Uses of Class mpicbg.spim.registration.ViewDataBeads (Fiji Javadocs 0-SNAPSHOT API)

Packages that use ViewDataBeads
Package	Description
mpicbg.spim
mpicbg.spim.fusion
mpicbg.spim.io
mpicbg.spim.mpicbg
mpicbg.spim.postprocessing.deconvolution
mpicbg.spim.preprocessing
mpicbg.spim.registration
mpicbg.spim.registration.bead
mpicbg.spim.registration.bead.error
mpicbg.spim.registration.detection
mpicbg.spim.registration.detection.descriptor
mpicbg.spim.registration.segmentation
mpicbg.spim.vis3d

Uses of ViewDataBeads in mpicbg.spim

Methods in mpicbg.spim with parameters of type ViewDataBeads
Modifier and Type	Method and Description
`protected ArrayList<Bead>`	Reconstruction.`getAveragedBeadList(ArrayList<ViewDataBeads> views, ViewDataBeads newView)`

Method parameters in mpicbg.spim with type arguments of type ViewDataBeads
Modifier and Type	Method and Description
`protected ArrayList<Bead>`	Reconstruction.`getAveragedBeadList(ArrayList<ViewDataBeads> views, ViewDataBeads newView)`

Uses of ViewDataBeads in mpicbg.spim.fusion

Methods in mpicbg.spim.fusion with parameters of type ViewDataBeads
Modifier and Type	Method and Description
`I`	IsolatedPixelWeightenerFactory.`createInstance(ViewDataBeads view)`
`GaussContent`	GaussContentFactory.`createInstance(ViewDataBeads view)`
`EntropyFast`	EntropyFastFactory.`createInstance(ViewDataBeads view)`
`AverageContent`	AverageContentFactory.`createInstance(ViewDataBeads view)`

Method parameters in mpicbg.spim.fusion with type arguments of type ViewDataBeads
Modifier and Type	Method and Description
`void`	SPIMImageFusion.`computeFinalImageSize(ArrayList<ViewDataBeads> views)`
`static void`	SPIMImageFusion.`computeImageSize(ArrayList<ViewDataBeads> views, Point3f min, Point3f max, Point3f size, int scale, int cropSizeX, int cropSizeY, int cropSizeZ, int debugLevel)`
`static void`	PreDeconvolutionFusionSequential.`computeOverlap(Image<FloatType> overlap, ArrayList<ViewDataBeads> views, ViewStructure viewStructure, int cropOffsetX, int cropOffsetY, int cropOffsetZ, int scale, Point3f min)`
`I`	CombinedPixelWeightenerFactory.`createInstance(ArrayList<ViewDataBeads> views)`
`BlendingSimple`	BlendingSimpleFactory.`createInstance(ArrayList<ViewDataBeads> views)`
`Blending`	BlendingFactory.`createInstance(ArrayList<ViewDataBeads> views)`

Constructors in mpicbg.spim.fusion with parameters of type ViewDataBeads
Constructor and Description
`AverageContent(ViewDataBeads view, ContainerFactory entropyContainer)`
`EntropyFast(ViewDataBeads view, ContainerFactory entropyContainerFactory)`
`GaussContent(ViewDataBeads view, ContainerFactory entropyContainer)`
`IsolatedPixelWeightener(ViewDataBeads view)`

Constructor parameters in mpicbg.spim.fusion with type arguments of type ViewDataBeads
Constructor and Description
`Blending(ArrayList<ViewDataBeads> views)`
`BlendingSimple(ArrayList<ViewDataBeads> views)`
`CombinedPixelWeightener(ArrayList<ViewDataBeads> views)`

Uses of ViewDataBeads in mpicbg.spim.io

Methods in mpicbg.spim.io with parameters of type ViewDataBeads
Modifier and Type	Method and Description
`static boolean`	IOFunctions.`readDim(ViewDataBeads view, String directory)`
`static ArrayList<Nucleus>`	IOFunctions.`readNuclei(ViewDataBeads view, String directory, NucleiConfiguration nConf)`
`static boolean`	IOFunctions.`readNucleiCorrespondences(ViewDataBeads view, String directory)`
`static boolean`	IOFunctions.`readNucleiCorrespondences(ViewDataBeads view, String directory, boolean removePreviousEntries)`
`static boolean`	IOFunctions.`readRegistration(ViewDataBeads view, String fileName)`
`static boolean`	IOFunctions.`readSegmentation(ViewDataBeads view, String directory, SPIMConfiguration conf)`
`static boolean`	IOFunctions.`writeDim(ViewDataBeads view, String directory)`
`static boolean`	IOFunctions.`writeNuclei(ViewDataBeads view, Collection<Nucleus> nuclei, String directory)`
`static boolean`	IOFunctions.`writeNucleiCorrespondences(ViewDataBeads view, String directory)`
`static boolean`	IOFunctions.`writeRegistration(ViewDataBeads view, String directory)`
`static boolean`	IOFunctions.`writeRegistration(ViewDataBeads view, String directory, String extension)`
`static boolean`	IOFunctions.`writeSegmentation(ViewDataBeads view, String directory)`

Uses of ViewDataBeads in mpicbg.spim.mpicbg

Fields in mpicbg.spim.mpicbg declared as ViewDataBeads
Modifier and Type Field and Description

protected ViewDataBeads TileSPIM.parent

Methods in mpicbg.spim.mpicbg that return ViewDataBeads
Modifier and Type Method and Description

ViewDataBeads TileSPIM.getParent()

Constructors in mpicbg.spim.mpicbg with parameters of type ViewDataBeads
Constructor and Description

TileSPIM(M model, ViewDataBeads parent)
Constructor

Fields in mpicbg.spim.mpicbg declared as ViewDataBeads
Modifier and Type	Field and Description
`protected ViewDataBeads`	TileSPIM.`parent`

Methods in mpicbg.spim.mpicbg that return ViewDataBeads
Modifier and Type	Method and Description
`ViewDataBeads`	TileSPIM.`getParent()`

Constructors in mpicbg.spim.mpicbg with parameters of type ViewDataBeads
Constructor and Description
`TileSPIM(M model, ViewDataBeads parent)` Constructor

Uses of ViewDataBeads in mpicbg.spim.postprocessing.deconvolution

Methods in mpicbg.spim.postprocessing.deconvolution with parameters of type ViewDataBeads
Modifier and Type	Method and Description
`protected static Image<FloatType>`	ExtractPSF.`extractPSF(ViewDataBeads view, int[] size)` Extracts the PSF by averaging the local neighborhood RANSAC correspondences

Uses of ViewDataBeads in mpicbg.spim.preprocessing

Methods in mpicbg.spim.preprocessing with parameters of type ViewDataBeads
Modifier and Type	Method and Description
`protected void`	AutomaticAngleSetup.`getCommonAreaPerpendicularViews(ViewDataBeads viewA, ViewDataBeads viewB)`

Uses of ViewDataBeads in mpicbg.spim.registration

Fields in mpicbg.spim.registration with type parameters of type ViewDataBeads
Modifier and Type	Field and Description
`protected ArrayList<ViewDataBeads>`	ViewStructure.`views` The link to the Views

Methods in mpicbg.spim.registration that return ViewDataBeads
Modifier and Type	Method and Description
`ViewDataBeads`	ViewStructure.`getViewFromID(int viewID)` For getting a View with a certain ID

Methods in mpicbg.spim.registration that return types with arguments of type ViewDataBeads
Modifier and Type	Method and Description
`ArrayList<ViewDataBeads>`	ViewStructure.`getViews()` Get the views

Methods in mpicbg.spim.registration with parameters of type ViewDataBeads
Modifier and Type	Method and Description
`int`	ViewDataBeads.`compareTo(ViewDataBeads o)`

Constructor parameters in mpicbg.spim.registration with type arguments of type ViewDataBeads
Constructor and Description
`ViewStructure(ArrayList<ViewDataBeads> views, SPIMConfiguration conf, String id, int timePoint, int numChannels)`
`ViewStructure(ArrayList<ViewDataBeads> views, SPIMConfiguration conf, String id, int timePoint, int numChannels, int debugLevel)`

Uses of ViewDataBeads in mpicbg.spim.registration.bead

Methods in mpicbg.spim.registration.bead with parameters of type ViewDataBeads
Modifier and Type	Method and Description
`static void`	BeadRegistration.`concatenateAxialScaling(ViewDataBeads view, int debugLevel)`
`protected BeadStructure`	BeadSegmentation.`extractBeadsDOM(ViewDataBeads view, SPIMConfiguration conf)` Computes potential beads based on the difference-of-mean (DOM).
`protected BeadStructure`	BeadSegmentation.`extractBeadsLaPlaceImgLib(ViewDataBeads view, SPIMConfiguration conf)`
`protected BeadStructure`	BeadSegmentation.`extractBeadsThresholdSegmentation(ViewDataBeads view, float thresholdI, int minSize, int maxSize, int minBlackBorder)`
`Image<FloatType>`	BeadSegmentation.`getFoundBeads(ViewDataBeads view)`

Method parameters in mpicbg.spim.registration.bead with type arguments of type ViewDataBeads
Modifier and Type	Method and Description
`static void`	BeadRegistration.`computeErrors(ArrayList<ViewDataBeads> views, TileConfigurationSPIM tc)`
`static void`	BeadRegistration.`concatenateAxialScaling(ArrayList<ViewDataBeads> views, int debugLevel)`
`static TileConfigurationSPIM`	BeadRegistration.`optimizeTiles(ArrayList<ViewDataBeads> views, GlobalErrorStatistics errorStatistics, int debugLevel)`
`static TileConfigurationSPIM`	BeadRegistration.`optimizeTiles(ArrayList<ViewDataBeads> views, int numFixed, GlobalErrorStatistics errorStatistics, int debugLevel)`
`void`	BeadSegmentation.`segment(SPIMConfiguration conf, ArrayList<ViewDataBeads> views)`

Constructors in mpicbg.spim.registration.bead with parameters of type ViewDataBeads
Constructor and Description
`Bead(int id, double[] location, ViewDataBeads myView)`
`Bead(int id, Point3d location, ViewDataBeads myView)`
`BeadIdentification(int detectionID, ViewDataBeads view)`

Uses of ViewDataBeads in mpicbg.spim.registration.bead.error

Methods in mpicbg.spim.registration.bead.error that return ViewDataBeads
Modifier and Type	Method and Description
`ViewDataBeads`	ViewErrorPairWise.`getView()`

Methods in mpicbg.spim.registration.bead.error with parameters of type ViewDataBeads
Modifier and Type	Method and Description
`int`	ViewErrorStatistics.`getNumCandidatePairs(ViewDataBeads otherView)` Returns the number of correspondence candidate pairs this view shares with another view
`int`	ViewErrorStatistics.`getNumTrueCorrespondencePairs(ViewDataBeads otherView)` Returns the number of true correspondence pairs this view shares with another view
`double`	ViewErrorStatistics.`getViewSpecificError(ViewDataBeads otherView)`
`void`	ViewErrorStatistics.`resetViewSpecificError(ViewDataBeads otherView)`
`void`	ViewErrorStatistics.`setViewConnected(ViewDataBeads otherView, boolean newStatus)`
`void`	ViewErrorStatistics.`setViewError(ViewDataBeads otherView, double error)`
`void`	ViewErrorStatistics.`setViewSpecificError(ViewDataBeads otherView, double error)`

Constructors in mpicbg.spim.registration.bead.error with parameters of type ViewDataBeads
Constructor and Description
`ViewErrorPairWise(ViewDataBeads view)`
`ViewErrorStatistics(ViewDataBeads view)`

Uses of ViewDataBeads in mpicbg.spim.registration.detection

Fields in mpicbg.spim.registration.detection declared as ViewDataBeads
Modifier and Type	Field and Description
`protected ViewDataBeads`	DetectionView.`myView`
`protected ViewDataBeads`	DetectionIdentification.`view`

Methods in mpicbg.spim.registration.detection that return ViewDataBeads
Modifier and Type	Method and Description
`ViewDataBeads`	DetectionView.`getView()`
`ViewDataBeads`	DetectionIdentification.`getView()` Returns the `ViewDataBeads` object of the view it belongs to.

Constructors in mpicbg.spim.registration.detection with parameters of type ViewDataBeads
Constructor and Description
`DetectionIdentification(int detectionID, ViewDataBeads view)` This constructor is used when a BeadIdenfication object is initialized from a file where only the BeadID and the `ViewDataBeads` are known.
`DetectionView(int id, double[] location, ViewDataBeads myView)`

Uses of ViewDataBeads in mpicbg.spim.registration.detection.descriptor

Constructors in mpicbg.spim.registration.detection.descriptor with parameters of type ViewDataBeads
Constructor and Description
`SparseCorrespondenceExtraction(ViewDataBeads viewA, ViewDataBeads viewB, M model)`

Uses of ViewDataBeads in mpicbg.spim.registration.segmentation

Constructors in mpicbg.spim.registration.segmentation with parameters of type ViewDataBeads
Constructor and Description
`Nucleus(int id, double[] location, ViewDataBeads myView)`
`NucleusIdentification(int detectionID, ViewDataBeads view)`

Uses of ViewDataBeads in mpicbg.spim.vis3d

Methods in mpicbg.spim.vis3d with parameters of type ViewDataBeads
Modifier and Type	Method and Description
`protected String`	VisualizeBeads.`drawFalseCorrespondences(ViewDataBeads view, ViewDataBeads correspondingView, float factor)`
`protected String`	VisualizeBeads.`drawPointDescriptorCorrespondences(ViewDataBeads view, ViewDataBeads correspondingView, float factor)`
`protected String`	VisualizeBeads.`drawRANSACCorrespondences(ViewDataBeads view, ViewDataBeads correspondingView, float factor)`
`static String`	VisualizationSketchTikZ.`drawView(ViewDataBeads view, double factor)`
`static String`	VisualizationSketchTikZ.`drawViews(ViewDataBeads[] views, float factor)`
`static ArrayList<Point3f>`	VisualizationFunctions.`getBoundingBox(ViewDataBeads view)`
`static ArrayList<Point3f>`	VisualizationFunctions.`getTransformedBoundingBox(ViewDataBeads view)`

Method parameters in mpicbg.spim.vis3d with type arguments of type ViewDataBeads
Modifier and Type	Method and Description
`protected String`	VisualizeBeads.`drawAllFalseCorrespondences(ArrayList<ViewDataBeads> views, float factor)`
`protected String`	VisualizeBeads.`drawAllRANSACCorrespondences(ArrayList<ViewDataBeads> views, float factor)`

Uses of Classmpicbg.spim.registration.ViewDataBeads

Uses of ViewDataBeads in mpicbg.spim

Uses of ViewDataBeads in mpicbg.spim.fusion

Uses of ViewDataBeads in mpicbg.spim.io

Uses of ViewDataBeads in mpicbg.spim.mpicbg

Uses of ViewDataBeads in mpicbg.spim.postprocessing.deconvolution

Uses of ViewDataBeads in mpicbg.spim.preprocessing

Uses of ViewDataBeads in mpicbg.spim.registration

Uses of ViewDataBeads in mpicbg.spim.registration.bead

Uses of ViewDataBeads in mpicbg.spim.registration.bead.error

Uses of ViewDataBeads in mpicbg.spim.registration.detection

Uses of ViewDataBeads in mpicbg.spim.registration.detection.descriptor

Uses of ViewDataBeads in mpicbg.spim.registration.segmentation

Uses of ViewDataBeads in mpicbg.spim.vis3d

Uses of Class
mpicbg.spim.registration.ViewDataBeads