Uses of Class
deformablemesh.MeshImageStack

Packages that use MeshImageStack

Package	Description
deformablemesh
deformablemesh.externalenergies
deformablemesh.geometry
deformablemesh.gui
deformablemesh.gui.meshinitialization
deformablemesh.io
deformablemesh.meshview
deformablemesh.ringdetection
deformablemesh.simulations
deformablemesh.util
deformablemesh.util.connectedcomponents

Uses of MeshImageStack in deformablemesh

Subclasses of MeshImageStack in deformablemesh

Modifier and Type	Class and Description
class	MeshImageSubStack Created by smithm3 on 20/02/18.

Methods in deformablemesh that return MeshImageStack

Modifier and Type	Method and Description
static MeshImageStack	MeshImageStack.getEmptyStack()
MeshImageStack	SegmentationController.getMeshImageStack() Gets the currently selected MeshImageStack.

Methods in deformablemesh with parameters of type MeshImageStack

Modifier and Type	Method and Description
static double	DeformableMesh3DTools.calculateAverageIntensity(MeshImageStack stack, List<Triangle3D> triangles, double thickness)
static double	DeformableMesh3DTools.calculateIntensity(Box3D bound, MeshImageStack stack)
static ij.ImagePlus	DeformableMesh3DTools.createBinaryRepresentation(MeshImageStack stack, DeformableMesh3D mesh)
static ij.ImagePlus	DeformableMesh3DTools.createBinaryRepresentation(MeshImageStack stack, ij.ImagePlus original, Map<Integer,DeformableMesh3D> meshes)
static ij.ImagePlus	DeformableMesh3DTools.createMosaicRepresentation(MeshImageStack stack, ij.ImagePlus original_plus, List<Track> allMeshTracks)
static ij.ImagePlus	DeformableMesh3DTools.createUniqueLabelsRepresentation(MeshImageStack stack, List<Track> allMeshTracks)
static List<int[]>	DeformableMesh3DTools.getContainedPixels(MeshImageStack stack, DeformableMesh3D mesh) Get pixels contained in the mesh.
static void	DeformableMesh3DTools.mosaicBinary(MeshImageStack stack, ij.ImageStack out, DeformableMesh3D mesh, int rgb)

Constructors in deformablemesh with parameters of type MeshImageStack

Constructor and Description
MeshDetector(MeshImageStack mis)
MeshImageSubStack(Box3D region, MeshImageStack backing, ij.ImagePlus sample)

Uses of MeshImageStack in deformablemesh.externalenergies

Constructors in deformablemesh.externalenergies with parameters of type MeshImageStack

Constructor and Description
GradientEnergy(MeshImageStack stack, double image_weight)
IntensityEnergy(MeshImageStack stack, double image_weight)
PerpendicularGradientEnergy(MeshImageStack stack, DeformableMesh3D mesh, double weight)
PerpendicularIntensityEnergy(MeshImageStack stack, DeformableMesh3D mesh, double weight)
TriangleAreaDistributor(MeshImageStack stack, DeformableMesh3D mesh, double weight)

Uses of MeshImageStack in deformablemesh.geometry

Methods in deformablemesh.geometry with parameters of type MeshImageStack

Modifier and Type	Method and Description
ArrayList<double[]>	DeformableMesh3D.calculateIntensity(MeshImageStack stack, double thickness) Thickness is in um.
ArrayList<double[]>	DeformableMesh3D.calculateNormalScan(MeshImageStack stack, double thickness)
void	Furrow3D.createTexturedPlane3DObject(MeshImageStack mis)
static DeformableMesh3D	BinaryMeshGenerator.generateVoxelPlane(MeshImageStack stack, int[] px, double[] normal)
static DeformableMesh3D	BinaryMeshGenerator.remesh(DeformableMesh3D mesh, MeshImageStack stack)
static DeformableMesh3D	RayCastMesh.sphericalRayCastBinaryStack(MeshImageStack stack, int divisions)

Constructors in deformablemesh.geometry with parameters of type MeshImageStack

Constructor and Description
BinaryInterceptible(List<int[]> pixels, MeshImageStack stack, int label)
BinaryMomentsOfInertia(DeformableMesh3D mesh, MeshImageStack stack)

Uses of MeshImageStack in deformablemesh.gui

Methods in deformablemesh.gui with parameters of type MeshImageStack

Modifier and Type	Method and Description
void	RingController.loadImage(MeshImageStack stack)
void	RingController.setStack(MeshImageStack stack)
void	RingController.writeFurrows(File f, MeshImageStack stack)

Uses of MeshImageStack in deformablemesh.gui.meshinitialization

Constructors in deformablemesh.gui.meshinitialization with parameters of type MeshImageStack

Constructor and Description
SlicePicker(MeshImageStack s, double[] normal, double[] center)

Uses of MeshImageStack in deformablemesh.io

Methods in deformablemesh.io with parameters of type MeshImageStack

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 double[]	TrackMateAdapter.getCenterRealCoordinates(DeformableMesh3D mesh, MeshImageStack stack) Uses the same algorithm that is used to get the real coordinates for spot/track generation.
static List<Track>	TrackMateAdapter.importTrackMateFile(MeshImageStack mis, Path trackMateFile)
static Map<Integer,Furrow3D>	FurrowWriter.loadFurrows(File f, MeshImageStack stack)
static void	TrackMateAdapter.saveAsTrackMateFile(MeshImageStack stack, List<Track> tracks, Path destination)
static void	FurrowWriter.writeFurrows(File f, MeshImageStack stack, ContractileRingDetector detector)

Uses of MeshImageStack in deformablemesh.meshview

Methods in deformablemesh.meshview that return MeshImageStack

Modifier and Type	Method and Description
MeshImageStack	TexturedPlaneDataObject.getMeshImageStack()

Methods in deformablemesh.meshview with parameters of type MeshImageStack

Modifier and Type	Method and Description
void	VolumeDataObject.setTextureData(MeshImageStack stack) For creating a volume representing the all of the pixes of the provided mesh image stack.
void	TexturedPlaneDataObject.setTextureData(MeshImageStack stack)
void	VolumeDataObject.setTextureData(MeshImageStack stack, List<int[]> pts) For creating a volume that shows part of an image stack.
void	MeshFrame3D.showEnergy(MeshImageStack stack, ExternalEnergy erg)
void	MeshFrame3D.showVolume(MeshImageStack stack) Backs the volume texture date with the supplied image stack.

Constructors in deformablemesh.meshview with parameters of type MeshImageStack

Constructor and Description
ChannelVolume(MeshImageStack stack, Color c)
TexturedPlaneDataObject(DeformableMesh3D mesh, MeshImageStack stack)

Uses of MeshImageStack in deformablemesh.ringdetection

Methods in deformablemesh.ringdetection with parameters of type MeshImageStack

Modifier and Type	Method and Description
void	ContractileRingDetector.setImageStack(MeshImageStack stack)

Constructors in deformablemesh.ringdetection with parameters of type MeshImageStack

Constructor and Description
FurrowTransformer(Furrow3D furrow, MeshImageStack stack)

Uses of MeshImageStack in deformablemesh.simulations

Methods in deformablemesh.simulations with parameters of type MeshImageStack

Modifier and Type	Method and Description
static DeformableMesh3D	FillingBinaryImage.fillBinaryWithMesh(MeshImageStack stack, List<int[]> points)

Constructors in deformablemesh.simulations with parameters of type MeshImageStack

Constructor and Description
FillingBinaryImage(MeshImageStack mis, List<DeformableMesh3D> meshes)

Uses of MeshImageStack in deformablemesh.util

Methods in deformablemesh.util with parameters of type MeshImageStack

Modifier and Type	Method and Description
static void	MeshFaceObscuring.analyzeTracks(List<Track> tracks, MeshImageStack stack, int frame, double cutoff)
static void	MeshAnalysis.calculateAllVolumes(List<Track> tracks, MeshImageStack stack) Generates a text window with the time series for all of the tracks provided.
static void	MeshAnalysis.plotDisplacementHistogram(List<Track> tracks, MeshImageStack meshImageStack)
static void	MeshAnalysis.plotDisplacementsVsTime(List<Track> tracks, MeshImageStack meshImageStack)
static void	MeshAnalysis.plotMeshesOverTime(List<Track> tracks, MeshImageStack mis) Plots the number of meshes over time.
static void	MeshAnalysis.plotVolumesOverTime(List<Track> tracks, MeshImageStack mis) Creates a plot of the volumes over time.

Constructors in deformablemesh.util with parameters of type MeshImageStack

Constructor and Description
IntensitySurfacePlot(DeformableMesh3D mesh, MeshImageStack stack)
MeshAnalysis(Map<Integer,DeformableMesh3D> meshes, Map<Integer,Furrow3D> furrows, MeshImageStack stack)

Uses of MeshImageStack in deformablemesh.util.connectedcomponents

Methods in deformablemesh.util.connectedcomponents with parameters of type MeshImageStack

Modifier and Type	Method and Description
DataObject	Region.getDataObject(MeshImageStack stack)
List<DeformableMesh3D>	BoxRegionConnectedComponents.guessMeshes(MeshImageStack stack)