Uses of Class
deformablemesh.geometry.DeformableMesh3D

Packages that use DeformableMesh3D

Package	Description
deformablemesh
deformablemesh.externalenergies
deformablemesh.geometry
deformablemesh.geometry.modifier
deformablemesh.gui.meshinitialization
deformablemesh.gui.render2d
deformablemesh.io
deformablemesh.meshview
deformablemesh.simulations
deformablemesh.track
deformablemesh.util
deformablemesh.util.connectedcomponents

Uses of DeformableMesh3D in deformablemesh

Methods in deformablemesh that return DeformableMesh3D

Modifier and Type	Method and Description
DeformableMesh3D	SegmentationController.copyMesh(DeformableMesh3D mesh) Creates a copy of the provided mesh.
static DeformableMesh3D	DeformableMesh3DTools.copyOf(DeformableMesh3D mesh)
static DeformableMesh3D	DeformableMesh3DTools.createRectangleMesh(double width, double height, double depth, double segment_size) Makes a rectangular prism mesh with triangular elements.
static DeformableMesh3D	DeformableMesh3DTools.createRhombicDodecahedron(double l)
DeformableMesh3D	SegmentationModel.createSubMesh(DeformableMesh3D mesh, Set<Triangle3D> triangles)
static DeformableMesh3D	DeformableMesh3DTools.createTestBlock() Creates a 2x2x2 test block.
static DeformableMesh3D	DeformableMesh3DTools.createTestBlock(double w, double h, double depth) -w/2,-h/2, d/2 0------------------1 / /| / / | / | / | 3------------------2 | | 4- - - - | -5 | / | / | | / | |/ 7------------------6 w/2,h/2, -d/2
DeformableMesh3D	SegmentationController.getMesh()
DeformableMesh3D	SegmentationController.getSelectedMesh()
DeformableMesh3D	SegmentationModel.getSelectedMesh(int frame)
static DeformableMesh3D	DeformableMesh3DTools.mergeMeshes(List<DeformableMesh3D> meshes) Each mesh is constructed of 3 essential data values: positions, triangles, connections.

Methods in deformablemesh with parameters of type DeformableMesh3D

Modifier and Type	Method and Description
void	SegmentationController.addMesh(DeformableMesh3D m) Adds the mesh to the currently selected track.
void	SegmentationController.addMesh(int frame, DeformableMesh3D m) Adds the provided mesh to the model.
void	SegmentationModel.addMeshToTrack(int f, DeformableMesh3D mesh, Track track)
static double	DeformableMesh3DTools.calculateSurfaceArea(DeformableMesh3D mesh)
void	SegmentationController.clearMesh(DeformableMesh3D mesh) Least efficient way to clear a mesh.
void	SegmentationController.clearMeshFromTrack(Track old, int f, DeformableMesh3D mesh) Clears the mesh specified mesh from the track at the specific time frame.
void	SegmentationController.confineMesh(DeformableMesh3D mesh) If a point is outside of the boundary, it is moved to the edge along that axis.
DeformableMesh3D	SegmentationController.copyMesh(DeformableMesh3D mesh) Creates a copy of the provided mesh.
static DeformableMesh3D	DeformableMesh3DTools.copyOf(DeformableMesh3D mesh)
static ij.ImagePlus	DeformableMesh3DTools.createBinaryRepresentation(MeshImageStack stack, DeformableMesh3D mesh)
DeformableMesh3D	SegmentationModel.createSubMesh(DeformableMesh3D mesh, Set<Triangle3D> triangles)
void	SegmentationModel.deformMesh(DeformableMesh3D mesh) Deforms the provided mesh using the prepared energies and values.
static List<List<Node3D>>	DeformableMesh3DTools.generateConnectionMap(DeformableMesh3D mesh)
ExternalEnergy	SegmentationModel.generateImageEnergy(DeformableMesh3D mesh)
static List<int[]>	DeformableMesh3DTools.getContainedPixels(MeshImageStack stack, DeformableMesh3D mesh) Get pixels contained in the mesh.
List<ExternalEnergy>	SegmentationModel.getExternalEnergies(DeformableMesh3D selectedMesh)
void	SegmentationController.initializeMesh(DeformableMesh3D mesh) For creating a new mesh, if there is a currently selected mesh in the current frame, this starts a new mesh track.
static void	DeformableMesh3DTools.mosaicBinary(MeshImageStack stack, ij.ImageStack out, DeformableMesh3D mesh, int rgb)
void	SegmentationModel.removeMeshFromTrack(int frame, DeformableMesh3D mesh, Track track)
void	SegmentationController.selectMesh(DeformableMesh3D mesh) Attempts to select the track that contains the provided mesh.
void	SegmentationModel.selectTrackWithMesh(DeformableMesh3D mesh)
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.showForces(DeformableMesh3D mesh) Creates a set of vectors to show how the mesh will deform based on the image energy and external forces.
Track	SegmentationModel.startMeshTrack(int frame, DeformableMesh3D freshMesh)
void	SegmentationController.startNewMeshTrack(int frame, DeformableMesh3D mesh) Starts a new mesh track with one mesh on the specified frame.

Method parameters in deformablemesh with type arguments of type DeformableMesh3D

Modifier and Type	Method and Description
static ij.ImagePlus	DeformableMesh3DTools.createBinaryRepresentation(MeshImageStack stack, ij.ImagePlus original, Map<Integer,DeformableMesh3D> meshes)
void	SegmentationModel.deformMeshes(List<DeformableMesh3D> meshes, int steps) A generic method for deforming all of the meshes provided.
static DeformableMesh3D	DeformableMesh3DTools.mergeMeshes(List<DeformableMesh3D> meshes) Each mesh is constructed of 3 essential data values: positions, triangles, connections.
void	SegmentationController.setMeshes(List<Track> tracks, int frame, List<DeformableMesh3D> meshes) Adds all of the provided meshes to the corresponding track.
void	SegmentationController.startNewMeshTracks(List<DeformableMesh3D> meshes) Starts a new Track for each of provided meshes.

Uses of DeformableMesh3D in deformablemesh.externalenergies

Constructors in deformablemesh.externalenergies with parameters of type DeformableMesh3D

Constructor and Description
BallooningEnergy(Interceptable constraint, DeformableMesh3D mesh, double weight)
PerpendicularGradientEnergy(MeshImageStack stack, DeformableMesh3D mesh, double weight)
PerpendicularIntensityEnergy(MeshImageStack stack, DeformableMesh3D mesh, double weight)
PressureForce(DeformableMesh3D mesh, double pressure)
SmoothingForce(DeformableMesh3D mesh, double magnitude)
SofterStericMesh(DeformableMesh3D id, DeformableMesh3D neighbor, double weight)
StericMesh(DeformableMesh3D id, DeformableMesh3D neighbor, double weight)
TriangleAreaDistributor(MeshImageStack stack, DeformableMesh3D mesh, double weight)
VolumeConservation(DeformableMesh3D mesh, double weight)

Uses of DeformableMesh3D in deformablemesh.geometry

Subclasses of DeformableMesh3D in deformablemesh.geometry

Modifier and Type	Class and Description
class	NewtonMesh3D Created by msmith on 3/4/16.

Methods in deformablemesh.geometry that return DeformableMesh3D

Modifier and Type	Method and Description
DeformableMesh3D	DeformableMesh3D.createSubMesh(List<Node3D> nodes) Creates a mesh consisting of all the provided nodes, and their immediate neighbors.
static DeformableMesh3D	RayCastMesh.fiveTriangleSphere()
static DeformableMesh3D	BinaryMeshGenerator.generateVoxelPlane(MeshImageStack stack, int[] px, double[] normal)
DeformableMesh3D	ProjectableMesh.getMesh()
static DeformableMesh3D	BinaryMeshGenerator.getQuad(double[] origin, double[] nx, double[] ny)
DeformableMesh3D	ShellMesh.getShellMesh()
DeformableMesh3D	WireframeMesh.getWireFrameMesh()
static DeformableMesh3D	DeformableMesh3D.loadMesh(double[] positions, int[] connection_indices, int[] triangle_indices)
static DeformableMesh3D	RayCastMesh.rayCastMesh(Interceptable object, double[] origin, int divisions)
static DeformableMesh3D	RayCastMesh.rayCastMesh(List<Interceptable> objects, double[] origin, int divisions) Checks for interceptsion of all of the included objects.
DeformableMesh3D	ConnectionRemesher.remesh(DeformableMesh3D original)
static DeformableMesh3D	BinaryMeshGenerator.remesh(DeformableMesh3D mesh, MeshImageStack stack)
static DeformableMesh3D	RayCastMesh.sixTriangleSphere()
static DeformableMesh3D	RayCastMesh.sphereRayCastMesh(int divisions)
static DeformableMesh3D	RayCastMesh.sphericalRayCastBinaryStack(MeshImageStack stack, int divisions)

Methods in deformablemesh.geometry with parameters of type DeformableMesh3D

Modifier and Type	Method and Description
static double	CurvatureCalculator.calculateAverageCurvature(DeformableMesh3D sharedFaces) Calculates the average kappaH value for the whole mesh.
void	ConnectionRemesher.prepareWorkSpace(DeformableMesh3D original)
DeformableMesh3D	ConnectionRemesher.remesh(DeformableMesh3D original)
static DeformableMesh3D	BinaryMeshGenerator.remesh(DeformableMesh3D mesh, MeshImageStack stack)
void	SpherePathTesting.setMesh(DeformableMesh3D mesh)
static void	RayCastMesh.subDivideMesh(DeformableMesh3D mesh) Quadruple the number of triangles in a mesh.

Constructors in deformablemesh.geometry with parameters of type DeformableMesh3D

Constructor and Description
BinaryMomentsOfInertia(DeformableMesh3D mesh, MeshImageStack stack)
CurvatureCalculator(DeformableMesh3D mesh)
InterceptingMesh3D(DeformableMesh3D mesh)
NewtonMesh3D(DeformableMesh3D mesh)
ProjectableMesh(DeformableMesh3D mesh)
ShellMesh(DeformableMesh3D mesh)
WireframeMesh(DeformableMesh3D mesh)

Uses of DeformableMesh3D in deformablemesh.geometry.modifier

Methods in deformablemesh.geometry.modifier that return DeformableMesh3D

Modifier and Type	Method and Description
DeformableMesh3D	MeshModifier.getMesh()
DeformableMesh3D	MeshModifier.getOriginalMesh()

Methods in deformablemesh.geometry.modifier with parameters of type DeformableMesh3D

Modifier and Type	Method and Description
void	MeshModifier.setMesh(DeformableMesh3D mesh)

Uses of DeformableMesh3D in deformablemesh.gui.meshinitialization

Methods in deformablemesh.gui.meshinitialization that return DeformableMesh3D

Modifier and Type	Method and Description
static DeformableMesh3D	CircularMeshInitializationDialog.createMeshFromSpheres(List<Sphere> spheres, int divisions)
DeformableMesh3D	CircularMeshInitializationDialog.fillSpheresWithMesh(List<Sphere> spheres, DeformableMesh3D mesh, double min, double max)

Methods in deformablemesh.gui.meshinitialization with parameters of type DeformableMesh3D

Modifier and Type	Method and Description
void	SlicePicker.addProjectableMesh(ProjectableMesh pm, DeformableMesh3D mesh)
DeformableMesh3D	CircularMeshInitializationDialog.fillSpheresWithMesh(List<Sphere> spheres, DeformableMesh3D mesh, double min, double max)

Uses of DeformableMesh3D in deformablemesh.gui.render2d

Method parameters in deformablemesh.gui.render2d with type arguments of type DeformableMesh3D

Modifier and Type	Method and Description
void	RaycastRender.setMeshes(List<DeformableMesh3D> meshes)

Uses of DeformableMesh3D in deformablemesh.io

Methods in deformablemesh.io with parameters of type DeformableMesh3D

Modifier and Type	Method and Description
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 void	MeshWriter.saveMesh(String filename, DeformableMesh3D mesh)
void	MeshWriter.write(DeformableMesh3D mesh, Integer frame)
static void	MeshWriter.writeMesh(DataOutput dos, DeformableMesh3D mesh, int frame)

Method parameters in deformablemesh.io with type arguments of type DeformableMesh3D

Modifier and Type	Method and Description
static void	MeshWriter.legacySaveMeshes(File output, Map<Integer,DeformableMesh3D> meshes)

Uses of DeformableMesh3D in deformablemesh.meshview

Constructors in deformablemesh.meshview with parameters of type DeformableMesh3D

Constructor and Description
TexturedPlaneDataObject(DeformableMesh3D mesh, MeshImageStack stack)
VectorField(DeformableMesh3D mesh)
VectorField(DeformableMesh3D mesh, List<ExternalEnergy> energies)

Uses of DeformableMesh3D in deformablemesh.simulations

Methods in deformablemesh.simulations that return DeformableMesh3D

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

Methods in deformablemesh.simulations with parameters of type DeformableMesh3D

Modifier and Type	Method and Description
void	GrowingDroplet.addMesh(DeformableMesh3D mesh)
void	ManyDrops.prepareEnergies(DeformableMesh3D mesh)
void	TwoDrops.stickVertexes(DeformableMesh3D a, DeformableMesh3D b)
void	TwoDrops.stickyCell(DeformableMesh3D sticky, DeformableMesh3D neighbor)

Constructor parameters in deformablemesh.simulations with type arguments of type DeformableMesh3D

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

Uses of DeformableMesh3D in deformablemesh.track

Methods in deformablemesh.track that return DeformableMesh3D

Modifier and Type	Method and Description
DeformableMesh3D	Track.getMesh(Integer i)
DeformableMesh3D	MeshTracker.getSelectedMesh(int frame)

Methods in deformablemesh.track that return types with arguments of type DeformableMesh3D

Modifier and Type	Method and Description
List<DeformableMesh3D>	MeshTracker.getCurrent(int frame)
Map<Integer,DeformableMesh3D>	Track.getTrack() Legacy method that returns a duplicate map that represents the time vs.

Methods in deformablemesh.track with parameters of type DeformableMesh3D

Modifier and Type	Method and Description
void	MeshTracker.addMesh(int frame, DeformableMesh3D replacementMesh) Adds a mesh to the currently selected.
void	Track.addMesh(Integer i, DeformableMesh3D mesh)
void	MeshTracker.addMeshToTrack(int f, DeformableMesh3D mesh, Track track)
boolean	Track.containsMesh(DeformableMesh3D mesh)
Track	MeshTracker.createNewMeshTrack(int frame, DeformableMesh3D freshMesh) Creates a new track, adds the provided mesh, adds it to the tracked tracks, and selects it.
int	Track.getFrame(DeformableMesh3D mesh)
void	Track.remove(DeformableMesh3D mesh)
void	MeshTracker.removeMeshFromTrack(int frame, DeformableMesh3D mesh, Track track)
void	MeshTracker.selectTrackContainingMesh(DeformableMesh3D mesh) changes the selected track to the track containing the mesh.

Method parameters in deformablemesh.track with type arguments of type DeformableMesh3D

Modifier and Type	Method and Description
static double[][]	FrameToFrameDisplacement.boundingBoxJaccardIndexMatrix(List<DeformableMesh3D> one, List<DeformableMesh3D> two)
static double[][]	FrameToFrameDisplacement.boundingBoxJaccardIndexMatrix(List<DeformableMesh3D> one, List<DeformableMesh3D> two)
static double[]	FrameToFrameDisplacement.centerOfMass(List<DeformableMesh3D> meshes)
static double[][]	FrameToFrameDisplacement.displacements(List<DeformableMesh3D> A, List<DeformableMesh3D> B, double[] aToB)
static double[][]	FrameToFrameDisplacement.displacements(List<DeformableMesh3D> A, List<DeformableMesh3D> B, double[] aToB)
static ij.ImagePlus	FrameToFrameDisplacement.generateMosaicImage(List<DeformableMesh3D> meshes)
static List<deformablemesh.track.FrameToFrameDisplacement.Mapping>	FrameToFrameDisplacement.jaccardIndex(List<DeformableMesh3D> one, List<DeformableMesh3D> two) Finds the jaccardIndexMatrix between the two lists of meshes.
static List<deformablemesh.track.FrameToFrameDisplacement.Mapping>	FrameToFrameDisplacement.jaccardIndex(List<DeformableMesh3D> one, List<DeformableMesh3D> two) Finds the jaccardIndexMatrix between the two lists of meshes.
static double[][]	FrameToFrameDisplacement.jaccardIndexMatrix(List<DeformableMesh3D> one, List<DeformableMesh3D> two)
static double[][]	FrameToFrameDisplacement.jaccardIndexMatrix(List<DeformableMesh3D> one, List<DeformableMesh3D> two)
List<deformablemesh.track.FrameToFrameDisplacement.Mapping>	FrameToFrameDisplacement.processJaccardIndexMap(List<DeformableMesh3D> m1, List<DeformableMesh3D> m2)
List<deformablemesh.track.FrameToFrameDisplacement.Mapping>	FrameToFrameDisplacement.processJaccardIndexMap(List<DeformableMesh3D> m1, List<DeformableMesh3D> m2)
List<double[]>	FrameToFrameDisplacement.processJaccardIndexMatrix(List<DeformableMesh3D> m1, List<DeformableMesh3D> m2)
List<double[]>	FrameToFrameDisplacement.processJaccardIndexMatrix(List<DeformableMesh3D> m1, List<DeformableMesh3D> m2)
void	Track.putAll(Map<Integer,DeformableMesh3D> newMeshes)
void	Track.setData(Map<Integer,DeformableMesh3D> data) For use when reading data from a file.

Uses of DeformableMesh3D in deformablemesh.util

Methods in deformablemesh.util that return types with arguments of type DeformableMesh3D

Modifier and Type	Method and Description
static List<DeformableMesh3D>	GroupDynamics.generateGrid()
static List<DeformableMesh3D>	GroupDynamics.getMeshInFrame(List<Track> tracks, int i)

Methods in deformablemesh.util with parameters of type DeformableMesh3D

Modifier and Type	Method and Description
Set<Triangle3D>	MeshFaceObscuring.getOverlapArea(DeformableMesh3D mesh)
void	MeshFaceObscuring.setNeighbor(DeformableMesh3D mesh)

Method parameters in deformablemesh.util with type arguments of type DeformableMesh3D

Modifier and Type	Method and Description
static MeshGroup	GroupDynamics.createMeshGroup(List<DeformableMesh3D> meshes)
static double[]	GroupDynamics.getAxisRotation(List<DeformableMesh3D> previous, List<DeformableMesh3D> next) Consider that a rigid body rotates the group of meshes.
static double[]	GroupDynamics.getAxisRotation(List<DeformableMesh3D> previous, List<DeformableMesh3D> next) Consider that a rigid body rotates the group of meshes.
static double[]	GroupDynamics.getCenterOfMass(List<DeformableMesh3D> meshes)
static double	GroupDynamics.getMass(List<DeformableMesh3D> meshes)
void	MeshFaceObscuring.setNeighbors(List<DeformableMesh3D> meshes)

Constructors in deformablemesh.util with parameters of type DeformableMesh3D

Constructor and Description
CurvatureSurfacePlot(DeformableMesh3D mesh)
IntensitySurfacePlot(DeformableMesh3D mesh, ij.ImagePlus plus)
IntensitySurfacePlot(DeformableMesh3D mesh, MeshImageStack stack)

Constructor parameters in deformablemesh.util with type arguments of type DeformableMesh3D

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

Uses of DeformableMesh3D in deformablemesh.util.connectedcomponents

Methods in deformablemesh.util.connectedcomponents that return types with arguments of type DeformableMesh3D

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