deformablemesh

Class DeformableMesh3DTools

java.lang.Object

deformablemesh.DeformableMesh3DTools

public class DeformableMesh3DTools
extends Object

Collection of static methods for creating meshes. Creating binary/mosaic images. Performing some basic operations.

Constructor Summary

Constructors

Constructor and Description
DeformableMesh3DTools()

Method Summary

Modifier and Type	Method and Description
static double	calculateAverageIntensity(MeshImageStack stack, List<Triangle3D> triangles, double thickness)
static double	calculateIntensity(Box3D bound, MeshImageStack stack)
static double	calculateSurfaceArea(DeformableMesh3D mesh)
static double	calculateVolume(double[] direction, double[] positions, List<Triangle3D> triangles) normal *dot* direction + |position|*direction
static double[]	centerAndRadius(List<Node3D> nodes) Calculates the center based on the position of the nodes.
static DeformableMesh3D	copyOf(DeformableMesh3D mesh)
static ij.ImagePlus	createBinaryRepresentation(MeshImageStack stack, DeformableMesh3D mesh)
static ij.ImagePlus	createBinaryRepresentation(MeshImageStack stack, ij.ImagePlus original, Map<Integer,DeformableMesh3D> meshes)
static ij.ImagePlus	createMosaicRepresentation(MeshImageStack stack, ij.ImagePlus original_plus, List<Track> allMeshTracks)
static DeformableMesh3D	createRectangleMesh(double width, double height, double depth, double segment_size) Makes a rectangular prism mesh with triangular elements.
static DeformableMesh3D	createRhombicDodecahedron(double l)
static DeformableMesh3D	createTestBlock() Creates a 2x2x2 test block.
static DeformableMesh3D	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
static ij.ImagePlus	createUniqueLabelsRepresentation(MeshImageStack stack, List<Track> allMeshTracks)
static double[]	findMinMax(List<Node3D> nodes, double[] centroid) Finds the closest and furthest away nodes from the centroid.
static List<Node3D>	findPath(List<List<Node3D>> connectionMap, Node3D origin, Node3D goal)
static List<List<Node3D>>	generateConnectionMap(DeformableMesh3D mesh)
static List<int[]>	getContainedPixels(MeshImageStack stack, DeformableMesh3D mesh) Get pixels contained in the mesh.
static void	main(String[] args)
static DeformableMesh3D	mergeMeshes(List<DeformableMesh3D> meshes) Each mesh is constructed of 3 essential data values: positions, triangles, connections.
static void	mosaicBinary(MeshImageStack stack, ij.ImageStack out, DeformableMesh3D mesh, int rgb)
static AStarBasic<Node3D>	pathFinder(List<List<Node3D>> connectionMap, Node3D destination)
static void	scanDirty(List<Intersection> sections) This puts topographical constraints on the intersections.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

DeformableMesh3DTools

public DeformableMesh3DTools()

Method Detail

createRectangleMesh

public static DeformableMesh3D createRectangleMesh(double width,
                                                   double height,
                                                   double depth,
                                                   double segment_size)

Makes a rectangular prism mesh with triangular elements.

Parameters:

width - size in x direction

height - size in y direction

depth - size in z direction

segment_size - size of each segment.

Returns:

a mesh that will deform according to an image.

createRhombicDodecahedron

public static DeformableMesh3D createRhombicDodecahedron(double l)

createTestBlock

public static DeformableMesh3D createTestBlock()

Creates a 2x2x2 test block.

Returns:

See Also:

createTestBlock(double, double, double)

createTestBlock

public static DeformableMesh3D 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

Parameters:

w -

h -

depth -

Returns:

calculateVolume

public static double calculateVolume(double[] direction,
                                     double[] positions,
                                     List<Triangle3D> triangles)

normal *dot* direction + |position|*direction

Parameters:

direction -

positions -

triangles -

Returns:

calculateAverageIntensity

public static double calculateAverageIntensity(MeshImageStack stack,
                                               List<Triangle3D> triangles,
                                               double thickness)

centerAndRadius

public static double[] centerAndRadius(List<Node3D> nodes)

Calculates the center based on the position of the nodes. Finds the mean distance from the center. Since the nodes are not evenly distributed this method can be biased.

Parameters:

nodes - Nodes of the current mesh.

Returns:

{x, y, z, r}

calculateSurfaceArea

public static double calculateSurfaceArea(DeformableMesh3D mesh)

calculateIntensity

public static double calculateIntensity(Box3D bound,
                                        MeshImageStack stack)

generateConnectionMap

public static List<List<Node3D>> generateConnectionMap(DeformableMesh3D mesh)

pathFinder

public static AStarBasic<Node3D> pathFinder(List<List<Node3D>> connectionMap,
                                            Node3D destination)

findPath

public static List<Node3D> findPath(List<List<Node3D>> connectionMap,
                                    Node3D origin,
                                    Node3D goal)

createBinaryRepresentation

public static ij.ImagePlus createBinaryRepresentation(MeshImageStack stack,
                                                      ij.ImagePlus original,
                                                      Map<Integer,DeformableMesh3D> meshes)

createBinaryRepresentation

public static ij.ImagePlus createBinaryRepresentation(MeshImageStack stack,
                                                      DeformableMesh3D mesh)

createMosaicRepresentation

public static ij.ImagePlus createMosaicRepresentation(MeshImageStack stack,
                                                      ij.ImagePlus original_plus,
                                                      List<Track> allMeshTracks)

createUniqueLabelsRepresentation

public static ij.ImagePlus createUniqueLabelsRepresentation(MeshImageStack stack,
                                                            List<Track> allMeshTracks)

scanDirty

public static void scanDirty(List<Intersection> sections)

This puts topographical constraints on the intersections. When an intersection is 'dirty' it means it was decided at a region of low confidence.

Parameters:

sections -

getContainedPixels

public static List<int[]> getContainedPixels(MeshImageStack stack,
                                             DeformableMesh3D mesh)

Get pixels contained in the mesh. This has repeated code with "mosaicBinary" and should be combined.

Parameters:

stack -

mesh -

Returns:

mosaicBinary

public static void mosaicBinary(MeshImageStack stack,
                                ij.ImageStack out,
                                DeformableMesh3D mesh,
                                int rgb)

copyOf

public static DeformableMesh3D copyOf(DeformableMesh3D mesh)

findMinMax

public static double[] findMinMax(List<Node3D> nodes,
                                  double[] centroid)

Finds the closest and furthest away nodes from the centroid.

Parameters:

nodes -

centroid -

Returns:

{min, max}

mergeMeshes

public static DeformableMesh3D mergeMeshes(List<DeformableMesh3D> meshes)

Each mesh is constructed of 3 essential data values: positions, triangles, connections. positions : double[] of length 3*vertex. trianges : int[] of length triangles. connection_index : int[] of length 2*connections

Parameters:

meshes -

Returns:

main

public static void main(String[] args)
                 throws IOException

Throws:

IOException