Uses of Class
net.preibisch.mvrecon.fiji.spimdata.SpimData2

Packages that use SpimData2

Package	Description
net.preibisch.mvrecon.fiji.datasetmanager
net.preibisch.mvrecon.fiji.plugin
net.preibisch.mvrecon.fiji.plugin.boundingbox
net.preibisch.mvrecon.fiji.plugin.fusion
net.preibisch.mvrecon.fiji.plugin.interactive
net.preibisch.mvrecon.fiji.plugin.interestpointdetection
net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global
net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise
net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters
net.preibisch.mvrecon.fiji.plugin.queryXML
net.preibisch.mvrecon.fiji.plugin.resave
net.preibisch.mvrecon.fiji.spimdata
net.preibisch.mvrecon.fiji.spimdata.explorer
net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror
net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint
net.preibisch.mvrecon.fiji.spimdata.explorer.popup
net.preibisch.mvrecon.fiji.spimdata.explorer.registration
net.preibisch.mvrecon.fiji.spimdata.explorer.selection
net.preibisch.mvrecon.fiji.spimdata.imgloaders
net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions
net.preibisch.mvrecon.headless.definedataset
net.preibisch.mvrecon.process.boundingbox
net.preibisch.mvrecon.process.chromaticabberation
net.preibisch.mvrecon.process.fusion
net.preibisch.mvrecon.process.fusion.blk
net.preibisch.mvrecon.process.fusion.lazy
net.preibisch.mvrecon.process.fusion.transformed.nonrigid
net.preibisch.mvrecon.process.interestpointdetection
net.preibisch.mvrecon.process.interestpointregistration
net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.loadcorrespondences
net.preibisch.mvrecon.process.interestpointremoval
net.preibisch.mvrecon.process.n5api
net.preibisch.mvrecon.process.psf
net.preibisch.mvrecon.process.splitting
util

Uses of SpimData2 in net.preibisch.mvrecon.fiji.datasetmanager

Methods in net.preibisch.mvrecon.fiji.datasetmanager that return SpimData2

Modifier and Type	Method	Description
SpimData2	DHM.createDataset(String xmlFileName)
SpimData2	FileListDatasetDefinition.createDataset(String xmlFileName)
SpimData2	LightSheetZ1.createDataset(String xmlFileName)
SpimData2	MicroManager.createDataset(String xmlFileName)
SpimData2	MultiViewDatasetDefinition.createDataset(String xmlFileName)	This method is supposed to (interactively, ideally ImageJ-macroscriptable) query all necessary data from the user to build up a SpimData object and save it as an XML file.
SpimData2	OMEZARR.createDataset(String xmlFileName)
SpimData2	SimView.createDataset(String xmlFileName)
SpimData2	SmartSPIM.createDataset(String xmlFileName)
SpimData2	StackList.createDataset(String xmlFileName)

Uses of SpimData2 in net.preibisch.mvrecon.fiji.plugin

Methods in net.preibisch.mvrecon.fiji.plugin that return SpimData2

Modifier and Type	Method	Description
static SpimData2	Switch_Attributes.switchAttributes(SpimData2 data, int in1, int in2)
static SpimData2	Switch_Attributes.switchAttributesGUI(SpimData2 data)

Methods in net.preibisch.mvrecon.fiji.plugin that return types with arguments of type SpimData2

Modifier and Type	Method	Description
ImgLib2Temp.Pair<SpimData2,String>	Define_Multi_View_Dataset.defineDataset(boolean save)

Methods in net.preibisch.mvrecon.fiji.plugin with parameters of type SpimData2

Modifier and Type	Method	Description
AdvancedRegistrationParameters	Interest_Point_Registration.advancedRegistrationParameters(BasicRegistrationParameters brp, List<mpicbg.spim.data.sequence.TimePoint> timepointToProcess, SpimData2 data, List<mpicbg.spim.data.sequence.ViewId> viewIds)
static boolean	PSF_Assign.assign(SpimData2 spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewCollection)
static boolean	PSF_Assign.assign(SpimData2 spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewCollection, String xmlFileName, boolean saveXml)
static boolean	PSF_Average.average(SpimData2 spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewCollection)
static boolean	PSF_Average.average(SpimData2 spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds, int choice, boolean subtractMinProjections)
static net.imglib2.img.Img<net.imglib2.type.numeric.real.FloatType>	PSF_Average.averagePSF(SpimData2 spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds)
static net.imglib2.img.Img<net.imglib2.type.numeric.real.FloatType>	PSF_View.averageTransformedPSF(SpimData2 spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds)
BasicRegistrationParameters	Interest_Point_Registration.basicRegistrationParameters(List<mpicbg.spim.data.sequence.TimePoint> timepointToProcess, int nAllTimepoints, SpimData2 data, List<mpicbg.spim.data.sequence.ViewId> viewIds)
static boolean	CreateFromCorresponding_Detections.create(SpimData2 data, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewCollection)
static boolean	Image_Deconvolution.deconvolve(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> views)
static boolean	Image_Deconvolution.deconvolve(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewList, ExecutorService service)
BoundingBox	Define_Bounding_Box.defineBoundingBox(SpimData2 data, List<mpicbg.spim.data.sequence.ViewId> viewIds)
BoundingBox	Define_Bounding_Box.defineBoundingBox(SpimData2 data, List<mpicbg.spim.data.sequence.ViewId> viewIds, String xmlFileName, boolean saveXML)
boolean	Interest_Point_Detection.detectInterestPoints(SpimData2 data, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewCollection)
boolean	Interest_Point_Detection.detectInterestPoints(SpimData2 data, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewCollection, String xmlFileName, boolean saveXML)
static double[]	Image_Fusion.determineInputBitDepth(Iterable<? extends mpicbg.spim.data.sequence.ViewDescription> group, SpimData2 spimData)
static double[]	Image_Fusion.determineInputBitDepth(Group<mpicbg.spim.data.sequence.ViewDescription> group, SpimData2 spimData, net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> virtual)
static boolean	PSF_View.display(SpimData2 spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewCollection)
static boolean	PSF_View.display(SpimData2 spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIdsIn, int choice)
protected void	Duplicate_Transformation.duplicateTransformations(int transformations, mpicbg.spim.data.sequence.ViewId sourceViewId, mpicbg.spim.data.sequence.ViewId targetViewId, SpimData2 spimData)
static boolean	Image_Quality.estimateFRC(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewsToProcess)
static boolean	PSF_Extract.extract(SpimData2 spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewCollection)
static boolean	PSF_Extract.extract(SpimData2 spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewCollection, String xmlFileName, boolean saveXml)
static boolean	Image_Fusion.fuse(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewsToProcess)
static String	Show_Histogram.getLabel(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIds)
static String[]	Show_Relative_Histogram.getLabels(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIds)
static CreateFromCorrespondencesParameters	CreateFromCorresponding_Detections.getParameters(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIds)
static RelativeThinOutParameters	RelativeThinOut_Detections.getParameters(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIds)
static ThinOutParameters	ThinOut_Detections.getParameters(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIds)
boolean	Intensity_Adjustment.intensityAdjustment(SpimData2 data, List<mpicbg.spim.data.sequence.ViewId> viewIds)
boolean	Intensity_Adjustment.intensityAdjustment(SpimData2 data, List<mpicbg.spim.data.sequence.ViewId> views, String xmlFileName, boolean saveXML)
static boolean	Show_Histogram.plotHistogram(SpimData2 spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewCollection)
static boolean	Show_Relative_Histogram.plotHistogram(SpimData2 spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewCollection)
static Visualize_Detections.Params	Visualize_Detections.queryDetails(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIds)
boolean	Interest_Point_Registration.register(SpimData2 data, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewCollection)
boolean	Interest_Point_Registration.register(SpimData2 data, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewCollection, String xmlFileName, boolean saveXML)
boolean	RemoveIntensity_Adjustment.removeAdjustment(SpimData2 data, List<mpicbg.spim.data.sequence.ViewId> viewIds)
boolean	RemoveIntensity_Adjustment.removeAdjustment(SpimData2 data, List<mpicbg.spim.data.sequence.ViewId> viewIds, String xmlFileName, boolean saveXML)
protected static net.imglib2.img.Img<net.imglib2.type.numeric.integer.UnsignedShortType>	Visualize_Detections.renderSegmentations(SpimData2 data, mpicbg.spim.data.sequence.ViewId viewId, String label, int detections, net.imglib2.Interval interval, double downsample)
static URI	XMLSaveAs.saveAs(SpimData2 data, String suggestedFileName)
static boolean	Split_Views.split(SpimData2 data, URI filePath)
static boolean	Split_Views.split(SpimData2 data, URI saveAs, SplitView splitting, boolean assingIlluminationsFromTileIds, Split_Views.InterestPointAdding ipAdding, double pointDensity, int minPoints, int maxPoints, double error, double excludeRadius, boolean display)
static boolean	Split_Views.split(SpimData2 data, URI saveAs, SplitView splitting, boolean assingIlluminationsFromTileIds, Split_Views.InterestPointAdding ipAdding, double pointDensity, int minPoints, int maxPoints, double error, double excludeRadius, boolean display, String fakeLabel, SplittingTools.InterestPointSaver saver, SplittingTools.CorrespondenceSaver corrSaver)
static boolean	Split_Views.split(SpimData2 data, URI saveAs, SplitView splitting, boolean assingIlluminationsFromTileIds, Split_Views.InterestPointAdding ipAdding, double pointDensity, int minPoints, int maxPoints, double error, double excludeRadius, boolean display, String fakeLabel, SplittingTools.InterestPointSaver saver, SplittingTools.CorrespondenceSaver corrSaver, Set<Integer> driveByChannelIds)
static SpimData2	Switch_Attributes.switchAttributes(SpimData2 data, int in1, int in2)
static SpimData2	Switch_Attributes.switchAttributesGUI(SpimData2 data)
static boolean	RelativeThinOut_Detections.thinOut(SpimData2 data, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewCollection)
static boolean	ThinOut_Detections.thinOut(SpimData2 data, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewCollection)
static void	Visualize_Detections.visualize(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIds, String label, int detections, double downsample, boolean displayInput)

Uses of SpimData2 in net.preibisch.mvrecon.fiji.plugin.boundingbox

Fields in net.preibisch.mvrecon.fiji.plugin.boundingbox declared as SpimData2

Modifier and Type	Field	Description
protected final SpimData2	BoundingBoxGUI.spimData

Methods in net.preibisch.mvrecon.fiji.plugin.boundingbox with parameters of type SpimData2

Modifier and Type	Method	Description
protected static boolean	BoundingBoxGUI.findRange(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIdsToProcess, int[] rangeMin, int[] rangeMax)
BoundingBoxGUI	AutomaticReorientationBoundingBoxGUI.newInstance(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIdsToProcess)
BoundingBoxGUI	BDVBoundingBoxGUI.newInstance(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIdsToProcess)
abstract BoundingBoxGUI	BoundingBoxGUI.newInstance(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIdsToProcess)
BoundingBoxGUI	MaximumBoundingBoxGUI.newInstance(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIdsToProcess)
BoundingBoxGUI	MinFilterThresholdBoundingBoxGUI.newInstance(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIdsToProcess)
ModifyDefinedBoundingBoxGUI	ModifyDefinedBoundingBoxGUI.newInstance(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIdsToProcess)
protected static final void	ModifyDefinedBoundingBoxGUI.update(SpimData2 spimData, Choice choice, Label label1, Label label2)

Constructors in net.preibisch.mvrecon.fiji.plugin.boundingbox with parameters of type SpimData2

Modifier	Constructor	Description
	AutomaticReorientationBoundingBoxGUI(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIdsToProcess)
	BDVBoundingBoxGUI(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIdsToProcess)
	BoundingBoxGUI(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIdsToProcess)
	BoundingBoxGUI(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIdsToProcess, BoundingBox bb)
	MaximumBoundingBoxGUI(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIdsToProcess)
	MinFilterThresholdBoundingBoxGUI(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIdsToProcess)
	ModifyDefinedBoundingBoxGUI(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIdsToProcess)

Uses of SpimData2 in net.preibisch.mvrecon.fiji.plugin.fusion

Fields in net.preibisch.mvrecon.fiji.plugin.fusion declared as SpimData2

Modifier and Type	Field	Description
protected final SpimData2	DeconvolutionGUI.spimData
protected final SpimData2	FusionGUI.spimData
protected final SpimData2	QualityGUI.spimData

Methods in net.preibisch.mvrecon.fiji.plugin.fusion that return SpimData2

Modifier and Type	Method	Description
SpimData2	DeconvolutionGUI.getSpimData()
SpimData2	FusionExportInterface.getSpimData()
SpimData2	FusionGUI.getSpimData()
SpimData2	QualityGUI.getSpimData()

Methods in net.preibisch.mvrecon.fiji.plugin.fusion with parameters of type SpimData2

Modifier and Type	Method	Description
static List<Group<mpicbg.spim.data.sequence.ViewDescription>>	FusionGUI.getFusionGroups(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> views, int splittingType)
static int	FusionGUI.inputBytePerPixel(mpicbg.spim.data.sequence.ViewId viewId, SpimData2 spimData)
static int	ManageDeconvolutionDialogListeners.maxNumGroups(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> views, DeconvolutionGUI decon, int splittingType)
static long	FusionGUI.maxNumInputPixelsPerInputGroup(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> views, int splittingType)

Constructors in net.preibisch.mvrecon.fiji.plugin.fusion with parameters of type SpimData2

Modifier	Constructor	Description
	DeconvolutionGUI(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> views, ExecutorService service)
	FusionGUI(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> views)
	NonRigidParametersGUI(SpimData2 spimData, List<? extends mpicbg.spim.data.sequence.ViewId> viewIds)
	QualityGUI(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> views)

Uses of SpimData2 in net.preibisch.mvrecon.fiji.plugin.interactive

Methods in net.preibisch.mvrecon.fiji.plugin.interactive with parameters of type SpimData2

Modifier and Type	Method	Description
static ArrayList<net.imglib2.util.Pair<net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>,net.imglib2.realtransform.AffineTransform3D>>	MultiResolutionTools.createMultiResolutionAffine(SpimData2 spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds, net.imglib2.Interval boundingBox, int minDS, int maxDS, int dsInc)
static ArrayList<net.imglib2.util.Pair<net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>,net.imglib2.realtransform.AffineTransform3D>>	MultiResolutionTools.createMultiResolutionNonRigid(SpimData2 spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewsToFuse, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewsToUse, ArrayList<String> labels, long controlPointDistance, net.imglib2.Interval boundingBox, ExecutorService service, int minDS, int maxDS, int dsInc)
static ArrayList<net.imglib2.util.Pair<net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>,net.imglib2.realtransform.AffineTransform3D>>	MultiResolutionTools.createMultiResolutionNonRigid(SpimData2 spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewsToFuse, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewsToUse, ArrayList<String> labels, FusionGUI.FusionType fusionType, boolean displayDistances, long controlPointDistance, double alpha, int interpolation, net.imglib2.Interval boundingBox, Map<? extends mpicbg.spim.data.sequence.ViewId,mpicbg.models.AffineModel1D> intensityAdjustments, ExecutorService service, int minDS, int maxDS, int dsInc)

Uses of SpimData2 in net.preibisch.mvrecon.fiji.plugin.interestpointdetection

Methods in net.preibisch.mvrecon.fiji.plugin.interestpointdetection with parameters of type SpimData2

Modifier and Type	Method	Description
DifferenceOfGaussianGUI	DifferenceOfGaussianGUI.newInstance(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIdsToProcess)
abstract InterestPointDetectionGUI	InterestPointDetectionGUI.newInstance(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIdsToProcess)

Constructors in net.preibisch.mvrecon.fiji.plugin.interestpointdetection with parameters of type SpimData2

Modifier	Constructor	Description
	DifferenceOfGaussianGUI(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIdsToProcess)
	DifferenceOfGUI(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIdsToProcess)
	InterestPointDetectionGUI(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIdsToProcess)

Uses of SpimData2 in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global

Constructors in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global with parameters of type SpimData2

Modifier	Constructor	Description
	IndividualTimepointGUI(SpimData2 data)

Uses of SpimData2 in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise

Methods in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise with parameters of type SpimData2

Modifier and Type	Method	Description
CenterOfMassGUI	CenterOfMassGUI.newInstance(SpimData2 spimData)
FRGLDMGUI	FRGLDMGUI.newInstance(SpimData2 spimData)
GeometricHashingGUI	GeometricHashingGUI.newInstance(SpimData2 spimData)
IterativeClosestPointGUI	IterativeClosestPointGUI.newInstance(SpimData2 spimData)
PairwiseGUI	LoadCorrespondencesGUI.newInstance(SpimData2 spimData)
abstract PairwiseGUI	PairwiseGUI.newInstance(SpimData2 spimData)
RGLDMGUI	RGLDMGUI.newInstance(SpimData2 spimData)

Constructors in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.pairwise with parameters of type SpimData2

Modifier	Constructor	Description
	LoadCorrespondencesGUI(SpimData2 spimData)

Uses of SpimData2 in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters

Methods in net.preibisch.mvrecon.fiji.plugin.interestpointregistration.parameters with parameters of type SpimData2

Modifier and Type	Method	Description
static HashSet<Group<mpicbg.spim.data.sequence.ViewId>>	AdvancedRegistrationParameters.getGroups(SpimData2 data, List<? extends mpicbg.spim.data.sequence.ViewId> views, boolean groupTiles, boolean groupIllums, boolean groupChannels, boolean groupTimePoints)
HashSet<Group<mpicbg.spim.data.sequence.ViewId>>	AdvancedRegistrationParameters.getGroups(SpimData2 data, List<mpicbg.spim.data.sequence.ViewId> views, boolean groupTiles, boolean groupIllums, boolean groupChannels)

Uses of SpimData2 in net.preibisch.mvrecon.fiji.plugin.queryXML

Methods in net.preibisch.mvrecon.fiji.plugin.queryXML that return SpimData2

Modifier and Type	Method	Description
protected SpimData2	LoadParseQueryXML.parseXML(URI xmlPath)

Uses of SpimData2 in net.preibisch.mvrecon.fiji.plugin.resave

Methods in net.preibisch.mvrecon.fiji.plugin.resave that return SpimData2

Modifier and Type	Method	Description
static SpimData2	Resave_HDF5.createXMLObject(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIds, Generic_Resave_HDF5.ParametersResaveHDF5 params, bdv.export.ProgressWriter progressWriter, boolean useRightAway)
static SpimData2	Resave_TIFF.createXMLObject(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIds, Resave_TIFF.ParametersResaveAsTIFF params)
static SpimData2	Resave_N5Api.resaveN5(SpimData2 data, Collection<? extends mpicbg.spim.data.sequence.ViewId> vidsToResave, ParametersResaveN5Api n5Params, boolean saveXML)

Methods in net.preibisch.mvrecon.fiji.plugin.resave with parameters of type SpimData2

Modifier and Type	Method	Description
static SpimData2	Resave_HDF5.createXMLObject(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIds, Generic_Resave_HDF5.ParametersResaveHDF5 params, bdv.export.ProgressWriter progressWriter, boolean useRightAway)
static SpimData2	Resave_TIFF.createXMLObject(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIds, Resave_TIFF.ParametersResaveAsTIFF params)
static boolean	Resave_HDF5.loadDimensions(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewSetup> viewsetups)
static SpimData2	Resave_N5Api.resaveN5(SpimData2 data, Collection<? extends mpicbg.spim.data.sequence.ViewId> vidsToResave, ParametersResaveN5Api n5Params, boolean saveXML)

Uses of SpimData2 in net.preibisch.mvrecon.fiji.spimdata

Methods in net.preibisch.mvrecon.fiji.spimdata that return SpimData2

Modifier and Type	Method	Description
static SpimData2	SpimData2.convert(mpicbg.spim.data.SpimData data1)
SpimData2	XmlIoSpimData2.fromXml(org.jdom2.Element root, URI xmlFile)
SpimData2	XmlIoSpimData2.load(URI xmlURI)

Methods in net.preibisch.mvrecon.fiji.spimdata with parameters of type SpimData2

Modifier and Type	Method	Description
static List<InterestPointsN5.InterestPointData>	XmlIoSpimData2.collectInterestPointData(SpimData2 spimData, boolean modifiedOnly)	Collect all modified interest points as serializable InterestPointData objects.
void	XmlIoSpimData2.save(SpimData2 spimData, String xmlPath)	Deprecated.
boolean	XmlIoSpimData2.save(SpimData2 spimData, URI xmlURI)
static void	XmlIoSpimData2.saveInterestPointsInParallel(SpimData2 spimData)	Save all interest points using a single shared N5Writer with parallel writes.
static void	XmlIoSpimData2.savePSFsInParallel(SpimData2 spimData)
URI	XmlIoSpimData2.saveWithFilename(SpimData2 data, String xmlFileName)	Saves a SpimData2 object using its own URI into a filename specified by xmlFilename
org.jdom2.Element	XmlIoSpimData2.toXml(SpimData2 spimData, File xmlFileDirectory)
org.jdom2.Element	XmlIoSpimData2.toXml(SpimData2 spimData, URI xmlFileDirectory)

Uses of SpimData2 in net.preibisch.mvrecon.fiji.spimdata.explorer

Classes in net.preibisch.mvrecon.fiji.spimdata.explorer with type parameters of type SpimData2

Modifier and Type	Interface	Description
interface	ExplorerWindow<AS extends SpimData2>
class	FilteredAndGroupedExplorer<AS extends SpimData2>
class	FilteredAndGroupedExplorerPanel<AS extends SpimData2>
class	FilteredAndGroupedTableModel<AS extends SpimData2>
interface	ISpimDataTableModel<AS extends SpimData2>
class	MissingViewsTableModelDecorator<AS extends SpimData2>
class	MultiViewTableModelDecorator<AS extends SpimData2>
class	ViewSetupExplorer<AS extends SpimData2>
class	ViewSetupExplorerPanel<AS extends SpimData2>

Fields in net.preibisch.mvrecon.fiji.spimdata.explorer declared as SpimData2

Modifier and Type	Field	Description
protected AS	FilteredAndGroupedExplorerPanel.data

Uses of SpimData2 in net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror

Methods in net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror with parameters of type SpimData2

Modifier and Type	Method	Description
static ArrayList<AnalyzeErrorsUtil.GroupPairResult>	AnalyzeErrorsUtil.computeGroupPairs(SpimData2 data, ArrayList<AnalyzeErrorsUtil.PairError> errors, AnalyzeErrorsUtil.Parameters p)	Bucket per-pair errors into per-group-pair buckets using Group.combineBy(java.util.List<V>, java.util.Set<java.lang.Class<? extends mpicbg.spim.data.generic.base.Entity>>) (collapse semantics — same as ViewSetupExplorer / Interest_Point_Registration grouping).
static ArrayList<AnalyzeErrorsUtil.SingleGroupError>	AnalyzeErrorsUtil.computeSingleGroupErrors(SpimData2 data, ArrayList<AnalyzeErrorsUtil.PairError> errors, AnalyzeErrorsUtil.Parameters p)	Aggregate AnalyzeErrorsUtil.PairErrors into one AnalyzeErrorsUtil.SingleGroupError per group that participates in at least one group-pair under the supplied grouping AnalyzeErrorsUtil.Parameters.
static ArrayList<AnalyzeErrorsUtil.PairError>	AnalyzeErrorsUtil.getErrors(SpimData2 data, List<mpicbg.spim.data.sequence.ViewId> viewIds, Map<String,Double> labelAndWeights)	Compute weighted error per (viewA, viewB) pair, returning the list sorted desc by error.
static HashMap<String,Double>	AnalyzeErrorsUtil.getParameters(SpimData2 data, List<mpicbg.spim.data.sequence.ViewId> viewIds)	Backwards-compatible wrapper that returns just the labels-and-weights map.
static AnalyzeErrorsUtil.Parameters	AnalyzeErrorsUtil.getParametersExtended(SpimData2 data, List<mpicbg.spim.data.sequence.ViewId> viewIds)	Extended dialog returning the full AnalyzeErrorsUtil.Parameters bundle (labels+weights, grouping, top/bottom caps).
static void	AnalyzeErrorsUtil.printResults(SpimData2 data, ArrayList<AnalyzeErrorsUtil.PairError> errors, AnalyzeErrorsUtil.Parameters p)	Print top-N worst, bottom-M best, and the per-old-tile-pair / per-old-tile rollup summary blocks that the AnalyzeErrorsUtil.Parameters dialog choices request.

Constructors in net.preibisch.mvrecon.fiji.spimdata.explorer.analyzeerror with parameters of type SpimData2

Modifier	Constructor	Description
	AnalyzeErrorsResultsWindow(SpimData2 data, ArrayList<AnalyzeErrorsUtil.PairError> errors, AnalyzeErrorsUtil.Parameters params, ViewSetupExplorerPanel<?> panel, Collection<? extends mpicbg.spim.data.sequence.ViewId> analyzedViews)

Uses of SpimData2 in net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint

Classes in net.preibisch.mvrecon.fiji.spimdata.explorer.interestpoint with type parameters of type SpimData2

Modifier and Type	Class	Description
class	InterestPointExplorer<AS extends SpimData2>

Uses of SpimData2 in net.preibisch.mvrecon.fiji.spimdata.explorer.popup

Constructors in net.preibisch.mvrecon.fiji.spimdata.explorer.popup with parameters of type SpimData2

Modifier	Constructor	Description
	HistogramListener(SpimData2 spimData, ArrayList<mpicbg.spim.data.sequence.ViewId> views, String label, int i)

Uses of SpimData2 in net.preibisch.mvrecon.fiji.spimdata.explorer.registration

Classes in net.preibisch.mvrecon.fiji.spimdata.explorer.registration with type parameters of type SpimData2

Modifier and Type	Class	Description
class	RegistrationExplorer<AS extends SpimData2>

Uses of SpimData2 in net.preibisch.mvrecon.fiji.spimdata.explorer.selection

Constructors in net.preibisch.mvrecon.fiji.spimdata.explorer.selection with parameters of type SpimData2

Modifier	Constructor	Description
	SelectionDialog(JFrame parent, SpimData2 data)

Uses of SpimData2 in net.preibisch.mvrecon.fiji.spimdata.imgloaders

Methods in net.preibisch.mvrecon.fiji.spimdata.imgloaders with parameters of type SpimData2

Modifier and Type	Method	Description
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>, IL extends mpicbg.spim.data.sequence.ImgLoader & FileMapGettable> void	LegacyFileMapImgLoaderLOCI.checkAndRemoveZeroVolume(SpimData2 spimData, IL loader)
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>, IL extends mpicbg.spim.data.sequence.ImgLoader & FileMapGettable> void	LegacyFileMapImgLoaderLOCI.checkAndRemoveZeroVolume(SpimData2 spimData, IL loader, boolean filesArePatterns)	check if views in spimData contain zero-valued planes at the end of the z-axis.
static boolean	LegacyFileMapImgLoaderLOCI.isZSizeEqualInEveryFile(SpimData2 spimData, FileMapGettable loader)	for every file in the dataset file list check if the z-size is equal for every series.

Uses of SpimData2 in net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions

Constructors in net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions with parameters of type SpimData2

Modifier	Constructor	Description
	PointSpreadFunction(SpimData2 spimData, mpicbg.spim.data.sequence.ViewId viewId, net.imglib2.img.Img<net.imglib2.type.numeric.real.FloatType> img)

Uses of SpimData2 in net.preibisch.mvrecon.headless.definedataset

Methods in net.preibisch.mvrecon.headless.definedataset that return SpimData2

Modifier and Type	Method	Description
static SpimData2	LightSheetZ1.createDataset(String cziFirstFile, DefineDataSetParameters params)
static SpimData2	MicroManager.createDataset(String tiffFile, DefineDataSetParameters params)
static SpimData2	StackListImageJ.createDataset(String file, StackListParameters params)
static SpimData2	StackListLOCI.createDataset(String file, StackListParameters params)

Methods in net.preibisch.mvrecon.headless.definedataset with parameters of type SpimData2

Modifier and Type	Method	Description
static boolean	LightSheetZ1MetaData.fixBioformats(SpimData2 spimData, File cziFile, LightSheetZ1MetaData meta)

Uses of SpimData2 in net.preibisch.mvrecon.process.boundingbox

Methods in net.preibisch.mvrecon.process.boundingbox with parameters of type SpimData2

Modifier and Type	Method	Description
static ArrayList<net.imglib2.RealLocalizable>	BoundingBoxReorientation.extractPoints(String label, boolean useCorresponding, boolean transform, List<mpicbg.spim.data.sequence.ViewId> viewIds, SpimData2 data)	Gets point locations in local or global coordinates
static ArrayList<net.imglib2.RealLocalizable>	BoundingBoxReorientation.extractPoints(HashMap<mpicbg.spim.data.sequence.ViewId,? extends Collection<? extends net.imglib2.RealLocalizable>> pointsIn, List<mpicbg.spim.data.sequence.ViewId> viewIdsForEstimation, SpimData2 spimData)
static List<BoundingBox>	BoundingBoxTools.getAllBoundingBoxes(SpimData2 spimData, Collection<mpicbg.spim.data.sequence.ViewId> currentlySelected, boolean addBoundingBoxForAllViews)
static BoundingBox	BoundingBoxTools.getBoundingBox(SpimData2 spimData, String bbTitle)	Finds a bounding box by title in the SpimData2 bounding box collection.
static <V extends mpicbg.spim.data.sequence.ViewId> BoundingBox	BoundingBoxTools.maximalBoundingBox(SpimData2 spimData, Collection<V> viewIds, String title)

Constructors in net.preibisch.mvrecon.process.boundingbox with parameters of type SpimData2

Modifier	Constructor	Description
	BoundingBoxMinFilterThreshold(SpimData2 spimData, ExecutorService service, Collection<? extends mpicbg.spim.data.sequence.ViewId> views, net.imglib2.img.ImgFactory<net.imglib2.type.numeric.real.FloatType> imgFactory, double background, int discardedObjectSize, boolean displaySegmentationImage, int downsampling)
	BoundingBoxReorientation(SpimData2 spimData, ArrayList<net.imglib2.RealLocalizable> points, double percent, boolean testRotations, List<mpicbg.spim.data.sequence.ViewId> viewIdsToApply)
	BoundingBoxReorientation(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIdsForEstimation, String label, boolean useCorresponding, double percent, boolean testRotations, List<mpicbg.spim.data.sequence.ViewId> viewIdsToApply)
	BoundingBoxReorientation(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIdsForEstimation, HashMap<mpicbg.spim.data.sequence.ViewId,? extends Collection<? extends net.imglib2.RealLocalizable>> points, double percent, boolean testRotations, List<mpicbg.spim.data.sequence.ViewId> viewIdsToApply)

Uses of SpimData2 in net.preibisch.mvrecon.process.chromaticabberation

Methods in net.preibisch.mvrecon.process.chromaticabberation with parameters of type SpimData2

Modifier and Type	Method	Description
static <V extends mpicbg.spim.data.sequence.ViewId> ArrayList<net.imglib2.util.Pair<mpicbg.spim.data.sequence.Channel,mpicbg.spim.data.sequence.Channel>>	DetectChromaticAbberation.identifyChannelPairs(SpimData2 spimData, List<V> viewIds)
static <V extends mpicbg.spim.data.sequence.ViewId> ArrayList<net.imglib2.util.Pair<V,V>>	DetectChromaticAbberation.identifyViewIdPairs(SpimData2 spimData, List<V> viewIds, net.imglib2.util.Pair<mpicbg.spim.data.sequence.Channel,mpicbg.spim.data.sequence.Channel> channelPair)

Uses of SpimData2 in net.preibisch.mvrecon.process.fusion

Methods in net.preibisch.mvrecon.process.fusion with parameters of type SpimData2

Modifier and Type	Method	Description
static final ArrayList<mpicbg.spim.data.sequence.ViewDescription>	FusionTools.assembleInputData(SpimData2 spimData, mpicbg.spim.data.sequence.TimePoint timepoint, mpicbg.spim.data.sequence.Channel channel, List<mpicbg.spim.data.sequence.ViewId> viewIdsToProcess)
static net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>	FusionTools.fuseVirtual(SpimData2 spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds, FusionGUI.FusionType fusionType, boolean adjustIntensities)	Virtually fuses views using a maximal bounding box around all views

Uses of SpimData2 in net.preibisch.mvrecon.process.fusion.blk

Methods in net.preibisch.mvrecon.process.fusion.blk with parameters of type SpimData2

Modifier and Type	Method	Description
static bdv.ViewerImgLoader	SplitImgLoaderThinPlateSplineFusion.getUnderlyingImageLoader(SpimData2 data)

Uses of SpimData2 in net.preibisch.mvrecon.process.fusion.lazy

Methods in net.preibisch.mvrecon.process.fusion.lazy with parameters of type SpimData2

Modifier and Type	Method	Description
static BoundingBox	LazyFusionTools.getBoundingBox(SpimData2 data, List<mpicbg.spim.data.sequence.ViewId> viewIds, String boundingBoxName)

Uses of SpimData2 in net.preibisch.mvrecon.process.fusion.transformed.nonrigid

Methods in net.preibisch.mvrecon.process.fusion.transformed.nonrigid with parameters of type SpimData2

Modifier and Type	Method	Description
static ArrayList<mpicbg.spim.data.sequence.ViewId>	NonRigidTools.assembleViewsToUse(SpimData2 spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewsToFuse, boolean nonRigidAcrossTime)
static net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>	NonRigidTools.fuseVirtualInterpolatedNonRigid(SpimData2 spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewsToFuse, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewsToUse, ArrayList<String> labels, FusionGUI.FusionType fusionType, boolean displayDistances, long[] controlPointDistance, double alpha, boolean virtualGrid, int interpolation, net.imglib2.Interval boundingBox1, Map<? extends mpicbg.spim.data.sequence.ViewId,mpicbg.models.AffineModel1D> intensityAdjustments, ExecutorService service)

Uses of SpimData2 in net.preibisch.mvrecon.process.interestpointdetection

Methods in net.preibisch.mvrecon.process.interestpointdetection with parameters of type SpimData2

Modifier and Type	Method	Description
static boolean	InterestPointTools.addInterestPoints(SpimData2 data, String label, HashMap<mpicbg.spim.data.sequence.ViewId,List<InterestPoint>> points)	Add interest points.
static boolean	InterestPointTools.addInterestPoints(SpimData2 data, String label, HashMap<mpicbg.spim.data.sequence.ViewId,List<InterestPoint>> points, String parameters)	Add interest points.
static String[]	InterestPointTools.getAllInterestPointLabels(SpimData2 spimData, List<? extends mpicbg.spim.data.sequence.ViewId> viewIdsToProcess)	Goes through all Views and checks all available labels for interest point detection

Uses of SpimData2 in net.preibisch.mvrecon.process.interestpointregistration

Methods in net.preibisch.mvrecon.process.interestpointregistration with parameters of type SpimData2

Modifier and Type	Method	Description
static Set<mpicbg.spim.data.sequence.ViewId>	ViewNeighbors.connectedFor(SpimData2 data, Collection<? extends mpicbg.spim.data.sequence.ViewId> actual, Collection<? extends mpicbg.spim.data.sequence.ViewId> universe, Map<String,Double> labelAndWeights)	Per-click connectivity query.
static Set<mpicbg.spim.data.sequence.ViewId>	ViewNeighbors.connectedTo(mpicbg.spim.data.sequence.ViewId v, SpimData2 data, Collection<? extends mpicbg.spim.data.sequence.ViewId> universe, Map<String,Double> labelAndWeights)	Convenience: connected set for a single view (returns empty set if v not in universe).
static Map<mpicbg.spim.data.sequence.ViewId,Set<mpicbg.spim.data.sequence.ViewId>>	ViewNeighbors.connectedViews(SpimData2 data, Collection<? extends mpicbg.spim.data.sequence.ViewId> universe, Map<String,Double> labelAndWeights)	For each view in universe, return the set of other views in universe that share at least one same-label correspondence with it.
static Set<mpicbg.spim.data.sequence.ViewId>	ViewNeighbors.overlappingFor(SpimData2 data, Collection<? extends mpicbg.spim.data.sequence.ViewId> actual, Collection<? extends mpicbg.spim.data.sequence.ViewId> universe)	Per-click overlap query.
static Map<mpicbg.spim.data.sequence.ViewId,Set<mpicbg.spim.data.sequence.ViewId>>	ViewNeighbors.overlappingViews(SpimData2 data, Collection<? extends mpicbg.spim.data.sequence.ViewId> universe)	For each view in universe, return the set of other views in universe whose registered bounding-box overlaps it.
static Set<mpicbg.spim.data.sequence.ViewId>	ViewNeighbors.overlappingWith(mpicbg.spim.data.sequence.ViewId v, SpimData2 data, Collection<? extends mpicbg.spim.data.sequence.ViewId> universe)	Convenience: overlap set for a single view.

Uses of SpimData2 in net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.loadcorrespondences

Constructors in net.preibisch.mvrecon.process.interestpointregistration.pairwise.methods.loadcorrespondences with parameters of type SpimData2

Modifier	Constructor	Description
	LoadCorrespondencesPairwise(SpimData2 spimData, int minNumMatches)

Uses of SpimData2 in net.preibisch.mvrecon.process.interestpointremoval

Methods in net.preibisch.mvrecon.process.interestpointremoval with parameters of type SpimData2

Modifier and Type	Method	Description
static boolean	CreateInterestPointsFromCorrespondences.createFor(SpimData2 spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds, CreateFromCorrespondencesParameters params)
static Histogram	DistanceHistogram.plotHistogram(SpimData2 spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds, String label, String title)
static Histogram	DistanceHistogram.plotHistogram(SpimData2 spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds, HashMap<? extends mpicbg.spim.data.sequence.ViewId,String> labelMap, String title)
static Histogram	RelativeDistanceHistogram.plotHistogram(SpimData2 spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds, String label, String relativeLabel, String title)
static Histogram	RelativeDistanceHistogram.plotHistogram(SpimData2 spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds, HashMap<? extends mpicbg.spim.data.sequence.ViewId,String> labelMap, HashMap<? extends mpicbg.spim.data.sequence.ViewId,String> labelMapRelative, String title)
static InteractiveProjections	InteractiveProjections.removeInteractively(SpimData2 spimData, mpicbg.spim.data.sequence.ViewId viewId, int dim, String label, String newLabel)
static boolean	RelativeThinOut.thinOut(SpimData2 spimData, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds, RelativeThinOutParameters rtop)
static boolean	ThinOut.thinOut(SpimData2 spimData, List<mpicbg.spim.data.sequence.ViewId> viewIds, ThinOutParameters top)

Constructors in net.preibisch.mvrecon.process.interestpointremoval with parameters of type SpimData2

Modifier	Constructor	Description
	InteractiveProjections(SpimData2 spimData, mpicbg.spim.data.sequence.ViewDescription vd, String label, String newLabel, int projectionDim)

Uses of SpimData2 in net.preibisch.mvrecon.process.n5api

Methods in net.preibisch.mvrecon.process.n5api that return SpimData2

Modifier and Type	Method	Description
static SpimData2	SpimData2Tools.createNewSpimDataForFusion(org.janelia.saalfeldlab.n5.universe.StorageFormat storageType, URI n5PathURI, URI xmlOutPathURI, Map<mpicbg.spim.data.sequence.ViewId,AllenOMEZarrLoader.OMEZARREntry> viewIdToPath, ArrayList<mpicbg.spim.data.sequence.ViewSetup> setups, ArrayList<mpicbg.spim.data.sequence.TimePoint> tps)
static SpimData2	SpimData2Tools.reduceSpimData2(SpimData2 oldSpimData, List<mpicbg.spim.data.sequence.ViewId> viewIds)	Reduces a given SpimData2 to the subset of timepoints and viewsetups as selected by the user, including the original imgloader and keeping the basepath (i.e. interest points still work) Note: PSF's will be lost.
static SpimData2	SpimData2Tools.reduceSpimData2(SpimData2 oldSpimData, List<mpicbg.spim.data.sequence.ViewId> viewIds, URI basePath)	Reduces a given SpimData2 to the subset of timepoints and viewsetups as selected by the user, including the original imgloader and changing the base path (you still need to save to materialize the returned object!)

Methods in net.preibisch.mvrecon.process.n5api with parameters of type SpimData2

Modifier and Type	Method	Description
static SpimData2	SpimData2Tools.reduceSpimData2(SpimData2 oldSpimData, List<mpicbg.spim.data.sequence.ViewId> viewIds)	Reduces a given SpimData2 to the subset of timepoints and viewsetups as selected by the user, including the original imgloader and keeping the basepath (i.e. interest points still work) Note: PSF's will be lost.
static SpimData2	SpimData2Tools.reduceSpimData2(SpimData2 oldSpimData, List<mpicbg.spim.data.sequence.ViewId> viewIds, URI basePath)	Reduces a given SpimData2 to the subset of timepoints and viewsetups as selected by the user, including the original imgloader and changing the base path (you still need to save to materialize the returned object!)
static <T extends net.imglib2.type.NativeType<T>> void	N5ApiTools.resaveS0Block(SpimData2 data, org.janelia.saalfeldlab.n5.N5Writer n5, org.janelia.saalfeldlab.n5.universe.StorageFormat storageType, org.janelia.saalfeldlab.n5.DataType dataType, Function<long[][],String> gridBlockToDataset, long[][] gridBlock)

Uses of SpimData2 in net.preibisch.mvrecon.process.psf

Methods in net.preibisch.mvrecon.process.psf with parameters of type SpimData2

Modifier and Type	Method	Description
static ArrayList<net.imglib2.RealLocalizable>	PSFExtraction.getPoints(SpimData2 data, mpicbg.spim.data.sequence.ViewId viewId, String label, boolean useCorresponding)

Constructors in net.preibisch.mvrecon.process.psf with parameters of type SpimData2

Modifier	Constructor	Description
	PSFExtraction(SpimData2 data, mpicbg.spim.data.sequence.ViewId viewId, String label, boolean useCorresponding, T type, long[] size)
	PSFExtraction(SpimData2 data, mpicbg.spim.data.sequence.ViewId viewId, String label, boolean useCorresponding, T type, long[] size, boolean multithreaded)

Uses of SpimData2 in net.preibisch.mvrecon.process.splitting

Methods in net.preibisch.mvrecon.process.splitting that return SpimData2

Modifier and Type	Method	Description
SpimData2	ConsensusSetCriterion.getSpimData()
SpimData2	CrossViewCorrespondenceCriterion.getSpimData()
SpimData2	OctTreeSplitCriterion.getSpimData()
static SpimData2	SplittingTools.splitImages(SpimData2 spimData, SplitView splitting, boolean assingIlluminationsFromTileIds, Split_Views.InterestPointAdding ipAdding, double pointDensity, int minPoints, int maxPoints, double error, double excludeRadius)
static SpimData2	SplittingTools.splitImages(SpimData2 spimData, SplitView splitting, boolean assingIlluminationsFromTileIds, Split_Views.InterestPointAdding ipAdding, double pointDensity, int minPoints, int maxPoints, double error, double excludeRadius, String fakeLabel, SplittingTools.InterestPointSaver saver, SplittingTools.CorrespondenceSaver corrSaver)
static SpimData2	SplittingTools.splitImages(SpimData2 spimData, SplitView splitting, boolean assingIlluminationsFromTileIds, Split_Views.InterestPointAdding ipAdding, double pointDensity, int minPoints, int maxPoints, double error, double excludeRadius, String fakeLabel, SplittingTools.InterestPointSaver saver, SplittingTools.CorrespondenceSaver corrSaver, Set<Integer> driveByChannelIds)	Split all ViewSetups of the dataset, optionally driving the split geometry from a single channel.

Methods in net.preibisch.mvrecon.process.splitting with parameters of type SpimData2

Modifier and Type	Method	Description
static mpicbg.spim.data.sequence.ViewId	SplittingTools.findFirstPresentViewId(SpimData2 spimData, int setupId)
static void	SplittingTools.processCorrespondingInterestPointsStatic(mpicbg.spim.data.sequence.ViewSetup oldSetup, int newSetupId, mpicbg.spim.data.sequence.TimePoint t, SpimData2 spimData, Map<Integer,? extends List<Integer>> old2NewSetups, Map<mpicbg.spim.data.sequence.ViewId,ViewInterestPointLists> newInterestpoints, AtomicInteger completed, int totalTasks, SplittingTools.CorrespondenceSaver corrSaver, Map<String,Map<Integer,InterestPoint>> ipMapCache)	Process corresponding interest points for a single (oldSetup, newSetupId, timepoint) combination.
static SplittingTools.SetupSplitResult	SplittingTools.processSetupStatic(mpicbg.spim.data.sequence.ViewSetup oldSetup, ArrayList<net.imglib2.Interval> intervals, int idRangeStart, int maxIntervalSpread, mpicbg.spim.data.sequence.TimePoints timepoints, mpicbg.spim.data.registration.ViewRegistrations oldRegistrations, SpimData2 spimData, boolean assingIlluminationsFromTileIds, Split_Views.InterestPointAdding ipAdding, String fakeLabel, double pointDensity, int minPoints, int maxPoints, double error, double excludeRadius, long rndSeed, String splittingDescription, SplittingTools.InterestPointSaver saver)	Process a single ViewSetup's split intervals in isolation.
static ConsensusSetCriterion	ConsensusSetCriterion.queryGUI(ij.gui.GenericDialog gd, SpimData2 data)	Query GUI components and create ConsensusSetCriterion instance.
static ConsensusSetCriterion	ConsensusSetCriterion.queryGUI(ij.gui.GenericDialog gd, SpimData2 data, Set<Integer> driveByChannelIds)	Query GUI components and create ConsensusSetCriterion instance.
static CrossViewCorrespondenceCriterion	CrossViewCorrespondenceCriterion.queryGUI(ij.gui.GenericDialog gd, SpimData2 data)	Query GUI components and create CrossViewCorrespondenceCriterion instance.
static CrossViewCorrespondenceCriterion	CrossViewCorrespondenceCriterion.queryGUI(ij.gui.GenericDialog gd, SpimData2 data, Set<Integer> driveByChannelIds)	Query GUI components and create CrossViewCorrespondenceCriterion instance.
static SplitDistributeEvenly	SplitDistributeEvenly.queryGUI(ij.gui.GenericDialog gd, SpimData2 data, long[] minStepSize)
static SplitOctTree	SplitOctTree.queryGUI(ij.gui.GenericDialog gd, SpimData2 data, long[] minStepSize)	Query GUI components and create SplitOctTree instance.
static SplitOctTree	SplitOctTree.queryGUI(ij.gui.GenericDialog gd, SpimData2 data, long[] minStepSize, Set<Integer> driveByChannelIds)	Query GUI components and create SplitOctTree instance.
static boolean	ConsensusSetCriterion.setupGUI(ij.gui.GenericDialog gd, SpimData2 data)	Setup GUI components for consensus set criterion.
static boolean	ConsensusSetCriterion.setupGUI(ij.gui.GenericDialog gd, SpimData2 data, Set<Integer> driveByChannelIds)	Setup GUI components for consensus set criterion.
static boolean	CrossViewCorrespondenceCriterion.setupGUI(ij.gui.GenericDialog gd, SpimData2 data)	Setup GUI components for cross-view correspondence criterion.
static boolean	CrossViewCorrespondenceCriterion.setupGUI(ij.gui.GenericDialog gd, SpimData2 data, Set<Integer> driveByChannelIds)	Setup GUI components for cross-view correspondence criterion.
static void	SplitDistributeEvenly.setupGUI(ij.gui.GenericDialog gd, SpimData2 data, long[] minStepSize)
static boolean	SplitOctTree.setupGUI(ij.gui.GenericDialog gd, SpimData2 data, long[] minStepSize)	Setup GUI components for oct-tree splitting parameters.
static boolean	SplitOctTree.setupGUI(ij.gui.GenericDialog gd, SpimData2 data, long[] minStepSize, Set<Integer> driveByChannelIds)	Setup GUI components for oct-tree splitting parameters.
static SpimData2	SplittingTools.splitImages(SpimData2 spimData, SplitView splitting, boolean assingIlluminationsFromTileIds, Split_Views.InterestPointAdding ipAdding, double pointDensity, int minPoints, int maxPoints, double error, double excludeRadius)
static SpimData2	SplittingTools.splitImages(SpimData2 spimData, SplitView splitting, boolean assingIlluminationsFromTileIds, Split_Views.InterestPointAdding ipAdding, double pointDensity, int minPoints, int maxPoints, double error, double excludeRadius, String fakeLabel, SplittingTools.InterestPointSaver saver, SplittingTools.CorrespondenceSaver corrSaver)
static SpimData2	SplittingTools.splitImages(SpimData2 spimData, SplitView splitting, boolean assingIlluminationsFromTileIds, Split_Views.InterestPointAdding ipAdding, double pointDensity, int minPoints, int maxPoints, double error, double excludeRadius, String fakeLabel, SplittingTools.InterestPointSaver saver, SplittingTools.CorrespondenceSaver corrSaver, Set<Integer> driveByChannelIds)	Split all ViewSetups of the dataset, optionally driving the split geometry from a single channel.

Constructors in net.preibisch.mvrecon.process.splitting with parameters of type SpimData2

Modifier	Constructor	Description
	ConsensusSetCriterion(SpimData2 spimData, Set<String> labels, int minCorrespondences, ConsensusSetCriterion.ToleranceMode toleranceMode, double toleranceValue)	Constructor.
	CrossViewCorrespondenceCriterion(SpimData2 spimData, Set<String> labels, int maxCorrespondences)	Constructor.
	SplitDistributeEvenly(SpimData2 spimData, long[] overlapPx, long[] targetSize, long[] minStepSize, boolean optimize)

Uses of SpimData2 in util

Methods in util that return SpimData2

Modifier and Type	Method	Description
static SpimData2	URITools.loadSpimData(URI xmlURI, XmlIoSpimData2 io)

Methods in util with parameters of type SpimData2

Modifier and Type	Method	Description
static void	URITools.saveSpimData(SpimData2 data, URI xmlURI, XmlIoSpimData2 io)