Uses of Class
deformablemesh.track.Track

Packages that use Track

Package	Description
deformablemesh
deformablemesh.examples
deformablemesh.gui.render2d
deformablemesh.io
deformablemesh.meshview
deformablemesh.track
deformablemesh.util

Uses of Track in deformablemesh

Methods in deformablemesh that return Track

Modifier and Type	Method and Description
Track	SegmentationController.getSelectedMeshTrack()
Track	SegmentationModel.getSelectedTrack()
Track	SegmentationModel.startEmptyTrack() Starts a track that is not used but has a name unique to the existing tracks.
Track	SegmentationModel.startMeshTrack(int frame, DeformableMesh3D freshMesh)

Methods in deformablemesh that return types with arguments of type Track

Modifier and Type	Method and Description
List<Track>	SegmentationModel.getAllTracks()
List<Track>	SegmentationController.getAllTracks()

Methods in deformablemesh with parameters of type Track

Modifier and Type	Method and Description
void	SegmentationModel.addMeshToTrack(int f, DeformableMesh3D mesh, Track track)
void	SegmentationModel.addMeshTrack(Track track)
void	SegmentationController.addTracer(Track t) Addes a line that follows the center of mass of the provided mesh track to the current frame.
void	SegmentationModel.calculateInterfaceLineScan(Track track)
void	SegmentationController.clearMeshFromTrack(Track t, int f)
void	SegmentationController.clearMeshFromTrack(Track old, int f, DeformableMesh3D mesh) Clears the mesh specified mesh from the track at the specific time frame.
void	SegmentationController.reMeshConnections(Track track, int frame, double minConnectionLength, double maxConnectionLength) Remeshes the current track by using the remesh connection algorithm.
void	SegmentationModel.removeMeshFromTrack(int frame, DeformableMesh3D mesh, Track track)
void	SegmentationModel.removeMeshTrack(Track track)
void	SegmentationModel.selectMeshTrack(Track track)
void	SegmentationController.selectMeshTrack(Track track) Overload for convenience.
void	SegmentationController.setMesh(Track track, int frame, DeformableMesh3D mesh) Sets the provided mesh to be the mesh for the provided track at the specified frame.
void	SegmentationController.trackMesh(Track track, int frame) Extands the track to (frame + 1) provided by copying the deformable mesh at frame.

Method parameters in deformablemesh with type arguments of type Track

Modifier and Type	Method and Description
void	SegmentationModel.calculateInterfaceLineScan(int index, List<Track> tracks)
void	SegmentationController.createLabelledImage(List<Track> tracks) Creates a labelled image of the provided tracks.
static ij.ImagePlus	DeformableMesh3DTools.createMosaicRepresentation(MeshImageStack stack, ij.ImagePlus original_plus, List<Track> allMeshTracks)
static ij.ImagePlus	DeformableMesh3DTools.createUniqueLabelsRepresentation(MeshImageStack stack, List<Track> allMeshTracks)
void	SegmentationController.lumpImports(List<Track> imports) Groups all of the meshes into the current frame.
void	SegmentationController.relateImports(List<Track> imports) Finds the earliest mesh frame, aligns that to the current frame
void	SegmentationController.selectImports(List<Track> imports) Reduces the provided meshes to only meshes in the currently selected frame.
void	SegmentationModel.setMeshes(List<Track> meshes)
void	SegmentationController.setMeshes(List<Track> tracks, int frame, List<DeformableMesh3D> meshes) Adds all of the provided meshes to the corresponding track.
void	SegmentationController.setMeshTracks(List<Track> replacements) Replaces the current tracks with the provided.

Uses of Track in deformablemesh.examples

Method parameters in deformablemesh.examples with type arguments of type Track

Modifier and Type	Method and Description
ij.ImagePlus	CreateCrossSectionMovies.threeDVersion(List<Track> solid, List<Track> outlines, int dw, int dh)
ij.ImagePlus	CreateCrossSectionMovies.threeDVersion(List<Track> solid, List<Track> outlines, int dw, int dh)

Uses of Track in deformablemesh.gui.render2d

Method parameters in deformablemesh.gui.render2d with type arguments of type Track

Modifier and Type	Method and Description
void	RenderFrame2D.setTracks(List<Track> tracks)

Uses of Track in deformablemesh.io

Methods in deformablemesh.io that return types with arguments of type Track

Modifier and Type	Method and Description
static List<Track>	TrackMateAdapter.applyTracking(List<Track> tracks, MeshImageStack mis, Path trackMateFile) Takes the provided Tracks for the provided image file and attempts to link them based on associated positions.
static List<Track>	TrackMateAdapter.createSpotList(Model model, MeshImageStack geometry)
static List<Track>	TrackMateAdapter.importTrackMateFile(MeshImageStack mis, Path trackMateFile)
static List<Track>	TrackMateAdapter.importTrackMateFile(Path image, Path trackMateFile) Overload in case the image hasn't been loaded yet.
List<Track>	MeshReader.loadMeshes()
static List<Track>	MeshReader.loadMeshes(File input)

Method parameters in deformablemesh.io with type arguments of type Track

Modifier and Type	Method and Description
static List<Track>	TrackMateAdapter.applyTracking(List<Track> tracks, MeshImageStack mis, Path trackMateFile) Takes the provided Tracks for the provided image file and attempts to link them based on associated positions.
static void	MeshWriter.exportToPly(File output, List<Track> tracks, int frame, double[] offsets, double scale) Save all of the tracks contained in the current frame.
static void	MeshWriter.exportToStlWireframe(File output, List<Track> tracks, double[] offset, double SCALE, Integer frame)
static void	TrackMateAdapter.saveAsTrackMateFile(MeshImageStack stack, List<Track> tracks, Path destination)
static void	MeshWriter.saveMeshes(File output, List<Track> tracks)
static void	MeshWriter.saveStlMesh(File output, List<Track> tracks, double[] offset, double SCALE, Integer frame) Saves the current mesh to an ascii

Uses of Track in deformablemesh.meshview

Methods in deformablemesh.meshview with parameters of type Track

Modifier and Type	Method and Description
void	MeshViewer.addMeshTrack(Track track)

Uses of Track in deformablemesh.track

Methods in deformablemesh.track that return Track

Modifier and Type	Method and Description
Track	MeshTracker.createNewMeshTrack(int frame, DeformableMesh3D freshMesh) Creates a new track, adds the provided mesh, adds it to the tracked tracks, and selects it.
Track	MeshTracker.getSelectedTrack()
Track	MeshTrackManager.getSelectedTrack()
Track	MeshTrackManager.getTrackAtColumn(int column)
Track	MeshTracker.prepareEmptyTrack()

Methods in deformablemesh.track that return types with arguments of type Track

Modifier and Type	Method and Description
List<Track>	MeshTracker.getAllMeshTracks()
List<Track>	MeshTrackManager.getTracks()
List<Track>	MeshTracker.prepareEmptyTracks(int n) Returns n tracks with a name that is not contained in the current set of tracks names.

Methods in deformablemesh.track with parameters of type Track

Modifier and Type	Method and Description
void	MeshTracker.addMeshToTrack(int f, DeformableMesh3D mesh, Track track)
void	MeshTracker.addTrack(Track track)
void	MeshTracker.removeMeshFromTrack(int frame, DeformableMesh3D mesh, Track track)
void	MeshTracker.removeTrack(Track track)
void	MeshTracker.selectMeshTrack(Track track)

Method parameters in deformablemesh.track with type arguments of type Track

Modifier and Type	Method and Description
void	MeshTracker.addMeshTracks(List<Track> meshes)
void	FrameToFrameDisplacement.calculateCenterOfMass(List<Track> tracks) Calculates the center of mass based on the provided tracks.

Uses of Track in deformablemesh.util

Methods in deformablemesh.util that return types with arguments of type Track

Modifier and Type	Method and Description
static List<Track>	GroupDynamics.steppingMeshes(List<Track> tracks, int i)

Methods in deformablemesh.util with parameters of type Track

Modifier and Type	Method and Description
static List<double[]>	MeshFaceObscuring.analyzeTracks(Track target, List<Track> others, double cutoff) Analyzes the provided tracks.

Method parameters in deformablemesh.util with type arguments of type Track

Modifier and Type	Method and Description
static void	MeshFaceObscuring.analyzeTimeCourses(List<Track> tracks, String meshFileName)
static void	MeshFaceObscuring.analyzeTracks(List<Track> tracks, MeshImageStack stack, int frame, double cutoff)
static List<double[]>	MeshFaceObscuring.analyzeTracks(Track target, List<Track> others, double cutoff) Analyzes the provided tracks.
static void	MeshAnalysis.calculateAllVolumes(List<Track> tracks, MeshImageStack stack) Generates a text window with the time series for all of the tracks provided.
static List<DeformableMesh3D>	GroupDynamics.getMeshInFrame(List<Track> tracks, int i)
static void	MeshAnalysis.plotDisplacementHistogram(List<Track> tracks, MeshImageStack meshImageStack)
static void	MeshAnalysis.plotDisplacementsVsTime(List<Track> tracks, MeshImageStack meshImageStack)
static void	MeshAnalysis.plotElongationsVsTime(List<Track> tracks)
static void	MeshAnalysis.plotMeshesOverTime(List<Track> tracks, MeshImageStack mis) Plots the number of meshes over time.
static void	TrackAnalysis.plotNextFrameTrackingResults(List<Track> tracks, int frame)
static void	MeshAnalysis.plotVolumesOverTime(List<Track> tracks, MeshImageStack mis) Creates a plot of the volumes over time.
static List<Track>	GroupDynamics.steppingMeshes(List<Track> tracks, int i)

Constructor parameters in deformablemesh.util with type arguments of type Track

Constructor and Description
Create3DTrainingDataFromMeshes(List<Track> tracks, ij.ImagePlus plus)