImgLib2

openSelectionDialog() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

OPTIMIZATION_I - Enum constant in enum class net.preibisch.mvrecon.process.deconvolution.DeconViewPSF.PSFTYPE

OPTIMIZATION_II - Enum constant in enum class net.preibisch.mvrecon.process.deconvolution.DeconViewPSF.PSFTYPE

ortho(double, double, double, double, double, double) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Creates an orthographic projection transform that mimics a standard, camera-based, view-model.

ORTHOGONAL - Static variable in class net.preibisch.mvrecon.vecmath.Transform3D

The four row vectors that make up an orthogonal matrix form a basis, meaning that they are mutually orthogonal; an orthogonal matrix with positive determinant is a pure rotation matrix; a negative determinant indicates a rotation and a reflection.

osemSpeedup - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

osemspeedupChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

out - Variable in class net.preibisch.mvrecon.fiji.plugin.resave.ProgressWriterIJ

out() - Method in class net.preibisch.mvrecon.fiji.plugin.resave.ProgressWriterIJ

outside - Variable in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccess

outsideValue - Variable in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccessible

outsideValueImg - Static variable in class net.preibisch.mvrecon.process.deconvolution.MultiViewDeconvolution

overlapChoices - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.BasicRegistrationParameters

OverlapDetection<V> - Interface in net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap

OVERLAPPING_ONLY - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.BasicRegistrationParameters.InterestPointOverlapType

OVERLAPPING_ONLY - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.BasicRegistrationParameters.OverlapType

overlappingFor(SpimData2, Collection<? extends ViewId>, Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.ViewNeighbors

Per-click overlap query.

overlappingGroups(Collection<Group<V>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

Identify all pairs of overlapping groups

overlappingViewIds(Interval, Collection<? extends ViewId>, Map<? extends ViewId, ? extends AffineTransform3D>, Map<? extends ViewId, ? extends Dimensions>, int) - Static method in class net.preibisch.mvrecon.process.fusion.lazy.LazyFusionTools

overlappingViews(SpimData2, Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.ViewNeighbors

For each view in universe, return the set of other views in universe whose registered bounding-box overlaps it.

overlappingWith(ViewId, SpimData2, Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.ViewNeighbors

Convenience: overlap set for a single view.

overlaps - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.grid.RegularTranformHelpers.RegularTranslationParameters

overlaps(Interval, Interval) - Static method in class net.preibisch.mvrecon.process.fusion.lazy.LazyFusionTools

overlaps(BoundingBox, BoundingBox) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap.SimpleBoundingBoxOverlap

overlaps(Group<V>, Group<V>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

Test if there is any overlap between two groups (at least one view part of both)

overlaps(V, V) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap.AllAgainstAllOverlap

overlaps(V, V) - Method in interface net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap.OverlapDetection

overlaps(V, V) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap.SimpleBoundingBoxOverlap

overlapType - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.BasicRegistrationParameters

P

p() - Method in class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.FlattenedMatches

paint(Graphics) - Method in class net.preibisch.mvrecon.fiji.plugin.util.MyMultiLineLabel

pair() - Method in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.PairwiseStitchingResult

PAIR - Enum constant in enum class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.Mode

PairError(ViewId, ViewId, double, int) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.PairError

pairs - Variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.PairwiseSetup

pairsSpanTimepoints(List<Pair<V, V>>, int) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.ReferenceTimepoint

Tests if pairs span over different timepoints (that are not the reference timepoint)

pairwiseGroupedMatchingInstance() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.CenterOfMassGUI

pairwiseGroupedMatchingInstance() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.FRGLDMGUI

pairwiseGroupedMatchingInstance() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.GeometricHashingGUI

pairwiseGroupedMatchingInstance() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.IterativeClosestPointGUI

pairwiseGroupedMatchingInstance() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.LoadCorrespondencesGUI

pairwiseGroupedMatchingInstance() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.PairwiseGUI

This is not good style, but when creating the object we do not know which generic parameter will be required as the user specifies this later (could be a factory)

pairwiseGroupedMatchingInstance() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.RGLDMGUI

PairwiseGUI - Class in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise

PairwiseGUI() - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.PairwiseGUI

PairwiseLinkImpl - Class in net.preibisch.mvrecon.fiji.spimdata.stitchingresults

PairwiseLinkImpl(Set<Pair<Group<ViewId>, Group<ViewId>>>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.PairwiseLinkImpl

PairwiseLinkInterface - Interface in net.preibisch.mvrecon.fiji.spimdata.stitchingresults

pairwiseMatchingInstance() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.CenterOfMassGUI

pairwiseMatchingInstance() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.FRGLDMGUI

pairwiseMatchingInstance() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.GeometricHashingGUI

pairwiseMatchingInstance() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.IterativeClosestPointGUI

pairwiseMatchingInstance() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.LoadCorrespondencesGUI

pairwiseMatchingInstance() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.PairwiseGUI

pairwiseMatchingInstance() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.RGLDMGUI

PairwiseResult<I> - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise

PairwiseResult(boolean) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.PairwiseResult

pairwiseResultToXml(PairwiseStitchingResult<ViewId>) - Method in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.XmlIoStitchingResults

PairwiseSetup<V> - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation

PairwiseSetup(List<V>) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.PairwiseSetup

PairwiseSetup(List<V>, Set<Group<V>>) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.PairwiseSetup

Sets up all pairwise comparisons 1) definePairs() 2) removeNonOverlappingPairs() - if wanted 3) reorderPairs() - if wanted 4) detectSubsets() 5) sortSubsets() - if wanted 6) getSubsets() within each subset 7) subset.fixViews( this.getDefaultFixedViews() ) 8) subset.fixViews() - fixed some of the views necessary for the strategy to work

pairwiseSetupInstance(BasicRegistrationParameters.RegistrationType, List<ViewId>, Set<Group<ViewId>>) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.AdvancedRegistrationParameters

PairwiseStitchingResult<C> - Class in net.preibisch.mvrecon.fiji.spimdata.stitchingresults

PairwiseStitchingResult(Pair<Group<C>, Group<C>>, RealInterval, AffineGet, double, double) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.PairwiseStitchingResult

PairwiseStitchingResult.CrossCorrelationPairwiseQualityMeasure - Class in net.preibisch.mvrecon.fiji.spimdata.stitchingresults

PairwiseStitchingResult.PairwiseQualityMeasure - Interface in net.preibisch.mvrecon.fiji.spimdata.stitchingresults

PairwiseStrategyTools - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise

PairwiseStrategyTools() - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.PairwiseStrategyTools

panel - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorer

panel - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BDVPopup

panel - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.LazyBDVPopup

panel() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointExplorer

panel() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationExplorer

paperURL - Static variable in class net.preibisch.mvrecon.fiji.plugin.util.GUIHelper

ParallelepipedOverlap - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap

Tight overlap test for two affine-transformed voxel cubes (parallelepipeds in world space) via the 3-D Separating Axis Theorem (SAT).

parameters - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.FRGLDMGUI

parameters - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.IterativeClosestPointGUI

parameters - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.RGLDMGUI

Parameters() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.Parameters

ParametersResaveAsTIFF() - Constructor for class net.preibisch.mvrecon.fiji.plugin.resave.Resave_TIFF.ParametersResaveAsTIFF

ParametersResaveHDF5(boolean, int[][], int[][], File, File, boolean, boolean, int, int, boolean, int, int, double, double) - Constructor for class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.ParametersResaveHDF5

ParametersResaveN5Api - Class in net.preibisch.mvrecon.fiji.plugin.resave

ParametersResaveN5Api() - Constructor for class net.preibisch.mvrecon.fiji.plugin.resave.ParametersResaveN5Api

Params(String, int, double, boolean) - Constructor for class net.preibisch.mvrecon.fiji.plugin.Visualize_Detections.Params

parseCompression(GenericDialog) - Static method in class net.preibisch.mvrecon.fiji.plugin.util.PluginHelper

parseDialog(GenericDialog) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGaussianGUI

parseDialog(GenericDialog) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.CenterOfMassGUI

parseDialog(GenericDialog) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.FRGLDMGUI

parseDialog(GenericDialog) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.GeometricHashingGUI

parseDialog(GenericDialog) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.IterativeClosestPointGUI

parseDialog(GenericDialog) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.LoadCorrespondencesGUI

parseDialog(GenericDialog) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.PairwiseGUI

parseDialog(GenericDialog) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.RGLDMGUI

parseDialog(GenericDialog) - Method in interface net.preibisch.mvrecon.fiji.plugin.util.GenericDialogAppender

parseDownsampleChoice(String) - Static method in class net.preibisch.mvrecon.process.downsampling.DownsampleTools

parseJSONSimple(String) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

parseJSONSimple(String) - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

parseMetaData(File, File) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData

parseMetaDataFile(URI) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM

parseName(String) - Static method in class net.preibisch.mvrecon.headless.definedataset.Rewrite_LuxendoXML

parseNameString(String, boolean) - Static method in class net.preibisch.mvrecon.fiji.spimdata.NamePattern

Parse a pattern provided by the user defining a range of integers.

ParsePattern - Class in net.preibisch.legacy.io

ParsePattern() - Constructor for class net.preibisch.legacy.io.ParsePattern

parseProperties(Properties) - Method in class net.preibisch.mvrecon.headless.definedataset.DefineDataSetParameters

parseProperties(Properties) - Method in class net.preibisch.mvrecon.headless.definedataset.StackListParameters

parseQuery(GenericDialog, boolean) - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.NonRigidParametersGUI

parseRansacQuery(GenericDialog) - Static method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.PairwiseGUI

Reads the fields added by PairwiseGUI.addRansacQuery(GenericDialog) (in the same order) and returns the resulting RANSACParameters, or null if the user cancels the advanced sub-dialog.

parseRegistrations(GenericDialog) - Method in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

parseResolutionsString(String) - Static method in class net.preibisch.mvrecon.fiji.plugin.util.PluginHelper

parseSimpleParametersFromDialog(GenericDialog) - Static method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters

parseSimViewXML(File) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData

parseString(String, int) - Static method in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

parseTimestamps(File, String) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.DHMMetaData

parseXML(URI) - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

parseXML(URI) - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.LoadParseQueryXML

pasteBlock(RandomAccessibleInterval<FloatType>, RandomAccessibleInterval<FloatType>) - Method in class net.preibisch.mvrecon.process.cuda.Block

pasteSelection(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationExplorerPanel

path - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoader

Pattern() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData.Pattern

patternParser - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData

peakTooLow - Variable in class net.preibisch.legacy.registration.bead.laplace.RejectStatistics

PERCENTAGE - Enum constant in enum class net.preibisch.mvrecon.process.splitting.ConsensusSetCriterion.ToleranceMode

percentGPUMem - Variable in class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGParameters

perimeterSamplingFactor - Variable in class net.preibisch.mvrecon.process.quality.FRC

The correlation is computed using intervals around the circle circumference.

perspective(double, double, double, double) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Creates a perspective projection transform that mimics a standard, camera-based, view-model.

PHASE_DIR_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoDHMImgLoader

PHASE_ID_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoDHMImgLoader

pixelDistanceX - Variable in class net.preibisch.mvrecon.headless.definedataset.DefineDataSetParameters

pixelDistanceY - Variable in class net.preibisch.mvrecon.headless.definedataset.DefineDataSetParameters

pixelDistanceZ - Variable in class net.preibisch.mvrecon.headless.definedataset.DefineDataSetParameters

pixelOffset - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader.IFDData

pixelOffset - Variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader.IFDData

pixelType - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

pixelType() - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

PIXELTYPE_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoSimViewImgLoader

pixelTypes1 - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

pixelTypeString() - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

pixelUnit - Variable in class net.preibisch.mvrecon.headless.definedataset.DefineDataSetParameters

PLANE_PATTERN - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData

plotData(TimePoints, ArrayList<RegistrationStatistics>) - Static method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.statistics.TimeLapseDisplay

plotData(TimePoints, ArrayList<RegistrationStatistics>, int, boolean) - Static method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.statistics.TimeLapseDisplay

plotData(TimePoints, ArrayList<RegistrationStatistics>, int, boolean, List<SelectTimepointEntry>) - Static method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.statistics.TimeLapseDisplay

plotHistogram(SpimData2, Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.fiji.plugin.Show_Histogram

plotHistogram(SpimData2, Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.fiji.plugin.Show_Relative_Histogram

plotHistogram(SpimData2, Collection<? extends ViewId>, String, String) - Static method in class net.preibisch.mvrecon.process.interestpointremoval.DistanceHistogram

plotHistogram(SpimData2, Collection<? extends ViewId>, String, String, String) - Static method in class net.preibisch.mvrecon.process.interestpointremoval.RelativeDistanceHistogram

plotHistogram(SpimData2, Collection<? extends ViewId>, HashMap<? extends ViewId, String>, String) - Static method in class net.preibisch.mvrecon.process.interestpointremoval.DistanceHistogram

plotHistogram(SpimData2, Collection<? extends ViewId>, HashMap<? extends ViewId, String>, HashMap<? extends ViewId, String>, String) - Static method in class net.preibisch.mvrecon.process.interestpointremoval.RelativeDistanceHistogram

PluginHelper - Class in net.preibisch.mvrecon.fiji.plugin.util

PluginHelper() - Constructor for class net.preibisch.mvrecon.fiji.plugin.util.PluginHelper

PluginHelper.ChooseDirectoryListener - Class in net.preibisch.mvrecon.fiji.plugin.util

PluginHelper.ChooseXmlFileListener - Class in net.preibisch.mvrecon.fiji.plugin.util

Point1D - Class in net.preibisch.mvrecon.process.fusion.intensity.mpicbg

A 1D point.

Point1D(double) - Constructor for class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.Point1D

Point1D(double, double) - Constructor for class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.Point1D

Point3d - Class in net.preibisch.mvrecon.vecmath

A 3 element point that is represented by double precision floating point x,y,z coordinates.

Point3d() - Constructor for class net.preibisch.mvrecon.vecmath.Point3d

Constructs and initializes a Point3d to (0,0,0).

Point3d(double[]) - Constructor for class net.preibisch.mvrecon.vecmath.Point3d

Constructs and initializes a Point3d from the array of length 3.

Point3d(double, double, double) - Constructor for class net.preibisch.mvrecon.vecmath.Point3d

Constructs and initializes a Point3d from the specified xyz coordinates.

Point3d(Point3d) - Constructor for class net.preibisch.mvrecon.vecmath.Point3d

Constructs and initializes a Point3d from the specified Point3d.

Point3d(Point3f) - Constructor for class net.preibisch.mvrecon.vecmath.Point3d

Constructs and initializes a Point3d from the specified Point3f.

Point3d(Tuple3d) - Constructor for class net.preibisch.mvrecon.vecmath.Point3d

Constructs and initializes a Point3d from the specified Tuple3d.

Point3d(Tuple3f) - Constructor for class net.preibisch.mvrecon.vecmath.Point3d

Constructs and initializes a Point3d from the specified Tuple3f.

Point3f - Class in net.preibisch.mvrecon.vecmath

A 3 element point that is represented by single precision floating point x,y,z coordinates.

Point3f() - Constructor for class net.preibisch.mvrecon.vecmath.Point3f

Constructs and initializes a Point3f to (0,0,0).

Point3f(float[]) - Constructor for class net.preibisch.mvrecon.vecmath.Point3f

Constructs and initializes a Point3f from the array of length 3.

Point3f(float, float, float) - Constructor for class net.preibisch.mvrecon.vecmath.Point3f

Constructs and initializes a Point3f from the specified xyz coordinates.

Point3f(Point3d) - Constructor for class net.preibisch.mvrecon.vecmath.Point3f

Constructs and initializes a Point3f from the specified Point3d.

Point3f(Point3f) - Constructor for class net.preibisch.mvrecon.vecmath.Point3f

Constructs and initializes a Point3f from the specified Point3f.

Point3f(Tuple3d) - Constructor for class net.preibisch.mvrecon.vecmath.Point3f

Constructs and initializes a Point3f from the specified Tuple3d.

Point3f(Tuple3f) - Constructor for class net.preibisch.mvrecon.vecmath.Point3f

Constructs and initializes a Point3f from the specified Tuple3f.

Point3i - Class in net.preibisch.mvrecon.vecmath

A 3 element point represented by signed integer x,y,z coordinates.

Point3i() - Constructor for class net.preibisch.mvrecon.vecmath.Point3i

Constructs and initializes a Point3i to (0,0,0).

Point3i(int[]) - Constructor for class net.preibisch.mvrecon.vecmath.Point3i

Constructs and initializes a Point3i from the array of length 3.

Point3i(int, int, int) - Constructor for class net.preibisch.mvrecon.vecmath.Point3i

Constructs and initializes a Point3i from the specified x, y, and z coordinates.

Point3i(Tuple3i) - Constructor for class net.preibisch.mvrecon.vecmath.Point3i

Constructs and initializes a Point3i from the specified Tuple3i.

Point4d - Class in net.preibisch.mvrecon.vecmath

A 4 element vector represented by double precision floating point x,y,z,w coordinates.

Point4d() - Constructor for class net.preibisch.mvrecon.vecmath.Point4d

Constructs and initializes a Point4d to (0,0,0,0).

Point4d(double[]) - Constructor for class net.preibisch.mvrecon.vecmath.Point4d

Constructs and initializes a Point4d from the coordinates contained in the array.

Point4d(double, double, double, double) - Constructor for class net.preibisch.mvrecon.vecmath.Point4d

Constructs and initializes a Point4d from the specified xyzw coordinates.

Point4d(Point4d) - Constructor for class net.preibisch.mvrecon.vecmath.Point4d

Constructs and initializes a Point4d from the specified Point4d.

Point4d(Point4f) - Constructor for class net.preibisch.mvrecon.vecmath.Point4d

Constructs and initializes a Point4d from the specified Point4f.

Point4d(Tuple3d) - Constructor for class net.preibisch.mvrecon.vecmath.Point4d

Constructs and initializes a Point4d from the specified Tuple3d.

Point4d(Tuple4d) - Constructor for class net.preibisch.mvrecon.vecmath.Point4d

Constructs and initializes a Point4d from the specified Tuple4d.

Point4d(Tuple4f) - Constructor for class net.preibisch.mvrecon.vecmath.Point4d

Constructs and initializes a Point4d from the specified Tuple4f.

Point4f - Class in net.preibisch.mvrecon.vecmath

A 4 element point represented by single precision floating point x,y,z,w coordinates.

Point4f() - Constructor for class net.preibisch.mvrecon.vecmath.Point4f

Constructs and initializes a Point4f to (0,0,0,0).

Point4f(float[]) - Constructor for class net.preibisch.mvrecon.vecmath.Point4f

Constructs and initializes a Point4f from the array of length 4.

Point4f(float, float, float, float) - Constructor for class net.preibisch.mvrecon.vecmath.Point4f

Constructs and initializes a Point4f from the specified xyzw coordinates.

Point4f(Point4d) - Constructor for class net.preibisch.mvrecon.vecmath.Point4f

Constructs and initializes a Point4f from the specified Point4d.

Point4f(Point4f) - Constructor for class net.preibisch.mvrecon.vecmath.Point4f

Constructs and initializes a Point4f from the specified Point4f.

Point4f(Tuple3f) - Constructor for class net.preibisch.mvrecon.vecmath.Point4f

Constructs and initializes a Point4f from the specified Tuple3f.

Point4f(Tuple4d) - Constructor for class net.preibisch.mvrecon.vecmath.Point4f

Constructs and initializes a Point4f from the specified Tuple4d.

Point4f(Tuple4f) - Constructor for class net.preibisch.mvrecon.vecmath.Point4f

Constructs and initializes a Point4f from the specified Tuple4f.

PointMatch1D - Class in net.preibisch.mvrecon.process.fusion.intensity.mpicbg

A match of two 1D points.

PointMatch1D(Point1D, Point1D) - Constructor for class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.PointMatch1D

PointMatch1D(Point1D, Point1D, double) - Constructor for class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.PointMatch1D

PointMatchCreator - Interface in net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating

PointMatchGeneric<P> - Class in net.preibisch.legacy.mpicbg

PointMatchGeneric(P, P) - Constructor for class net.preibisch.legacy.mpicbg.PointMatchGeneric

PointMatchGeneric(P, P, double) - Constructor for class net.preibisch.legacy.mpicbg.PointMatchGeneric

PointMatchGeneric(P, P, double[]) - Constructor for class net.preibisch.legacy.mpicbg.PointMatchGeneric

PointMatchGeneric(P, P, double[], double) - Constructor for class net.preibisch.legacy.mpicbg.PointMatchGeneric

PointMatchGeneric(P, P, double, double) - Constructor for class net.preibisch.legacy.mpicbg.PointMatchGeneric

PointMatchIdentification<P> - Interface in net.preibisch.mvrecon.process.pointcloud.icp

PointNode - Class in net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test

PointNode(double[]) - Constructor for class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test.PointNode

PointNode(double[], double[]) - Constructor for class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test.PointNode

PointNode(Point) - Constructor for class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test.PointNode

PointSpreadFunction - Class in net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions

PointSpreadFunction(URI, String) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions.PointSpreadFunction

PointSpreadFunction(URI, String, Img<FloatType>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions.PointSpreadFunction

PointSpreadFunction(SpimData2, ViewId, Img<FloatType>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions.PointSpreadFunction

PointSpreadFunctions - Class in net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions

PointSpreadFunctions() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions.PointSpreadFunctions

PointSpreadFunctions(HashMap<ViewId, PointSpreadFunction>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions.PointSpreadFunctions

PointSpreadFunctionsPopup - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

PointSpreadFunctionsPopup() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.PointSpreadFunctionsPopup

populateAttributesEntities(int, ArrayList<HashSet<Integer>>) - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

populateImage(ArrayImg<T, ?>, File, String, String, List<String>, String, String) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyDHMImgLoader

populateImage(Img<T>, BasicViewDescription<?>, MultipageTiffReader) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyMicroManagerImgLoader

populateImageSize(SmartSPIM.SmartSPIMMetaData, boolean) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM

popups - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

pow(double) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

pow(double) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

pow(NumericAffineModel3D) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

pow(NumericAffineTransform3D) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

preAlign - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters

preciseAvgMax - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

precomputeBoundingBoxes(Collection<V>) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap.SimpleBoundingBoxOverlap

Pre-compute all bounding boxes for a collection of views in parallel.

PRECOMPUTED - Enum constant in enum class net.preibisch.mvrecon.process.fusion.FusionTools.ImgDataType

preConcatenateTransform(SpimData, ViewId, AffineTransform3D, String) - Static method in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

predictTilesAndAngles(IFormatReader) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil

predictTimepointsChannelsAndIllums(IFormatReader) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil

prefetch(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitViewerImgLoader

prefetch(BasicImgLoader, int) - Static method in class util.URITools

prepareCachedImage(String, int, int, int, CacheHints, T) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AllenOMEZarrLoader

preprocess() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

preprocess() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.InterestPointDetectionGUI

if any preprocessing is necessary

preserveAnisotropy - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

preserveAnisotropy - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

presetNames - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.grid.RegularTranformHelpers

presets - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.grid.RegularTranformHelpers

printAffine3D(Affine3D<?>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

printAffine3D(AffineGet) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

printAndSummarizeTransformations(Iterable<? extends ViewId>, Map<? extends ViewId, ? extends Tile>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

Print per-view transformation models (capped at TransformationTools.maxPerViewTransformLog) followed by a one-line summary of identity vs non-identity counts.

printDimensions(Dimensions) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.SimViewSetupImgLoader

printDownsampling(double) - Static method in class net.preibisch.mvrecon.process.downsampling.DownsampleTools

For double-based downsampling Double.NaN means no downsampling to avoid unnecessary computations, here we return a String for that number that says "None" if it is Double.NaN

printErr() - Static method in class net.preibisch.legacy.io.IOFunctions

printErr(Object) - Static method in class net.preibisch.legacy.io.IOFunctions

printErr(String) - Static method in class net.preibisch.legacy.io.IOFunctions

printIJLog - Static variable in class net.preibisch.legacy.io.IOFunctions

printInterval(RealInterval) - Static method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxTools

println() - Static method in class net.preibisch.legacy.io.IOFunctions

println(Object) - Static method in class net.preibisch.legacy.io.IOFunctions

println(String) - Static method in class net.preibisch.legacy.io.IOFunctions

printlnTS() - Static method in class net.preibisch.legacy.io.IOFunctions

printlnTS(Object) - Static method in class net.preibisch.legacy.io.IOFunctions

printlnTS(String) - Static method in class net.preibisch.legacy.io.IOFunctions

printMetaData(Hashtable<String, Object>) - Static method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

printMetaData(IFormatReader) - Static method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

printRealInterval(RealInterval) - Static method in class net.preibisch.legacy.io.IOFunctions

printRealInterval(RealInterval) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

get String representation of RealInterval TODO: PR to ImgLib2 (Util) ?

printResult() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm.RGLDMPairwise

printResults(SpimData2, ArrayList<AnalyzeErrorsUtil.PairError>, AnalyzeErrorsUtil.Parameters) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil

Print top-N worst, bottom-M best, and the per-old-tile-pair / per-old-tile rollup summary blocks that the AnalyzeErrorsUtil.Parameters dialog choices request.

printStatistics() - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.loadcorrespondences.LoadCorrespondencesPairwise

Print timing statistics for the LoadCorrespondencesPairwise matcher

process(Interval, int[], T, Set<AccessFlags>, Consumer<RandomAccessibleInterval<T>>) - Static method in class util.Lazy

processCorrespondingInterestPointsStatic(ViewSetup, int, TimePoint, SpimData2, Map<Integer, ? extends List<Integer>>, Map<ViewId, ViewInterestPointLists>, AtomicInteger, int, SplittingTools.CorrespondenceSaver, Map<String, Map<Integer, InterestPoint>>) - Static method in class net.preibisch.mvrecon.process.splitting.SplittingTools

Process corresponding interest points for a single (oldSetup, newSetupId, timepoint) combination.

processFailures(Set<T>) - Method in class net.preibisch.mvrecon.process.export.RetryTracker

Remove successful blocks from the failed set and update retry counts.

processingInterval - Variable in class net.preibisch.mvrecon.process.interestpointdetection.methods.lazygauss.LazyWeightedGauss

ProcessInputImages<V> - Class in net.preibisch.mvrecon.process.deconvolution.util

ProcessInputImages(AbstractSpimData<?>, Collection<Group<V>>, ExecutorService, Interval, double, boolean, float, float, boolean, float, float, Map<? extends ViewId, AffineModel1D>) - Constructor for class net.preibisch.mvrecon.process.deconvolution.util.ProcessInputImages

ProcessInputImages(AbstractSpimData<?>, Collection<Group<V>>, ExecutorService, Interval, double, Map<? extends ViewId, AffineModel1D>) - Constructor for class net.preibisch.mvrecon.process.deconvolution.util.ProcessInputImages

ProcessInputImages(AbstractSpimData<?>, Collection<Group<V>>, ExecutorService, Interval, Map<? extends ViewId, AffineModel1D>) - Constructor for class net.preibisch.mvrecon.process.deconvolution.util.ProcessInputImages

processRegistration(PairwiseSetup<ViewId>, Map<Integer, ? extends BasicViewSetup>, PairwiseGUI, GroupParameters.InterestpointGroupingType, BasicRegistrationParameters.InterestPointOverlapType, double, Set<ViewId>, Model<?>, Map<Subset<ViewId>, Pair<ViewId, Dimensions>>, Map<ViewId, ViewRegistration>, Map<ViewId, ViewDescription>, Map<ViewId, ViewInterestPointLists>, Map<ViewId, HashMap<String, Double>>, GlobalOptimizationParameters, boolean, boolean) - Method in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

processSetupStatic(ViewSetup, ArrayList<Interval>, int, int, TimePoints, ViewRegistrations, SpimData2, boolean, Split_Views.InterestPointAdding, String, double, int, int, double, double, long, String, SplittingTools.InterestPointSaver) - Static method in class net.preibisch.mvrecon.process.splitting.SplittingTools

Process a single ViewSetup's split intervals in isolation.

processWithFutures(List<Future<T>>, Collection<T>) - Method in class net.preibisch.mvrecon.process.export.RetryTracker

Method to process all results when running with a service that returns futures.

ProgressWriterIJ - Class in net.preibisch.mvrecon.fiji.plugin.resave

ProgressWriterIJ() - Constructor for class net.preibisch.mvrecon.fiji.plugin.resave.ProgressWriterIJ

project(Point4d) - Method in class net.preibisch.mvrecon.vecmath.Point3d

Multiplies each of the x,y,z components of the Point4d parameter by 1/w and places the projected values into this point.

project(Point4d) - Method in class net.preibisch.mvrecon.vecmath.Point4d

Multiplies each of the x,y,z components of the Point4d parameter by 1/w, places the projected values into this point, and places a 1 as the w parameter of this point.

project(Point4f) - Method in class net.preibisch.mvrecon.vecmath.Point3f

Multiplies each of the x,y,z components of the Point4f parameter by 1/w and places the projected values into this point.

project(Point4f) - Method in class net.preibisch.mvrecon.vecmath.Point4f

Multiplies each of the x,y,z components of the Point4f parameter by 1/w, places the projected values into this point, and places a 1 as the w parameter of this point.

proposedMipmaps - Variable in class net.preibisch.mvrecon.fiji.plugin.resave.ParametersResaveN5Api

proposeMipmaps(Collection<? extends BasicViewSetup>) - Static method in class net.preibisch.mvrecon.fiji.plugin.resave.Resave_HDF5

PSF_Assign - Class in net.preibisch.mvrecon.fiji.plugin

PSF_Assign() - Constructor for class net.preibisch.mvrecon.fiji.plugin.PSF_Assign

PSF_Average - Class in net.preibisch.mvrecon.fiji.plugin

PSF_Average() - Constructor for class net.preibisch.mvrecon.fiji.plugin.PSF_Average

PSF_Extract - Class in net.preibisch.mvrecon.fiji.plugin

PSF_Extract() - Constructor for class net.preibisch.mvrecon.fiji.plugin.PSF_Extract

PSF_FILE_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions.XmlKeysPointSpreadFunctions

PSF_SETUP_ATTRIBUTE_NAME - Static variable in class net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions.XmlKeysPointSpreadFunctions

PSF_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions.XmlKeysPointSpreadFunctions

PSF_TIMEPOINT_ATTRIBUTE_NAME - Static variable in class net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions.XmlKeysPointSpreadFunctions

PSF_View - Class in net.preibisch.mvrecon.fiji.plugin

PSF_View() - Constructor for class net.preibisch.mvrecon.fiji.plugin.PSF_View

PSFCombination - Class in net.preibisch.mvrecon.process.psf

PSFCombination() - Constructor for class net.preibisch.mvrecon.process.psf.PSFCombination

PSFExtraction<T> - Class in net.preibisch.mvrecon.process.psf

PSFExtraction(RandomAccessible<T>, Collection<RealLocalizable>, T, long[]) - Constructor for class net.preibisch.mvrecon.process.psf.PSFExtraction

PSFExtraction(RandomAccessible<T>, Collection<RealLocalizable>, T, long[], boolean) - Constructor for class net.preibisch.mvrecon.process.psf.PSFExtraction

PSFExtraction(RandomAccessibleInterval<T>, Collection<RealLocalizable>, T, long[]) - Constructor for class net.preibisch.mvrecon.process.psf.PSFExtraction

PSFExtraction(RandomAccessibleInterval<T>, Collection<RealLocalizable>, T, long[], boolean) - Constructor for class net.preibisch.mvrecon.process.psf.PSFExtraction

PSFExtraction(RealRandomAccessible<T>, Collection<RealLocalizable>, T, long[]) - Constructor for class net.preibisch.mvrecon.process.psf.PSFExtraction

PSFExtraction(RealRandomAccessible<T>, Collection<RealLocalizable>, T, long[], boolean) - Constructor for class net.preibisch.mvrecon.process.psf.PSFExtraction

PSFExtraction(SpimData2, ViewId, String, boolean, T, long[]) - Constructor for class net.preibisch.mvrecon.process.psf.PSFExtraction

PSFExtraction(SpimData2, ViewId, String, boolean, T, long[], boolean) - Constructor for class net.preibisch.mvrecon.process.psf.PSFExtraction

PSFPreparation - Class in net.preibisch.mvrecon.process.deconvolution.util

PSFPreparation() - Constructor for class net.preibisch.mvrecon.process.deconvolution.util.PSFPreparation

PSFS_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions.XmlKeysPointSpreadFunctions

psfToXml(PointSpreadFunction, ViewId) - Method in class net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions.XmlIoPointSpreadFunctions

psfType - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

psfTypeChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

psiCopyBlockSize - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

psiFactory - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

psiInit - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

PsiInit - Interface in net.preibisch.mvrecon.process.deconvolution.init

PsiInit.PsiInitType - Enum Class in net.preibisch.mvrecon.process.deconvolution.init

PsiInitAvgApprox - Class in net.preibisch.mvrecon.process.deconvolution.init

PsiInitAvgApprox() - Constructor for class net.preibisch.mvrecon.process.deconvolution.init.PsiInitAvgApprox

PsiInitAvgApproxFactory - Class in net.preibisch.mvrecon.process.deconvolution.init

PsiInitAvgApproxFactory() - Constructor for class net.preibisch.mvrecon.process.deconvolution.init.PsiInitAvgApproxFactory

PsiInitAvgApproxThread - Class in net.preibisch.mvrecon.process.deconvolution.init

PsiInitAvgApproxThread(DeconView, int) - Constructor for class net.preibisch.mvrecon.process.deconvolution.init.PsiInitAvgApproxThread

PsiInitAvgApproxThread(DeconView, int, int) - Constructor for class net.preibisch.mvrecon.process.deconvolution.init.PsiInitAvgApproxThread

PsiInitAvgPrecise - Class in net.preibisch.mvrecon.process.deconvolution.init

PsiInitAvgPrecise() - Constructor for class net.preibisch.mvrecon.process.deconvolution.init.PsiInitAvgPrecise

PsiInitAvgPreciseFactory - Class in net.preibisch.mvrecon.process.deconvolution.init

PsiInitAvgPreciseFactory() - Constructor for class net.preibisch.mvrecon.process.deconvolution.init.PsiInitAvgPreciseFactory

PsiInitAvgPreciseThread - Class in net.preibisch.mvrecon.process.deconvolution.init

Fuse one portion of a paralell fusion, supports no weights

PsiInitAvgPreciseThread(ImagePortion, RandomAccessibleInterval<FloatType>, ArrayList<RandomAccessibleInterval<FloatType>>) - Constructor for class net.preibisch.mvrecon.process.deconvolution.init.PsiInitAvgPreciseThread

PsiInitBlurredFused - Class in net.preibisch.mvrecon.process.deconvolution.init

PsiInitBlurredFused() - Constructor for class net.preibisch.mvrecon.process.deconvolution.init.PsiInitBlurredFused

PsiInitBlurredFused(double) - Constructor for class net.preibisch.mvrecon.process.deconvolution.init.PsiInitBlurredFused

PsiInitBlurredFusedFactory - Class in net.preibisch.mvrecon.process.deconvolution.init

PsiInitBlurredFusedFactory() - Constructor for class net.preibisch.mvrecon.process.deconvolution.init.PsiInitBlurredFusedFactory

PsiInitBlurredFusedThread - Class in net.preibisch.mvrecon.process.deconvolution.init

Fuse one portion of a paralell fusion, supports no weights

PsiInitBlurredFusedThread(ImagePortion, RandomAccessibleInterval<FloatType>, ArrayList<RandomAccessibleInterval<FloatType>>) - Constructor for class net.preibisch.mvrecon.process.deconvolution.init.PsiInitBlurredFusedThread

psiInitChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

PsiInitFactory - Interface in net.preibisch.mvrecon.process.deconvolution.init

PsiInitFromFile - Class in net.preibisch.mvrecon.process.deconvolution.init

PsiInitFromFile(File, boolean) - Constructor for class net.preibisch.mvrecon.process.deconvolution.init.PsiInitFromFile

PsiInitFromFileFactory - Class in net.preibisch.mvrecon.process.deconvolution.init

PsiInitFromFileFactory(File, boolean) - Constructor for class net.preibisch.mvrecon.process.deconvolution.init.PsiInitFromFileFactory

PsiInitFromRAI - Class in net.preibisch.mvrecon.process.deconvolution.init

PsiInitFromRAI(RandomAccessibleInterval<FloatType>, boolean) - Constructor for class net.preibisch.mvrecon.process.deconvolution.init.PsiInitFromRAI

PsiInitFromRAIFactory - Class in net.preibisch.mvrecon.process.deconvolution.init

PsiInitFromRAIFactory(RandomAccessibleInterval<FloatType>, boolean) - Constructor for class net.preibisch.mvrecon.process.deconvolution.init.PsiInitFromRAIFactory

psiStartFile - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

put(double, double, double) - Method in class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.FlattenedMatches

put(PointMatch) - Method in class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.FlattenedMatches

putTextEntry(float, float, String) - Method in class net.preibisch.legacy.mpicbg.SketchTikZFileObject

pvid(ViewId) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

pvids(ViewId) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

pwr - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.BasicRegistrationParameters

Q

q() - Method in class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.FlattenedMatches

quadrFuncValue - Variable in class net.preibisch.legacy.registration.bead.laplace.DoGMaximum

QualityGUI - Class in net.preibisch.mvrecon.fiji.plugin.fusion

QualityGUI(SpimData2, List<ViewId>) - Constructor for class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

QualityPointMatch - Class in net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating

QualityPointMatch(Point, Point, double) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.QualityPointMatch

QualityPopup - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

QualityPopup() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.QualityPopup

QualityPopup.MyActionListener - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

Quat4d - Class in net.preibisch.mvrecon.vecmath

A 4-element quaternion represented by double precision floating point x,y,z,w coordinates.

Quat4d() - Constructor for class net.preibisch.mvrecon.vecmath.Quat4d

Constructs and initializes a Quat4d to (0,0,0,0).

Quat4d(double[]) - Constructor for class net.preibisch.mvrecon.vecmath.Quat4d

Constructs and initializes a Quat4d from the array of length 4.

Quat4d(double, double, double, double) - Constructor for class net.preibisch.mvrecon.vecmath.Quat4d

Constructs and initializes a Quat4d from the specified xyzw coordinates.

Quat4d(Quat4d) - Constructor for class net.preibisch.mvrecon.vecmath.Quat4d

Constructs and initializes a Quat4d from the specified Quat4d.

Quat4d(Quat4f) - Constructor for class net.preibisch.mvrecon.vecmath.Quat4d

Constructs and initializes a Quat4d from the specified Quat4f.

Quat4d(Tuple4d) - Constructor for class net.preibisch.mvrecon.vecmath.Quat4d

Constructs and initializes a Quat4d from the specified Tuple4d.

Quat4d(Tuple4f) - Constructor for class net.preibisch.mvrecon.vecmath.Quat4d

Constructs and initializes a Quat4d from the specified Tuple4f.

Quat4f - Class in net.preibisch.mvrecon.vecmath

A 4 element unit quaternion represented by single precision floating point x,y,z,w coordinates.

Quat4f() - Constructor for class net.preibisch.mvrecon.vecmath.Quat4f

Constructs and initializes a Quat4f to (0.0,0.0,0.0,0.0).

Quat4f(float[]) - Constructor for class net.preibisch.mvrecon.vecmath.Quat4f

Constructs and initializes a Quat4f from the array of length 4.

Quat4f(float, float, float, float) - Constructor for class net.preibisch.mvrecon.vecmath.Quat4f

Constructs and initializes a Quat4f from the specified xyzw coordinates.

Quat4f(Quat4d) - Constructor for class net.preibisch.mvrecon.vecmath.Quat4f

Constructs and initializes a Quat4f from the specified Quat4d.

Quat4f(Quat4f) - Constructor for class net.preibisch.mvrecon.vecmath.Quat4f

Constructs and initializes a Quat4f from the specified Quat4f.

Quat4f(Tuple4d) - Constructor for class net.preibisch.mvrecon.vecmath.Quat4f

Constructs and initializes a Quat4f from the specified Tuple4d.

Quat4f(Tuple4f) - Constructor for class net.preibisch.mvrecon.vecmath.Quat4f

Constructs and initializes a Quat4f from the specified Tuple4f.

Quaternion - Class in net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher

Quaternion(float, float, float, float) - Constructor for class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.Quaternion

Quaternion(float, float, float, float, float, float, float, float, float) - Constructor for class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.Quaternion

query() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.NonRigidParametersGUI

query(int, String, List<E>, List<E>) - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

queryAdditionalParameters(GenericDialog) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGaussianGUI

queryAdditionalParameters(GenericDialog) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

queryAdvancedRANSAC(boolean) - Static method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.PairwiseGUI

If the user enabled "Advanced_RANSAC_options", query maxTrust / minimal inlier ratio / filter-RANSAC in a follow-up dialog, updating the RANSACParameters statics that the GUI uses to build its RANSACParameters.

queryBigDataViewer(SpimData, List<ViewId>, ApplyParameters) - Method in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

queryCUDADetails(CUDAStandardFunctions, boolean) - Static method in class net.preibisch.mvrecon.process.cuda.CUDATools

queryCUDADetails(CUDAStandardFunctions, boolean, GenericDialogAppender) - Static method in class net.preibisch.mvrecon.process.cuda.CUDATools

queryCZIFile() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.LightSheetZ1

queryDetails() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

queryDetails() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

queryDetails() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

queryDetails() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

queryDetails() - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

queryDetails(SpimData2, List<ViewId>) - Static method in class net.preibisch.mvrecon.fiji.plugin.Visualize_Detections

queryDirectoryAndRatio() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.DHM

queryGeneralInformation() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

queryGUI(GenericDialog, SpimData2) - Static method in class net.preibisch.mvrecon.process.splitting.ConsensusSetCriterion

Query GUI components and create ConsensusSetCriterion instance.

queryGUI(GenericDialog, SpimData2) - Static method in class net.preibisch.mvrecon.process.splitting.CrossViewCorrespondenceCriterion

Query GUI components and create CrossViewCorrespondenceCriterion instance.

queryGUI(GenericDialog, SpimData2, long[]) - Static method in class net.preibisch.mvrecon.process.splitting.SplitDistributeEvenly

queryGUI(GenericDialog, SpimData2, long[]) - Static method in class net.preibisch.mvrecon.process.splitting.SplitOctTree

Query GUI components and create SplitOctTree instance.

queryGUI(GenericDialog, SpimData2, long[], Set<Integer>) - Static method in class net.preibisch.mvrecon.process.splitting.SplitOctTree

Query GUI components and create SplitOctTree instance.

queryGUI(GenericDialog, SpimData2, Set<Integer>) - Static method in class net.preibisch.mvrecon.process.splitting.ConsensusSetCriterion

Query GUI components and create ConsensusSetCriterion instance.

queryGUI(GenericDialog, SpimData2, Set<Integer>) - Static method in class net.preibisch.mvrecon.process.splitting.CrossViewCorrespondenceCriterion

Query GUI components and create CrossViewCorrespondenceCriterion instance.

queryIndividualEntry(String, String[], int) - Static method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

Querys a single element from the list

queryInformation() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

queryMetaDataFile() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM

queryMMFile() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.MicroManager

queryMultipleEntries(String, String[], boolean[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

Querys a multiple element from the list

queryNames() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

queryNewCal(ArrayList<Specify_Calibration.Cal>, Specify_Calibration.Cal) - Static method in class net.preibisch.mvrecon.fiji.plugin.Specify_Calibration

queryParameters() - Method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.BoundingBoxGUI

queryParameters() - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoaderIJ

queryParameters(boolean, boolean, boolean, boolean, boolean) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

queryParameters(boolean, boolean, boolean, boolean, boolean) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.InterestPointDetectionGUI

Query the necessary parameters for the interestpoint detection

queryParameters(String, int) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.grid.RegularTranformHelpers

queryParameters(FusionExportInterface) - Method in class net.preibisch.mvrecon.process.export.DisplayImage

queryParameters(FusionExportInterface) - Method in class net.preibisch.mvrecon.process.export.ExportLarge2DTIFF

queryParameters(FusionExportInterface) - Method in class net.preibisch.mvrecon.process.export.ExportN5Api

queryParameters(FusionExportInterface) - Method in interface net.preibisch.mvrecon.process.export.ImgExport

queryParameters(FusionExportInterface) - Method in class net.preibisch.mvrecon.process.export.OpenSeaDragon

queryParameters(FusionExportInterface) - Method in class net.preibisch.mvrecon.process.export.Save3dTIFF

queryParams(SpimData, List<ViewId>) - Method in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

queryPattern(String, String[], String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

Querys a pattern of element from the list

queryRegularizedModel() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.TransformationModelGUI

queryRootDir() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.SimView

queryRotationAxis(SpimData, List<ViewId>, ApplyParameters) - Method in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

queryString(SpimData, List<ViewId>, ApplyParameters) - Method in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

queryXML() - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

queryXML(boolean, boolean, boolean, boolean, boolean) - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.LoadParseQueryXML

queryXML(String) - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

queryXML(String, boolean, boolean, boolean, boolean, boolean) - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.LoadParseQueryXML

queryXML(String, String, boolean, boolean, boolean, boolean, boolean) - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.LoadParseQueryXML

Asks the user for a valid XML (real time parsing)

queryXML(String, String, List<String>) - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

queryXML(String, String, List<String>) - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.LoadParseQueryXML

queryXML(String, List<String>) - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

queryXML(List<String>) - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

quickDownsampling - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.DisplayFusedImagesPopup

quit() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointExplorer

quit() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationExplorer

quit() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.SelectedViewDescriptionListener

quit() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorer

R

r() - Method in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.PairwiseStitchingResult

radiusDoG(double) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2

RadiusSearchFilter<S,T> - Class in net.preibisch.mvrecon.imglib2.st.filter

RadiusSearchFilter(RadiusNeighborSearch<S>, double) - Constructor for class net.preibisch.mvrecon.imglib2.st.filter.RadiusSearchFilter

RadiusSearchFilterFactory<S,T> - Class in net.preibisch.mvrecon.imglib2.st.filter

RadiusSearchFilterFactory() - Constructor for class net.preibisch.mvrecon.imglib2.st.filter.RadiusSearchFilterFactory

raiMap - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.LazyLoadingFlatFieldCorrectionMap

randomAccess() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.FlatFieldCorrectedRandomAccessibleInterval

randomAccess() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.VirtuallyNormalizedRandomAccessibleInterval

randomAccess() - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccessibleInterval

randomAccess() - Method in class net.preibisch.mvrecon.process.deconvolution.util.FusedNonZeroRandomAccessibleInterval

randomAccess() - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval

randomAccess() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.DistanceVisualizingRandomAccessible

randomAccess() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGrid

randomAccess() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.InterpolatingNonRigidRandomAccessible

randomAccess() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidRandomAccessible

randomAccess() - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputGeneralRandomAccessible

randomAccess() - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccessible

randomAccess() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccessibleInterval

randomAccess() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.InterpolatingNonRigidRasteredRandomAccessible

randomAccess() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.NonRigidRasteredRandomAccessible

randomAccess() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.TransformedRasteredRandomAccessible

randomAccess(Interval) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.FlatFieldCorrectedRandomAccessibleInterval

randomAccess(Interval) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.VirtuallyNormalizedRandomAccessibleInterval

randomAccess(Interval) - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccessibleInterval

randomAccess(Interval) - Method in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccessible

randomAccess(Interval) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval

randomAccess(Interval) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGrid

randomAccess(Interval) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputGeneralRandomAccessible

randomAccess(Interval) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccessibleInterval

randomAccess(Interval) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.InterpolatingNonRigidRasteredRandomAccessible

randomAccess(Interval) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.NonRigidRasteredRandomAccessible

randomAccess(Interval) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.TransformedRasteredRandomAccessible

range - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.AdvancedRegistrationParameters

RangeComparator<V> - Interface in net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.range

RANSAC - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac

RANSAC() - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac.RANSAC

ransacChoices - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac.RANSACParameters

ransacChoicesIterations - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac.RANSACParameters

RANSACParameters - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac

RANSACParameters() - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac.RANSACParameters

RANSACParameters(double, double, int, int, boolean) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac.RANSACParameters

RANSACParameters(double, double, int, int, boolean, double, boolean) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac.RANSACParameters

ransacParams - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.FRGLDMGUI

ransacParams - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.GeometricHashingGUI

ransacParams - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.RGLDMGUI

RansacRegressionReduceFilter - Class in net.preibisch.mvrecon.process.fusion.intensity.mpicbg

RansacRegressionReduceFilter(FastAffineModel1D, int, double, double, int, double) - Constructor for class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.RansacRegressionReduceFilter

raster(RealRandomAccessible<T>, Interval) - Static method in class net.preibisch.mvrecon.imglib2.st.render.Render

ratioOfDistance - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.fastrgldm.FRGLDMParameters

ratioOfDistance - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.geometrichashing.GeometricHashingParameters

ratioOfDistance - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm.RGLDMParameters

re - Variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.fastrgldm.FRGLDMParameters

re - Variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.geometrichashing.GeometricHashingParameters

re - Variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm.RGLDMParameters

read() - Method in class net.preibisch.mvrecon.process.export.OpenSeaDragon.OpenSeaDragonImgLib2

read(Rectangle) - Method in class net.preibisch.mvrecon.process.export.OpenSeaDragon.OpenSeaDragonImgLib2

read(ViewId, ViewId) - Method in class net.preibisch.mvrecon.process.fusion.intensity.ViewPairCoefficientMatchesIO

readApproxAffine(N5Reader, String) - Static method in class net.preibisch.mvrecon.process.fusion.blk.DisplacementFieldN5Tools

Read the per-view approximate affine from a dfield dataset's attributes.

readBbox(N5Reader, String) - Static method in class net.preibisch.mvrecon.process.fusion.blk.DisplacementFieldN5Tools

Read the back-projected bbox (render coordinates) of the source view from a previously-written dfield dataset's attributes.

readBytes(byte[], Cursor<T>, int) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyLightSheetZ1ImgLoader

readBytesArray(byte[], Cursor<T>, int) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyLightSheetZ1ImgLoader

readCoefficients(N5Reader, String, String, ViewId) - Static method in class net.preibisch.mvrecon.process.fusion.intensity.IntensityCorrection

readCoefficientsSize() - Method in class net.preibisch.mvrecon.process.fusion.intensity.ViewPairCoefficientMatchesIO

readDisplacementFieldAsArrayImg(N5Reader, String, D) - Static method in class net.preibisch.mvrecon.process.fusion.blk.DisplacementFieldN5Tools

Read a dfield dataset (previously written by DisplacementFieldN5Tools.writeDisplacementField(net.imglib2.realtransform.RealTransform, net.imglib2.Interval, double[], org.janelia.saalfeldlab.n5.N5Writer, java.lang.String, int[], D, org.janelia.saalfeldlab.n5.Compression)) into a full ArrayImg and reconstruct the DisplacementFields.TransformedDisplacementField.

readDisplacementFieldAsCellImg(N5Reader, String, D) - Static method in class net.preibisch.mvrecon.process.fusion.blk.DisplacementFieldN5Tools

Read a dfield dataset (previously written by DisplacementFieldN5Tools.writeDisplacementField(net.imglib2.realtransform.RealTransform, net.imglib2.Interval, double[], org.janelia.saalfeldlab.n5.N5Writer, java.lang.String, int[], D, org.janelia.saalfeldlab.n5.Compression) or DisplacementFieldN5Tools.createEmptyDataset(org.janelia.saalfeldlab.n5.N5Writer, java.lang.String, net.imglib2.Interval, double[], int[], D, org.janelia.saalfeldlab.n5.Compression)+DisplacementFieldN5Tools.writeDisplacementFieldBlock(net.imglib2.realtransform.RealTransform, net.imglib2.Interval, double[], int[], long[], org.janelia.saalfeldlab.n5.N5Writer, java.lang.String, D)) as a lazy CellImg and reconstruct the DisplacementFields.TransformedDisplacementField.

readFloats(byte[], Cursor<T>, int, boolean) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyLightSheetZ1ImgLoader

readFloatsArray(byte[], Cursor<T>, int, boolean) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyLightSheetZ1ImgLoader

readImage(String) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

readImage(String) - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

readSignedShorts(byte[], Cursor<T>, int, boolean) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyLightSheetZ1ImgLoader

readSignedShortsArray(byte[], Cursor<T>, int, boolean) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyLightSheetZ1ImgLoader

readUnsignedInts(byte[], Cursor<T>, int, boolean) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyLightSheetZ1ImgLoader

readUnsignedIntsArray(byte[], Cursor<T>, int, boolean) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyLightSheetZ1ImgLoader

readUnsignedShorts(byte[], Cursor<T>, int, boolean) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyLightSheetZ1ImgLoader

readUnsignedShortsArray(byte[], Cursor<T>, int, boolean) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyLightSheetZ1ImgLoader

realMax(double[]) - Method in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox

realMax(double[]) - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccessibleInterval

realMax(double[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval

realMax(double[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGrid

realMax(double[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccessibleInterval

realMax(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox

realMax(int) - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccessibleInterval

realMax(int) - Method in class net.preibisch.mvrecon.process.fusion.intensity.IntensityCorrection.SerializableRealInterval

realMax(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval

realMax(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGrid

realMax(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccessibleInterval

realMax(RealPositionable) - Method in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox

realMax(RealPositionable) - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccessibleInterval

realMax(RealPositionable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval

realMax(RealPositionable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGrid

realMax(RealPositionable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccessibleInterval

realMin(double[]) - Method in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox

realMin(double[]) - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccessibleInterval

realMin(double[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval

realMin(double[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGrid

realMin(double[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccessibleInterval

realMin(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox

realMin(int) - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccessibleInterval

realMin(int) - Method in class net.preibisch.mvrecon.process.fusion.intensity.IntensityCorrection.SerializableRealInterval

realMin(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval

realMin(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGrid

realMin(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccessibleInterval

realMin(RealPositionable) - Method in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox

realMin(RealPositionable) - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccessibleInterval

realMin(RealPositionable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval

realMin(RealPositionable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGrid

realMin(RealPositionable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccessibleInterval

realRandomAccess() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGrid

realRandomAccess() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccessible

realRandomAccess() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.ContentBasedFFTRealRandomAccessible

realRandomAccess() - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.ContentBasedRealRandomAccessible

realRandomAccess() - Method in class net.preibisch.mvrecon.process.quality.FRCRealRandomAccessible

realRandomAccess() - Method in class util.StackingRealRandomAccessible

realRandomAccess(RealInterval) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGrid

realRandomAccess(RealInterval) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccessible

realRandomAccess(RealInterval) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.ContentBasedFFTRealRandomAccessible

realRandomAccess(RealInterval) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.ContentBasedRealRandomAccessible

realRandomAccess(RealInterval) - Method in class net.preibisch.mvrecon.process.quality.FRCRealRandomAccessible

realRandomAccess(RealInterval) - Method in class util.StackingRealRandomAccessible

To be overridden for RealTransform that can estimate the boundaries of a transferred RealInterval.

realUnion(RealInterval, RealInterval) - Static method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxMaximalGroupOverlap

Compute the smallest interval that contains both input intervals.

RealViews - Class in util

RealViews() - Constructor for class util.RealViews

reCenterViews(BigDataViewer, Collection<BasicViewDescription<?>>, ViewRegistrations) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

record(ViewerPanel) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough

reduceBlockNumbers(int[], int) - Static method in class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2

reduceSpimData2(SpimData2, List<ViewId>) - Static method in class net.preibisch.mvrecon.process.n5api.SpimData2Tools

Reduces a given SpimData2 to the subset of timepoints and viewsetups as selected by the user, including the original imgloader and keeping the basepath (i.e. interest points still work) Note: PSF's will be lost.

reduceSpimData2(SpimData2, List<ViewId>, URI) - Static method in class net.preibisch.mvrecon.process.n5api.SpimData2Tools

Reduces a given SpimData2 to the subset of timepoints and viewsetups as selected by the user, including the original imgloader and changing the base path (you still need to save to materialize the returned object!)

redundancy - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.fastrgldm.FRGLDMParameters

redundancy - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.geometrichashing.GeometricHashingParameters

redundancy - Static variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm.RGLDMParameters

referenceTimePoint - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.AdvancedRegistrationParameters

ReferenceTimepoint - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation

ReferenceTimepoint(List<ViewId>, Set<Group<ViewId>>, int) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.ReferenceTimepoint

ReferenceTimepoint(List<ViewId>, Set<Group<ViewId>>, TimePoint) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.ReferenceTimepoint

ReferenceTimepointRange<V> - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.range

ReferenceTimepointRange(int) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.range.ReferenceTimepointRange

ReferenceTimepointRange(TimePoint) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.range.ReferenceTimepointRange

refineTileOrAngleInfo(IFormatReader, List<FileListDatasetDefinitionUtil.TileOrAngleInfo>) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.metadatarefinement.CZITileOrAngleRefiner

refineTileOrAngleInfo(IFormatReader, List<FileListDatasetDefinitionUtil.TileOrAngleInfo>) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.metadatarefinement.NikonND2TileOrAngleRefiner

refineTileOrAngleInfo(IFormatReader, List<FileListDatasetDefinitionUtil.TileOrAngleInfo>) - Method in interface net.preibisch.mvrecon.fiji.datasetmanager.metadatarefinement.TileOrAngleRefiner

register(SpimData2, Collection<? extends ViewId>) - Method in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

register(SpimData2, Collection<? extends ViewId>, String, boolean) - Method in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

RegisterInterestPointsPopup - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

RegisterInterestPointsPopup() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.RegisterInterestPointsPopup

RegisterInterestPointsPopup.MyActionListener - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

RegistrationExplorer<AS> - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.registration

RegistrationExplorer(URI, XmlIoSpimData2, FilteredAndGroupedExplorer<AS>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationExplorer

RegistrationExplorerPanel - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.registration

RegistrationExplorerPanel(ViewRegistrations, RegistrationExplorer<?>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationExplorerPanel

RegistrationExplorerPopup - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

RegistrationExplorerPopup() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.RegistrationExplorerPopup

RegistrationExplorerPopup.MyActionListener - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

RegistrationStatistics - Class in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.statistics

RegistrationStatistics(int, double, double, double, double, double, double, int, int) - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.statistics.RegistrationStatistics

RegistrationStatistics(int, List<? extends Pair<? extends Pair<ViewId, ViewId>, ? extends PairwiseResult<?>>>) - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.statistics.RegistrationStatistics

RegistrationTableModel - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.registration

RegistrationTableModel(ViewRegistrations, RegistrationExplorerPanel) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationTableModel

registrationType - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.BasicRegistrationParameters

registrationTypeChoices - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.BasicRegistrationParameters

regularizationModelChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.TransformationModelGUI

RegularTranformHelpers - Class in net.preibisch.mvrecon.fiji.datasetmanager.grid

RegularTranformHelpers() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.grid.RegularTranformHelpers

RegularTranformHelpers.GridPreset - Class in net.preibisch.mvrecon.fiji.datasetmanager.grid

RegularTranformHelpers.RegularTranslationParameters - Class in net.preibisch.mvrecon.fiji.datasetmanager.grid

RegularTranslationParameters() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.grid.RegularTranformHelpers.RegularTranslationParameters

RejectStatistics - Class in net.preibisch.legacy.registration.bead.laplace

RejectStatistics() - Constructor for class net.preibisch.legacy.registration.bead.laplace.RejectStatistics

RelativeDistanceHistogram - Class in net.preibisch.mvrecon.process.interestpointremoval

RelativeDistanceHistogram() - Constructor for class net.preibisch.mvrecon.process.interestpointremoval.RelativeDistanceHistogram

RelativeDistanceHistogramListener() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.RemoveDetectionsPopup.RelativeDistanceHistogramListener

relativeDownsampling - Variable in class net.preibisch.mvrecon.process.n5api.N5ApiTools.MultiResolutionLevelInfo

relativeFRCDist - Static variable in class net.preibisch.mvrecon.process.quality.FRCRealRandomAccessible

relativeLabel - Variable in class net.preibisch.mvrecon.process.interestpointremoval.RelativeThinOutParameters

RelativeThinOut - Class in net.preibisch.mvrecon.process.interestpointremoval

RelativeThinOut() - Constructor for class net.preibisch.mvrecon.process.interestpointremoval.RelativeThinOut

RelativeThinOut_Detections - Class in net.preibisch.mvrecon.fiji.plugin

RelativeThinOut_Detections() - Constructor for class net.preibisch.mvrecon.fiji.plugin.RelativeThinOut_Detections

RelativeThinOutListener() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.RemoveDetectionsPopup.RelativeThinOutListener

RelativeThinOutParameters - Class in net.preibisch.mvrecon.process.interestpointremoval

RelativeThinOutParameters() - Constructor for class net.preibisch.mvrecon.process.interestpointremoval.RelativeThinOutParameters

relativeThreshold - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters

removeAdjustment(SpimData2, List<ViewId>) - Method in class net.preibisch.mvrecon.fiji.plugin.RemoveIntensity_Adjustment

removeAdjustment(SpimData2, List<ViewId>, String, boolean) - Method in class net.preibisch.mvrecon.fiji.plugin.RemoveIntensity_Adjustment

removeAmbigousMatches(List<PointMatchGeneric<P>>) - Static method in class net.preibisch.mvrecon.process.pointcloud.icp.ICP

Detects ambigous (and duplicate) PointMatches, i.e. if a Point corresponds with more than one other Point

removeBrackets(String) - Static method in class net.preibisch.mvrecon.fiji.plugin.util.GUIHelper

Removes any of those characters from a String: (, ), [, ], {, }, <, >

removeCorrespondencesForViewLabel(ViewInterestPoints, ViewId, String, int) - Static method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.CorrespondenceTools

Removes correspondences pointing to a specific view+label from all other views.

removeCorrespondencesNotToViews(ViewInterestPoints, Set<ViewId>, int) - Static method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.CorrespondenceTools

Inverse of CorrespondenceTools.removeCorrespondencesToViews(net.preibisch.mvrecon.fiji.spimdata.interestpoints.ViewInterestPoints, java.util.Set<mpicbg.spim.data.sequence.ViewId>, int): removes correspondences whose correspondingViewId is NOT in the given set of views to keep.

removeCorrespondencesToLabel(ViewInterestPoints, String, int) - Static method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.CorrespondenceTools

Removes correspondences whose correspondingLabel equals the given label, from every view's every (other) interest-point list.

removeCorrespondencesToViews(ViewInterestPoints, Set<ViewId>, int) - Static method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.CorrespondenceTools

Removes all correspondences pointing TO the specified views from ALL other views.

RemoveDetectionsPopup - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

RemoveDetectionsPopup() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.RemoveDetectionsPopup

RemoveDetectionsPopup.CreateFromCorrespondencesListener - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

RemoveDetectionsPopup.HistogramListener - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

RemoveDetectionsPopup.InteractiveListener - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

RemoveDetectionsPopup.RelativeDistanceHistogramListener - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

RemoveDetectionsPopup.RelativeThinOutListener - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

RemoveDetectionsPopup.ThinOutListener - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

removeEmptyGroups(List<Group<V>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

removeInconsistentMatches(List<P>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac.RANSAC

removeInliers(List<P>, List<P>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.ransac.RANSAC

RemoveInsideROIButtonListener(ImagePlus, Map<Integer, InterestPoint>, int, boolean) - Constructor for class net.preibisch.mvrecon.process.interestpointremoval.InteractiveProjections.RemoveInsideROIButtonListener

RemoveIntensity_Adjustment - Class in net.preibisch.mvrecon.fiji.plugin

RemoveIntensity_Adjustment() - Constructor for class net.preibisch.mvrecon.fiji.plugin.RemoveIntensity_Adjustment

removeInteractively(SpimData2, ViewId, int, String, String) - Static method in class net.preibisch.mvrecon.process.interestpointremoval.InteractiveProjections

removeKeepChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.ThinOut_Detections

removeLink(TileConfiguration, HashMap<ViewId, ? extends Tile<?>>) - Method in interface net.preibisch.mvrecon.process.interestpointregistration.global.linkremoval.LinkRemovalStrategy

removeLink(TileConfiguration, HashMap<ViewId, ? extends Tile<?>>) - Method in class net.preibisch.mvrecon.process.interestpointregistration.global.linkremoval.MaxErrorLinkRemoval

removeMinProjections() - Method in class net.preibisch.mvrecon.process.psf.PSFExtraction

removeMinProjections(Img<T>) - Static method in class net.preibisch.mvrecon.process.psf.PSFExtraction

removeNonExistentViewsInGroups(List<V>, Set<Group<V>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.PairwiseSetup

Remove all views in groups that do not exist in the views list - called from constructor

removeNonOverlappingPairs(List<Pair<V, V>>, OverlapDetection<V>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.PairwiseSetup

Remove pairs that are not overlapping

removeNonOverlappingPairs(OverlapDetection<V>) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.PairwiseSetup

Remove pairs that are not overlapping.

removeNonOverlappingPairsOptimized(List<Pair<V, V>>, Collection<V>) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap.SimpleBoundingBoxOverlap

Combined method: pre-compute bounding boxes and filter pairs in parallel.

removeNonOverlappingPairsParallel(List<Pair<V, V>>, Map<V, BoundingBox>) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap.SimpleBoundingBoxOverlap

Filter overlapping pairs using pre-computed bounding boxes in parallel.

removeOnDeselect - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.LazyBDVPopup

If true, deselecting a view in the explorer calls state.removeSource(...) — frees BDV state, lower memory.

removePairwiseResultForPair(Pair<Group<ViewId>, Group<ViewId>>) - Method in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.StitchingResults

removeRedundantPairs(List<Pair<V, V>>, Set<Group<V>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.PairwiseSetup

Checks all pairs if both views are contained in the same group, and if so removes the pair from the list - called from definePairs()

removeSequences(String, String[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.util.GUIHelper

removeTableModelListener(TableModelListener) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MissingViewsTableModelDecorator

removeTableModelListener(TableModelListener) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MultiViewTableModelDecorator

RemoveTransformationPopup - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

RemoveTransformationPopup() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.RemoveTransformationPopup

RemoveTransformationPopup.MyActionListener - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

render(IterableRealInterval<S>, RadiusSearchFilterFactory<S, T>) - Static method in class net.preibisch.mvrecon.imglib2.st.render.Render

Render - Class in net.preibisch.mvrecon.imglib2.st.render

Render() - Constructor for class net.preibisch.mvrecon.imglib2.st.render.Render

renderBoxes(MultiBoxOverlayRenderer, BDVFlyThrough.MyTarget, ViewerState, int, int) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough

renderNN(IterableRealInterval<T>) - Static method in class net.preibisch.mvrecon.imglib2.st.render.Render

renderNN(IterableRealInterval<T>, T, double) - Static method in class net.preibisch.mvrecon.imglib2.st.render.Render

renderScalebar(ScaleBarOverlayRenderer, BDVFlyThrough.MyTarget, ViewerState, int, int) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough

renderScreenshot(ViewerPanel) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough

renderSegmentations(SpimData2, ViewId, String, int, Interval, double) - Static method in class net.preibisch.mvrecon.fiji.plugin.Visualize_Detections

reorderPairs() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.PairwiseSetup

Reorder the pairs so that the "smaller" view comes first

reorderPairs(List<Pair<V, V>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.PairwiseSetup

reorientationChoice - Variable in class net.preibisch.mvrecon.fiji.plugin.boundingbox.AutomaticReorientationBoundingBoxGUI

reorientationDescription - Static variable in class net.preibisch.mvrecon.fiji.plugin.boundingbox.AutomaticReorientationBoundingBoxGUI

reorientationDescription - Static variable in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxReorientation

ReorientSamplePopup - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

ReorientSamplePopup() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.ReorientSamplePopup

ReorientSamplePopup.MyActionListener - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

replaceAngles - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData.Pattern

replaceAngles - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

replaceAngles - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoader

replaceCams - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData.Pattern

replaceChannels - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData.Pattern

replaceChannels - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

replaceChannels - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoader

replaceIlluminations - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

replaceIlluminations - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoader

replacePlanes - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData.Pattern

replaceTiles - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

replaceTiles - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoader

replaceTimepoints - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData.Pattern

replaceTimepoints - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

replaceTimepoints - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoader

requiresInterestPointDuplication() - Method in interface net.preibisch.mvrecon.process.interestpointregistration.pairwise.MatcherPairwise

Determines if this pairwise matching requires a duplication of the input InterestPoints as these instances are ran multithreaded.

requiresInterestPointDuplication() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.centerofmass.CenterOfMassPairwise

We only read l[]

requiresInterestPointDuplication() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.fastrgldm.FRGLDMPairwise

We run RANSAC on these points which makes copies, so no need to duplicate points

requiresInterestPointDuplication() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.geometrichashing.GeometricHashingPairwise

We run RANSAC on these points which makes copies, so no need to duplicate points

requiresInterestPointDuplication() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.icp.IterativeClosestPointPairwise

We modify w[] on these points, which is not a good idea when running things multithreaded

requiresInterestPointDuplication() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.loadcorrespondences.LoadCorrespondencesPairwise

requiresInterestPointDuplication() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm.RGLDMPairwise

We only read the points, no reason to duplicate, RANSAC does its own duplication

Resave_HDF5 - Class in net.preibisch.mvrecon.fiji.plugin.resave

Resave_HDF5() - Constructor for class net.preibisch.mvrecon.fiji.plugin.resave.Resave_HDF5

Resave_N5Api - Class in net.preibisch.mvrecon.fiji.plugin.resave

Resave_N5Api() - Constructor for class net.preibisch.mvrecon.fiji.plugin.resave.Resave_N5Api

Resave_TIFF - Class in net.preibisch.mvrecon.fiji.plugin.resave

Resave_TIFF() - Constructor for class net.preibisch.mvrecon.fiji.plugin.resave.Resave_TIFF

Resave_TIFF.ParametersResaveAsTIFF - Class in net.preibisch.mvrecon.fiji.plugin.resave

ResaveImaris - Class in net.preibisch.mvrecon.headless.definedataset

ResaveImaris() - Constructor for class net.preibisch.mvrecon.headless.definedataset.ResaveImaris

resaveN5(SpimData2, Collection<? extends ViewId>, ParametersResaveN5Api, boolean) - Static method in class net.preibisch.mvrecon.fiji.plugin.resave.Resave_N5Api

ResavePopup - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

ResavePopup() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.ResavePopup

ResavePopup.MyActionListener - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

resaveS0Block(SpimData2, N5Writer, StorageFormat, DataType, Function<long[][], String>, long[][]) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

reset() - Method in interface net.preibisch.legacy.registration.bead.error.GlobalErrorStatistics

reset() - Method in class net.preibisch.legacy.registration.bead.error.GlobalErrorStatisticsImpl

resetBDVManualTransformations(BigDataViewer) - Static method in class util.BDVTools

Resets manual transformations for all views to identity.

resetLogCounters() - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.PairwiseResult

Reset the per-pair load-log counter and one-shot notice flag.

resetStatistics() - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.loadcorrespondences.LoadCorrespondencesPairwise

Reset all timing statistics (call before starting a new batch of computePairs)

resetW() - Method in class net.preibisch.legacy.registration.detection.AbstractDetection

resetWorldCoordinates() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.AbstractPointDescriptor

Resets the world coordinates of the descriptorPoints

resetWorldCoordinatesAfterMatching() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.AbstractPointDescriptor

Tells if the descriptormatching should reset the world coordinates after the matching

resetWorldCoordinatesAfterMatching() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.LocalCoordinateSystemPointDescriptor

resetWorldCoordinatesAfterMatching() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.ModelPointDescriptor

resetWorldCoordinatesAfterMatching() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.SimplePointDescriptor

resetWorldCoordinatesAfterMatching() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.TranslationInvariantLocalCoordinateSystemPointDescriptor

resolutions - Variable in class net.preibisch.mvrecon.fiji.plugin.resave.ParametersResaveN5Api

resolveAmbiguity(Map<Class<? extends Entity>, FileListDatasetDefinitionUtil.CheckResult>, boolean, boolean, boolean, boolean) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil

resortMapNamed(Map<T, List<FileMapEntry>>) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil

reStartBDV() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BDVPopup

RetryTracker<T> - Class in net.preibisch.mvrecon.process.export

Simple utility to track retry attempts and handle retry logic for failed blocks.

RetryTracker(Function<T, String>, String, int, boolean, long, boolean, int) - Constructor for class net.preibisch.mvrecon.process.export.RetryTracker

Rewrite_LuxendoXML - Class in net.preibisch.mvrecon.headless.definedataset

Rewrite_LuxendoXML() - Constructor for class net.preibisch.mvrecon.headless.definedataset.Rewrite_LuxendoXML

reWriteRegistrationFile(File, AffineModel3D, AffineModel3D, AffineModel3D) - Static method in class net.preibisch.legacy.io.IOFunctions

RGLDMGUI - Class in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise

Redundant Geometric Local Descriptor Matching (RGLDM)

RGLDMGUI() - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise.RGLDMGUI

RGLDMMatcher<I> - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm

RGLDMMatcher() - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm.RGLDMMatcher

RGLDMPairwise<I> - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm

RGLDMPairwise(RANSACParameters, RGLDMParameters) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm.RGLDMPairwise

RGLDMParameters - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm

RGLDMParameters(Model<?>) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm.RGLDMParameters

RGLDMParameters(Model<?>, double, double, boolean, double, int, int) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm.RGLDMParameters

RIGID - Static variable in class net.preibisch.mvrecon.vecmath.Transform3D

This matrix is a rotation and a translation with unity scale; The upper 3x3 of the matrix is orthogonal, and there is a translation component.

rnd - Static variable in class net.preibisch.mvrecon.process.deconvolution.normalization.AdjustInput

rod - Variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.fastrgldm.FRGLDMParameters

rod - Variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.geometrichashing.GeometricHashingParameters

rod - Variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm.RGLDMParameters

ROI - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoG.ValueChange

ROIListener - Class in net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive

Tests whether the ROI was changed and will recompute the preview

ROIListener(InteractiveDoG, ImagePlus) - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.ROIListener

rotationAngle(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

rotationAngle(int) - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

rotationAngleAxis(double, double[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

rotationAround - Variable in class net.preibisch.mvrecon.headless.definedataset.DefineDataSetParameters

rotationAxis() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

rotationAxis() - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

rotationAxis() - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

rotationAxisIndex() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

rotationAxisIndex() - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

rotationAxisName() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

rotationAxisName() - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

rotationAxisName() - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

rotAxes - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.LightSheetZ1

rotAxes - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.MicroManager

rotAxis - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

rotAxis - Variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

rotX(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Sets the value of this matrix to a counter clockwise rotation about the x axis.

rotX(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the value of this matrix to a counter-clockwise rotation about the x axis.

rotX(double) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the value of this transform to a counter clockwise rotation about the x axis.

rotX(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Sets the value of this matrix to a counter clockwise rotation about the x axis.

rotX(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the value of this matrix to a counter clockwise rotation about the x axis.

rotY(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Sets the value of this matrix to a counter clockwise rotation about the y axis.

rotY(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the value of this matrix to a counter-clockwise rotation about the y axis.

rotY(double) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the value of this transform to a counter clockwise rotation about the y axis.

rotY(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Sets the value of this matrix to a counter clockwise rotation about the y axis.

rotY(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the value of this matrix to a counter clockwise rotation about the y axis.

rotZ(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Sets the value of this matrix to a counter clockwise rotation about the z axis.

rotZ(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the value of this matrix to a counter-clockwise rotation about the z axis.

rotZ(double) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the value of this transform to a counter clockwise rotation about the z axis.

rotZ(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Sets the value of this matrix to a counter clockwise rotation about the z axis.

rotZ(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the value of this matrix to a counter clockwise rotation about the z axis.

roundMipmapResolutions - Static variable in class net.preibisch.mvrecon.process.splitting.SplittingTools

rs - Static variable in class util.ColorStream

run() - Method in class net.preibisch.mvrecon.fiji.plugin.apply.BigDataViewerTransformationWindow.BDVChecker

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.Analyze_Errors

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.CreateFromCorresponding_Detections

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.Data_Explorer

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.Define_Bounding_Box

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.Define_Multi_View_Dataset

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.Display_View

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.Image_Deconvolution

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.Image_Fusion

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.Image_Quality

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.Intensity_Adjustment

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Detection

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.Max_Project

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.PSF_Assign

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.PSF_Average

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.PSF_Extract

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.PSF_View

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.RelativeThinOut_Detections

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.RemoveIntensity_Adjustment

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.resave.Resave_HDF5

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.resave.Resave_N5Api

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.resave.Resave_TIFF

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.Show_Histogram

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.Show_Relative_Histogram

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.Specify_Calibration

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.Split_Views

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.Switch_Attributes

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.ThinOut_Detections

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.Visualize_Detections

run(String) - Method in class net.preibisch.mvrecon.fiji.plugin.XMLSaveAs

run(String) - Method in class net.preibisch.mvrecon.headless.definedataset.Rewrite_LuxendoXML

runAfterFinished - Variable in class net.preibisch.mvrecon.process.interestpointremoval.InteractiveProjections

runGlobal(HashMap<Pair<Integer, Integer>, ArrayList<PointMatch>>, HashMap<Integer, ViewId>, M) - Static method in class net.preibisch.mvrecon.process.fusion.intensityadjust.IntensityAdjustmentTools

runICPIteration(Model<?>, Model<?>) - Method in class net.preibisch.mvrecon.process.pointcloud.icp.ICP

Performs one iteration of the ICP.

runInitialization(Img<FloatType>, List<DeconView>, ExecutorService) - Method in interface net.preibisch.mvrecon.process.deconvolution.init.PsiInit

runInitialization(Img<FloatType>, List<DeconView>, ExecutorService) - Method in class net.preibisch.mvrecon.process.deconvolution.init.PsiInitAvgApprox

runInitialization(Img<FloatType>, List<DeconView>, ExecutorService) - Method in class net.preibisch.mvrecon.process.deconvolution.init.PsiInitAvgPrecise

runInitialization(Img<FloatType>, List<DeconView>, ExecutorService) - Method in class net.preibisch.mvrecon.process.deconvolution.init.PsiInitBlurredFused

runInitialization(Img<FloatType>, List<DeconView>, ExecutorService) - Method in class net.preibisch.mvrecon.process.deconvolution.init.PsiInitFromFile

runInitialization(Img<FloatType>, List<DeconView>, ExecutorService) - Method in class net.preibisch.mvrecon.process.deconvolution.init.PsiInitFromRAI

runIteration(List<DeconView>, List<RandomAccessibleInterval<FloatType>>, List<RandomAccessibleInterval<FloatType>>, List<Float>, List<ArrayImg<FloatType, ?>>, List<ArrayImg<FloatType, ?>>) - Method in interface net.preibisch.mvrecon.process.deconvolution.iteration.mul.ComputeBlockMulThread

run an iteration on the block

runIteration(List<DeconView>, List<RandomAccessibleInterval<FloatType>>, List<RandomAccessibleInterval<FloatType>>, List<Float>, List<ArrayImg<FloatType, ?>>, List<ArrayImg<FloatType, ?>>) - Method in class net.preibisch.mvrecon.process.deconvolution.iteration.mul.ComputeBlockMulThreadCPU

runIteration(DeconView, Block, RandomAccessibleInterval<FloatType>, RandomAccessibleInterval<FloatType>, float, ArrayImg<FloatType, ?>, ArrayImg<FloatType, ?>) - Method in interface net.preibisch.mvrecon.process.deconvolution.iteration.sequential.ComputeBlockSeqThread

run an iteration on the block

runIteration(DeconView, Block, RandomAccessibleInterval<FloatType>, RandomAccessibleInterval<FloatType>, float, ArrayImg<FloatType, ?>, ArrayImg<FloatType, ?>) - Method in class net.preibisch.mvrecon.process.deconvolution.iteration.sequential.ComputeBlockSeqThreadCPU

runIteration(DeconView, Block, RandomAccessibleInterval<FloatType>, RandomAccessibleInterval<FloatType>, float, ArrayImg<FloatType, ?>, ArrayImg<FloatType, ?>) - Method in class net.preibisch.mvrecon.process.deconvolution.iteration.sequential.ComputeBlockSeqThreadCUDA

runIterations() - Method in class net.preibisch.mvrecon.process.deconvolution.MultiViewDeconvolution

runNextIteration() - Method in class net.preibisch.mvrecon.process.deconvolution.MultiViewDeconvolution

runNextIteration() - Method in class net.preibisch.mvrecon.process.deconvolution.MultiViewDeconvolutionMul

runNextIteration() - Method in class net.preibisch.mvrecon.process.deconvolution.MultiViewDeconvolutionSeq

runningBdvPopup() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.ExplorerWindow

Returns whichever BDV popup currently has a running BDV (eager or lazy).

runningBdvPopup() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

Returns whichever BDV popup currently has a running BDV (eager BDVPopup or lazy variant — both implement BasicBDVPopup).

runSetup(IFormatReader) - Method in interface net.preibisch.mvrecon.fiji.spimdata.imgloaders.util.BioformatsReaderSetupHook

runSetup(IFormatReader) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.util.CZIReaderSetupHook

runThreads(Thread[]) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

runWhenDone(Thread) - Method in class net.preibisch.mvrecon.process.interestpointremoval.InteractiveProjections

S

s3Region - Static variable in class util.URITools

S3Tools - Class in util

AWS-SDK-touching S3 configuration, intentionally isolated from URITools.

S3Tools() - Constructor for class util.S3Tools

sameColorSources(List<ConverterSetup>, int, int, int, int) - Static method in class util.BDVTools

Deprecated.

Use the batch methods instead

sameModelAngles - Variable in class net.preibisch.mvrecon.fiji.plugin.apply.ApplyParameters

sameModelChannels - Variable in class net.preibisch.mvrecon.fiji.plugin.apply.ApplyParameters

sameModelIlluminations - Variable in class net.preibisch.mvrecon.fiji.plugin.apply.ApplyParameters

sameModelTiles - Variable in class net.preibisch.mvrecon.fiji.plugin.apply.ApplyParameters

sameModelTimePoints - Variable in class net.preibisch.mvrecon.fiji.plugin.apply.ApplyParameters

sample(Random, int) - Method in class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.MatchIndices

SAMPLES_PER_PIXEL - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

SAMPLES_PER_PIXEL - Static variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

save() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointExplorer

save() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationExplorer

save() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.SelectedViewDescriptionListener

save() - Method in class net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions.PointSpreadFunction

save(SpimData2, String) - Method in class net.preibisch.mvrecon.fiji.spimdata.XmlIoSpimData2

Deprecated.

save(SpimData2, URI) - Method in class net.preibisch.mvrecon.fiji.spimdata.XmlIoSpimData2

Save3dTIFF - Class in net.preibisch.mvrecon.process.export

Save3dTIFF(String) - Constructor for class net.preibisch.mvrecon.process.export.Save3dTIFF

Save3dTIFF(String, boolean) - Constructor for class net.preibisch.mvrecon.process.export.Save3dTIFF

saveAs(SpimData2, String) - Static method in class net.preibisch.mvrecon.fiji.plugin.XMLSaveAs

saveCorrespondences(ViewInterestPointLists) - Method in interface net.preibisch.mvrecon.process.splitting.SplittingTools.CorrespondenceSaver

saveCorrespondencesStatic(URI, int, int, String, List<CorrespondingInterestPoints>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

Convenience overload that constructs n5path from timepoint/setup/label.

saveCorrespondencesStatic(URI, String, List<CorrespondingInterestPoints>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

Core static method for saving correspondences to N5.

saveCorrespondencesStatic(N5Writer, String, List<CorrespondingInterestPoints>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

Core static method for saving correspondences to N5 using an already-open N5Writer.

saveCorrespondingInterestPoints(boolean) - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoints

saveCorrespondingInterestPoints(boolean) - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

saveCorrespondingInterestPoints(boolean, N5Writer) - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

Save correspondences using an already-open N5Writer, clearing the modified flag on success.

saveInterestPointDataStatic(URI, InterestPointsN5.InterestPointData) - Static method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

Static wrapper to save all data from an InterestPointData object.

saveInterestPointDataStatic(N5Writer, InterestPointsN5.InterestPointData) - Static method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

Static wrapper to save all data from an InterestPointData object using an already-open N5Writer.

saveInterestPoints(boolean) - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoints

saveInterestPoints(boolean) - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

saveInterestPoints(boolean, N5Writer) - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

Save interest points using an already-open N5Writer, clearing the modified flag on success.

saveInterestPoints(Map<ViewId, ViewInterestPointLists>) - Method in interface net.preibisch.mvrecon.process.splitting.SplittingTools.InterestPointSaver

saveInterestPointsInParallel(SpimData2) - Static method in class net.preibisch.mvrecon.fiji.spimdata.XmlIoSpimData2

Save all interest points using a single shared N5Writer with parallel writes.

saveInterestPointsStatic(URI, int, int, String, int[], double[][]) - Static method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

Convenience overload that constructs n5path from timepoint/setup/label.

saveInterestPointsStatic(URI, String, int[], double[][]) - Static method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

Core static method for saving interest points to N5.

saveInterestPointsStatic(N5Writer, String, int[], double[][]) - Static method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

Core static method for saving interest points to N5 using an already-open N5Writer.

savePSFsInParallel(SpimData2) - Static method in class net.preibisch.mvrecon.fiji.spimdata.XmlIoSpimData2

saveSelectionToHistory() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

saveSpimData(SpimData2, URI, XmlIoSpimData2) - Static method in class util.URITools

saveTiffStack(ImagePlus, String) - Static method in class net.preibisch.mvrecon.process.export.Save3dTIFF

saveViewerTransforms() - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough

saveViewerTransforms(File) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough

saveWithFilename(SpimData2, String) - Method in class net.preibisch.mvrecon.fiji.spimdata.XmlIoSpimData2

Saves a SpimData2 object using its own URI into a filename specified by xmlFilename

saveXML() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.ExplorerWindow

saveXML() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

scale(double) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Sets the value of this tuple to the scalar multiplication of itself.

scale(double) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Sets the value of this tuple to the scalar multiplication of the scale factor with this.

scale(double, Tuple3d) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Sets the value of this tuple to the scalar multiplication of tuple t1.

scale(double, Tuple4d) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Sets the value of this tuple to the scalar multiplication of the scale factor with the tuple t1.

scale(float) - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Sets the value of this tuple to the scalar multiplication of the scale factor with this.

scale(float) - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Sets the value of this tuple to the scalar multiplication of the scale factor with this.

scale(float, Tuple3f) - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Sets the value of this vector to the scalar multiplication of tuple t1.

scale(float, Tuple4f) - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Sets the value of this tuple to the scalar multiplication of tuple t1.

scale(int) - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Sets the value of this tuple to the scalar multiplication of the scale factor with this.

scale(int, Tuple3i) - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Sets the value of this tuple to the scalar multiplication of tuple t1.

SCALE - Static variable in class net.preibisch.mvrecon.vecmath.Transform3D

A Uniform scale matrix with no translation or other off-diagonal components.

scaleAdd(double, Transform3D) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Scales this transform by a Uniform scale matrix with scale factor s and then adds transform t1 (this = S*this + t1).

scaleAdd(double, Transform3D, Transform3D) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Scales transform t1 by a Uniform scale matrix with scale factor s and then adds transform t2 (this = S*t1 + t2).

scaleAdd(double, Tuple3d) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Sets the value of this tuple to the scalar multiplication of itself and then adds tuple t1 (this = s*this + t1).

scaleAdd(double, Tuple3d, Tuple3d) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Sets the value of this tuple to the scalar multiplication of tuple t1 and then adds tuple t2 (this = s*t1 + t2).

scaleAdd(double, Tuple4d) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Sets the value of this tuple to the scalar multiplication of itself and then adds tuple t1 (this = s*this + t1).

scaleAdd(double, Tuple4d, Tuple4d) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Sets the value of this tuple to the scalar multiplication by s of tuple t1 plus tuple t2 (this = s*t1 + t2).

scaleAdd(float, Tuple3f) - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Sets the value of this tuple to the scalar multiplication of itself and then adds tuple t1 (this = s*this + t1).

scaleAdd(float, Tuple3f, Tuple3f) - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Sets the value of this tuple to the scalar multiplication of tuple t1 and then adds tuple t2 (this = s*t1 + t2).

scaleAdd(float, Tuple4d) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

scaleAdd(float, Tuple4f) - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Sets the value of this tuple to the scalar multiplication of itself and then adds tuple t1 (this = s*this + t1).

scaleAdd(float, Tuple4f, Tuple4f) - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Sets the value of this tuple to the scalar multiplication of tuple t1 plus tuple t2 (this = s*t1 + t2).

scaleAdd(int, Tuple3i) - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Sets the value of this tuple to the scalar multiplication of itself and then adds tuple t1 (this = s*this + t1).

scaleAdd(int, Tuple3i, Tuple3i) - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Sets the value of this tuple to the scalar multiplication of tuple t1 plus tuple t2 (this = s*t1 + t2).

scaleBoundingBox(Interval, double) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.TransformVirtual

Scale the bounding box (use with scaleTransform so it is the right image, but just smaller)

scaleBoundingBox(Interval, double[]) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.TransformVirtual

scaleBoundingBox(Interval, double, double[]) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.TransformVirtual

scaleDisplayRangeMax(BigDataViewer, double, boolean) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVUtils

Multiply the display-range maximum (white point) of BDV sources by factor, leaving the minimum (black point) untouched.

scaleTransform(AffineTransform3D, double) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.TransformVirtual

Scale the affine transform (use with scaleBoundingBox so it is the right image, but just smaller)

scaleTransform(AffineTransform3D, double[]) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.TransformVirtual

scaling(Dimensions, AffineTransform3D) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

scalingRange - Static variable in class net.preibisch.mvrecon.process.deconvolution.MultiViewDeconvolution

scoreSplit(List<OctTreeSplitCriterion.SplitCorrespondence>, List<OctTreeSplitCriterion.SplitCorrespondence>) - Method in class net.preibisch.mvrecon.process.splitting.ConsensusSetCriterion

scoreSplit(List<OctTreeSplitCriterion.SplitCorrespondence>, List<OctTreeSplitCriterion.SplitCorrespondence>) - Method in class net.preibisch.mvrecon.process.splitting.CrossViewCorrespondenceCriterion

scoreSplit(List<OctTreeSplitCriterion.SplitCorrespondence>, List<OctTreeSplitCriterion.SplitCorrespondence>) - Method in interface net.preibisch.mvrecon.process.splitting.OctTreeSplitCriterion

Score a candidate binary split.

ScrollableBrightnessDialog - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.bdv

Adjust brightness and colors for individual (or groups of) setups and having a scrollpane if necessary

ScrollableBrightnessDialog(Frame, SetupAssignments) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.ScrollableBrightnessDialog

search - Variable in class net.preibisch.mvrecon.imglib2.st.render.IntegratingNeighborSearchInterpolator

search(RealLocalizable) - Method in class net.preibisch.mvrecon.imglib2.st.render.FilteredMaxDistanceSearchOnKDTree

search(RealLocalizable) - Method in interface net.preibisch.mvrecon.imglib2.st.render.IntegratingNeighborSearch

Perform intgrating-neighbor search for a reference coordinate.

search(RealLocalizable) - Method in class net.preibisch.mvrecon.imglib2.st.render.NearestNeighborMaxDistanceSearchOnKDTree

searchRadius - Variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm.RGLDMParameters

searchRadius() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm.RGLDMParameters

SegmentationBenchmark - Class in net.preibisch.legacy.registration.bead

SegmentationBenchmark() - Constructor for class net.preibisch.legacy.registration.bead.SegmentationBenchmark

selectedRows - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

selectedRows() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.ExplorerWindow

selectedRows() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

selectedRowsGroups() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

selectedRowsGroups() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.GroupedRowWindow

selectedRowsViewId() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.ExplorerWindow

selectedRowsViewId() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

selectedRowsViewIdGroups() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

selectedRowsViewIdGroups() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.GroupedRowWindow

SelectedViewDescriptionListener<AS> - Interface in net.preibisch.mvrecon.fiji.spimdata.explorer

selectedViewDescriptions(List<List<BasicViewDescription<?>>>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointExplorer

selectedViewDescriptions(List<List<BasicViewDescription<?>>>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationExplorer

selectedViewDescriptions(List<List<BasicViewDescription<?>>>) - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.SelectedViewDescriptionListener

selectImgFactory(LightSheetZ1MetaData) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.LightSheetZ1

SelectionDialog - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.selection

Dialog for selecting views based on predefined ranges and values.

SelectionDialog(JFrame, SpimData2) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.selection.SelectionDialog

SelectTimepointEntry - Class in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.statistics

SelectTimepointEntry(String, ArrayList<RegistrationStatistics>) - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.statistics.SelectTimepointEntry

selectViews(List<BasicViewDescription<?>>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

selectViewsAndRecenter(ViewSetupExplorerPanel<?>, AnalyzeErrorsUtil.Parameters, Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil

Bring the explorer into the grouping state AnalyzeErrors was run with (only if it isn't already there), then select rows whose view-set intersects the given views, update BDV coloring, and recenter on the selection.

selectViewsAndRecenter(ViewSetupExplorerPanel<?>, AnalyzeErrorsUtil.Parameters, Collection<? extends ViewId>, boolean) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil

Same as AnalyzeErrorsUtil.selectViewsAndRecenter(ViewSetupExplorerPanel, Parameters, Collection) but skips the TransformationTools.reCenterViews(...) call when recenter == false.

semicolonSeparatedList(List<String>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoDHMImgLoader

sensitivity - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoG

Separator - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

Separator() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.Separator

sequenceDescription - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoader

serializable(RealInterval) - Static method in class net.preibisch.mvrecon.process.fusion.intensity.IntensityCorrection.SerializableRealInterval

SerializableRealInterval(RealInterval) - Constructor for class net.preibisch.mvrecon.process.fusion.intensity.IntensityCorrection.SerializableRealInterval

serialize(AffineTransform3D, Type, JsonSerializationContext) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough.AffineTransform3DAdapter

series() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.FileMapEntry

seriesIndex - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.TileInfo

service - Static variable in class net.preibisch.mvrecon.process.export.DisplayImage

service - Static variable in class net.preibisch.mvrecon.process.export.ExportLarge2DTIFF

set(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Sets the value of this matrix to a scale matrix with the passed scale amount.

set(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the value of this matrix to a scale matrix with the passed scale amount.

set(double) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the value of this transform to a uniform scale; all of the matrix values are modified.

set(double[]) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4d

Sets the value of this axis angle to the specified x,y,z,angle.

set(double[]) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Sets the values in this Matrix3d equal to the row-major array parameter (ie, the first three elements of the array will be copied into the first row of this matrix, etc.).

set(double[]) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the values in this Matrix4d equal to the row-major array parameter (ie, the first four elements of the array will be copied into the first row of this matrix, etc.).

set(double[]) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the matrix values of this transform to the matrix values in the double precision array parameter.

set(double[]) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Sets the value of this tuple to the value of the xyz coordinates located in the array of length 3.

set(double[]) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Sets the value of this tuple to the specified xyzw coordinates.

set(double, double, double) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Sets the value of this tuple to the specified xyz coordinates.

set(double, double, double, double) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4d

Sets the value of this axis angle to the specified x,y,z,angle.

set(double, double, double, double) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Sets the value of this tuple to the specified xyzw coordinates.

set(double, Vector3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the value of this transform to a scale and translation matrix; the scale is not applied to the translation and all of the matrix values are modified.

set(double, Vector3d) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the value of this transform to a scale and translation matrix; the scale is not applied to the translation and all of the matrix values are modified.

set(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Sets the value of this matrix to a scale matrix with the passed scale amount.

set(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the value of this matrix to a scale matrix with the the passed scale amount.

set(float[]) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4f

Sets the value of this axis-angle to the specified values in the array of length 4.

set(float[]) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Sets the values in this Matrix3f equal to the row-major array parameter (ie, the first three elements of the array will be copied into the first row of this matrix, etc.).

set(float[]) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the values in this Matrix4f equal to the row-major array parameter (ie, the first four elements of the array will be copied into the first row of this matrix, etc.).

set(float[]) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the matrix values of this transform to the matrix values in the single precision array parameter.

set(float[]) - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Sets the value of this tuple to the xyz coordinates specified in the array of length 3.

set(float[]) - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Sets the value of this tuple to the specified coordinates in the array of length 4.

set(float, float, float) - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Sets the value of this tuple to the specified xyz coordinates.

set(float, float, float, float) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4f

Sets the value of this axis-angle to the specified x,y,z,angle.

set(float, float, float, float) - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Sets the value of this tuple to the specified xyzw coordinates.

set(float, Vector3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the value of this transform to a scale and translation matrix; the scale is not applied to the translation and all of the matrix values are modified.

set(float, Vector3f) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the value of this transform to a scale and translation matrix; the scale is not applied to the translation and all of the matrix values are modified.

set(int[]) - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Sets the value of this tuple to the specified coordinates in the array of length 3.

set(int, int, int) - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Sets the value of this tuple to the specified x, y, and z coordinates.

set(Color) - Method in class net.preibisch.mvrecon.vecmath.Color3f

Sets the r,g,b values of this Color3f object to those of the specified AWT Color object.

set(MatchIndices) - Method in class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.MatchIndices

set(NumericAffineModel3D) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

set(NumericAffineTransform3D) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

set(FixedModel) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.FixedModel

set(TranslationInvariantAffineModel3D) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantAffineModel3D

set(TranslationInvariantFixedModel) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantFixedModel

set(TranslationInvariantRigidModel2D) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel2D

set(TranslationInvariantRigidModel3D) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel3D

set(TranslationInvariantSimilarityModel3D) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantSimilarityModel3D

set(AxisAngle4d) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4d

Sets the value of this axis angle to the value of axis angle a1.

set(AxisAngle4d) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4f

Sets the value of this axis-angle to the value of axis-angle a1.

set(AxisAngle4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Sets the value of this matrix to the matrix conversion of the double precision axis and angle argument.

set(AxisAngle4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Sets the value of this matrix to the matrix conversion of the (double precision) axis and angle argument.

set(AxisAngle4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the value of this matrix to the matrix conversion of the double precision axis and angle argument.

set(AxisAngle4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the value of this matrix to the matrix conversion of the double precision axis and angle argument.

set(AxisAngle4d) - Method in class net.preibisch.mvrecon.vecmath.Quat4d

Sets the value of this quaternion to the equivalent rotation of the AxisAngle argument.

set(AxisAngle4d) - Method in class net.preibisch.mvrecon.vecmath.Quat4f

Sets the value of this quaternion to the equivalent rotation of the AxisAngle argument.

set(AxisAngle4d) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the value of this transform to the matrix conversion of the double precision axis-angle argument; all of the matrix values are modified.

set(AxisAngle4f) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4d

Sets the value of this axis angle to the value of axis angle a1.

set(AxisAngle4f) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4f

Sets the value of this axis-angle to the value of axis-angle a1.

set(AxisAngle4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Sets the value of this matrix to the matrix conversion of the single precision axis and angle argument.

set(AxisAngle4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Sets the value of this matrix to the matrix conversion of the (single precision) axis and angle argument.

set(AxisAngle4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the value of this matrix to the matrix conversion of the single precision axis and angle argument.

set(AxisAngle4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the value of this matrix to the matrix conversion of the (single precision) axis and angle argument.

set(AxisAngle4f) - Method in class net.preibisch.mvrecon.vecmath.Quat4d

Sets the value of this quaternion to the equivalent rotation of the AxisAngle argument.

set(AxisAngle4f) - Method in class net.preibisch.mvrecon.vecmath.Quat4f

Sets the value of this quaternion to the equivalent rotation of the AxisAngle argument.

set(AxisAngle4f) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the value of this transform to the matrix conversion of the single precision axis-angle argument; all of the matrix values are modified.

set(Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4d

Sets the value of this axis-angle to the rotational component of the passed matrix.

set(Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4f

Sets the value of this axis-angle to the rotational component of the passed matrix.

set(Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Sets the value of this matrix to the value of the Matrix3d argument.

set(Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Sets the value of this matrix to the float value of the Matrix3d argument.

set(Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the rotational component (upper 3x3) of this matrix to the matrix values in the double precision Matrix3d argument; the other elements of this matrix are initialized as if this were an identity matrix (i.e., affine matrix with no translational component).

set(Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the rotational component (upper 3x3) of this matrix to the matrix values in the double precision Matrix3d argument; the other elements of this matrix are initialized as if this were an identity matrix (i.e., affine matrix with no translational component).

set(Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Quat4d

Sets the value of this quaternion to the rotational component of the passed matrix.

set(Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Quat4f

Sets the value of this quaternion to the rotational component of the passed matrix.

set(Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the rotational component (upper 3x3) of this transform to the matrix values in the double precision Matrix3d argument; the other elements of this transform are initialized as if this were an identity matrix (ie, affine matrix with no translational component).

set(Matrix3d, Vector3d, double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the value of this matrix from the rotation expressed by the rotation matrix m1, the translation t1, and the scale factor.

set(Matrix3d, Vector3d, double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the value of this matrix from the rotation expressed by the rotation matrix m1, the translation t1, and the scale factor.

set(Matrix3d, Vector3d, double) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the value of this matrix from the rotation expressed by the rotation matrix m1, the translation t1, and the scale s.

set(Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4d

Sets the value of this axis-angle to the rotational component of the passed matrix.

set(Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4f

Sets the value of this axis-angle to the rotational component of the passed matrix.

set(Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Sets the value of this matrix to the double value of the Matrix3f argument.

set(Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Sets the value of this matrix to the value of the Matrix3f argument.

set(Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the rotational component (upper 3x3) of this matrix to the matrix values in the single precision Matrix3f argument; the other elements of this matrix are initialized as if this were an identity matrix (i.e., affine matrix with no translational component).

set(Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the rotational component (upper 3x3) of this matrix to the matrix values in the single precision Matrix3f argument; the other elements of this matrix are initialized as if this were an identity matrix (i.e., affine matrix with no translational component).

set(Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Quat4d

Sets the value of this quaternion to the rotational component of the passed matrix.

set(Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Quat4f

Sets the value of this quaternion to the rotational component of the passed matrix.

set(Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the rotational component (upper 3x3) of this transform to the matrix values in the single precision Matrix3f argument; the other elements of this transform are initialized as if this were an identity matrix (i.e., affine matrix with no translational component).

set(Matrix3f, Vector3d, double) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the value of this matrix from the rotation expressed by the rotation matrix m1, the translation t1, and the scale s.

set(Matrix3f, Vector3f, float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the value of this matrix from the rotation expressed by the rotation matrix m1, the translation t1, and the scale factor.

set(Matrix3f, Vector3f, float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the value of this matrix from the rotation expressed by the rotation matrix m1, the translation t1, and the scale factor.

set(Matrix3f, Vector3f, float) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the value of this matrix from the rotation expressed by the rotation matrix m1, the translation t1, and the scale s.

set(Matrix4d) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4d

Sets the value of this axis-angle to the rotational component of the passed matrix.

set(Matrix4d) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4f

Sets the value of this axis-angle to the rotational component of the passed matrix.

set(Matrix4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the value of this matrix to a copy of the passed matrix m1.

set(Matrix4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the value of this matrix to the float value of the passed matrix4d m1.

set(Matrix4d) - Method in class net.preibisch.mvrecon.vecmath.Quat4d

Sets the value of this quaternion to the rotational component of the passed matrix.

set(Matrix4d) - Method in class net.preibisch.mvrecon.vecmath.Quat4f

Sets the value of this quaternion to the rotational component of the passed matrix.

set(Matrix4d) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the matrix values of this transform to the matrix values in the double precision Matrix4d argument.

set(Matrix4f) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4d

Sets the value of this axis-angle to the rotational component of the passed matrix.

set(Matrix4f) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4f

Sets the value of this axis-angle to the rotational component of the passed matrix.

set(Matrix4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the value of this matrix to a copy of the passed matrix m1.

set(Matrix4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the value of this matrix to a copy of the passed matrix m1.

set(Matrix4f) - Method in class net.preibisch.mvrecon.vecmath.Quat4d

Sets the value of this quaternion to the rotational component of the passed matrix.

set(Matrix4f) - Method in class net.preibisch.mvrecon.vecmath.Quat4f

Sets the value of this quaternion to the rotational component of the passed matrix.

set(Matrix4f) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the matrix values of this transform to the matrix values in the single precision Matrix4f argument.

set(Quat4d) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4d

Sets the value of this axis-angle to the rotational equivalent of the passed quaternion.

set(Quat4d) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4f

Sets the value of this axis-angle to the rotational equivalent of the passed quaternion.

set(Quat4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Sets the value of this matrix to the matrix conversion of the double precision quaternion argument.

set(Quat4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Sets the value of this matrix to the matrix conversion of the (single precision) quaternion argument.

set(Quat4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the value of this matrix to the matrix conversion of the (double precision) quaternion argument.

set(Quat4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the value of this matrix to the matrix conversion of the double precision quaternion argument.

set(Quat4d) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the value of this transform to the matrix conversion of the double precision quaternion argument; the non-rotational components are set as if this were an identity matrix.

set(Quat4d, Vector3d, double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the value of this matrix from the rotation expressed by the quaternion q1, the translation t1, and the scale s.

set(Quat4d, Vector3d, double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the value of this matrix from the rotation expressed by the quaternion q1, the translation t1, and the scale s.

set(Quat4d, Vector3d, double) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the value of this matrix from the rotation expressed by the quaternion q1, the translation t1, and the scale s.

set(Quat4f) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4d

Sets the value of this axis-angle to the rotational equivalent of the passed quaternion.

set(Quat4f) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4f

Sets the value of this axis-angle to the rotational equivalent of the passed quaternion.

set(Quat4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Sets the value of this matrix to the matrix conversion of the single precision quaternion argument.

set(Quat4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Sets the value of this matrix to the matrix conversion of the (single precision) quaternion argument.

set(Quat4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the value of this matrix to the matrix conversion of the single precision quaternion argument.

set(Quat4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the value of this matrix to the matrix conversion of the single precision quaternion argument.

set(Quat4f) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the value of this transform to the matrix conversion of the single precision quaternion argument; the non-rotational components are set as if this were an identity matrix.

set(Quat4f, Vector3d, double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the value of this matrix from the rotation expressed by the quaternion q1, the translation t1, and the scale s.

set(Quat4f, Vector3d, double) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the value of this matrix from the rotation expressed by the quaternion q1, the translation t1, and the scale s.

set(Quat4f, Vector3f, float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the value of this matrix from the rotation expressed by the quaternion q1, the translation t1, and the scale s.

set(Quat4f, Vector3f, float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the value of this matrix from the rotation expressed by the quaternion q1, the translation t1, and the scale s.

set(Quat4f, Vector3f, float) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the value of this matrix from the rotation expressed by the quaternion q1, the translation t1, and the scale s.

set(Transform3D) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the matrix, type, and state of this transform to the matrix, type, and state of transform t1.

set(Tuple3d) - Method in class net.preibisch.mvrecon.vecmath.Point4d

Sets the x,y,z components of this point to the corresponding components of tuple t1.

set(Tuple3d) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Sets the value of this tuple to the value of tuple t1.

set(Tuple3d) - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Sets the value of this tuple to the value of tuple t1.

set(Tuple3d) - Method in class net.preibisch.mvrecon.vecmath.Vector4d

Sets the x,y,z components of this vector to the corresponding components of tuple t1.

set(Tuple3f) - Method in class net.preibisch.mvrecon.vecmath.Point4f

Sets the x,y,z components of this point to the corresponding components of tuple t1.

set(Tuple3f) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Sets the value of this tuple to the value of tuple t1.

set(Tuple3f) - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Sets the value of this tuple to the value of tuple t1.

set(Tuple3f) - Method in class net.preibisch.mvrecon.vecmath.Vector4f

Sets the x,y,z components of this vector to the corresponding components of tuple t1.

set(Tuple3i) - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Sets the value of this tuple to the value of tuple t1.

set(Tuple4d) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Sets the value of this tuple to the value of tuple t1.

set(Tuple4d) - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Sets the value of this tuple to the value of tuple t1.

set(Tuple4f) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Sets the value of this tuple to the value of tuple t1.

set(Tuple4f) - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Sets the value of this tuple to the value of tuple t1.

set(Vector3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the value of this matrix to a translate matrix by the passed translation value.

set(Vector3d) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the translational value of this matrix to the Vector3d paramter values, and sets the other components of the matrix as if this transform were an identity matrix.

set(Vector3d, double) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4d

Sets the value of this AxisAngle4d to the specified axis and angle.

set(Vector3d, double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the value of this transform to a scale and translation matrix; the translation is scaled by the scale factor and all of the matrix values are modified.

set(Vector3d, double) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the value of this transform to a scale and translation matrix; the translation is scaled by the scale factor and all of the matrix values are modified.

set(Vector3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the value of this matrix to a translate matrix with the passed translation value.

set(Vector3f) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the translational value of this matrix to the Vector3f parameter values, and sets the other components of the matrix as if this transform were an identity matrix.

set(Vector3f, float) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4f

Sets the value of this AxisAngle4f to the specified axis and angle.

set(Vector3f, float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the value of this transform to a scale and translation matrix; the translation is scaled by the scale factor and all of the matrix values are modified.

set(Vector3f, float) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the value of this transform to a scale and translation matrix; the translation is scaled by the scale factor and all of the matrix values are modified.

setAbsoluteLocalAlignmentError(double) - Method in interface net.preibisch.legacy.registration.bead.error.GlobalErrorStatistics

setAbsoluteLocalAlignmentError(double) - Method in class net.preibisch.legacy.registration.bead.error.GlobalErrorStatisticsImpl

setActive(boolean) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.DefaultFlatfieldCorrectionWrappedImgLoader

setActive(boolean) - Method in interface net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.FlatfieldCorrectionWrappedImgLoader

setActive(boolean) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.MultiResolutionFlatfieldCorrectionWrappedImgLoader

setAdvancedValues() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGaussianGUI

setAdvancedValues() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

setAffineModel(AffineModel3D) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

setAffineModel(AffineTransform3D) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

setAlignmentErrorCount(int) - Method in interface net.preibisch.legacy.registration.bead.error.GlobalErrorStatistics

setAlignmentErrorCount(int) - Method in class net.preibisch.legacy.registration.bead.error.GlobalErrorStatisticsImpl

setAmbiguousAngleTile(Boolean) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListViewDetectionState

setAmbiguousIllumChannel(Boolean) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListViewDetectionState

setAngle(double) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4d

Set the axis angle, in radians.
An axis angle is a rotation angle about the vector (x,y,z).

setAngle(float) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4f

Set the axis angle, in radians.
An axis angle is a rotation angle about the vector (x,y,z).

setAngleNames(List<String>) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

setAngleNames(List<String>) - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

setApplyAxis(boolean) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

setApplyAxis(boolean) - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

setApplyAxis(boolean) - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

setAsBrightnessDialog(BigDataViewer) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.ScrollableBrightnessDialog

setAtBase(int, double) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

setAtBase(int, double) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

setAutoNormalize(boolean) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets a flag that enables or disables automatic SVD normalization.

setAutoStitch(boolean) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.util.CZIReaderSetupHook

setAverageAlignmentError(double) - Method in interface net.preibisch.legacy.registration.bead.error.GlobalErrorStatistics

setAverageAlignmentError(double) - Method in class net.preibisch.legacy.registration.bead.error.GlobalErrorStatisticsImpl

setBasePath(URI) - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoints

setBasePath(URI) - Method in class net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions.PointSpreadFunction

setBDV(BigDataViewer) - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BasicBDVPopup

Adopt an already-running BigDataViewer instance (e.g. when an explorer transfers a live BDV across a panel rebuild, such as the BigStitcher Stitching <-> Multiview mode switch).

setBDV(BigDataViewer) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BDVPopup

setBDV(BigDataViewer) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.LazyBDVPopup

Adopt an already-running (lazy) BDV when the explorer transfers it across a panel rebuild (e.g. the BigStitcher Stitching <-> Multiview mode switch).

setBoundingBox(Interval) - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

setBoundingBox(Interval) - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

setBoundingBoxes(BoundingBoxes) - Method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

setBrightImage(ViewId, File) - Method in interface net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.FlatfieldCorrectionWrappedImgLoader

setBrightImage(ViewId, File) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.LazyLoadingFlatFieldCorrectionMap

setCached(boolean) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.DefaultFlatfieldCorrectionWrappedImgLoader

setCached(boolean) - Method in interface net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.FlatfieldCorrectionWrappedImgLoader

setCached(boolean) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.MultiResolutionFlatfieldCorrectionWrappedImgLoader

setCalibration(double[], String) - Method in interface net.preibisch.mvrecon.process.export.Calibrateable

setCalibration(double[], String) - Method in class net.preibisch.mvrecon.process.export.DisplayImage

setCalibration(double[], String) - Method in class net.preibisch.mvrecon.process.export.ExportN5Api

setCalibration(double[], String) - Method in class net.preibisch.mvrecon.process.export.Save3dTIFF

setCalibration(ImagePlus, Interval, double, double, double[], String) - Static method in class net.preibisch.mvrecon.process.export.DisplayImage

setCalUnit(String) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

setCalUnit(String) - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

setCalUnit(String) - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

setCalX(double) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

setCalX(double) - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

setCalX(double) - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

setCalY(double) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

setCalY(double) - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

setCalY(double) - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

setCalZ(double) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

setCalZ(double) - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

setCalZ(double) - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

setCandidates(List<PointMatchGeneric<I>>) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.PairwiseResult

setCanvasSize(int, int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointOverlay

setCanvasSize(int, int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupIdOverlay

setChannelNames(List<String>) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

setChannelNames(List<String>) - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

setChartPanel(ChartPanel) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.statistics.SelectTimepointEntry

setColumn(int, double[]) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Sets the specified column of this matrix3d to the three values provided.

setColumn(int, double[]) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the specified column of this matrix4d to the four values provided.

setColumn(int, double, double, double) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Sets the specified column of this matrix3d to the three values provided.

setColumn(int, double, double, double, double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the specified column of this matrix4d to the four values provided.

setColumn(int, float[]) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Sets the specified column of this matrix3f to the three values provided.

setColumn(int, float[]) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the specified column of this matrix4f to the four values provided.

setColumn(int, float, float, float) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Sets the specified column of this matrix3f to the three values provided.

setColumn(int, float, float, float, float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the specified column of this matrix4f to the four values provided.

setColumn(int, Vector3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Sets the specified column of this matrix3d to the vector provided.

setColumn(int, Vector3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Sets the specified column of this matrix3f to the vector provided.

setColumn(int, Vector4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the specified column of this matrix4d to the vector provided.

setColumn(int, Vector4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the specified column of this matrix4f to the vector provided.

setColumnClasses(List<Class<? extends Entity>>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedTableModel

setColumnClasses(List<Class<? extends Entity>>) - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.ISpimDataTableModel

setColumnClasses(List<Class<? extends Entity>>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MissingViewsTableModelDecorator

setColumnClasses(List<Class<? extends Entity>>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MultiViewTableModelDecorator

setComparator(Comparator<String>) - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

setComputeComplexConjugate(boolean) - Method in class util.FFTConvolution

setCorrespondingInterestPoints(Collection<CorrespondingInterestPoints>) - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoints

setCorrespondingInterestPointsLocal(Collection<CorrespondingInterestPoints>) - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoints

setCorrespondingInterestPointsLocal(Collection<CorrespondingInterestPoints>) - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

setDarkImage(ViewId, File) - Method in interface net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.FlatfieldCorrectionWrappedImgLoader

setDarkImage(ViewId, File) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.LazyLoadingFlatFieldCorrectionMap

setDebug(boolean) - Method in class net.preibisch.mvrecon.process.deconvolution.MultiViewDeconvolution

setDebugInterval(int) - Method in class net.preibisch.mvrecon.process.deconvolution.MultiViewDeconvolution

setDefaultMultipleAngles(int) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

setDefaultMultipleAngles(int) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListImageJ

setDefaultMultipleAngles(int) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListLOCI

setDefaultMultipleChannels(int) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

setDefaultMultipleChannels(int) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListImageJ

setDefaultMultipleChannels(int) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListLOCI

setDefaultMultipleIlluminations(int) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

setDefaultMultipleIlluminations(int) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListImageJ

setDefaultMultipleIlluminations(int) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListLOCI

setDefaultMultipleTiles(int) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

setDefaultMultipleTiles(int) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListImageJ

setDefaultMultipleTiles(int) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListLOCI

setDefaultMultipleTimepoints(int) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

setDefaultMultipleTimepoints(int) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListImageJ

setDefaultMultipleTimepoints(int) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListLOCI

setDefaultValues(int) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGaussianGUI

setDefaultValues(int) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

setDeflate(boolean) - Method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.ParametersResaveHDF5

setDescription(String) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.PairwiseResult

setDescriptions(String) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.PairwiseResult

setDistance(double) - Method in class net.preibisch.legacy.registration.detection.AbstractDetection

setDistanceFade(double, boolean) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

setDistanceThreshold(double) - Method in class net.preibisch.mvrecon.process.pointcloud.icp.SimplePointMatchIdentification

setElement(int, int, double) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Sets the specified element of this matrix3f to the value provided.

setElement(int, int, double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the specified element of this matrix4f to the value provided.

setElement(int, int, float) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Sets the specified element of this matrix3f to the value provided.

setElement(int, int, float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the specified element of this matrix4f to the value provided.

setEuler(Vector3d) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the rotational component (upper 3x3) of this transform to the rotation matrix converted from the Euler angles provided; the other non-rotational elements are set as if this were an identity matrix.

setExecutorService(ExecutorService) - Method in class util.FFTConvolution

setExplorerWindow(ExplorerWindow<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.AnalyzeErrorPopup

setExplorerWindow(ExplorerWindow<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.ApplyTransformationPopup

setExplorerWindow(ExplorerWindow<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BakeManualTransformationPopup

setExplorerWindow(ExplorerWindow<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BDVPopup

setExplorerWindow(ExplorerWindow<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BoundingBoxPopup

setExplorerWindow(ExplorerWindow<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.DeconvolutionPopup

setExplorerWindow(ExplorerWindow<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.DetectInterestPointsPopup

setExplorerWindow(ExplorerWindow<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.DisplayFusedImagesPopup

setExplorerWindow(ExplorerWindow<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.DisplayRawImagesPopup

setExplorerWindow(ExplorerWindow<?>) - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.popup.ExplorerWindowSetable

setExplorerWindow(ExplorerWindow<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.FlatFieldCorrectionPopup

setExplorerWindow(ExplorerWindow<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.FusionPopup

setExplorerWindow(ExplorerWindow<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.IntensityAdjustmentPopup

setExplorerWindow(ExplorerWindow<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.InterestPointsExplorerPopup

setExplorerWindow(ExplorerWindow<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.LabelPopUp

setExplorerWindow(ExplorerWindow<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.LazyBDVPopup

setExplorerWindow(ExplorerWindow<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.MaxProjectPopup

setExplorerWindow(ExplorerWindow<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.MissingViewsPopup

setExplorerWindow(ExplorerWindow<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.PointSpreadFunctionsPopup

setExplorerWindow(ExplorerWindow<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.QualityPopup

setExplorerWindow(ExplorerWindow<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.RegisterInterestPointsPopup

setExplorerWindow(ExplorerWindow<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.RegistrationExplorerPopup

setExplorerWindow(ExplorerWindow<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.RemoveDetectionsPopup

setExplorerWindow(ExplorerWindow<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.RemoveTransformationPopup

setExplorerWindow(ExplorerWindow<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.ReorientSamplePopup

setExplorerWindow(ExplorerWindow<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.ResavePopup

setExplorerWindow(ExplorerWindow<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.Separator

setExplorerWindow(ExplorerWindow<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.SimpleHyperlinkPopup

setExplorerWindow(ExplorerWindow<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.SpecifyCalibrationPopup

setExplorerWindow(ExplorerWindow<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.VisualizeDetectionsPopup

setExplorerWindow(ExplorerWindow<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.VisualizeNonRigid

setExtraSpaceFactor(double) - Method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxMinFilterThreshold

setFFTImgFactory(ImgFactory<ComplexFloatType>) - Method in class util.FFTConvolution

setFixedViews(Set<V>) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.Subset

setFlippedMatches(Collection<PointMatch>) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.PairwiseResult

setFont(Font) - Method in class net.preibisch.mvrecon.fiji.plugin.util.MyMultiLineLabel

setFusedModeSimple(BigDataViewer, AbstractSpimData<?>) - Static method in class util.BDVTools

Sets BDV to FUSED display mode and deactivates all sources.

setFusion(FusedRandomAccessibleInterval.Fusion) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval

setGroupedFormat(Boolean) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListViewDetectionState

setHDF5File(File) - Method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.ParametersResaveHDF5

setHideMissingViews(boolean) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedTableModel

setId(V, ArrayList<HashSet<V>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.PairwiseSetup

setIdentity() - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Sets this Matrix3d to identity.

setIdentity() - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Sets this Matrix3f to identity.

setIdentity() - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets this Matrix4d to identity.

setIdentity() - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets this Matrix4f to identity.

setIdentity() - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets this transform to the identity matrix.

setImg(RandomAccessible<R>, Interval) - Method in class util.FFTConvolution

setImg(RandomAccessibleInterval<R>) - Method in class util.FFTConvolution

setImgFactory(ImgFactory<? extends NativeType<?>>) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AbstractImgFactoryImgLoader

setImgFactory(ImgFactory<? extends NativeType<?>>) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.FileMapImgLoaderLOCI

setImgFFT(Img<ComplexFloatType>) - Method in class util.FFTConvolution

Sets the FFT image as computed, be very careful with this method, if any parameters of the FFT are wrong, this will fail WARNING: if you do not set keepImgFFT, this image will be modified during convolution

setImgToAvg(boolean) - Method in class net.preibisch.mvrecon.process.deconvolution.init.PsiInitAvgApprox

setImgToAvg(boolean) - Method in class net.preibisch.mvrecon.process.deconvolution.init.PsiInitAvgPrecise

setInliers(List<PointMatchGeneric<I>>, double) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.PairwiseResult

setInliers(List<PointMatchGeneric<I>>, double, List<Integer>) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.PairwiseResult

setIntensityAdjustments(IntensityAdjustments) - Method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

setInteractiveValues() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGaussianGUI

setInteractiveValues() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

setInterestPoints(Collection<InterestPoint>) - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoints

setInterestPointsLocal(Collection<InterestPoint>) - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoints

setInterestPointsLocal(Collection<InterestPoint>) - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5

setKeepImgFFT(boolean) - Method in class util.FFTConvolution

setKernel(RandomAccessible<R>, Interval) - Method in class util.FFTConvolution

setKernel(RandomAccessibleInterval<R>) - Method in class util.FFTConvolution

setKernelFFT(Img<ComplexFloatType>) - Method in class util.FFTConvolution

Sets the FFT kernel as computed, be very careful with this method, if any parameters of the FFT are wrong, this will fail

setLabelA(String) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.PairwiseResult

setLabelB(String) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.PairwiseResult

setLinearInterpolation() - Method in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccessible

setM00(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Set the first matrix element in the first row.

setM00(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Set the first matrix element in the first row.

setM00(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Set the first matrix element in the first row.

setM00(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Set the first matrix element in the first row.

setM01(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Set the second matrix element in the first row.

setM01(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Set the second matrix element in the first row.

setM01(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Set the second matrix element in the first row.

setM01(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Set the second matrix element in the first row.

setM02(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Set the third matrix element in the first row.

setM02(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Set the third matrix element in the first row.

setM02(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Set the third matrix element in the first row.

setM02(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Set the third matrix element in the first row.

setM03(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Set the fourth element of the first row.

setM03(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Set the fourth element of the first row.

setM10(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Set first matrix element in the second row.

setM10(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Set first matrix element in the second row.

setM10(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Set first matrix element in the second row.

setM10(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Set first matrix element in the second row.

setM11(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Set the second matrix element in the second row.

setM11(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Set the second matrix element in the second row.

setM11(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Set the second matrix element in the second row.

setM11(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Set the second matrix element in the second row.

setM12(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Set the third matrix element in the second row.

setM12(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Set the third matrix element in the second row.

setM12(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Set the third matrix element in the second row.

setM12(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Set the third matrix element in the second row.

setM13(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Set the fourth element of the second row.

setM13(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Set the fourth element of the second row.

setM20(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Set the first matrix element in the third row.

setM20(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Set the first matrix element in the third row.

setM20(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Set the first matrix element in the third row.

setM20(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Set the first matrix element in the third row.

setM21(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Set the second matrix element in the third row.

setM21(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Set the second matrix element in the third row.

setM21(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Set the second matrix element in the third row.

setM21(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Set the second matrix element in the third row.

setM22(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Set the third matrix element in the third row.

setM22(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Set the third matrix element in the third row.

setM22(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Set the third matrix element in the third row.

setM22(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Set the third matrix element in the third row.

setM23(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Set the fourth element of the third row.

setM23(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Set the fourth element of the third row.

setM30(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Set the first element of the fourth row.

setM30(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Set the first element of the fourth row.

setM31(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Set the second element of the fourth row.

setM31(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Set the second element of the fourth row.

setM32(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Set the third element of the fourth row.

setM32(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Set the third element of the fourth row.

setM33(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Set the fourth element of the fourth row.

setM33(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Set the fourth element of the fourth row.

setMax(double) - Method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.ParametersResaveHDF5

setMaxAlignmentError(double) - Method in interface net.preibisch.legacy.registration.bead.error.GlobalErrorStatistics

setMaxAlignmentError(double) - Method in class net.preibisch.legacy.registration.bead.error.GlobalErrorStatisticsImpl

setMin(double) - Method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.ParametersResaveHDF5

setMinAlignmentError(double) - Method in interface net.preibisch.legacy.registration.bead.error.GlobalErrorStatistics

setMinAlignmentError(double) - Method in class net.preibisch.legacy.registration.bead.error.GlobalErrorStatisticsImpl

setMipmapManual(boolean) - Method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.ParametersResaveHDF5

setModel(double[], String) - Method in class net.preibisch.mvrecon.fiji.plugin.apply.ModelLink

setModelToCalibration(SpimData, ViewId, double) - Static method in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

setModelToIdentity(SpimData, ViewId) - Static method in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

setName(String) - Method in class net.preibisch.mvrecon.fiji.spimdata.EmptyEntity

setNearestNeighborInterpolation() - Method in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccessible

setNonUniformScale(double, double, double) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Deprecated.

Use setScale(Vector3d) instead of setNonUniformScale; note that the setScale only modifies the scale component

setNumCandidates(int) - Method in interface net.preibisch.legacy.registration.bead.error.GlobalErrorStatistics

setNumCandidates(int) - Method in class net.preibisch.legacy.registration.bead.error.GlobalErrorStatisticsImpl

setNumCorrespondences(int) - Method in interface net.preibisch.legacy.registration.bead.error.GlobalErrorStatistics

setNumCorrespondences(int) - Method in class net.preibisch.legacy.registration.bead.error.GlobalErrorStatisticsImpl

setNumDetections(int) - Method in interface net.preibisch.legacy.registration.bead.error.GlobalErrorStatistics

setNumDetections(int) - Method in class net.preibisch.legacy.registration.bead.error.GlobalErrorStatisticsImpl

setNumFetcherThreads(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitViewerImgLoader

setNumFetcherThreads(BasicImgLoader, int) - Static method in class util.URITools

setNumViews(int) - Method in class net.preibisch.mvrecon.process.deconvolution.iteration.mul.ComputeBlockMulThreadCPUFactory

setOne() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

setOne() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

setOSEMspeedup(double) - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccessibleInterval

setOutput(RandomAccessibleInterval<R>) - Method in class util.FFTConvolution

setPairs(List<Pair<V, V>>) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.PairwiseSetup

Directly set the pairs list (used for optimized pair generation that bypasses definePairs()).

setPairwiseResultForPair(Pair<Group<ViewId>, Group<ViewId>>, PairwiseStitchingResult<ViewId>) - Method in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.StitchingResults

setParameters(String) - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoints

setPlaneThickness(double) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

setPointMatchIdentification(PointMatchIdentification<P>) - Method in class net.preibisch.mvrecon.process.pointcloud.icp.ICP

Sets the PointMatchIdentification that defines how PointMatches between reference and target are identified.

setPointSizeScale(double) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

setPointSpreadFunctions(PointSpreadFunctions) - Method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

setPosition(double[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridAccess

setPosition(double[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccess

setPosition(double[]) - Method in class util.StackingRealRandomAccessible.StackingRealRandomAccess

setPosition(double, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridAccess

setPosition(double, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccess

setPosition(double, int) - Method in class util.StackingRealRandomAccessible.StackingRealRandomAccess

setPosition(float[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridAccess

setPosition(float[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccess

setPosition(float[]) - Method in class util.StackingRealRandomAccessible.StackingRealRandomAccess

setPosition(float, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridAccess

setPosition(float, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccess

setPosition(float, int) - Method in class util.StackingRealRandomAccessible.StackingRealRandomAccess

setPosition(int[]) - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccess

setPosition(int[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccess

setPosition(int[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccess

setPosition(int[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessFirstWins

setPosition(int[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessMax

setPosition(int[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessNoWeights

setPosition(int[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridAccess

setPosition(int[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGridRandomAccess

setPosition(int[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputGeneralRandomAccess

setPosition(int[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccess2d

setPosition(int[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccess

setPosition(int[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccess

setPosition(int[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.InterpolatingNonRigidRasteredRandomAccess

setPosition(int[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.NonRigidRasteredRandomAccess

setPosition(int[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.TransformedRasteredRandomAccess

setPosition(int[]) - Method in class util.StackingRealRandomAccessible.StackingRealRandomAccess

setPosition(int, int) - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccess

setPosition(int, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccess

setPosition(int, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccess

setPosition(int, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessFirstWins

setPosition(int, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessMax

setPosition(int, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessNoWeights

setPosition(int, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridAccess

setPosition(int, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGridRandomAccess

setPosition(int, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputGeneralRandomAccess

setPosition(int, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccess2d

setPosition(int, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccess

setPosition(int, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccess

setPosition(int, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.InterpolatingNonRigidRasteredRandomAccess

setPosition(int, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.NonRigidRasteredRandomAccess

setPosition(int, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.TransformedRasteredRandomAccess

setPosition(int, int) - Method in class util.StackingRealRandomAccessible.StackingRealRandomAccess

setPosition(long[]) - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccess

setPosition(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccess

setPosition(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccess

setPosition(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessFirstWins

setPosition(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessMax

setPosition(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessNoWeights

setPosition(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridAccess

setPosition(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGridRandomAccess

setPosition(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputGeneralRandomAccess

setPosition(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccess2d

setPosition(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccess

setPosition(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccess

setPosition(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.InterpolatingNonRigidRasteredRandomAccess

setPosition(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.NonRigidRasteredRandomAccess

setPosition(long[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.TransformedRasteredRandomAccess

setPosition(long[]) - Method in class util.StackingRealRandomAccessible.StackingRealRandomAccess

setPosition(long, int) - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccess

setPosition(long, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccess

setPosition(long, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccess

setPosition(long, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessFirstWins

setPosition(long, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessMax

setPosition(long, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessNoWeights

setPosition(long, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridAccess

setPosition(long, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGridRandomAccess

setPosition(long, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputGeneralRandomAccess

setPosition(long, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccess2d

setPosition(long, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccess

setPosition(long, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccess

setPosition(long, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.InterpolatingNonRigidRasteredRandomAccess

setPosition(long, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.NonRigidRasteredRandomAccess

setPosition(long, int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.TransformedRasteredRandomAccess

setPosition(long, int) - Method in class util.StackingRealRandomAccessible.StackingRealRandomAccess

setPosition(Localizable) - Method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccess

setPosition(Localizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccess

setPosition(Localizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccess

setPosition(Localizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessFirstWins

setPosition(Localizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessMax

setPosition(Localizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessNoWeights

setPosition(Localizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridAccess

setPosition(Localizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGridRandomAccess

setPosition(Localizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputGeneralRandomAccess

setPosition(Localizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccess2d

setPosition(Localizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccess

setPosition(Localizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccess

setPosition(Localizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.InterpolatingNonRigidRasteredRandomAccess

setPosition(Localizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.NonRigidRasteredRandomAccess

setPosition(Localizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.TransformedRasteredRandomAccess

setPosition(Localizable) - Method in class util.StackingRealRandomAccessible.StackingRealRandomAccess

setPosition(RealLocalizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.ModelGridAccess

setPosition(RealLocalizable) - Method in class net.preibisch.mvrecon.process.fusion.transformed.weights.BlendingRealRandomAccess

setPosition(RealLocalizable) - Method in class util.StackingRealRandomAccessible.StackingRealRandomAccess

setPrintOut(boolean) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.PairwiseResult

setPrintResult(boolean) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.rgldm.RGLDMPairwise

setProgress(double) - Method in class net.preibisch.mvrecon.fiji.plugin.resave.ProgressWriterIJ

setPSF(Img<FloatType>) - Method in class net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions.PointSpreadFunction

setReferenceTimepoint(TimePoints, int) - Static method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.statistics.MouseListenerTimelapse

setRelativePositions(boolean) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.util.CZIReaderSetupHook

setRenderResult(BufferedImageRenderResult) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough.MyTarget

setResolutions(int[][]) - Method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.ParametersResaveHDF5

setResult(long, String) - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.PairwiseResult

setRotation(AxisAngle4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the rotational component (upper 3x3) of this matrix to the matrix equivalent values of the axis-angle argument; the other elements of this matrix are unchanged; a singular value decomposition is performed on this object's upper 3x3 matrix to factor out the scale, then this object's upper 3x3 matrix components are replaced by the matrix equivalent of the axis-angle, and then the scale is reapplied to the rotational components.

setRotation(AxisAngle4d) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the rotational component (upper 3x3) of this transform to the matrix equivalent values of the axis-angle argument; the other elements of this transform are unchanged; any pre-existing scale in the transform is preserved.

setRotation(AxisAngle4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the rotational component (upper 3x3) of this matrix to the matrix equivalent values of the axis-angle argument; the other elements of this matrix are unchanged; a singular value decomposition is performed on this object's upper 3x3 matrix to factor out the scale, then this object's upper 3x3 matrix components are replaced by the matrix equivalent of the axis-angle, and then the scale is reapplied to the rotational components.

setRotation(AxisAngle4f) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the rotational component (upper 3x3) of this transform to the matrix equivalent values of the axis-angle argument; the other elements of this transform are unchanged; any pre-existing scale in the transform is preserved.

setRotation(Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the rotational component (upper 3x3) of this matrix to the matrix values in the double precision Matrix3d argument; the other elements of this matrix are unchanged; a singular value decomposition is performed on this object's upper 3x3 matrix to factor out the scale, then this object's upper 3x3 matrix components are replaced by the passed rotation components, and then the scale is reapplied to the rotational components.

setRotation(Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the rotational component (upper 3x3) of this matrix to the matrix values in the double precision Matrix3d argument; the other elements of this matrix are unchanged; a singular value decomposition is performed on this object's upper 3x3 matrix to factor out the scale, then this object's upper 3x3 matrix components are replaced by the passed rotation components, and then the scale is reapplied to the rotational components.

setRotation(Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the rotational component (upper 3x3) of this transform to the matrix values in the double precision Matrix3d argument; the other elements of this transform are unchanged; any pre-existing scale will be preserved; the argument matrix m1 will be checked for proper normalization when this transform is internally classified.

setRotation(Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the rotational component (upper 3x3) of this matrix to the matrix values in the single precision Matrix3f argument; the other elements of this matrix are unchanged; a singular value decomposition is performed on this object's upper 3x3 matrix to factor out the scale, then this object's upper 3x3 matrix components are replaced by the passed rotation components, and then the scale is reapplied to the rotational components.

setRotation(Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the rotational component (upper 3x3) of this matrix to the matrix values in the single precision Matrix3f argument; the other elements of this matrix are unchanged; a singular value decomposition is performed on this object's upper 3x3 matrix to factor out the scale, then this object's upper 3x3 matrix components are replaced by the passed rotation components, and then the scale is reapplied to the rotational components.

setRotation(Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the rotational component (upper 3x3) of this transform to the matrix values in the single precision Matrix3f argument; the other elements of this transform are unchanged; any pre-existing scale will be preserved; the argument matrix m1 will be checked for proper normalization when this transform is internally classified.

setRotation(Quat4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the rotational component (upper 3x3) of this matrix to the matrix equivalent values of the quaternion argument; the other elements of this matrix are unchanged; a singular value decomposition is performed on this object's upper 3x3 matrix to factor out the scale, then this object's upper 3x3 matrix components are replaced by the matrix equivalent of the quaternion, and then the scale is reapplied to the rotational components.

setRotation(Quat4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the rotational component (upper 3x3) of this matrix to the matrix equivalent values of the quaternion argument; the other elements of this matrix are unchanged; a singular value decomposition is performed on this object's upper 3x3 matrix to factor out the scale, then this object's upper 3x3 matrix components are replaced by the matrix equivalent of the quaternion, and then the scale is reapplied to the rotational components.

setRotation(Quat4d) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the rotational component (upper 3x3) of this transform to the matrix equivalent values of the quaternion argument; the other elements of this transform are unchanged; any pre-existing scale in the transform is preserved.

setRotation(Quat4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the rotational component (upper 3x3) of this matrix to the matrix equivalent values of the quaternion argument; the other elements of this matrix are unchanged; a singular value decomposition is performed on this object's upper 3x3 matrix to factor out the scale, then this object's upper 3x3 matrix components are replaced by the matrix equivalent of the quaternion, and then the scale is reapplied to the rotational components.

setRotation(Quat4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the rotational component (upper 3x3) of this matrix to the matrix equivalent values of the quaternion argument; the other elements of this matrix are unchanged; a singular value decomposition is performed on this object's upper 3x3 matrix to factor out the scale, then this object's upper 3x3 matrix components are replaced by the matrix equivalent of the quaternion, and then the scale is reapplied to the rotational components.

setRotation(Quat4f) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the rotational component (upper 3x3) of this transform to the matrix equivalent values of the quaternion argument; the other elements of this transform are unchanged; any pre-existing scale in the transform is preserved.

setRotationAxis(int) - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

setRotationScale(Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Replaces the upper 3x3 matrix values of this matrix with the values in the matrix m1.

setRotationScale(Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Replaces the upper 3x3 matrix values of this transform with the values in the matrix m1.

setRotationScale(Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Replaces the upper 3x3 matrix values of this matrix with the values in the matrix m1.

setRotationScale(Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Replaces the upper 3x3 matrix values of this matrix with the values in the matrix m1.

setRotationScale(Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Replaces the upper 3x3 matrix values of this transform with the values in the matrix m1.

setRotAxis(double[]) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

setRotAxis(double[]) - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

setRow(int, double[]) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Sets the specified row of this matrix3d to the three values provided.

setRow(int, double[]) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the specified row of this matrix4d to the four values provided.

setRow(int, double, double, double) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Sets the specified row of this matrix3d to the 4 values provided.

setRow(int, double, double, double, double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the specified row of this matrix4d to the four values provided.

setRow(int, float[]) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Sets the specified row of this matrix3f to the three values provided.

setRow(int, float[]) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the specified row of this matrix4f to the four values provided in the passed array.

setRow(int, float, float, float) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Sets the specified row of this matrix3f to the three values provided.

setRow(int, float, float, float, float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the specified row of this matrix4f to the four values provided.

setRow(int, Vector3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Sets the specified row of this matrix3d to the Vector provided.

setRow(int, Vector3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Sets the specified row of this matrix3f to the Vector provided.

setRow(int, Vector4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the specified row of this matrix4d to the Vector provided.

setRow(int, Vector4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the specified row of this matrix4f to the Vector provided.

setScale(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Sets the scale component of the current matrix by factoring out the current scale (by doing an SVD) and multiplying by the new scale.

setScale(double) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the scale component of the current matrix by factoring out the current scale (by doing an SVD) from the rotational component and multiplying by the new scale.

setScale(double) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the scale component of the current transform; any existing scale is first factored out of the existing transform before the new scale is applied.

setScale(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Sets the scale component of the current matrix by factoring out the current scale (by doing an SVD) and multiplying by the new scale.

setScale(float) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the scale component of the current matrix by factoring out the current scale (by doing an SVD) from the rotational component and multiplying by the new scale.

setScale(Vector3d) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets the possibly non-uniform scale component of the current transform; any existing scale is first factored out of the existing transform before the new scale is applied.

setSelected(int, int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

setSelectedState(int) - Method in interface net.preibisch.mvrecon.fiji.plugin.util.MouseOverPopUpStateChanger.StateChanger

setSeqFile(File) - Method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.ParametersResaveHDF5

setSetupsPerPartition(int) - Method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.ParametersResaveHDF5

setSimilarityMeasure(SimilarityMeasure) - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.AbstractPointDescriptor

Sets the SimilarityMeasure object that is used to compute how similar two descriptors are

setSize(int) - Method in class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.MatchIndices

setSpimData(Object) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

setSplit(boolean) - Method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.ParametersResaveHDF5

setStitchingResults(StitchingResults) - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.StitchingResultsSettable

setStitchingResults(StitchingResults) - Method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

setSubdivisions(int[][]) - Method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.ParametersResaveHDF5

setTargetW(double[]) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.SimpleReferenceIP

setText(String[]) - Method in class net.preibisch.mvrecon.fiji.plugin.util.MyMultiLineLabel

setTimepointsPerPartition(int) - Method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.ParametersResaveHDF5

setTitle(String) - Method in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox

setTitle(String) - Method in class net.preibisch.mvrecon.process.deconvolution.DeconView

setTranslation(Vector3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Modifies the translational components of this matrix to the values of the Vector3d argument; the other values of this matrix are not modified.

setTranslation(Vector3d) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Replaces the translational components of this transform to the values in the Vector3d argument; the other values of this transform are not modified.

setTranslation(Vector3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Modifies the translational components of this matrix to the values of the Vector3f argument; the other values of this matrix are not modified.

setTranslation(Vector3f) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Replaces the translational components of this transform to the values in the Vector3f argument; the other values of this transform are not modified.

setUnit(String) - Method in class net.preibisch.mvrecon.fiji.plugin.Specify_Calibration.Cal

setupBdvDatasetsHDF5(N5Writer, ViewId, DataType, long[], Compression, int[], int[][]) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

setupBdvDatasetsN5(N5Writer, ViewId, DataType, long[], Compression, int[], int[][]) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

setupBdvDatasetsOMEZARR_ResaveRaw(N5Writer, ViewId, DataType, long[], double[], String, Compression, int[], int[][], boolean, int[]) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

setUpDefaultValues(int[], int[]) - Method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.AutomaticReorientationBoundingBoxGUI

setUpDefaultValues(int[], int[]) - Method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.BDVBoundingBoxGUI

setUpDefaultValues(int[], int[]) - Method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.BoundingBoxGUI

populates this.min[] and this.max[] from the defaultMin and defaultMax

setUpDefaultValues(int[], int[]) - Method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.MaximumBoundingBoxGUI

setUpDefaultValues(int[], int[]) - Method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.MinFilterThresholdBoundingBoxGUI

setUpDefaultValues(int[], int[]) - Method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.ModifyDefinedBoundingBoxGUI

setupFFTs(Interval, Interval, long[], long[]) - Static method in class util.FFTConvolution

setupFromXML(Element, HashMap<Integer, Integer>, HashMap<Integer, Interval>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.XmlIoSplitViewerImgLoader

setupGUI(GenericDialog, SpimData2) - Static method in class net.preibisch.mvrecon.process.splitting.ConsensusSetCriterion

Setup GUI components for consensus set criterion.

setupGUI(GenericDialog, SpimData2) - Static method in class net.preibisch.mvrecon.process.splitting.CrossViewCorrespondenceCriterion

Setup GUI components for cross-view correspondence criterion.

setupGUI(GenericDialog, SpimData2, long[]) - Static method in class net.preibisch.mvrecon.process.splitting.SplitDistributeEvenly

setupGUI(GenericDialog, SpimData2, long[]) - Static method in class net.preibisch.mvrecon.process.splitting.SplitOctTree

Setup GUI components for oct-tree splitting parameters.

setupGUI(GenericDialog, SpimData2, long[], Set<Integer>) - Static method in class net.preibisch.mvrecon.process.splitting.SplitOctTree

Setup GUI components for oct-tree splitting parameters.

setupGUI(GenericDialog, SpimData2, Set<Integer>) - Static method in class net.preibisch.mvrecon.process.splitting.ConsensusSetCriterion

Setup GUI components for consensus set criterion.

setupGUI(GenericDialog, SpimData2, Set<Integer>) - Static method in class net.preibisch.mvrecon.process.splitting.CrossViewCorrespondenceCriterion

Setup GUI components for cross-view correspondence criterion.

setupId - Variable in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5.InterestPointData

SETUPIDS_NAME - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.XmlIoSplitViewerImgLoader

SETUPIDS_NEW - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.XmlIoSplitViewerImgLoader

SETUPIDS_OLD - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.XmlIoSplitViewerImgLoader

SETUPIDS_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.XmlIoSplitViewerImgLoader

setUpMultiRes(int, int, Interval, double[][], Dimensions[], Interval[]) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitViewerSetupImgLoader

setupMultiResolutionPyramid(N5Writer, Function<Integer, String>, DataType, long[], Compression, int[], int[][]) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

setupMultiResolutionPyramid(N5Writer, Function<Integer, String>, DataType, long[], Compression, int[], int[][], boolean, int[]) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

setupMultiResolutionPyramid(N5Writer, ViewId, BiFunction<ViewId, Integer, String>, DataType, long[], Compression, int[], int[][], boolean, int[]) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

SetupSplitResult(int, List<ViewSetup>, Map<Integer, Integer>, Map<Integer, Interval>, List<Integer>, Map<ViewId, ViewRegistration>, Map<ViewId, ViewInterestPointLists>) - Constructor for class net.preibisch.mvrecon.process.splitting.SplittingTools.SetupSplitResult

setupToXml(int, int, Interval) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.XmlIoSplitViewerImgLoader

setUsed(boolean) - Method in class net.preibisch.legacy.registration.detection.AbstractDetection

setUseW(boolean) - Method in class net.preibisch.legacy.registration.detection.AbstractDetection

setValueAt(Object, int, int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

setValueAt(Object, int, int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MissingViewsTableModelDecorator

setValueAt(Object, int, int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MultiViewTableModelDecorator

setValueAt(Object, int, int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationTableModel

setViewsInterestPoints(ViewInterestPoints) - Method in class net.preibisch.mvrecon.fiji.spimdata.SpimData2

setVisible(boolean) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupIdOverlay

setVisibleSources(ViewerState, Collection<? extends SourceAndConverter<?>>) - Static method in class util.BDVTools

Sets source visibility using batch API.

setVisibleSourcesBatch(BigDataViewer, Set<Integer>) - Static method in class util.BDVTools

Sets source visibility by setup ID using BDV's batch API.

setW(double) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Set the w coordinate.

setW(double[]) - Method in class net.preibisch.legacy.registration.detection.AbstractDetection

setW(float) - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Set the w coordinate.

setWasZGrouped(Boolean) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListViewDetectionState

setWeight(double) - Method in class net.preibisch.legacy.registration.detection.AbstractDetection

setWeighted(boolean) - Method in class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.FlattenedMatches

setX(double) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4d

Set a new value for x coordinate.

setX(double) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Set the x coordinate.

setX(double) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Set the x coordinate.

setX(float) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4f

Set a new value for x coordinate.

setX(float) - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Set the x coordinate.

setX(float) - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Set the x coordinate.

setX(int) - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Set the x coordinate.

setY(double) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4d

Set a new value for y coordinate.

setY(double) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Set the y coordinate.

setY(double) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Set the y coordinate.

setY(float) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4f

Set a new value for y coordinate.

setY(float) - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Set the y coordinate.

setY(float) - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Set the y coordinate.

setY(int) - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Set the y coordinate.

setZ(double) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4d

Set a new value for z coordinate.

setZ(double) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Set the z coordinate.

setZ(double) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Set the z coordinate.

setZ(float) - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4f

Set a new value for z coordinate.

setZ(float) - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Set the Z coordinate.

setZ(float) - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Set the z coordinate.

setZ(int) - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Set the z coordinate.

setZero() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

setZero() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

setZero() - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Sets this matrix to all zeros.

setZero() - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Sets this matrix to all zeros.

setZero() - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets this matrix to all zeros.

setZero() - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets this matrix to all zeros.

setZero() - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Sets this transform to all zeros.

shardSize - Variable in class net.preibisch.mvrecon.process.n5api.N5ApiTools.MultiResolutionLevelInfo

shouldSplit(List<OctTreeSplitCriterion.SplitCorrespondence>) - Method in class net.preibisch.mvrecon.process.splitting.ConsensusSetCriterion

shouldSplit(List<OctTreeSplitCriterion.SplitCorrespondence>) - Method in class net.preibisch.mvrecon.process.splitting.CrossViewCorrespondenceCriterion

shouldSplit(List<OctTreeSplitCriterion.SplitCorrespondence>) - Method in interface net.preibisch.mvrecon.process.splitting.OctTreeSplitCriterion

Evaluates whether to continue splitting based on pre-filtered correspondences.

Show_Histogram - Class in net.preibisch.mvrecon.fiji.plugin

Show_Histogram() - Constructor for class net.preibisch.mvrecon.fiji.plugin.Show_Histogram

Show_Relative_Histogram - Class in net.preibisch.mvrecon.fiji.plugin

Show_Relative_Histogram() - Constructor for class net.preibisch.mvrecon.fiji.plugin.Show_Relative_Histogram

showDebugFileNames - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

showDialogs(SimViewMetaData) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.SimView

showDialogs(MultipageTiffReader) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.MicroManager

showDialogs(LightSheetZ1MetaData) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.LightSheetZ1

showDistanceMap - Variable in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidParameters

showDistanceMap() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidParameters

showExpertGrouping - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters

showHelp() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointExplorerPanel

showHistogram() - Method in class net.preibisch.mvrecon.process.interestpointremoval.histogram.Histogram

showInfoBox() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

showInfoBox() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorerPanel

showNote - Static variable in class net.preibisch.mvrecon.fiji.plugin.Data_Explorer

showNote() - Static method in class net.preibisch.mvrecon.fiji.plugin.Data_Explorer

showProgress() - Method in class net.preibisch.mvrecon.process.interestpointdetection.methods.InterestPointParameters

showProgress(double, double) - Method in class net.preibisch.mvrecon.process.interestpointdetection.methods.InterestPointParameters

showProgressMax - Variable in class net.preibisch.mvrecon.process.interestpointdetection.methods.InterestPointParameters

showProgressMin - Variable in class net.preibisch.mvrecon.process.interestpointdetection.methods.InterestPointParameters

showProjection(Img<FloatType>) - Method in class net.preibisch.mvrecon.process.interestpointremoval.InteractiveProjections

showStatistics - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.AdvancedRegistrationParameters

showWarning - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.ApplyTransformationPopup

showWarning - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.MaxProjectPopup

showWarning - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.ReorientSamplePopup

showWarning - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.SpecifyCalibrationPopup

sigma - Variable in class net.preibisch.legacy.registration.bead.laplace.DoGMaximum

sigma - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoGParams

sigma - Variable in class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGParameters

SIGMA - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoG.ValueChange

SigmaListener - Class in net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive

SigmaListener(InteractiveDoG, Label, float, float, int, Scrollbar) - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.SigmaListener

sigmaMax - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoG

sigmaMin - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoG

silent - Static variable in class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2

SimilarityMeasure - Interface in net.preibisch.mvrecon.process.pointcloud.pointdescriptor.similarity

simple2x(RandomAccessibleInterval<T>) - Static method in class net.preibisch.mvrecon.process.downsampling.Downsample

simple2x(RandomAccessibleInterval<T>, boolean[]) - Static method in class net.preibisch.mvrecon.process.downsampling.Downsample

SimpleBoundingBoxOverlap<V> - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap

SimpleBoundingBoxOverlap(Map<Integer, ? extends BasicViewSetup>, Map<ViewId, ViewRegistration>) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap.SimpleBoundingBoxOverlap

SimpleBoundingBoxOverlap(AbstractSpimData<? extends AbstractSequenceDescription<? extends BasicViewSetup, ?, ?>>) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap.SimpleBoundingBoxOverlap

SimpleBoundingBoxOverlap(SequenceDescription, ViewRegistrations) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.overlap.SimpleBoundingBoxOverlap

SimpleDirectoryFileListChooser() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition.SimpleDirectoryFileListChooser

SimpleHyperlinkPopup - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

SimpleHyperlinkPopup(String, URI) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.SimpleHyperlinkPopup

SimpleInfoBox - Class in net.preibisch.mvrecon.fiji.spimdata.explorer

SimpleInfoBox(String, String) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.SimpleInfoBox

SimpleIterativeConvergenceStrategy - Class in net.preibisch.mvrecon.process.interestpointregistration.global.convergence

SimpleIterativeConvergenceStrategy(double, double, double) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.global.convergence.SimpleIterativeConvergenceStrategy

SimpleIterativeConvergenceStrategy(double, int, int, double, double) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.global.convergence.SimpleIterativeConvergenceStrategy

SimpleMatcher - Class in net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher

SimpleMatcher(int) - Constructor for class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.SimpleMatcher

SimplePeak - Class in net.preibisch.legacy.segmentation

SimplePeak(int[], float, boolean, boolean) - Constructor for class net.preibisch.legacy.segmentation.SimplePeak

SimplePointDescriptor<P> - Class in net.preibisch.mvrecon.process.pointcloud.pointdescriptor

SimplePointDescriptor(P, ArrayList<P>, SimilarityMeasure, Matcher) - Constructor for class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.SimplePointDescriptor

SimplePointMatchIdentification<P> - Class in net.preibisch.mvrecon.process.pointcloud.icp

SimplePointMatchIdentification() - Constructor for class net.preibisch.mvrecon.process.pointcloud.icp.SimplePointMatchIdentification

SimplePointMatchIdentification(double) - Constructor for class net.preibisch.mvrecon.process.pointcloud.icp.SimplePointMatchIdentification

SimpleRealLocalizable - Class in net.preibisch.mvrecon.imglib2.st.render.util

SimpleRealLocalizable(double[]) - Constructor for class net.preibisch.mvrecon.imglib2.st.render.util.SimpleRealLocalizable

SimpleReferenceIP - Class in net.preibisch.mvrecon.process.fusion.transformed.nonrigid

SimpleReferenceIP(double[], double[]) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.SimpleReferenceIP

SimpleReferenceIP(double[], double[], double[]) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.SimpleReferenceIP

SimpleSampler<T> - Class in net.preibisch.mvrecon.imglib2.st.render.util

SimpleSampler(T) - Constructor for class net.preibisch.mvrecon.imglib2.st.render.util.SimpleSampler

SimView - Class in net.preibisch.mvrecon.fiji.datasetmanager

SimView() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.SimView

SimView.DirectoryFilter - Class in net.preibisch.mvrecon.fiji.datasetmanager

SimViewChannel() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData.SimViewChannel

SimViewImgLoader - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

SimViewImgLoader(AbstractSequenceDescription<?, ?, ?>, File, String, int, boolean) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.SimViewImgLoader

SimViewMetaData - Class in net.preibisch.mvrecon.fiji.datasetmanager

SimViewMetaData() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData

SimViewMetaData.Pattern - Class in net.preibisch.mvrecon.fiji.datasetmanager

SimViewMetaData.SimViewChannel - Class in net.preibisch.mvrecon.fiji.datasetmanager

SimViewSetupImgLoader - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

SimViewSetupImgLoader(int, AbstractSequenceDescription<?, ?, ?>, File, String, SimViewMetaData.Pattern, int, boolean) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.SimViewSetupImgLoader

sin - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel2D

SINGLE - Enum constant in enum class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.CheckResult

SINGLE_VIEW - Enum constant in enum class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.Mode

SingleGroupError(Group<ViewDescription>, List<Group<ViewDescription>>, int, double, double, double) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.SingleGroupError

SingleViewError(ViewId, List<ViewId>, int, double, double, double) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.SingleViewError

SingularMatrixException - Exception Class in net.preibisch.mvrecon.vecmath

Indicates that inverse of a matrix can not be computed.

SingularMatrixException() - Constructor for exception class net.preibisch.mvrecon.vecmath.SingularMatrixException

Create the exception object with default values.

SingularMatrixException(String) - Constructor for exception class net.preibisch.mvrecon.vecmath.SingularMatrixException

Create the exception object that outputs message.

size - Variable in class net.preibisch.legacy.registration.threshold.ComponentProperties

size - Static variable in class net.preibisch.mvrecon.process.interestpointremoval.InteractiveProjections

size() - Method in class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.FlattenedMatches

size() - Method in class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.MatchIndices

size() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

sizeX - Variable in class net.preibisch.legacy.registration.threshold.ComponentProperties

sizeY - Variable in class net.preibisch.legacy.registration.threshold.ComponentProperties

sizeZ - Variable in class net.preibisch.legacy.registration.threshold.ComponentProperties

SketchTikZFileObject - Class in net.preibisch.legacy.mpicbg

SketchTikZFileObject(BufferedReader, PrintWriter) - Constructor for class net.preibisch.legacy.mpicbg.SketchTikZFileObject

skipDialog - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough

SLICE - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoG.ValueChange

sliceChanged(ImagePlus) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.ImagePlusListener

smallStatusFont - Static variable in class net.preibisch.mvrecon.fiji.plugin.util.GUIHelper

SmartSPIM - Class in net.preibisch.mvrecon.fiji.datasetmanager

SmartSPIM() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM

SmartSPIM.SmartSPIMMetaData - Class in net.preibisch.mvrecon.fiji.datasetmanager

SmartSPIMImgLoader - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

SmartSPIMImgLoader(SmartSPIM.SmartSPIMMetaData, AbstractSequenceDescription<?, ?, ?>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.SmartSPIMImgLoader

SmartSPIMMetaData(URI) - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM.SmartSPIMMetaData

SmartSPIMSetupImgLoader - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

SmartSPIMSetupImgLoader(int, SmartSPIM.SmartSPIMMetaData, AbstractSequenceDescription<?, ?, ?>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.SmartSPIMSetupImgLoader

smoothWeights(float, double, float, float) - Static method in class net.preibisch.mvrecon.process.deconvolution.normalization.NormalizingRandomAccess

solve(int[], Collection<ViewPairCoefficientMatches>, int) - Static method in class net.preibisch.mvrecon.process.fusion.intensity.IntensityCorrection

sortBlocksBySmallestFootprint(List<Block>, Interval, int) - Static method in class net.preibisch.mvrecon.process.cuda.BlockSorter

Here are some assumptions: - the first block is in the top/left/upper... corner - the effective size of this block was used to compute the number of blocks - all blocks have the same dimensions, tightly stacked next to each other - only the effective blocksize of the last blocks in each dimension can be smaller

sortByColumn(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedTableModel

clicking on a column adds that columns class as the last class to sort by

sortByColumn(int) - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.ISpimDataTableModel

sortByColumn(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MissingViewsTableModelDecorator

sortByColumn(int) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MultiViewTableModelDecorator

sortedFileNames - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM.SmartSPIMMetaData

sortedSlicesFor(URI) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM.SmartSPIMMetaData

sortedSlicesFor(Pair<Integer, Integer>, long, long) - Method in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM.SmartSPIMMetaData

sortSets(ArrayList<Subset<V>>, Comparator<Pair<V, V>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.PairwiseSetup

Sorts each list using a given comparator, and then the lists according to their first element

sortSubsets() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.PairwiseSetup

Sorts each subset by comparing the first view of each pair, and then all subsets according to their first pair

source - Variable in class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion.LandmarkRecord

source - Variable in class util.StackingRealRandomAccessible

sourceAccess - Variable in class util.StackingRealRandomAccessible.StackingRealRandomAccess

sourceNumDimensions - Variable in class util.StackingRealRandomAccessible

Specify_Calibration - Class in net.preibisch.mvrecon.fiji.plugin

Specify_Calibration() - Constructor for class net.preibisch.mvrecon.fiji.plugin.Specify_Calibration

Specify_Calibration.Cal - Class in net.preibisch.mvrecon.fiji.plugin

SpecifyCalibrationPopup - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

SpecifyCalibrationPopup() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.SpecifyCalibrationPopup

SpecifyCalibrationPopup.MyActionListener - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

spimData - Variable in class net.preibisch.mvrecon.fiji.plugin.boundingbox.BoundingBoxGUI

spimData - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

spimData - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

spimData - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

SpimData2 - Class in net.preibisch.mvrecon.fiji.spimdata

Extends the SpimData class; has additonally detections

SpimData2() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.SpimData2

SpimData2(URI, SequenceDescription, ViewRegistrations, ViewInterestPoints, BoundingBoxes, PointSpreadFunctions, StitchingResults, IntensityAdjustments) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.SpimData2

SpimData2Tools - Class in net.preibisch.mvrecon.process.n5api

SpimData2Tools() - Constructor for class net.preibisch.mvrecon.process.n5api.SpimData2Tools

SpimData2Tools.InstantiateViewSetup - Interface in net.preibisch.mvrecon.process.n5api

SpimData2Tools.InstantiateViewSetupBigStitcher - Class in net.preibisch.mvrecon.process.n5api

SpimData2Tools.InstantiateViewSetupBigStitcherSpark - Class in net.preibisch.mvrecon.process.n5api

SpimDataExample - Class in net.preibisch.mvrecon.fiji.spimdata

SpimDataExample() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.SpimDataExample

SpimDataTools - Class in net.preibisch.mvrecon.fiji.spimdata

SpimDataTools() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.SpimDataTools

split(ViewId) - Method in class net.preibisch.mvrecon.process.splitting.SplitDistributeEvenly

split(ViewId) - Method in class net.preibisch.mvrecon.process.splitting.SplitOctTree

split(ViewId) - Method in interface net.preibisch.mvrecon.process.splitting.SplitView

Split a single view into sub-intervals.

split(Interval) - Method in interface net.preibisch.mvrecon.process.splitting.SplitInterval

split(SpimData2, URI) - Static method in class net.preibisch.mvrecon.fiji.plugin.Split_Views

split(SpimData2, URI, SplitView, boolean, Split_Views.InterestPointAdding, double, int, int, double, double, boolean) - Static method in class net.preibisch.mvrecon.fiji.plugin.Split_Views

split(SpimData2, URI, SplitView, boolean, Split_Views.InterestPointAdding, double, int, int, double, double, boolean, String, SplittingTools.InterestPointSaver, SplittingTools.CorrespondenceSaver) - Static method in class net.preibisch.mvrecon.fiji.plugin.Split_Views

split(SpimData2, URI, SplitView, boolean, Split_Views.InterestPointAdding, double, int, int, double, double, boolean, String, SplittingTools.InterestPointSaver, SplittingTools.CorrespondenceSaver, Set<Integer>) - Static method in class net.preibisch.mvrecon.fiji.plugin.Split_Views

Split_Views - Class in net.preibisch.mvrecon.fiji.plugin

Split_Views() - Constructor for class net.preibisch.mvrecon.fiji.plugin.Split_Views

Split_Views.InterestPointAdding - Enum Class in net.preibisch.mvrecon.fiji.plugin

splitBy(List<V>, Set<Class<? extends Entity>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

Split means to make a group for every instance of an attribute, e.g. channel (for example group everthing that is GFP and everything that it RFP) v1: angle 0, channel 0 v2: angle 1, channel 0 v3: angle 1, channel 1 split by channel: [v1 v2], [v3]

SplitCorrespondence(double[], int, String, int) - Constructor for class net.preibisch.mvrecon.process.splitting.OctTreeSplitCriterion.SplitCorrespondence

splitCount - Variable in class net.preibisch.mvrecon.process.splitting.SplitOctTree.OctTreeSplitResult

splitDim(Interval, int, long, long) - Static method in class net.preibisch.mvrecon.process.splitting.SplitDistributeEvenly

SplitDistributeEvenly - Class in net.preibisch.mvrecon.process.splitting

SplitDistributeEvenly(SpimData2, long[], long[], long[], boolean) - Constructor for class net.preibisch.mvrecon.process.splitting.SplitDistributeEvenly

splitImages(SpimData2, SplitView, boolean, Split_Views.InterestPointAdding, double, int, int, double, double) - Static method in class net.preibisch.mvrecon.process.splitting.SplittingTools

splitImages(SpimData2, SplitView, boolean, Split_Views.InterestPointAdding, double, int, int, double, double, String, SplittingTools.InterestPointSaver, SplittingTools.CorrespondenceSaver) - Static method in class net.preibisch.mvrecon.process.splitting.SplittingTools

splitImages(SpimData2, SplitView, boolean, Split_Views.InterestPointAdding, double, int, int, double, double, String, SplittingTools.InterestPointSaver, SplittingTools.CorrespondenceSaver, Set<Integer>) - Static method in class net.preibisch.mvrecon.process.splitting.SplittingTools

Split all ViewSetups of the dataset, optionally driving the split geometry from a single channel.

SplitImgLoader - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting

SplitImgLoader(ImgLoader, HashMap<Integer, Integer>, HashMap<Integer, Interval>, SequenceDescription) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitImgLoader

SplitImgLoaderThinPlateSplineFusion - Class in net.preibisch.mvrecon.process.fusion.blk

SplitImgLoaderThinPlateSplineFusion() - Constructor for class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion

SplitImgLoaderThinPlateSplineFusion.DonatedNail - Class in net.preibisch.mvrecon.process.fusion.blk

A single nail landmark donated from one split sub-view's surface onto the recipient underlying view's TPS.

SplitImgLoaderThinPlateSplineFusion.LandmarkRecord - Class in net.preibisch.mvrecon.process.fusion.blk

One TPS landmark, classified by category.

splitInterval(Interval) - Method in class net.preibisch.mvrecon.process.splitting.SplitDistributeEvenly

Split an interval into uniform sub-intervals with overlap.

SplitInterval - Interface in net.preibisch.mvrecon.process.splitting

splitIntoPathAndPattern(String, String...) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition

splitIntoPrefixAndPattern(FilenamePatternDetector) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition

SplitMultiResolutionImgLoader - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting

SplitMultiResolutionImgLoader(MultiResolutionImgLoader, HashMap<Integer, Integer>, HashMap<Integer, Interval>, SequenceDescription) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitMultiResolutionImgLoader

SplitMultiResolutionSetupImgLoader<T> - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting

SplitMultiResolutionSetupImgLoader(MultiResolutionSetupImgLoader<T>, Interval) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitMultiResolutionSetupImgLoader

SplitOctTree - Class in net.preibisch.mvrecon.process.splitting

Adaptive oct-tree based image splitting with recursive correspondence partitioning.

SplitOctTree(long[], int[], OctTreeSplitCriterion, int, double[]) - Constructor for class net.preibisch.mvrecon.process.splitting.SplitOctTree

Constructor with all parameters.

SplitOctTree.OctTreeSplitResult - Class in net.preibisch.mvrecon.process.splitting

Result of a split operation, including intervals and statistics.

SplitResult - Class in net.preibisch.mvrecon.process.splitting

Base result of splitting a single view.

SplitResult(ArrayList<Interval>) - Constructor for class net.preibisch.mvrecon.process.splitting.SplitResult

SplitSetupImgLoader<T> - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting

SplitSetupImgLoader(SetupImgLoader<T>, Interval) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitSetupImgLoader

splitTasks(List<Callable<T>>, int) - Static method in class net.preibisch.mvrecon.Threads

SplittingTools - Class in net.preibisch.mvrecon.process.splitting

SplittingTools() - Constructor for class net.preibisch.mvrecon.process.splitting.SplittingTools

SplittingTools.CorrespondenceSaver - Interface in net.preibisch.mvrecon.process.splitting

Callback for saving correspondences on-the-fly.

SplittingTools.InterestPointSaver - Interface in net.preibisch.mvrecon.process.splitting

Callback for saving interest points (detections + correspondences) on-the-fly.

SplittingTools.SetupSplitResult - Class in net.preibisch.mvrecon.process.splitting

Result of processing a single ViewSetup's split intervals.

splittingType - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

splittingType - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

splittingType - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

splittingTypes - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

splittingTypes - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

splittingTypes - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

SplitView - Interface in net.preibisch.mvrecon.process.splitting

Interface for splitting views into sub-intervals.

SplitViewerImgLoader - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting

SplitViewerImgLoader(ViewerImgLoader, Map<Integer, Integer>, Map<Integer, Interval>, SequenceDescription) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitViewerImgLoader

SplitViewerSetupImgLoader<T,V> - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting

SplitViewerSetupImgLoader(ViewerSetupImgLoader<T, V>, Interval, long[][]) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitViewerSetupImgLoader

splitViewIds(Collection<? extends ViewId>, Map<Integer, List<Integer>>) - Static method in class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion

squareDistance(double, double, double, double, double, double) - Static method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxReorientation

SquareDistance - Class in net.preibisch.mvrecon.process.pointcloud.pointdescriptor.similarity

SquareDistance() - Constructor for class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.similarity.SquareDistance

src - Variable in class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion.DonatedNail

STACK_DIR_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoDHMImgLoader

StackImgLoader<I> - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

StackImgLoader(I) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.StackImgLoader

StackImgLoaderIJ - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

StackImgLoaderIJ(File, String, int, int, int, int, int, AbstractSequenceDescription<?, ?, ?>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.StackImgLoaderIJ

StackImgLoaderLOCI - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

StackImgLoaderLOCI(File, String, int, int, int, int, int, AbstractSequenceDescription<?, ?, ?>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.StackImgLoaderLOCI

StackingRealRandomAccess() - Constructor for class util.StackingRealRandomAccessible.StackingRealRandomAccess

StackingRealRandomAccessible<T> - Class in util

A RealRandomAccessible whose samples are generated by trivial projection of the lower dimensional source into a higher dimensional target by continuous stacking, i.e. when projecting from 1D to 3D, the samples at f(5) = g(5,2,3) = g(5,1,6) = g(5,18,-20)...

StackingRealRandomAccessible(RealRandomAccessible<T>, int) - Constructor for class util.StackingRealRandomAccessible

StackingRealRandomAccessible.StackingRealRandomAccess - Class in util

RealRandomAccess that generates its samples from a lower dimensional source

StackList - Class in net.preibisch.mvrecon.fiji.datasetmanager

StackList - Class in net.preibisch.mvrecon.headless.definedataset

Base StackList class for various kinds of DataSet definition class

StackList() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.StackList

StackList() - Constructor for class net.preibisch.mvrecon.headless.definedataset.StackList

StackList.Calibration - Class in net.preibisch.mvrecon.fiji.datasetmanager

StackList.Calibration - Class in net.preibisch.mvrecon.headless.definedataset

StackList.ViewSetupPrecursor - Class in net.preibisch.mvrecon.fiji.datasetmanager

StackList.ViewSetupPrecursor - Class in net.preibisch.mvrecon.headless.definedataset

StackListImageJ - Class in net.preibisch.mvrecon.fiji.datasetmanager

StackListImageJ - Class in net.preibisch.mvrecon.headless.definedataset

DataSet definition for ImageJ

StackListImageJ() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.StackListImageJ

StackListImageJ() - Constructor for class net.preibisch.mvrecon.headless.definedataset.StackListImageJ

StackListLOCI - Class in net.preibisch.mvrecon.fiji.datasetmanager

StackListLOCI - Class in net.preibisch.mvrecon.headless.definedataset

DataSet definition for LOCI

StackListLOCI() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.StackListLOCI

StackListLOCI() - Constructor for class net.preibisch.mvrecon.headless.definedataset.StackListLOCI

StackListParameters - Class in net.preibisch.mvrecon.headless.definedataset

Created by moon on 7/2/15.

StackListParameters() - Constructor for class net.preibisch.mvrecon.headless.definedataset.StackListParameters

StackListParameters.AngleOption - Enum Class in net.preibisch.mvrecon.headless.definedataset

StackListParameters.ChannelOption - Enum Class in net.preibisch.mvrecon.headless.definedataset

StackListParameters.Container - Enum Class in net.preibisch.mvrecon.headless.definedataset

StackListParameters.IlluminationOption - Enum Class in net.preibisch.mvrecon.headless.definedataset

StackListParameters.TileOption - Enum Class in net.preibisch.mvrecon.headless.definedataset

StackListParameters.TimePointOption - Enum Class in net.preibisch.mvrecon.headless.definedataset

standardDevice - Static variable in class net.preibisch.mvrecon.process.cuda.CUDATools

startPosition - Variable in class net.preibisch.mvrecon.process.fusion.ImagePortion

state - Variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Bool

staticAlgorithms - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Detection

staticBoundingBoxAlgorithms - Static variable in class net.preibisch.mvrecon.fiji.plugin.Define_Bounding_Box

staticDatasetDefinitions - Static variable in class net.preibisch.mvrecon.fiji.plugin.Define_Multi_View_Dataset

staticfont - Static variable in class net.preibisch.mvrecon.fiji.plugin.util.GUIHelper

staticImgExportAlgorithms - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

staticImgExportAlgorithms - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI

staticImgExportAlgorithms - Static variable in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

staticPairwiseAlgorithms - Static variable in class net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

stepSize - Static variable in class util.ColorStream

STICHING_BBOX_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.XmlKeysStitchingResults

STICHING_CORRELATION_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.XmlKeysStitchingResults

STICHING_SHIFT_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.XmlKeysStitchingResults

STITCHING_HASH_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.XmlKeysStitchingResults

STITCHING_TP_A_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.XmlKeysStitchingResults

STITCHING_TP_B_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.XmlKeysStitchingResults

STITCHING_VS_A_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.XmlKeysStitchingResults

STITCHING_VS_B_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.XmlKeysStitchingResults

STITCHINGRESULT_PW_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.XmlKeysStitchingResults

StitchingResults - Class in net.preibisch.mvrecon.fiji.spimdata.stitchingresults

StitchingResults() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.StitchingResults

STITCHINGRESULTS_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.XmlKeysStitchingResults

StitchingResultsSettable - Interface in net.preibisch.mvrecon.fiji.spimdata.explorer

Interface to be implemented by classes that need access to the global stitching results

storeCorrespondences() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.PairwiseResult

storeTransformation(ViewRegistration, V, Tile<?>, AffineGet, String) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

STRIP_BYTE_COUNTS - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

STRIP_BYTE_COUNTS - Static variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

STRIP_OFFSETS - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

STRIP_OFFSETS - Static variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

sub(NumericAffineModel3D) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

sub(NumericAffineTransform3D) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

sub(Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Sets the value of this matrix to the matrix difference of itself and matrix m1 (this = this - m1).

sub(Matrix3d, Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Sets the value of this matrix to the matrix difference of matrices m1 and m2.

sub(Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Sets the value of this matrix to the matrix difference of itself and matrix m1 (this = this - m1).

sub(Matrix3f, Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Sets the value of this matrix to the matrix difference of matrices m1 and m2.

sub(Matrix4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the value of this matrix to the matrix difference of itself and matrix m1 (this = this - m1).

sub(Matrix4d, Matrix4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the value of this matrix to the matrix difference of matrices m1 and m2.

sub(Matrix4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets this matrix to the matrix difference of itself and matrix m1 (this = this - m1).

sub(Matrix4f, Matrix4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Performs an element-by-element subtraction of matrix m2 from matrix m1 and places the result into matrix this (this = m2 - m1).

sub(Transform3D) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Subtracts transform t1 from this transform and places the result into this: this = this - t1.

sub(Transform3D, Transform3D) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Subtracts transform t2 from transform t1 and places the result into this: this = t1 - t2.

sub(Tuple3d) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Sets the value of this tuple to the difference of itself and t1 (this = this - t1).

sub(Tuple3d, Tuple3d) - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Sets the value of this tuple to the difference of tuples t1 and t2 (this = t1 - t2).

sub(Tuple3f) - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Sets the value of this tuple to the vector difference of itself and tuple t1 (this = this - t1) .

sub(Tuple3f, Tuple3f) - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Sets the value of this tuple to the vector difference of tuples t1 and t2 (this = t1 - t2).

sub(Tuple3i) - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Sets the value of this tuple to the difference of itself and t1 (this = this - t1).

sub(Tuple3i, Tuple3i) - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Sets the value of this tuple to the difference of tuples t1 and t2 (this = t1 - t2).

sub(Tuple4d) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Sets the value of this tuple to the difference of itself and tuple t1 (this = this - t1).

sub(Tuple4d, Tuple4d) - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Sets the value of this tuple to the difference of tuples t1 and t2 (this = t1 - t2).

sub(Tuple4f) - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Sets the value of this tuple to the difference of itself and t1 (this = this - t1).

sub(Tuple4f, Tuple4f) - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Sets the value of this tuple to the difference of tuples t1 and t2 (this = t1 - t2).

subdivisions - Variable in class net.preibisch.mvrecon.fiji.plugin.resave.ParametersResaveN5Api

subsampling - Static variable in class net.preibisch.mvrecon.process.interestpointremoval.DistanceHistogram

subsampling - Static variable in class net.preibisch.mvrecon.process.interestpointremoval.RelativeDistanceHistogram

Subset<V> - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation

Subset(Set<V>, List<Pair<V, V>>, Set<Group<V>>) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.Subset

SubsetMatcher - Class in net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher

SubsetMatcher(int, int) - Constructor for class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.SubsetMatcher

Matches n out of m neighbor points, the effort increases exponentially(!)

subsets - Variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.PairwiseSetup

subsetsLinkedByGroup(List<? extends Set<V>>, Group<V>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.PairwiseSetup

which subsets are part of a group - called by detectSubsets()

subtractProjection(RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, int) - Static method in class net.preibisch.mvrecon.process.psf.PSFExtraction

suggestTiles(int) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.grid.RegularTranformHelpers

SUM - Enum constant in enum class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccessibleInterval.CombineType

sumChange - Variable in class net.preibisch.mvrecon.process.deconvolution.iteration.ComputeBlockThread.IterationStatistics

sumImg(IterableInterval<T>) - Static method in class net.preibisch.mvrecon.process.deconvolution.normalization.AdjustInput

SUMMARY_MD_HEADER - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

SUMMARY_MD_HEADER - Static variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

sumValue - Variable in class net.preibisch.legacy.registration.bead.laplace.DoGMaximum

supportDHM() - Static method in class net.preibisch.mvrecon.fiji.plugin.Define_Multi_View_Dataset

supportRadiusMax - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoG

supportRadiusMin - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoG

supportsMultipleAnglesPerFile() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

supportsMultipleAnglesPerFile() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListImageJ

supportsMultipleAnglesPerFile() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListLOCI

supportsMultipleChannelsPerFile() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

supportsMultipleChannelsPerFile() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListImageJ

supportsMultipleChannelsPerFile() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListLOCI

supportsMultipleIlluminationsPerFile() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

supportsMultipleIlluminationsPerFile() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListImageJ

supportsMultipleIlluminationsPerFile() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListLOCI

supportsMultipleTilesPerFile() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

supportsMultipleTilesPerFile() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListImageJ

supportsMultipleTilesPerFile() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListLOCI

supportsMultipleTimepointsPerFile() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

supportsMultipleTimepointsPerFile() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListImageJ

supportsMultipleTimepointsPerFile() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackListLOCI

supportsRemoteXMLLocation() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition

supportsRemoteXMLLocation() - Method in interface net.preibisch.mvrecon.fiji.datasetmanager.MultiViewDatasetDefinition

supportsRemoteXMLLocation() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.OMEZARR

Switch_Attributes - Class in net.preibisch.mvrecon.fiji.plugin

Switch_Attributes() - Constructor for class net.preibisch.mvrecon.fiji.plugin.Switch_Attributes

switchAttributes(SpimData2, int, int) - Static method in class net.preibisch.mvrecon.fiji.plugin.Switch_Attributes

switchAttributesGUI(SpimData2) - Static method in class net.preibisch.mvrecon.fiji.plugin.Switch_Attributes

SWITCHING_STATES - Enum constant in enum class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsResultsWindow.BdvResetPolicy

T

t - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList.ViewSetupPrecursor

table - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

table - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointExplorerPanel

table - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationExplorerPanel

tableModel - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

tableModel - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointExplorerPanel

tableModel - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationExplorerPanel

tag - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader.IFDEntry

tag - Variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader.IFDEntry

target - Variable in class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion.DonatedNail

target - Variable in class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion.LandmarkRecord

testAxis(Vector3d, List<RealLocalizable>) - Method in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxReorientation

Test one major axis for the minimal bounding box volume required

testBlockIntegrity() - Method in class net.preibisch.mvrecon.process.deconvolution.MultiViewDeconvolutionMul

testEmptyBlocks - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

testEmptyBlocks() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

TestPointDescriptor - Class in net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test

TestPointDescriptor() - Constructor for class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test.TestPointDescriptor

testQuaternions() - Static method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test.TestPointDescriptor

testStability(int, int, int, double, double, boolean, boolean) - Static method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test.TestPointDescriptor

TextFileAccess - Class in net.preibisch.legacy.io

TextFileAccess() - Constructor for class net.preibisch.legacy.io.TextFileAccess

thinOut(SpimData2, Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.fiji.plugin.RelativeThinOut_Detections

thinOut(SpimData2, Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.fiji.plugin.ThinOut_Detections

thinOut(SpimData2, Collection<? extends ViewId>, RelativeThinOutParameters) - Static method in class net.preibisch.mvrecon.process.interestpointremoval.RelativeThinOut

thinOut(SpimData2, List<ViewId>, ThinOutParameters) - Static method in class net.preibisch.mvrecon.process.interestpointremoval.ThinOut

ThinOut - Class in net.preibisch.mvrecon.process.interestpointremoval

ThinOut() - Constructor for class net.preibisch.mvrecon.process.interestpointremoval.ThinOut

ThinOut_Detections - Class in net.preibisch.mvrecon.fiji.plugin

ThinOut_Detections() - Constructor for class net.preibisch.mvrecon.fiji.plugin.ThinOut_Detections

ThinOutListener() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.RemoveDetectionsPopup.ThinOutListener

ThinOutParameters - Class in net.preibisch.mvrecon.process.interestpointremoval

ThinOutParameters() - Constructor for class net.preibisch.mvrecon.process.interestpointremoval.ThinOutParameters

Threads - Class in net.preibisch.mvrecon

Threads() - Constructor for class net.preibisch.mvrecon.Threads

THREE_SIGMA - Enum constant in enum class net.preibisch.mvrecon.process.quality.FRC.ThresholdMethod

threshold - Variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoGParams

threshold - Variable in class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGParameters

THRESHOLD - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoG.ValueChange

ThresholdListener - Class in net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive

ThresholdListener(InteractiveDoG, Label, float, float) - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.ThresholdListener

thresholdMax - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoG

thresholdMin - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoG

TILE_PATTERN - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

tileChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

TileInfo() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.TileInfo

tileLocations() - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

tileNameList - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

tileNameList - Variable in class net.preibisch.mvrecon.headless.definedataset.StackList.ViewSetupPrecursor

TileOrAngleInfo() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.TileOrAngleInfo

TileOrAngleRefiner - Interface in net.preibisch.mvrecon.fiji.datasetmanager.metadatarefinement

tiles - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

tiles - Variable in class net.preibisch.mvrecon.headless.definedataset.StackListParameters

tiles() - Method in class net.preibisch.mvrecon.headless.definedataset.LightSheetZ1MetaData

tilesGrouped() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.ExplorerWindow

tilesGrouped() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorerPanel

TimeLapseDisplay - Class in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.statistics

TimeLapseDisplay() - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.statistics.TimeLapseDisplay

TIMEPOINT_PATTERN - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.SimViewMetaData

TIMEPOINT_PATTERN - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

timepointId - Variable in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5.InterestPointData

timepointIndex(Group<? extends ViewDescription>, ArrayList<TimePoint>) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

timepointNameList - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

TimepointRange<V> - Class in net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.range

TimepointRange(int) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.range.TimepointRange

timepoints - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.StackList

timepoints - Variable in class net.preibisch.mvrecon.headless.definedataset.StackListParameters

timepoints(List<? extends Group<? extends ViewDescription>>) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

TIMEPOINTS_INDIVIDUALLY - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.BasicRegistrationParameters.RegistrationType

TIMEPOINTS_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoDHMImgLoader

timepointsToProcess - Variable in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

timer - Variable in class net.preibisch.mvrecon.fiji.plugin.apply.BigDataViewerTransformationWindow

title - Variable in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox

TO_REFERENCE_TIMEPOINT - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.BasicRegistrationParameters.RegistrationType

toggle() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.viewneighbours.ViewNeighboursWindow

Toggle expand ↔ collapse for the explorer's `n`/`N` shortcut.

toggle() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.viewneighbours.ViewOverlapWindow

Toggle expand ↔ collapse for the explorer's `o`/`O` shortcut.

ToggleDialogActionBrightness - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.bdv

ToggleDialogActionBrightness(String, ScrollableBrightnessDialog) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.ToggleDialogActionBrightness

toGroup(Collection<V>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

toGroups(Collection<V>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

TOLERANCE_CHOICES - Static variable in class net.preibisch.mvrecon.process.splitting.ConsensusSetCriterion

toModels(HashMap<ViewId, Tile<M>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.global.GlobalOpt

tooHighEigenValueRatio - Variable in class net.preibisch.legacy.registration.bead.laplace.RejectStatistics

topN - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.Parameters

toProcess - Variable in class net.preibisch.mvrecon.process.interestpointdetection.methods.InterestPointParameters

toProcessor(Img<? extends RealType<?>>) - Static method in class net.preibisch.mvrecon.fiji.plugin.Max_Project

toString() - Method in class net.preibisch.legacy.registration.detection.AbstractDetection

toString() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.ChannelInfo

toString() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.ChannelOrIlluminationInfo

toString() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.TileInfo

toString() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.TileOrAngleInfo

toString() - Method in class net.preibisch.mvrecon.fiji.datasetmanager.StackList.ViewSetupPrecursor

toString() - Method in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.BoundingBox

toString() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AllenOMEZarrLoader.OMEZARREntry

toString() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.FileMapImgLoaderLOCI

toString() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyLightSheetZ1ImgLoader

toString() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyMicroManagerImgLoader

toString() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoaderIJ

toString() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoaderLOCI

toString() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LightSheetZ1ImgLoader

toString() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MicroManagerImgLoader

toString() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.StackImgLoader

toString() - Method in class net.preibisch.mvrecon.headless.definedataset.StackList.ViewSetupPrecursor

toString() - Method in class net.preibisch.mvrecon.process.cuda.CUDADevice

toString() - Method in class net.preibisch.mvrecon.process.deconvolution.DeconView

toString() - Method in class net.preibisch.mvrecon.process.deconvolution.iteration.mul.ComputeBlockMulThreadCPUFactory

toString() - Method in class net.preibisch.mvrecon.process.deconvolution.iteration.sequential.ComputeBlockSeqThreadCPUFactory

toString() - Method in class net.preibisch.mvrecon.process.deconvolution.iteration.sequential.ComputeBlockSeqThreadCUDAFactory

toString() - Method in class net.preibisch.mvrecon.process.fusion.ImagePortion

toString() - Method in class net.preibisch.mvrecon.process.fusion.intensity.IntensityCorrection.SerializableRealInterval

toString() - Method in class net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.Link

toString() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

toString() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.LinkedInterestPoint

toString() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.AbstractPointDescriptor

Overwrites the toString method

toString() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.LinkedPoint

toString() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.Quaternion

toString() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.FixedModel

toString() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantAffineModel3D

toString() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantFixedModel

toString() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel3D

toString() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantSimilarityModel3D

toString() - Method in enum class net.preibisch.mvrecon.process.quality.FRC.ThresholdMethod

toString() - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4d

Returns a string that contains the values of this AxisAngle4d.

toString() - Method in class net.preibisch.mvrecon.vecmath.AxisAngle4f

Returns a string that contains the values of this AxisAngle4f.

toString() - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Returns a string that contains the values of this Matrix3d.

toString() - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Returns a string that contains the values of this Matrix3f.

toString() - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Returns a string that contains the values of this Matrix4d.

toString() - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Returns a string that contains the values of this Matrix4f.

toString() - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Returns the matrix elements of this transform as a string.

toString() - Method in class net.preibisch.mvrecon.vecmath.Tuple3d

Returns a string that contains the values of this Tuple3d.

toString() - Method in class net.preibisch.mvrecon.vecmath.Tuple3f

Returns a string that contains the values of this Tuple3f.

toString() - Method in class net.preibisch.mvrecon.vecmath.Tuple3i

Returns a string that contains the values of this Tuple3i.

toString() - Method in class net.preibisch.mvrecon.vecmath.Tuple4d

Returns a string that contains the values of this Tuple4d.

toString() - Method in class net.preibisch.mvrecon.vecmath.Tuple4f

Returns a string that contains the values of this Tuple4f.

totalRAM(long, int) - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.ManageDeconvolutionDialogListeners

totalRAM(long, int) - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.ManageFusionDialogListeners

totalRAM(long, int) - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.ManageQualityDialogListeners

toUnit(double[]) - Static method in class net.preibisch.mvrecon.fiji.plugin.Apply_Transformation

toURI(String) - Static method in class util.URITools

toViewIdGroup(Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

toViewIdGroups(Collection<? extends ViewId>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

toXml(BoundingBoxes) - Method in class net.preibisch.mvrecon.fiji.spimdata.boundingbox.XmlIoBoundingBoxes

toXml(AllenOMEZarrLoader, File) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoAllenOMEZarrLoader

toXml(AllenOMEZarrLoader, URI) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoAllenOMEZarrLoader

toXml(DHMImgLoader, File) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoDHMImgLoader

toXml(FileMapImgLoaderLOCI2, File) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.XmlIOFileMapImgLoaderLOCI2

toXml(FileMapImgLoaderLOCI2, URI) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.XmlIOFileMapImgLoaderLOCI2

toXml(FileMapImgLoaderLOCI, File) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoFileListImgLoaderLOCI

toXml(FlatfieldCorrectionWrappedImgLoader<? extends ImgLoader>, File) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.XmlIoFlatfieldCorrectedWrappedImgLoader

toXml(LightSheetZ1ImgLoader, File) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoLightSheetZ1ImgLoader

toXml(MicroManagerImgLoader, File) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoMicroManagerImgLoader

toXml(SimViewImgLoader, File) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoSimViewImgLoader

toXml(SmartSPIMImgLoader, File) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoSmartSPIMImgLoader

toXml(SmartSPIMImgLoader, URI) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoSmartSPIMImgLoader

toXml(SplitImgLoader, File) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.XmlIoSplitImgLoader

toXml(SplitMultiResolutionImgLoader, File) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.XmlIoSplitMultiResolutionImgLoader

toXml(SplitViewerImgLoader, File) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.XmlIoSplitViewerImgLoader

toXml(IntensityAdjustments) - Method in class net.preibisch.mvrecon.fiji.spimdata.intensityadjust.XmlIoIntensityAdjustments

toXml(ViewInterestPoints) - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.XmlIoViewInterestPoints

toXml(PointSpreadFunctions) - Method in class net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions.XmlIoPointSpreadFunctions

toXml(SpimData2, File) - Method in class net.preibisch.mvrecon.fiji.spimdata.XmlIoSpimData2

toXml(SpimData2, URI) - Method in class net.preibisch.mvrecon.fiji.spimdata.XmlIoSpimData2

toXml(StitchingResults) - Method in class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.XmlIoStitchingResults

toXml(T, File) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoStackImgLoader

tpChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

transform(RandomAccessibleInterval<T>, AffineTransform3D, long[], double[]) - Static method in class net.preibisch.mvrecon.process.psf.PSFExtraction

transform(AffineTransform3D, AffineTransform3D) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.CorrespondingIP

transform(Point3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Transforms the point parameter with this Matrix4d and places the result back into point.

transform(Point3d) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Transforms the point parameter with this transform and places the result back into point.

transform(Point3d, Point3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Transforms the point parameter with this Matrix4d and places the result into pointOut.

transform(Point3d, Point3d) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Transforms the point parameter with this transform and places the result into pointOut.

transform(Point3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Transforms the point parameter with this Matrix4d and places the result back into point.

transform(Point3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Transforms the point parameter with this Matrix4f and places the result back into point.

transform(Point3f) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Transforms the point parameter with this transform and places the result back into point.

transform(Point3f, Point3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Transforms the point parameter with this Matrix4d and places the result into pointOut.

transform(Point3f, Point3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Transforms the point parameter with this Matrix4f and places the result into pointOut.

transform(Point3f, Point3f) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Transforms the point parameter with this transform and places the result into pointOut.

transform(Tuple3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Multiply this matrix by the tuple t and place the result back into the tuple (t = this*t).

transform(Tuple3d, Tuple3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Multiply this matrix by the tuple t and and place the result into the tuple "result" (result = this*t).

transform(Tuple3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Multiply this matrix by the tuple t and place the result back into the tuple (t = this*t).

transform(Tuple3f, Tuple3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Multiply this matrix by the tuple t and and place the result into the tuple "result" (result = this*t).

transform(Tuple4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Transform the vector vec using this Matrix4d and place the result back into vec.

transform(Tuple4d, Tuple4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Transform the vector vec using this Matrix4d and place the result into vecOut.

transform(Tuple4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Transform the vector vec using this Transform and place the result back into vec.

transform(Tuple4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Transform the vector vec using this Transform and place the result back into vec.

transform(Tuple4f, Tuple4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Transform the vector vec using this Matrix4d and place the result into vecOut.

transform(Tuple4f, Tuple4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Transform the vector vec using this Matrix4f and place the result into vecOut.

transform(Vector3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Transforms the normal parameter by this transform and places the value back into normal.

transform(Vector3d) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Transforms the normal parameter by this transform and places the value back into normal.

transform(Vector3d, Vector3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Transforms the normal parameter by this Matrix4d and places the value into normalOut.

transform(Vector3d, Vector3d) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Transforms the normal parameter by this transform and places the value into normalOut.

transform(Vector3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Transforms the normal parameter by this transform and places the value back into normal.

transform(Vector3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Transforms the normal parameter by this transform and places the value back into normal.

transform(Vector3f) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Transforms the normal parameter by this transform and places the value back into normal.

transform(Vector3f, Vector3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Transforms the normal parameter by this Matrix4d and places the value into normalOut.

transform(Vector3f, Vector3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Transforms the normal parameter by this Matrix4f and places the value into normalOut.

transform(Vector3f, Vector3f) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Transforms the normal parameter by this transform and places the value into normalOut.

transform(Vector4d) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Transform the vector vec using this Transform and place the result back into vec.

transform(Vector4d, Vector4d) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Transform the vector vec using this transform and place the result into vecOut.

transform(Vector4f) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Transform the vector vec using this Transform and place the result back into vec.

transform(Vector4f, Vector4f) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Transform the vector vec using this Transform and place the result into vecOut.

Transform3D - Class in net.preibisch.mvrecon.vecmath

A generalized transform object represented internally as a 4x4 double-precision floating point matrix.

Transform3D() - Constructor for class net.preibisch.mvrecon.vecmath.Transform3D

Constructs and initializes a transform to the identity matrix.

Transform3D(double[]) - Constructor for class net.preibisch.mvrecon.vecmath.Transform3D

Constructs and initializes a transform from the double precision array of length 16; the top row of the matrix is initialized to the first four elements of the array, and so on.

Transform3D(float[]) - Constructor for class net.preibisch.mvrecon.vecmath.Transform3D

Constructs and initializes a transform from the float array of length 16; the top row of the matrix is initialized to the first four elements of the array, and so on.

Transform3D(Matrix3d, Vector3d, double) - Constructor for class net.preibisch.mvrecon.vecmath.Transform3D

Constructs and initializes a transform from the rotation matrix, translation, and scale values.

Transform3D(Matrix3f, Vector3d, double) - Constructor for class net.preibisch.mvrecon.vecmath.Transform3D

Constructs and initializes a transform from the rotation matrix, translation, and scale values.

Transform3D(Matrix3f, Vector3f, float) - Constructor for class net.preibisch.mvrecon.vecmath.Transform3D

Constructs and initializes a transform from the rotation matrix, translation, and scale values.

Transform3D(Matrix4d) - Constructor for class net.preibisch.mvrecon.vecmath.Transform3D

Constructs and initializes a transform from the 4 x 4 matrix.

Transform3D(Matrix4f) - Constructor for class net.preibisch.mvrecon.vecmath.Transform3D

Constructs and initializes a transform from the 4 x 4 matrix.

Transform3D(Quat4d, Vector3d, double) - Constructor for class net.preibisch.mvrecon.vecmath.Transform3D

Constructs and initializes a transform from the quaternion, translation, and scale values.

Transform3D(Quat4f, Vector3d, double) - Constructor for class net.preibisch.mvrecon.vecmath.Transform3D

Constructs and initializes a transform from the quaternion, translation, and scale values.

Transform3D(Quat4f, Vector3f, float) - Constructor for class net.preibisch.mvrecon.vecmath.Transform3D

Constructs and initializes a transform from the quaternion, translation, and scale values.

Transform3D(Transform3D) - Constructor for class net.preibisch.mvrecon.vecmath.Transform3D

Constructs and initializes a transform from the Transform3D object.

transformationChoice - Static variable in class net.preibisch.mvrecon.fiji.plugin.Duplicate_Transformation

TransformationModelGUI - Class in net.preibisch.mvrecon.fiji.plugin.interestpointregistration

TransformationModelGUI(int) - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.TransformationModelGUI

TransformationModelGUI(int, int, double, boolean) - Constructor for class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.TransformationModelGUI

TransformationTools - Class in net.preibisch.mvrecon.process.interestpointregistration

TransformationTools() - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

transformBlending(Interval, float[], float[], AffineTransform3D, Interval) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.TransformWeight

transformChanged(AffineTransform3D) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointOverlay

transformChanged(AffineTransform3D) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupIdOverlay

transformContentBased(RandomAccessibleInterval<T>, double[], double[], int[], float, AffineTransform3D, Interval) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.TransformWeight

transformCorrespondingIPs(Collection<CorrespondingIP>, Map<ViewId, AffineTransform3D>) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidTools

TransformedInputGeneralRandomAccess<T> - Class in net.preibisch.mvrecon.process.fusion.transformed

Virtually transforms any RandomAccessibleInterval<RealType> into a RandomAccess<FloatType> using an AffineTransformation

TransformedInputGeneralRandomAccess(RandomAccessibleInterval<T>, AffineTransform3D, InterpolatorFactory<FloatType, RandomAccessible<FloatType>>, OutOfBoundsFactory<T, RandomAccessible<T>>, long[]) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputGeneralRandomAccess

TransformedInputGeneralRandomAccessible<T> - Class in net.preibisch.mvrecon.process.fusion.transformed

TransformedInputGeneralRandomAccessible(RandomAccessibleInterval<T>, AffineTransform3D, OutOfBoundsFactory<T, RandomAccessible<T>>, InterpolatorFactory<FloatType, RandomAccessible<FloatType>>, long[]) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputGeneralRandomAccessible

TransformedInputRandomAccess<T> - Class in net.preibisch.mvrecon.process.fusion.transformed

Virtually transforms any RandomAccessibleInterval<RealType> into a RandomAccess<FloatType> using an AffineTransformation and Linear Interpolation.

TransformedInputRandomAccess(RandomAccessibleInterval<T>, AffineTransform3D, InterpolatorFactory<FloatType, RandomAccessible<FloatType>>, boolean, float, FloatType, long[]) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccess

TransformedInputRandomAccess2d<T> - Class in net.preibisch.mvrecon.process.fusion.transformed

Virtually transforms any RandomAccessibleInterval<RealType> into a RandomAccess<FloatType> using an AffineTransformation and Linear Interpolation.

TransformedInputRandomAccess2d(RandomAccessibleInterval<T>, AffineTransform3D, InterpolatorFactory<FloatType, RandomAccessible<FloatType>>, boolean, float, FloatType, long[]) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccess2d

TransformedInputRandomAccessible<T> - Class in net.preibisch.mvrecon.process.fusion.transformed

TransformedInputRandomAccessible(RandomAccessibleInterval<T>, AffineTransform3D, boolean, float, FloatType, Interval) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccessible

TransformedInputRandomAccessible(RandomAccessibleInterval<T>, AffineTransform3D, Interval) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.TransformedInputRandomAccessible

TransformedRasteredRandomAccess<T> - Class in net.preibisch.mvrecon.process.fusion.transformed.weights

TransformedRasteredRandomAccess(RealRandomAccessible<T>, T, AffineTransform3D, int[]) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.weights.TransformedRasteredRandomAccess

TransformedRasteredRandomAccessible<T> - Class in net.preibisch.mvrecon.process.fusion.transformed.weights

TransformedRasteredRandomAccessible(RealRandomAccessible<T>, T, AffineTransform3D, long[]) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.weights.TransformedRasteredRandomAccessible

transformPSF(RandomAccessibleInterval<T>, AffineTransform3D) - Static method in class net.preibisch.mvrecon.process.psf.PSFExtraction

Transforms the extracted PSF using the affine transformation of the corresponding view

transformUniqueIPs(ArrayList<HashSet<CorrespondingIP>>, Map<ViewId, AffineTransform3D>) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidTools

transformView(ImgLoader, ViewId, AffineTransform3D, FinalInterval, OutOfBoundsFactory<T, RandomAccessible<T>>, InterpolatorFactory<FloatType, RandomAccessible<FloatType>>) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.TransformView

transformView(ImgLoader, ViewId, AffineTransform3D, Interval, float, int) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.TransformView

transformView(SpimData, ViewId, FinalInterval, OutOfBoundsFactory<T, RandomAccessible<T>>, InterpolatorFactory<FloatType, RandomAccessible<FloatType>>) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.TransformView

transformView(SpimData, ViewId, Interval, float, int) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.TransformView

transformView(RandomAccessibleInterval<T>, AffineTransform3D, Interval, float, float, int) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.TransformView

Creates a virtual construct that transforms and zero-mins.

transformView(RandomAccessibleInterval<T>, AffineTransform3D, Interval, float, int) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.TransformView

Creates a virtual construct that transforms and zero-mins.

transformView(RandomAccessibleInterval<T>, AffineTransform3D, Interval, OutOfBoundsFactory<T, RandomAccessible<T>>, InterpolatorFactory<FloatType, RandomAccessible<FloatType>>) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.TransformView

Creates a virtual construct that transforms and zero-mins using a user-defined outofbounds & interpolation.

TransformView - Class in net.preibisch.mvrecon.process.fusion.transformed

TransformView() - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.TransformView

transformViewNonRigid(RandomAccessibleInterval<T>, Collection<? extends NonrigidIP>, double, AffineModel3D, Interval, float, int) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidTools

transformViewNonRigidInterpolated(RandomAccessibleInterval<T>, ModelGrid, AffineModel3D, Interval, float, int) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidTools

TransformVirtual - Class in net.preibisch.mvrecon.process.fusion.transformed

TransformVirtual() - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.TransformVirtual

transformWeight(RealRandomAccessible<FloatType>, AffineTransform3D, Interval) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.TransformWeight

create a transformed, rastered image

TransformWeight - Class in net.preibisch.mvrecon.process.fusion.transformed

TransformWeight() - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.TransformWeight

transformWeightNonRigid(RealRandomAccessible<FloatType>, Collection<? extends NonrigidIP>, double, AffineModel3D, Interval) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidWeightTools

transformWeightNonRigidInterpolated(RealRandomAccessible<FloatType>, ModelGrid, AffineModel3D, Interval) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidWeightTools

translateIfNecessary(Interval, RandomAccessibleInterval<T>) - Static method in class net.preibisch.mvrecon.process.fusion.FusionTools

TRANSLATION - Static variable in class net.preibisch.mvrecon.vecmath.Transform3D

A translation-only matrix with ones on the diagonal.

TranslationInvariantAffineModel3D - Class in net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model

3d-affine transformation models to be applied to points in 3d-space.

TranslationInvariantAffineModel3D() - Constructor for class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantAffineModel3D

TranslationInvariantFixedModel - Class in net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model

This model just applies some other TranslationInvariantModel without computing anything.

TranslationInvariantFixedModel() - Constructor for class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantFixedModel

TranslationInvariantFixedModel(double, double, double, double, double, double, double, double, double) - Constructor for class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantFixedModel

TranslationInvariantLocalCoordinateSystemPointDescriptor<P> - Class in net.preibisch.mvrecon.process.pointcloud.pointdescriptor

TranslationInvariantLocalCoordinateSystemPointDescriptor(P, P, P, P) - Constructor for class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.TranslationInvariantLocalCoordinateSystemPointDescriptor

TranslationInvariantModel<M> - Class in net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model

This class is a subtle hint that Models which are used to fit AbstractPointDescriptors should be translation invariant.

TranslationInvariantModel() - Constructor for class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantModel

TranslationInvariantRigidModel2D - Class in net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model

2d-rigid transformation models to be applied to points in 2d-space.

TranslationInvariantRigidModel2D() - Constructor for class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel2D

TranslationInvariantRigidModel3D - Class in net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model

3d-rigid transformation models to be applied to points in 3d-space.

TranslationInvariantRigidModel3D() - Constructor for class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel3D

TranslationInvariantSimilarityModel3D - Class in net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model

3d-rigid transformation models to be applied to points in 3d-space.

TranslationInvariantSimilarityModel3D() - Constructor for class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantSimilarityModel3D

transpose() - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Sets the value of this matrix to its transpose.

transpose() - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Sets the value of this matrix to its transpose.

transpose() - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the value of this matrix to its transpose.

transpose() - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the value of this matrix to its transpose in place.

transpose() - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Transposes this matrix in place.

transpose(Matrix3d) - Method in class net.preibisch.mvrecon.vecmath.Matrix3d

Sets the value of this matrix to the transpose of the argument matrix.

transpose(Matrix3f) - Method in class net.preibisch.mvrecon.vecmath.Matrix3f

Sets the value of this matrix to the transpose of the argument matrix.

transpose(Matrix4d) - Method in class net.preibisch.mvrecon.vecmath.Matrix4d

Sets the value of this matrix to the transpose of the argument matrix

transpose(Matrix4f) - Method in class net.preibisch.mvrecon.vecmath.Matrix4f

Sets the value of this matrix to the transpose of the argument matrix.

transpose(Transform3D) - Method in class net.preibisch.mvrecon.vecmath.Transform3D

Transposes transform t1 and places the value into this transform.

TRUE - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters.PreAlign

tryParsing(URI, boolean) - Method in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

Tuple3d - Class in net.preibisch.mvrecon.vecmath

A generic 3-element tuple that is represented by double-precision floating point x,y,z coordinates.

Tuple3d() - Constructor for class net.preibisch.mvrecon.vecmath.Tuple3d

Constructs and initializes a Tuple3d to (0,0,0).

Tuple3d(double[]) - Constructor for class net.preibisch.mvrecon.vecmath.Tuple3d

Constructs and initializes a Tuple3d from the array of length 3.

Tuple3d(double, double, double) - Constructor for class net.preibisch.mvrecon.vecmath.Tuple3d

Constructs and initializes a Tuple3d from the specified xyz coordinates.

Tuple3d(Tuple3d) - Constructor for class net.preibisch.mvrecon.vecmath.Tuple3d

Constructs and initializes a Tuple3d from the specified Tuple3d.

Tuple3d(Tuple3f) - Constructor for class net.preibisch.mvrecon.vecmath.Tuple3d

Constructs and initializes a Tuple3d from the specified Tuple3f.

Tuple3f - Class in net.preibisch.mvrecon.vecmath

A generic 3-element tuple that is represented by single precision-floating point x,y,z coordinates.

Tuple3f() - Constructor for class net.preibisch.mvrecon.vecmath.Tuple3f

Constructs and initializes a Tuple3f to (0,0,0).

Tuple3f(float[]) - Constructor for class net.preibisch.mvrecon.vecmath.Tuple3f

Constructs and initializes a Tuple3f from the array of length 3.

Tuple3f(float, float, float) - Constructor for class net.preibisch.mvrecon.vecmath.Tuple3f

Constructs and initializes a Tuple3f from the specified xyz coordinates.

Tuple3f(Tuple3d) - Constructor for class net.preibisch.mvrecon.vecmath.Tuple3f

Constructs and initializes a Tuple3f from the specified Tuple3d.

Tuple3f(Tuple3f) - Constructor for class net.preibisch.mvrecon.vecmath.Tuple3f

Constructs and initializes a Tuple3f from the specified Tuple3f.

Tuple3i - Class in net.preibisch.mvrecon.vecmath

A 3-element tuple represented by signed integer x,y,z coordinates.

Tuple3i() - Constructor for class net.preibisch.mvrecon.vecmath.Tuple3i

Constructs and initializes a Tuple3i to (0,0,0).

Tuple3i(int[]) - Constructor for class net.preibisch.mvrecon.vecmath.Tuple3i

Constructs and initializes a Tuple3i from the array of length 3.

Tuple3i(int, int, int) - Constructor for class net.preibisch.mvrecon.vecmath.Tuple3i

Constructs and initializes a Tuple3i from the specified x, y, and z coordinates.

Tuple3i(Tuple3i) - Constructor for class net.preibisch.mvrecon.vecmath.Tuple3i

Constructs and initializes a Tuple3i from the specified Tuple3i.

Tuple4d - Class in net.preibisch.mvrecon.vecmath

A 4 element tuple represented by double precision floating point x,y,z,w coordinates.

Tuple4d() - Constructor for class net.preibisch.mvrecon.vecmath.Tuple4d

Constructs and initializes a Tuple4d to (0,0,0,0).

Tuple4d(double[]) - Constructor for class net.preibisch.mvrecon.vecmath.Tuple4d

Constructs and initializes a Tuple4d from the coordinates contained in the array.

Tuple4d(double, double, double, double) - Constructor for class net.preibisch.mvrecon.vecmath.Tuple4d

Constructs and initializes a Tuple4d from the specified xyzw coordinates.

Tuple4d(Tuple4d) - Constructor for class net.preibisch.mvrecon.vecmath.Tuple4d

Constructs and initializes a Tuple4d from the specified Tuple4d.

Tuple4d(Tuple4f) - Constructor for class net.preibisch.mvrecon.vecmath.Tuple4d

Constructs and initializes a Tuple4d from the specified Tuple4f.

Tuple4f - Class in net.preibisch.mvrecon.vecmath

A 4-element tuple represented by single-precision floating point x,y,z,w coordinates.

Tuple4f() - Constructor for class net.preibisch.mvrecon.vecmath.Tuple4f

Constructs and initializes a Tuple4f to (0,0,0,0).

Tuple4f(float[]) - Constructor for class net.preibisch.mvrecon.vecmath.Tuple4f

Constructs and initializes a Tuple4f from the array of length 4.

Tuple4f(float, float, float, float) - Constructor for class net.preibisch.mvrecon.vecmath.Tuple4f

Constructs and initializes a Tuple4f from the specified xyzw coordinates.

Tuple4f(Tuple4d) - Constructor for class net.preibisch.mvrecon.vecmath.Tuple4f

Constructs and initializes a Tuple4f from the specified Tuple4d.

Tuple4f(Tuple4f) - Constructor for class net.preibisch.mvrecon.vecmath.Tuple4f

Constructs and initializes a Tuple4f from the specified Tuple4f.

TWO_ROUND_ITERATIVE - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters.GlobalOptType

TWO_ROUND_SIMPLE - Enum constant in enum class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters.GlobalOptType

tx - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel2D

ty - Variable in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.model.TranslationInvariantRigidModel2D

type - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader.IFDEntry

type - Variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader.IFDEntry

type - Variable in class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion.LandmarkRecord

TYPE_CORR_COM - Static variable in class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion.LandmarkRecord

TYPE_MIDPOINT - Static variable in class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion.LandmarkRecord

TYPE_NAIL - Static variable in class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion.LandmarkRecord

types - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.SimView

types - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.IntensityAdjustmentPopup

types - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.RemoveTransformationPopup

types - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.ResavePopup

U

unbleach(double, int) - Method in interface net.preibisch.mvrecon.process.fusion.intensity.UnbleachFunction

Compute the corrected intensity when intensity was observed in a pixel that has been nBleachIterations times imaged already.

UnbleachFunction - Interface in net.preibisch.mvrecon.process.fusion.intensity

Compute the corrected intensity when intensity was observed in a pixel that has been bleached by previously being imaged.

underlyingSequenceDescription() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitViewerImgLoader

underlyingViewId - Variable in class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion.LandmarkRecord

underlyingViewIds(Collection<? extends ViewId>, Map<Integer, Integer>) - Static method in class net.preibisch.mvrecon.process.fusion.blk.SplitImgLoaderThinPlateSplineFusion

uniqueInterestPointCounts(List<HashSet<CorrespondingIP>>) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidTools

unit - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

unit - Variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

unit() - Method in class net.preibisch.mvrecon.fiji.plugin.Specify_Calibration.Cal

unitCube() - Static method in class net.preibisch.mvrecon.process.interestpointregistration.TransformationTools

unwrapPointMatches(List<? extends PointMatchGeneric<? extends LinkedInterestPoint<P>>>) - Static method in class net.preibisch.mvrecon.process.pointcloud.icp.ICP

Return the List of PointMatches (target, reference) of the last ICP iteration

update() - Method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.BoundingBoxGUI.ManageListeners

update() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.ManageDeconvolutionDialogListeners

update() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.ManageFusionDialogListeners

update() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.ManageQualityDialogListeners

update(ViewRegistrations) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationTableModel

update(ViewInterestPoints) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

update(SpimData2, Choice, Label, Label) - Static method in class net.preibisch.mvrecon.fiji.plugin.boundingbox.ModifyDefinedBoundingBoxGUI

updateAndGetMinMax(RandomAccessibleInterval<T>, Generic_Resave_HDF5.ParametersResaveHDF5) - Static method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyStackImgLoaderIJ

updateBDV() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BasicBDVPopup

updateBDV() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BDVPopup

updateBDV() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.LazyBDVPopup

updateBDV(BigDataViewer, boolean, AbstractSpimData<?>, BasicViewDescription<?>, Collection<List<BasicViewDescription<?>>>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

updateBDV(BigDataViewer, boolean, AbstractSpimData<?>, BasicViewDescription<?>, Collection<List<BasicViewDescription<?>>>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorerPanel

updateBDV(Bdv) - Static method in class net.preibisch.mvrecon.fiji.plugin.interactive.MultiResolutionTools

updateBrightnessPanels(BigDataViewer) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.ScrollableBrightnessDialog

updateContainer(Object) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

updateContainer(Object) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

updateContent() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.ExplorerWindow

updateContent() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

updateContent(AS) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointExplorer

updateContent(AS) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationExplorer

updateContent(AS) - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.SelectedViewDescriptionListener

updateDefaultName(String, List<BoundingBox>) - Method in class net.preibisch.mvrecon.fiji.plugin.Define_Bounding_Box

updateElements() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedTableModel

updateElements() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.ISpimDataTableModel

updateElements() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MissingViewsTableModelDecorator

updateElements() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.MultiViewTableModelDecorator

updateFilter(Class<? extends Entity>, Entity) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

updateHideMissingViewsCheckbox() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorerPanel

Updates the enabled state and label of the "Hide Missing Views" checkbox.

updateIndex(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

updateIndex(int) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

updateLabel() - Method in class net.preibisch.mvrecon.fiji.plugin.util.MyMultiLineLabel

updateMetaDataCache(ViewId, int, int, int, double, double, double) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AbstractImgLoader

updateModelTmp() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

updatePanels() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.ScrollableBrightnessDialog

updatePanels() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.ToggleDialogActionBrightness

updatePreview(InteractiveDoG.ValueChange) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoG

Updates the Preview with the current parameters (sigma, threshold, roi, slice number + RANSAC parameters)

updateScaledIntervals(Interval[], int, int, Interval) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.SplitMultiResolutionSetupImgLoader

Sometimes because of scaling the max is too high exceeding the actual downsampled image as provided

updateTransformTmp() - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

updateViewDescription(List<BasicViewDescription<?>>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointExplorerPanel

updateViewDescription(List<BasicViewDescription<?>>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint.InterestPointTableModel

updateViewDescription(BasicViewDescription<?>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationTableModel

updateViewDescriptions(List<BasicViewDescription<?>>) - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationExplorerPanel

updateViewSetup(String, Collection<ViewSetup>, Pair<DatasetAttributes, Pair<VoxelDimensions, double[]>>, int, int, int, int, int, long, int) - Static method in class net.preibisch.mvrecon.fiji.datasetmanager.OMEZARR

updateWithNewChart(TimePoints, JFreeChart, boolean, List<SelectTimepointEntry>, ArrayList<RegistrationStatistics>, int, boolean) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.statistics.GraphFrame

updateXMLMetaData(List<? extends ViewSetup>, boolean) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AbstractImgLoader

Updates a list of ViewSetups using the imageMetaDataCache

updateXMLMetaData(ViewSetup, boolean) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AbstractImgLoader

Updates one specific ViewSetup using the imageMetaDataCache

updateXMLMetaData(SpimData, boolean) - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.AbstractImgLoader

Updates the ViewSetups using the imageMetaDataCache

upperThreshold - Variable in class net.preibisch.mvrecon.process.interestpointremoval.ThinOutParameters

URITools - Class in util

URITools() - Constructor for class util.URITools

useAllViews - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.Parameters

When true, the caller should analyse all views in the dataset, not just the explorer's selection.

useAverageMapBack - Static variable in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.DifferenceOfGUI

useHalfCircle - Variable in class net.preibisch.mvrecon.process.quality.FRC

The correlation is computed using intervals around the circle circumference of the Fourier transform.

useLazyMode - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BDVPopup

Set by Data_Explorer's large-dataset dialog.

useRANSAC() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.icp.IterativeClosestPointParameters

useRelativeFRC - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.QualityGUI

userSelectedAdvancedParameters() - Method in class net.preibisch.mvrecon.fiji.plugin.fusion.NonRigidParametersGUI

useS3CredentialsRead - Static variable in class util.URITools

useS3CredentialsWrite - Static variable in class util.URITools

useSharding - Variable in class net.preibisch.mvrecon.fiji.plugin.resave.ParametersResaveN5Api

useTikhonov - Variable in class net.preibisch.mvrecon.fiji.plugin.fusion.DeconvolutionGUI

useW - Variable in class net.preibisch.legacy.registration.detection.AbstractDetection

useWorldCoordinatesForDescriptorBuildUp() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.AbstractPointDescriptor

Tells if the build up of the descriptor should use the world coordinates or rather the local coordinates

useWorldCoordinatesForDescriptorBuildUp() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.LocalCoordinateSystemPointDescriptor

useWorldCoordinatesForDescriptorBuildUp() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.ModelPointDescriptor

useWorldCoordinatesForDescriptorBuildUp() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.SimplePointDescriptor

useWorldCoordinatesForDescriptorBuildUp() - Method in class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.TranslationInvariantLocalCoordinateSystemPointDescriptor

util - package util

V

v - Variable in class net.preibisch.mvrecon.process.fusion.transformed.AbstractTransformedIntervalRandomAccess

vA - Variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.MatcherPairwiseTools.MatchingTask

validPair(V, V, Collection<V>, Collection<? extends Collection<V>>) - Static method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.PairwiseStrategyTools

value - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader.IFDEntry

value - Variable in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader.IFDEntry

value - Variable in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccess

VALUE - Enum constant in enum class net.preibisch.mvrecon.process.cuda.CUDASeparableConvolutionFunctions.OutOfBounds

valueEquals(NumericAffineModel3D) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineModel3D

valueEquals(NumericAffineTransform3D) - Method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.NumericAffineTransform3D

valueOf(String) - Static method in enum class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.CheckResult

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI.FusionType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoG.ValueChange

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters.GlobalOptType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters.PreAlign

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.BasicRegistrationParameters.InterestPointOverlapType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.BasicRegistrationParameters.OverlapType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.BasicRegistrationParameters.RegistrationType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.GroupParameters.InterestpointGroupingType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.preibisch.mvrecon.fiji.plugin.Split_Views.InterestPointAdding

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsResultsWindow.BdvResetPolicy

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.Mode

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.preibisch.mvrecon.fiji.spimdata.explorer.ISpimDataTableModel.SpecialColumnType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.preibisch.mvrecon.fiji.spimdata.explorer.viewneighbours.ViewNeighboursWindow.ResetPolicy

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.preibisch.mvrecon.fiji.spimdata.explorer.viewneighbours.ViewOverlapWindow.ResetPolicy

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.preibisch.mvrecon.headless.definedataset.DefineDataSetParameters.RotationAxis

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.preibisch.mvrecon.headless.definedataset.StackListParameters.AngleOption

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.preibisch.mvrecon.headless.definedataset.StackListParameters.ChannelOption

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.preibisch.mvrecon.headless.definedataset.StackListParameters.Container

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.preibisch.mvrecon.headless.definedataset.StackListParameters.IlluminationOption

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.preibisch.mvrecon.headless.definedataset.StackListParameters.TileOption

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.preibisch.mvrecon.headless.definedataset.StackListParameters.TimePointOption

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.preibisch.mvrecon.imglib2.st.filter.GaussianFilterFactory.WeightType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.preibisch.mvrecon.process.cuda.CUDASeparableConvolutionFunctions.OutOfBounds

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.preibisch.mvrecon.process.deconvolution.DeconViewPSF.PSFTYPE

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.preibisch.mvrecon.process.deconvolution.init.PsiInit.PsiInitType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.preibisch.mvrecon.process.fusion.FusionTools.ImgDataType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval.Fusion

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccessibleInterval.CombineType

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2.SpecialPoint

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.preibisch.mvrecon.process.quality.FRC.ThresholdMethod

Returns the enum constant of this class with the specified name.

valueOf(String) - Static method in enum class net.preibisch.mvrecon.process.splitting.ConsensusSetCriterion.ToleranceMode

Returns the enum constant of this class with the specified name.

ValuePair(A, B) - Constructor for class net.preibisch.mvrecon.fiji.ImgLib2Temp.ValuePair

values() - Static method in enum class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.CheckResult

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.preibisch.mvrecon.fiji.plugin.fusion.FusionGUI.FusionType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoG.ValueChange

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters.GlobalOptType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters.PreAlign

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.BasicRegistrationParameters.InterestPointOverlapType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.BasicRegistrationParameters.OverlapType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.BasicRegistrationParameters.RegistrationType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters.GroupParameters.InterestpointGroupingType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.preibisch.mvrecon.fiji.plugin.Split_Views.InterestPointAdding

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsResultsWindow.BdvResetPolicy

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.Mode

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.preibisch.mvrecon.fiji.spimdata.explorer.ISpimDataTableModel.SpecialColumnType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.preibisch.mvrecon.fiji.spimdata.explorer.viewneighbours.ViewNeighboursWindow.ResetPolicy

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.preibisch.mvrecon.fiji.spimdata.explorer.viewneighbours.ViewOverlapWindow.ResetPolicy

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.preibisch.mvrecon.headless.definedataset.DefineDataSetParameters.RotationAxis

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.preibisch.mvrecon.headless.definedataset.StackListParameters.AngleOption

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.preibisch.mvrecon.headless.definedataset.StackListParameters.ChannelOption

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.preibisch.mvrecon.headless.definedataset.StackListParameters.Container

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.preibisch.mvrecon.headless.definedataset.StackListParameters.IlluminationOption

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.preibisch.mvrecon.headless.definedataset.StackListParameters.TileOption

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.preibisch.mvrecon.headless.definedataset.StackListParameters.TimePointOption

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.preibisch.mvrecon.imglib2.st.filter.GaussianFilterFactory.WeightType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.preibisch.mvrecon.process.cuda.CUDASeparableConvolutionFunctions.OutOfBounds

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.preibisch.mvrecon.process.deconvolution.DeconViewPSF.PSFTYPE

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.preibisch.mvrecon.process.deconvolution.init.PsiInit.PsiInitType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.preibisch.mvrecon.process.fusion.FusionTools.ImgDataType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessibleInterval.Fusion

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.preibisch.mvrecon.process.fusion.transformed.weightcombination.CombineWeightsRandomAccessibleInterval.CombineType

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2.SpecialPoint

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.preibisch.mvrecon.process.quality.FRC.ThresholdMethod

Returns an array containing the constants of this enum class, in the order they are declared.

values() - Static method in enum class net.preibisch.mvrecon.process.splitting.ConsensusSetCriterion.ToleranceMode

Returns an array containing the constants of this enum class, in the order they are declared.

ValueTriple(A, B, C) - Constructor for class net.preibisch.mvrecon.fiji.ImgLib2Temp.ValueTriple

vB - Variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.MatcherPairwiseTools.MatchingTask

Vector3d - Class in net.preibisch.mvrecon.vecmath

A 3-element vector that is represented by double-precision floating point x,y,z coordinates.

Vector3d() - Constructor for class net.preibisch.mvrecon.vecmath.Vector3d

Constructs and initializes a Vector3d to (0,0,0).

Vector3d(double[]) - Constructor for class net.preibisch.mvrecon.vecmath.Vector3d

Constructs and initializes a Vector3d from the array of length 3.

Vector3d(double, double, double) - Constructor for class net.preibisch.mvrecon.vecmath.Vector3d

Constructs and initializes a Vector3d from the specified xyz coordinates.

Vector3d(Tuple3d) - Constructor for class net.preibisch.mvrecon.vecmath.Vector3d

Constructs and initializes a Vector3d from the specified Tuple3d.

Vector3d(Tuple3f) - Constructor for class net.preibisch.mvrecon.vecmath.Vector3d

Constructs and initializes a Vector3d from the specified Tuple3f.

Vector3d(Vector3d) - Constructor for class net.preibisch.mvrecon.vecmath.Vector3d

Constructs and initializes a Vector3d from the specified Vector3d.

Vector3d(Vector3f) - Constructor for class net.preibisch.mvrecon.vecmath.Vector3d

Constructs and initializes a Vector3d from the specified Vector3f.

Vector3f - Class in net.preibisch.mvrecon.vecmath

A 3-element vector that is represented by single-precision floating point x,y,z coordinates.

Vector3f() - Constructor for class net.preibisch.mvrecon.vecmath.Vector3f

Constructs and initializes a Vector3f to (0,0,0).

Vector3f(float[]) - Constructor for class net.preibisch.mvrecon.vecmath.Vector3f

Constructs and initializes a Vector3f from the array of length 3.

Vector3f(float, float, float) - Constructor for class net.preibisch.mvrecon.vecmath.Vector3f

Constructs and initializes a Vector3f from the specified xyz coordinates.

Vector3f(Tuple3d) - Constructor for class net.preibisch.mvrecon.vecmath.Vector3f

Constructs and initializes a Vector3f from the specified Tuple3d.

Vector3f(Tuple3f) - Constructor for class net.preibisch.mvrecon.vecmath.Vector3f

Constructs and initializes a Vector3f from the specified Tuple3f.

Vector3f(Vector3d) - Constructor for class net.preibisch.mvrecon.vecmath.Vector3f

Constructs and initializes a Vector3f from the specified Vector3d.

Vector3f(Vector3f) - Constructor for class net.preibisch.mvrecon.vecmath.Vector3f

Constructs and initializes a Vector3f from the specified Vector3f.

Vector4d - Class in net.preibisch.mvrecon.vecmath

A 4-element vector represented by double-precision floating point x,y,z,w coordinates.

Vector4d() - Constructor for class net.preibisch.mvrecon.vecmath.Vector4d

Constructs and initializes a Vector4d to (0,0,0,0).

Vector4d(double[]) - Constructor for class net.preibisch.mvrecon.vecmath.Vector4d

Constructs and initializes a Vector4d from the coordinates contained in the array.

Vector4d(double, double, double, double) - Constructor for class net.preibisch.mvrecon.vecmath.Vector4d

Constructs and initializes a Vector4d from the specified xyzw coordinates.

Vector4d(Tuple3d) - Constructor for class net.preibisch.mvrecon.vecmath.Vector4d

Constructs and initializes a Vector4d from the specified Tuple3d.

Vector4d(Tuple4d) - Constructor for class net.preibisch.mvrecon.vecmath.Vector4d

Constructs and initializes a Vector4d from the specified Tuple4d.

Vector4d(Tuple4f) - Constructor for class net.preibisch.mvrecon.vecmath.Vector4d

Constructs and initializes a Vector4d from the specified Tuple4f.

Vector4d(Vector4d) - Constructor for class net.preibisch.mvrecon.vecmath.Vector4d

Constructs and initializes a Vector4d from the specified Vector4d.

Vector4d(Vector4f) - Constructor for class net.preibisch.mvrecon.vecmath.Vector4d

Constructs and initializes a Vector4d from the specified Vector4f.

Vector4f - Class in net.preibisch.mvrecon.vecmath

A 4-element vector represented by single-precision floating point x,y,z,w coordinates.

Vector4f() - Constructor for class net.preibisch.mvrecon.vecmath.Vector4f

Constructs and initializes a Vector4f to (0,0,0,0).

Vector4f(float[]) - Constructor for class net.preibisch.mvrecon.vecmath.Vector4f

Constructs and initializes a Vector4f from the array of length 4.

Vector4f(float, float, float, float) - Constructor for class net.preibisch.mvrecon.vecmath.Vector4f

Constructs and initializes a Vector4f from the specified xyzw coordinates.

Vector4f(Tuple3f) - Constructor for class net.preibisch.mvrecon.vecmath.Vector4f

Constructs and initializes a Vector4f from the specified Tuple3f.

Vector4f(Tuple4d) - Constructor for class net.preibisch.mvrecon.vecmath.Vector4f

Constructs and initializes a Vector4f from the specified Tuple4d.

Vector4f(Tuple4f) - Constructor for class net.preibisch.mvrecon.vecmath.Vector4f

Constructs and initializes a Vector4f from the specified Tuple4f.

Vector4f(Vector4d) - Constructor for class net.preibisch.mvrecon.vecmath.Vector4f

Constructs and initializes a Vector4f from the specified Vector4d.

Vector4f(Vector4f) - Constructor for class net.preibisch.mvrecon.vecmath.Vector4f

Constructs and initializes a Vector4f from the specified Vector4f.

VectorUtil - Class in net.preibisch.mvrecon.fiji.spimdata.stitchingresults

VectorUtil() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.VectorUtil

Version - Class in net.preibisch.mvrecon

view - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror.AnalyzeErrorsUtil.SingleViewError

VIEW_REGISTRATION_COLUMN - Enum constant in enum class net.preibisch.mvrecon.fiji.spimdata.explorer.ISpimDataTableModel.SpecialColumnType

view1() - Method in class net.preibisch.mvrecon.process.fusion.intensity.ViewPairCoefficientMatches

view2() - Method in class net.preibisch.mvrecon.process.fusion.intensity.ViewPairCoefficientMatches

viewDescriptions() - Method in class net.preibisch.mvrecon.fiji.plugin.apply.ModelLink

viewerTransforms - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough

viewIdSourceName(BasicViewSetup, AbstractSequenceDescription<?, ?, ?>) - Static method in class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BDVSourceNaming

viewIdsToProcess - Variable in class net.preibisch.mvrecon.fiji.plugin.boundingbox.BoundingBoxGUI

viewIdToDatasetBdv(int, StorageFormat) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

viewIdToDatasetBdv(StorageFormat) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

ViewInterestPointLists - Class in net.preibisch.mvrecon.fiji.spimdata.interestpoints

Maps from a String label to a list of interest points for a specific viewid

ViewInterestPointLists(int, int) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.interestpoints.ViewInterestPointLists

ViewInterestPoints - Class in net.preibisch.mvrecon.fiji.spimdata.interestpoints

A class that organizes all interest point detections of all ViewDescriptions (which extend ViewId)

ViewInterestPoints() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.interestpoints.ViewInterestPoints

ViewInterestPoints(Collection<ViewInterestPointLists>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.interestpoints.ViewInterestPoints

ViewInterestPoints(Map<ViewId, ViewInterestPointLists>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.interestpoints.ViewInterestPoints

VIEWINTERESTPOINTS_LABEL_ATTRIBUTE_NAME - Static variable in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.XmlKeysInterestPoints

VIEWINTERESTPOINTS_PARAMETERS_ATTRIBUTE_NAME - Static variable in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.XmlKeysInterestPoints

VIEWINTERESTPOINTS_SETUP_ATTRIBUTE_NAME - Static variable in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.XmlKeysInterestPoints

VIEWINTERESTPOINTS_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.XmlKeysInterestPoints

VIEWINTERESTPOINTS_TIMEPOINT_ATTRIBUTE_NAME - Static variable in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.XmlKeysInterestPoints

VIEWINTERESTPOINTSFILE_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.XmlKeysInterestPoints

viewInterestPointsToXml(InterestPoints, int, int, String) - Method in class net.preibisch.mvrecon.fiji.spimdata.interestpoints.XmlIoViewInterestPoints

ViewNeighbors - Class in net.preibisch.mvrecon.process.interestpointregistration

Reusable per-view neighbour queries: ViewNeighbors.connectedViews(SpimData2, Collection, Map) — interest-point correspondence neighbours ViewNeighbors.overlappingViews(SpimData2, Collection) — geometric (bounding-box) neighbours Both restrict their results to the universe set passed in (typically the views the caller is already analysing).

ViewNeighboursWindow - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.viewneighbours

Companion window of FilteredAndGroupedExplorerPanel that highlights views in BDV which are correspondence-connected to the explorer's current selection.

ViewNeighboursWindow(FilteredAndGroupedExplorerPanel<?>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.viewneighbours.ViewNeighboursWindow

ViewNeighboursWindow.ResetPolicy - Enum Class in net.preibisch.mvrecon.fiji.spimdata.explorer.viewneighbours

ViewOverlapWindow - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.viewneighbours

Companion window of FilteredAndGroupedExplorerPanel that highlights views in BDV which geometrically overlap the explorer's current selection.

ViewOverlapWindow(FilteredAndGroupedExplorerPanel<?>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.viewneighbours.ViewOverlapWindow

ViewOverlapWindow.ResetPolicy - Enum Class in net.preibisch.mvrecon.fiji.spimdata.explorer.viewneighbours

ViewPairCoefficientMatches - Class in net.preibisch.mvrecon.process.fusion.intensity

ViewPairCoefficientMatches(ViewId, ViewId, List<IntensityMatcher.CoefficientMatch>) - Constructor for class net.preibisch.mvrecon.process.fusion.intensity.ViewPairCoefficientMatches

ViewPairCoefficientMatchesIO - Class in net.preibisch.mvrecon.process.fusion.intensity

ViewPairCoefficientMatchesIO(URI) - Constructor for class net.preibisch.mvrecon.process.fusion.intensity.ViewPairCoefficientMatchesIO

viewRegistrations - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.registration.RegistrationExplorerPanel

views - Variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group

views - Variable in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.PairwiseSetup

viewsAsList() - Method in class net.preibisch.mvrecon.process.interestpointregistration.pairwise.MatcherPairwiseTools.MatchingTask

ViewSetupExplorer<AS> - Class in net.preibisch.mvrecon.fiji.spimdata.explorer

ViewSetupExplorer(AS, URI, XmlIoSpimData2) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorer

ViewSetupExplorer(AS, URI, XmlIoSpimData2, boolean) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorer

ViewSetupExplorerInfoBox<AS> - Class in net.preibisch.mvrecon.fiji.spimdata.explorer

ViewSetupExplorerInfoBox(AS) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorerInfoBox

ViewSetupExplorerPanel<AS> - Class in net.preibisch.mvrecon.fiji.spimdata.explorer

ViewSetupExplorerPanel(FilteredAndGroupedExplorer<AS>, AS, URI, XmlIoSpimData2, boolean) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorerPanel

viewSetupIdOverlay - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

ViewSetupIdOverlay - Class in net.preibisch.mvrecon.fiji.spimdata.explorer

ViewSetupIdOverlay(ViewerPanel) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupIdOverlay

ViewSetupPrecursor(int, int, int, int) - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.StackList.ViewSetupPrecursor

ViewSetupPrecursor(int, int, int, int, ArrayList<String>, ArrayList<String>, ArrayList<String>, ArrayList<String>) - Constructor for class net.preibisch.mvrecon.headless.definedataset.StackList.ViewSetupPrecursor

ViewSetupUtils - Class in net.preibisch.mvrecon.fiji.spimdata

ViewSetupUtils() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.ViewSetupUtils

viewsWithUniquePSFs(PointSpreadFunctions) - Static method in class net.preibisch.mvrecon.fiji.plugin.PSF_Assign

virtual - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.SimViewSetupImgLoader

VIRTUAL - Enum constant in enum class net.preibisch.mvrecon.process.fusion.FusionTools.ImgDataType

VirtualGrid - Class in net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid

VirtualGrid(long[], long[], long[], double, Collection<? extends NonrigidIP>) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGrid

VirtualGridRandomAccess - Class in net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid

VirtualGridRandomAccess(long[], long[], double, Collection<? extends NonrigidIP>, int) - Constructor for class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.grid.VirtualGridRandomAccess

VirtuallyNormalizedRandomAccessibleInterval<T> - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield

VirtuallyNormalizedRandomAccessibleInterval(RandomAccessibleInterval<T>) - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.VirtuallyNormalizedRandomAccessibleInterval

VirtualPointNode<P> - Class in net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test

VirtualPointNode(P) - Constructor for class net.preibisch.mvrecon.process.pointcloud.pointdescriptor.test.VirtualPointNode

visualize(SpimData2, List<ViewId>, String, int, double, boolean) - Static method in class net.preibisch.mvrecon.fiji.plugin.Visualize_Detections

Visualize_Detections - Class in net.preibisch.mvrecon.fiji.plugin

Visualize_Detections() - Constructor for class net.preibisch.mvrecon.fiji.plugin.Visualize_Detections

Visualize_Detections.Params - Class in net.preibisch.mvrecon.fiji.plugin

VisualizeDetectionsPopup - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

VisualizeDetectionsPopup() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.VisualizeDetectionsPopup

VisualizeDetectionsPopup.MyActionListener - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

visualizeDistancesViewNonRigidInterpolated(Interval, ModelGrid, AffineTransform3D, Interval, float, int) - Static method in class net.preibisch.mvrecon.process.fusion.transformed.nonrigid.NonRigidTools

VisualizeIntensityCorrection - Class in net.preibisch.mvrecon.process.fusion.intensity

VisualizeNonRigid - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

VisualizeNonRigid() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.explorer.popup.VisualizeNonRigid

VisualizeNonRigid.MyActionListener - Class in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

vrs - Variable in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxMaximalGroupOverlap

vss - Variable in class net.preibisch.mvrecon.process.boundingbox.BoundingBoxMaximalGroupOverlap

W

w - Variable in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccess

w - Variable in class net.preibisch.mvrecon.process.fusion.transformed.FusedRandomAccessFirstWins

w - Variable in class net.preibisch.mvrecon.vecmath.Tuple4d

The w coordinate.

w - Variable in class net.preibisch.mvrecon.vecmath.Tuple4f

The w coordinate.

w() - Method in class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.FlattenedMatches

warning - Static variable in class net.preibisch.mvrecon.fiji.plugin.util.GUIHelper

warningLabel - Static variable in class net.preibisch.mvrecon.process.interestpointdetection.InterestPointTools

warningMsg1 - Static variable in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

wasCanceled - Variable in class net.preibisch.mvrecon.process.interestpointremoval.InteractiveProjections

wasCanceled() - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.InteractiveDoG

wasCanceled() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.selection.SelectionDialog

wasCanceled() - Method in class net.preibisch.mvrecon.process.interestpointremoval.InteractiveProjections

wasCancelled - Variable in class net.preibisch.mvrecon.fiji.plugin.apply.BigDataViewerTransformationWindow

wasCancelled() - Method in class net.preibisch.mvrecon.fiji.plugin.apply.BigDataViewerTransformationWindow

wavelength - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.ChannelInfo

wavelength - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinitionUtil.ChannelOrIlluminationInfo

WeakLinkFactory - Interface in net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.weak

WeakLinkPointMatchCreator<M> - Class in net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.weak

WeakLinkPointMatchCreator(HashMap<ViewId, Tile<M>>) - Constructor for class net.preibisch.mvrecon.process.interestpointregistration.global.pointmatchcreating.weak.WeakLinkPointMatchCreator

weight - Variable in class net.preibisch.legacy.registration.detection.AbstractDetection

weighted() - Method in class net.preibisch.mvrecon.process.fusion.intensity.mpicbg.FlattenedMatches

Returns true if the weights of the matches should be considered for model fitting.

whiteSources(List<ConverterSetup>) - Static method in class util.BDVTools

Deprecated.

Use BDVTools.whiteSourcesBatch(BigDataViewer) instead

whiteSourcesBatch(BigDataViewer) - Static method in class util.BDVTools

Sets all sources to white color using the proper ConverterSetups API.

width() - Method in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.MultipageTiffReader

width() - Method in class net.preibisch.mvrecon.headless.definedataset.MultipageTiffReader

WildcardDirectoryListChooser() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.OMEZARR.WildcardDirectoryListChooser

WildcardFileListChooser() - Constructor for class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition.WildcardFileListChooser

windowClosing(WindowEvent) - Method in class net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.FrameListener

windowClosing(WindowEvent) - Method in class net.preibisch.mvrecon.process.interestpointremoval.histogram.Histogram

windowsHack - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition

withinTolerancePercent - Variable in class net.preibisch.mvrecon.process.splitting.SplitOctTree.OctTreeSplitResult

WRAPPED_IMGLOADER_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.XmlIoFlatfieldCorrectedWrappedImgLoader

wrapWithIntensityCorrectedSource(SourceAndConverter<?>, SharedQueue, IntFunction<Coefficients>, BooleanSupplier) - Static method in class net.preibisch.mvrecon.process.fusion.intensity.VisualizeIntensityCorrection

Wrap the given SourceAndConverter, allowing to switch between unmodified and on-the-fly intensity-corrected images.

write(ViewId, ViewId, List<IntensityMatcher.CoefficientMatch>) - Method in class net.preibisch.mvrecon.process.fusion.intensity.ViewPairCoefficientMatchesIO

write(ViewPairCoefficientMatches) - Method in class net.preibisch.mvrecon.process.fusion.intensity.ViewPairCoefficientMatchesIO

writeApproxAffine(N5Writer, String, AffineTransform3D) - Static method in class net.preibisch.mvrecon.process.fusion.blk.DisplacementFieldN5Tools

Write the per-view approximate affine (the affine that fits from the TPS landmarks for blending-weight adjustment) as an N5 attribute on the dfield dataset.

writeBack(Img<FloatType>, Vector<Pair<Pair<Integer, Block>, Img<FloatType>>>) - Static method in class net.preibisch.mvrecon.process.deconvolution.MultiViewDeconvolution

writeBDVMetaData(N5Writer, StorageFormat, DataType, long[], Compression, int[], int[][], ViewId, URI, URI, SpimData2Tools.InstantiateViewSetup) - Static method in class net.preibisch.mvrecon.process.n5api.SpimData2Tools

writeCoefficients(N5Writer, String, String, Map<ViewId, Coefficients>) - Static method in class net.preibisch.mvrecon.process.fusion.intensity.IntensityCorrection

writeCoefficientsSize(int[]) - Method in class net.preibisch.mvrecon.process.fusion.intensity.ViewPairCoefficientMatchesIO

writeDisplacementField(RealTransform, Interval, double[], N5Writer, String, int[], D, Compression) - Static method in class net.preibisch.mvrecon.process.fusion.blk.DisplacementFieldN5Tools

Sample the given transform over bbox at spacing and write the resulting displacement field to an N5/Zarr dataset.

writeDisplacementFieldBlock(RealTransform, Interval, double[], int[], long[], N5Writer, String, D) - Static method in class net.preibisch.mvrecon.process.fusion.blk.DisplacementFieldN5Tools

Sample one block of the displacement field and write it via N5Utils.saveBlock(net.imglib2.RandomAccessibleInterval<T>, org.janelia.saalfeldlab.n5.N5Writer, java.lang.String, org.janelia.saalfeldlab.n5.DatasetAttributes, long[]).

writeDownsampledBlock(N5Writer, N5ApiTools.MultiResolutionLevelInfo, N5ApiTools.MultiResolutionLevelInfo, long[][]) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

writeDownsampledBlock5dOMEZARR(N5Writer, N5ApiTools.MultiResolutionLevelInfo, N5ApiTools.MultiResolutionLevelInfo, long[][], long, long) - Static method in class net.preibisch.mvrecon.process.n5api.N5ApiTools

writeHDF5(AbstractSpimData<?>, Generic_Resave_HDF5.ParametersResaveHDF5, ProgressWriter) - Static method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5

writeSpimData(ViewId, StorageFormat, long[], URI, URI, AllenOMEZarrLoader.OMEZARREntry, SpimData2Tools.InstantiateViewSetup) - Static method in class net.preibisch.mvrecon.process.n5api.SpimData2Tools

writeTIFF(SpimData, List<ViewId>, String, boolean, ProgressWriter) - Static method in class net.preibisch.mvrecon.fiji.plugin.resave.Resave_TIFF

writeXML(T, XmlIoAbstractSpimData<A, T>, Generic_Resave_HDF5.ParametersResaveHDF5, ProgressWriter) - Static method in class net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5

X

x - Variable in class net.preibisch.legacy.registration.bead.laplace.DoGMaximum

x - Variable in class net.preibisch.mvrecon.headless.definedataset.StackList.ViewSetupPrecursor

x - Variable in class net.preibisch.mvrecon.vecmath.AxisAngle4d

The x coordinate.

x - Variable in class net.preibisch.mvrecon.vecmath.AxisAngle4f

The x coordinate.

x - Variable in class net.preibisch.mvrecon.vecmath.Tuple3d

The x coordinate.

x - Variable in class net.preibisch.mvrecon.vecmath.Tuple3f

The x coordinate.

x - Variable in class net.preibisch.mvrecon.vecmath.Tuple3i

The x coordinate.

x - Variable in class net.preibisch.mvrecon.vecmath.Tuple4d

The x coordinate.

x - Variable in class net.preibisch.mvrecon.vecmath.Tuple4f

The x coordinate.

X - Variable in class net.preibisch.legacy.registration.bead.laplace.DoGMaximum

X_Axis - Enum constant in enum class net.preibisch.mvrecon.headless.definedataset.DefineDataSetParameters.RotationAxis

X_TILES_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoSmartSPIMImgLoader

xd - Variable in class net.preibisch.legacy.registration.bead.laplace.DoGMaximum

xml - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

xml() - Method in interface net.preibisch.mvrecon.fiji.spimdata.explorer.ExplorerWindow

xml() - Method in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

xmlFileName - Variable in class net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML

xmlFilenameToFullPath(AbstractSpimData<?>, String) - Static method in class util.URITools

XmlIoAllenOMEZarrLoader - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

XmlIoAllenOMEZarrLoader() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoAllenOMEZarrLoader

XmlIoBoundingBoxes - Class in net.preibisch.mvrecon.fiji.spimdata.boundingbox

XmlIoBoundingBoxes() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.boundingbox.XmlIoBoundingBoxes

XmlIoDHMImgLoader - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

XmlIoDHMImgLoader() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoDHMImgLoader

XmlIoFileListImgLoaderLOCI - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

XmlIoFileListImgLoaderLOCI() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoFileListImgLoaderLOCI

XmlIOFileMapImgLoaderLOCI2 - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2

XmlIOFileMapImgLoaderLOCI2() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.XmlIOFileMapImgLoaderLOCI2

XmlIoFlatfieldCorrectedWrappedImgLoader - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield

XmlIoFlatfieldCorrectedWrappedImgLoader() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.XmlIoFlatfieldCorrectedWrappedImgLoader

XmlIoFlatfieldCorrectedWrappedImgLoaderMR - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield

Dummy class so we can use XmlIoFlatfieldCorrectedWrappedImgLoader for both multiresolution and non-multiresolution ImgLoaders with flatfield correction

XmlIoFlatfieldCorrectedWrappedImgLoaderMR() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.flatfield.XmlIoFlatfieldCorrectedWrappedImgLoaderMR

XmlIoIntensityAdjustments - Class in net.preibisch.mvrecon.fiji.spimdata.intensityadjust

XmlIoIntensityAdjustments() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.intensityadjust.XmlIoIntensityAdjustments

XmlIoLightSheetZ1ImgLoader - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

XmlIoLightSheetZ1ImgLoader() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoLightSheetZ1ImgLoader

XmlIoMicroManagerImgLoader - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

XmlIoMicroManagerImgLoader() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoMicroManagerImgLoader

XmlIoPointSpreadFunctions - Class in net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions

XmlIoPointSpreadFunctions() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions.XmlIoPointSpreadFunctions

XmlIoSimViewImgLoader - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

XmlIoSimViewImgLoader() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoSimViewImgLoader

XmlIoSmartSPIMImgLoader - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

XmlIoSmartSPIMImgLoader() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoSmartSPIMImgLoader

XmlIoSpimData2 - Class in net.preibisch.mvrecon.fiji.spimdata

XmlIoSpimData2() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.XmlIoSpimData2

XmlIoSplitImgLoader - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting

XmlIoSplitImgLoader() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.XmlIoSplitImgLoader

XmlIoSplitMultiResolutionImgLoader - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting

XmlIoSplitMultiResolutionImgLoader() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.XmlIoSplitMultiResolutionImgLoader

XmlIoSplitViewerImgLoader - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting

XmlIoSplitViewerImgLoader() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.splitting.XmlIoSplitViewerImgLoader

XmlIoStackImgLoader<T> - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

XmlIoStackImgLoader() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoStackImgLoader

XmlIoStackImgLoaderIJ - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

XmlIoStackImgLoaderIJ() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoStackImgLoaderIJ

XmlIoStackImgLoaderLOCI - Class in net.preibisch.mvrecon.fiji.spimdata.imgloaders

XmlIoStackImgLoaderLOCI() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoStackImgLoaderLOCI

XmlIoStitchingResults - Class in net.preibisch.mvrecon.fiji.spimdata.stitchingresults

XmlIoStitchingResults() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.XmlIoStitchingResults

XmlIoViewInterestPoints - Class in net.preibisch.mvrecon.fiji.spimdata.interestpoints

XmlIoViewInterestPoints() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.interestpoints.XmlIoViewInterestPoints

XmlKeysBoundingBox - Class in net.preibisch.mvrecon.fiji.spimdata.boundingbox

XmlKeysBoundingBox() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.boundingbox.XmlKeysBoundingBox

XmlKeysIntensityAdjustments - Class in net.preibisch.mvrecon.fiji.spimdata.intensityadjust

XmlKeysIntensityAdjustments() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.intensityadjust.XmlKeysIntensityAdjustments

XmlKeysInterestPoints - Class in net.preibisch.mvrecon.fiji.spimdata.interestpoints

XmlKeysInterestPoints() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.interestpoints.XmlKeysInterestPoints

XmlKeysPointSpreadFunctions - Class in net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions

XmlKeysPointSpreadFunctions() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions.XmlKeysPointSpreadFunctions

XmlKeysStitchingResults - Class in net.preibisch.mvrecon.fiji.spimdata.stitchingresults

XmlKeysStitchingResults() - Constructor for class net.preibisch.mvrecon.fiji.spimdata.stitchingresults.XmlKeysStitchingResults

xmlLabel - Variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel

xmlPath - Variable in class net.preibisch.mvrecon.fiji.plugin.resave.Resave_TIFF.ParametersResaveAsTIFF

XMLSaveAs - Class in net.preibisch.mvrecon.fiji.plugin

XMLSaveAs() - Constructor for class net.preibisch.mvrecon.fiji.plugin.XMLSaveAs

xmlURI - Variable in class net.preibisch.mvrecon.fiji.plugin.resave.ParametersResaveN5Api

xPos - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorer

xPosLog - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorer

xTileLocations - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM.SmartSPIMMetaData

xyRes - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM.SmartSPIMMetaData

xzLevel - Static variable in class net.preibisch.mvrecon.fiji.plugin.util.PluginHelper

Y

y - Variable in class net.preibisch.legacy.registration.bead.laplace.DoGMaximum

y - Variable in class net.preibisch.mvrecon.vecmath.AxisAngle4d

The y coordinate.

y - Variable in class net.preibisch.mvrecon.vecmath.AxisAngle4f

The y coordinate.

y - Variable in class net.preibisch.mvrecon.vecmath.Tuple3d

The y coordinate.

y - Variable in class net.preibisch.mvrecon.vecmath.Tuple3f

The y coordinate.

y - Variable in class net.preibisch.mvrecon.vecmath.Tuple3i

The y coordinate.

y - Variable in class net.preibisch.mvrecon.vecmath.Tuple4d

The y coordinate.

y - Variable in class net.preibisch.mvrecon.vecmath.Tuple4f

The y coordinate.

Y_Axis - Enum constant in enum class net.preibisch.mvrecon.headless.definedataset.DefineDataSetParameters.RotationAxis

Y_TILES_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoSmartSPIMImgLoader

yd - Variable in class net.preibisch.legacy.registration.bead.laplace.DoGMaximum

yPos - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorer

yPosLog - Static variable in class net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorer

yTileLocations - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM.SmartSPIMMetaData

Z

z - Variable in class net.preibisch.legacy.registration.bead.laplace.DoGMaximum

z - Variable in class net.preibisch.mvrecon.vecmath.AxisAngle4d

The z coordinate.

z - Variable in class net.preibisch.mvrecon.vecmath.AxisAngle4f

The z coordinate.

z - Variable in class net.preibisch.mvrecon.vecmath.Tuple3d

The z coordinate.

z - Variable in class net.preibisch.mvrecon.vecmath.Tuple3f

The z coordinate.

z - Variable in class net.preibisch.mvrecon.vecmath.Tuple3i

The z coordinate.

z - Variable in class net.preibisch.mvrecon.vecmath.Tuple4d

The z coordinate.

z - Variable in class net.preibisch.mvrecon.vecmath.Tuple4f

The z coordinate.

Z_Axis - Enum constant in enum class net.preibisch.mvrecon.headless.definedataset.DefineDataSetParameters.RotationAxis

Z_LAYERS - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoSmartSPIMImgLoader

Z_OFFSETS_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoSmartSPIMImgLoader

Z_VARIABLE_CHOICE - Static variable in class net.preibisch.mvrecon.fiji.datasetmanager.FileListDatasetDefinition

ZARR_V2_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoAllenOMEZarrLoader

ZARR_V3_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoAllenOMEZarrLoader

zd - Variable in class net.preibisch.legacy.registration.bead.laplace.DoGMaximum

ZERO - Enum constant in enum class net.preibisch.mvrecon.process.cuda.CUDASeparableConvolutionFunctions.OutOfBounds

ZERO - Static variable in class net.preibisch.mvrecon.vecmath.Transform3D

A zero matrix.

zGrouped - Variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.FileMapImgLoaderLOCI

ZGROUPED_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.XmlIOFileMapImgLoaderLOCI2

ZGROUPED_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoFileListImgLoaderLOCI

zOffsets - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM.SmartSPIMMetaData

ZPLANES_TAG - Static variable in class net.preibisch.mvrecon.fiji.spimdata.imgloaders.XmlIoDHMImgLoader

zRes - Variable in class net.preibisch.mvrecon.fiji.datasetmanager.SmartSPIM.SmartSPIMMetaData

zstdLevel - Static variable in class net.preibisch.mvrecon.fiji.plugin.util.PluginHelper

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