- a - Variable in class edu.utexas.clm.archipelago.data.Duplex
-
- A(int[], int) - Static method in class fiji.threshold.Auto_Threshold
-
- a - Variable in class fiji.util.Levenshtein
-
- a - Variable in class ini.trakem2.display.Tree.Pair
-
Two nodes of a tree; there is a unique path that goes from a to b.
- a - Variable in class math3d.Triangle
-
- a - Variable in class mpicbg.models.InterpolatedCoordinateTransform
-
- a - Variable in class mpicbg.models.InterpolatedModel
-
- a - Variable in class mpicbg.models.PolynomialTransform2D
-
holds two coefficients for each polynomial coefficient, including 1
initialized at 0 order, i.e.
- A - Variable in class mpicbg.spim.registration.bead.laplace.DoGMaximum
-
- a - Variable in class mpicbg.trakem2.transform.ExportUnsignedShort.PatchIntensityRange
-
- a - Variable in class mpicbg.trakem2.util.Downsampler.Pair
-
- a - Variable in class mpicbg.trakem2.util.Pair
-
- a - Variable in class mpicbg.trakem2.util.Triple
-
- A - Variable in class net.imglib2.display.ARGBARGBColorConverter
-
- A - Variable in class net.imglib2.display.ARGBtoRandomARGBColorConverter
-
- a - Variable in class sc.fiji.timelapse.LinearRegression
-
- a() - Method in class script.imglib.math.fn.BinaryOperation
-
- a() - Method in class script.imglib.math.fn.UnaryOperation
-
Call a().eval() to obtain the result as a double of the computation encapsulated by the @field a.
- a - Variable in class spim.fiji.datasetmanager.StackList.ViewSetupPrecursor
-
- a00 - Variable in class vib.FastMatrix
-
- a00 - Variable in class vib.FloatMatrix
-
- a01 - Variable in class vib.FastMatrix
-
- a01 - Variable in class vib.FloatMatrix
-
- a02 - Variable in class vib.FastMatrix
-
- a02 - Variable in class vib.FloatMatrix
-
- a03 - Variable in class vib.FastMatrix
-
- a03 - Variable in class vib.FloatMatrix
-
- a10 - Variable in class vib.FastMatrix
-
- a10 - Variable in class vib.FloatMatrix
-
- a11 - Variable in class vib.FastMatrix
-
- a11 - Variable in class vib.FloatMatrix
-
- a12 - Variable in class vib.FastMatrix
-
- a12 - Variable in class vib.FloatMatrix
-
- a13 - Variable in class vib.FastMatrix
-
- a13 - Variable in class vib.FloatMatrix
-
- a20 - Variable in class vib.FastMatrix
-
- a20 - Variable in class vib.FloatMatrix
-
- a21 - Variable in class vib.FastMatrix
-
- a21 - Variable in class vib.FloatMatrix
-
- a22 - Variable in class vib.FastMatrix
-
- a22 - Variable in class vib.FloatMatrix
-
- a23 - Variable in class vib.FastMatrix
-
- a23 - Variable in class vib.FloatMatrix
-
- A_Image5D_test - Class in sc.fiji.i5d.plugin
-
- A_Image5D_test() - Constructor for class sc.fiji.i5d.plugin.A_Image5D_test
-
- abort() - Method in class bdv.tools.bookmarks.BookmarksEditor
-
- abort() - Method in class bdv.tools.transformation.ManualTransformationEditor
-
- abort() - Method in class ini.trakem2.display.FreeHandProfile
-
for abort (ESC pressed for instance)
- abortCurrentOperation() - Method in class sc.fiji.snt.SNTUI
-
- About - Class in loci.plugins
-
Displays a small information dialog about the Bio-Formats Plugins package.
- About() - Constructor for class loci.plugins.About
-
- about() - Static method in class loci.plugins.About
-
- About_RATS - Class in <Unnamed>
-
- About_RATS() - Constructor for class About_RATS
-
- AboutDialog - Class in org.imagearchive.lsm.toolbox.gui
-
- AboutDialog(JFrame, MasterModel) - Constructor for class org.imagearchive.lsm.toolbox.gui.AboutDialog
-
- AboutDialog() - Constructor for class org.imagearchive.lsm.toolbox.gui.AboutDialog
-
- aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.ActionChooserDescriptor
-
- aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.ConfigureViewsDescriptor
-
- aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.DetectionDescriptor
-
- aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.DetectorChoiceDescriptor
-
- aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.DetectorConfigurationDescriptor
-
- aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.GrapherDescriptor
-
- aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.InitFilterDescriptor
-
- aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.LogPanelDescriptor
-
- aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.SomeDialogDescriptor
-
- aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.SpotFilterDescriptor
-
- aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.StartDialogDescriptor
-
- aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.TrackerChoiceDescriptor
-
- aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.TrackerConfigurationDescriptor
-
- aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.TrackFilterDescriptor
-
- aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.TrackingDescriptor
-
- aboutToDisplayPanel() - Method in class fiji.plugin.trackmate.gui.descriptors.ViewChoiceDescriptor
-
- aboutToDisplayPanel() - Method in interface fiji.plugin.trackmate.gui.descriptors.WizardPanelDescriptor
-
This method is used to provide functionality that will be performed just
before the panel is to be displayed.
- aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.ActionChooserDescriptor
-
- aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.ConfigureViewsDescriptor
-
- aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.DetectionDescriptor
-
- aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.DetectorChoiceDescriptor
-
- aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.DetectorConfigurationDescriptor
-
- aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.GrapherDescriptor
-
- aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.InitFilterDescriptor
-
- aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.LogPanelDescriptor
-
- aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.SomeDialogDescriptor
-
- aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.SpotFilterDescriptor
-
- aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.StartDialogDescriptor
-
- aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.TrackerChoiceDescriptor
-
- aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.TrackerConfigurationDescriptor
-
- aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.TrackFilterDescriptor
-
- aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.TrackingDescriptor
-
- aboutToHidePanel() - Method in class fiji.plugin.trackmate.gui.descriptors.ViewChoiceDescriptor
-
- aboutToHidePanel() - Method in interface fiji.plugin.trackmate.gui.descriptors.WizardPanelDescriptor
-
This method is used to perform functionality just before the panel is to
be hidden.
- aboveThresholdLengthAlong(PrincipalComponents, int, ImagePlus, Threshold) - Method in class vib.oldregistration.PCA_Registration
-
- Abs(int[]) - Method in class GrayMorphology_
-
Calculates the absolute value of an array
- Abs - Class in imglib.ops.operator.unary
-
TODO
- Abs() - Constructor for class imglib.ops.operator.unary.Abs
-
- abs() - Method in class loci.plugins.util.RecordedImageProcessor
-
- Abs - Class in script.imglib.math
-
TODO
- Abs(Image<? extends RealType<?>>) - Constructor for class script.imglib.math.Abs
-
- Abs(IFunction) - Constructor for class script.imglib.math.Abs
-
- Abs(Number) - Constructor for class script.imglib.math.Abs
-
- ABS_PATH - Static variable in class ini.trakem2.persistence.FSLoader
-
- absFreq - Variable in class mpicbg.spim.fusion.entropy.Entropy
-
- absFreq - Variable in class mpicbg.spim.fusion.entropy.EntropyFloatArray3D
-
- absolute(Tuple3d) - Method in class spim.vecmath.Tuple3d
-
Sets each component of the tuple parameter to its absolute value and
places the modified values into this tuple.
- absolute() - Method in class spim.vecmath.Tuple3d
-
Sets each component of this tuple to its absolute value.
- absolute(Tuple3f) - Method in class spim.vecmath.Tuple3f
-
Sets each component of the tuple parameter to its absolute value and
places the modified values into this tuple.
- absolute() - Method in class spim.vecmath.Tuple3f
-
Sets each component of this tuple to its absolute value.
- absolute(Tuple3i) - Method in class spim.vecmath.Tuple3i
-
Sets each component of the tuple parameter to its absolute value and
places the modified values into this tuple.
- absolute() - Method in class spim.vecmath.Tuple3i
-
Sets each component of this tuple to its absolute value.
- absolute(Tuple4d) - Method in class spim.vecmath.Tuple4d
-
Sets each component of the tuple parameter to its absolute value and
places the modified values into this tuple.
- absolute() - Method in class spim.vecmath.Tuple4d
-
Sets each component of this tuple to its absolute value.
- absolute(Tuple4f) - Method in class spim.vecmath.Tuple4f
-
Sets each component of the tuple parameter to its absolute value and
places the modified values into this tuple.
- absolute() - Method in class spim.vecmath.Tuple4f
-
Sets each component of this tuple to its absolute value.
- AbsoluteFloatComparator() - Constructor for class fiji.features.Frangi_.AbsoluteFloatComparator
-
- absoluteThreshold - Variable in class mpicbg.stitching.StitchingParameters
-
- AbstractAffine3D<T extends NumericType<T>> - Class in script.imglib.algorithm.fn
-
TODO
- AbstractAffine3D(Image<T>, float[], AbstractAffine3D.Mode, Number) - Constructor for class script.imglib.algorithm.fn.AbstractAffine3D
-
- AbstractAffine3D(Image<T>, float[], AbstractAffine3D.Mode, OutOfBoundsStrategyFactory<T>) - Constructor for class script.imglib.algorithm.fn.AbstractAffine3D
-
- AbstractAffine3D(Image<T>, float, float, float, float, float, float, AbstractAffine3D.Mode, Number) - Constructor for class script.imglib.algorithm.fn.AbstractAffine3D
-
- AbstractAffine3D(Image<T>, float, float, float, float, float, float, AbstractAffine3D.Mode, OutOfBoundsStrategyFactory<T>) - Constructor for class script.imglib.algorithm.fn.AbstractAffine3D
-
- AbstractAffine3D.Mode - Enum in script.imglib.algorithm.fn
-
- AbstractAffineModel1D<M extends AbstractAffineModel1D<M>> - Class in mpicbg.models
-
- AbstractAffineModel1D() - Constructor for class mpicbg.models.AbstractAffineModel1D
-
- AbstractAffineModel2D<M extends AbstractAffineModel2D<M>> - Class in mpicbg.models
-
- AbstractAffineModel2D() - Constructor for class mpicbg.models.AbstractAffineModel2D
-
- AbstractAffineModel3D<M extends AbstractAffineModel3D<M>> - Class in mpicbg.models
-
- AbstractAffineModel3D() - Constructor for class mpicbg.models.AbstractAffineModel3D
-
- AbstractAffineModelChunk - Class in edu.utexas.clm.archipelago.ijsupport
-
- AbstractAffineModelChunk(AbstractAffineModel2D<?>) - Constructor for class edu.utexas.clm.archipelago.ijsupport.AbstractAffineModelChunk
-
- AbstractAffineTile2D<A extends Model<A> & Affine2D<A>> - Class in mpicbg.trakem2.align
-
- AbstractAffineTile2D(A, Patch) - Constructor for class mpicbg.trakem2.align.AbstractAffineTile2D
-
- AbstractAnimator - Class in bdv.viewer.animate
-
Mother abstract class for animators that can animate the current view in a
ViewerFrame
instance.
- AbstractAnimator(long) - Constructor for class bdv.viewer.animate.AbstractAnimator
-
Create new animator with the given duration.
- AbstractAnnotation - Class in fiji.util.gui
-
- AbstractAnnotation() - Constructor for class fiji.util.gui.AbstractAnnotation
-
- AbstractBlockFilter - Class in mpicbg.ij.plugin
-
Abstract base class for variance and STD filters.
- AbstractBlockFilter() - Constructor for class mpicbg.ij.plugin.AbstractBlockFilter
-
- AbstractBlockMatching - Class in mpicbg.ij.plugin
-
- AbstractBlockMatching() - Constructor for class mpicbg.ij.plugin.AbstractBlockMatching
-
- AbstractBlockStatistics - Class in mpicbg.ij.plugin
-
Abstract base class for variance and STD filters.
- AbstractBlockStatistics() - Constructor for class mpicbg.ij.plugin.AbstractBlockStatistics
-
- AbstractCachedViewerSetupImgLoader<T extends NativeType<T>,V extends Volatile<T> & NativeType<V>,A extends VolatileAccess> - Class in bdv
-
- AbstractCachedViewerSetupImgLoader(int, long[][], int[][], double[][], T, V, CacheArrayLoader<A>, VolatileGlobalCellCache) - Constructor for class bdv.AbstractCachedViewerSetupImgLoader
-
- AbstractCorrelationFit - Class in org.janelia.thickness.inference.fits
-
- AbstractCorrelationFit() - Constructor for class org.janelia.thickness.inference.fits.AbstractCorrelationFit
-
- AbstractDetection<T extends AbstractDetection<T>> - Class in mpicbg.spim.registration.detection
-
- AbstractDetection(int, double[]) - Constructor for class mpicbg.spim.registration.detection.AbstractDetection
-
- AbstractDetection(int, double[], double) - Constructor for class mpicbg.spim.registration.detection.AbstractDetection
-
- AbstractFeatureGrapher - Class in fiji.plugin.trackmate.features
-
- AbstractFeatureGrapher(String, Set<String>, Model) - Constructor for class fiji.plugin.trackmate.features.AbstractFeatureGrapher
-
- AbstractImgFactoryImgLoader - Class in spim.fiji.spimdata.imgloaders
-
- AbstractImgFactoryImgLoader() - Constructor for class spim.fiji.spimdata.imgloaders.AbstractImgFactoryImgLoader
-
- AbstractImgLoader - Class in spim.fiji.spimdata.imgloaders
-
- AbstractImgLoader() - Constructor for class spim.fiji.spimdata.imgloaders.AbstractImgLoader
-
- AbstractInteractiveBlockFilter - Class in mpicbg.ij.integral
-
- AbstractInteractiveBlockFilter() - Constructor for class mpicbg.ij.integral.AbstractInteractiveBlockFilter
-
- AbstractInteractiveBlockFilter.PaintThread - Class in mpicbg.ij.integral
-
- AbstractLayerAlignmentParam - Class in mpicbg.trakem2.align
-
- AbstractLayerAlignmentParam() - Constructor for class mpicbg.trakem2.align.AbstractLayerAlignmentParam
-
- AbstractLayerAlignmentParam(int, int, float, int, int, int, boolean, int, float, int, int, float, float, int, int, int, int, int, float, int, boolean, boolean, boolean, boolean) - Constructor for class mpicbg.trakem2.align.AbstractLayerAlignmentParam
-
- AbstractLegacyViewerImgLoader<T,V extends Volatile<T>> - Class in bdv.spimdata.legacy
-
- AbstractLegacyViewerImgLoader(T, V) - Constructor for class bdv.spimdata.legacy.AbstractLegacyViewerImgLoader
-
- AbstractLUTGrid - Class in org.janelia.thickness.lut
-
- AbstractLUTGrid(int, int, RandomAccessibleInterval<DoubleType>) - Constructor for class org.janelia.thickness.lut.AbstractLUTGrid
-
- AbstractLUTGrid(int, int, RandomAccessibleInterval<DoubleType>, double[], double[]) - Constructor for class org.janelia.thickness.lut.AbstractLUTGrid
-
- AbstractLUTRealTransform - Class in org.janelia.thickness.lut
-
Abstract base class for LUT based transforms.
- AbstractLUTRealTransform(double[], int, int) - Constructor for class org.janelia.thickness.lut.AbstractLUTRealTransform
-
- AbstractLUTRealTransformField - Class in org.janelia.thickness.lut
-
Abstract base class for LUT based transforms in 2D fields.
- AbstractLUTRealTransformField(double[], int, int, long...) - Constructor for class org.janelia.thickness.lut.AbstractLUTRealTransformField
-
- AbstractLUTRealTransformField(int, int, RandomAccessibleInterval<DoubleType>) - Constructor for class org.janelia.thickness.lut.AbstractLUTRealTransformField
-
- AbstractMappingThread(ImagePlus, ImagePlus, ImageProcessor) - Constructor for class mpicbg.panorama.AbstractPanorama_View.AbstractMappingThread
-
- AbstractModel<M extends AbstractModel<M>> - Class in mpicbg.models
-
Abstract class for arbitrary transformation models to be applied
to
Points
in n-dimensional space.
- AbstractModel() - Constructor for class mpicbg.models.AbstractModel
-
- AbstractMovingLeastSquaresTransform - Class in mpicbg.models
-
Smooth coordinate transformation interpolating between a set of control
points that are maped exactly on top of each other using landmark based deformation by means
of Moving Least Squares as described by \citet{SchaeferAl06}.
- AbstractMovingLeastSquaresTransform() - Constructor for class mpicbg.models.AbstractMovingLeastSquaresTransform
-
- AbstractNormalize<T extends NumericType<T>> - Class in script.imglib.algorithm.fn
-
TODO
- AbstractNormalize(Image<T>) - Constructor for class script.imglib.algorithm.fn.AbstractNormalize
-
- AbstractOffscreenThread - Class in ini.trakem2.display
-
To be used in combination with the AbstractRepaintThread, as a thread to create graphics offscreen.
- AbstractOffscreenThread.RepaintProperties - Interface in ini.trakem2.display
-
- AbstractPanorama_View - Class in mpicbg.panorama
-
- AbstractPanorama_View() - Constructor for class mpicbg.panorama.AbstractPanorama_View
-
- AbstractPanorama_View.AbstractMappingThread - Class in mpicbg.panorama
-
- AbstractPanorama_View.GUI - Class in mpicbg.panorama
-
- AbstractPanorama_View.Mapper - Class in mpicbg.panorama
-
- AbstractPerumtationTransform - Class in org.janelia.thickness.lut
-
Bijective integer transform mapping between integer coordinates in [0,n-1].
- AbstractPerumtationTransform(int[]) - Constructor for class org.janelia.thickness.lut.AbstractPerumtationTransform
-
- AbstractPointDescriptor<P extends Point,F extends AbstractPointDescriptor<P,F>> - Class in mpicbg.pointdescriptor
-
- AbstractPointDescriptor(P, ArrayList<P>, SimilarityMeasure, Matcher) - Constructor for class mpicbg.pointdescriptor.AbstractPointDescriptor
-
- AbstractPointEdit - Class in bigwarp.landmarks.actions
-
- AbstractPointEdit(LandmarkTableModel) - Constructor for class bigwarp.landmarks.actions.AbstractPointEdit
-
- AbstractProvider<K extends TrackMateModule> - Class in fiji.plugin.trackmate.providers
-
- AbstractProvider(Class<K>) - Constructor for class fiji.plugin.trackmate.providers.AbstractProvider
-
- AbstractRegionalExtremaFinder<T extends RealType<T>> - Class in mpicbg.imglib.algorithm.extremafinder
-
TODO
- AbstractRegionalExtremaFinder() - Constructor for class mpicbg.imglib.algorithm.extremafinder.AbstractRegionalExtremaFinder
-
- AbstractRepaintThread - Class in ini.trakem2.display
-
- AbstractRepaintThread(Component, String, AbstractOffscreenThread) - Constructor for class ini.trakem2.display.AbstractRepaintThread
-
- AbstractSemiAutoTracker<T extends RealType<T> & NativeType<T>> - Class in fiji.plugin.trackmate.detection.semiauto
-
A class made to perform semi-automated tracking of spots in TrackMate &
friends
- AbstractSemiAutoTracker(Model, SelectionModel, Logger) - Constructor for class fiji.plugin.trackmate.detection.semiauto.AbstractSemiAutoTracker
-
- AbstractSemiAutoTracker.SearchRegion<R> - Class in fiji.plugin.trackmate.detection.semiauto
-
A utility class made to return the information on a neighborhood
generated from a source around a
Spot
.
- AbstractSequenceDescription<V extends BasicViewSetup,D extends BasicViewDescription<V>,L extends BasicImgLoader> - Class in mpicbg.spim.data.generic.sequence
-
A SPIM sequence consisting of a list of timepoints and a list of view setups.
- AbstractSequenceDescription(TimePoints, Map<Integer, ? extends V>, L, MissingViews) - Constructor for class mpicbg.spim.data.generic.sequence.AbstractSequenceDescription
-
- AbstractSequenceDescription() - Constructor for class mpicbg.spim.data.generic.sequence.AbstractSequenceDescription
-
- AbstractSequenceDescriptionUtils - Class in mpicbg.spim.data.generic.sequence
-
- AbstractSequenceDescriptionUtils() - Constructor for class mpicbg.spim.data.generic.sequence.AbstractSequenceDescriptionUtils
-
- AbstractSortedGrayLevelIterator<T extends IntegerType<T>> - Class in mpicbg.imglib.cursor.special
-
Iterate over all pixels ordered by their gray level
- AbstractSortedGrayLevelIterator(Image<T>) - Constructor for class mpicbg.imglib.cursor.special.AbstractSortedGrayLevelIterator
-
- AbstractSource<T extends NumericType<T>> - Class in bdv.util
-
- AbstractSource(T, String, VoxelDimensions) - Constructor for class bdv.util.AbstractSource
-
- AbstractSource(T, String) - Constructor for class bdv.util.AbstractSource
-
- AbstractSource(Supplier<T>, String) - Constructor for class bdv.util.AbstractSource
-
- AbstractSpecialCursor<T extends Type<T>> - Class in mpicbg.imglib.cursor.special
-
This abstract cursor offer facilities for specialized cursor that are based
on a
LocalizableByDimCursor
whose iteration domain is imposed.
- AbstractSpecialCursor() - Constructor for class mpicbg.imglib.cursor.special.AbstractSpecialCursor
-
- AbstractSpimData<S extends AbstractSequenceDescription<?,?,?>> - Class in mpicbg.spim.data.generic
-
- AbstractSpimData(File, S, ViewRegistrations) - Constructor for class mpicbg.spim.data.generic.AbstractSpimData
-
- AbstractSpimData() - Constructor for class mpicbg.spim.data.generic.AbstractSpimData
-
- AbstractSpimSource<T extends NumericType<T>> - Class in bdv
-
- AbstractSpimSource(AbstractSpimData<?>, int, String) - Constructor for class bdv.AbstractSpimSource
-
- AbstractSpimSource.ImgKey - Class in bdv
-
- AbstractStampFormat(String[], String, boolean, boolean, boolean) - Constructor for class Series_Labeler.AbstractStampFormat
-
- AbstractTMAction - Class in fiji.plugin.trackmate.action
-
- AbstractTMAction() - Constructor for class fiji.plugin.trackmate.action.AbstractTMAction
-
- AbstractTool - Class in fiji.tool
-
- AbstractTool() - Constructor for class fiji.tool.AbstractTool
-
- AbstractTool.KeyProxy - Class in fiji.tool
-
- AbstractTool.KeyProxyIfNotConsumed - Class in fiji.tool
-
- AbstractTool.MouseMotionProxy - Class in fiji.tool
-
- AbstractTool.MouseMotionProxyIfNotConsumed - Class in fiji.tool
-
- AbstractTool.MouseProxy - Class in fiji.tool
-
- AbstractTool.MouseWheelProxy - Class in fiji.tool
-
- AbstractTool.MouseWheelProxyIfNotConsumed - Class in fiji.tool
-
- AbstractTool.ToolbarMouseAdapter - Class in fiji.tool
-
This class is used to monitor tool toggles and double-clicks on the toolbar icon of this concrete tool.
- AbstractTrackingTool - Class in fiji.tool
-
- AbstractTrackingTool() - Constructor for class fiji.tool.AbstractTrackingTool
-
- AbstractTrackMateModelView - Class in fiji.plugin.trackmate.visualization
-
An abstract class for spot displayers, that can overlay detected spots and
tracks on top of the image data.
- AbstractTrackMateModelView(Model, SelectionModel) - Constructor for class fiji.plugin.trackmate.visualization.AbstractTrackMateModelView
-
- AbstractTransformAnimator - Class in bdv.viewer.animate
-
Mother abstract class for animators that animate the current view in a
ViewerFrame
instance by modifying the viewer transform.
- AbstractTransformAnimator(long) - Constructor for class bdv.viewer.animate.AbstractTransformAnimator
-
Create new animator with the given duration.
- AbstractTransformedBoxModel - Class in bdv.tools.boundingbox
-
A transformed box that can be modified and notifies listeners about changes.
- AbstractTransformedBoxModel(AffineTransform3D) - Constructor for class bdv.tools.boundingbox.AbstractTransformedBoxModel
-
- AbstractTransformedBoxModel.IntervalChangedListener - Interface in bdv.tools.boundingbox
-
- AbstractTransformedBoxSelectionDialog<R> - Class in bdv.tools.boundingbox
-
- AbstractTransformedBoxSelectionDialog(Window, String) - Constructor for class bdv.tools.boundingbox.AbstractTransformedBoxSelectionDialog
-
- AbstractTransformedBoxSelectionDialog.OkCancelPanel - Class in bdv.tools.boundingbox
-
A panel containing OK and Cancel buttons, and callback lists for both.
- AbstractTransformedBoxSelectionDialog.TimepointSelectionPanel - Class in bdv.tools.boundingbox
-
A panel that contains sliders to adjust timepoint, timepoint range, or
nothing.
- AbstractTransformMapping<T> - Class in mpicbg.ij.stack
-
Abstract base class
Mapping
from an source
into an target.
- AbstractTransformMapping(T) - Constructor for class mpicbg.ij.stack.AbstractTransformMapping
-
- AbstractTransformMapping.ByteInterpolator - Class in mpicbg.ij.stack
-
- AbstractTransformMapping.FloatInterpolator - Class in mpicbg.ij.stack
-
- AbstractTransformMapping.Interpolator - Class in mpicbg.ij.stack
-
- AbstractTransformMapping.RGBInterpolator - Class in mpicbg.ij.stack
-
- AbstractTransformMapping.ShortInterpolator - Class in mpicbg.ij.stack
-
- AbstractTreeTransferHandler - Class in ini.trakem2.tree
-
- AbstractTreeTransferHandler(DNDTree, int, boolean) - Constructor for class ini.trakem2.tree.AbstractTreeTransferHandler
-
- AbstractVector<V extends AbstractVector<V>> - Class in mpicbg.imglib.cursor.vector
-
TODO
- AbstractVector(Dimensionality) - Constructor for class mpicbg.imglib.cursor.vector.AbstractVector
-
- AbstractVector(int) - Constructor for class mpicbg.imglib.cursor.vector.AbstractVector
-
- AbstractViewerSetupImgLoader<T,V extends Volatile<T>> - Class in bdv
-
- AbstractViewerSetupImgLoader(T, V) - Constructor for class bdv.AbstractViewerSetupImgLoader
-
- accept(File) - Method in class fiji.plugin.trackmate.util.DefaultFileFilter
-
Returns true if file
is a directory or ends with the
specified extension.
- accept(File) - Method in class fiji.plugin.trackmate.util.DefaultFileFilter.EditorFileFilter
-
Returns true if the file is a directory or has a .xml or .xml.gz
extension.
- accept(File) - Method in class fiji.plugin.trackmate.util.DefaultFileFilter.ImageFileFilter
-
Returns true if the file is a directory or ends with a known image
extension.
- accept(File) - Method in class fsalign.FolderWatcher.FolderFilter
-
- accept(Node<I>) - Method in class ini.trakem2.display.Node.BranchAndEndNodeIterator
-
- accept(Node<I>) - Method in class ini.trakem2.display.Node.BranchNodeIterator
-
- accept(Node<I>) - Method in class ini.trakem2.display.Node.EndNodeIterator
-
- accept(Node<I>) - Method in class ini.trakem2.display.Node.FilteredIterator
-
- accept(File, String) - Method in class ini.trakem2.io.ImageFileFilter
-
- accept(File, String) - Method in class ini.trakem2.io.XMLFileFilter
-
- accept(T) - Method in interface ini.trakem2.utils.Filter
-
- accept(File) - Method in class org.imagearchive.lsm.toolbox.gui.AllKnownFilter
-
- accept(File) - Method in class org.imagearchive.lsm.toolbox.gui.BatchFilter
-
- accept(File) - Method in class org.imagearchive.lsm.toolbox.gui.ImageFilter
-
- accept(BytePointer, int, int, int) - Method in class org.janelia.it.jacs.shared.ffmpeg.ByteGatherAcceptor
-
Accept one "page" of data, of width x height given, and with linesize
bytes on each line of the page.
- accept(byte[], int, int, int) - Method in class org.janelia.it.jacs.shared.ffmpeg.ByteGatherAcceptor
-
Accept one "page" of data, of width x height given, and with linesize
bytes on each line of the page.
- accept(BytePointer, int, int, int) - Method in interface org.janelia.it.jacs.shared.ffmpeg.FFMPGByteAcceptor
-
- accept(byte[], int, int, int) - Method in interface org.janelia.it.jacs.shared.ffmpeg.FFMPGByteAcceptor
-
- accept(byte[], int, int, int) - Method in interface org.janelia.it.jacs.shared.ffmpeg.H5JLoader.DataAcceptor
-
- accept(BytePointer, int, int, int) - Method in class org.janelia.it.jacs.shared.ffmpeg.PPMFileAcceptor
-
- accept(byte[], int, int, int) - Method in class org.janelia.it.jacs.shared.ffmpeg.PPMFileAcceptor
-
- accept(File) - Method in class org.siox.example.ExtensionFileFilter
-
Whether the given file is regular file with recognized extension or a
directory.
- accept(T, T) - Method in class sc.fiji.coloc.algorithms.Accumulator
-
- acceptingNodes() - Method in class edu.utexas.clm.archipelago.Cluster
-
- accepts(Object) - Method in class edu.utexas.clm.archipelago.ijsupport.bottle.LayerBottler
-
- accepts(Object) - Method in class edu.utexas.clm.archipelago.ijsupport.bottle.PatchBottler
-
- accepts(Object) - Method in class edu.utexas.clm.archipelago.ijsupport.bottle.PointBottler
-
- accepts(Object) - Method in class edu.utexas.clm.archipelago.ijsupport.bottle.SIFTParamBottler
-
- accepts(Object) - Method in interface edu.utexas.clm.archipelago.network.translation.Bottler
-
Return true if this Bottler accepts the given Object.
- accepts(Object) - Method in class edu.utexas.clm.archipelago.network.translation.FileBottler
-
- Access() - Constructor for class bdv.tools.boundingbox.BoxRealRandomAccessible.Access
-
- Access(BoxRealRandomAccessible<T>.Access) - Constructor for class bdv.tools.boundingbox.BoxRealRandomAccessible.Access
-
- access - Variable in class mpicbg.imglib.labeling.LabelingType
-
- access - Variable in class org.janelia.thickness.lut.AbstractLUTGrid
-
- access - Variable in class org.janelia.thickness.lut.AbstractLUTRealTransformField
-
- accessible - Variable in class bdv.util.RealRandomAccessibleSource
-
- accessor - Variable in class mpicbg.imglib.cursor.dynamic.DynamicCursor
-
- accessToValidImageData() - Method in class sc.fiji.snt.SNT
-
- accumulate(Cursor<? extends A>[], B) - Method in class bdv.viewer.render.AccumulateProjector
-
- accumulate(Cursor<? extends ARGBType>[], ARGBType) - Method in class bdv.viewer.render.AccumulateProjectorARGB
-
- accumulate(RoiStatistics.Accessor) - Method in class fiji.statistics.RoiStatistics
-
- AccumulateProjector<A,B> - Class in bdv.viewer.render
-
- AccumulateProjector(ArrayList<VolatileProjector>, ArrayList<? extends RandomAccessible<? extends A>>, RandomAccessibleInterval<B>, int, ExecutorService) - Constructor for class bdv.viewer.render.AccumulateProjector
-
- AccumulateProjectorARGB - Class in bdv.viewer.render
-
- AccumulateProjectorARGB(ArrayList<VolatileProjector>, ArrayList<? extends RandomAccessible<? extends ARGBType>>, RandomAccessibleInterval<ARGBType>, int, ExecutorService) - Constructor for class bdv.viewer.render.AccumulateProjectorARGB
-
- accumulateProjectorFactory(AccumulateProjectorFactory<ARGBType>) - Method in class bdv.util.BdvOptions
-
- AccumulateProjectorFactory<A> - Interface in bdv.viewer.render
-
- accumulateProjectorFactory - Variable in class bdv.viewer.render.MultiResolutionRenderer
-
TODO
- accumulateProjectorFactory(AccumulateProjectorFactory<ARGBType>) - Method in class bdv.viewer.ViewerOptions
-
- accumulator - Variable in class fiji.statistics.RoiStatistics
-
- Accumulator<T extends RealType<T>> - Class in sc.fiji.coloc.algorithms
-
A class allowing an easy accumulation of values visited by a
TwinCursor.
- Accumulator(TwinCursor<T>) - Constructor for class sc.fiji.coloc.algorithms.Accumulator
-
The two values x and y from each cursor iteration to get
summed up as single values and their combinations.
- Accumulator(TwinCursor<T>, double, double) - Constructor for class sc.fiji.coloc.algorithms.Accumulator
-
The two values (x - xDiff) and (y - yDiff) from each cursor
iteration to get summed up as single values and their combinations.
- Accumulator(TwinCursor<T>, boolean, double, double) - Constructor for class sc.fiji.coloc.algorithms.Accumulator
-
- accuracy - Variable in class ini.trakem2.imaging.filters.GaussianBlur
-
- ACCURATE - Static variable in class Despeckle_
-
- ACCURATE_MODE - Static variable in class bunwarpj.MainDialog
-
accurate mode constant
- ACos - Class in script.imglib.math
-
TODO
- ACos(Image<? extends RealType<?>>) - Constructor for class script.imglib.math.ACos
-
- ACos(IFunction) - Constructor for class script.imglib.math.ACos
-
- ACos(Number) - Constructor for class script.imglib.math.ACos
-
- acronym() - Method in class sc.fiji.snt.annotation.AllenCompartment
-
- acronym() - Method in interface sc.fiji.snt.annotation.BrainAnnotation
-
- acronym() - Method in class sc.fiji.snt.annotation.InsectBrainCompartment
-
- act(int, RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, double[], int[], int[], double[], RandomAccessibleInterval<double[]>) - Method in class org.janelia.thickness.inference.visitor.CorrelationFitVisitor
-
- act(int, RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, double[], int[], int[], double[], RandomAccessibleInterval<double[]>) - Method in class org.janelia.thickness.inference.visitor.GlobalCorrelationFitVisitor
-
- act(int, RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, double[], int[], int[], double[], RandomAccessibleInterval<double[]>) - Method in class org.janelia.thickness.inference.visitor.LazyVisitor
-
- act(int, RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, double[], int[], int[], double[], RandomAccessibleInterval<double[]>) - Method in class org.janelia.thickness.inference.visitor.ListVisitor
-
- act(int, RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, double[], int[], int[], double[], RandomAccessibleInterval<double[]>) - Method in class org.janelia.thickness.inference.visitor.LUTVisitor
-
- act(int, RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, double[], int[], int[], double[], RandomAccessibleInterval<double[]>) - Method in class org.janelia.thickness.inference.visitor.MatrixVisitor
-
- act(int, RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, double[], int[], int[], double[], RandomAccessibleInterval<double[]>) - Method in class org.janelia.thickness.inference.visitor.PermutedLUTVisitor
-
- act(int, RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, double[], int[], int[], double[], RandomAccessibleInterval<double[]>) - Method in class org.janelia.thickness.inference.visitor.PermutedScalingFactorsVisitor
-
- act(int, RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, double[], int[], int[], double[], RandomAccessibleInterval<double[]>) - Method in class org.janelia.thickness.inference.visitor.ScalingFactorsVisitor
-
- act(int, RandomAccessibleInterval<T>, RandomAccessibleInterval<T>, double[], int[], int[], double[], RandomAccessibleInterval<double[]>) - Method in interface org.janelia.thickness.inference.visitor.Visitor
-
- ActElement() - Method in class view5d.My3DData
-
- action(String) - Method in class fiji.help.Context_Help
-
- Action(String, String) - Constructor for class fiji.util.gui.CommandFinderBase.Action
-
- action(String) - Method in class fiji.util.MenuItemDiverter
-
- ACTION_FINISHED - Variable in class fiji.plugin.trackmate.gui.panels.ActionChooserPanel
-
- ACTION_STARTED - Variable in class fiji.plugin.trackmate.gui.panels.ActionChooserPanel
-
- ActionChooserDescriptor - Class in fiji.plugin.trackmate.gui.descriptors
-
- ActionChooserDescriptor(ActionProvider, TrackMate, TrackMateGUIController) - Constructor for class fiji.plugin.trackmate.gui.descriptors.ActionChooserDescriptor
-
- actionChooserDescriptor - Variable in class fiji.plugin.trackmate.gui.TrackMateGUIController
-
- ActionChooserPanel - Class in fiji.plugin.trackmate.gui.panels
-
- ActionChooserPanel(ActionProvider, TrackMate, TrackMateGUIController) - Constructor for class fiji.plugin.trackmate.gui.panels.ActionChooserPanel
-
- ActionListenablePanel - Class in fiji.plugin.trackmate.gui.panels
-
- ActionListenablePanel() - Constructor for class fiji.plugin.trackmate.gui.panels.ActionListenablePanel
-
- actionListeners - Variable in class fiji.plugin.trackmate.gui.panels.ActionListenablePanel
-
- actionPerformed(ActionEvent) - Method in class bdv.ij.util.PluginHelper.ChooseXmlFileListener
-
- actionPerformed(ActionEvent) - Method in class bdv.tools.ToggleDialogAction
-
- actionPerformed(ActionEvent) - Method in class bdv.viewer.LandmarkPointMenu.ActivateSelectedHandler
-
- actionPerformed(ActionEvent) - Method in class bdv.viewer.LandmarkPointMenu.ClearHandler
-
- actionPerformed(ActionEvent) - Method in class bdv.viewer.LandmarkPointMenu.ClearSelectedHandler
-
- actionPerformed(ActionEvent) - Method in class bdv.viewer.LandmarkPointMenu.DeactivateSelectedHandler
-
- actionPerformed(ActionEvent) - Method in class bdv.viewer.LandmarkPointMenu.DeleteHandler
-
- actionPerformed(ActionEvent) - Method in class bdv.viewer.LandmarkPointMenu.DeleteSelectedHandler
-
- actionPerformed(ActionEvent) - Method in class bdv.viewer.WarpNavigationActions.AlignPlaneAction
-
- actionPerformed(ActionEvent) - Method in class bdv.viewer.WarpNavigationActions.CardAction
-
- actionPerformed(ActionEvent) - Method in class bdv.viewer.WarpNavigationActions.CollapseCardAction
-
- actionPerformed(ActionEvent) - Method in class bdv.viewer.WarpNavigationActions.DisplayXfmAction
-
- actionPerformed(ActionEvent) - Method in class bdv.viewer.WarpNavigationActions.ExpandCardAction
-
- actionPerformed(ActionEvent) - Method in class bdv.viewer.WarpNavigationActions.RotatePlaneAction
-
- actionPerformed(ActionEvent) - Method in class bdv.viewer.WarpNavigationActions.SetCurrentSourceOrGroupAction
-
- actionPerformed(ActionEvent) - Method in class bdv.viewer.WarpNavigationActions.ToggleFusedModeAction
-
- actionPerformed(ActionEvent) - Method in class bdv.viewer.WarpNavigationActions.ToggleGroupingAction
-
- actionPerformed(ActionEvent) - Method in class bdv.viewer.WarpNavigationActions.ToggleInterPolationAction
-
- actionPerformed(ActionEvent) - Method in class bdv.viewer.WarpNavigationActions.ToggleSourceOrGroupVisibilityAction
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.AlignViewerPanelAction
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.DebugAction
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.EstimateWarpAction
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.ExportAffineAction
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.ExportImagePlusAction
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.ExportWarpAction
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.GarbageCollectionAction
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.GoToBookmarkAction
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.GoToBookmarkRotationAction
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.LandmarkGridDialogAction
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.LandmarkModeAction
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.LoadLandmarksAction
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.LoadSettingsAction
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.PrintTransformAction
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.ResetActiveViewerAction
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.SaveLandmarksAction
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.SaveSettingsAction
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.SaveWarpedAction
-
Deprecated.
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.SaveWarpedXmlAction
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.SetBookmarkAction
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.SetWarpMagBaseAction
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.SetWarpVisGridTypeAction
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.SetWarpVisTypeAction
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.TableSelectionAction
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.ToggleAlwaysEstimateTransformAction
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.ToggleBoxAndTexOverlayVisibility
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.ToggleLandmarkModeAction
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.ToggleMovingImageDisplayAction
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.TogglePointNameVisibleAction
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.TogglePointsVisibleAction
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.UndoRedoAction
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.WarpToNearest
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.WarpToNextAction
-
- actionPerformed(ActionEvent) - Method in class bigwarp.BigWarpActions.WarpToSelectedAction
-
- actionPerformed(ActionEvent) - Method in class bunwarpj.ClearAll
-
Actions to take place with the dialog for clearing everything
- actionPerformed(ActionEvent) - Method in class bunwarpj.IODialog
-
Actions to be taking during the dialog.
- actionPerformed(ActionEvent) - Method in class bunwarpj.MainDialog
-
Actions to be taken during the dialog.
- actionPerformed(ActionEvent) - Method in class edu.utexas.clm.archipelago.ui.ClusterNodeStatusUI
-
- actionPerformed(ActionEvent) - Method in class edu.utexas.clm.archipelago.ui.NodeConfigurationUI
-
- actionPerformed(ActionEvent) - Method in class edu.utexas.clm.archipelago.ui.RootNodeConfigDialog
-
- actionPerformed(ActionEvent) - Method in class fiji.plugin.timelapsedisplay.FileOpenMenuEntry
-
- actionPerformed(ActionEvent) - Method in class fiji.plugin.timelapsedisplay.GraphFrame
-
- actionPerformed(ActionEvent) - Method in class fiji.plugin.trackmate.gui.TrackMateGUIController
-
- actionPerformed(ActionEvent) - Method in class fiji.plugin.trackmate.gui.TrackMateWizard
-
Simply forwards the caught event to listeners of this main frame.
- actionPerformed(ActionEvent) - Method in class fiji.plugin.trackmate.visualization.trackscheme.SaveAction
-
- actionPerformed(ActionEvent) - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackSchemeActions.EditAction
-
- actionPerformed(ActionEvent) - Method in class fiji.plugin.volumeviewer.Gui
-
- actionPerformed(ActionEvent) - Method in class fiji.util.ArrowTool
-
Is called when the user change a property using the option panel.
- actionPerformed(ActionEvent) - Method in class fiji.util.gui.CommandFinderBase
-
- actionPerformed(ActionEvent) - Method in class fiji.util.Recent_Commands
-
- actionPerformed(ActionEvent) - Method in class fiji.Wiki_Editor
-
- actionPerformed(ActionEvent) - Method in class ij3d.contextmenu.ContextMenu
-
- actionPerformed(ActionEvent) - Method in class ij3d.gui.LUTDialog
-
- actionPerformed(ActionEvent) - Method in class ij3d.Image3DMenubar
-
- actionPerformed(ActionEvent) - Method in class ij3d.pointlist.PointListPanel
-
Handling the events coming from the popup menu.
- actionPerformed(ActionEvent) - Method in class ij3d.RegistrationMenubar
-
- actionPerformed(ActionEvent) - Method in class ini.trakem2.display.Display
-
- actionPerformed(ActionEvent) - Method in class ini.trakem2.display.DisplayableChooser
-
- actionPerformed(ActionEvent) - Method in class ini.trakem2.display.YesNoDialog
-
- actionPerformed(ActionEvent) - Method in class ini.trakem2.tree.LayerTree
-
- actionPerformed(ActionEvent) - Method in class ini.trakem2.tree.ProjectTree
-
- actionPerformed(ActionEvent) - Method in class ini.trakem2.tree.TemplateTree
-
- actionPerformed(ActionEvent) - Method in class IntSlider
-
- actionPerformed(ActionEvent) - Method in class landmarks.ProgressWindow
-
- actionPerformed(ActionEvent) - Method in class loci.plugins.config.ConfigWindow
-
- actionPerformed(ActionEvent) - Method in class loci.plugins.in.SeriesDialog
-
- actionPerformed(ActionEvent) - Method in class loci.plugins.shortcut.ShortcutPanel
-
Handles button presses.
- actionPerformed(ActionEvent) - Method in class loci.plugins.util.DataBrowser
-
- actionPerformed(ActionEvent) - Method in class loci.plugins.util.SearchableWindow
-
- actionPerformed(ActionEvent) - Method in class Manual_Tracking
-
- actionPerformed(ActionEvent) - Method in class mpicbg.spim.segmentation.InteractiveDoG.ApplyButtonListener
-
- actionPerformed(ActionEvent) - Method in class mpicbg.spim.segmentation.InteractiveDoG.FinishedButtonListener
-
- actionPerformed(ActionEvent) - Method in class mpicbg.spim.segmentation.InteractiveIntegral.FinishButtonListener
-
- actionPerformed(ActionEvent) - Method in class net.imagej.ui.swing.ops.OpFinder
-
- actionPerformed(ActionEvent) - Method in class sc.fiji.balloonSegmentation.BalloonSegmentation_
-
- actionPerformed(ActionEvent) - Method in class sc.fiji.cellCounter.CellCounter
-
- actionPerformed(ActionEvent) - Method in class sc.fiji.coloc.results.SingleWindowDisplay
-
- actionPerformed(ActionEvent) - Method in class sc.fiji.hdf5.HDF5_Reader_Vibez
-
- actionPerformed(ActionEvent) - Method in class sc.fiji.hdf5.HDF5_Writer_Vibez
-
- actionPerformed(ActionEvent) - Method in class sc.fiji.i5d.gui.ChannelControl
-
- actionPerformed(ActionEvent) - Method in class sc.fiji.i5d.gui.ChannelControl.ChannelColorChooser
-
- actionPerformed(ActionEvent) - Method in class sc.fiji.i5d.gui.ChannelControl.ChannelSelectorOverlay
-
- actionPerformed(ActionEvent) - Method in class sc.fiji.snt.FillManagerUI
-
- actionPerformed(ActionEvent) - Method in class sc.fiji.snt.gui.EnhancedGenericDialog
-
Deprecated.
- actionPerformed(ActionEvent) - Method in class sc.fiji.snt.gui.ShollAnalysisDialog
-
Deprecated.
- actionPerformed(ActionEvent) - Method in class sc.fiji.snt.gui.SWCImportOptionsDialog
-
- actionPerformed(ActionEvent) - Method in class selection.DoneButtonListener
-
- actionPerformed(ActionEvent) - Method in class selection.LoadListener
-
- actionPerformed(ActionEvent) - Method in class selection.RemoveItemListener
-
- actionPerformed(ActionEvent) - Method in class selection.SaveListener
-
- actionPerformed(ActionEvent) - Method in class siox.SegmentationGUI
-
- actionPerformed(ActionEvent) - Method in class spim.fiji.plugin.apply.BigDataViewerTransformationWindow.ApplyButtonListener
-
- actionPerformed(ActionEvent) - Method in class spim.fiji.plugin.apply.BigDataViewerTransformationWindow.CancelButtonListener
-
- actionPerformed(ActionEvent) - Method in class spim.fiji.plugin.removedetections.InteractiveProjections.FinishedButtonListener
-
- actionPerformed(ActionEvent) - Method in class spim.fiji.plugin.removedetections.InteractiveProjections.RemoveInsideROIButtonListener
-
- actionPerformed(ActionEvent) - Method in class spim.fiji.plugin.resave.PluginHelper.ChooseXmlFileListener
-
- actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.ApplyTransformationPopup.MyActionListener
-
- actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.BDVPopup.MyActionListener
-
- actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.BoundingBoxPopup.MyActionListener
-
- actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.DetectInterestPointsPopup.MyActionListener
-
- actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.DisplayViewPopup.MyActionListener
-
- actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.FusionPopup.MyActionListener
-
- actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.InterestPointsExplorerPopup.MyActionListener
-
- actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.MaxProjectPopup.MyActionListener
-
- actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.RegisterInterestPointsPopup.MyActionListener
-
- actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.RegistrationExplorerPopup.MyActionListener
-
- actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.RemoveDetectionsPopup.MyActionListener
-
- actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.RemoveTransformationPopup.MyActionListener
-
- actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.ReorientSamplePopup.MyActionListener
-
- actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.ResavePopup.MyActionListener
-
- actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.SpecifyCalibrationPopup.MyActionListener
-
- actionPerformed(ActionEvent) - Method in class spim.fiji.spimdata.explorer.popup.VisualizeDetectionsPopup.MyActionListener
-
- actionPerformed(ActionEvent) - Method in class spim.process.interestpointregistration.registrationstatistics.GraphFrame
-
- actionPerformed(ActionEvent) - Method in class spim.process.interestpointregistration.registrationstatistics.SelectTimepointEntry
-
- actionPerformed(ActionEvent) - Method in class spimopener.OpenerGenericDialog
-
- actionPerformed(ActionEvent) - Method in class Sync_Measure_3D
-
Implementation of ActionListener interface.
- actionPerformed(ActionEvent) - Method in class Sync_Windows
-
Implementation of ActionListener interface.
- actionPerformed(ActionEvent) - Method in class tools.RoiPicker
-
- actionPerformed(ActionEvent) - Method in class util.ModelessQuestions
-
- actionPerformed(ActionEvent) - Method in class util.Quantile_Based_Normalization
-
- actionPerformed(ActionEvent) - Method in class vib.app.gui.FileGroupDialog
-
- actionPerformed(ActionEvent) - Method in class vib.EditAmiraParameters_
-
- actionPerformed(ActionEvent) - Method in class vib.Points_Dialog
-
- actionPerformed(ActionEvent) - Method in class vib.Relabel_
-
- actionPerformed(ActionEvent) - Method in class vib.segment.CustomStackWindow
-
- actionPerformed(ActionEvent) - Method in class vib.segment.MaterialList
-
- actionPerformed(ActionEvent) - Method in class vib.ShowHistogram
-
- actionPerformed(ActionEvent) - Method in class VIB_Protocol
-
- actionPerformed(ActionEvent) - Method in class video.Edit_Video
-
- actionPerformed(ActionEvent) - Method in class view4d.TimelineGUI
-
- actionProvider - Variable in class fiji.plugin.trackmate.gui.TrackMateGUIController
-
- ActionProvider - Class in fiji.plugin.trackmate.providers
-
- ActionProvider() - Constructor for class fiji.plugin.trackmate.providers.ActionProvider
-
- actions - Variable in class fiji.util.gui.CommandFinderBase
-
- actions - Static variable in class fiji.util.MenuItemDiverter
-
- ACTIVATE - Static variable in class bdv.viewer.LandmarkPointMenu
-
- activate() - Method in class fiji.plugin.trackmate.visualization.DummySpotColorGenerator
-
- activate() - Method in class fiji.plugin.trackmate.visualization.DummyTrackColorGenerator
-
- activate() - Method in interface fiji.plugin.trackmate.visualization.FeatureColorGenerator
-
When this color generator is reused, calling this method ensures that it
is registered again, and will follow whatever changes subsequently
happening to the model.
- activate() - Method in class fiji.plugin.trackmate.visualization.ManualEdgeColorGenerator
-
- activate() - Method in class fiji.plugin.trackmate.visualization.ManualSpotColorGenerator
-
- activate() - Method in class fiji.plugin.trackmate.visualization.PerEdgeFeatureColorGenerator
-
- activate() - Method in class fiji.plugin.trackmate.visualization.PerTrackFeatureColorGenerator
-
- activate() - Method in class fiji.plugin.trackmate.visualization.SpotColorGenerator
-
- activate() - Method in class fiji.plugin.trackmate.visualization.SpotColorGeneratorPerTrackFeature
-
- ACTIVATE_SELECTED - Static variable in class bdv.viewer.LandmarkPointMenu
-
- activateAllHandler - Variable in class bdv.viewer.LandmarkPointMenu
-
- activateAllItem - Variable in class bdv.viewer.LandmarkPointMenu
-
- activated5d - Variable in class sc.fiji.i5d.Image5D
-
- activateFinishedPath - Variable in class sc.fiji.snt.SNT
-
- activateRow(int) - Method in class bigwarp.landmarks.LandmarkTableModel
-
- ActivateSelectedHandler(String) - Constructor for class bdv.viewer.LandmarkPointMenu.ActivateSelectedHandler
-
- active() - Method in class edu.utexas.clm.archipelago.network.server.ArchipelagoServer
-
- ACTIVE_DISPL_COLOR - Static variable in class ini.trakem2.tree.ProjectTree
-
- activeCluster() - Static method in class edu.utexas.clm.archipelago.Cluster
-
- ACTIVECOLUMN - Static variable in class bigwarp.landmarks.LandmarkTableModel
-
- ActiveContours - Class in levelsets.algorithm
-
Implementation of the Levelset algorithm as originally implemented by Arne-Michael Toersel.
- ActiveContours(ImageContainer, ImageProgressContainer, StateContainer, double, double, double, double) - Constructor for class levelsets.algorithm.ActiveContours
-
- activeCursorIndex - Variable in class mpicbg.imglib.cursor.special.HyperSphereIterator
-
- ActiveElement - Variable in class view5d.My3DData
-
- activeHandle - Variable in class fiji.tool.AbstractTrackingTool
-
- activeList - Variable in class bigwarp.landmarks.LandmarkTableModel
-
- activeSourcesDialog - Variable in class bdv.BigDataViewer
-
- activeSourcesDialogP - Variable in class bigwarp.BigWarp
-
- activeSourcesDialogQ - Variable in class bigwarp.BigWarp
-
- ActiveTime - Variable in class view5d.My3DData
-
- actualSize - Variable in class fiji.util.ArrayBase
-
- ADAPT_COEFFICIENTS - Static variable in class bunwarpj.IODialog
-
bUnwarpJ_ method name to adapt B-spline coefficients to a scale
- adaptCanvasses(Image5DCanvas) - Method in class sc.fiji.i5d.gui.Image5DWindow
-
- adaptChannelCanvasses() - Method in class sc.fiji.i5d.gui.Image5DCanvas
-
- adaptChannelMouse() - Method in class sc.fiji.i5d.gui.Image5DCanvas
-
- adaptChannelRois(boolean) - Method in class sc.fiji.i5d.gui.Image5DCanvas
-
- adaptCoefficients(String, String, String) - Static method in class bunwarpj.bUnwarpJ_
-
Adapt the B-spline coefficients to a new image size.
- adaptCoefficients(String, double, String) - Static method in class bunwarpj.MiscTools
-
Adapt B-spline coefficients based on a scale factor.
- adaptCoefficients(double, double, int, double[][], double[][]) - Static method in class bunwarpj.MiscTools
-
Adapt B-spline coefficients to a scale factor
- adaptCoefficientsMacro(String, String, String, String, String) - Static method in class bunwarpj.bUnwarpJ_
-
Method to adapt an elastic transformation given a new image size.
- adaptedRandIndex3D(ImagePlus, ImagePlus) - Static method in class trainableSegmentation.metrics.RandError
-
Calculate the Rand index between to 3D clusters, as described by
William M.
- adaptedRandIndexFScore3D(ImagePlus, ImagePlus) - Static method in class trainableSegmentation.metrics.RandError
-
Calculate the F-score of the Rand index between to 3D clusters, as described by
William M.
- adaptedRandIndexStats3D(ImagePlus, ImagePlus) - Static method in class trainableSegmentation.metrics.RandError
-
Calculate the Rand index between to 3D clusters, as described by
William M.
- adaptedRandIndexStats3DN2(ImagePlus, ImagePlus) - Static method in class trainableSegmentation.metrics.RandError
-
Calculate the Rand index stats between to 3D clusters, as described by
William M.
- adapter - package adapter
-
- adapter - Variable in class Manual_Tracking
-
- adapter - Variable in class sc.fiji.snt.viewer.geditor.SNTGraphComponent
-
- AdaptiveNonMaximalSuppression<T extends RealType<T>> - Class in mpicbg.imglib.algorithm.scalespace
-
TODO
- AdaptiveNonMaximalSuppression(List<DifferenceOfGaussianPeak<T>>, double) - Constructor for class mpicbg.imglib.algorithm.scalespace.AdaptiveNonMaximalSuppression
-
Performs adaptive non maximal suppression in the local neighborhood of each detection, seperately
for minima and maxima.
- adaptMouse(Image5DCanvas) - Method in class sc.fiji.i5d.gui.Image5DWindow
-
Hands on the cursor location and modifiers of i5dc
to all
channel canvasses of this window except i5dc
.
- adaptRois(Image5DCanvas) - Method in class sc.fiji.i5d.gui.Image5DWindow
-
Hands on the roi
, cursor location and modifiers of
i5dc
to all channel canvasses of this window except
i5dc
.
- add(BasicViewSetup, AbstractSequenceDescription<?, ?, ?>, ViewRegistrations, int[][], int[][]) - Method in class bdv.ij.export.SetupAggregator
-
Deprecated.
- add(E) - Method in class bdv.util.WrappedList
-
- add(int, E) - Method in class bdv.util.WrappedList
-
- add(String) - Method in class bdv.viewer.animate.MessageOverlayAnimator
-
- add(BigWarp.BigWarpData, Source<T>, int, int, boolean) - Static method in class bigwarp.BigWarpInit
-
- add(double[], boolean) - Method in class bigwarp.landmarks.LandmarkTableModel
-
- add(double[], boolean, RealTransform) - Method in class bigwarp.landmarks.LandmarkTableModel
-
- add(CustomMesh) - Method in class customnode.CustomMultiMesh
-
- add(Pnt) - Method in class delaunay.Pnt
-
Add.
- add(float, float) - Method in class distance.Correlation
-
- add(float, float) - Method in class distance.Euclidean
-
- add(float, float) - Method in class distance.MutualInformation
-
- add(float, float) - Method in interface distance.PixelPairs
-
- add(float, float) - Method in class distance.Thresholded
-
- add(float, float) - Method in class distance.TwoValues
-
- add(Spot, Integer) - Method in class fiji.plugin.trackmate.SpotCollection
-
Adds the given spot to this collection, at the specified frame, and mark
it as visible.
- add(double) - Method in class fiji.plugin.trackmate.tracking.sparselap.costmatrix.ResizableDoubleArray
-
- add(K, Point4d, Color4f) - Method in class fiji.plugin.trackmate.visualization.threedviewer.SpotGroupNode
-
- add(double) - Method in class fiji.util.DoubleArray
-
Deprecated.
- add(float) - Method in class fiji.util.FloatArray
-
Deprecated.
- add(int) - Method in class fiji.util.IntArray
-
Deprecated.
- ADD - Static variable in class ij3d.Executer
-
- add(String, String, String, String, String, String, String, String, String) - Static method in class ij3d.ImageJ3DViewer
-
- add(Content) - Method in class ij3d.ViewAdjuster
-
Add another Content which should be completely visible in the canvas.
- add(Transform3D, Point3d) - Method in class ij3d.ViewAdjuster
-
Add another point which should be visible in the canvas; the point is
expected to be in local coordinates, with the given local-to-vworld
transformation.
- add(Point3d) - Method in class ij3d.ViewAdjuster
-
Add another point which should be visible in the canvas; the point is
expected to be in vworld coordinates.
- add(DisplayChangeListener, DisplayChangeListener) - Static method in class IJEventMulticaster
-
Adds DisplayChange-listener-a with DisplayChange-listener-b and
returns the resulting multicast listener.
- Add - Class in imglib.ops.operator.binary
-
TODO
- Add() - Constructor for class imglib.ops.operator.binary.Add
-
- add(Project, TemplateTree, ProjectTree, LayerTree) - Static method in class ini.trakem2.ControlWindow
-
Beware that this method is asynchronous, as it delegates the launching to the SwingUtilities.invokeLater method to avoid havoc with Swing components.
- add(long, ShapeRoi) - Method in class ini.trakem2.display.AreaList
-
Adds the given ROI, which is expected in world/LayerSet coordinates, to the area present at Layer with id layer_id, or set it if none present yet.
- add(Area, Layer) - Method in class ini.trakem2.display.AreaWrapper
-
Add an area in world coordinates.
- add(Area, AffineTransform) - Method in class ini.trakem2.display.AreaWrapper
-
Add an area that needs to be transformed by tmp first to bring it to world coordinates;
will MODIFY the to_world AffineTransform object.
- add(Layer, Displayable, boolean) - Static method in class ini.trakem2.display.Display
-
Find the displays that show the given Layer, and add the given Displayable to the GUI and sets it active only in the front Display and only if 'activate' is true.
- add(Layer, Displayable) - Static method in class ini.trakem2.display.Display
-
- add(LayerSet, ZDisplayable) - Static method in class ini.trakem2.display.Display
-
Add the ZDisplayable to all Displays that show a Layer belonging to the given LayerSet.
- add(DoStep) - Method in class ini.trakem2.display.Displayable.DoEdit
-
- add(String, Object) - Method in class ini.trakem2.display.Displayable.DoEdit
-
- add(Displayable) - Method in class ini.trakem2.display.Layer
-
Add a displayable and update all Display instances showing this Layer.
- add(Displayable, boolean) - Method in class ini.trakem2.display.Layer
-
- add(Displayable, boolean, boolean) - Method in class ini.trakem2.display.Layer
-
- add(Layer) - Method in class ini.trakem2.display.LayerSet
-
Add a new Layer, inserted according to its Z.
- add(ZDisplayable) - Method in class ini.trakem2.display.LayerSet
-
Add a Displayable to be painted in all Layers, such as a Pipe.
- add(Layer, double, double) - Method in class ini.trakem2.display.ManualAlignMode.Landmarks
-
Returns the index of the newly added point, or -1 if the layer doesn't match.
- add(Node<T>, byte) - Method in class ini.trakem2.display.Node
-
Returns -1 when not added (e.g.
- add(Shape, Color, Stroke) - Method in class ini.trakem2.display.Overlay
-
Add a new Shape to be painted above all other elements in the canvas.
- add(Shape, Color, Stroke, boolean) - Method in class ini.trakem2.display.Overlay
-
- add(Shape, Color, Stroke, boolean, boolean, float) - Method in class ini.trakem2.display.Overlay
-
- add(Displayable) - Method in class ini.trakem2.display.Selection
-
- add(Area, CoordinateTransform) - Method in class ini.trakem2.display.VectorDataTransform
-
Add a coordinate transform @param ct that applies to the @param roi Area only;
ASSUMES all rois added do not overlap.
- add(Patch) - Static method in class ini.trakem2.persistence.FilePathRepair
-
- add(History.Step<?>) - Method in class ini.trakem2.utils.History
-
Append a new step.
- add(String) - Method in class ini.trakem2.utils.Montage
-
- add(String) - Method in class ini.trakem2.utils.ReconstructArea
-
To reconstruct from XML, takes a "M ....
- add(Vector3, Vector3) - Method in class ini.trakem2.utils.Vector3
-
- add(NamedPointWorld) - Method in class landmarks.NamedPointSet
-
- add(double) - Method in class loci.plugins.util.RecordedImageProcessor
-
- add(int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- add(Point3d) - Method in class math3d.NormalEstimator
-
- add(LocalHistogram) - Method in class mmorpho.LocalHistogram
-
- add(int) - Method in class mpicbg.imglib.cursor.vector.AbstractVector
-
- add(V) - Method in class mpicbg.imglib.cursor.vector.AbstractVector
-
- add(Vector) - Method in class mpicbg.imglib.cursor.vector.Vector
-
- add(int) - Method in class mpicbg.imglib.cursor.vector.Vector
-
- add(Vector1d) - Method in class mpicbg.imglib.cursor.vector.Vector1d
-
- add(int) - Method in class mpicbg.imglib.cursor.vector.Vector1d
-
- add(Vector2d) - Method in class mpicbg.imglib.cursor.vector.Vector2d
-
- add(int) - Method in class mpicbg.imglib.cursor.vector.Vector2d
-
- add(Vector3d) - Method in class mpicbg.imglib.cursor.vector.Vector3d
-
- add(int) - Method in class mpicbg.imglib.cursor.vector.Vector3d
-
- add(Vector4d) - Method in class mpicbg.imglib.cursor.vector.Vector4d
-
- add(int) - Method in class mpicbg.imglib.cursor.vector.Vector4d
-
- add(T) - Method in class mpicbg.imglib.image.Image
-
- add(BitType) - Method in class mpicbg.imglib.type.logic.BitType
-
- add(ComplexFloatType) - Method in class mpicbg.imglib.type.numeric.complex.ComplexFloatType
-
- add(T) - Method in class mpicbg.imglib.type.numeric.complex.ComplexTypeImpl
-
- add(T) - Method in class mpicbg.imglib.type.numeric.integer.GenericByteType
-
- add(T) - Method in class mpicbg.imglib.type.numeric.integer.GenericIntType
-
- add(T) - Method in class mpicbg.imglib.type.numeric.integer.GenericShortType
-
- add(LongType) - Method in class mpicbg.imglib.type.numeric.integer.LongType
-
- add(T) - Method in interface mpicbg.imglib.type.numeric.NumericType
-
- add(FloatType) - Method in class mpicbg.imglib.type.numeric.real.FloatType
-
- add(T) - Method in class mpicbg.imglib.type.numeric.real.RealTypeImpl
-
- add(RGBALegacyType) - Method in class mpicbg.imglib.type.numeric.RGBALegacyType
-
- add(E) - Method in class mpicbg.models.CoordinateTransformList
-
- add(double) - Method in class mpicbg.models.ErrorStatistic
-
- add(E) - Method in class mpicbg.models.InverseCoordinateTransformList
-
- add(E) - Method in class mpicbg.models.InvertibleCoordinateTransformList
-
- add(E) - Method in interface mpicbg.models.TransformList
-
- add(Point, Point) - Static method in class mpicbg.pointdescriptor.test.TestPointDescriptor
-
- add(LRFFT) - Method in class mpicbg.spim.postprocessing.deconvolution2.LRInput
-
- add(double, double) - Method in class mpicbg.util.RealStreamPMCC
-
- add(double) - Method in class mpicbg.util.RealSum
-
Add an element to the sum.
- add(T) - Method in class mpicbg.util.RingBuffer
-
- add(int, T) - Method in class mpicbg.util.RingBuffer
- add(T) - Method in class mpicbg.util.RingBuffer.RingBufferListIterator
-
- add(OpTreeTableNode) - Method in class net.imagej.ui.swing.ops.OpTreeTableNode
-
Add a child to this node.
- add(Frame) - Method in class org.janelia.it.jacs.shared.ffmpeg.ImageStack
-
Add a Frame to the end of the stack
- add(int, int, double, double) - Method in class org.janelia.thickness.inference.fits.AbstractCorrelationFit
-
- add(int, int, double, double) - Method in class org.janelia.thickness.inference.fits.GlobalCorrelationFitAverage
-
- add(int, int, double, double) - Method in class org.janelia.thickness.inference.fits.GlobalCorrelationFitAverageRegularized
-
- add(int, int, double, double) - Method in class org.janelia.thickness.inference.fits.LocalCorrelationFitAverage
-
- add(double, Color) - Method in class org.jfree.chart.renderer.InterpolatePaintScale
-
Add a color to the color list of this paint scale, at the position given
by value
.
- add(int, int) - Method in class org.siox.util.IntArrayList
-
Inserts the specified element at the specified position in this list.
- add(int) - Method in class org.siox.util.IntArrayList
-
Appends the specified element to the end of this list.
- add(double[], double[]) - Method in class sc.fiji.balloonSegmentation.structure.Balloon
-
Math vector operators: addition of 2 vectors a+b (I made this before I start using JAMA library)
- add(ProfileEntry) - Method in class sc.fiji.snt.analysis.sholl.Profile
-
- add(int, int, int, double, int, boolean) - Method in class sc.fiji.snt.Fill
-
- add(Path) - Method in class sc.fiji.snt.Path
-
- add(Path) - Method in class sc.fiji.snt.Tree
-
Adds a new Path to this Tree.
- add(Tree) - Method in class sc.fiji.snt.viewer.Viewer2D
-
Appends a tree to the viewer using default options.
- add(List<Tree>, String) - Method in class sc.fiji.snt.viewer.Viewer2D
-
Adds a list of trees while assigning each tree to a LUT index.
- add(Tree, ColorRGB) - Method in class sc.fiji.snt.viewer.Viewer2D
-
Appends a tree to the viewer.
- add(Tree, String) - Method in class sc.fiji.snt.viewer.Viewer2D
-
Appends a tree to the viewer.
- add(Tree, String, ColorTable, double, double) - Method in class sc.fiji.snt.viewer.Viewer2D
-
Appends a tree to the viewer rendered after the specified measurement.
- add(Tree, String, String) - Method in class sc.fiji.snt.viewer.Viewer2D
-
Appends a tree to the viewer rendered after the specified measurement.
- add(Tree, String, String, double, double) - Method in class sc.fiji.snt.viewer.Viewer2D
-
Appends a tree to the viewer rendered after the specified measurement.
- add(Object) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Script friendly method to add a supported object (
Tree
,
OBJMesh
,
AbstractDrawable
, etc.) to this viewer.
- add(double, double) - Method in class sc.fiji.timelapse.LinearRegression
-
- add(double) - Method in class sc.fiji.timelapse.StandardDeviation
-
- Add - Class in script.imglib.math
-
TODO
- Add(Image<? extends RealType<?>>, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.Add
-
- Add(IFunction, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.Add
-
- Add(Image<? extends RealType<?>>, IFunction) - Constructor for class script.imglib.math.Add
-
- Add(IFunction, IFunction) - Constructor for class script.imglib.math.Add
-
- Add(Image<? extends RealType<?>>, Number) - Constructor for class script.imglib.math.Add
-
- Add(Number, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.Add
-
- Add(IFunction, Number) - Constructor for class script.imglib.math.Add
-
- Add(Number, IFunction) - Constructor for class script.imglib.math.Add
-
- Add(Number, Number) - Constructor for class script.imglib.math.Add
-
- Add(Object...) - Constructor for class script.imglib.math.Add
-
- add(ViewDescription) - Method in class spim.fiji.plugin.apply.ModelLink
-
- add(MVDeconFFT) - Method in class spim.process.fusion.deconvolution.MVDeconInput
-
- add(double) - Method in class spim.vecmath.Matrix3d
-
Adds a scalar to each component of this matrix.
- add(double, Matrix3d) - Method in class spim.vecmath.Matrix3d
-
Adds a scalar to each component of the matrix m1 and places the result
into this.
- add(Matrix3d, Matrix3d) - Method in class spim.vecmath.Matrix3d
-
Sets the value of this matrix to the matrix sum of matrices m1 and m2.
- add(Matrix3d) - Method in class spim.vecmath.Matrix3d
-
Sets the value of this matrix to the sum of itself and matrix m1.
- add(float) - Method in class spim.vecmath.Matrix3f
-
Adds a scalar to each component of this matrix.
- add(float, Matrix3f) - Method in class spim.vecmath.Matrix3f
-
Adds a scalar to each component of the matrix m1 and places the result
into this.
- add(Matrix3f, Matrix3f) - Method in class spim.vecmath.Matrix3f
-
Sets the value of this matrix to the matrix sum of matrices m1 and m2.
- add(Matrix3f) - Method in class spim.vecmath.Matrix3f
-
Sets the value of this matrix to the matrix sum of itself and matrix m1.
- add(double) - Method in class spim.vecmath.Matrix4d
-
Adds a scalar to each component of this matrix.
- add(double, Matrix4d) - Method in class spim.vecmath.Matrix4d
-
Adds a scalar to each component of the matrix m1 and places the result
into this.
- add(Matrix4d, Matrix4d) - Method in class spim.vecmath.Matrix4d
-
Sets the value of this matrix to the matrix sum of matrices m1 and m2.
- add(Matrix4d) - Method in class spim.vecmath.Matrix4d
-
Sets the value of this matrix to sum of itself and matrix m1.
- add(float) - Method in class spim.vecmath.Matrix4f
-
Adds a scalar to each component of this matrix.
- add(float, Matrix4f) - Method in class spim.vecmath.Matrix4f
-
Adds a scalar to each component of the matrix m1 and places the result
into this.
- add(Matrix4f, Matrix4f) - Method in class spim.vecmath.Matrix4f
-
Sets the value of this matrix to the matrix sum of matrices m1 and m2.
- add(Matrix4f) - Method in class spim.vecmath.Matrix4f
-
Sets the value of this matrix to the sum of itself and matrix m1.
- add(Transform3D) - Method in class spim.vecmath.Transform3D
-
Adds this transform to transform t1 and places the result into this: this
= this + t1.
- add(Transform3D, Transform3D) - Method in class spim.vecmath.Transform3D
-
Adds transforms t1 and t2 and places the result into this transform.
- add(Tuple3d, Tuple3d) - Method in class spim.vecmath.Tuple3d
-
Sets the value of this tuple to the sum of tuples t1 and t2.
- add(Tuple3d) - Method in class spim.vecmath.Tuple3d
-
Sets the value of this tuple to the sum of itself and t1.
- add(Tuple3f, Tuple3f) - Method in class spim.vecmath.Tuple3f
-
Sets the value of this tuple to the vector sum of tuples t1 and t2.
- add(Tuple3f) - Method in class spim.vecmath.Tuple3f
-
Sets the value of this tuple to the vector sum of itself and tuple t1.
- add(Tuple3i, Tuple3i) - Method in class spim.vecmath.Tuple3i
-
Sets the value of this tuple to the sum of tuples t1 and t2.
- add(Tuple3i) - Method in class spim.vecmath.Tuple3i
-
Sets the value of this tuple to the sum of itself and t1.
- add(Tuple4d, Tuple4d) - Method in class spim.vecmath.Tuple4d
-
Sets the value of this tuple to the tuple sum of tuples t1 and t2.
- add(Tuple4d) - Method in class spim.vecmath.Tuple4d
-
Sets the value of this tuple to the sum of itself and tuple t1.
- add(Tuple4f, Tuple4f) - Method in class spim.vecmath.Tuple4f
-
Sets the value of this tuple to the sum of tuples t1 and t2.
- add(Tuple4f) - Method in class spim.vecmath.Tuple4f
-
Sets the value of this tuple to the sum of itself and t1.
- add(ImageProcessor) - Method in class spimopener.GaussianStackFocuser
-
- add(ImageProcessor) - Method in class spimopener.MaximumProjector
-
- add(ImageProcessor) - Method in class spimopener.MinimumProjector
-
- add(ImageProcessor) - Method in interface spimopener.Projector
-
- add(double) - Method in class stitching.model.ErrorStatistic
-
- add(T, Object) - Method in class util.FibonacciHeap
-
- add(double, Object) - Method in class util.FibonacciHeapDouble
-
- add(int, Object) - Method in class util.FibonacciHeapInt
-
- add(String) - Method in class vib.app.FileGroup
-
- add(ImagePlus) - Method in class vib.Average_Images
-
- add(int) - Method in class vib.NaiveResampler.Averager
-
- add(int) - Method in class vib.NaiveResampler.IntAverager
-
- add(int) - Method in class vib.NaiveResampler.MaxLikelihood
-
- add(int) - Method in class vib.NaiveResampler.MinEntropy
-
- add(BenesNamedPoint) - Method in class vib.PointList
-
- add(String, double, double, double) - Method in class vib.PointList
-
- add(double, double, double) - Method in class vib.PointList
-
- add2Command(Container, String, String, String, String, ActionListener) - Static method in class gui.GuiBuilder
-
- add3Command(Container, String, String, String, String, String, String, ActionListener) - Static method in class gui.GuiBuilder
-
- add3DCube(int, int, int, int, int, int, Color) - Method in class jRenderer3D.JRenderer3D
-
Adds a cube (drawn with 12 lines) to the 3D scene.
- add3DCube(int, int, int, int, int, int, int) - Method in class jRenderer3D.JRenderer3D
-
Adds a cube (drawn with 12 lines) to the 3D scene.
- ADD_BOX - Static variable in class ij3d.Executer
-
- ADD_CONE - Static variable in class ij3d.Executer
-
- ADD_CROSS - Static variable in class bunwarpj.PointAction
-
constant to identify the add cross tool
- ADD_EDGE - Static variable in class org.siox.SioxSegmentator
-
Add mode for the subpixel refinement.
- Add_Empty_Channel - Class in sc.fiji.i5d.plugin
-
- Add_Empty_Channel() - Constructor for class sc.fiji.i5d.plugin.Add_Empty_Channel
-
- Add_Empty_Frame - Class in video2
-
- Add_Empty_Frame() - Constructor for class video2.Add_Empty_Frame
-
- Add_Empty_Slice - Class in sc.fiji.i5d.plugin
-
- Add_Empty_Slice() - Constructor for class sc.fiji.i5d.plugin.Add_Empty_Slice
-
- ADD_SPHERE - Static variable in class ij3d.Executer
-
- ADD_TRACE - Static variable in class trainableSegmentation.Weka_Segmentation
-
name of the macro method to add the current trace to a class
- ADD_TUBE_POINT - Static variable in class ij3d.Executer
-
- addAccelerator(Component, JComponent, ActionListener, int, int) - Static method in class Bug_Submitter.Bug_Submitter
-
Add a keyboard accelerator to a container.
- addActionListender(JRadioButton) - Method in class bdv.gui.TransformTypeSelectDialog
-
- addActionListener(ActionListener) - Method in class fiji.plugin.trackmate.gui.descriptors.SpotFilterDescriptor
-
- addActionListener(ActionListener) - Method in class fiji.plugin.trackmate.gui.descriptors.StartDialogDescriptor
-
- addActionListener(ActionListener) - Method in class fiji.plugin.trackmate.gui.descriptors.TrackFilterDescriptor
-
- addActionListener(ActionListener) - Method in class fiji.plugin.trackmate.gui.panels.ActionListenablePanel
-
- addActionListener(ActionListener) - Method in class fiji.plugin.trackmate.gui.panels.components.ImagePlusChooser
-
- addActionListener(ActionListener) - Method in class fiji.plugin.trackmate.gui.TrackMateWizard
-
Adds an
ActionListener
to the list of listeners of this GUI, that
will be notified when one the of push buttons is pressed.
- addActionListener(ActionListener) - Method in class fiji.util.ArrowOptionPanel
-
- addActionListener(ActionListener) - Method in class IntSlider
-
- addActionListener(ActionListener) - Method in class vib.segment.CustomStackWindow
-
- addActionListener(ActionListener) - Method in class vib.segment.ImageButton
-
- addAddtionalParameters(GenericDialog) - Method in class spim.fiji.plugin.interestpointdetection.DifferenceOf
-
- addAddtionalParameters(GenericDialog) - Method in class spim.fiji.plugin.interestpointdetection.DifferenceOfGaussian
-
- addAddtionalParameters(GenericDialog) - Method in class spim.fiji.plugin.interestpointdetection.DifferenceOfMean
-
- addAdjustmentListener(AdjustmentListener) - Method in class sc.fiji.i5d.gui.ScrollbarWithLabel
-
- addAdvancedPoints(ArrayList<Point>, ArrayList<Point>) - Method in class mpicbg.pointdescriptor.test.TestPointDescriptor
-
- addAlignmentFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.Param
-
- addAlignmentFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.ParamOptimize
-
- addAll(Collection<? extends E>) - Method in class bdv.util.WrappedList
-
- addAll(int, Collection<? extends E>) - Method in class bdv.util.WrappedList
-
- addAll(Layer, Collection<? extends Displayable>) - Static method in class ini.trakem2.display.Display
-
- addAll(LayerSet, Collection<? extends ZDisplayable>) - Static method in class ini.trakem2.display.Display
-
- addAll(Collection<? extends ZDisplayable>) - Method in class ini.trakem2.display.LayerSet
-
- addAll(String[]) - Method in class ini.trakem2.utils.Montage
-
- addAll(Collection<? extends T>) - Method in class mpicbg.imglib.image.Image
-
- addAll(int[]) - Method in class org.siox.util.IntArrayList
-
Appends all of the elements in the specified array, in the order that
they appear in the array.
- addAll(Collection) - Method in class org.siox.util.IntArrayList
-
Appends all of the elements in the specified collection, in the order that
they appear in the array.
- addAll(int, Collection) - Method in class org.siox.util.IntArrayList
-
Inserts all of the elements in the specified array into this list,
starting at the specified position.
- addAll(int, int[]) - Method in class org.siox.util.IntArrayList
-
Inserts all of the elements in the specified array into this list,
starting at the specified position.
- addAllAnalyzers() - Method in class fiji.plugin.trackmate.Settings
-
All the spot analyzers, edge analyzers and track analyzers discovered at
runtime.
- addAllClasses(ClassifiedRegion) - Method in class mpicbg.stitching.fusion.ClassifiedRegion
-
Merges the classes attached to another region with the classes of this
region.
- addAllEdges(Collection<DefaultWeightedEdge>) - Method in class fiji.plugin.trackmate.ModelChangeEvent
-
- addAllSpots(Collection<Spot>) - Method in class fiji.plugin.trackmate.ModelChangeEvent
-
- addAlphaMask(Roi, int) - Method in class ini.trakem2.display.Patch
-
Add the given roi, in world coords, to the alpha mask, using the given fill value.
- addAlphaMask(Area, int) - Method in class ini.trakem2.display.Patch
-
Add the given area, in world coords, to the alpha mask, using the given fill value.
- addAlphaMaskLocal(Area, int) - Method in class ini.trakem2.display.Patch
-
Add the given area, in local coordinates, to the alpha mask, using the given fill value.
- addAmiraLabelsList(GenericDialog, String) - Static method in class amira.AmiraParameters
-
- addAmiraMeshList(GenericDialog, String) - Static method in class amira.AmiraParameters
-
- addAmiraTableList(GenericDialog, String) - Static method in class amira.AmiraParameters
-
- addAndFixTiles(List<ViewId>, HashMap<ViewId, Tile<M>>, GlobalOptimizationType, GlobalOptimizationSubset, boolean) - Static method in class spim.process.interestpointregistration.GlobalOpt
-
- addAnisotropicDiffusion(ImagePlus, int, int, int, float, float, float) - Method in class trainableSegmentation.FeatureStack
-
Add anisotropic diffusion filtering images to current stack
- addAppleA() - Method in class spim.fiji.spimdata.explorer.ViewSetupExplorerPanel
-
- addArea(long, Area) - Method in class ini.trakem2.display.AreaList
-
Add a copy of an Area object to the existing, if any, area object at Layer with layer_id as given, or if not existing, just set the copy as it.
- addAreaList(AreaList) - Method in class edu.utexas.clm.crop.AreaListCrop
-
- AddARGBComposite - Class in ini.trakem2.display.graphics
-
- addAsLinesTo3DViewer(Image3DUniverse, Color, ImagePlus) - Method in class sc.fiji.snt.Path
-
Deprecated.
- addAsLinesTo3DViewer(Image3DUniverse, Color3f, ImagePlus) - Method in class sc.fiji.snt.Path
-
Deprecated.
- addBall(double, double, double, long) - Method in class ini.trakem2.display.Ball
-
Used to add individual ball objects when parsing.
- addBilateralFilter(ImagePlus, double, double) - Method in class trainableSegmentation.FeatureStack
-
Add bilateral filter image to current stack
- addBinaryData(ImagePlus, FeatureStack, String) - Method in class trainableSegmentation.WekaSegmentation
-
Add instances to a specific class from a label (binary) image.
- addBinaryData(ImagePlus, FeatureStack, String, String) - Method in class trainableSegmentation.WekaSegmentation
-
Add instances to two classes from a label (binary) image.
- addBinaryData(List<Point3f>[], FeatureStackArray, String, String) - Method in class trainableSegmentation.WekaSegmentation
-
Add instances to two classes from lists of coordinates.
- addBinaryData(ImagePlus, int, String, String) - Method in class trainableSegmentation.WekaSegmentation
-
Add label image as binary data
- addBinaryData(ImagePlus, ImagePlus, String, String) - Method in class trainableSegmentation.WekaSegmentation
-
Add binary training data from input and label images.
- addBinaryData(ImagePlus, ImagePlus, ImagePlus, String, String) - Method in class trainableSegmentation.WekaSegmentation
-
Add binary training data from input and label images.
- addBottler(Bottler) - Method in class edu.utexas.clm.archipelago.Cluster
-
- addBottler(Bottler) - Method in class edu.utexas.clm.archipelago.network.MessageXC
-
- addBottler(Bottler) - Method in class edu.utexas.clm.archipelago.network.node.ClusterNode
-
- addBottler(Bottler) - Method in class edu.utexas.clm.archipelago.network.node.NodeCoordinator
-
- addBoundingBox(BoundingBox) - Method in class spim.fiji.spimdata.boundingbox.BoundingBoxes
-
- addBox() - Method in class ij3d.Executer
-
- addBox(Image3DUniverse) - Static method in class ij3d.gui.PrimitiveDialogs
-
- addBox(String, String, String) - Static method in class ij3d.ImageJ3DViewer
-
Add a box into the current 3D universe
- addBrowseToCellVoyagerFolder(GenericDialogPlus, String, String, int) - Static method in class bdv.ij.ExportCellVoyagerPlugIn
-
- addButton(String, ActionListener) - Method in class fiji.util.gui.GenericDialogPlus
-
Add button to the dialog
- addButton(String, ActionListener) - Method in class spim.fiji.plugin.queryXML.GenericLoadParseQueryXML
-
- addCacheControl(CacheControl, int) - Method in class bdv.cache.CacheControl.CacheControls
-
- addCacheControl(CacheControl) - Method in class bdv.cache.CacheControl.CacheControls
-
- addCanvasListener(CustomCanvas.CanvasListener) - Method in class vib.segment.CustomCanvas
-
- addCard(String, JComponent, boolean, Insets) - Method in class bdv.ui.CardPanel
-
- addCard(Object, String, JComponent, boolean, Insets) - Method in class bdv.ui.CardPanel
-
- addCard(String, JComponent, boolean) - Method in class bdv.ui.CardPanel
-
- addCard(Object, String, JComponent, boolean) - Method in class bdv.ui.CardPanel
-
- addCenter() - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay
-
- addCenterLinesBinaryData(ImagePlus, int, String, String) - Method in class trainableSegmentation.WekaSegmentation
-
Add center lines of label image as binary data
- addCenterOf(Iterable<Content>) - Method in class ij3d.ViewAdjuster
-
Make sure that the average center of all contents is visible in the canvas.
- addChangeListener(ChangeListener) - Method in class fiji.plugin.trackmate.gui.descriptors.SpotFilterDescriptor
-
- addChangeListener(ChangeListener) - Method in class fiji.plugin.trackmate.gui.descriptors.TrackFilterDescriptor
-
- addChangeListener(ChangeListener) - Method in class fiji.plugin.trackmate.gui.panels.components.FilterGuiPanel
-
- addChangeListener(ChangeListener) - Method in class fiji.plugin.trackmate.gui.panels.FilterPanel
-
- addChangeTreesStep() - Method in class ini.trakem2.display.LayerSet
-
Add a step to undo the addition or deletion of one or more objects in this project and LayerSet.
- addChangeTreesStep(Set<DoStep>) - Method in class ini.trakem2.display.LayerSet
-
Add a step to undo the addition or deletion of one or more objects in this project and LayerSet,
along with an arbitrary set of steps that may alter, for example the data.
- addCheckBox(Container, String) - Static method in class gui.GuiBuilder
-
- addCheckbox(String, boolean) - Method in class ini.trakem2.utils.OptionPanel
-
- addCheckbox(String, boolean, OptionPanel.Setter) - Method in class ini.trakem2.utils.OptionPanel
-
- addCheckbox(GenericDialog, String) - Method in class loci.plugins.prefs.OptionsDialog
-
Adds a checkbox to the given dialog object corresponding
to the boolean option identified by the specified key.
- addCheckbox(String) - Method in class util.ModelessQuestions
-
- addChild(Thing, DefaultMutableTreeNode) - Method in class ini.trakem2.tree.DNDTree
-
Appends at the end of the parent_node child list, and waits until the tree's UI is updated.
- addChild(Thing) - Method in class ini.trakem2.tree.LayerThing
-
- addChild(Thing) - Method in class ini.trakem2.tree.ProjectThing
-
- addChild(ProjectThing, int) - Method in class ini.trakem2.tree.ProjectThing
-
In addition, if the child contains an object of class ini.trakem2.display.Profile, reorders all children of the parent Thing by the Z of the layers of the profiles.
- addChild(ProjectThing, String, Displayable) - Method in class ini.trakem2.tree.ProjectTree
-
- addChild(Thing) - Method in class ini.trakem2.tree.TemplateThing
-
- addChild(Thing) - Method in interface ini.trakem2.tree.Thing
-
- addChoice(GenericDialog, String, Vector) - Static method in class amira.AmiraParameters
-
- addChoice(GenericDialog, String, Vector, String) - Static method in class amira.AmiraParameters
-
- addChoice(String, String[], int) - Method in class ini.trakem2.utils.OptionPanel
-
- addChoice(String, String[], int, OptionPanel.Setter) - Method in class ini.trakem2.utils.OptionPanel
-
- addChoice(GenericDialog, String) - Method in class loci.plugins.prefs.OptionsDialog
-
Adds a choice to the given dialog object corresponding
to the string option identified by the specified key.
- addChoice(String, String[]) - Method in class spimopener.OpenerGenericDialog
-
- addCircle(ImagePlus, int, int, double) - Method in class selection.Select_Points
-
- addCitationMessage() - Method in class sc.fiji.snt.gui.EnhancedGenericDialog
-
Deprecated.
Allows users to visit the manuscript from a dialog prompt
- addClass(int) - Method in class mpicbg.stitching.fusion.ClassifiedRegion
-
Add a class, in the form an int value, to this region.
- addClass(List<IFT_.Cls>, int, int, int, byte) - Static method in class process3d.IFT_
-
- addClass() - Method in class trainableSegmentation.WekaSegmentation
-
Add new segmentation class.
- addClickableURLtoLabel(Component, String, Color) - Static method in class sc.fiji.snt.gui.EnhancedGenericDialog
-
Deprecated.
- addColorBarLegend(String, double, double) - Method in class sc.fiji.snt.viewer.Viewer2D
-
- addColorBarLegend(ColorTable, double, double) - Method in class sc.fiji.snt.viewer.Viewer2D
-
Adds a color bar legend (LUT ramp).
- addColorBarLegend(T) - Method in class sc.fiji.snt.viewer.Viewer2D
-
- addColorBarLegend() - Method in class sc.fiji.snt.viewer.Viewer2D
-
Adds a color bar legend (LUT ramp) to the viewer.
- addColorBarLegend(T) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Adds a color bar legend (LUT ramp) from a ColorMapper
.
- addColorBarLegend(ColorTable, double, double) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Adds a color bar legend (LUT ramp) using default settings.
- addColorBarLegend(ColorTable, double, double, Font, int, int) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Adds a color bar legend (LUT ramp).
- addColorChangedListener(ColorChangedListener) - Method in class sc.fiji.snt.gui.ColorChooserButton
-
- addColorMode() - Method in class spim.fiji.spimdata.explorer.ViewSetupExplorerPanel
-
- addColorMouseListener(ImageCanvas, double, double) - Static method in class fiji.analyze.directionality.Directionality_
-
- addCommand(Container, String, String, ActionListener) - Static method in class gui.GuiBuilder
-
- addCompletingButton(String, String) - Method in class util.ModelessQuestions
-
- addComponent(Component) - Method in class fiji.util.gui.GenericDialogPlus
-
- addComponent(Component, int, double) - Method in class fiji.util.gui.GenericDialogPlus
-
- addComponentToGrid(Component, Container, int, int, int, int, int, int, double, double) - Static method in class org.imagearchive.lsm.toolbox.gui.GUIMaker
-
- addCone() - Method in class ij3d.Executer
-
- addCone(Image3DUniverse) - Static method in class ij3d.gui.PrimitiveDialogs
-
- addCone(String, String, String, String) - Static method in class ij3d.ImageJ3DViewer
-
Add a cone into the current 3D universe
- addConnectedTile(Tile<?>) - Method in class mpicbg.models.Tile
-
Add a
Tile
to the set of connected tiles.
- addConnectedTile(Tile) - Method in class stitching.model.Tile
-
Add a
Tile
to the set of connected tiles.
- AddConstant - Class in imglib.ops.operator.unary
-
TODO
- AddConstant(double) - Constructor for class imglib.ops.operator.unary.AddConstant
-
- addContent(ImagePlus, File) - Method in class ij3d.Executer
-
- addContent(ImagePlus, Color3f, String, int, boolean[], int, int) - Method in class ij3d.Image3DUniverse
-
Add the specified image as a new Content to the universe.
- addContent(ImagePlus, int, int) - Method in class ij3d.Image3DUniverse
-
Add the specified image as a new Content to the universe.
- addContent(ImagePlus, int) - Method in class ij3d.Image3DUniverse
-
Add the specified image as a new Content to the universe.
- addContent(Content) - Method in class ij3d.Image3DUniverse
-
Add the specified Content to the universe.
- addContent(Collection<Content>) - Method in class ini.trakem2.display.Display3D
-
- addContent(Content) - Method in class ini.trakem2.display.Display3D
-
- addContentFromFile() - Method in class ij3d.Executer
-
- addContentFromImage(ImagePlus) - Method in class ij3d.Executer
-
- addContentLater(Content) - Method in class ij3d.Image3DUniverse
-
Add the specified Content to the universe.
- addContentLater(String) - Method in class ij3d.Image3DUniverse
-
- addContentLater(Collection<Content>) - Method in class ij3d.Image3DUniverse
-
Add the specified collection of Content to the universe.
- addContour(Element, ReconstructSection) - Method in interface edu.utexas.clm.reconstructreader.reconstruct.ContourSet
-
- addContour(Element, ReconstructSection) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructAreaList
-
- addContour(Element, ReconstructSection) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructProfileList
-
- addContour(Element, ReconstructSection) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructZTrace
-
- addCorrespondence(ExtendedPointMatch) - Method in class selection.Select_Points
-
- addCorrespondences(List<PairwiseMatch>) - Method in class spim.process.interestpointregistration.optimizationtypes.GlobalOptimizationType
-
Add all correspondences the list for those that are compared here
This method can be overwritten if saving, adding & clearing of correspondences is different for a certain type of registration
- addCross(ImagePlus, int, int) - Method in class selection.Select_Points
-
- addCrossLink(long, long, long) - Method in class ini.trakem2.persistence.DBLoader
-
- addCrossLink(long, long, long) - Method in class ini.trakem2.persistence.Loader
-
- addCtrlHint() - Method in class ij3d.gui.LUTDialog
-
- addCursor(Cursor<T>) - Method in class mpicbg.imglib.image.Image
-
- addCustomMesh(CustomMesh, String) - Method in class ij3d.Image3DUniverse
-
Add a custom mesh to the universe.
- addCustomMesh(CustomMultiMesh, String) - Method in class ij3d.Image3DUniverse
-
Add a CustomMultiMesh to the universe.
- addData(byte) - Method in class adt.PixelStats
-
- addDataEditStep(Set<? extends Displayable>) - Method in class ini.trakem2.display.LayerSet
-
A new undo step for the "data" field of all Displayable in the set.
- addDefaultFeatures() - Method in class trainableSegmentation.FeatureStack
-
Add the default features to the feature stack
- addDefaultFiles() - Method in class fiji.packaging.Packager
-
- addDefaultTableMouseListener() - Method in class bigwarp.BigWarp
-
- addDependent(double[]) - Method in class ini.trakem2.vector.VectorString3D
-
Add an array that will get resampled along; must be of the same length as the value returned by length()
- addDependents(Collection<DoStep>) - Method in class ini.trakem2.display.Displayable.DoEdits
-
- addDependents(Set<DoStep>) - Method in class ini.trakem2.display.LayerSet.DoChangeTrees
-
- addDerivatives(double, int, int) - Method in class trainableSegmentation.FeatureStack
-
Add derivatives features to current stack
- addDetection(T) - Method in class mpicbg.spim.registration.detection.DetectionStructure
-
- addDirectoryField(String, String) - Method in class fiji.util.gui.GenericDialogPlus
-
- addDirectoryField(String, String, int) - Method in class fiji.util.gui.GenericDialogPlus
-
- addDirectoryField(Container, String) - Static method in class gui.GuiBuilder
-
- addDirectoryOrFileField(String, String) - Method in class fiji.util.gui.GenericDialogPlus
-
- addDirectoryOrFileField(String, String, int) - Method in class fiji.util.gui.GenericDialogPlus
-
- addDiscsTo3DViewer(Image3DUniverse, Color, ImagePlus) - Method in class sc.fiji.snt.Path
-
Deprecated.
- addDiscsTo3DViewer(Image3DUniverse, Color3f, ImagePlus) - Method in class sc.fiji.snt.Path
-
Deprecated.
- addDisplayChangeListener(ImageWindow, DisplayChangeListener) - Static method in class OpenImage5DAdapter
-
- addDisplayChangeListener(DisplayChangeListener) - Method in class OpenImage5DWindow
-
- addDisplayChangeListener(ImageWindow, DisplayChangeListener) - Static method in class OpenStackAdapter
-
- addDisplayChangeListener(DisplayChangeListener) - Method in class OpenStackWindow
-
- addDisplaySettingsChangeListener(DisplaySettingsListener) - Method in class fiji.plugin.trackmate.gui.panels.ConfigureViewsPanel
-
Adds the specified
DisplaySettingsListener
to the collection of
listeners that will be notified when a display settings change is made on
this GUI.
- addDoG(float, float) - Method in class trainableSegmentation.FeatureStack
-
Add difference of Gaussians to feature stack (single thread version)
- addDoubleSlider(String, int, int) - Method in class spimopener.OpenerGenericDialog
-
- addDoubleSlider(String, int, int, int, int) - Method in class spimopener.OpenerGenericDialog
-
- addDragOverlay(BigWarpDragOverlay) - Method in class bdv.viewer.BigWarpViewerPanel
-
- added(BenesNamedPoint) - Method in class ij3d.pointlist.PointListPanel
-
- added(BenesNamedPoint) - Method in class ij3d.pointlist.PointListShape
-
- added(BenesNamedPoint) - Method in interface vib.PointList.PointListListener
-
- added(BenesNamedPoint) - Method in class vib.Points_Dialog
-
- addEdge(Spot, Spot, double) - Method in class fiji.plugin.trackmate.Model
-
Creates a new edge between two spots, with the specified weight.
- addEdge(DefaultWeightedEdge) - Method in class fiji.plugin.trackmate.ModelChangeEvent
-
- addEdge(double, double, double, double) - Method in class fiji.plugin.trackmate.util.XYEdgeSeries
-
- addEdge(Edge) - Method in class sc.fiji.analyzeSkeleton.Graph
-
Add edge to the graph.
- addEdgeAnalyzer(EdgeAnalyzer) - Method in class fiji.plugin.trackmate.Settings
-
- addEdgeAnalyzer(int, EdgeAnalyzer) - Method in class fiji.plugin.trackmate.Settings
-
Adds a
EdgeAnalyzer
to the
List
of edge analyzers
configured, at the specified index.
- addEdgeManually(mxCell) - Method in class fiji.plugin.trackmate.visualization.trackscheme.TrackScheme
-
This method is called when the user has created manually an edge in the
graph, by dragging a link between two spot cells.
- addEdgeToSelection(DefaultWeightedEdge) - Method in class fiji.plugin.trackmate.SelectionModel
-
- addEdgeToSelection(Collection<DefaultWeightedEdge>) - Method in class fiji.plugin.trackmate.SelectionModel
-
- addEditor() - Method in class fiji.Wiki_Editor
-
- addedPatchFrom(String, Patch) - Method in class ini.trakem2.persistence.FSLoader
-
All backslashes are converted to slashes to avoid havoc in MSWindows.
- addedPatchFrom(String, Patch) - Method in class ini.trakem2.persistence.Loader
-
Subclasses can override this method to register the URL of the imported image.
- AddElement(byte[], int, int, int, int, int) - Method in class view5d.View5D
-
- AddElement(short[], int, int, int, int, int) - Method in class view5d.View5D
-
- AddElement(char[], int, int, int, int, int) - Method in class view5d.View5D
-
- AddElement(float[], int, int, int, int, int) - Method in class view5d.View5D
-
- AddElement(double[], int, int, int, int, int) - Method in class view5d.View5D
-
- AddElementC(float[], int, int, int, int, int) - Method in class view5d.View5D
-
- addEmptyPoint() - Method in class vib.Points_Dialog
-
- addEnablerListener(Checkbox, Component[], Component[]) - Static method in class ini.trakem2.utils.Utils
-
A helper for GenericDialog checkboxes to control other the enabled state of other GUI elements in the same dialog.
- addEnablerListener(Checkbox, Component[], Component[]) - Static method in class Stitching_3D
-
- addEntropy(int, int) - Method in class trainableSegmentation.FeatureStack
-
Add entropy filter to current stack
- addEntry(Comparable<Object>, DefaultListModel) - Static method in class loci.plugins.config.ConfigWindow
-
- addEqualLabels(int, int) - Method in class mpicbg.spim.registration.threshold.ConnectedComponent
-
- addErodedBinaryData(ImagePlus, int, String, String) - Method in class trainableSegmentation.WekaSegmentation
-
Add eroded version of label image as binary data
- addExample(int, Roi, int) - Method in class trainableSegmentation.WekaSegmentation
-
Adds a ROI to the list of examples for a certain class
and slice.
- addExternalTransformation(ViewStructure) - Method in class mpicbg.spim.Reconstruction
-
- addFace(int, int, int) - Method in class customnode.FullInfoMesh
-
- addFatPoint(String, LayerSet, double, double, double, double, Color) - Static method in class ini.trakem2.display.Display3D
-
Expects uncalibrated wx,wy,wz, (i.e.
- addFeaturePenaltyToSettings(Map<?, ?>, Object, Object, Object, StringBuilder) - Static method in class fiji.plugin.trackmate.tracking.LAPUtils
-
Utility method to put a value in a map, contained in a mother map.
- addFeaturesMT(ImagePlus) - Method in class trainableSegmentation.FeatureStack
-
Add features based on a list of filters in a multi-thread fashion
- addFields(GenericDialog) - Method in class lenscorrection.Distortion_Correction.BasicParam
-
- addFields(GenericDialog) - Method in class lenscorrection.Distortion_Correction.PluginParam
-
- addFields(GenericDialog, FloatArray2DMOPS.Param) - Static method in class mpicbg.ij.MOPS
-
- addFields(GenericDialog) - Method in class mpicbg.ij.plugin.AbstractBlockMatching
-
- addFields(GenericDialog, FloatArray2DSIFT.Param) - Static method in class mpicbg.ij.SIFT
-
- addFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.Param
-
- addFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.ParamOptimize
-
- addFile(String, boolean) - Method in class fiji.packaging.Packager
-
- addFile(File) - Method in class org.imagearchive.lsm.toolbox.gui.LsmImageTableModel
-
- addFileField(String, String) - Method in class fiji.util.gui.GenericDialogPlus
-
- addFileField(String, String, int) - Method in class fiji.util.gui.GenericDialogPlus
-
- addFileField(Container, String) - Static method in class gui.GuiBuilder
-
- addFileField(String, String) - Method in class org.janelia.thickness.plugin.NonBlockingGenericDialogWithFileField
-
- addFileField(String, String, int) - Method in class org.janelia.thickness.plugin.NonBlockingGenericDialogWithFileField
-
- addFileSaveField(Container, String) - Static method in class gui.GuiBuilder
-
- addFill(Fill) - Method in class sc.fiji.snt.PathAndFillManager
-
- addFilterPanel() - Method in class fiji.plugin.trackmate.gui.panels.components.FilterGuiPanel
-
- addFilterPanel(FeatureFilter) - Method in class fiji.plugin.trackmate.gui.panels.components.FilterGuiPanel
-
- addFilterPanel(String) - Method in class fiji.plugin.trackmate.gui.panels.components.FilterGuiPanel
-
- addFirst(Transform) - Method in class vib.transforms.OrderedTransformations
-
- addFirst(OrderedTransformations) - Method in class vib.transforms.OrderedTransformations
-
- addFittedMinimum(int) - Method in class sc.fiji.timelapse.Extrema
-
Fit a parabola to the interval [left;right].
- addFixedPoint(RealPoint, boolean) - Method in class bigwarp.BigWarp.MouseLandmarkListener
-
Adds a point in the moving and fixed images at the same point.
- addFrame() - Method in class video.Edit_Video
-
- addFrames(ImagePlus, int, int) - Static method in class video2.Add_Empty_Frame
-
- addGabor(ImagePlus, double, double, double, double, int) - Method in class trainableSegmentation.FeatureStack
-
Add Gabor features to current stack
- addGaussianBlur(float) - Method in class trainableSegmentation.FeatureStack
-
Add Gaussian blur slice to current stack
- addGaussianNoise(Image<FloatType>, Random, float, boolean) - Static method in class mpicbg.spim.postprocessing.deconvolution2.AdjustInput
-
Adds additive gaussian noise: i = i + gauss(x, sigma)
- addGaussianNoiseAddMul(Image<FloatType>, Random, float, boolean) - Static method in class mpicbg.spim.postprocessing.deconvolution2.AdjustInput
-
Adds additive and multiplicative gaussian noise: i = i*gauss(x,sigma) + gauss(x, sigma)
- addGeometricConsensusFilterFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.Param
-
- addGradient(float) - Method in class trainableSegmentation.FeatureStack
-
Add Sobel filter version of the original image
- addGroup(SourceGroup) - Method in class bdv.viewer.BasicViewerState
-
Add group
to the state.
- addGroup(SourceGroup) - Method in class bdv.viewer.state.ViewerState
-
Deprecated.
- addGroup(SourceGroup) - Method in class bdv.viewer.SynchronizedViewerState
-
Add group
to the state.
- addGroup(SourceGroup) - Method in class bdv.viewer.ViewerPanel
-
- addGroup(SourceGroup) - Method in interface bdv.viewer.ViewerState
-
Add group
to the state (optional operation).
- addGroup(Collection<Tree>, String) - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics
-
Adds a comparison group to the analysis queue.
- addGroup(Collection<Tree>, String, String...) - Method in class sc.fiji.snt.analysis.GroupedTreeStatistics
-
Adds a comparison group to the analysis queue.
- addGroups(Collection<? extends SourceGroup>) - Method in class bdv.viewer.BasicViewerState
-
Add all groups in collection
to the state.
- addGroups(Collection<? extends SourceGroup>) - Method in class bdv.viewer.SynchronizedViewerState
-
Add all groups in collection
to the state.
- addGroups(Collection<? extends SourceGroup>) - Method in interface bdv.viewer.ViewerState
-
Add all groups in collection
to the state (optional operation).
- addHandle(int, int) - Method in class mpicbg.ij.InteractiveMapping
-
- addHandle(int, int) - Method in class sc.fiji.timelapse.PolygonRoiPublic
-
- addHandle(int, int) - Method in class Transform_MovingLeastSquaresMesh
-
- addHandle(int, int) - Method in class Transform_ThinPlateSpline
-
- addHessian(float) - Method in class trainableSegmentation.FeatureStack
-
Add Hessian features from original image (single thread version).
- addHSB() - Method in class trainableSegmentation.FeatureStack
-
Add HSB features
- addHyperlink(String) - Method in class sc.fiji.snt.gui.EnhancedWaitForUserDialog
-
Deprecated.
- addHyperLink(GenericDialog, String, String) - Static method in class spim.fiji.plugin.util.GUIHelper
-
- addHyperLinkListener(MultiLineLabel, String) - Static method in class fiji.plugin.Bead_Registration
-
- addHyperLinkListener(MultiLineLabel, String) - Static method in class spim.fiji.plugin.util.GUIHelper
-
- addHyperLinkListener(MultiLineLabel, String) - Static method in class stitching.CommonFunctions
-
- addHyperlinkMessage(String, Font, Color, String) - Method in class sc.fiji.snt.gui.EnhancedGenericDialog
-
Deprecated.
Appends a message to the specified dialog consisting of one or more lines
of text, and assigns a functional URL to it.
- addIcospheres(List<Point3f>, Color3f, int, float, String) - Method in class ij3d.Image3DUniverse
-
At every
Point3f
in @param points, place an icosphere created with @param
subdivisions and @param radius.
- addICPCorrespondence(T) - Method in class mpicbg.spim.registration.detection.DetectionView
-
- addICPCorrespondence(T, double) - Method in class mpicbg.spim.registration.detection.DetectionView
-
- addIfValid(Algorithm<T>, List<Algorithm<T>>) - Method in class sc.fiji.coloc.Coloc_2
-
Adds the provided Algorithm to the list if it is not null.
- addImage(String) - Method in class fiji.util.gui.GenericDialogPlus
-
Adds an image to the generic dialog
- addImage(URL) - Method in class fiji.util.gui.GenericDialogPlus
-
Adds an image to the generic dialog
- addImage(ImageIcon) - Method in class fiji.util.gui.GenericDialogPlus
-
Adds an image to the generic dialog
- addImage(Image, String, String) - Method in class sc.fiji.coloc.results.PDFWriter
-
Prints an image into the opened PDF.
- addImage(Image, String) - Method in class sc.fiji.io.PDF_Writer
-
- addImageChoice(String, String) - Method in class fiji.util.gui.GenericDialogPlus
-
- addImageList(GenericDialog, String, String, AmiraParameters.IsA) - Static method in class amira.AmiraParameters
-
- addImagePlusPair(ImagePlus, ImagePlus) - Method in class util.Histogram_2D
-
- addImagePlusPair(ImagePlus, ImagePlus, int) - Method in class util.Histogram_2D
-
- addImagePlusPair(ImagePlus, ImagePlus, double, double, double, double, int, int) - Method in class util.Histogram_2D
-
- addImageToList(ImagePlus, String) - Method in class sc.fiji.coloc.results.PDFWriter
-
- addImageWindowListener(WindowListener) - Method in class org.siox.example.ControlJPanel
-
Add a WindowListener
to any image display window (except
internal frames), wether it is now open or opened in the future.
- addImageWindowListener(InternalFrameListener) - Method in class org.siox.example.ControlJPanel
-
Add an InternalFrameListener
to any internal frame
for displaying an image.
- addImgLibAlgorithms() - Method in class fiji.expressionparser.ImgLibParser
-
Add ImgLib algorithms to the parser, such as gaussian convolution.
- addingNode(SearchNode) - Method in class sc.fiji.snt.SearchThread
-
This method can be overridden if one needs to find out when a point was
first discovered.
- addInstant(ContentInstant) - Method in class ij3d.Content
-
- addInteractiveBehavior(InteractiveBehavior) - Method in class ij3d.DefaultUniverse
-
- addInterestPointList(String, InterestPointList) - Method in class spim.fiji.spimdata.interestpoints.ViewInterestPointLists
-
- addInterpolationModeListener(InterpolationModeListener) - Method in class bdv.viewer.ViewerPanel
-
- addInverseEnablerListener(Checkbox, Component[], Component[]) - Static method in class Stitching_3D
-
- addIOButtons(GenericDialogPlus) - Method in class fiji.tool.AbstractTrackingTool
-
- addItem(int, int, String) - Method in class ini.trakem2.display.Dissector
-
For reconstruction purposes from XML.
- additionalSigmaX - Variable in class spim.fiji.plugin.interestpointdetection.DifferenceOf
-
- additionalSigmaY - Variable in class spim.fiji.plugin.interestpointdetection.DifferenceOf
-
- additionalSigmaZ - Variable in class spim.fiji.plugin.interestpointdetection.DifferenceOf
-
- addJGraphTEdge(DefaultWeightedEdge) - Method in class fiji.plugin.trackmate.visualization.trackscheme.JGraphXAdapter
-
- addJGraphTVertex(Spot) - Method in class fiji.plugin.trackmate.visualization.trackscheme.JGraphXAdapter
-
- addJob(Bureaucrat) - Method in class ini.trakem2.persistence.Loader
-
Adds a new job to monitor.
- addKey(String, File) - Method in class edu.utexas.clm.archipelago.network.shell.NodeShellParameters
-
- addKey(String, String) - Method in class edu.utexas.clm.archipelago.network.shell.NodeShellParameters
-
- addKey(String, int) - Method in class edu.utexas.clm.archipelago.network.shell.NodeShellParameters
-
- addKey(String, float) - Method in class edu.utexas.clm.archipelago.network.shell.NodeShellParameters
-
- addKeyEventPostProcessor(KeyEventPostProcessor) - Method in class bigwarp.BigWarp
-
- addKeyListener(Component) - Method in class fiji.tool.AbstractTool
-
- addKeyListener(KeyListener) - Method in class sc.fiji.i5d.gui.ScrollbarWithLabel
-
- addKuwaharaFeatures(ImagePlus, int, int, int) - Method in class trainableSegmentation.FeatureStack
-
Add Kuwahara filter features to the current stack
- addLabel(int) - Method in class mpicbg.spim.registration.threshold.ConnectedComponent
-
- addLabel(String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Adds an annotation label to the scene.
- addLabel(String) - Method in class util.ModelessQuestions
-
- addLabeledData(ImagePlus, FeatureStack) - Method in class trainableSegmentation.WekaSegmentation
-
Add instances from a labeled image.
- addLabeledData(ImageProcessor, FeatureStack, String[], int) - Method in class trainableSegmentation.WekaSegmentation
-
Add instances reading the pixel classes from a label image.
- addLabeledData(ImageProcessor, FeatureStack, int[], int) - Method in class trainableSegmentation.WekaSegmentation
-
Add instances reading the pixel classes from a label image.
- addLabeledData(ImagePlus, ImagePlus) - Method in class trainableSegmentation.WekaSegmentation
-
Add labeled training data from input and label images.
- addLabeledData(ImagePlus, ImagePlus, String[], int) - Method in class trainableSegmentation.WekaSegmentation
-
Add training data from input and labeled images.
- addLabeledData(ImagePlus, ImagePlus, int[], int) - Method in class trainableSegmentation.WekaSegmentation
-
Add training data from input and labeled images.
- addLabeledNumericSpinner(Container, String, int, int, int, ChangeListener) - Static method in class gui.GuiBuilder
-
- addLabeledSpinner(Container, String, SpinnerModel) - Static method in class gui.GuiBuilder
-
- addLabelList(Container) - Static method in class oldsegmenters.Segmentator_
-
- addLabelList(Container) - Static method in class oldsegmenters.Segmenter_
-
- addLaplacian(double) - Method in class trainableSegmentation.FeatureStack
-
Add Laplacian features to current stack
- addLast(Transform) - Method in class vib.transforms.OrderedTransformations
-
- addLast(OrderedTransformations) - Method in class vib.transforms.OrderedTransformations
-
- addLayer(LayerSet, Layer) - Method in class ini.trakem2.tree.LayerTree
-
Used by the Loader.importStack and the "many new layers" command.
- addLayerChoice(String, Layer, GenericDialog) - Static method in class ini.trakem2.utils.Utils
-
- addLayerContentStep(Layer) - Method in class ini.trakem2.display.LayerSet
-
For the Displayable contained in a Layer: their number, and their stack order.
- addLayerEditedStep(Layer) - Method in class ini.trakem2.display.LayerSet
-
For the Z and thickness of a layer.
- addLayerEditedStep(List<Layer>) - Method in class ini.trakem2.display.LayerSet
-
For the Z and thickness of a list of layers.
- addLayerRangeChoices(Layer, GenericDialog) - Static method in class ini.trakem2.utils.Utils
-
- addLayerRangeChoices(Layer, Layer, GenericDialog) - Static method in class ini.trakem2.utils.Utils
-
- addLayoutComponent(Component, Object) - Method in class sc.fiji.i5d.gui.Image5DLayout
-
- addLayoutComponent(String, Component) - Method in class sc.fiji.i5d.gui.Image5DLayout
-
- addLeafs(List<? extends Thing>, Runnable) - Method in class ini.trakem2.tree.DNDTree
-
Will add only those for which a node doesn't exist already.
- addLine3D(Line3D) - Method in class jRenderer3D.JRenderer3D
-
Adds a single 3D line to the 3D scene.
- addLine3D(int, int, int, int, int, int, Color) - Method in class jRenderer3D.JRenderer3D
-
Adds a single 3D line to the 3D scene.
- addLineMesh(List<Point3f>, Color3f, String, boolean) - Method in class ij3d.Image3DUniverse
-
Add a custom mesh, in particular a line mesh (a set of lines in 3D) to the
universe.
- addLines(Point3f[]) - Method in class customnode.CustomLineMesh
-
- addLines3D(Line3D[]) - Method in class jRenderer3D.JRenderer3D
-
Adds an array of lines to the 3D scene.
- addLipschitzFilter(ImagePlus, boolean, boolean, double) - Method in class trainableSegmentation.FeatureStack
-
Add Lipschitz filter image to current stack
- addListener(NodeStateListener) - Method in class edu.utexas.clm.archipelago.network.node.ClusterNode
-
Adds a NodeStateListener to the list of listeners that are notified when the state of this
ClusterNode changes.
- addListener(FileListener) - Method in class fsalign.FolderWatcher
-
- addListener(LUTDialog.Listener) - Method in class ij3d.gui.LUTDialog
-
- addListener(SNTListener) - Method in class sc.fiji.snt.SNT
-
- addListener(SelectedViewDescriptionListener<AS>) - Method in class spim.fiji.spimdata.explorer.ViewSetupExplorer
-
- addListener(SelectedViewDescriptionListener<AS>) - Method in class spim.fiji.spimdata.explorer.ViewSetupExplorerPanel
-
- addListeners() - Method in class bigwarp.WarpVisFrame
-
- addListeners(GenericDialog, Choice, MyMultiLineLabel, ArrayList<MultiViewDatasetDefinition>) - Method in class spim.fiji.plugin.Define_Multi_View_Dataset
-
- addListeners(GenericDialog, TextField, TextField, TextField, Checkbox, Label) - Method in class spim.fiji.plugin.Merge_Cluster_Jobs
-
- addListeners(GenericDialog, TextField, Label, Label) - Method in class spim.fiji.plugin.queryXML.GenericLoadParseQueryXML
-
- addListeners(GenericDialog, Vector<?>, Label, long[]) - Method in class spim.process.fusion.boundingbox.AutomaticBoundingBox
-
- addListeners(ImgExport) - Method in class spim.process.fusion.boundingbox.BoundingBoxGUI.ManageListeners
-
- addListeners(GenericDialog, Choice, Label, Label) - Method in class spim.process.fusion.boundingbox.PreDefinedBoundingBox
-
- AddLookUpTable(int, byte[], byte[], byte[]) - Static method in class view5d.Bundle
-
- AddLookUpTable(int, byte[], byte[], byte[]) - Method in class view5d.My3DData
-
- addLowerRightPoint(Point) - Method in class adt.Connectivity2D
-
the contract of calling this method is that the new point must be gauranteed to
be the most far right lowest point (i.e.
- addLThresh(double) - Method in class view5d.My3DData
-
- AddMarkedElement() - Method in class view5d.My3DData
-
- addMarker(CellCntrMarker) - Method in class sc.fiji.cellCounter.CellCntrMarkerVector
-
- addMaskPoint(int, int) - Method in class bunwarpj.PointHandler
-
Add a point to the mask.
- addMatch(PointMatch) - Method in class mpicbg.models.Tile
-
- addMatch(PointMatch) - Method in class stitching.model.Tile
-
Add one match.
- addMatches(Collection<PointMatch>) - Method in class mpicbg.models.Tile
-
- addMatches(Collection<PointMatch>) - Method in class stitching.model.Tile
-
- addMatchWeightedByDistance(PointMatch, double) - Method in class mpicbg.models.MovingLeastSquaresMesh
-
Add a PointMatch to all Tiles weighted by its distance to the
corresponding vertex.
- addMaterial(String, double, double, double) - Method in class amira.AmiraParameters
-
- addMaterial(String, int, int, int) - Static method in class Segmentation_Editor
-
- addMaterial() - Method in class vib.segment.MaterialList
-
- addMax(float) - Method in class trainableSegmentation.FeatureStack
-
Add maximum filter to current feature stack.
- addMean(float) - Method in class trainableSegmentation.FeatureStack
-
Add mean filter to current stack
- addMedian(float) - Method in class trainableSegmentation.FeatureStack
-
Add median filter to the current feature stack.
- addMembraneFeatures(int, int) - Method in class trainableSegmentation.FeatureStack
-
Add membrane features to the stack (single thread version)
- addMesh(ImagePlus) - Method in class ij3d.Image3DUniverse
-
Add a new image as a content, displaying it as an isosurface.
- addMesh(ImagePlus, int) - Method in class ij3d.Image3DUniverse
-
Add a new image as a content, displaying it as an isosurface.
- addMesh(ImagePlus, Color3f, String, int, boolean[], int) - Method in class ij3d.Image3DUniverse
-
Add a new image as a content, displaying it as an iso-surface.
- addMesh(List, Color3f, String, float, int) - Method in class ij3d.Image3DUniverse
-
- addMesh(List<Point3f>, Color3f, String, int) - Method in class ij3d.Image3DUniverse
-
- addMesh(LayerSet, VectorString3D, String, Color) - Static method in class ini.trakem2.display.Display3D
-
Creates a mesh from the given VectorString3D, which is unbound to any existing Pipe.
- addMesh(LayerSet, VectorString3D, String, Color, double[], float) - Static method in class ini.trakem2.display.Display3D
-
Creates a mesh from the given VectorString3D, which is unbound to any existing Pipe.
- addMesh(OBJMesh) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Loads a Wavefront .OBJ file.
- addMeshes(Image3DUniverse, String) - Static method in class isosurface.AmiraSurface
-
- addMessage(String) - Method in class ini.trakem2.utils.OptionPanel
-
- addMessage(GenericDialog, String[], Font, Color) - Static method in class spim.fiji.plugin.util.MyMultiLineLabel
-
Adds a message consisting of one or more lines of text,
which will be displayed using the specified font and color.
- addMin(float) - Method in class trainableSegmentation.FeatureStack
-
Add minimum filter to current feature stack.
- addMinimum(int) - Method in class sc.fiji.timelapse.Extrema
-
- addModelChangeListener(ModelChangeListener) - Method in class fiji.plugin.trackmate.Model
-
- addModuleListener(ModuleListener) - Static method in class vib.app.module.Module
-
- addMouseMotionListener(ImageCanvas) - Method in class fiji.tool.AbstractTool
-
- addMouseWheelListener(ImageWindow) - Method in class fiji.tool.AbstractTool
-
- addNatMethBeadsPaper(GenericDialog) - Static method in class spim.fiji.plugin.util.GUIHelper
-
- addNatMethBeadsPaper(GenericDialog, String) - Static method in class spim.fiji.plugin.util.GUIHelper
-
- addNeighborPair(int, byte[], int, int) - Method in class SRM_
-
- addNeighborPair(int, byte[], byte[], int) - Method in class SRM_
-
- addNeighbors(int, int) - Method in class trainableSegmentation.FeatureStack
-
Add 8 neighbors of the original image as features
- AddNewBalloon(int[], int[]) - Method in class sc.fiji.balloonSegmentation.structure.BalloonPopulation
-
Add a balloon with custom shape defined by arrays X and Y
- AddNewBalloon(int, int) - Method in class sc.fiji.balloonSegmentation.structure.BalloonPopulation
-
Add a circular balloon centrerd on x,y with id ID
- addNewChildType(ProjectThing, String) - Method in class ini.trakem2.tree.TemplateTree
-
Add a new template thing to an existing ProjectThing, so that new instances of template new_child_type can be added to the ProjectThing pt.
- addNewChildType(TemplateThing, String) - Method in class ini.trakem2.tree.TemplateTree
-
tt_parent is the parent TemplateThing
tet_child is the child to add to tt parent, and to insert as child to all nodes that host the tt parent.
- addNewImage(ImagePlus) - Method in class ini.trakem2.persistence.Loader
-
- addNewImage(ImagePlus, double, double) - Method in class ini.trakem2.persistence.Loader
-
Mipmaps for this image are generated asynchronously.
- addNewPoint() - Method in class landmarks.NamedPointSet
-
- addNode(Node<T>, Node<T>, byte) - Method in class ini.trakem2.display.Tree
-
Will call calculateBoundingBox and repaint.
- addNode(PointInImage) - Method in class sc.fiji.snt.Path
-
Appends a node to this Path.
- addNode(SearchNode, boolean) - Method in class sc.fiji.snt.SearchThread
-
- AddNoise - Class in imglib.ops.operator.unary
-
TODO
- AddNoise(double, double, double) - Constructor for class imglib.ops.operator.unary.AddNoise
-
- addNotify() - Method in class spim.fiji.plugin.util.MyMultiLineLabel
-
- addNumericField(String, double, int) - Method in class ini.trakem2.utils.OptionPanel
-
- addNumericField(String, double, int, OptionPanel.Setter) - Method in class ini.trakem2.utils.OptionPanel
-
- addNumericField(String, int) - Method in class ini.trakem2.utils.OptionPanel
-
- addNumericField(String, int, OptionPanel.Setter) - Method in class ini.trakem2.utils.OptionPanel
-
- addObject(Object3D) - Method in class Utilities.Counter3D
-
Add the provided Object3D to the list
- addObserver(Observer) - Method in class imglib.ops.operation.AssignOperation
-
- addOctree(String, String) - Method in class ij3d.Image3DUniverse
-
- addOrthoslice(ImagePlus) - Method in class ij3d.Image3DUniverse
-
Add a new image as a content, displaying it as orthoslices.
- addOrthoslice(ImagePlus, int) - Method in class ij3d.Image3DUniverse
-
Add a new image as a content, displaying it as orthoslices.
- addOrthoslice(ImagePlus, Color3f, String, int, boolean[], int) - Method in class ij3d.Image3DUniverse
-
Add a new image as a content, displaying it as orthoslices.
- addOrthoslice(String, String, String, String, String, String, String) - Static method in class ij3d.ImageJ3DViewer
-
- addOverlay(BigWarpOverlay) - Method in class bdv.viewer.BigWarpViewerPanel
-
- addOverlay(Roi) - Method in class fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayer
-
- addOverlay(OverlayedImageCanvas.Overlay) - Method in class fiji.util.gui.OverlayedImageCanvas
-
- addOverlay(Collection<OverlayedImageCanvas.Overlay>) - Method in class fiji.util.gui.OverlayedImageCanvas
-
Add the collection of overlays to the display list of this canvas
- addOverlayAnimator(OverlayAnimator) - Method in class bdv.viewer.ViewerPanel
-
- addp(int, int, double) - Method in class parObject
-
- addp(double, double, double) - Method in class parObject
-
- addPanel(Panel) - Method in class ij3d.pointlist.PointListDialog
-
Displays an optional panel at the bottom of the window.
- addPanelIntoDialog(Panel) - Method in class Series_Labeler
-
The container Panel is added to the generic dialog.
- addPanelsToDialog(Panel, Panel[]) - Method in class Series_Labeler
-
Adds different Panels to a container Panel.
- addPassiveVertex(Vertex) - Method in class mpicbg.models.SpringMesh
-
- addPath(Path) - Method in class sc.fiji.snt.PathAndFillManager
-
Adds a new path.
- addPath(Path, boolean, boolean) - Method in class sc.fiji.snt.PathAndFillManager
-
- addPath(Path, boolean, boolean, boolean) - Method in class sc.fiji.snt.PathAndFillManager
-
- addPath(Path, int, int) - Method in class sc.fiji.snt.PathAndFillManager
-
- addPathAndFillListener(PathAndFillListener) - Method in class sc.fiji.snt.PathAndFillManager
-
Adds a PathAndFillListener.
- addPathPointsToShollList(Path, double, double, double, List<ShollAnalysisDialog.ShollPoint>) - Static method in class sc.fiji.snt.gui.ShollAnalysisDialog
-
Deprecated.
- addPeak(int) - Method in class sc.fiji.timelapse.Peak_Counter_Tool
-
- addPlugIns(JPopupMenu, String, Project, Callable<Displayable>) - Static method in class ini.trakem2.utils.Utils
-
Returns false if none to add.
- addPlugIns(String, Project, Callable<Displayable>) - Static method in class ini.trakem2.utils.Utils
-
Returns null if none to add.
- addPoint(int, int) - Method in class adt.Connectivity2D
-
- addPoint(Point) - Method in class adt.Connectivity2D
-
- addPoint(int, int) - Method in class adt.Points
-
- addPoint(Point) - Method in class adt.Points
-
- addPoint(double[], boolean, BigWarpViewerPanel) - Method in class bigwarp.BigWarp
-
Updates the global variable ptBack
- addPoint(double[], boolean) - Method in class bigwarp.BigWarp
-
Updates the global variable ptBack
- addPoint(int, int) - Method in class bunwarpj.PointHandler
-
Add a point to the list of points.
- addPoint(Point3f) - Method in class customnode.CustomPointMesh
-
- addPoint(Content, int, int) - Method in class ij3d.behaviors.Picker
-
Adds a landmark point specfied by the canvas position
- addPoint(Content, MouseEvent) - Method in class ij3d.behaviors.Picker
-
Adds a landmark point specfied by the position of the MouseEvent.
- addPoint(double, double, long, double) - Method in class ini.trakem2.display.Ball
-
Add a point either at the end or between two existing points, with accuracy depending on magnification.
- addPoint(int, int, double, double, long) - Method in class ini.trakem2.display.Pipe
-
Add a point either at the end or between two existing points, with accuracy depending on magnification.
- addPoint(int, int, long, double) - Method in class ini.trakem2.display.Polyline
-
Add a point either at the end or between two existing points, with accuracy depending on magnification.
- addPoint(double, double, double, double) - Method in class ini.trakem2.display.Profile
-
Add a point either at the end or between two existing points, with accuracy depending on magnification.
- addPoint(Point) - Method in class sc.fiji.analyzeSkeleton.Vertex
-
Add point to the vertex.
- addPoint(ShollPoint) - Method in class sc.fiji.snt.analysis.sholl.ProfileEntry
-
- addPoint3D(Point3D) - Method in class jRenderer3D.JRenderer3D
-
Adds a single
Point3D
to the 3D scene.
- addPoint3D(int, int, int, int, Color, int) - Method in class jRenderer3D.JRenderer3D
-
Adds a point to the 3D scene.
- addPoint3D(int, int, int, int, int, int) - Method in class jRenderer3D.JRenderer3D
-
Adds a point to the 3D scene.
- addPointDescriptorCorrespondence(T) - Method in class mpicbg.spim.registration.detection.DetectionView
-
- addPointDescriptorCorrespondence(T, double) - Method in class mpicbg.spim.registration.detection.DetectionView
-
- addPointDouble(double, double, double) - Method in class sc.fiji.snt.Path
-
- AddPointEdit - Class in bigwarp.landmarks.actions
-
- AddPointEdit(LandmarkTableModel, int, double[], boolean) - Constructor for class bigwarp.landmarks.actions.AddPointEdit
-
- addPointList(String, PointListPanel) - Method in class ij3d.pointlist.PointListDialog
-
Adds the specified PointListPanel.
- addPointListListener(PointList.PointListListener) - Method in class vib.PointList
-
- addPointListPoint(Point3d) - Method in class ij3d.Content
-
Deprecated.
- addPointListPoint(Point3d) - Method in class ij3d.ContentInstant
-
Deprecated.
- addPointMatches(ArrayList<PointMatchGeneric<T>>, Tile<?>, Tile<?>) - Static method in class mpicbg.spim.registration.detection.DetectionRegistration
-
- addPointMatches(ArrayList<PointMatch>, Tile<?>, Tile<?>) - Static method in class process.Matching
-
- addPointMatches(ArrayList<PointMatchGeneric<Detection>>, Tile<?>, Tile<?>) - Static method in class spim.process.interestpointregistration.GlobalOpt
-
- addPointMesh(List<Point3f>, Color3f, String) - Method in class ij3d.Image3DUniverse
-
Add a custom mesh, in particular a point mesh, to the universe.
- addPointMesh(List<Point3f>, Color3f, float, String) - Method in class ij3d.Image3DUniverse
-
Add a custom mesh, in particular a point mesh, to the universe.
- addPoints(Points) - Method in class adt.Points
-
- addPoints(Point3f[]) - Method in class customnode.CustomPointMesh
-
- addPoints(double[], double[], int) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollPlot
-
- addPoints3D(Point3D[]) - Method in class jRenderer3D.JRenderer3D
-
Adds an array with
Point3D
to the 3D scene.
- addPointsAtBegin(double[][], double[][], double[][]) - Method in class ini.trakem2.display.Profile
-
- addPointsAtEnd(double[][], double[][], double[][]) - Method in class ini.trakem2.display.Profile
-
- addPopupMenu(JTable) - Method in class spim.fiji.spimdata.explorer.interestpoint.InterestPointExplorerPanel
-
- addPopupMenu(JTable) - Method in class spim.fiji.spimdata.explorer.registration.RegistrationExplorerPanel
-
- addPopupMenu(JTable) - Method in class spim.fiji.spimdata.explorer.ViewSetupExplorerPanel
-
- addPossible(String) - Method in class loci.plugins.prefs.StringOption
-
Adds a possible value to the list.
- addPostTask(Runnable) - Method in class ini.trakem2.utils.Bureaucrat
-
Add a task to run after the Worker has finished or quit.
- addPreibischLabWebsite(GenericDialog) - Static method in class spim.fiji.plugin.util.GUIHelper
-
- addProfile(ReconstructProfile) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructSection
-
- addProgressListener(SearchProgressCallback) - Method in class sc.fiji.snt.ManualTracerThread
-
- addProgressListener(SearchProgressCallback) - Method in class sc.fiji.snt.SearchThread
-
- addProgressListener(SearchProgressCallback) - Method in class sc.fiji.snt.TubularGeodesicsTracer
-
- addQuad(Point3f, Point3f, Point3f, Point3f) - Method in class customnode.CustomQuadMesh
-
- addQuadMesh(List<Point3f>, Color3f, String) - Method in class ij3d.Image3DUniverse
-
Add a custom mesh, in particular a mesh consisting of quads, to the
universe.
- addQuads(Point3f[]) - Method in class customnode.CustomQuadMesh
-
- addQuery(GenericDialog) - Method in class spim.fiji.plugin.interestpointdetection.DifferenceOfGaussian
-
- addQuery(GenericDialog, Interest_Point_Registration.RegistrationType) - Method in class spim.fiji.plugin.interestpointregistration.InterestPointRegistration
-
adds the questions this registration wants to ask
- addQuery(GenericDialog) - Method in interface spim.fiji.plugin.util.GenericDialogAppender
-
adds the questions this registration wants to ask
- addQuery(GenericDialog, Interest_Point_Registration.RegistrationType) - Method in class spim.process.interestpointregistration.centerofmass.CenterOfMass
-
- addQuery(GenericDialog, Interest_Point_Registration.RegistrationType) - Method in class spim.process.interestpointregistration.geometricdescriptor.RGLDM
-
- addQuery(GenericDialog, Interest_Point_Registration.RegistrationType) - Method in class spim.process.interestpointregistration.geometrichashing.GeometricHashing
-
- addQuery(GenericDialog, Interest_Point_Registration.RegistrationType) - Method in class spim.process.interestpointregistration.icp.IterativeClosestPoint
-
- addRadio(String, String) - Method in class util.ModelessQuestions
-
- addRandomBalancedBinaryData(ImageProcessor, FeatureStack, String, String, int) - Method in class trainableSegmentation.WekaSegmentation
-
Add instances to two classes from a label (binary) image in a random
and balanced way.
- addRandomBalancedBinaryData(ImageProcessor, ImageProcessor, FeatureStack, String, String, int) - Method in class trainableSegmentation.WekaSegmentation
-
Add instances to two classes from a label (binary) image in a random
and balanced way (with repetition).
- addRandomBalancedBinaryData(List<Point3f>[], FeatureStackArray, String, String, int) - Method in class trainableSegmentation.WekaSegmentation
-
Add instances to two classes from lists of coordinates in a random
and balanced way.
- addRandomBalancedBinaryData(List<Point3f>[], FeatureStackArray, ImagePlus, String, String, int) - Method in class trainableSegmentation.WekaSegmentation
-
Add instances to two classes from lists of coordinates in a random
and balanced way.
- addRandomBalancedBinaryData(ImageProcessor, ImageProcessor, ImageProcessor, FeatureStack, String, String, int) - Method in class trainableSegmentation.WekaSegmentation
-
Add instances to two classes from a label (binary) image in a random
and balanced way (with repetition).
- addRandomBalancedBinaryData(ImagePlus, ImagePlus, String, String, int) - Method in class trainableSegmentation.WekaSegmentation
-
Add binary training data from input and label images in a
random and balanced way (same number of samples per class).
- addRandomBalancedBinaryData(ImagePlus, ImagePlus, String, String, int, ImagePlus) - Method in class trainableSegmentation.WekaSegmentation
-
Add binary training data from input and label images in a
random and balanced way (same number of samples per class).
- addRandomBalancedBinaryData(ImagePlus, ImagePlus, String, String, int, ImagePlus, ImagePlus) - Method in class trainableSegmentation.WekaSegmentation
-
Add binary training data from input and label images in a
random and balanced way (same number of samples per class).
- addRandomBalancedBinaryData(ImagePlus, ImagePlus, ImagePlus, String, String, int) - Method in class trainableSegmentation.WekaSegmentation
-
Add binary training data from input and label images in a
random and balanced way (same number of samples per class).
- addRandomBalancedLabeledData(ImageProcessor, FeatureStack, int) - Method in class trainableSegmentation.WekaSegmentation
-
Add instances from a labeled image in a random and balanced way.
- addRandomBalancedLabeledData(ImageProcessor, int[], FeatureStack, int) - Method in class trainableSegmentation.WekaSegmentation
-
Add instances from a labeled image in a random and balanced way.
- addRandomBalancedLabeledData(ImageProcessor, FeatureStack, String[], int) - Method in class trainableSegmentation.WekaSegmentation
-
Add instances reading the pixel classes from a label image in a random
and balanced way.
- addRandomBalancedLabeledData(ImagePlus, ImagePlus, int) - Method in class trainableSegmentation.WekaSegmentation
-
Add training data from input and labeled images in a
random and balanced way (same number of samples per class).
- addRandomBalancedLabeledData(ImagePlus, ImagePlus, int[], int) - Method in class trainableSegmentation.WekaSegmentation
-
Add training data from input and labeled images in a
random and balanced way (same number of samples per class).
- addRandomBalancedLabeledData(ImagePlus, ImagePlus, String[], int) - Method in class trainableSegmentation.WekaSegmentation
-
Add training data from input and labeled images in a
random and balanced way (same number of samples per class).
- addRandomData(ImagePlus, FeatureStack, String, int) - Method in class trainableSegmentation.WekaSegmentation
-
Add instances defined by a label (binary) image in a random
way.
- addRandomData(ImagePlus, ImagePlus, String, int) - Method in class trainableSegmentation.WekaSegmentation
-
Add training data from input and a binary label image in a
random way.
- addRANSACCorrespondence(T) - Method in class mpicbg.spim.registration.detection.DetectionView
-
- addRANSACCorrespondence(T, double) - Method in class mpicbg.spim.registration.detection.DetectionView
-
- addRegularizationFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.Param
-
- addRenderTransformListener(TransformListener<AffineTransform3D>) - Method in class bdv.viewer.ViewerPanel
-
- addRenderTransformListener(TransformListener<AffineTransform3D>, int) - Method in class bdv.viewer.ViewerPanel
-
- addRGBColorSliders(GenericDialog, Color) - Static method in class ini.trakem2.utils.Utils
-
- addRoi - Variable in class siox.SegmentationGUI
-
- addRoiListener(RoiListener) - Method in class events.RoiWatcher
-
- addRow(ResultsTable) - Method in class util.FindConnectedRegions.Region
-
- addSaveAsFileField(GenericDialogPlus, String, String, int) - Static method in class bdv.ij.util.PluginHelper
-
- addSaveAsFileField(GenericDialogPlus, String, String, int) - Static method in class spim.fiji.plugin.resave.PluginHelper
-
- addScrollBars(Container) - Static method in class loci.plugins.util.WindowTools
-
Adds AWT scroll bars to the given container.
- addScrollBars(Container) - Static method in class spim.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
- addScrollListener(ImagePlus, AdjustmentListener, MouseWheelListener) - Static method in class sc.fiji.i5d.Main
-
- addSection(List<Document>, DocumentBuilder, File) - Static method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructTranslator
-
- addSelectionChangeListener(SelectionChangeListener) - Method in class fiji.plugin.trackmate.SelectionModel
-
- addSeparator(JComponent, String, boolean, GridBagConstraints) - Static method in class sc.fiji.snt.gui.GuiUtils
-
- addSeparator(JComponent, JLabel, boolean, GridBagConstraints) - Static method in class sc.fiji.snt.gui.GuiUtils
-
- addSeries(XYEdgeSeries) - Method in class fiji.plugin.trackmate.util.XYEdgeSeriesCollection
-
- addSetup(SpimRegistrationSequence, int, String, String) - Method in class bdv.ij.export.SetupAggregator
-
Deprecated.
- addSetup(SpimRegistrationSequence, int, int[][], int[][]) - Method in class bdv.ij.export.SetupAggregator
-
Deprecated.
- addSetup(ConverterSetup) - Method in class bdv.tools.brightness.MinMaxGroup
-
- addSetup(ConverterSetup) - Method in class bdv.tools.brightness.SetupAssignments
-
Deprecated.
Add the setup in a new group.
- addSetups(SpimRegistrationSequence, String, String) - Method in class bdv.ij.export.SetupAggregator
-
Deprecated.
- addSetups(SpimRegistrationSequence, int[][], int[][]) - Method in class bdv.ij.export.SetupAggregator
-
Deprecated.
- addSetups(FusionResult, String, String) - Method in class bdv.ij.export.SetupAggregator
-
Deprecated.
- addSetups(FusionResult, int[][], int[][]) - Method in class bdv.ij.export.SetupAggregator
-
Deprecated.
- addShape(Shape, T, int[]) - Method in class mpicbg.imglib.container.shapelist.ShapeList
-
- addSibling(Displayable, Displayable) - Method in class ini.trakem2.tree.ProjectTree
-
Finds the node for the elder and adds the sibling next to it, under the same parent.
- addSIFTFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.Param
-
- addSilently(DBObject) - Method in class ini.trakem2.display.Layer
-
Used for reconstruction purposes.
- addSilently(Layer) - Method in class ini.trakem2.display.LayerSet
-
Add a new Layer silently, ordering by z as well.
- addSilently(ZDisplayable) - Method in class ini.trakem2.display.LayerSet
-
Used for reconstruction purposes, avoids repainting or updating.
- addSimplePoints(ArrayList<Point>, ArrayList<Point>) - Method in class mpicbg.pointdescriptor.test.TestPointDescriptor
-
- addSlice(String, Object) - Method in class ini.trakem2.imaging.LayerStack
-
Does nothing.
- addSlice(String, ImageProcessor) - Method in class ini.trakem2.imaging.LayerStack
-
Does nothing.
- addSlice(String, ImageProcessor, int) - Method in class ini.trakem2.imaging.LayerStack
-
Does nothing.
- addSlice(String) - Method in class ini.trakem2.imaging.LazyVirtualStack
-
- addSlice(Callable<ImageProcessor>) - Method in class ini.trakem2.imaging.LazyVirtualStack
-
- addSlice(String, ImageProcessor) - Method in class mpicbg.imglib.image.display.imagej.ImageJVirtualDisplay
-
Adds the image in 'ip' to the end of the stack.
- addSlice(String, ImageProcessor, int) - Method in class mpicbg.imglib.image.display.imagej.ImageJVirtualDisplay
-
Adds the image in 'ip' to the stack following slice 'n'.
- addSlice(String, ImageProcessor) - Method in class mpicbg.imglib.image.display.imagej.ImageJVirtualStack
-
Adds the image in 'ip' to the end of the stack.
- addSlice(String, ImageProcessor, int) - Method in class mpicbg.imglib.image.display.imagej.ImageJVirtualStack
-
Adds the image in 'ip' to the stack following slice 'n'.
- addSlice(String) - Method in class sc.fiji.i5d.I5DVirtualStack
-
Adds an image to the end of the stack.
- addSlice(String, Object) - Method in class sc.fiji.i5d.I5DVirtualStack
-
Does nothing.
- addSlice(String, ImageProcessor) - Method in class sc.fiji.i5d.I5DVirtualStack
-
Does nothing..
- addSlice(String, ImageProcessor, int) - Method in class sc.fiji.i5d.I5DVirtualStack
-
Does noting.
- addSlice(String) - Method in class spimopener.SPIMRegularStack
-
- addSlice(ImageProcessor) - Method in class spimopener.SPIMRegularStack
-
- addSlice(String) - Method in class spimopener.SPIMStack
-
- addSlice(ImageProcessor) - Method in class spimopener.SPIMStack
-
- addSlice(String) - Method in class spimopener.SPIMVirtualStack
-
Adds an image to the end of the stack.
- addSlice(ImageProcessor) - Method in class spimopener.SPIMVirtualStack
-
- addSlice(String, Object) - Method in class spimopener.SPIMVirtualStack
-
Does nothing.
- addSlice(String, ImageProcessor) - Method in class spimopener.SPIMVirtualStack
-
Does nothing..
- addSlice(String, ImageProcessor, int) - Method in class spimopener.SPIMVirtualStack
-
Does noting.
- addSlice(int, ImageProcessor) - Method in class video.VideoStack
-
- addSlice(String) - Method in class video2.WritableVirtualStack
-
Adds a slice to the end of the stack.
- addSlice(String, Object) - Method in class video2.WritableVirtualStack
-
Adds a slice with the given pixels to the end of the stack.
- addSlice(String, ImageProcessor) - Method in class video2.WritableVirtualStack
-
Adds the given ImageProcessor as a slice to the end of the stack.
- addSlice(String, ImageProcessor, int) - Method in class video2.WritableVirtualStack
-
Adds the given ImageProcessor as a slice at the specified
position in the stack.
- addSliceListener(SliceListener) - Method in class events.SliceWatcher
-
- addSource(SourceAndConverter<?>) - Method in class bdv.viewer.BasicViewerState
-
Add source
to the state.
- addSource(int) - Method in class bdv.viewer.state.SourceGroup
-
Deprecated.
- addSource(SourceAndConverter<?>) - Method in class bdv.viewer.state.ViewerState
-
Deprecated.
- addSource(SourceAndConverter<?>) - Method in class bdv.viewer.SynchronizedViewerState
-
Add source
to the state.
- addSource(SourceAndConverter<?>) - Method in class bdv.viewer.ViewerPanel
-
- addSource(SourceAndConverter<?>) - Method in interface bdv.viewer.ViewerState
-
Add source
to the state (optional operation).
- addSources(Collection<? extends SourceAndConverter<?>>) - Method in class bdv.viewer.BasicViewerState
-
Add all sources in collection
to the state.
- addSources(Collection<? extends SourceAndConverter<?>>) - Method in class bdv.viewer.SynchronizedViewerState
-
Add all sources in collection
to the state.
- addSources(Collection<SourceAndConverter<?>>) - Method in class bdv.viewer.ViewerPanel
-
- addSources(Collection<? extends SourceAndConverter<?>>) - Method in interface bdv.viewer.ViewerState
-
Add all sources in collection
to the state (optional operation).
- addSourcesToGroup(Collection<? extends SourceAndConverter<?>>, SourceGroup) - Method in class bdv.viewer.BasicViewerState
-
Add all sources in collection
to group
.
- addSourcesToGroup(Collection<? extends SourceAndConverter<?>>, SourceGroup) - Method in class bdv.viewer.SynchronizedViewerState
-
Add all sources in collection
to group
.
- addSourcesToGroup(Collection<? extends SourceAndConverter<?>>, SourceGroup) - Method in interface bdv.viewer.ViewerState
-
Add all sources in collection
to group
(optional
operation).
- addSourceToGroup(SourceAndConverter<?>, SourceGroup) - Method in class bdv.viewer.BasicViewerState
-
Add source
to group
.
- addSourceToGroup(SourceAndConverter<?>, SourceGroup) - Method in class bdv.viewer.SynchronizedViewerState
-
Add source
to group
.
- addSourceToGroup(SourceAndConverter<?>, SourceGroup) - Method in interface bdv.viewer.ViewerState
-
Add source
to group
(optional operation).
- addSourceToGroup(int, int) - Method in class bdv.viewer.VisibilityAndGrouping
-
Deprecated.
- addSphere() - Method in class ij3d.Executer
-
- addSphere(Image3DUniverse) - Static method in class ij3d.gui.PrimitiveDialogs
-
- addSphere(String, String, String) - Static method in class ij3d.ImageJ3DViewer
-
Add a sphere into the current 3D universe
- addSphere(String, double, double, double, Color, double) - Method in class sc.fiji.snt.SNT
-
- addSpot(Spot) - Method in class fiji.plugin.trackmate.ModelChangeEvent
-
- addSpotAnalyzerFactory(SpotAnalyzerFactory<?>) - Method in class fiji.plugin.trackmate.Settings
-
- addSpotAnalyzerFactory(int, SpotAnalyzerFactory<?>) - Method in class fiji.plugin.trackmate.Settings
-
- addSpotFilter(FeatureFilter) - Method in class fiji.plugin.trackmate.Settings
-
Add a filter to the list of spot filters.
- addSpotTo(Spot, Integer) - Method in class fiji.plugin.trackmate.Model
-
Adds a single spot to the collections managed by this model, mark it as
visible, then update its features.
- addSpotToSelection(Spot) - Method in class fiji.plugin.trackmate.SelectionModel
-
- addSpotToSelection(Collection<Spot>) - Method in class fiji.plugin.trackmate.SelectionModel
-
- addSpring(Vertex, Spring) - Method in class mpicbg.models.Vertex
-
- addSpring(Vertex, double[]) - Method in class mpicbg.models.Vertex
-
- addSpring(Vertex, double[], double) - Method in class mpicbg.models.Vertex
-
- addSpring(Vertex, double) - Method in class mpicbg.models.Vertex
-
- addSpring(Vertex, double, double) - Method in class mpicbg.models.Vertex
-
- addStandardFunctions() - Method in class fiji.expressionparser.ImgLibParser
-
- addStateListener(ClusterStateListener) - Method in class edu.utexas.clm.archipelago.Cluster
-
- addStatusListener(StatusListener) - Method in class loci.plugins.in.ImagePlusReader
-
- addStatusListener(StatusListener) - Method in class loci.plugins.in.ImportProcess
-
- addStatusListener(StatusListener) - Method in class mpicbg.imglib.io.ImageOpener
-
Adds a listener to those informed when progress occurs.
- addStringField(String, String, int) - Method in class fiji.util.gui.GenericDialogPlus
-
- addStructure(double, double) - Method in class trainableSegmentation.FeatureStack
-
Add structure tensor features to current stack
It computes, for all pixels in the input image, the eigenvalues of the so-called structure tensor.
- addSurfacePlot(ImagePlus) - Method in class ij3d.Image3DUniverse
-
Add a new image as a content, displaying it as a 2D surface plot.
- addSurfacePlot(ImagePlus, int) - Method in class ij3d.Image3DUniverse
-
Add a new image as a content, displaying it as a 2D surface plot.
- addSurfacePlot(ImagePlus, Color3f, String, int, boolean[], int) - Method in class ij3d.Image3DUniverse
-
Add a new image as a content, displaying it as a 2D surface plot.
- AddSymbol(long, long) - Method in class customnode.u3d.ContextManager
-
- addTab(String, Component) - Method in class ini.trakem2.display.Display
-
Returns the tab index in this Display's JTabbedPane.
- addTag(Tag) - Method in class ini.trakem2.display.Node
-
- addTag(Tag) - Method in interface ini.trakem2.display.Taggable
-
- addTarget(float, float, long, float) - Method in class ini.trakem2.display.Connector
-
- addTarget(double, double, long, double) - Method in class ini.trakem2.display.Connector
-
- addText(String, Transform3D, Appearance) - Method in class ij3d.shapes.CoordinateSystem
-
- addText3D(Text3D[]) - Method in class jRenderer3D.JRenderer3D
-
Adds an array of text to the 3D scene.
- addText3D(String, int, int, int, Color, int) - Method in class jRenderer3D.JRenderer3D
-
Adds a text to the 3D scene.
- addText3D(String, int, int, int, int, int) - Method in class jRenderer3D.JRenderer3D
-
Adds a text to the 3D scene.
- addText3D(Text3D) - Method in class jRenderer3D.JRenderer3D
-
Adds a single 3D text to the 3D scene.
- addTextField(String, int, String) - Method in class util.ModelessQuestions
-
- addTextPair3D(Text3D, Text3D) - Method in class jRenderer3D.JRenderer3D
-
- addTile(Tile<?>) - Method in class mpicbg.models.TileConfiguration
-
- addTile(TileSPIM) - Method in class mpicbg.spim.mpicbg.TileConfigurationSPIM
-
- addTile(Tile) - Method in class stitching.model.TileConfiguration
-
Add a single tile.
- addTiles(Collection<? extends Tile<?>>) - Method in class mpicbg.models.TileConfiguration
-
- addTiles(TileConfiguration) - Method in class mpicbg.models.TileConfiguration
-
- addTiles(Collection<? extends TileSPIM>) - Method in class mpicbg.spim.mpicbg.TileConfigurationSPIM
-
- addTiles(TileConfigurationSPIM) - Method in class mpicbg.spim.mpicbg.TileConfigurationSPIM
-
- addTiles(Collection<Tile>) - Method in class stitching.model.TileConfiguration
-
Add a collection of tiles.
- addTilesAsRois - Variable in class mpicbg.stitching.StitchingParameters
-
- AddTime(byte[], int, int, int, int, int) - Method in class view5d.View5D
-
- AddTime(short[], int, int, int, int, int) - Method in class view5d.View5D
-
- AddTime(char[], int, int, int, int, int) - Method in class view5d.View5D
-
- AddTime(float[], int, int, int, int, int) - Method in class view5d.View5D
-
- AddTime(double[], int, int, int, int, int) - Method in class view5d.View5D
-
- AddTimeC(float[], int, int, int, int, int) - Method in class view5d.View5D
-
- addTimelapseFromFile() - Method in class ij3d.Executer
-
- addTimelapseFromFolder() - Method in class ij3d.Executer
-
- addTimelapseFromHyperstack(ImagePlus) - Method in class ij3d.Executer
-
- addTimelapseListener(TimelapseListener) - Method in class ij3d.Image3DUniverse
-
- addTimePointListener(TimePointListener) - Method in class bdv.viewer.ViewerPanel
-
- addTimePointListener(TimePointListener, int) - Method in class bdv.viewer.ViewerPanel
-
- addTo(Bdv) - Method in class bdv.util.BdvOptions
-
When showing content using one of the
BdvFunctions
methods, this
option can be given to specify that the content should be added to an
existing window.
- addTo() - Method in class bdv.util.BdvOptions.Values
-
- addTo3DViewer(Image3DUniverse, Color, ImagePlus) - Method in class sc.fiji.snt.Path
-
Deprecated.
- addTo3DViewer(Image3DUniverse, Color3f, ImagePlus) - Method in class sc.fiji.snt.Path
-
Deprecated.
- addToActionMap(ActionMap, BigWarpViewerFrame, int) - Static method in class bdv.viewer.WarpNavigationActions
-
- addToDatabase(DBObject) - Method in class ini.trakem2.persistence.DBLoader
-
- addToDatabase() - Method in class ini.trakem2.persistence.DBObject
-
- addToDatabase(DBObject) - Method in class ini.trakem2.persistence.FSLoader
-
- addToDatabase(DBObject) - Method in class ini.trakem2.persistence.Loader
-
- addToDatabase(Project) - Method in class ini.trakem2.tree.TemplateThing
-
Recursive into children! Will add the attributes as well and grab an id for this instance.
- addToLinkLater(Node<T>) - Method in class ini.trakem2.display.Tree
-
- addTooltip(JComponent, String) - Method in class sc.fiji.snt.gui.GuiUtils
-
- addToResultsTable() - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults
-
Deprecated.
- addToRoiManager(int, Roi) - Method in class sc.fiji.timelapse.LOI_Interpolator
-
- addToViewer() - Method in class bdv.tools.boundingbox.TransformedBoxOverlaySource
-
- addTrace(String, String) - Static method in class trainableSegmentation.Weka_Segmentation
-
Add the current ROI to a specific class and slice.
- addTrackAnalyzer(TrackAnalyzer) - Method in class fiji.plugin.trackmate.Settings
-
- addTrackAnalyzer(int, TrackAnalyzer) - Method in class fiji.plugin.trackmate.Settings
-
Adds a
TrackAnalyzer
to the
List
of track analyzers
configured, at the specified index.
- addTrackFilter(FeatureFilter) - Method in class fiji.plugin.trackmate.Settings
-
Add a filter to the list of track filters.
- addTransformListener(TransformListener<AffineTransform3D>) - Method in class bdv.viewer.render.TransformAwareBufferedImageOverlayRenderer
-
- addTransformListener(TransformListener<AffineTransform3D>, int) - Method in class bdv.viewer.render.TransformAwareBufferedImageOverlayRenderer
-
- addTransformListener(TransformListener<AffineTransform3D>) - Method in interface bdv.viewer.render.TransformAwareRenderTarget
-
- addTransformListener(TransformListener<AffineTransform3D>, int) - Method in interface bdv.viewer.render.TransformAwareRenderTarget
-
- addTransformListener(TransformListener<AffineTransform3D>) - Method in class bdv.viewer.ViewerPanel
-
- addTransformListener(TransformListener<AffineTransform3D>, int) - Method in class bdv.viewer.ViewerPanel
-
- addTransformListener(TransformListener<InvertibleRealTransform>) - Method in class bigwarp.BigWarp
-
- addTransformStep(Layer) - Method in class ini.trakem2.display.LayerSet
-
Add an undo step for the transformations of all Displayable in the layer.
- addTransformStep(List<Layer>) - Method in class ini.trakem2.display.LayerSet
-
- addTransformStep(Collection<? extends Displayable>) - Method in class ini.trakem2.display.LayerSet
-
Add an undo step for the transformations of all Displayable in hs.
- addTransformStep() - Method in class ini.trakem2.display.LayerSet
-
Add an undo step for the transformations of all Displayable in all layers.
- addTransformStepWithData(Collection<? extends Displayable>) - Method in class ini.trakem2.display.LayerSet
-
Add an undo step for the transformations of all Displayable in col, with data as well (for Patch, data includes the CoordinateTransform).
- addTransformStepWithDataForAll(Collection<Layer>) - Method in class ini.trakem2.display.LayerSet
-
Includes all ZDisplayable that paint at any of the given layers.
- addTree(Tree) - Method in class sc.fiji.snt.PathAndFillManager
-
- addTree(Tree) - Method in class sc.fiji.snt.SciViewSNT
-
Adds a tree to the associated SciView instance.
- addTree(Tree) - Method in class sc.fiji.snt.viewer.Viewer2D
-
- addTree(Tree) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Adds a tree to this viewer.
- addTreeModelListener(TreeModelListener) - Method in class bdv.ui.sourcegrouptree.SourceGroupTreeModel
-
Adds a listener for the TreeModelEvent posted after the tree changes.
- addTrees(Collection<Tree>, String, String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Adds a collection of trees.
- addTrees(Collection<Tree>, String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Adds a collection of trees.
- addTrees(Collection<Tree>, boolean) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Adds a collection of trees.
- addTriangle(Point3f, Point3f, Point3f) - Method in class customnode.CustomTriangleMesh
-
- addTriangle(ArrayList<PointMatch>) - Method in class mpicbg.models.TransformMesh
-
Add a triangle defined by 3 PointMatches that defines an
AffineTransform2D.
- addTriangleMesh(List<Point3f>, Color3f, String) - Method in class ij3d.Image3DUniverse
-
Add a custom mesh, in particular a triangle mesh, to the universe.
- addTriangleMesh(List<Point3f>, List<Color3f>, String) - Method in class ij3d.Image3DUniverse
-
Add a custom mesh, in particular a triangle mesh, to the universe.
- addTriangles(Point3f[]) - Method in class customnode.CustomTriangleMesh
-
- addTube() - Method in class ij3d.Executer
-
- addTube(Image3DUniverse) - Static method in class ij3d.gui.PrimitiveDialogs
-
- addTubePoint(String) - Static method in class ij3d.ImageJ3DViewer
-
Add a point to the list that will conform a tube into the current
3D universe
- addUndoMoveStep(Displayable) - Method in class ini.trakem2.display.LayerSet
-
To undo moving up/down/top/bottom.
- addUndoStep(DoStep) - Method in class ini.trakem2.display.LayerSet
-
- addUniqueType(TemplateThing) - Method in class ini.trakem2.Project
-
Returns false if the type exists already.
- addUniverseListener(UniverseListener) - Method in class ij3d.DefaultUniverse
-
Register the specified UniverseListener
- addUnseenChildrenOf(V) - Method in class fiji.plugin.trackmate.graph.SortedDepthFirstIterator
-
This is where we add the multiple children in proper sorted order.
- addUnseenChildrenOf(Spot) - Method in class fiji.plugin.trackmate.graph.TimeDirectedDepthFirstIterator
-
- addUnseenChildrenOf(Spot) - Method in class fiji.plugin.trackmate.graph.TimeDirectedSortedDepthFirstIterator
-
- addUnsignedShortSlice(String, Object) - Method in class mpicbg.imglib.image.display.imagej.ImageJVirtualDisplay
-
Obsolete.
- addUnsignedShortSlice(String, Object) - Method in class mpicbg.imglib.image.display.imagej.ImageJVirtualStack
-
Obsolete.
- addUpdateListener(VisibilityAndGrouping.UpdateListener) - Method in class bdv.viewer.VisibilityAndGrouping
-
Deprecated.
- addUThresh(double) - Method in class view5d.My3DData
-
- addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.AveragePixelFusion
-
- addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.AveragePixelFusionIgnoreZero
-
- addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.BlendingPixelFusion
-
- addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.BlendingPixelFusionIgnoreZero
-
- addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.MaxPixelFusion
-
- addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.MaxPixelFusionIgnoreZero
-
- addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.MedianPixelFusion
-
- addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.MedianPixelFusionIgnoreZero
-
- addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.MinPixelFusion
-
- addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.MinPixelFusionIgnoreZero
-
- addValue(double, int, double[]) - Method in class mpicbg.stitching.fusion.OverlapFusion
-
- addValue(double, int, double[]) - Method in interface mpicbg.stitching.fusion.PixelFusion
-
add a new value for the current output pixel
- addVariance(float) - Method in class trainableSegmentation.FeatureStack
-
Add variance-filtered image to the stack (single thread version)
- addVertex(Point3f) - Method in class customnode.FullInfoMesh
-
- addVertex(Image3DUniverse, Color3f, float, float, float) - Method in class MC_Test
-
- addVertex(Vertex, double) - Method in class mpicbg.models.SpringMesh
-
- addVertex(Vertex) - Method in class sc.fiji.analyzeSkeleton.Graph
-
Add vertex to the graph.
- addVertex(Extract_Surface.SurfaceVoxel) - Method in class vib.Extract_Surface
-
- addVertexWeightedByDistance(Vertex, double, double) - Method in class mpicbg.models.SpringMesh
-
- addVertices(Point3f[]) - Method in class customnode.CustomIndexedTriangleMesh
-
- addVertices(Point3f[]) - Method in class customnode.CustomMesh
-
- addVerticesToGeometryArray(Point3f[]) - Method in class customnode.CustomIndexedTriangleMesh
-
- addVerticesToGeometryArray(Point3f[]) - Method in class customnode.CustomMesh
-
- addVerticesToGeometryStripArray(Point3f[]) - Method in class customnode.CustomIndexedTriangleMesh
-
- addVerticesToGeometryStripArray(Point3f[]) - Method in class customnode.CustomMesh
-
- addView(TrackMateModelView) - Method in class fiji.plugin.trackmate.gui.TrackMateGUIModel
-
- addViewer(Viewer3D) - Static method in class sc.fiji.snt.SNTUtils
-
- addVirtualMatch(PointMatch) - Method in class mpicbg.trakem2.align.AbstractAffineTile2D
-
- addVisibilityChangeListener(PlaceHolderOverlayInfo.VisibilityChangeListener) - Method in class bdv.util.PlaceHolderOverlayInfo
-
- addVisitor(Visitor) - Method in class org.janelia.thickness.inference.visitor.ListVisitor
-
- addVisitor(String, Visitor) - Static method in class org.janelia.thickness.plugin.ZPositionCorrection
-
- addVisitor(String, ZPositionCorrection.VisitorFactory) - Static method in class org.janelia.thickness.plugin.ZPositionCorrection
-
- addVoltex(ImagePlus) - Method in class ij3d.Image3DUniverse
-
Add a new image as a content, displaying it as a volume rendering.
- addVoltex(ImagePlus, int) - Method in class ij3d.Image3DUniverse
-
Add a new image as a content, displaying it as a volume rendering.
- addVoltex(ImagePlus, Color3f, String, int, boolean[], int) - Method in class ij3d.Image3DUniverse
-
Add a new image as a content, displaying it as a volume rendering.
- addVolume(String, String, String, String, String, String, String) - Static method in class ij3d.ImageJ3DViewer
-
- addVolumeColor(Color) - Method in class volumeCalculator.Volumes
-
The user has created another Volume Color.
- addVoxel(int, int, int, int, boolean, float) - Method in class Utilities.Object3D
-
Adds a new voxel to the specified Object3D, at the next available slot in the object.
- addWarning(String, String) - Method in class sc.fiji.coloc.algorithms.Algorithm
-
Adds a warning to the list of warnings.
- addWebsite(GenericDialog) - Static method in class spim.fiji.plugin.util.GUIHelper
-
- addWebsite(GenericDialog, String) - Static method in class spim.fiji.plugin.util.GUIHelper
-
- addWeight(double) - Method in class mpicbg.models.Spring
-
- addWindowList(GenericDialog, String, boolean) - Static method in class amira.AmiraParameters
-
- addWorkload(int) - Static method in class bunwarpj.ProgressBar
-
Extend the amount of work to perform by batch
.
- addWorldAreaTo(Node<?>, Area) - Method in class ini.trakem2.display.AreaTree
-
Assumes nd
is an AreaNode.
- addZDisplayable(ZDisplayable) - Method in class ini.trakem2.display.LayerSet
-
Useful for typeless scripts so that a ZDisplayable can be added; the
overloaded method add(Layer) and add(ZDisplayable) is not distinguishable otherwise.
- ADJUST_BOTH - Static variable in class ij3d.ViewAdjuster
-
Fit the points both horizontally and vertically
- ADJUST_HORIZONTAL - Static variable in class ij3d.ViewAdjuster
-
Fit the points horizontally
- ADJUST_VERTICAL - Static variable in class ij3d.ViewAdjuster
-
Fit the points vertically
- adjustChannels(ImagePlus, boolean[]) - Static method in class ij3d.ColorTable
-
- adjustChannels(Image) - Method in class ini.trakem2.display.Patch
-
Takes an image and scales its channels according to the values packed in this.channels.
- adjustChannels(Patch, int) - Method in class ini.trakem2.persistence.Loader
-
- adjustColorMapLThresh(double) - Method in class view5d.My3DData
-
- adjustColorMapUThresh(double) - Method in class view5d.My3DData
-
- adjustColumn(int) - Method in class sc.fiji.hdf5.TableColumnAdjuster
-
- adjustColumns() - Method in class sc.fiji.hdf5.TableColumnAdjuster
-
- adjustConfidence(int) - Method in class ini.trakem2.display.Node
-
Adjust the confidence value of this node with its parent.
- adjustDimensions() - Method in class ini.trakem2.display.DisplayCanvas
-
Adjust srcRect and internal variables to the canvas' bounds.
- adjustDisplayedImage(RandomAccessibleInterval<? extends RealType<?>>) - Method in class sc.fiji.coloc.results.SingleWindowDisplay
-
- adjustEdgeConfidence(int, float, float, Layer, DisplayCanvas) - Method in class ini.trakem2.display.Tree
-
Expects world coordinates.
- AdjustedRandError - Class in trainableSegmentation.metrics
-
This class implements the adjusted Rand error, defined as the 1 - adjusted Rand index.
- AdjustedRandError(ImagePlus, ImagePlus) - Constructor for class trainableSegmentation.metrics.AdjustedRandError
-
Initialize adjusted Rand error metric.
- adjustedRandError(ImageProcessor, ImageProcessor, double) - Static method in class trainableSegmentation.metrics.AdjustedRandError
-
Calculate the adjusted Rand error between some 2D original labels
and the corresponding proposed labels.
- adjustedRandIndex(ShortProcessor, ShortProcessor) - Static method in class trainableSegmentation.metrics.AdjustedRandError
-
Calculate the adjusted Rand index between to clusters, as described by
Lawrence Hubert and Phipps Arabie \cite{Rand71}.
- adjustGroupProperties(Collection<Displayable>) - Method in class ini.trakem2.display.Display
-
Pops up a dialog to adjust the alpha, visible, color, locked and compositeMode of all Displayables in col
.
- adjustImage(Image<FloatType>, float, float) - Static method in class mpicbg.spim.postprocessing.deconvolution2.AdjustInput
-
Adjusts an image so that the minimal intensity is minValue and the average is average
- AdjustInput - Class in mpicbg.spim.postprocessing.deconvolution2
-
- AdjustInput() - Constructor for class mpicbg.spim.postprocessing.deconvolution2.AdjustInput
-
- AdjustInput - Class in spim.process.fusion.deconvolution
-
- AdjustInput() - Constructor for class spim.process.fusion.deconvolution.AdjustInput
-
- adjustLight() - Method in class ij3d.Executer
-
- adjustListPlaceholder() - Method in class sc.fiji.snt.FillManagerUI
-
- adjustLUTs(Content) - Method in class ij3d.Executer
-
- adjustMeasurementOptions() - Method in class ini.trakem2.display.Display
-
- adjustmentValueChanged(AdjustmentEvent) - Method in class _3D_objects_counter
-
- adjustmentValueChanged(AdjustmentEvent) - Method in class fiji.tool.SliceObserver
-
- adjustmentValueChanged(AdjustmentEvent) - Method in class fiji.util.CurrentSlice
-
- adjustmentValueChanged(AdjustmentEvent) - Method in class ini.trakem2.display.Displayable.SliderListener
-
- adjustmentValueChanged(AdjustmentEvent) - Method in class ini.trakem2.display.RollingPanel
-
Adjust the sublist of displayed DisplayablePanel.
- adjustmentValueChanged(AdjustmentEvent) - Method in class IntSlider
-
- adjustmentValueChanged(AdjustmentEvent) - Method in class loci.plugins.util.DataBrowser
-
- adjustmentValueChanged(AdjustmentEvent) - Method in class mpicbg.spim.segmentation.InteractiveDoG.Sigma2Listener
-
- adjustmentValueChanged(AdjustmentEvent) - Method in class mpicbg.spim.segmentation.InteractiveDoG.SigmaListener
-
- adjustmentValueChanged(AdjustmentEvent) - Method in class mpicbg.spim.segmentation.InteractiveDoG.ThresholdListener
-
- adjustmentValueChanged(AdjustmentEvent) - Method in class mpicbg.spim.segmentation.InteractiveIntegral.Radius1Listener
-
- adjustmentValueChanged(AdjustmentEvent) - Method in class mpicbg.spim.segmentation.InteractiveIntegral.Radius2Listener
-
- adjustmentValueChanged(AdjustmentEvent) - Method in class mpicbg.spim.segmentation.InteractiveIntegral.ThresholdListener
-
- adjustmentValueChanged(AdjustmentEvent) - Method in class OpenImage5DWindow
-
Handles changes in the scrollbars for z and t.
- adjustmentValueChanged(AdjustmentEvent) - Method in class OpenStackWindow
-
Calls super.updateSliceSelector() and issues a DisplayChangeEvent to registered listeners.
- adjustmentValueChanged(AdjustmentEvent) - Method in class sc.fiji.balloonSegmentation.BalloonSegmentation_
-
- adjustmentValueChanged(AdjustmentEvent) - Method in class sc.fiji.i5d.gui.ChannelControl
-
Executed if scrollbar has been moved.
- adjustmentValueChanged(AdjustmentEvent) - Method in class sc.fiji.i5d.gui.Image5DWindow
-
Handles changes in the scrollbars for z and t.
- adjustmentValueChanged(AdjustmentEvent) - Method in class sc.fiji.i5d.gui.ScrollbarWithLabel
-
- adjustmentValueChanged(AdjustmentEvent) - Method in class sc.fiji.timelapse.LOI_Interpolator.SliderListener
-
- adjustmentValueChanged(AdjustmentEvent) - Method in class Stack_Rotate
-
- adjustmentValueChanged(AdjustmentEvent) - Method in class surfaceplot.SurfacePlotGroup
-
Implements AdjustmentListener interface to automatically update the surface
plot when the slice slider in the stack window is dragged.
- adjustmentValueChanged(AdjustmentEvent) - Method in class vib.segment.CustomStackWindow
-
- adjustmentValueChanged(AdjustmentEvent) - Method in class view5d.ImageCanvas
-
- adjustMinAndMaxGUI() - Method in class ini.trakem2.display.Display
-
- adjustNodeColors(Node<T>) - Method in class ini.trakem2.display.Tree
-
- adjustNodeRadius(float, float, float, Layer, DisplayCanvas) - Method in class ini.trakem2.display.Treeline
-
- AdjustOffset() - Method in class view5d.ImgPanel
-
- AdjustOffsetToROIMean() - Method in class view5d.My3DData
-
- adjustProperties() - Method in class ini.trakem2.display.AreaList
-
- adjustProperties() - Method in class ini.trakem2.display.Ball
-
- adjustProperties() - Method in class ini.trakem2.display.Display
-
- adjustProperties() - Method in class ini.trakem2.display.Displayable
-
Shows a dialog to adjust properties of this object.
- adjustProperties() - Method in class ini.trakem2.display.DLabel
-
- adjustProperties() - Method in class ini.trakem2.Project
-
- adjustRoiOffset(long[], long[], long[]) - Method in class sc.fiji.coloc.gadgets.DataContainer
-
Make sure that the ROI offset has the same dimensionality
as the image.
- adjustRoiSize(long[], long[], long[], long[]) - Method in class sc.fiji.coloc.gadgets.DataContainer
-
Transforms a ROI size array to a dimensionality.
- adjustSegmentationStateToData(Instances) - Method in class trainableSegmentation.WekaSegmentation
-
Adjust current segmentation state (attributes and classes) to
loaded data
- adjustSourceRect(double, int, int) - Method in class fiji.util.gui.JImagePanel
-
- adjustSourceRectI5d(double, int, int) - Method in class sc.fiji.i5d.gui.Image5DCanvas
-
- adjustSrcRect(int, int) - Method in class ini.trakem2.display.DisplayCanvas
-
Adjust srcRect to new dimensions.
- AdjustThresh(int) - Method in class view5d.My3DData
-
- AdjustThresh(boolean) - Method in class view5d.My3DData
-
- AdjustThresh() - Method in class view5d.My3DData
-
- AdjustThreshGlobal() - Method in class view5d.My3DData
-
- adjustView() - Method in class ij3d.Image3DUniverse
-
Fit all contents optimally into the canvas.
- adjustView(int) - Method in class ij3d.Image3DUniverse
-
Fit all contents optimally into the canvas.
- adjustView(Iterable<Content>) - Method in class ij3d.Image3DUniverse
-
Fit the specified contents optimally into the canvas.
- adjustView(Iterable<Content>, int) - Method in class ij3d.Image3DUniverse
-
Fit the specified contents optimally into the canvas.
- adjustView(Content, int) - Method in class ij3d.Image3DUniverse
-
Fit the specified content optimally into the canvas.
- adjustView(Content) - Method in class ij3d.Image3DUniverse
-
Fit the specified content optimally into the canvas.
- adt - package adt
-
- advance() - Method in class mpicbg.imglib.labeling.LocalizableLabelingCursor
-
- advanced - Variable in class mpicbg.imglib.labeling.LocalizableLabelingCursor
-
- ADVANCED - Variable in class org.imagearchive.lsm.toolbox.info.LUTInfo
-
- advanced - Static variable in class register_virtual_stack.Register_Virtual_Stack_MT
-
advance options flag
- advanceElement(int) - Method in class view5d.My3DData
-
- AdvancePos() - Method in class view5d.ImgPanel
-
- advanceTime(int) - Method in class view5d.My3DData
-
- ADVECTION_FORCE - Variable in class levelsets.algorithm.ActiveContours
-
- affine - Variable in class bdv.BehaviourTransformEventHandler3D
-
Current source to screen transform.
- AFFINE - Static variable in class bdv.gui.TransformTypeSelectDialog
-
- affine - Variable in class bdv.util.BehaviourTransformEventHandlerPlanar
-
Current source to screen transform.
- affine() - Method in class bigwarp.BigWarp
-
Returns an AffineGet that represents the the transform if the transform
is linear, or is the affine part of the transform if it is non-linear.
- affine - Variable in class lenscorrection.Distortion_Correction.PointMatchCollectionAndAffine
-
- AFFINE - Static variable in class Moving_Least_Squares
-
- affine - Variable in class mpicbg.models.InterpolatedAffineModel1D
-
- affine - Variable in class mpicbg.models.InterpolatedAffineModel2D
-
- affine - Variable in class mpicbg.models.InterpolatedAffineModel3D
-
- affine - Variable in class mpicbg.spim.data.registration.ViewTransformAffine
-
- affine - Variable in class net.imglib2.ui.TransformEventHandler2Dto3D
-
Current source to screen transform.
- AFFINE - Static variable in class register_virtual_stack.Register_Virtual_Stack_MT
-
affine registration model id
- AFFINE - Static variable in class spim.vecmath.Transform3D
-
An affine matrix can translate, rotate, reflect, scale anisotropically,
and shear.
- Affine1D<T extends Affine1D<T>> - Interface in mpicbg.models
-
- affine2d() - Method in class bigwarp.BigWarp
-
Returns an AffineTransform2D that represents the the transform if the transform
is linear, or is the affine part of the transform if it is non-linear.
- Affine2D<T extends Affine2D<T>> - Interface in mpicbg.models
-
- Affine2D<N extends NumericType<N>> - Class in script.imglib.algorithm
-
TODO
- Affine2D(Object, Number, Number, Number, Number, Number, Number) - Constructor for class script.imglib.algorithm.Affine2D
-
Affine transform the image with the best interpolation mode available.
- Affine2D(Object, Number, Number, Number, Number, Number, Number, AbstractAffine3D.Mode, Number) - Constructor for class script.imglib.algorithm.Affine2D
-
Affine transform the image with the best interpolation mode available.
- Affine2D(Object, AffineTransform) - Constructor for class script.imglib.algorithm.Affine2D
-
- Affine2D(Object, AffineTransform, AbstractAffine3D.Mode) - Constructor for class script.imglib.algorithm.Affine2D
-
- Affine2D(Object, AffineTransform, Number) - Constructor for class script.imglib.algorithm.Affine2D
-
- Affine2D(Object, AffineTransform, AbstractAffine3D.Mode, Number) - Constructor for class script.imglib.algorithm.Affine2D
-
- Affine2D(Object, float, float, float, float, float, float, AbstractAffine3D.Mode, OutOfBoundsStrategyFactory<N>) - Constructor for class script.imglib.algorithm.Affine2D
-
- affine3d() - Method in class bigwarp.BigWarp
-
Returns an AffineTransform3D that represents the the transform if the transform
is linear, or is the affine part of the transform if it is non-linear.
- affine3d - Variable in class bigwarp.TransformHandler3DWrapping2D
-
- Affine3D<T extends Affine3D<T>> - Interface in mpicbg.models
-
- Affine3D<T extends NumericType<T>> - Class in script.imglib.algorithm
-
Performs a mathematically correct transformation of an image.
- Affine3D(Image<T>, float[], AbstractAffine3D.Mode) - Constructor for class script.imglib.algorithm.Affine3D
-
- Affine3D(Object, float[], AbstractAffine3D.Mode, Number) - Constructor for class script.imglib.algorithm.Affine3D
-
- Affine3D(Object, float[], AbstractAffine3D.Mode, OutOfBoundsStrategyFactory<T>) - Constructor for class script.imglib.algorithm.Affine3D
-
- Affine3D(Object, float, float, float, float, float, float, AbstractAffine3D.Mode, Number) - Constructor for class script.imglib.algorithm.Affine3D
-
- Affine3D(Object, float, float, float, float, float, float, AbstractAffine3D.Mode, OutOfBoundsStrategyFactory<T>) - Constructor for class script.imglib.algorithm.Affine3D
-
- Affine3DHelpers - Class in bdv.util
-
- Affine3DHelpers() - Constructor for class bdv.util.Affine3DHelpers
-
- Affine_From_Landmarks - Class in landmarks
-
- Affine_From_Landmarks() - Constructor for class landmarks.Affine_From_Landmarks
-
- affineDragStart - Variable in class bdv.BehaviourTransformEventHandler3D
-
- affineDragStart - Variable in class bdv.util.BehaviourTransformEventHandlerPlanar
-
- affineDragStart - Variable in class net.imglib2.ui.TransformEventHandler2Dto3D
-
- AffineFromLandmarks - Class in landmarks
-
- AffineFromLandmarks() - Constructor for class landmarks.AffineFromLandmarks
-
- AffineFromLandmarks.CandidateAffine - Class in landmarks
-
- AffineModel1D - Class in mpicbg.models
-
- AffineModel1D() - Constructor for class mpicbg.models.AffineModel1D
-
- AffineModel2D - Class in mpicbg.models
-
2d-affine transformation models to be applied to points in 2d-space.
- AffineModel2D() - Constructor for class mpicbg.models.AffineModel2D
-
- AffineModel2D - Class in mpicbg.trakem2.transform
-
- AffineModel2D() - Constructor for class mpicbg.trakem2.transform.AffineModel2D
-
- AffineModel3D - Class in mpicbg.models
-
3d-affine transformation models to be applied to points in 3d-space.
- AffineModel3D() - Constructor for class mpicbg.models.AffineModel3D
-
- AffineModel3D - Class in mpicbg.trakem2.transform
-
- AffineModel3D() - Constructor for class mpicbg.trakem2.transform.AffineModel3D
-
- affinePartOfTpsHC() - Method in class bigwarp.BigWarp
-
Returns the affine part of the thin plate spline model,
as a matrix in homogeneous coordinates.
- AffineTile2D - Class in mpicbg.trakem2.align
-
- AffineTile2D(AffineModel2D, Patch) - Constructor for class mpicbg.trakem2.align.AffineTile2D
-
- AffineTile2D(Patch) - Constructor for class mpicbg.trakem2.align.AffineTile2D
-
- affineToString() - Method in class bigwarp.BigWarp
-
- affineTransform3DElement(String, AffineGet) - Static method in class mpicbg.spim.data.XmlHelpers
-
- AffineTransform3DJsonSerializer - Class in bdv.img.remote
-
- AffineTransform3DJsonSerializer() - Constructor for class bdv.img.remote.AffineTransform3DJsonSerializer
-
- AffineTransformMode - Class in ini.trakem2.display
-
- AffineTransformMode(Display) - Constructor for class ini.trakem2.display.AffineTransformMode
-
- afs - Variable in class mpicbg.models.InterpolatedAffineModel1D
-
- afs - Variable in class mpicbg.models.InterpolatedAffineModel2D
-
- afs - Variable in class mpicbg.models.InterpolatedAffineModel3D
-
- afterEachPlane(boolean) - Method in interface bdv.export.ExportScalePyramid.AfterEachPlane
-
Called after a "plane of blocks" is written.
- age - Variable in class mpicbg.imglib.algorithm.labeling.Watershed.PixelIntensity
-
- ai - package ai
-
- ai - Variable in class lenscorrection.DistortionCorrectionTask.AppendCoordinateTransformThread
-
- ai - Variable in class lenscorrection.DistortionCorrectionTask.SetCoordinateTransformThread
-
- ai - Variable in class mpicbg.trakem2.align.Align.ExtractFeaturesThread
-
- ai - Variable in class mpicbg.trakem2.align.Align.MatchFeaturesAndFindModelThread
-
- AI1 - Variable in class sc.fiji.io.FIBSEM_Reader.FIBSEMData
-
- AI2 - Variable in class sc.fiji.io.FIBSEM_Reader.FIBSEMData
-
- AI3 - Variable in class sc.fiji.io.FIBSEM_Reader.FIBSEMData
-
- AI4 - Variable in class sc.fiji.io.FIBSEM_Reader.FIBSEMData
-
- AIdelay - Variable in class sc.fiji.io.FIBSEM_Reader.FIBSEMData
-
- Algorithm - Interface in mpicbg.imglib.algorithm
-
TODO
- Algorithm<T extends RealType<T>> - Class in sc.fiji.coloc.algorithms
-
An algorithm is an abstraction of techniques like the
calculation of the Persons coefficient or Li'S ICQ.
- Algorithm(String) - Constructor for class sc.fiji.coloc.algorithms.Algorithm
-
- AlgorithmUtil - Class in script.imglib.algorithm.fn
-
TODO
- AlgorithmUtil() - Constructor for class script.imglib.algorithm.fn.AlgorithmUtil
-
- aliases() - Method in class sc.fiji.snt.annotation.AllenCompartment
-
- aliases() - Method in interface sc.fiji.snt.annotation.BrainAnnotation
-
- aliases() - Method in class sc.fiji.snt.annotation.InsectBrainCompartment
-
- align(ImageProcessor, Line, ImageProcessor, Line) - Static method in class Align_Image
-
Align an image to another image given line selections in each.
- align(ImageProcessor, Line, ImageProcessor, Line, boolean, boolean) - Static method in class Align_Image
-
Align an image to another image given line selections in each.
- align(ViewerPanel.AlignPlane) - Method in class bdv.viewer.BigWarpViewerPanel
-
- align(ViewerPanel.AlignPlane) - Method in class bdv.viewer.ViewerPanel
-
Align the XY, ZY, or XZ plane of the local coordinate system of the
currently active source with the viewer coordinate system.
- Align - Class in mpicbg.trakem2.align
-
A collection of methods regarding SIFT-based alignment
TODO Bring the methods and tasks into a class for each method and clean up this mess.
- Align() - Constructor for class mpicbg.trakem2.align.Align
-
- Align.ExtractFeaturesThread - Class in mpicbg.trakem2.align
-
- Align.MatchFeaturesAndFindModelThread - Class in mpicbg.trakem2.align
-
- Align.Param - Class in mpicbg.trakem2.align
-
- Align.ParamOptimize - Class in mpicbg.trakem2.align
-
- Align_Image - Class in <Unnamed>
-
Select two images with a Line ROI in each, and rotate/translate/scale one to
the other.
- Align_Image() - Constructor for class Align_Image
-
- Align_Image.BilinearInterpolator - Class in <Unnamed>
-
- Align_Image.Interpolator - Class in <Unnamed>
-
- ALIGN_PLANE - Static variable in class bdv.viewer.NavigationActions
-
- ALIGN_PLANE - Static variable in class bdv.viewer.WarpNavigationActions
-
- ALIGN_VIEW_TRANSFORMS - Static variable in class bigwarp.BigWarpActions
-
- AlignDisplayTo(AnElement) - Method in class view5d.AnElement
-
- AlignImage(ImagePlus, ImageProcessor) - Method in class MultipleImageProcessor
-
- alignImagesBatch(ImagePlus, ImagePlus, ImageProcessor, ImageProcessor, int, int, int, int, double, double, double, double, double, double) - Static method in class bunwarpj.bUnwarpJ_
-
Method for images alignment with no graphical interface.
- alignImagesBatch(ImagePlus, ImagePlus, ImageProcessor, ImageProcessor, Param) - Static method in class bunwarpj.bUnwarpJ_
-
Method for images alignment with no graphical interface.
- alignImagesBatch(ImagePlus, ImagePlus, ImageProcessor, ImageProcessor, int, int, int, int, double, double, double, double, double, double, double, double) - Static method in class bunwarpj.bUnwarpJ_
-
Method for images alignment with no graphical interface.
- alignLayer(Layer, int) - Static method in class mpicbg.trakem2.align.Align
-
- alignLayers(Layer) - Static method in class mpicbg.trakem2.align.AlignLayersTask
-
- alignLayers(Layer, Rectangle) - Static method in class mpicbg.trakem2.align.AlignLayersTask
-
- alignLayersLinearly(List<Layer>, int) - Static method in class mpicbg.trakem2.align.Align
-
Align a range of layers by accumulating pairwise alignments of contiguous layers.
- alignLayersLinearly(List<Layer>, int, Filter<Patch>) - Static method in class mpicbg.trakem2.align.Align
-
Align a range of layers by accumulating pairwise alignments of contiguous layers.
- alignLayersLinearlyJob(LayerSet, int, int, boolean, Rectangle, Filter<Patch>) - Static method in class mpicbg.trakem2.align.AlignLayersTask
-
- alignLayersNonLinearlyJob(LayerSet, int, int, boolean, Rectangle, Filter<Patch>) - Static method in class mpicbg.trakem2.align.AlignLayersTask
-
- AlignLayersTask - Class in mpicbg.trakem2.align
-
Register a range of layers using linear or non-linear transformations.
- alignLayersTask(Layer) - Static method in class mpicbg.trakem2.align.AlignLayersTask
-
- alignLayersTask(Layer, Rectangle) - Static method in class mpicbg.trakem2.align.AlignLayersTask
-
- AlignmentUtils - Class in mpicbg.trakem2.align
-
- AlignmentUtils.ParamPointMatch - Class in mpicbg.trakem2.align
-
- alignMultiLayerMosaic(Layer, Patch) - Static method in class mpicbg.trakem2.align.AlignTask
-
Align a multi-layer mosaic.
- alignMultiLayerMosaicTask(Layer) - Static method in class mpicbg.trakem2.align.AlignTask
-
- alignMultiLayerMosaicTask(Layer, Patch) - Static method in class mpicbg.trakem2.align.AlignTask
-
- alignMultiLayerMosaicTask(List<Layer>, Patch, Align.Param, Align.ParamOptimize, Align.ParamOptimize, boolean, boolean, boolean, boolean, boolean) - Static method in class mpicbg.trakem2.align.AlignTask
-
- alignPatches(List<Patch>, Set<Patch>, int) - Static method in class mpicbg.trakem2.align.AlignTask
-
- alignPatches(Align.ParamOptimize, List<Patch>, Collection<Patch>, boolean, boolean, boolean, boolean, boolean) - Static method in class mpicbg.trakem2.align.AlignTask
-
- alignPatches(Align.ParamOptimize, List<Patch>, Collection<Patch>, boolean, boolean, boolean, boolean) - Static method in class mpicbg.trakem2.align.AlignTask
-
- alignPatchesTask(List<Patch>, Set<Patch>) - Static method in class mpicbg.trakem2.align.AlignTask
-
- alignPlaneAction(ViewerPanel, ViewerPanel.AlignPlane, String...) - Method in class bdv.viewer.NavigationActions
-
- AlignPlaneAction(ViewerPanel, ViewerPanel.AlignPlane) - Constructor for class bdv.viewer.WarpNavigationActions.AlignPlaneAction
-
- alignPlanes(ViewerPanel) - Method in class bdv.viewer.NavigationActions
-
- alignSelectedPatches(Selection, int) - Static method in class mpicbg.trakem2.align.Align
-
Align a selection of
patches
in a Layer.
- alignSelection(Selection, int) - Static method in class mpicbg.trakem2.align.AlignTask
-
- alignSelectionTask(Selection) - Static method in class mpicbg.trakem2.align.AlignTask
-
- AlignStacksWithLandmarks - Class in mpicbg.ij.plugin
-
- AlignStacksWithLandmarks() - Constructor for class mpicbg.ij.plugin.AlignStacksWithLandmarks
-
- AlignTask - Class in mpicbg.trakem2.align
-
Methods collection to be called from the GUI for alignment tasks.
- AlignTask() - Constructor for class mpicbg.trakem2.align.AlignTask
-
- AlignTask.ReferenceData - Class in mpicbg.trakem2.align
-
- alignTileCollections(Align.Param, Collection<AbstractAffineTile2D<?>>, Collection<AbstractAffineTile2D<?>>) - Static method in class mpicbg.trakem2.align.Align
-
Align two collections of tiles
- alignTiles(Align.ParamOptimize, List<AbstractAffineTile2D<?>>, List<AbstractAffineTile2D<?>>, boolean, int) - Static method in class mpicbg.trakem2.align.Align
-
- alignTiles(Align.ParamOptimize, List<AbstractAffineTile2D<?>>, List<AbstractAffineTile2D<?>>, int) - Static method in class mpicbg.trakem2.align.Align
-
- alignTiles(Align.ParamOptimize, List<AbstractAffineTile2D<?>>, List<AbstractAffineTile2D<?>>, boolean, boolean, boolean, boolean, boolean) - Static method in class mpicbg.trakem2.align.AlignTask
-
- alignTiles(Align.ParamOptimize, List<AbstractAffineTile2D<?>>, List<AbstractAffineTile2D<?>>, boolean, boolean, boolean, boolean) - Static method in class mpicbg.trakem2.align.AlignTask
-
- AlignTo4Byte() - Method in class customnode.u3d.BitStreamWrite
-
- AlignToByte() - Method in class customnode.u3d.BitStreamWrite
-
- AlignViewerPanelAction(BigWarp, BigWarpActions.AlignViewerPanelAction.TYPE) - Constructor for class bigwarp.BigWarpActions.AlignViewerPanelAction
-
- ALIVE - Static variable in class levelsets.algorithm.FastMarching
-
Constant for ALIVE elements
- ALL_FLAGS - Static variable in class sc.fiji.snt.analysis.MultiTreeStatistics
-
- ALL_PLOTS - Static variable in class sc.fiji.snt.plugin.ij1.ShollOptions
-
Deprecated.
- allAttributeInstances - Variable in class spim.fiji.plugin.queryXML.GenericLoadParseQueryXML
-
- allChannels - Static variable in class bdv.ij.ExportSpimFusionPlugIn
-
Deprecated.
- allChannels - Static variable in class bdv.ij.ExportSpimSequencePlugIn
-
Deprecated.
- allChoices - Static variable in class plugin.GridType
-
- AllConnectedComponents - Class in mpicbg.imglib.algorithm.labeling
-
Label all 8-connected components of a binary image
- AllConnectedComponents() - Constructor for class mpicbg.imglib.algorithm.labeling.AllConnectedComponents
-
- AllConnectedComponents.PositionStack - Class in mpicbg.imglib.algorithm.labeling
-
- allContentsString() - Method in class ij3d.Image3DUniverse
-
- AllenCompartment - Class in sc.fiji.snt.annotation
-
Defines an Allen Reference Atlas (ARA) [Allen Mouse Common Coordinate
Framework] annotation.
- AllenCompartment(UUID) - Constructor for class sc.fiji.snt.annotation.AllenCompartment
-
Instantiates a new ARA annotation from an UUID (as used by MouseLight's
database).
- AllenCompartment(int) - Constructor for class sc.fiji.snt.annotation.AllenCompartment
-
Instantiates a new ARA annotation from its identifier.
- AllenCompartment(JSONObject, UUID) - Constructor for class sc.fiji.snt.annotation.AllenCompartment
-
- AllenUtils - Class in sc.fiji.snt.annotation
-
- allIdentical(List<T>) - Method in class fiji.util.KDTree
-
- allIdentical(List<T>) - Method in class mpicbg.imglib.algorithm.kdtree.KDTree
-
- allImageSizesEqual() - Method in class spim.fiji.datasetmanager.LightSheetZ1MetaData
-
- AllKnownFilter - Class in org.imagearchive.lsm.toolbox.gui
-
- AllKnownFilter() - Constructor for class org.imagearchive.lsm.toolbox.gui.AllKnownFilter
-
- allocated - Variable in class fiji.util.ArrayBase
-
- allowCZIAutostitch() - Static method in class loci.plugins.util.LociPrefs
-
- allowed - Variable in class fiji.plugin.trackmate.tracking.oldlap.costfunction.GapClosingCostFunction
-
If false, gap closing will be prohibited.
- allowedBitDepth(int) - Method in class util.Histogram_2D
-
- allowEdgeExtrema(boolean) - Method in class mpicbg.imglib.algorithm.extremafinder.AbstractRegionalExtremaFinder
-
- allowEdgeExtrema(boolean) - Method in interface mpicbg.imglib.algorithm.extremafinder.RegionalExtremaFinder
-
If set to true before the
Algorithm.process()
method is called, then extrema found
at the edges of the image bounds (including time edges) will not be pruned, and will
be included in the result array.
- allowEdgeMax - Variable in class mpicbg.imglib.algorithm.extremafinder.AbstractRegionalExtremaFinder
-
- allowShow - Variable in class loci.plugins.util.DataBrowser
-
- allPeaks - Variable in class sc.fiji.timelapse.Peak_Counter_Tool
-
- allPeaksMap - Variable in class sc.fiji.timelapse.Peak_Counter_Tool
-
- allPointsIterator() - Method in class sc.fiji.snt.PathAndFillManager
-
- AllPointsIterator() - Constructor for class sc.fiji.snt.PathAndFillManager.AllPointsIterator
-
- allRegions - Variable in class util.FindConnectedRegions.Results
-
- allSame - Variable in class ai.SplitFunction
-
- AllToAllRegistration - Class in spim.process.interestpointregistration.optimizationtypes
-
- AllToAllRegistration(SpimData2, List<ViewId>, List<ChannelProcess>, boolean) - Constructor for class spim.process.interestpointregistration.optimizationtypes.AllToAllRegistration
-
- AllToAllRegistrationWithRange - Class in spim.process.interestpointregistration.optimizationtypes
-
- AllToAllRegistrationWithRange(SpimData2, List<ViewId>, List<ChannelProcess>, int, boolean) - Constructor for class spim.process.interestpointregistration.optimizationtypes.AllToAllRegistrationWithRange
-
- alpha - Variable in class fiji.features.Frangi_.VesselnessCalculator
-
- alpha - Variable in class ini.trakem2.display.Displayable
-
- alpha(int) - Static method in class mpicbg.imglib.type.numeric.RGBALegacyType
-
- alpha - Variable in class mpicbg.models.AbstractMovingLeastSquaresTransform
-
- alpha - Variable in class mpicbg.models.ElasticMovingLeastSquaresMesh
-
- alpha - Variable in class mpicbg.spim.io.SPIMConfiguration
-
- Alpha - Class in script.imglib.color
-
TODO
- Alpha(Image<? extends RGBALegacyType>) - Constructor for class script.imglib.color.Alpha
-
Extract the alpha channel of each pixel, in the range [0, 255].
- alpha - Variable in class Stitch_Image_Collection
-
- alpha - Variable in class Stitch_Multiple_Series_File
-
- alpha - Variable in class stitching.GridLayout
-
- alpha - Variable in class Stitching_2D
-
- alpha - Variable in class Stitching_3D
-
- ALPHA_ADVECTION - Variable in class levelsets.algorithm.GeodesicActiveContour
-
- alphaColor(Color, double) - Static method in class sc.fiji.snt.util.SNTColor
-
Adds an alpha component to a AWT color.
- AlphaMaskPath() - Constructor for class ini.trakem2.persistence.StaleFiles.AlphaMaskPath
-
- AlphanumComparator - Class in fiji.plugin.trackmate.util
-
The Alphanum Algorithm is an improved sorting algorithm for strings
containing numbers.
- alphaStatic - Static variable in class Stitch_Image_Collection
-
- alphaStatic - Static variable in class Stitch_Image_Directory
-
- alphaStatic - Static variable in class Stitch_Image_Grid
-
- alphaStatic - Static variable in class Stitch_Image_Grid_Sequence
-
- alphaStatic - Static variable in class Stitch_Many_Images
-
- alphaStatic - Static variable in class Stitch_Multiple_Series_File
-
- alphaStatic - Static variable in class Stitching_2D
-
- alphaStatic - Static variable in class Stitching_3D
-
- AlternateViewer - Class in view5d
-
- AlternateViewer(Container) - Constructor for class view5d.AlternateViewer
-
- AlternateViewer(Container, int, int) - Constructor for class view5d.AlternateViewer
-
- alternatingPath(int) - Method in class fiji.plugin.trackmate.tracking.oldlap.hungarian.MunkresKuhnAlgorithm
-
- aLUT - Variable in class ij3d.ContentInstant
-
- always_interpolate_areas_with_distance_map - Static variable in class ini.trakem2.utils.AreaUtils
-
Project property key.
- alwaysCopy - Static variable in class mpicbg.stitching.StitchingParameters
-
If you want to force that the
ContainerFactory
above is always used set this to true
- alwaysShowWindow - Static variable in class vib.VIB
-
- aMatrix - Variable in class jitk.spline.ThinPlateR2LogRSplineKernelTransform
-
- ambigous - Static variable in class ini.trakem2.utils.MCCube
-
- ambigous - Static variable in class marchingcubes.MCCube
-
- amira - package amira
-
- AmiraImporter - Class in ini.trakem2.io
-
Parses an amira labelfield and imports the labels as AreaList instances into the project tree.
- AmiraImporter() - Constructor for class ini.trakem2.io.AmiraImporter
-
- AmiraMeshDecoder - Class in amira
-
- AmiraMeshDecoder() - Constructor for class amira.AmiraMeshDecoder
-
- AmiraMeshDecoder() - Method in class amira.AmiraMeshDecoder
-
- AmiraMeshEncoder - Class in amira
-
- AmiraMeshEncoder(String) - Constructor for class amira.AmiraMeshEncoder
-
- AmiraMeshReader_ - Class in <Unnamed>
-
- AmiraMeshReader_() - Constructor for class AmiraMeshReader_
-
- AmiraMeshWriter_ - Class in <Unnamed>
-
- AmiraMeshWriter_() - Constructor for class AmiraMeshWriter_
-
- AmiraParameters - Class in amira
-
- AmiraParameters(ImagePlus) - Constructor for class amira.AmiraParameters
-
- AmiraParameters(Properties) - Constructor for class amira.AmiraParameters
-
- AmiraParameters(String) - Constructor for class amira.AmiraParameters
-
- AmiraParameters.IsA - Interface in amira
-
- AmiraParameters.Material - Class in amira
-
- AmiraSurface - Class in isosurface
-
- AmiraSurface() - Constructor for class isosurface.AmiraSurface
-
- AmiraTable - Class in amira
-
- AmiraTable(String, String, String) - Constructor for class amira.AmiraTable
-
- AmiraTable(String, String, String, boolean) - Constructor for class amira.AmiraTable
-
- AmiraTableEncoder - Class in amira
-
- AmiraTableEncoder(TextWindow) - Constructor for class amira.AmiraTableEncoder
-
- AmiraTableWriter_ - Class in <Unnamed>
-
- AmiraTableWriter_() - Constructor for class AmiraTableWriter_
-
- AMPLITUDE_DIR_TAG - Static variable in class spim.fiji.spimdata.imgloaders.XmlIoDHMImgLoader
-
- AMPLITUDE_ID_TAG - Static variable in class spim.fiji.spimdata.imgloaders.XmlIoDHMImgLoader
-
- Analyse_Particles - Class in QuickPALM
-
This plugin detectes sub-diffraction particles in a sequence of images, it
is the main plugin for the QuickPALM package.
- Analyse_Particles() - Constructor for class QuickPALM.Analyse_Particles
-
- ANALYSER_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
-
- ANALYSER_KEY_ATTRIBUTE - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
-
- AnalysisResults<T extends RealType<T>> - Class in sc.fiji.coloc.results
-
Data structure housing all colocalisation results.
- AnalysisResults() - Constructor for class sc.fiji.coloc.results.AnalysisResults
-
- analyze2D(int, int, double[], double, int, int, ImagePlus) - Method in class sc.fiji.snt.plugin.ij1.Sholl_Analysis
-
Deprecated.
- analyze3D(int, int, int, double[], ImagePlus) - Method in class sc.fiji.snt.plugin.ij1.Sholl_Analysis
-
Deprecated.
- Analyze_Reader - Class in sc.fiji.io
-
This plugin loads Analyze format files.
- Analyze_Reader() - Constructor for class sc.fiji.io.Analyze_Reader
-
- Analyze_Writer - Class in sc.fiji.io
-
This plugin saves Analyze format files.
- Analyze_Writer() - Constructor for class sc.fiji.io.Analyze_Writer
-
- analyzeMaximum(LocalizableByDimCursor3D<FloatType>, float, int, int, int, float, float, float, RejectStatistics, ArrayList<DoGMaximum>) - Static method in class mpicbg.spim.registration.bead.laplace.LaPlaceFunctions
-
- analyzePeak(DifferenceOfGaussianPeak<T>) - Method in class mpicbg.imglib.algorithm.scalespace.SubpixelLocalization
-
- analyzeProfile(double[], double[], boolean) - Method in class sc.fiji.snt.plugin.ij1.Sholl_Analysis
-
Deprecated.
Analyzes a sampled profile.
- ANALYZER_COLLECTION_ELEMENT_KEY - Static variable in class fiji.plugin.trackmate.io.TmXmlKeys
-
- AnalyzerCmd - Class in sc.fiji.snt.plugin
-
Command for measuring Tree(s).
- AnalyzerCmd() - Constructor for class sc.fiji.snt.plugin.AnalyzerCmd
-
- AnalyzeSkeleton_ - Class in sc.fiji.analyzeSkeleton
-
Main class of the ImageJ/Fiji plugin for skeleton analysis.
- AnalyzeSkeleton_() - Constructor for class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_
-
- analyzeTabularInput(ResultsTable, int, int, boolean) - Method in class sc.fiji.snt.plugin.ij1.Sholl_Analysis
-
Deprecated.
Instructs the plugin to parse the specified table expected to contain a
sampled profile.
- analyzeTabularInput(File, int, int, boolean) - Method in class sc.fiji.snt.plugin.ij1.Sholl_Analysis
-
Deprecated.
Instructs the plugin to parse the specified file expected to contain a
sampled profile.
- analyzeWithShollAnalysisPlugin(String, double) - Method in class sc.fiji.snt.gui.ShollAnalysisDialog.ShollResults
-
Deprecated.
- ANCHORS - Static variable in class ini.trakem2.display.LayerSet
-
- And() - Constructor for class fiji.expressionparser.function.ImgLibLogical.And
-
- And<T extends RealType<T>> - Class in imglib.ops.condition
-
TODO
- And(Condition<T>, Condition<T>) - Constructor for class imglib.ops.condition.And
-
- And - Class in imglib.ops.operator.binary
-
TODO
- And() - Constructor for class imglib.ops.operator.binary.And
-
- and(int) - Method in class loci.plugins.util.RecordedImageProcessor
-
- and(T) - Method in interface mpicbg.imglib.type.BooleanType
-
- and(BitType) - Method in class mpicbg.imglib.type.logic.BitType
-
- And - Class in script.imglib.math
-
TODO
- And(Image<? extends RealType<?>>, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.And
-
- And(IFunction, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.And
-
- And(Image<? extends RealType<?>>, IFunction) - Constructor for class script.imglib.math.And
-
- And(IFunction, IFunction) - Constructor for class script.imglib.math.And
-
- And(Image<? extends RealType<?>>, Number) - Constructor for class script.imglib.math.And
-
- And(Number, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.And
-
- And(IFunction, Number) - Constructor for class script.imglib.math.And
-
- And(Number, IFunction) - Constructor for class script.imglib.math.And
-
- And(Number, Number) - Constructor for class script.imglib.math.And
-
- And(Object...) - Constructor for class script.imglib.math.And
-
- AndConstant - Class in imglib.ops.operator.unary
-
TODO
- AndConstant(long) - Constructor for class imglib.ops.operator.unary.AndConstant
-
- AnElement - Class in view5d
-
- angle(Pnt) - Method in class delaunay.Pnt
-
Angle (in radians) between two Pnts (treated as vectors).
- Angle - Class in mpicbg.spim.data.sequence
-
Defines an angle which is part of the ViewSetup.
- Angle(int, String, double, double[]) - Constructor for class mpicbg.spim.data.sequence.Angle
-
- Angle(int, String) - Constructor for class mpicbg.spim.data.sequence.Angle
-
- Angle(int) - Constructor for class mpicbg.spim.data.sequence.Angle
-
- Angle() - Constructor for class mpicbg.spim.data.sequence.Angle
-
- angle - Variable in class mpicbg.spim.registration.ViewDataBeads
-
the acquisition angle
- angle(double, double, double, double) - Method in class sc.fiji.balloonSegmentation.structure.Balloon
-
Math vector operators: determine angle between v2 (x2, y2) and v1 (x1,y1) (I made this before I start using JAMA library)
- angle - Variable in class spim.vecmath.AxisAngle4d
-
The angle of rotation in radians.
- angle - Variable in class spim.vecmath.AxisAngle4f
-
The angle of rotation in radians.
- angle(Vector3d) - Method in class spim.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 spim.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 spim.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 spim.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].
- angle2d(AffineTransform3D, int) - Static method in class bigwarp.util.Rotation2DHelpers
-
- ANGLE_PATTERN - Static variable in class spim.fiji.datasetmanager.StackList
-
- ANGLE_ROTATIONAXIS_TAG - Static variable in class mpicbg.spim.data.XmlKeys
-
- ANGLE_ROTATIONDEGREES_TAG - Static variable in class mpicbg.spim.data.XmlKeys
-
- ANGLE_TAG - Static variable in class mpicbg.spim.data.XmlKeys
-
- angleAttributeKey - Static variable in class mpicbg.spim.data.sequence.ViewSetup
-
- angleBetween(double[], double[]) - Static method in class vib.FastMatrix
-
- angleBetween(float[], float[]) - Static method in class vib.FloatMatrix
-
- angleChoice - Static variable in class spim.fiji.plugin.Duplicate_Transformation
-
- angleEnd - Variable in class spimopener.SPIMExperiment
-
- angleIndicies - Variable in class mpicbg.spim.fusion.MappingFusionSequentialDifferentOutput
-
- angleIndiciesStatic - Static variable in class mpicbg.spim.fusion.MappingFusionSequentialDifferentOutput
-
- angleMult(double[], double[], double) - Static method in class bigwarp.util.Rotation2DHelpers
-
- angleNameList - Variable in class spim.fiji.datasetmanager.StackList
-
- angleNames - Variable in class spim.fiji.spimdata.imgloaders.MultipageTiffReader
-
- anglePattern - Variable in class mpicbg.spim.io.SPIMConfiguration
-
- angles - Static variable in class fiji.plugin.Bead_Registration
-
- angles - Variable in class mpicbg.spim.io.SPIMConfiguration
-
- angles() - Method in class spim.fiji.datasetmanager.LightSheetZ1MetaData
-
- angles - Variable in class spim.fiji.datasetmanager.SlideBook6Image
-
- angles(int) - Method in class spim.fiji.datasetmanager.SlideBook6MetaData
-
- angles - Variable in class spim.fiji.datasetmanager.StackList
-
- angles() - Method in class spim.fiji.plugin.apply.ModelLink
-
- angles - Variable in class spimopener.SPIMExperiment
-
- ANGLES_TAG - Static variable in class mpicbg.spim.data.XmlKeys
-
- angleStart - Variable in class spimopener.SPIMExperiment
-
- anim - Variable in class loci.plugins.util.DataBrowser
-
- animate - Variable in class loci.plugins.util.DataBrowser
-
- ANIMATE_TG - Static variable in class ij3d.DefaultUniverse
-
The index of the transform group in the viewing platform's
MultiTransformGroup which is responsible for animation
- animateBrowsing(int, int) - Method in class ini.trakem2.display.DisplayCanvas
-
Smoothly move the canvas from x0,y0,layer0 to x1,y1,layer1
- animateBrowsing(Rectangle, Layer) - Method in class ini.trakem2.display.DisplayCanvas
-
Smoothly move the canvas from its current position until the given rectangle is included within the srcRect.
- animateBrowsingTo(Coordinate<?>) - Method in class ini.trakem2.display.Display
-
- Animated_Gif_Reader - Class in sc.fiji.io
-
- Animated_Gif_Reader() - Constructor for class sc.fiji.io.Animated_Gif_Reader
-
- animateLayoutChange - Variable in class sc.fiji.snt.viewer.geditor.GraphEditor
-
- animateTransformation(AffineTransform3D, int) - Method in class bdv.viewer.BigWarpViewerPanel
-
- animateTransformation(AffineTransform3D) - Method in class bdv.viewer.BigWarpViewerPanel
-
- anisotropic_diffusion - package anisotropic_diffusion
-
- ANISOTROPIC_DIFFUSION - Static variable in class trainableSegmentation.FeatureStack
-
Anisotropic diffusion filter flag index
- Anisotropic_Diffusion_2D - Class in anisotropic_diffusion
-
- Anisotropic_Diffusion_2D() - Constructor for class anisotropic_diffusion.Anisotropic_Diffusion_2D
-
- AnisotropicDiffusion<T extends RealType<T>> - Class in mpicbg.imglib.algorithm.pde
-
Perona & Malik Anisotropic diffusion
- AnisotropicDiffusion(Image<T>, double, AnisotropicDiffusion.DiffusionFunction) - Constructor for class mpicbg.imglib.algorithm.pde.AnisotropicDiffusion
-
Instantiate the Perona & Malik anisotropic diffusion process, with a custom diffusion function.
- AnisotropicDiffusion(Image<T>, double, double) - Constructor for class mpicbg.imglib.algorithm.pde.AnisotropicDiffusion
-
Instantiate the Perona & Malik anisotropic diffusion process, with the default strong-edge
diffusion function.
- AnisotropicDiffusion.DiffusionFunction - Interface in mpicbg.imglib.algorithm.pde
-
The interface that function suitable to be diffusion function must implement.
- AnisotropicDiffusion.StrongEdgeEnhancer - Class in mpicbg.imglib.algorithm.pde
-
The first diffusion function proposed by Perona & Malik.
- AnisotropicDiffusion.WideRegionEnhancer - Class in mpicbg.imglib.algorithm.pde
-
The second diffusion function proposed by Perona & Malik.
- annotate(String) - Method in class sc.fiji.snt.analysis.SNTChart
-
Adds a subtitle to the chart.
- annotateCategory(String, String) - Method in class sc.fiji.snt.analysis.SNTChart
-
Annotates the specified category (Category plots only)
- annotateCategory(String, String, String) - Method in class sc.fiji.snt.analysis.SNTChart
-
Annotates the specified category (Category plots only).
- annotateLine(Collection<? extends SNTPoint>, String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Adds a line annotation to this viewer.
- annotatePoint(double, double, String) - Method in class sc.fiji.snt.analysis.SNTChart
-
Highlights a point in a histogram/XY plot by drawing a labeled arrow at the
specified location.
- annotatePoint(double, double, String, String) - Method in class sc.fiji.snt.analysis.SNTChart
-
Highlights a point in a histogram/XY plot by drawing a labeled arrow at the
specified location.
- annotatePoint(SNTPoint, String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Adds an highlighting point annotation to this viewer.
- annotatePoints(Collection<? extends SNTPoint>, String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Adds a scatter (point cloud) annotation to this viewer.
- annotateSurface(Collection<? extends SNTPoint>, String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
- annotateSurface(Collection<? extends SNTPoint>, String, boolean) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Computes a convex hull from a collection of points and adds it to the
scene as an annotation.
- annotateXline(double, String) - Method in class sc.fiji.snt.analysis.SNTChart
-
Annotates the specified X-value (XY plots and histograms).
- annotateXline(double, String, String) - Method in class sc.fiji.snt.analysis.SNTChart
-
Annotates the specified X-value (XY plots and histograms).
- annotateYline(double, String) - Method in class sc.fiji.snt.analysis.SNTChart
-
Annotates the specified Y-value (XY plots and histograms).
- annotateYline(double, String, String) - Method in class sc.fiji.snt.analysis.SNTChart
-
Annotates the specified Y-value (XY plots and histograms).
- annotation - Variable in class ini.trakem2.display.Displayable
-
- Annotation3D - Class in sc.fiji.snt.viewer
-
An Annotation3D is a triangulated surface or a cloud of points (scatter)
rendered in
Viewer3D
that can be used to highlight nodes in a
Tree
or locations in a
mesh
.
- Annotation3D(Viewer3D, Collection<Annotation3D>) - Constructor for class sc.fiji.snt.viewer.Annotation3D
-
- Annotation3D(Viewer3D, Collection<? extends SNTPoint>, int) - Constructor for class sc.fiji.snt.viewer.Annotation3D
-
- Annotation3D(Viewer3D, SNTPoint) - Constructor for class sc.fiji.snt.viewer.Annotation3D
-
- AnnotationGraph - Class in sc.fiji.snt.analysis.graph
-
- AnnotationGraph() - Constructor for class sc.fiji.snt.analysis.graph.AnnotationGraph
-
- AnnotationGraph(Collection<Tree>, String, double, int) - Constructor for class sc.fiji.snt.analysis.graph.AnnotationGraph
-
- AnnotationGraphAdapter - Class in sc.fiji.snt.viewer.geditor
-
- AnnotationGraphAdapter(AnnotationGraph) - Constructor for class sc.fiji.snt.viewer.geditor.AnnotationGraphAdapter
-
- AnnotationGraphAdapter(AnnotationGraph, String) - Constructor for class sc.fiji.snt.viewer.geditor.AnnotationGraphAdapter
-
- AnnotationGraphComponent - Class in sc.fiji.snt.viewer.geditor
-
- AnnotationGraphComponent(AnnotationGraphAdapter, Context) - Constructor for class sc.fiji.snt.viewer.geditor.AnnotationGraphComponent
-
- AnnotationGraphGeneratorCmd - Class in sc.fiji.snt.gui.cmds
-
- AnnotationGraphGeneratorCmd() - Constructor for class sc.fiji.snt.gui.cmds.AnnotationGraphGeneratorCmd
-
- AnnotationGraphRecViewerCmd - Class in sc.fiji.snt.gui.cmds
-
- AnnotationGraphRecViewerCmd() - Constructor for class sc.fiji.snt.gui.cmds.AnnotationGraphRecViewerCmd
-
- AnnotationGraphUtils - Class in sc.fiji.snt.analysis.graph
-
Utilities for AnnotationGraph handling and manipulation.
- AnnotationGraphUtils() - Constructor for class sc.fiji.snt.analysis.graph.AnnotationGraphUtils
-
- annotationsDescriptionChanged() - Method in class sc.fiji.snt.plugin.ShollAnalysisImgCmd
-
- AnnotationWeightedEdge - Class in sc.fiji.snt.analysis.graph
-
- AnnotationWeightedEdge() - Constructor for class sc.fiji.snt.analysis.graph.AnnotationWeightedEdge
-
- ANNULUS - Static variable in interface sc.fiji.snt.analysis.sholl.math.ShollStats
-
Flag for annulus normalization (Semi-log/Log-log method)
- antiAliasedText - Static variable in class Series_Labeler
-
- antiSymmetricPadding(double[][], int) - Static method in class bunwarpj.MathTools
-
- antiSymmetricPadding(double[], int, int) - Static method in class bunwarpj.MathTools
-
- antiSymmetricPadding(float[], int, int) - Static method in class bunwarpj.MathTools
-
- ANY_HEMISPHERE - Static variable in interface sc.fiji.snt.annotation.BrainAnnotation
-
- anyListeners() - Method in class sc.fiji.snt.SNT
-
- anySelected() - Method in class sc.fiji.snt.PathAndFillManager
-
Checks whether at least one Path is currently selected in the UI.
- ap - Variable in class mpicbg.trakem2.align.Align.ExtractFeaturesThread
-
- ap - Variable in class mpicbg.trakem2.align.Align.MatchFeaturesAndFindModelThread
-
- ap - Variable in class org.janelia.thickness.plugin.RealSumFloatNCC
-
- ap - Variable in class org.janelia.thickness.trakem2.RealSumARGBNCC
-
- appCreator - Variable in class voltex.VolumeRenderer
-
The AppearanceCreator, which creates the textures.
- AppearanceCreator - Class in octree
-
- AppearanceCreator - Class in voltex
-
This class is a helper class whose main task is to create Appearance objects
for a specified axis and direction.
- AppearanceCreator(VoltexVolume) - Constructor for class voltex.AppearanceCreator
-
Constructor.
- AppearanceCreator(VoltexVolume, Color3f, float) - Constructor for class voltex.AppearanceCreator
-
Initializes this AppearanceCreator with the given image data, color and
transparency values.
- append(Line3D) - Method in class ini.trakem2.analysis.Compare.Chain
-
- append(History.Step<?>) - Method in class ini.trakem2.utils.History
-
Appends a step at the end of the list, without modifying the current index.
- append(ILoggingEvent) - Method in class loci.plugins.util.IJStatusEchoer
-
- append(StringBuilder, HashSet<String>, String) - Static method in class mpicbg.trakem2.transform.DTD
-
- append(String) - Method in class vib.app.gui.Console
-
- appendBezierPathXML(StringBuilder, double[]) - Static method in class edu.utexas.clm.reconstructreader.Utils
-
- appendCalibration(StringBuilder) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructTranslator
-
- appendClosedPathXML(StringBuilder, double[]) - Static method in class edu.utexas.clm.reconstructreader.Utils
-
- appendCoordinateTransform(CoordinateTransform) - Method in class ini.trakem2.display.Patch
-
- appendCoordinateTransform(List<Patch>, CoordinateTransform, int) - Static method in class lenscorrection.DistortionCorrectionTask
-
- AppendCoordinateTransformThread(List<Patch>, CoordinateTransform, AtomicInteger) - Constructor for class lenscorrection.DistortionCorrectionTask.AppendCoordinateTransformThread
-
- appendDisplay(StringBuilder) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructTranslator
-
- appendDTD(StringBuilder) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructTranslator
-
- appendFilters(IFilter[]) - Method in class ini.trakem2.display.Patch
-
- appendGUIState(TrackMateGUIModel) - Method in class fiji.plugin.trackmate.io.TmXmlWriter
-
Appends the current GUI state as a state string to the document.
- appendLayerSet(StringBuilder) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructTranslator
-
- appendLayerSetXML(StringBuilder, List<ReconstructSection>) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructAreaList
-
- appendLog(String) - Method in class fiji.plugin.trackmate.io.TmXmlWriter
-
Appends the log content to the document.
- appendModel(Model) - Method in class fiji.plugin.trackmate.io.TmXmlWriter
-
Appends the content of a
Model
to the file generated by this
writer.
- appendOpenPathXML(StringBuilder, double[]) - Static method in class edu.utexas.clm.reconstructreader.Utils
-
- appendPatch(StringBuilder, Element) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructSection
-
- appendPoint(int, int, long) - Method in class ini.trakem2.display.Polyline
-
Append a point at the end.
- appendPoints(double[], double[], long[], int) - Method in class ini.trakem2.display.Polyline
-
- appendProject(StringBuilder) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructTranslator
-
- appendProjectXML(StringBuilder) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructAreaList
-
- appendProjectXML(StringBuilder) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructProfileList
-
- appendProjectXML(StringBuilder) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructZTrace
-
- appendSettings(Settings) - Method in class fiji.plugin.trackmate.io.TmXmlWriter
-
Appends the content of a
Settings
object to the document.
- appendShortest(float, float, StringBuilder) - Static method in class ini.trakem2.utils.M
-
Appends to @param sb the shortest possible String representation of a float number, according to the desired decimal @param precision.
- AppendSpimData2 - Class in spim.process.fusion.export
-
- AppendSpimData2() - Constructor for class spim.process.fusion.export.AppendSpimData2
-
- appendSpimData2(SpimData2, List<TimePoint>, List<ViewSetup>) - Static method in class spim.process.fusion.export.AppendSpimData2
-
Assembles a new SpimData2 based on the timepoints and viewsetups.
- AppendSpimData2HDF5 - Class in spim.process.fusion.export
-
- AppendSpimData2HDF5() - Constructor for class spim.process.fusion.export.AppendSpimData2HDF5
-
- appendText(String) - Static method in class vib.BatchLog_
-
- AppendTo - Variable in class view5d.My3DData
-
- AppendTo - Variable in class view5d.View5D_
-
- appendToExistingFile(ExportSpimFusionPlugIn.Parameters) - Static method in class bdv.ij.ExportSpimFusionPlugIn
-
Deprecated.
- appendToLastRow(String, Object) - Method in class sc.fiji.snt.analysis.SNTTable
-
- appendToPath(String, String) - Static method in class fiji.scripting.Compiler
-
- appendXML(StringBuilder) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructProfile
-
- appendXML(StringBuilder) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructSection
-
- appendXML(StringBuilder) - Method in class edu.utexas.clm.reconstructreader.reconstruct.ReconstructZTrace
-
- applet - Variable in class view5d.My3DData
-
- applied() - Method in interface ij3d.gui.LUTDialog.Listener
-
- applies(Object) - Method in class edu.utexas.clm.archipelago.ijsupport.TrakEM2Archipelago
-
- applies(Object) - Method in class edu.utexas.clm.crop.AreaList_Crop
-
- applies(Object) - Method in class edu.utexas.clm.reconstructreader.trakem2.Reconstruct_Writer
-
- applies(Object) - Method in interface ini.trakem2.plugin.TPlugIn
-
Returns true if this plugin can be applied to an Object like @param ob.
- applies(Object) - Method in class lineage.Identify
-
- applies(Object) - Method in class org.janelia.intensity.MatchIntensities
-
- applies(Object) - Method in class org.janelia.thickness.trakem2.LayerZPosition
-
- applies(Object) - Method in class treeline.TreelineGraphEditor
-
- apply(ImagePlus, ImagePlus, LandmarkTableModel, String, String, String, double[], double[], double[], Interpolation, boolean, int) - Static method in class bdv.ij.ApplyBigwarpPlugin
-
- apply(BigWarp.BigWarpData<T>, LandmarkTableModel, String, String, String, double[], double[], double[], Interpolation, boolean, int) - Static method in class bdv.ij.ApplyBigwarpPlugin
-
- apply(Interpolation) - Method in class bdv.util.DefaultInterpolators
-
- apply(double[]) - Method in class bdv.viewer.animate.SimilarityModel3D
-
- apply(double[], double[]) - Method in class bigwarp.BigWarp.WrappedCoordinateTransform
-
- apply(RealLocalizable, RealPositionable) - Method in class bigwarp.BigWarp.WrappedCoordinateTransform
-
- apply(double[]) - Method in class bunwarpj.trakem2.transform.CubicBSplineTransform
-
- apply(PathIterator) - Method in class fiji.geom.AreaCalculations.Calculation
-
- apply(V) - Method in class fiji.plugin.trackmate.graph.RecursiveCumSum
-
- apply(HashMap<String, String>, Image3DUniverse) - Method in class ij3d.SaveSession
-
- apply(Image3DUniverse) - Static method in class ij3d.UniverseSettings
-
- apply() - Method in class ij3d.ViewAdjuster
-
After all points/contents were added, apply() finally adjusts center and
zoom transformations of the view.
- apply() - Method in class ini.trakem2.display.AffineTransformMode
-
- apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.AreaList
-
- apply(VectorDataTransform) - Method in class ini.trakem2.display.AreaList
-
- apply(CoordinateTransform, Area) - Method in class ini.trakem2.display.AreaTree.AreaNode
-
- apply(VectorDataTransform) - Method in class ini.trakem2.display.AreaTree.AreaNode
-
- apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.Ball
-
- apply(VectorDataTransform) - Method in class ini.trakem2.display.Ball
-
- apply() - Method in class ini.trakem2.display.ContrastAdjustmentMode
-
- apply() - Method in class ini.trakem2.display.DefaultMode
-
- apply(int) - Method in class ini.trakem2.display.Displayable.DoEdit
-
Set the stored data to the stored Displayable.
- apply(int) - Method in class ini.trakem2.display.Displayable.DoEdits
-
- apply(int) - Method in class ini.trakem2.display.Displayable.DoTransforms
-
- apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.Dissector
-
- apply(VectorDataTransform) - Method in class ini.trakem2.display.Dissector
-
- apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.DLabel
-
- apply(VectorDataTransform) - Method in class ini.trakem2.display.DLabel
-
- apply(int) - Method in interface ini.trakem2.display.DoStep
-
Returns true on success.
- apply() - Method in class ini.trakem2.display.inspect.InspectPatchTrianglesMode
-
- apply(Class<?>, AffineTransform) - Method in class ini.trakem2.display.Layer
-
Preconcatenate the given AffineTransform to all Displayable objects of class c, without respecting their links.
- apply(int) - Method in class ini.trakem2.display.Layer.DoMoveDisplayable
-
- apply(int) - Method in class ini.trakem2.display.LayerSet.DoChangeTrees
-
- apply(int) - Method in class ini.trakem2.display.LayerSet.DoMoveZDisplayable
-
- apply() - Method in class ini.trakem2.display.ManualAlignMode
-
- apply() - Method in interface ini.trakem2.display.Mode
-
- apply(CoordinateTransform, Area) - Method in class ini.trakem2.display.Node
-
- apply(VectorDataTransform) - Method in class ini.trakem2.display.Node
-
- apply(Node.Operation<T>, Iterator<Node<T>>) - Method in class ini.trakem2.display.Node
-
- apply(Node<I>) - Method in interface ini.trakem2.display.Node.Operation
-
- apply() - Method in class ini.trakem2.display.NonLinearTransformMode
-
- apply(Set<Layer>) - Method in class ini.trakem2.display.NonLinearTransformMode
-
- apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.Pipe
-
- apply(VectorDataTransform) - Method in class ini.trakem2.display.Pipe
-
- apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.Polyline
-
- apply(VectorDataTransform) - Method in class ini.trakem2.display.Polyline
-
- apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.Profile
-
- apply(VectorDataTransform) - Method in class ini.trakem2.display.Profile
-
- apply(int, double[]) - Method in class ini.trakem2.display.Selection
-
- apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.Tree
-
- apply(VectorDataTransform) - Method in class ini.trakem2.display.Tree
-
- apply(CoordinateTransform, Area) - Method in class ini.trakem2.display.Treeline.RadiusNode
-
- apply(VectorDataTransform) - Method in class ini.trakem2.display.Treeline.RadiusNode
-
- apply(Layer, Area, CoordinateTransform) - Method in interface ini.trakem2.display.VectorData
-
Applies the 2D transform @ict (which is expected to operate on the
world coordinates version of the data contained here) only to the
data that falls within the @param roi (in world coords), and then
recomputes the bounding box and affine transform (to a translation
or identity).
- apply(VectorDataTransform) - Method in interface ini.trakem2.display.VectorData
-
- apply(Collection<Displayable>) - Method in class ini.trakem2.imaging.ContrastEnhancerWrapper
-
- apply(int) - Method in class ini.trakem2.tree.RenameThingStep
-
- apply(CoordinateTransform, Area, Area) - Static method in class ini.trakem2.utils.M
-
Apply in place the @param ict to the Area @param a, but only for the part that intersects the roi.
- apply(VectorDataTransform, Area) - Static method in class ini.trakem2.utils.M
-
- apply(VectorDataTransform, Area, boolean) - Static method in class ini.trakem2.utils.M
-
Parts of @param a not intersected by any of @param vdt rois will be left untouched if @param remove_outside is false.
- apply(CoordinateTransform, double[][], int, double[]) - Static method in class ini.trakem2.utils.M
-
Reuses the @param fp to apply in place.
- apply(O) - Method in interface ini.trakem2.utils.Operation
-
- apply(double[], double[]) - Method in class jitk.spline.ThinPlateR2LogRSplineKernelTransform
-
- apply(double[], double[], boolean) - Method in class jitk.spline.ThinPlateR2LogRSplineKernelTransform
-
Transform a source vector pt into a target vector result.
- apply(double[]) - Method in class jitk.spline.ThinPlateR2LogRSplineKernelTransform
-
Transforms the input point according to the thin plate spline stored by
this object.
- apply(double[]) - Method in class lenscorrection.PolynomialModel2D
-
- apply(Point3d) - Method in class math3d.Bookstein
-
- apply(double[][], double[]) - Static method in class math3d.FastMatrixN
-
Calculates b in Ax = b
- apply(float[][], float[]) - Static method in class math3d.FloatMatrixN
-
Calculates b in Ax = b
- apply(double[]) - Method in class mpicbg.models.AbstractMovingLeastSquaresTransform
-
- apply(double[]) - Method in class mpicbg.models.AffineModel1D
-
- apply(double[]) - Method in class mpicbg.models.AffineModel2D
-
- apply(double[]) - Method in class mpicbg.models.AffineModel3D
-
- apply(double[]) - Method in class mpicbg.models.ConstantModel
-
- apply(double[]) - Method in interface mpicbg.models.CoordinateTransform
-
- apply(double[]) - Method in class mpicbg.models.CoordinateTransformList
-
- apply(double[]) - Method in class mpicbg.models.CoordinateTransformMap2D
-
- apply(double[]) - Method in class mpicbg.models.HomographyModel2D
-
- apply(double[]) - Method in class mpicbg.models.IdentityModel
-
- apply(double[]) - Method in class mpicbg.models.InterpolatedAffineModel1D
-
- apply(double[]) - Method in class mpicbg.models.InterpolatedAffineModel2D
-
- apply(double[]) - Method in class mpicbg.models.InterpolatedAffineModel3D
-
- apply(double[]) - Method in class mpicbg.models.InterpolatedCoordinateTransform
-
- apply(double[]) - Method in class mpicbg.models.InterpolatedModel
-
- apply(double[]) - Method in class mpicbg.models.InvertibleCoordinateTransformList
-
- apply(CoordinateTransform) - Method in class mpicbg.models.MovingLeastSquaresMesh
-
Apply an arbitrary coordinate transformation to each Tile's
PointMatches.
- apply(CoordinateTransform) - Method in class mpicbg.models.Point
-
- apply(CoordinateTransform, double) - Method in class mpicbg.models.Point
-
- apply(CoordinateTransform, Iterable<P>) - Static method in class mpicbg.models.Point
-
- apply(CoordinateTransform) - Method in class mpicbg.models.PointMatch
-
- apply(CoordinateTransform, double) - Method in class mpicbg.models.PointMatch
-
- apply(Collection<? extends PointMatch>, CoordinateTransform) - Static method in class mpicbg.models.PointMatch
-
- apply(double[]) - Method in class mpicbg.models.PolynomialTransform2D
-
- apply(double[]) - Method in class mpicbg.models.RigidModel2D
-
- apply(double[]) - Method in class mpicbg.models.RigidModel3D
-
- apply(double[]) - Method in class mpicbg.models.SimilarityModel2D
-
- apply(double[]) - Method in class mpicbg.models.SimilarityModel3D
-
- apply() - Method in class mpicbg.models.Tile
-
- apply(double) - Method in class mpicbg.models.Tile
-
- apply() - Method in class mpicbg.models.TileConfiguration
-
- apply(double[]) - Method in class mpicbg.models.TransformMesh
-
- apply(double[]) - Method in class mpicbg.models.TranslationModel1D
-
- apply(double[]) - Method in class mpicbg.models.TranslationModel2D
-
- apply(double[]) - Method in class mpicbg.models.TranslationModel3D
-
- apply(double[]) - Method in class mpicbg.panorama.EquirectangularProjection
-
- apply(double[]) - Method in class mpicbg.panorama.RectlinearCamera
-
- apply(double[]) - Method in class mpicbg.pointdescriptor.model.FixedModel
-
- apply(double[]) - Method in class mpicbg.pointdescriptor.model.TranslationInvariantAffineModel3D
-
- apply(double[]) - Method in class mpicbg.pointdescriptor.model.TranslationInvariantFixedModel
-
- apply(double[]) - Method in class mpicbg.pointdescriptor.model.TranslationInvariantRigidModel2D
-
- apply(double[]) - Method in class mpicbg.pointdescriptor.model.TranslationInvariantRigidModel3D
-
- apply(double[]) - Method in class mpicbg.pointdescriptor.model.TranslationInvariantSimilarityModel3D
-
- apply(double[]) - Method in class mpicbg.trakem2.transform.NonLinearCoordinateTransform
-
- apply(double[]) - Method in class mpicbg.trakem2.transform.ThinPlateSplineTransform
-
- apply(double[], double[]) - Method in class net.imglib2.realtransform.Wrapped2DTransformAs3D
-
- apply(RealLocalizable, RealPositionable) - Method in class net.imglib2.realtransform.Wrapped2DTransformAs3D
-
- apply(double) - Method in class org.janelia.thickness.lut.AbstractLUTGrid
-
- apply(double) - Method in class org.janelia.thickness.lut.AbstractLUTRealTransform
-
- apply(double, int, int) - Method in class org.janelia.thickness.lut.AbstractLUTRealTransformField
-
- apply(int) - Method in class org.janelia.thickness.lut.AbstractPerumtationTransform
-
- apply(double[], double[]) - Method in class org.janelia.thickness.lut.LUTGrid
-
- apply(float[], float[]) - Method in class org.janelia.thickness.lut.LUTGrid
-
- apply(RealLocalizable, RealPositionable) - Method in class org.janelia.thickness.lut.LUTGrid
-
- apply(double[], double[]) - Method in class org.janelia.thickness.lut.LUTRealTransform
-
- apply(float[], float[]) - Method in class org.janelia.thickness.lut.LUTRealTransform
-
- apply(RealLocalizable, RealPositionable) - Method in class org.janelia.thickness.lut.LUTRealTransform
-
- apply(double[], double[]) - Method in class org.janelia.thickness.lut.LUTRealTransformField
-
- apply(float[], float[]) - Method in class org.janelia.thickness.lut.LUTRealTransformField
-
- apply(RealLocalizable, RealPositionable) - Method in class org.janelia.thickness.lut.LUTRealTransformField
-
- apply(long[], long[]) - Method in class org.janelia.thickness.lut.PermutationTransform
-
- apply(int[], int[]) - Method in class org.janelia.thickness.lut.PermutationTransform
-
- apply(Localizable, Positionable) - Method in class org.janelia.thickness.lut.PermutationTransform
-
- apply(double[], double[]) - Method in class org.janelia.thickness.lut.SingleDimensionLUTGrid
-
- apply(float[], float[]) - Method in class org.janelia.thickness.lut.SingleDimensionLUTGrid
-
- apply(RealLocalizable, RealPositionable) - Method in class org.janelia.thickness.lut.SingleDimensionLUTGrid
-
- apply(double[], double[]) - Method in class org.janelia.thickness.lut.SingleDimensionLUTRealTransform
-
- apply(float[], float[]) - Method in class org.janelia.thickness.lut.SingleDimensionLUTRealTransform
-
- apply(RealLocalizable, RealPositionable) - Method in class org.janelia.thickness.lut.SingleDimensionLUTRealTransform
-
- apply(double[], double[]) - Method in class org.janelia.thickness.lut.SingleDimensionLUTRealTransformField
-
- apply(float[], float[]) - Method in class org.janelia.thickness.lut.SingleDimensionLUTRealTransformField
-
- apply(RealLocalizable, RealPositionable) - Method in class org.janelia.thickness.lut.SingleDimensionLUTRealTransformField
-
- apply(long[], long[]) - Method in class org.janelia.thickness.lut.SingleDimensionPermutationTransform
-
- apply(int[], int[]) - Method in class org.janelia.thickness.lut.SingleDimensionPermutationTransform
-
- apply(Localizable, Positionable) - Method in class org.janelia.thickness.lut.SingleDimensionPermutationTransform
-
- apply(IFunction, R, int) - Static method in class script.imglib.math.Compute
-
Execute the given
IFunction
, which runs for each pixel,
and store the results in an
Image
with the type defined by ,
which has to be a subclass of
RealType
.
- apply(IFunction, RGBALegacyType, int) - Static method in class script.imglib.math.Compute
-
- apply(float[]) - Method in interface stitching.model.CoordinateTransform
-
- apply(Model) - Method in class stitching.model.Point
-
- apply(Model, float) - Method in class stitching.model.Point
-
- apply(Model) - Method in class stitching.model.PointMatch
-
- apply(float[]) - Method in class stitching.model.TranslationModel2D
-
- apply(float[]) - Method in class stitching.model.TranslationModel3D
-
- apply() - Method in class trainableSegmentation.utils.WatershedTransform2D
-
Apply fast watersheds using flooding simulations, as described
by Soille, Pierre, and Luc M.
- apply() - Method in class Transform_SpringMesh
-
- apply(double, double, double) - Method in class vib.FastMatrix
-
- apply(Point3d) - Method in class vib.FastMatrix
-
- apply(double[]) - Method in class vib.FastMatrix
-
- apply(float, float, float) - Method in class vib.FloatMatrix
-
- apply(Point3d) - Method in class vib.FloatMatrix
-
- apply(float[]) - Method in class vib.FloatMatrix
-
- apply() - Method in class vib.segment.Thresholder
-
- apply(ImageProcessor, Roi, int, int, int, boolean) - Method in class vib.segment.Thresholder
-
- apply(double, double, double, double[]) - Method in class vib.transforms.BooksteinTransform
-
- apply(double, double, double) - Method in class vib.transforms.BooksteinTransform
-
- apply(double, double, double, double[]) - Method in class vib.transforms.FastMatrixTransform
-
- apply(double, double, double, double[]) - Method in class vib.transforms.OrderedTransformations
-
- apply(double, double, double) - Method in class vib.transforms.OrderedTransformations
-
- apply(Point3d) - Method in class vib.transforms.OrderedTransformations
-
- apply(double, double, double, double[]) - Method in interface vib.transforms.Transform
-
- apply_bandpass_filter - Variable in class ini.trakem2.imaging.Segmentation.FastMarchingParam
-
- APPLY_CLASSIFIER - Static variable in class trainableSegmentation.Weka_Segmentation
-
name of the macro method to apply the current classifier to an image or stack
- Apply_External_Transformation - Class in fiji.plugin
-
- Apply_External_Transformation() - Constructor for class fiji.plugin.Apply_External_Transformation
-
- apply_grey_value_erosion - Variable in class ini.trakem2.imaging.Segmentation.FastMarchingParam
-
- APPLY_TRANSFORM - Static variable in class ij3d.Executer
-
- Apply_Transformation - Class in spim.fiji.plugin
-
- Apply_Transformation() - Constructor for class spim.fiji.plugin.Apply_Transformation
-
- applyAndPropagate(Set<Layer>) - Method in class ini.trakem2.display.AffineTransformMode
-
Skips current layer, since its done already.
- applyAngles(LoadParseQueryXML) - Method in class spim.fiji.plugin.Duplicate_Transformation
-
- applyAxis() - Method in class spim.fiji.datasetmanager.LightSheetZ1MetaData
-
- applyAxis(SpimData, double) - Static method in class spim.fiji.datasetmanager.SlideBook6
-
- applyAxis(SpimData) - Static method in class spim.fiji.plugin.Apply_Transformation
-
- applyAxis - Variable in class spim.fiji.spimdata.imgloaders.MultipageTiffReader
-
- applyAxis() - Method in class spim.fiji.spimdata.imgloaders.MultipageTiffReader
-
- applyBigWarpHelper(AbstractSpimData<?>[], AbstractSpimData<?>[], ImagePlus, LandmarkTableModel, Interpolation) - Static method in class bigwarp.BigWarpBatchTransformFOV
-
- ApplyBigwarpPlugin - Class in bdv.ij
-
Apply a bigwarp transform to a 2d or 3d ImagePlus
- ApplyBigwarpPlugin() - Constructor for class bdv.ij.ApplyBigwarpPlugin
-
- ApplyButtonListener() - Constructor for class mpicbg.spim.segmentation.InteractiveDoG.ApplyButtonListener
-
- ApplyButtonListener(Frame, BigDataViewer) - Constructor for class spim.fiji.plugin.apply.BigDataViewerTransformationWindow.ApplyButtonListener
-
- applyByStrength(Model, float) - Method in class stitching.model.PointMatch
-
- applyCal(Specify_Calibration.Cal, SpimData, List<ViewId>) - Static method in class spim.fiji.plugin.Specify_Calibration
-
- applyCalibration(ImagePlus) - Method in class loci.plugins.in.Calibrator
-
Applies spatial calibrations to an image stack.
- applyCanvasOffset(double, double, double) - Method in class sc.fiji.snt.Tree
-
Specifies the offset to be used when rendering this Tree in a
TracerCanvas
.
- applyChannels(LoadParseQueryXML) - Method in class spim.fiji.plugin.Duplicate_Transformation
-
- applyChecked(double) - Method in class org.janelia.thickness.lut.AbstractLUTGrid
-
- applyChecked(double) - Method in class org.janelia.thickness.lut.AbstractLUTRealTransform
-
- applyChecked(double, int, int) - Method in class org.janelia.thickness.lut.AbstractLUTRealTransformField
-
- applyChecked(int) - Method in class org.janelia.thickness.lut.AbstractPerumtationTransform
-
- applyClassifier(Instances, int, int, int) - Method in class trainableSegmentation.Trainable_Segmentation
-
Deprecated.
Apply current classifier to set of instances
- applyClassifier(String, String, String, String, String, String) - Static method in class trainableSegmentation.Weka_Segmentation
-
Apply current classifier to specific image (2D or stack)
- applyClassifier(ImagePlus) - Method in class trainableSegmentation.WekaSegmentation
-
Apply current classifier to a given image.
- applyClassifier(ImagePlus, int, boolean) - Method in class trainableSegmentation.WekaSegmentation
-
Apply current classifier to a given image.
- applyClassifier(ImagePlus, ImagePlus, int, boolean) - Method in class trainableSegmentation.WekaSegmentation
-
Apply current classifier to a given image with precomputed features.
- applyClassifier(ImagePlus, FeatureStackArray, int, boolean) - Method in class trainableSegmentation.WekaSegmentation
-
Apply current classifier to a given image with precomputed features.
- applyClassifier(boolean) - Method in class trainableSegmentation.WekaSegmentation
-
Apply current classifier to current image.
- applyClassifier(int, boolean) - Method in class trainableSegmentation.WekaSegmentation
-
Apply current classifier to current image.
- applyClassifier(ImagePlus, int[], int, boolean) - Method in class trainableSegmentation.WekaSegmentation
-
Apply the current classifier to an image subdividing the
image in tiles for memory saving.
- applyClassifier(ImagePlus, int[], int[], int, boolean) - Method in class trainableSegmentation.WekaSegmentation
-
Apply current classifier to a user-defined ROI of a given image.
- applyClassifier(Instances, int, int, int, boolean) - Method in class trainableSegmentation.WekaSegmentation
-
Apply current classifier to set of instances
- applyClassifier(FeatureStackArray, int, boolean) - Method in class trainableSegmentation.WekaSegmentation
-
Apply current classifier to a set of feature vectors (given in a feature
stack array).
- applyClassifierMT(ImagePlus, int, boolean) - Method in class trainableSegmentation.WekaSegmentation
-
Apply current classifier to a given image in a complete concurrent way.
- applyClassifierToTestData() - Method in class trainableSegmentation.Trainable_Segmentation
-
Deprecated.
Apply classifier to test data
- applyClassifierToTestData() - Method in class trainableSegmentation.Weka_Segmentation
-
Apply classifier to test data.
- applyClassifierToTestImage(ImagePlus, int) - Method in class trainableSegmentation.Trainable_Segmentation
-
Deprecated.
Apply current classifier to image
- applyColors(List<ImagePlus>) - Method in class loci.plugins.in.Colorizer
-
- applyColors(ImagePlus, int, Color[], int) - Static method in class org.imagearchive.lsm.toolbox.ReaderToolkit
-
- applyCoordinateTransform(ImagePlus, CoordinateTransform, int, boolean, int[]) - Static method in class register_virtual_stack.Transform_Virtual_Stack_MT
-
Apply a coordinate transform to a given image
- applyCorrection - Variable in class lenscorrection.Distortion_Correction.PluginParam
-
- applyEntropy(ImageProcessor, int, int) - Method in class trainableSegmentation.filters.Entropy_Filter
-
Apply entropy filter to an image
- applyFilter(Filter) - Method in class levelsets.ij.ImageContainer
-
Applies the passed Filter on every image in the container.
- applyFilter(Filter, int, int) - Method in class levelsets.ij.ImageContainer
-
Applies the passed filter on the selected range of images
- applyFilter(ImageProcessor, int, int, int) - Method in class trainableSegmentation.filters.Kuwahara
-
Apply filter to input image (in place)
- applyFilters(Image) - Method in class ini.trakem2.display.Display
-
- applyFilters(ImageProcessor) - Method in class ini.trakem2.display.Display
-
- applyFilters(ImagePlus) - Method in class ini.trakem2.display.Display
-
- ApplyHistSelection() - Method in class view5d.My3DData
-
- applyIcon(AbstractButton, float, IconFactory.GLYPH) - Static method in class sc.fiji.snt.gui.IconFactory
-
- applyIllums(LoadParseQueryXML) - Method in class spim.fiji.plugin.Duplicate_Transformation
-
- applyInPlace(double[]) - Method in class bdv.viewer.animate.SimilarityModel3D
-
- applyInPlace(double[]) - Method in class bunwarpj.trakem2.transform.CubicBSplineTransform
-
- applyInPlace(double[]) - Method in class jitk.spline.ThinPlateR2LogRSplineKernelTransform
-
Transform pt in place.
- applyInPlace(double[]) - Method in class lenscorrection.PolynomialModel2D
-
- applyInPlace(double[]) - Method in class mpicbg.models.AffineModel1D
-
- applyInPlace(double[]) - Method in class mpicbg.models.AffineModel2D
-
- applyInPlace(double[]) - Method in class mpicbg.models.AffineModel3D
-
- applyInPlace(double[]) - Method in class mpicbg.models.ConstantModel
-
- applyInPlace(double[]) - Method in interface mpicbg.models.CoordinateTransform
-
- applyInPlace(double[]) - Method in class mpicbg.models.CoordinateTransformList
-
- applyInPlace(double[]) - Method in class mpicbg.models.CoordinateTransformMap2D
-
- applyInPlace(double[]) - Method in class mpicbg.models.HomographyModel2D
-
- applyInPlace(double[]) - Method in class mpicbg.models.IdentityModel
-
- applyInPlace(double[]) - Method in class mpicbg.models.InterpolatedAffineModel1D
-
- applyInPlace(double[]) - Method in class mpicbg.models.InterpolatedAffineModel2D
-
- applyInPlace(double[]) - Method in class mpicbg.models.InterpolatedAffineModel3D
-
- applyInPlace(double[]) - Method in class mpicbg.models.InterpolatedCoordinateTransform
-
- applyInPlace(double[]) - Method in class mpicbg.models.InterpolatedModel
-
- applyInPlace(double[]) - Method in class mpicbg.models.InvertibleCoordinateTransformList
-
- applyInPlace(double[]) - Method in class mpicbg.models.MovingLeastSquaresTransform
-
- applyInPlace(double[]) - Method in class mpicbg.models.MovingLeastSquaresTransform2
-
- applyInPlace(double[]) - Method in class mpicbg.models.PolynomialTransform2D
-
- applyInPlace(double[]) - Method in class mpicbg.models.RigidModel2D
-
- applyInPlace(double[]) - Method in class mpicbg.models.RigidModel3D
-
- applyInPlace(double[]) - Method in class mpicbg.models.SimilarityModel2D
-
- applyInPlace(double[]) - Method in class mpicbg.models.SimilarityModel3D
-
- applyInPlace(double[]) - Method in class mpicbg.models.TransformMesh
-
- applyInPlace(double[]) - Method in class mpicbg.models.TranslationModel1D
-
- applyInPlace(double[]) - Method in class mpicbg.models.TranslationModel2D
-
- applyInPlace(double[]) - Method in class mpicbg.models.TranslationModel3D
-
- applyInPlace(double[]) - Method in class mpicbg.panorama.EquirectangularProjection
-
- applyInPlace(double[]) - Method in class mpicbg.panorama.RectlinearCamera
-
- applyInPlace(double[]) - Method in class mpicbg.pointdescriptor.model.FixedModel
-
- applyInPlace(double[]) - Method in class mpicbg.pointdescriptor.model.TranslationInvariantAffineModel3D
-
- applyInPlace(double[]) - Method in class mpicbg.pointdescriptor.model.TranslationInvariantFixedModel
-
- applyInPlace(double[]) - Method in class mpicbg.pointdescriptor.model.TranslationInvariantRigidModel2D
-
- applyInPlace(double[]) - Method in class mpicbg.pointdescriptor.model.TranslationInvariantRigidModel3D
-
- applyInPlace(double[]) - Method in class mpicbg.pointdescriptor.model.TranslationInvariantSimilarityModel3D
-
- applyInPlace(AbstractAffineModel3D<?>, Point3d) - Static method in class mpicbg.spim.mpicbg.Java3d
-
- applyInPlace(AbstractAffineModel3D<?>, Point3d, double[]) - Static method in class mpicbg.spim.mpicbg.Java3d
-
- applyInPlace(double[]) - Method in class mpicbg.trakem2.transform.MovingLeastSquaresTransform
-
- applyInPlace(double[]) - Method in class mpicbg.trakem2.transform.MovingLeastSquaresTransform2
-
Multi-threading safe version of the original applyInPlace method.
- applyInPlace(double[]) - Method in class mpicbg.trakem2.transform.NonLinearCoordinateTransform
-
- applyInPlace(double[]) - Method in class mpicbg.trakem2.transform.ThinPlateSplineTransform
-
- applyInPlace(float[]) - Method in interface stitching.model.CoordinateTransform
-
- applyInPlace(float[]) - Method in class stitching.model.TranslationModel2D
-
- applyInPlace(float[]) - Method in class stitching.model.TranslationModel3D
-
- applyInverse(double[]) - Method in class bdv.viewer.animate.SimilarityModel3D
-
- applyInverse(double[], double[]) - Method in class bigwarp.BigWarp.WrappedCoordinateTransform
-
- applyInverse(RealPositionable, RealLocalizable) - Method in class bigwarp.BigWarp.WrappedCoordinateTransform
-
- applyInverse(double[]) - Method in class mpicbg.models.AffineModel1D
-
- applyInverse(double[]) - Method in class mpicbg.models.AffineModel2D
-
- applyInverse(double[]) - Method in class mpicbg.models.AffineModel3D
-
- applyInverse(double[]) - Method in class mpicbg.models.HomographyModel2D
-
- applyInverse(double[]) - Method in class mpicbg.models.IdentityModel
-
- applyInverse(double[]) - Method in class mpicbg.models.InterpolatedAffineModel1D
-
- applyInverse(double[]) - Method in class mpicbg.models.InterpolatedAffineModel2D
-
- applyInverse(double[]) - Method in class mpicbg.models.InterpolatedAffineModel3D
-
- applyInverse(double[]) - Method in interface mpicbg.models.InverseCoordinateTransform
-
Apply the inverse of the model to a point location
- applyInverse(double[]) - Method in class mpicbg.models.InverseCoordinateTransformList
-
- applyInverse(double[]) - Method in class mpicbg.models.InverseCoordinateTransformMap2D
-
- applyInverse(double[]) - Method in class mpicbg.models.InvertibleConstantModel
-
- applyInverse(double[]) - Method in class mpicbg.models.InvertibleCoordinateTransformList
-
- applyInverse(double[]) - Method in class mpicbg.models.InvertibleInterpolatedModel
-
- applyInverse(InverseCoordinateTransform) - Method in class mpicbg.models.Point
-
- applyInverse(InverseCoordinateTransform, Iterable<Point>) - Static method in class mpicbg.models.Point
-
- applyInverse(double[]) - Method in class mpicbg.models.RigidModel2D
-
- applyInverse(double[]) - Method in class mpicbg.models.RigidModel3D
-
- applyInverse(double[]) - Method in class mpicbg.models.SimilarityModel2D
-
- applyInverse(double[]) - Method in class mpicbg.models.SimilarityModel3D
-
- applyInverse(double[]) - Method in class mpicbg.models.TransformMesh
-
- applyInverse(double[]) - Method in class mpicbg.models.TranslationModel1D
-
- applyInverse(double[]) - Method in class mpicbg.models.TranslationModel2D
-
- applyInverse(double[]) - Method in class mpicbg.models.TranslationModel3D
-
- applyInverse(double[]) - Method in class mpicbg.panorama.EquirectangularProjection
-
- applyInverse(double[]) - Method in class mpicbg.panorama.RectlinearCamera
-
- applyInverse(double[], double[]) - Method in class net.imglib2.realtransform.Wrapped2DTransformAs3D
-
- applyInverse(RealPositionable, RealLocalizable) - Method in class net.imglib2.realtransform.Wrapped2DTransformAs3D
-
- applyInverse(double) - Method in class org.janelia.thickness.lut.AbstractLUTGrid
-
- applyInverse(double) - Method in class org.janelia.thickness.lut.AbstractLUTRealTransform
-
- applyInverse(double, int, int) - Method in class org.janelia.thickness.lut.AbstractLUTRealTransformField
-
- applyInverse(int) - Method in class org.janelia.thickness.lut.AbstractPerumtationTransform
-
- applyInverse(double[], double[]) - Method in class org.janelia.thickness.lut.LUTGrid
-
- applyInverse(float[], float[]) - Method in class org.janelia.thickness.lut.LUTGrid
-
- applyInverse(RealPositionable, RealLocalizable) - Method in class org.janelia.thickness.lut.LUTGrid
-
- applyInverse(double[], double[]) - Method in class org.janelia.thickness.lut.LUTRealTransform
-
- applyInverse(float[], float[]) - Method in class org.janelia.thickness.lut.LUTRealTransform
-
- applyInverse(RealPositionable, RealLocalizable) - Method in class org.janelia.thickness.lut.LUTRealTransform
-
- applyInverse(double[], double[]) - Method in class org.janelia.thickness.lut.LUTRealTransformField
-
- applyInverse(float[], float[]) - Method in class org.janelia.thickness.lut.LUTRealTransformField
-
- applyInverse(RealPositionable, RealLocalizable) - Method in class org.janelia.thickness.lut.LUTRealTransformField
-
- applyInverse(long[], long[]) - Method in class org.janelia.thickness.lut.PermutationTransform
-
- applyInverse(int[], int[]) - Method in class org.janelia.thickness.lut.PermutationTransform
-
- applyInverse(Positionable, Localizable) - Method in class org.janelia.thickness.lut.PermutationTransform
-
- applyInverse(double[], double[]) - Method in class org.janelia.thickness.lut.SingleDimensionLUTGrid
-
- applyInverse(float[], float[]) - Method in class org.janelia.thickness.lut.SingleDimensionLUTGrid
-
- applyInverse(RealPositionable, RealLocalizable) - Method in class org.janelia.thickness.lut.SingleDimensionLUTGrid
-
- applyInverse(double[], double[]) - Method in class org.janelia.thickness.lut.SingleDimensionLUTRealTransform
-
- applyInverse(float[], float[]) - Method in class org.janelia.thickness.lut.SingleDimensionLUTRealTransform
-
- applyInverse(RealPositionable, RealLocalizable) - Method in class org.janelia.thickness.lut.SingleDimensionLUTRealTransform
-
- applyInverse(double[], double[]) - Method in class org.janelia.thickness.lut.SingleDimensionLUTRealTransformField
-
- applyInverse(float[], float[]) - Method in class org.janelia.thickness.lut.SingleDimensionLUTRealTransformField
-
- applyInverse(RealPositionable, RealLocalizable) - Method in class org.janelia.thickness.lut.SingleDimensionLUTRealTransformField
-
- applyInverse(long[], long[]) - Method in class org.janelia.thickness.lut.SingleDimensionPermutationTransform
-
- applyInverse(int[], int[]) - Method in class org.janelia.thickness.lut.SingleDimensionPermutationTransform
-
- applyInverse(Positionable, Localizable) - Method in class org.janelia.thickness.lut.SingleDimensionPermutationTransform
-
- applyInverse(float[]) - Method in interface stitching.model.InvertibleCoordinateTransform
-
Apply the inverse of the model to a point location
- applyInverse(InvertibleModel) - Method in class stitching.model.Point
-
- applyInverse(float[]) - Method in class stitching.model.TranslationModel2D
-
- applyInverse(float[]) - Method in class stitching.model.TranslationModel3D
-
- applyInverseChecked(double) - Method in class org.janelia.thickness.lut.AbstractLUTGrid
-
- applyInverseChecked(double) - Method in class org.janelia.thickness.lut.AbstractLUTRealTransform
-
- applyInverseChecked(double, int, int) - Method in class org.janelia.thickness.lut.AbstractLUTRealTransformField
-
- applyInverseChecked(int) - Method in class org.janelia.thickness.lut.AbstractPerumtationTransform
-
- applyInverseInPlace(double[]) - Method in class bdv.viewer.animate.SimilarityModel3D
-
- applyInverseInPlace(double[]) - Method in class mpicbg.models.AffineModel1D
-
- applyInverseInPlace(double[]) - Method in class mpicbg.models.AffineModel2D
-
- applyInverseInPlace(double[]) - Method in class mpicbg.models.AffineModel3D
-
- applyInverseInPlace(double[]) - Method in class mpicbg.models.HomographyModel2D
-
- applyInverseInPlace(double[]) - Method in class mpicbg.models.IdentityModel
-
- applyInverseInPlace(double[]) - Method in class mpicbg.models.InterpolatedAffineModel1D
-
- applyInverseInPlace(double[]) - Method in class mpicbg.models.InterpolatedAffineModel2D
-
- applyInverseInPlace(double[]) - Method in class mpicbg.models.InterpolatedAffineModel3D
-
- applyInverseInPlace(double[]) - Method in interface mpicbg.models.InverseCoordinateTransform
-
apply the inverse of the model to a point location
- applyInverseInPlace(double[]) - Method in class mpicbg.models.InverseCoordinateTransformList
-
- applyInverseInPlace(double[]) - Method in class mpicbg.models.InverseCoordinateTransformMap2D
-
- applyInverseInPlace(double[]) - Method in class mpicbg.models.InvertibleConstantModel
-
- applyInverseInPlace(double[]) - Method in class mpicbg.models.InvertibleCoordinateTransformList
-
- applyInverseInPlace(double[]) - Method in class mpicbg.models.InvertibleInterpolatedModel
-
- applyInverseInPlace(double[]) - Method in class mpicbg.models.RigidModel2D
-
- applyInverseInPlace(double[]) - Method in class mpicbg.models.RigidModel3D
-
- applyInverseInPlace(double[]) - Method in class mpicbg.models.SimilarityModel2D
-
- applyInverseInPlace(double[]) - Method in class mpicbg.models.SimilarityModel3D
-
- applyInverseInPlace(double[]) - Method in class mpicbg.models.TransformMesh
-
- applyInverseInPlace(double[]) - Method in class mpicbg.models.TranslationModel1D
-
- applyInverseInPlace(double[]) - Method in class mpicbg.models.TranslationModel2D
-
- applyInverseInPlace(double[]) - Method in class mpicbg.models.TranslationModel3D
-
- applyInverseInPlace(double[]) - Method in class mpicbg.panorama.EquirectangularProjection
-
- applyInverseInPlace(double[]) - Method in class mpicbg.panorama.RectlinearCamera
-
- applyInverseInPlace(AbstractAffineModel3D<?>, Point3d) - Static method in class mpicbg.spim.mpicbg.Java3d
-
- applyInverseInPlace(AbstractAffineModel3D<?>, Point3d, double[]) - Static method in class mpicbg.spim.mpicbg.Java3d
-
- applyInverseInPlace(double[]) - Method in class mpicbg.trakem2.transform.TransformMesh
-
Catch non-invertible locations outside of the meshes boundaries and
transfer them with the affine defined by the `closest' affine (the affine
whose summed up control points distances to location are smallest).
- applyInverseInPlace(float[]) - Method in interface stitching.model.InvertibleCoordinateTransform
-
apply the inverse of the model to a point location
- applyInverseInPlace(float[]) - Method in class stitching.model.TranslationModel2D
-
- applyInverseInPlace(float[]) - Method in class stitching.model.TranslationModel3D
-
- applyLayerTransformToPatch(Patch, CoordinateTransform) - Static method in class mpicbg.trakem2.align.Util
-
- applyLayerWise(Collection<Layer>) - Method in class ini.trakem2.imaging.ContrastEnhancerWrapper
-
- applyLayout(mxIGraphLayout) - Method in class sc.fiji.snt.viewer.geditor.GraphEditor
-
- applyLocalizedPattern(String) - Method in class HybridDateFormat
-
This method sets the formatting pattern that should be used by this
object.
- ApplyLog(double) - Method in class view5d.PixelDisplay
-
- applyLSTAMP(ImagePlus, LSMFileInfo) - Method in class org.imagearchive.lsm.toolbox.gui.ControlPanelFrame
-
- applyMedianFilter(RandomAccessibleInterval<R>) - Static method in class fiji.plugin.trackmate.detection.DetectionUtils
-
Apply a simple 3x3 median filter to the target image.
- applyMetaData(Image<?>, IFormatReader) - Static method in class mpicbg.imglib.io.LOCI
-
- applyMethodStack(List<RecordedImageProcessor.MethodEntry>) - Method in class loci.plugins.util.RecordedImageProcessor
-
- applyModels(SpimData, double, int, Map<ViewDescription, Pair<double[], String>>) - Method in class spim.fiji.plugin.Apply_Transformation
-
- ApplyParameters - Class in spim.fiji.plugin.apply
-
- ApplyParameters() - Constructor for class spim.fiji.plugin.apply.ApplyParameters
-
- applyPatchTask(List<Patch>, String, Operation<Boolean, Patch>, Filter<Patch>) - Method in class ini.trakem2.display.Display
-
Meant for tasks that require setting an undo and regenerating mipmaps.
- applyPattern(String) - Method in class HybridDateFormat
-
This method sets the formatting pattern that should be used by this
object.
- applyPrecomputedSignatures(int[], float[], int, double) - Method in class org.siox.SioxSegmentator
-
Segments the given image with the previously calculated color signatures.
- applyRawTransformationToSource(double[][], double[][]) - Method in class bunwarpj.MainDialog
-
Apply a raw transformation to the source image.
- applyRawTransformationToSource(ImagePlus, ImagePlus, BSplineModel, double[][], double[][]) - Static method in class bunwarpj.MiscTools
-
Apply a given raw transformation to the source image.
- applyRawTransformToSource(String, ImagePlus, ImagePlus) - Static method in class bunwarpj.bUnwarpJ_
-
Apply a raw transform loaded from file to the source image.
- applyRotation(int, double) - Method in class ij3d.Content
-
- applyScaling - Static variable in class process.Matching
-
- applySelection(float) - Method in class org.siox.example.ScrollDisplay
-
Applies the given value to the confidence matrix entries
within the selected area.
- applySelectionFilter(String, Number, Number) - Method in class sc.fiji.snt.PathManagerUI
-
Selects paths matching a morphometric criteria.
- applySelectionFilter(String) - Method in class sc.fiji.snt.PathManagerUI
-
Selects paths matching a text-based criteria.
- applySelectionFilter(String, Number) - Method in class sc.fiji.snt.PathManagerUI
-
Selects paths matching a morphometric criteria.
- applyShifts(double[], double[], double[], PermutationTransform, Options) - Method in class org.janelia.thickness.inference.InferFromMatrix
-
- applySurfaceColors(ImagePlus) - Method in class ij3d.Content
-
- applySurfaceColors(ImagePlus) - Method in class ij3d.ContentInstant
-
- applySurfaceColors(Content) - Method in class ij3d.Executer
-
- applyTable(int[]) - Method in class loci.plugins.util.RecordedImageProcessor
-
- applyTag(String) - Method in class sc.fiji.snt.PathManagerUI
-
Applies a tag/ color to selected Path(s).
- applyThreshold(ImageProcessor, Roi, int, int) - Static method in class vib.Local_Threshold
-
- applyTimepoints(LoadParseQueryXML) - Method in class spim.fiji.plugin.Duplicate_Transformation
-
- applyTo - Variable in class spim.fiji.plugin.apply.ApplyParameters
-
- applyToChoice - Static variable in class spim.fiji.plugin.Apply_Transformation
-
- applyToSlab(Node.Operation<T>) - Method in class ini.trakem2.display.Node
-
Apply @param op to this Node and all its subtree nodes until reaching a branch node or end node, inclusive.
- applyToSubtree(Node.Operation<T>) - Method in class ini.trakem2.display.Node
-
Apply @param op to this Node and all its subtree nodes.
- applyTransform(double[]) - Method in class ij3d.Content
-
- applyTransform(Transform3D) - Method in class ij3d.Content
-
- applyTransform(double[]) - Method in class ij3d.ContentInstant
-
- applyTransform(Transform3D) - Method in class ij3d.ContentInstant
-
- applyTransform(Content) - Method in class ij3d.Executer
-
- applyTransform(String) - Static method in class ij3d.ImageJ3DViewer
-
- applyTransform() - Method in class ini.trakem2.display.DisplayCanvas
-
- applyTransform(ArrayList<Point>) - Method in class mpicbg.pointdescriptor.test.TestPointDescriptor
-
- applyTransformationMT(ImagePlus, ImagePlus, BSplineModel, int, double[][], double[][]) - Static method in class bunwarpj.MiscTools
-
Apply a given B-spline transformation to the source (gray-scale) image.
- ApplyTransformationPopup - Class in spim.fiji.spimdata.explorer.popup
-
- ApplyTransformationPopup() - Constructor for class spim.fiji.spimdata.explorer.popup.ApplyTransformationPopup
-
- ApplyTransformationPopup.MyActionListener - Class in spim.fiji.spimdata.explorer.popup
-
- applyTransformationToSource(int, double[][], double[][]) - Method in class bunwarpj.MainDialog
-
Apply the transformation defined by the spline coefficients to the source
image.
- applyTransformationToSource(ImagePlus, ImagePlus, BSplineModel, int, double[][], double[][]) - Static method in class bunwarpj.MiscTools
-
Deprecated.
- applyTransformationToSource(ImagePlus, ImagePlus, BSplineModel, BSplineModel, BSplineModel, int, double[][], double[][]) - Static method in class bunwarpj.MiscTools
-
Deprecated.
- applyTransformationToSourceMT(ImagePlus, ImagePlus, int, double[][], double[][]) - Static method in class bunwarpj.MiscTools
-
Apply a given B-spline transformation to the source (gray-scale) image.
- applyTransformationToSourceMT(ImagePlus, ImagePlus, BSplineModel, int, double[][], double[][]) - Static method in class bunwarpj.MiscTools
-
Apply a given B-spline transformation to the source (gray-scale) image.
- applyTransformReverse(List<PointMatch>, CoordinateTransform) - Static method in class register_virtual_stack.Register_Virtual_Stack_MT
-
Apply a transformation to the second point (P2) of a list of Point matches
- applyTransformRotationXYZ(double, double, double) - Method in class jRenderer3D.JRenderer3D
-
Changes the rotation of x-, y-, and z-axis by the values of changeX and changeY.
- applyTransforms(Map<Displayable, AffineTransform>) - Static method in class ini.trakem2.display.LayerSet
-
- applyTransformToLayer(Layer, CoordinateTransform, Filter<Patch>) - Static method in class mpicbg.trakem2.align.ElasticLayerAlignment
-
- applyTransformToLayer(Layer, AffineTransform, Filter<Patch>) - Static method in class mpicbg.trakem2.align.RegularizedAffineLayerAlignment
-
- applyTransformToSource(String, ImagePlus, ImagePlus) - Static method in class bunwarpj.bUnwarpJ_
-
Apply transform loaded from file to source image (in place).
- applyTransformToStack(String, ImagePlus, ImagePlus) - Static method in class bunwarpj.MiscTools
-
Apply transform saved on a file to all slices of moving image
- applyTranslation(float, float, float) - Method in class ij3d.Content
-
- applyTSTAMP(ImagePlus, LSMFileInfo) - Method in class org.imagearchive.lsm.toolbox.gui.ControlPanelFrame
-
- applyWithoutTranslation(double, double, double) - Method in class vib.FastMatrix
-
- applyWithoutTranslation(Point3d) - Method in class vib.FastMatrix
-
- applyWithoutTranslation(float, float, float) - Method in class vib.FloatMatrix
-
- applyWithoutTranslation(Point3d) - Method in class vib.FloatMatrix
-
- applyZSTAMP(ImagePlus, LSMFileInfo) - Method in class org.imagearchive.lsm.toolbox.gui.ControlPanelFrame
-
- approximateEntropy(RandomAccessibleInterval<FloatType>, ImgFactory<ComplexFloatType>, double[], double[]) - Method in class spim.process.fusion.weights.ContentBased
-
- approximateInverseCoords(double[], ImagePlus, double[][], double[][]) - Static method in class bunwarpj.MiscTools
-
Approximate the transformed coordinates of a point from the
moving image into the fixed image.
- approximateTransferPixel(int[]) - Method in class ini.trakem2.display.Patch
-
Transfer an 8-bit or RGB pixel to this image color space, interpolating;
the pvalue is modified in place.
- approxNumberOfPoints() - Method in class bigwarp.landmarks.LandmarkGridGenerator
-
- appTitle - Variable in class sc.fiji.snt.viewer.geditor.GraphEditor
-
- apv - Variable in class mpicbg.models.SpringMesh
-
- ArchipelagoClient - Class in edu.utexas.clm.archipelago.network.client
-
- ArchipelagoClient(long, InputStream, OutputStream) - Constructor for class edu.utexas.clm.archipelago.network.client.ArchipelagoClient
-
- ArchipelagoClient(long, InputStream, OutputStream, TransceiverExceptionListener) - Constructor for class edu.utexas.clm.archipelago.network.client.ArchipelagoClient
-
- ArchipelagoFuture<T> - Class in edu.utexas.clm.archipelago.compute
-
- ArchipelagoFuture(Scheduler) - Constructor for class edu.utexas.clm.archipelago.compute.ArchipelagoFuture
-
- ArchipelagoFuture(Scheduler, T) - Constructor for class edu.utexas.clm.archipelago.compute.ArchipelagoFuture
-
- ArchipelagoServer - Class in edu.utexas.clm.archipelago.network.server
-
- ArchipelagoUI - Interface in edu.utexas.clm.archipelago.ui
-
- ArchipelagoUtils - Class in edu.utexas.archipelago
-
- ArchiveClient - Class in client
-
- ArchiveClient(Applet) - Constructor for class client.ArchiveClient
-
- ArchiveClient(Applet, String) - Constructor for class client.ArchiveClient
-
- area(PathIterator) - Static method in class fiji.geom.AreaCalculations
-
Computes the surface area of the path or multiple specified paths.
- Area() - Constructor for class fiji.geom.AreaCalculations.Area
-
- area - Variable in class ini.trakem2.display.Patch.TransformProperties
-
- area - Variable in class sc.fiji.balloonSegmentation.structure.Balloon
-
- area - Variable in class sc.fiji.balloonSegmentation.structure.BalloonPopulation
-
- AREA - Static variable in interface sc.fiji.snt.analysis.sholl.math.ShollStats
-
Flag for area normalization (Semi-log/Log-log method)
- area_color_cues - Variable in class ini.trakem2.display.LayerSet
-
- AREA_DOWNSAMPLING - Static variable in class ini.trakem2.persistence.Loader
-
- AreaCalculations - Class in fiji.geom
-
- AreaCalculations() - Constructor for class fiji.geom.AreaCalculations
-
- AreaCalculations.Area - Class in fiji.geom
-
- AreaCalculations.Calculation - Class in fiji.geom
-
- AreaCalculations.Centroid - Class in fiji.geom
-
- AreaCalculations.Circumference - Class in fiji.geom
-
- AreaContainer - Interface in ini.trakem2.display
-
- areaInInts(Area) - Static method in class ini.trakem2.utils.M
-
Converts all points in @param area to ints by casting.
- areaInIntsByRounding(Area) - Static method in class ini.trakem2.utils.M
-
Converts all points in @param area to ints by rounding.
- AreaList - Class in ini.trakem2.display
-
A list of brush painted areas similar to a set of labelfields in Amira.
- AreaList(Project, String, double, double) - Constructor for class ini.trakem2.display.AreaList
-
- AreaList(Project, long, HashMap<String, String>, HashMap<Displayable, String>) - Constructor for class ini.trakem2.display.AreaList
-
Reconstruct from XML.
- AreaList(Project, long, String, float, float, float, boolean, Color, boolean, ArrayList<Long>, AffineTransform) - Constructor for class ini.trakem2.display.AreaList
-
Reconstruct from the database.
- AreaList_Crop - Class in edu.utexas.clm.crop
-
- AreaList_Crop() - Constructor for class edu.utexas.clm.crop.AreaList_Crop
-
- AreaListCrop - Class in edu.utexas.clm.crop
-
- AreaListCrop() - Constructor for class edu.utexas.clm.crop.AreaListCrop
-
- AreaListVolume - Class in ij3d
-
Wraps a list of
Area
s to be triangulated.
- AreaListVolume(List<List<Area>>, double, double, double, double) - Constructor for class ij3d.AreaListVolume
-
- areAllRoisEmpty() - Method in class vib.segment.CustomStackWindow
-
- AreaNode(float, float, Layer) - Constructor for class ini.trakem2.display.AreaTree.AreaNode
-
- AreaNode(HashMap<String, String>) - Constructor for class ini.trakem2.display.AreaTree.AreaNode
-
To reconstruct from XML, without a layer.
- AreaTree - Class in ini.trakem2.display
-
- AreaTree(Project, String) - Constructor for class ini.trakem2.display.AreaTree
-
- AreaTree(Project, long, HashMap<String, String>, HashMap<Displayable, String>) - Constructor for class ini.trakem2.display.AreaTree
-
Reconstruct from XML.
- AreaTree(Project, long, String, float, float, float, boolean, Color, boolean, AffineTransform) - Constructor for class ini.trakem2.display.AreaTree
-
For cloning purposes, does not call addToDatabase()
- AreaTree.AreaNode - Class in ini.trakem2.display
-
- AreaUtils - Class in ini.trakem2.utils
-
- AreaWrapper - Class in ini.trakem2.display
-
- AreaWrapper(Displayable, Area) - Constructor for class ini.trakem2.display.AreaWrapper
-
- AreaWrapper() - Constructor for class ini.trakem2.display.AreaWrapper
-
- AreaWrapper(Area) - Constructor for class ini.trakem2.display.AreaWrapper
-
- AreaWrapper.PaintParameters - Class in ini.trakem2.display
-
- areLandmarksVisible() - Method in class bdv.viewer.BigWarpViewerSettings
-
- areNamesVisible() - Method in class bdv.viewer.BigWarpViewerSettings
-
- areThereLayerCrossLinks(Set<Layer>, boolean) - Static method in class ini.trakem2.display.Displayable
-
Returns true if any Displayable objects of different layers in sublist are linked to each other.
- areTransformsTheSame(RealTransform, RealTransform, Interval, double) - Static method in class bdv.ij.BigWarpToDeformationFieldPlugIn
-
- arg - Variable in class loci.plugins.LociExporter
-
Argument passed to setup method.
- argb(int, int, int) - Static method in class mpicbg.util.ColorStream
-
- ARGB(double, double) - Constructor for class net.imglib2.display.ScaledARGBConverter.ARGB
-
- argb(int, int, int) - Static method in class spim.fiji.spimdata.explorer.util.ColorStream
-
- ARGBARGBColorConverter<R> - Class in net.imglib2.display
-
- ARGBARGBColorConverter(double, double) - Constructor for class net.imglib2.display.ARGBARGBColorConverter
-
- ARGBARGBColorConverter.ToGray - Class in net.imglib2.display
-
A converter from a ARGB to ARGB that initially converts the input color to grayscale,
then scales the resulting grayscale value with the set color.
- ARGBARGBColorConverter.VolatileToGray - Class in net.imglib2.display
-
- ARGBtoRandomARGBColorConverter<R> - Class in net.imglib2.display
-
- ARGBtoRandomARGBColorConverter(double, double) - Constructor for class net.imglib2.display.ARGBtoRandomARGBColorConverter
-
- ARGBtoRandomARGBColorConverter.ToGray - Class in net.imglib2.display
-
A converter from a ARGB to ARGB that initially converts the input color to grayscale,
then scales the resulting grayscale value with the set color.
- ARGBtoRandomARGBColorConverter.VolatileToGray - Class in net.imglib2.display
-
- args - Static variable in class loci.plugins.shortcut.ShortcutPanel
-
Details for installed plugins.
- ARMED - Static variable in class vib.segment.ImageButton
-
- armijoCondition(double, double) - Method in class jitk.spline.TransformInverseGradientDescent
-
Returns true if the armijo condition is satisfied.
- arrangement - Variable in class stitching.GridLayout
-
- Array<T extends Type<T>,A extends DataAccess> - Class in mpicbg.imglib.container.array
-
TODO
- Array(ArrayContainerFactory, A, int[], int) - Constructor for class mpicbg.imglib.container.array.Array
-
- Array3D<T extends Type<T>,A extends DataAccess> - Class in mpicbg.imglib.container.array
-
TODO
- Array3D(ArrayContainerFactory, A, int, int, int, int) - Constructor for class mpicbg.imglib.container.array.Array3D
-
- Array3DLocalizableByDimCursor<T extends Type<T>> - Class in mpicbg.imglib.cursor.array
-
TODO
- Array3DLocalizableByDimCursor(Array3D<T, ?>, Image<T>, T) - Constructor for class mpicbg.imglib.cursor.array.Array3DLocalizableByDimCursor
-
- Array3DLocalizableByDimOutOfBoundsCursor<T extends Type<T>> - Class in mpicbg.imglib.cursor.array
-
TODO
- Array3DLocalizableByDimOutOfBoundsCursor(Array3D<T, ?>, Image<T>, T, OutOfBoundsStrategyFactory<T>) - Constructor for class mpicbg.imglib.cursor.array.Array3DLocalizableByDimOutOfBoundsCursor
-
- Array3DLocalizableCursor<T extends Type<T>> - Class in mpicbg.imglib.cursor.array
-
TODO
- Array3DLocalizableCursor(Array3D<T, ?>, Image<T>, T) - Constructor for class mpicbg.imglib.cursor.array.Array3DLocalizableCursor
-
- ArrayBase<ArrayType,BaseType> - Class in fiji.util
-
- ArrayBase(int, int, Class) - Constructor for class fiji.util.ArrayBase
-
- ArrayBase(int, Class) - Constructor for class fiji.util.ArrayBase
-
- ArrayContainerFactory - Class in mpicbg.imglib.container.array
-
TODO
- ArrayContainerFactory() - Constructor for class mpicbg.imglib.container.array.ArrayContainerFactory
-
- ArrayConverter - Class in mpi.fruitfly.general
-
Title:
- ArrayConverter() - Constructor for class mpi.fruitfly.general.ArrayConverter
-
- ArrayCursor<T extends Type<T>> - Class in mpicbg.imglib.cursor.array
-
TODO
- ArrayCursor(Array<T, ?>, Image<T>, T) - Constructor for class mpicbg.imglib.cursor.array.ArrayCursor
-
- ArrayDataAccess<A> - Interface in mpicbg.imglib.container.basictypecontainer.array
-
TODO
- ArrayImgLoader(T) - Constructor for class bdv.ij.export.imgloader.FusionImageLoader.ArrayImgLoader
-
Deprecated.
- arrayIndex - Variable in class mpicbg.imglib.labeling.LocalizableLabelingCursor
-
- ArrayIterable(Iterable<double[]>) - Constructor for class org.janelia.thickness.inference.visitor.CorrelationFitVisitor.ArrayIterable
-
- ArrayLocalizableByDimCursor<T extends Type<T>> - Class in mpicbg.imglib.cursor.array
-
TODO
- ArrayLocalizableByDimCursor(Array<T, ?>, Image<T>, T) - Constructor for class mpicbg.imglib.cursor.array.ArrayLocalizableByDimCursor
-
- ArrayLocalizableByDimOutOfBoundsCursor<T extends Type<T>> - Class in mpicbg.imglib.cursor.array
-
TODO
- ArrayLocalizableByDimOutOfBoundsCursor(Array<T, ?>, Image<T>, T, OutOfBoundsStrategyFactory<T>) - Constructor for class mpicbg.imglib.cursor.array.ArrayLocalizableByDimOutOfBoundsCursor
-
- ArrayLocalizableCursor<T extends Type<T>> - Class in mpicbg.imglib.cursor.array
-
TODO
- ArrayLocalizableCursor(Array<T, ?>, Image<T>, T) - Constructor for class mpicbg.imglib.cursor.array.ArrayLocalizableCursor
-
- ArrayLocalizablePlaneCursor<T extends Type<T>> - Class in mpicbg.imglib.cursor.array
-
TODO
- ArrayLocalizablePlaneCursor(Array<T, ?>, Image<T>, T) - Constructor for class mpicbg.imglib.cursor.array.ArrayLocalizablePlaneCursor
-
- ArraySortedIndices - Class in org.janelia.utility.arrays
-
- ArraySortedIndices() - Constructor for class org.janelia.utility.arrays.ArraySortedIndices
-
- ArrayToByteProcessor(ImageProcessor, int[][]) - Static method in class mpi.fruitfly.general.ImageArrayConverter
-
- ArrayToByteProcessor(ImageProcessor, float[][]) - Static method in class mpi.fruitfly.general.ImageArrayConverter
-
- ArrayToFloatProcessor(ImageProcessor, double[], int, int) - Static method in class mpi.fruitfly.general.ImageArrayConverter
-
- ArrayToFloatProcessor(ImageProcessor, float[], int, int) - Static method in class mpi.fruitfly.general.ImageArrayConverter
-
- arrayType - Variable in class mpicbg.imglib.cursor.special.SortedGrayLevelIteratorArrayContainerOnly
-
- ARROW - Static variable in class ini.trakem2.display.DLabel
-
- Arrow - Class in util
-
- Arrow(Color, double, double, double, double, double, double, int) - Constructor for class util.Arrow
-
- ArrowDisplayer - Interface in util
-
- ArrowOptionPanel - Class in fiji.util
-
- ArrowOptionPanel(ArrowShape, BasicStroke) - Constructor for class fiji.util.ArrowOptionPanel
-
Instantiates the config panel with using settings from arguments.
- ArrowOptionPanel() - Constructor for class fiji.util.ArrowOptionPanel
-
- ArrowShape - Class in fiji.util
-
- ArrowShape() - Constructor for class fiji.util.ArrowShape
-
- ArrowShape(ArrowShape.ArrowStyle) - Constructor for class fiji.util.ArrowShape
-
- ArrowShape(ArrowShape.ArrowStyle, double) - Constructor for class fiji.util.ArrowShape
-
- ArrowShape.ArrowStyle - Enum in fiji.util
-
- ArrowTool - Class in fiji.util
-
ArrowTool plugin
- ArrowTool() - Constructor for class fiji.util.ArrowTool
-
- asAffine3D() - Method in interface mpicbg.spim.data.registration.ViewTransform
-
- asAffine3D() - Method in class mpicbg.spim.data.registration.ViewTransformAffine
-
- asArray(int, double) - Static method in class script.imglib.algorithm.fn.AlgorithmUtil
-
Copy the given double value into each index of a double[] array of length .
- asBufferedImage(Image) - Static method in class ini.trakem2.io.ImageSaver
-
- asChart() - Method in class script.imglib.analysis.Histogram
-
- asChart(boolean) - Method in class script.imglib.analysis.Histogram
-
Return the JFreeChart with this histogram, and as a side effect, show it in a JFrame
that provides the means to edit the dimensions and also the plot properties via a popup menu.
- ASCII - Variable in class amira.AmiraMeshDecoder
-
- ASCII - Static variable in class isosurface.MeshExporter
-
- asContent(Display3D) - Method in class ini.trakem2.display.Display3D.VectorStringContent
-
- asDoubleArray(Collection<Number>) - Static method in class script.imglib.algorithm.fn.AlgorithmUtil
-
- asDoubleArray(float[]) - Static method in class script.imglib.algorithm.fn.AlgorithmUtil
-
- asGrey(BufferedImage) - Static method in class ini.trakem2.io.ImageSaver
-
If the given BufferedImage is of type TYPE_BYTE_GRAY, it will simply return it.
- asHexRGBColor(Color) - Static method in class ini.trakem2.utils.Utils
-
- asHexRGBColor(StringBuilder, Color) - Static method in class ini.trakem2.utils.Utils
-
- asImage() - Method in class script.imglib.analysis.BarChart
-
- asImage(JFreeChart) - Static method in class script.imglib.analysis.ChartUtils
-
- asImage(JFreeChart, int, int) - Static method in class script.imglib.analysis.ChartUtils
-
- asImage() - Method in class script.imglib.analysis.Histogram
-
- asImage() - Method in class script.imglib.color.fn.ColorFunction
-
- asImage(int) - Method in class script.imglib.color.fn.ColorFunction
-
- asImage() - Method in class script.imglib.math.fn.FloatImageOperation
-
Evaluate this operation as an Image<FloatType>
.
- asImage(int) - Method in class script.imglib.math.fn.FloatImageOperation
-
Evaluate this operation as an Image<FloatType>
using the defined number of parallel threads.
- asImage() - Method in interface script.imglib.math.fn.ImageComputation
-
- asImage(int) - Method in interface script.imglib.math.fn.ImageComputation
-
- ASin - Class in script.imglib.math
-
TODO
- ASin(Image<? extends RealType<?>>) - Constructor for class script.imglib.math.ASin
-
- ASin(IFunction) - Constructor for class script.imglib.math.ASin
-
- ASin(Number) - Constructor for class script.imglib.math.ASin
-
- ask_params - Variable in class levelsets.ij.LevelSet
-
- askAdjustRadius(Node<Float>) - Method in class ini.trakem2.display.Treeline
-
- askForFileForLoading(File, String, Frame, Logger) - Static method in class fiji.plugin.trackmate.io.IOUtils
-
Prompts the user for a xml file to load from.
- askForFileForSaving(File, Frame, Logger) - Static method in class fiji.plugin.trackmate.io.IOUtils
-
Prompts the user for a xml file to save to.
- askForFixedTiles(GlobalOptimizationSubset, GlobalOptimizationType, Set<ViewId>, String) - Method in class spim.fiji.plugin.Interest_Point_Registration
-
- askForFolder(File, String, Frame, Logger) - Static method in class fiji.plugin.trackmate.io.IOUtils
-
Prompts the user for a target folder.
- askForNewTag(int) - Method in class ini.trakem2.display.LayerSet
-
- askForReferenceTile(GlobalOptimizationSubset, GlobalOptimizationType, String) - Method in class spim.fiji.plugin.Interest_Point_Registration
-
- askForRegistrations(GenericDialog) - Method in class spim.fiji.plugin.Duplicate_Transformation
-
- askForXMLTemplate(Project) - Method in class ini.trakem2.persistence.Loader
-
Ask for the user to provide a template XML file to extract a root TemplateThing.
- askToFinish() - Method in class landmarks.FineTuneThread
-
- askToRemoveTag(int) - Method in class ini.trakem2.display.LayerSet
-
Returns false if the dialog was canceled or there wasn't any tag to remove.
- askUserConfirmation - Variable in class sc.fiji.snt.SNTUI
-
- askWhenMoreThan - Static variable in class spim.fiji.spimdata.explorer.popup.DisplayViewPopup
-
- askWhenMoreThan - Static variable in class spim.fiji.spimdata.explorer.popup.RemoveTransformationPopup
-
- askWhenMoreThan - Static variable in class spim.fiji.spimdata.explorer.popup.ResavePopup
-
- asList(long[]) - Static method in class ini.trakem2.utils.Utils
-
- asList(long[], int, int) - Static method in class ini.trakem2.utils.Utils
-
- asMask() - Method in class bdv.tools.boundingbox.TransformedRealBoxSelectionDialog.Result
-
Returns the transformed box as an imglib2 roi.
- asOptionPanel() - Method in class ini.trakem2.display.AreaWrapper.PaintParameters
-
- asOptionPanel() - Method in class ini.trakem2.imaging.Segmentation.FastMarchingParam
-
- asPaintable(List<? extends Paintable>) - Method in class ini.trakem2.display.graphics.DefaultGraphicsSource
-
Returns the list given as argument without any modification.
- asPaintable(List<? extends Paintable>) - Method in interface ini.trakem2.display.graphics.GraphicsSource
-
Takes as list of Paintable and returns the same or another list with perhaps a different number of Paintable objects, or some replaced by new Paintable instances.
- asPaintable(List<? extends Paintable>) - Method in class ini.trakem2.display.graphics.TestGraphicsSource
-
Replaces all Patch instances by a smiley face.
- asPaintable(List<? extends Paintable>) - Method in class ini.trakem2.display.GroupingMode.GroupedGraphicsSource
-
Returns the list given as argument without any modification.
- asPath(double, double, double, String) - Method in class sc.fiji.snt.SearchNode
-
- asPathReversed(double, double, double, String) - Method in class sc.fiji.snt.SearchNode
-
- asPoint() - Method in class ini.trakem2.display.Node
-
- asPoint(Node<T>, boolean) - Method in class ini.trakem2.display.Tree
-
Return the
Node
as a point in space.
- asPoints(float[]) - Method in class script.imglib.analysis.DoGPeaks
-
Returns a list of peaks as Java3D points if possible:
Point2f
for 2D images
Point3f
for 3D images
Point4f
for 4D images
- asPoints() - Method in class script.imglib.analysis.DoGPeaks
-
Returns a list of peaks as Java3D points: Point2f for 2D images, Point3f for 3D images, and Point4f for 4D images.
- asPoints(Number) - Method in class script.imglib.analysis.DoGPeaks
-
Returns a list of peaks as Java3D points: Point2f for 2D images, Point3f for 3D images, and Point4f for 4D images.
- asRGBABytes(int[], byte[], byte[]) - Static method in class ini.trakem2.imaging.P
-
- asRGBBytes(int[]) - Static method in class ini.trakem2.imaging.P
-
- asSafePath(String) - Static method in class ini.trakem2.persistence.FSLoader
-
Takes a String and returns a copy with the following conversions: / to -, space to _, and \ to -.
- assembleAllMetaData(SequenceDescription, Collection<? extends ViewId>) - Static method in class spim.fiji.plugin.Apply_Transformation
-
Should be called before registration to make sure all metadata is right
- assembleAllViewPairs() - Method in class spim.process.interestpointregistration.optimizationtypes.AllToAllRegistration
-
- assembleAllViewPairs() - Method in class spim.process.interestpointregistration.optimizationtypes.AllToAllRegistrationWithRange
-
- assembleAllViewPairs() - Method in class spim.process.interestpointregistration.optimizationtypes.GlobalOptimizationType
-
- assembleAllViewPairs() - Method in class spim.process.interestpointregistration.optimizationtypes.IndividualTimepointRegistration
-
- assembleAllViewPairs() - Method in class spim.process.interestpointregistration.optimizationtypes.ReferenceTimepointRegistration
-
- assembleAngles(List<Angle>) - Method in class spim.fiji.plugin.Duplicate_Transformation
-
- assembleAvailableCorrespondences(HashMap<Channel, ArrayList<EfficientBayesianBased.Correspondence>>, HashMap<Channel, Integer>, boolean) - Method in class spim.process.fusion.deconvolution.EfficientBayesianBased
-
- assembleChannels(List<Channel>) - Method in class spim.fiji.plugin.Duplicate_Transformation
-
- assembleChannels(List<Channel>) - Method in class spim.process.fusion.boundingbox.AutomaticBoundingBox
-
- assembleDefaultPattern() - Method in class spim.fiji.datasetmanager.StackList
-
- assembleFixedTiles(SpimData2, List<ViewId>, List<ChannelProcess>, TimePoint) - Static method in class spim.process.interestpointregistration.optimizationtypes.ReferenceTimepointRegistration
-
All tiles of the reference timepoint are fixed, nothing else
- assembleIllums(List<Illumination>) - Method in class spim.fiji.plugin.Duplicate_Transformation
-
- assembleInputData(SpimData2, TimePoint, Channel, List<ViewId>) - Static method in class spim.process.fusion.FusionHelper
-
- assembleNewViewSetupsFusion(SpimData2, List<ViewId>, BoundingBoxGUI, String, String) - Static method in class spim.process.fusion.weightedavg.WeightedAverageFusion
-
Creates one new Angle and one new Illumination for the fused dataset.
- assembleNewViewSetupsSequential(SpimData2, List<ViewId>, BoundingBoxGUI) - Static method in class spim.process.fusion.weightedavg.WeightedAverageFusion
-
Duplicates all Angles and Illuminations that are processed.
- assemblePartialSpimData2(SpimData2, List<ViewId>, File, List<String>) - Static method in class spim.fiji.plugin.resave.Resave_TIFF
-
Assembles a new SpimData2 based on the subset of timepoints and viewsetups as selected by the user.
- assembleRegistrationNames(SpimData, List<ViewId>) - Static method in class spim.fiji.plugin.util.GUIHelper
-
- assembleResults() - Method in class sc.fiji.analyzeSkeleton.AnalyzeSkeleton_
-
Returns the analysis results in a SkeletonResult object.
- assembleSpimData2(List<TimePoint>, List<ViewSetup>, File) - Static method in class spim.process.fusion.export.ExportSpimData2TIFF
-
Assembles a new SpimData2 based on the timepoints and viewsetups.
- assembleStats(TreeStatistics.StatisticsInstance, String) - Method in class sc.fiji.snt.analysis.MultiTreeStatistics
-
- assembleStats(TreeStatistics.StatisticsInstance, String) - Method in class sc.fiji.snt.analysis.TreeStatistics
-
- assembleTimepoints(List<TimePoint>) - Method in class spim.fiji.plugin.Duplicate_Transformation
-
- assembleTimepoints(TimePoints) - Static method in class spim.fiji.plugin.Interest_Point_Registration
-
- assembleTimepoints(List<TimePoint>) - Method in class spim.process.fusion.boundingbox.AutomaticBoundingBox
-
- assertEquals(String, Object, String, Object) - Static method in class sc.fiji.timelapse.PolygonRoiPublic
-
- assertEquals(String, Object, String, Object, int) - Static method in class sc.fiji.timelapse.PolygonRoiPublic
-
- assertEquals(String, boolean, String, boolean) - Static method in class sc.fiji.timelapse.PolygonRoiPublic
-
- assertEquals(String, byte, String, byte) - Static method in class sc.fiji.timelapse.PolygonRoiPublic
-
- assertEquals(String, short, String, short) - Static method in class sc.fiji.timelapse.PolygonRoiPublic
-
- assertEquals(String, int, String, int) - Static method in class sc.fiji.timelapse.PolygonRoiPublic
-
- assertEquals(String, long, String, long) - Static method in class sc.fiji.timelapse.PolygonRoiPublic
-
- assertEquals(String, float, String, float) - Static method in class sc.fiji.timelapse.PolygonRoiPublic
-
- assertEquals(String, double, String, double) - Static method in class sc.fiji.timelapse.PolygonRoiPublic
-
- assertEquals(String, String, String, String) - Static method in class sc.fiji.timelapse.PolygonRoiPublic
-
- assessIfBranchesHaveBeenAssigned() - Method in class sc.fiji.snt.analysis.NodeStatistics
-
- Assign3DData(Container, ImgPanel, My3DData) - Method in class view5d.AlternateViewer
-
- assignBranches(Tree) - Method in class sc.fiji.snt.analysis.NodeStatistics
-
Associates the nodes being analyzed to the branches of the specified tree
- ASSIGNED_VALUE - Static variable in class sc.fiji.snt.analysis.MultiTreeColorMapper
-
Mapping property: Assigned Tree value
- ASSIGNED_VALUE - Static variable in class sc.fiji.snt.analysis.MultiTreeStatistics
-
- assignEdgeWeightsEuclidean() - Method in class sc.fiji.snt.analysis.graph.DirectedWeightedGraph
-
For all edges, sets the Euclidean distance between the source and target
vertex as the weight.
- assignEditor(GraphEditor) - Method in class sc.fiji.snt.viewer.geditor.SNTGraphComponent
-
Assigns an editor.
- assignHemisphereTags(DirectedWeightedGraph) - Static method in class sc.fiji.snt.annotation.AllenUtils
-
- assignHemisphereTags(Tree) - Static method in class sc.fiji.snt.annotation.AllenUtils
-
- assignImage(ImagePlus) - Method in class sc.fiji.snt.analysis.sholl.Profile
-
- assignImage(ImagePlus) - Method in class sc.fiji.snt.Tree
-
Assigns the spatial calibration of an image to this Tree.
- assignListenerToHelpButton(String, ActionListener) - Method in class sc.fiji.snt.gui.EnhancedGenericDialog
-
Deprecated.
Adds a "Help" button and attaches the specified listener to it.
- Assignment(int, int, double) - Constructor for class fiji.plugin.trackmate.tracking.sparselap.costmatrix.DefaultCostMatrixCreator.Assignment
-
- AssignmentAlgorithm - Interface in fiji.plugin.trackmate.tracking.oldlap.hungarian
-
Just in case I want to try more than one implementation of the assignment algorithm.
- AssignmentProblem - Class in fiji.plugin.trackmate.tracking.oldlap.hungarian
-
An implementation of this: http://en.wikipedia.org/wiki/Hungarian_algorithm
- AssignmentProblem(double[][]) - Constructor for class fiji.plugin.trackmate.tracking.oldlap.hungarian.AssignmentProblem
-
- assignNewAttributeIds(AbstractSpimData<?>, Map<String, Set<Integer>>) - Static method in class bdv.spimdata.tools.ChangeAttributeId
-
For the specified spimData
data set, re-assign attribute id's
that are already in use.
- assignNewViewSetupIds(AbstractSpimData<?>, Set<Integer>) - Static method in class bdv.spimdata.tools.ChangeViewSetupId
-
For the specified spimData
data set, re-assign setup id's that
are already in use.
- AssignOperation<T extends RealType<T>> - Class in imglib.ops.operation
-
An AssignOperation computes values in an output image.
- AssignOperation(Image<T>[], Image<T>, RealFunction<T>) - Constructor for class imglib.ops.operation.AssignOperation
-
- assignOtherChannel(Channel, HashMap<Channel, ChannelPSF>) - Method in class spim.process.fusion.deconvolution.ProcessForDeconvolution
-
- AssignPixelDisplay(PixelDisplay) - Method in class view5d.AlternateViewer
-
- assignPointMatches(List<P>, List<P>) - Method in interface mpicbg.icp.PointMatchIdentification
-
- assignPointMatches(List<P>, List<P>) - Method in class mpicbg.icp.SimplePointMatchIdentification
-
- assignPoints(Set<ShollPoint>) - Method in class sc.fiji.snt.analysis.sholl.ProfileEntry
-
- assignPopupToHelpButton(JPopupMenu) - Method in class sc.fiji.snt.gui.EnhancedGenericDialog
-
Deprecated.
Attaches the specified JPopupMenu to the GenericDialog "Help" button
renamed "More »".
- assignPopupToHelpButton(String, JPopupMenu) - Method in class sc.fiji.snt.gui.EnhancedGenericDialog
-
Deprecated.
Adds a "Help" button and attaches the specified JPopupMenu to it.
- assignProperty(String) - Method in class sc.fiji.snt.analysis.sholl.gui.ShollOverlay
-
- assignSliceTo(int, Roi, int) - Method in class vib.segment.CustomStackWindow
-
- assignSpatialSettings(ImagePlus) - Method in class sc.fiji.snt.PathAndFillManager
-
- assignToLeftHemisphere(Tree) - Static method in class sc.fiji.snt.annotation.AllenUtils
-
- assignToRightHemisphere(Tree) - Static method in class sc.fiji.snt.annotation.AllenUtils
-
- assignUniqueColors(Collection<Tree>) - Static method in class sc.fiji.snt.Tree
-
- assignUniqueColors(Collection<String>) - Method in class sc.fiji.snt.viewer.Viewer3D
-
- assignValue(double) - Method in class sc.fiji.snt.Tree
-
Assigns a numeric property to this Tree.
- assignValues() - Method in class sc.fiji.snt.analysis.PathProfiler
-
- assignValues(int) - Method in class sc.fiji.snt.analysis.PathProfiler
-
- assignValues(Path) - Method in class sc.fiji.snt.analysis.PathProfiler
-
Retrieves pixel intensities at each node of the Path storing them as Path
values
- assignValues(Path, int) - Method in class sc.fiji.snt.analysis.PathProfiler
-
- assignValues(boolean) - Method in class sc.fiji.snt.SNTService
-
Assigns pixel intensities at each Path node, storing them as Path values.
- assignViewsToTiles(M, List<ViewId>, boolean) - Static method in class spim.process.interestpointregistration.GlobalOpt
-
- assoc(BufferedImage) - Method in class ini.trakem2.display.DisplayCanvas.Screenshot
-
Associate @param img to this, with a new sid.
- asVectorString2D(Polygon, double) - Static method in class ini.trakem2.utils.M
-
- asVectorString3D() - Method in interface ini.trakem2.display.Line3D
-
- asVectorString3D() - Method in class ini.trakem2.display.Pipe
-
Returns a non-calibrated VectorString3D.
- asVectorString3D() - Method in class ini.trakem2.display.Polyline
-
Returns a non-calibrated VectorString3D.
- asVertices() - Method in class ini.trakem2.display.Tree
-
Return a representation of this Tree with Vertex instead of Node.
- asVolatile(V, SharedQueue) - Method in class bdv.util.RandomAccessibleIntervalMipmapSource
-
- asVolatile(Supplier<V>, SharedQueue) - Method in class bdv.util.RandomAccessibleIntervalMipmapSource
-
- asVolatile(SharedQueue) - Method in class bdv.util.RandomAccessibleIntervalMipmapSource
-
- asVolatile() - Method in class bdv.viewer.SourceAndConverter
-
- asVolatile() - Method in class bdv.viewer.state.SourceState
-
Deprecated.
- asWorldPoints() - Method in class ini.trakem2.display.Ball
-
Returns a Point3f for every x,y,z ball, in calibrated world space.
- at - Variable in class ini.trakem2.display.Displayable
-
- at - Variable in class ini.trakem2.display.Displayable.DataPackage
-
- at - Variable in class ini.trakem2.display.Patch.TransformProperties
-
- ATan - Class in script.imglib.math
-
TODO
- ATan(Image<? extends RealType<?>>) - Constructor for class script.imglib.math.ATan
-
- ATan(IFunction) - Constructor for class script.imglib.math.ATan
-
- ATan(Number) - Constructor for class script.imglib.math.ATan
-
- ATan2 - Class in script.imglib.math
-
TODO
- ATan2(Image<? extends RealType<?>>, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.ATan2
-
- ATan2(IFunction, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.ATan2
-
- ATan2(Image<? extends RealType<?>>, IFunction) - Constructor for class script.imglib.math.ATan2
-
- ATan2(IFunction, IFunction) - Constructor for class script.imglib.math.ATan2
-
- ATan2(Image<? extends RealType<?>>, Number) - Constructor for class script.imglib.math.ATan2
-
- ATan2(Number, Image<? extends RealType<?>>) - Constructor for class script.imglib.math.ATan2
-
- ATan2(IFunction, Number) - Constructor for class script.imglib.math.ATan2
-
- ATan2(Number, IFunction) - Constructor for class script.imglib.math.ATan2
-
- ATan2(Number, Number) - Constructor for class script.imglib.math.ATan2
-
- atGoal(int, int, int, boolean) - Method in class sc.fiji.snt.SearchThread
-
- atGoal(int, int, int, boolean) - Method in class sc.fiji.snt.TracerThread
-
- attNumVals - Variable in class hr.irb.fastRandomForest.DataCache
-
Attribute description - holds a 0 for numeric attributes, and the number
of available categories for nominal attributes.
- ATTRIBUTE_COORD_SYSTEM - Static variable in class ij3d.DefaultUniverse
-
Constant used in showAttribute() specifying whether a global coordinate
system should be displayed or not.
- ATTRIBUTE_SCALEBAR - Static variable in class ij3d.DefaultUniverse
-
Constant used in showAttribute() specifying whether a scalebar should be
displayed or not.
- attributeChoice - Variable in class spim.fiji.plugin.queryXML.GenericLoadParseQueryXML
-
- attributeChoiceList - Static variable in class spim.fiji.plugin.queryXML.GenericLoadParseQueryXML
-
- AttributeClassPair - Class in ai
-
Inner class to order attributes while preserving class indices
- attributeInstancesToProcess - Variable in class spim.fiji.plugin.queryXML.GenericLoadParseQueryXML
-
- attributeMap - Variable in class mpicbg.spim.data.generic.sequence.XmlIoBasicViewSetup
-
Maps attribute tag name to map from id to entity.
- attributes - Variable in class spim.fiji.plugin.queryXML.GenericLoadParseQueryXML
-
- ATTRIBUTES_NAME_ATTRIBUTE_NAME - Static variable in class mpicbg.spim.data.XmlKeys
-
- ATTRIBUTES_SPECIALIZED_ATTRIBUTE_NAME - Static variable in class mpicbg.spim.data.XmlKeys
-
- ATTRIBUTES_TAG - Static variable in class mpicbg.spim.data.XmlKeys
-
- attributesSwitch - Variable in class ij3d.DefaultUniverse
-
Switch which holds the optionally displayable scalebar and coordinate
system.
- attributeValue - Variable in class ai.AttributeClassPair
-
real value of the corresponding attribute
- attrs - Static variable in class lineage.LineageClassifier
-
- ATYPICAL_MONOCHROMACY - Static variable in class Daltonize_
-
- AugmentedLandmarkWarp_ - Class in vib
-
- AugmentedLandmarkWarp_() - Constructor for class vib.AugmentedLandmarkWarp_
-
- augmentPath(int) - Method in class fiji.plugin.trackmate.tracking.oldlap.hungarian.MunkresKuhnAlgorithm
-
- AuthenticationException - Exception in edu.utexas.clm.archipelago.exception
-
- AuthenticationException() - Constructor for exception edu.utexas.clm.archipelago.exception.AuthenticationException
-
- AuthenticationException(String) - Constructor for exception edu.utexas.clm.archipelago.exception.AuthenticationException
-
- AuthenticationException(String, Throwable) - Constructor for exception edu.utexas.clm.archipelago.exception.AuthenticationException
-
- AuthenticationException(Throwable) - Constructor for exception edu.utexas.clm.archipelago.exception.AuthenticationException
-
- Auto_Threshold - Class in fiji.threshold
-
- Auto_Threshold() - Constructor for class fiji.threshold.Auto_Threshold
-
- autoCanvasActivation - Variable in class sc.fiji.snt.SNT
-
- AutoLabeller - Class in oldsegmenters
-
User: Tom Larkworthy
Date: 12-Jul-2006
Time: 19:10:47
- AutoLabeller(String) - Constructor for class oldsegmenters.AutoLabeller
-
- AutoLabeller.LabelStats - Class in oldsegmenters
-
- AutoLabellerNaive - Class in oldsegmenters
-
User: Tom Larkworthy
Date: 12-Jul-2006
Time: 19:12:08
- AutoLabellerNaive(String) - Constructor for class oldsegmenters.AutoLabellerNaive
-
- AutomaticAngleSetup - Class in mpicbg.spim.preprocessing
-
- AutomaticAngleSetup(ViewStructure) - Constructor for class mpicbg.spim.preprocessing.AutomaticAngleSetup
-
- AutomaticBoundingBox - Class in spim.process.fusion.boundingbox
-
- AutomaticBoundingBox(SpimData2, List<ViewId>) - Constructor for class spim.process.fusion.boundingbox.AutomaticBoundingBox
-
- AutomaticReorientation - Class in spim.process.fusion.boundingbox
-
- AutomaticReorientation(SpimData2, List<ViewId>) - Constructor for class spim.process.fusion.boundingbox.AutomaticReorientation
-
- AutomaticReorientation.Reorientation - Enum in spim.process.fusion.boundingbox
-
- autoMinMax() - Method in class fiji.plugin.trackmate.gui.panels.components.ColorByFeatureGUIPanel
-
- autoMinMax() - Method in class fiji.plugin.trackmate.gui.panels.components.SetColorScaleDialog
-
- autoMinMax() - Method in class fiji.plugin.trackmate.visualization.DummySpotColorGenerator
-
- autoMinMax() - Method in class fiji.plugin.trackmate.visualization.DummyTrackColorGenerator
-
- autoMinMax() - Method in class fiji.plugin.trackmate.visualization.ManualEdgeColorGenerator
-
- autoMinMax() - Method in class fiji.plugin.trackmate.visualization.ManualSpotColorGenerator
-