Friday, November 14, 2014

Graphics: Marching Cubes - Implementation




A javascript implementation of the Marching cubes algorithm...

1- Description


TODO

MarchingCubes.svg
Fig.1: The originally published 15 cube configurations. By Jmtrivial (License GPL, [Wikipedia])

2-  The script

In the last update of ImageJ (version 1.49k), it is now possible to call multiple files in a script.
Note: [2018/04/03] The code is updated for ES6 (2015+) JavaScript
However, this feature is only available for java Sun/Oracle (it does not seem to work with OpenJDK). In this case, copy and paste the contents of the two scripts marchingCubes_Cube.js and marchingCubes_Slice.js in the main script.

This - long - script is divided in three parts:
  • the class Cube for computing the configuration case and vertices along the edges.
  • the class Slice involved in the storage of temporary cubes
  • the main script marchingCubes.js

class Cube
+++ Javascript: MarchingCubes_Cube.js +++
// Marching Cubes
// Jean-Christophe Taveau
// http://crazybiocomputing.blogspot.com
// Nov 2014
// class Cube
function Cube(x,y,z,size) {
this.x = x;
this.y = y;
this.z = z;
this.size = size;
this.voxels = [];
this.edges=[-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1];
this.key=0;
}
Cube.prototype.getVertex = function (index) {
switch (index) {
case 0:
return {'x':this.x, 'y':this.y, 'z':this.z, 'voxel':this.voxels[0] }; // v0
case 1:
return {'x':this.x+this.size, 'y':this.y, 'z':this.z, 'voxel':this.voxels[1] }; // v1
case 2:
return {'x':this.x+this.size, 'y':this.y+this.size, 'z':this.z, 'voxel':this.voxels[2] }; // v2
case 3:
return {'x':this.x, 'y':this.y+this.size, 'z':this.z, 'voxel':this.voxels[3] }; // v3
case 4:
return {'x':this.x, 'y':this.y, 'z':this.z+this.size, 'voxel':this.voxels[4] }; // v4
case 5:
return {'x':this.x+this.size, 'y':this.y, 'z':this.z+this.size, 'voxel':this.voxels[5] }; // v5
case 6:
return {'x':this.x+this.size, 'y':this.y+this.size, 'z':this.z+this.size, 'voxel':this.voxels[6] }; // v6
case 7:
return {'x':this.x, 'y':this.y+this.size, 'z':this.z+this.size, 'voxel':this.voxels[7] }; // v7
}
}
Cube.prototype.setVoxels = function (stack) {
this.voxels[0]=stack.getVoxel(x ,y ,z ); // v0
this.voxels[1]=stack.getVoxel(x+this.size,y ,z ); // v1
this.voxels[2]=stack.getVoxel(x+this.size,y+this.size,z ); // v2
this.voxels[3]=stack.getVoxel(x ,y+this.size,z ); // v3
this.voxels[4]=stack.getVoxel(x ,y ,z+this.size); // v4
this.voxels[5]=stack.getVoxel(x+this.size,y ,z+this.size); // v5
this.voxels[6]=stack.getVoxel(x+this.size,y+this.size,z+this.size); // v6
this.voxels[7]=stack.getVoxel(x ,y+this.size,z+this.size); // v7
}
Cube.prototype.calcKey = function (threshold) {
var keystr = '';
keystr +=(this.voxels[7] > threshold)?"1":"0";
keystr +=(this.voxels[6] > threshold)?"1":"0";
keystr +=(this.voxels[5] > threshold)?"1":"0";
keystr +=(this.voxels[4] > threshold)?"1":"0";
keystr +=(this.voxels[3] > threshold)?"1":"0";
keystr +=(this.voxels[2] > threshold)?"1":"0";
keystr +=(this.voxels[1] > threshold)?"1":"0";
keystr +=(this.voxels[0] > threshold)?"1":"0";
this.key = parseInt(keystr,2);
}
Cube.prototype.toString = function () {
var str='[';
for (var i=0;i<12;i++) str+=(this.edges[i]+"; ");
return ("Cube["+this.key+"]=(" + this.x +" "+this.y+" "+this.z +") "+str+"]");
}
view raw marchingCubes_Cube.js hosted with ❤ by GitHub

+++ End of Script: +++

class Slice
+++ Javascript: MarchingCubes_Slice.js +++
// Marching Cubes
// Jean-Christophe Taveau
// http://crazybiocomputing.blogspot.com
// Nov 2014
// class Slice
function Slice(cubes_per_row, cubes_per_column) {
this.cubes = [];
this.count = 0;
this.w = cubes_per_row;
this.h = cubes_per_column;
}
Slice.prototype.reset_count = function () {
this.count=0;
}
Slice.prototype.push = function (a_cube) {
this.cubes[this.count++] = a_cube;
}
Slice.prototype.previous = function () {
//IJ.log('index previous '+this.count+' '+(this.count - 1) );
return this.cubes[this.count - 1];
}
Slice.prototype.above = function () {
//IJ.log('index above'+this.count+' '+(this.count - this.w) );
return this.cubes[this.count - this.w];
}
Slice.prototype.back = function () {
//IJ.log('index back'+this.count );
return this.cubes[this.count];
}
view raw marchingCubes_Slice.js hosted with ❤ by GitHub

+++ End of Script +++

Main Script
+++ Javascript: MarchingCubes_Slice.js +++
// Marching Cubes
// Jean-Christophe Taveau
// http://crazybiocomputing.blogspot.com
// Nov 2014
// Updated 2014/11/25: Bug fixes
// Updated 2018/04/03 - Upgrade ES6 + Bug Fixes
const require = load;
// C L A S S
// requires ImageJ 1.51u and later + java Oracle
// Nashorn JavaScript Engine
// Modify the path to fit where you store the two other files
require('./plugins/0Homemade/marchingCubes_Cube.js');
require('./plugins/0Homemade/marchingCubes_Slice.js');
// triangles to be drawn in each case
const triangles=[
[],
[0,8,3],
[0,1,9],
[1,8,3,9,8,1],
[1,2,11],
[0,8,3,1,2,11],
[9,2,11,0,2,9],
[2,8,3,2,11,8,11,9,8],
[3,10,2],
[0,10,2,8,10,0],
[1,9,0,2,3,10],
[1,10,2,1,9,10,9,8,10],
[3,11,1,10,11,3],
[0,11,1,0,8,11,8,10,11],
[3,9,0,3,10,9,10,11,9],
[9,8,11,11,8,10],
[4,7,8],
[4,3,0,7,3,4],
[0,1,9,8,4,7],
[4,1,9,4,7,1,7,3,1],
[1,2,11,8,4,7],
[3,4,7,3,0,4,1,2,11],
[9,2,11,9,0,2,8,4,7],
[2,11,9,2,9,7,2,7,3,7,9,4],
[8,4,7,3,10,2],
[10,4,7,10,2,4,2,0,4],
[9,0,1,8,4,7,2,3,10],
[4,7,10,9,4,10,9,10,2,9,2,1],
[3,11,1,3,10,11,7,8,4],
[1,10,11,1,4,10,1,0,4,7,10,4],
[4,7,8,9,0,10,9,10,11,10,0,3],
[4,7,10,4,10,9,9,10,11],
[9,5,4],
[9,5,4,0,8,3],
[0,5,4,1,5,0],
[8,5,4,8,3,5,3,1,5],
[1,2,11,9,5,4],
[3,0,8,1,2,11,4,9,5],
[5,2,11,5,4,2,4,0,2],
[2,11,5,3,2,5,3,5,4,3,4,8],
[9,5,4,2,3,10],
[0,10,2,0,8,10,4,9,5],
[0,5,4,0,1,5,2,3,10],
[2,1,5,2,5,8,2,8,10,4,8,5],
[11,3,10,11,1,3,9,5,4],
[4,9,5,0,8,1,8,11,1,8,10,11],
[5,4,0,5,0,10,5,10,11,10,0,3],
[5,4,8,5,8,11,11,8,10],
[9,7,8,5,7,9],
[9,3,0,9,5,3,5,7,3],
[0,7,8,0,1,7,1,5,7],
[1,5,3,3,5,7],
[9,7,8,9,5,7,11,1,2],
[11,1,2,9,5,0,5,3,0,5,7,3],
[8,0,2,8,2,5,8,5,7,11,5,2],
[2,11,5,2,5,3,3,5,7],
[7,9,5,7,8,9,3,10,2],
[9,5,7,9,7,2,9,2,0,2,7,10],
[2,3,10,0,1,8,1,7,8,1,5,7],
[10,2,1,10,1,7,7,1,5],
[9,5,8,8,5,7,11,1,3,11,3,10],
[5,7,0,5,0,9,7,10,0,1,0,11,10,11,0],
[10,11,0,10,0,3,11,5,0,8,0,7,5,7,0],
[10,11,5,7,10,5],
[11,6,5],
[0,8,3,5,11,6],
[9,0,1,5,11,6],
[1,8,3,1,9,8,5,11,6],
[1,6,5,2,6,1],
[1,6,5,1,2,6,3,0,8],
[9,6,5,9,0,6,0,2,6],
[5,9,8,5,8,2,5,2,6,3,2,8],
[2,3,10,11,6,5],
[10,0,8,10,2,0,11,6,5],
[0,1,9,2,3,10,5,11,6],
[5,11,6,1,9,2,9,10,2,9,8,10],
[6,3,10,6,5,3,5,1,3],
[0,8,10,0,10,5,0,5,1,5,10,6],
[3,10,6,0,3,6,0,6,5,0,5,9],
[6,5,9,6,9,10,10,9,8],
[5,11,6,4,7,8],
[4,3,0,4,7,3,6,5,11],
[1,9,0,5,11,6,8,4,7],
[11,6,5,1,9,7,1,7,3,7,9,4],
[6,1,2,6,5,1,4,7,8],
[1,2,5,5,2,6,3,0,4,3,4,7],
[8,4,7,9,0,5,0,6,5,0,2,6],
[7,3,9,7,9,4,3,2,9,5,9,6,2,6,9],
[3,10,2,7,8,4,11,6,5],
[5,11,6,4,7,2,4,2,0,2,7,10],
[0,1,9,4,7,8,2,3,10,5,11,6],
[9,2,1,9,10,2,9,4,10,7,10,4,5,11,6],
[8,4,7,3,10,5,3,5,1,5,10,6],
[5,1,10,5,10,6,1,0,10,7,10,4,0,4,10],
[0,5,9,0,6,5,0,3,6,10,6,3,8,4,7],
[6,5,9,6,9,10,4,7,9,7,10,9],
[11,4,9,6,4,11],
[4,11,6,4,9,11,0,8,3],
[11,0,1,11,6,0,6,4,0],
[8,3,1,8,1,6,8,6,4,6,1,11],
[1,4,9,1,2,4,2,6,4],
[3,0,8,1,2,9,2,4,9,2,6,4],
[0,2,4,4,2,6],
[8,3,2,8,2,4,4,2,6],
[11,4,9,11,6,4,10,2,3],
[0,8,2,2,8,10,4,9,11,4,11,6],
[3,10,2,0,1,6,0,6,4,6,1,11],
[6,4,1,6,1,11,4,8,1,2,1,10,8,10,1],
[9,6,4,9,3,6,9,1,3,10,6,3],
[8,10,1,8,1,0,10,6,1,9,1,4,6,4,1],
[3,10,6,3,6,0,0,6,4],
[6,4,8,10,6,8],
[7,11,6,7,8,11,8,9,11],
[0,7,3,0,11,7,0,9,11,6,7,11],
[11,6,7,1,11,7,1,7,8,1,8,0],
[11,6,7,11,7,1,1,7,3],
[1,2,6,1,6,8,1,8,9,8,6,7],
[2,6,9,2,9,1,6,7,9,0,9,3,7,3,9],
[7,8,0,7,0,6,6,0,2],
[7,3,2,6,7,2],
[2,3,10,11,6,8,11,8,9,8,6,7],
[2,0,7,2,7,10,0,9,7,6,7,11,9,11,7],
[1,8,0,1,7,8,1,11,7,6,7,11,2,3,10],
[10,2,1,10,1,7,11,6,1,6,7,1],
[8,9,6,8,6,7,9,1,6,10,6,3,1,3,6],
[0,9,1,10,6,7],
[7,8,0,7,0,6,3,10,0,10,6,0],
[7,10,6],
[7,6,10],
[3,0,8,10,7,6],
[0,1,9,10,7,6],
[8,1,9,8,3,1,10,7,6],
[11,1,2,6,10,7],
[1,2,11,3,0,8,6,10,7],
[2,9,0,2,11,9,6,10,7],
[6,10,7,2,11,3,11,8,3,11,9,8],
[7,2,3,6,2,7],
[7,0,8,7,6,0,6,2,0],
[2,7,6,2,3,7,0,1,9],
[1,6,2,1,8,6,1,9,8,8,7,6],
[11,7,6,11,1,7,1,3,7],
[11,7,6,1,7,11,1,8,7,1,0,8],
[0,3,7,0,7,11,0,11,9,6,11,7],
[7,6,11,7,11,8,8,11,9],
[6,8,4,10,8,6],
[3,6,10,3,0,6,0,4,6],
[8,6,10,8,4,6,9,0,1],
[9,4,6,9,6,3,9,3,1,10,3,6],
[6,8,4,6,10,8,2,11,1],
[1,2,11,3,0,10,0,6,10,0,4,6],
[4,10,8,4,6,10,0,2,9,2,11,9],
[11,9,3,11,3,2,9,4,3,10,3,6,4,6,3],
[8,2,3,8,4,2,4,6,2],
[0,4,2,4,6,2],
[1,9,0,2,3,4,2,4,6,4,3,8],
[1,9,4,1,4,2,2,4,6],
[8,1,3,8,6,1,8,4,6,6,11,1],
[11,1,0,11,0,6,6,0,4],
[4,6,3,4,3,8,6,11,3,0,3,9,11,9,3],
[11,9,4,6,11,4],
[4,9,5,7,6,10],
[0,8,3,4,9,5,10,7,6],
[5,0,1,5,4,0,7,6,10],
[10,7,6,8,3,4,3,5,4,3,1,5],
[9,5,4,11,1,2,7,6,10],
[6,10,7,1,2,11,0,8,3,4,9,5],
[7,6,10,5,4,11,4,2,11,4,0,2],
[3,4,8,3,5,4,3,2,5,11,5,2,10,7,6],
[7,2,3,7,6,2,5,4,9],
[9,5,4,0,8,6,0,6,2,6,8,7],
[3,6,2,3,7,6,1,5,0,5,4,0],
[6,2,8,6,8,7,2,1,8,4,8,5,1,5,8],
[9,5,4,11,1,6,1,7,6,1,3,7],
[1,6,11,1,7,6,1,0,7,8,7,0,9,5,4],
[4,0,11,4,11,5,0,3,11,6,11,7,3,7,11],
[7,6,11,7,11,8,5,4,11,4,8,11],
[6,9,5,6,10,9,10,8,9],
[3,6,10,0,6,3,0,5,6,0,9,5],
[0,10,8,0,5,10,0,1,5,5,6,10],
[6,10,3,6,3,5,5,3,1],
[1,2,11,9,5,10,9,10,8,10,5,6],
[0,10,3,0,6,10,0,9,6,5,6,9,1,2,11],
[10,8,5,10,5,6,8,0,5,11,5,2,0,2,5],
[6,10,3,6,3,5,2,11,3,11,5,3],
[5,8,9,5,2,8,5,6,2,3,8,2],
[9,5,6,9,6,0,0,6,2],
[1,5,8,1,8,0,5,6,8,3,8,2,6,2,8],
[1,5,6,2,1,6],
[1,3,6,1,6,11,3,8,6,5,6,9,8,9,6],
[11,1,0,11,0,6,9,5,0,5,6,0],
[0,3,8,5,6,11],
[11,5,6],
[10,5,11,7,5,10],
[10,5,11,10,7,5,8,3,0],
[5,10,7,5,11,10,1,9,0],
[11,7,5,11,10,7,9,8,1,8,3,1],
[10,1,2,10,7,1,7,5,1],
[0,8,3,1,2,7,1,7,5,7,2,10],
[9,7,5,9,2,7,9,0,2,2,10,7],
[7,5,2,7,2,10,5,9,2,3,2,8,9,8,2],
[2,5,11,2,3,5,3,7,5],
[8,2,0,8,5,2,8,7,5,11,2,5],
[9,0,1,5,11,3,5,3,7,3,11,2],
[9,8,2,9,2,1,8,7,2,11,2,5,7,5,2],
[1,3,5,3,7,5],
[0,8,7,0,7,1,1,7,5],
[9,0,3,9,3,5,5,3,7],
[9,8,7,5,9,7],
[5,8,4,5,11,8,11,10,8],
[5,0,4,5,10,0,5,11,10,10,3,0],
[0,1,9,8,4,11,8,11,10,11,4,5],
[11,10,4,11,4,5,10,3,4,9,4,1,3,1,4],
[2,5,1,2,8,5,2,10,8,4,5,8],
[0,4,10,0,10,3,4,5,10,2,10,1,5,1,10],
[0,2,5,0,5,9,2,10,5,4,5,8,10,8,5],
[9,4,5,2,10,3],
[2,5,11,3,5,2,3,4,5,3,8,4],
[5,11,2,5,2,4,4,2,0],
[3,11,2,3,5,11,3,8,5,4,5,8,0,1,9],
[5,11,2,5,2,4,1,9,2,9,4,2],
[8,4,5,8,5,3,3,5,1],
[0,4,5,1,0,5],
[8,4,5,8,5,3,9,0,5,0,3,5],
[9,4,5],
[4,10,7,4,9,10,9,11,10],
[0,8,3,4,9,7,9,10,7,9,11,10],
[1,11,10,1,10,4,1,4,0,7,4,10],
[3,1,4,3,4,8,1,11,4,7,4,10,11,10,4],
[4,10,7,9,10,4,9,2,10,9,1,2],
[9,7,4,9,10,7,9,1,10,2,10,1,0,8,3],
[10,7,4,10,4,2,2,4,0],
[10,7,4,10,4,2,8,3,4,3,2,4],
[2,9,11,2,7,9,2,3,7,7,4,9],
[9,11,7,9,7,4,11,2,7,8,7,0,2,0,7],
[3,7,11,3,11,2,7,4,11,1,11,0,4,0,11],
[1,11,2,8,7,4],
[4,9,1,4,1,7,7,1,3],
[4,9,1,4,1,7,0,8,1,8,7,1],
[4,0,3,7,4,3],
[4,8,7],
[9,11,8,11,10,8],
[3,0,9,3,9,10,10,9,11],
[0,1,11,0,11,8,8,11,10],
[3,1,11,10,3,11],
[1,2,10,1,10,9,9,10,8],
[3,0,9,3,9,10,1,2,9,2,10,9],
[0,2,10,8,0,10],
[3,2,10],
[2,3,8,2,8,11,11,8,9],
[9,11,2,0,9,2],
[2,3,8,2,8,11,0,1,8,1,11,8],
[1,11,2],
[1,3,8,9,1,8],
[0,9,1],
[0,3,8],
[]
];
// M A I N
// Default Marching Cubes Parameters
var threshold=128;
var SIZE=2;
var mode=0; // No interpolation
var interpolate = null;
var mesh = {};
mesh.vertices = [];
mesh.faces = [];
// Dialog window to set parameters
dialog();
// Get input stack/volume information and initialize slice of cubes
var imp=IJ.getImage();
var stack=imp.getImageStack();
var nx=imp.getWidth();
var ny=imp.getHeight();
var nz=imp.getStackSize();
var center = {'x':(nx-1)/2.0, 'y':(ny-1)/2.0,'z':(nz-1)/2.0};
var slice= new Slice(Math.floor( (nx -1)/SIZE ),Math.floor( (ny-1)/SIZE ) );
// M a i n L o o p
IJ.log("\\Clear");
IJ.log("Start of the main loop... Please wait.");
for (var z=0; z < nz-SIZE; z+=SIZE) {
slice.reset_count();
for (var y=0; y < ny-SIZE; y+=SIZE) {
for (var x=0; x < nx-SIZE; x+=SIZE) {
// 1- Create a new marching cube
var cube = new Cube(x,y,z,SIZE);
// 2- Set voxels in the cube
cube.setVoxels(stack);
// 3- Calc configuration
cube.calcKey(threshold);
// 4- Create vertices and triangles
if (cube.key != 0 && cube.key != 255) {
createTriangles(cube);
}
// 5- Update slice
slice.push(cube);
}
}
if ( (z%10) == 0) IJ.log("z="+z);
}
saveAsOBJ();
throw("-- End of Script --");
// F U N C T I O N S
function dialog() {
var gd = new GenericDialog("Marching Cubes");
gd.addNumericField("Threshold: ", threshold, 0);
gd.addNumericField("Cube Size: ", SIZE, 0);
gd.addChoice("Interpolation: ", ["None","Bilinear"], 0);
gd.showDialog();
if (gd.wasCanceled()) {
return;
}
threshold = gd.getNextNumber();
SIZE = gd.getNextNumber();
mode = gd.getNextChoiceIndex();
if (mode ==0) {
interpolate = function (v0,v1) {
return interpolateNone(v0,v1);
}
}
else {
interpolate = function (v0,v1) {
return interpolateBilinear(v0,v1);
}
}
var saveDialog = new SaveDialog("Save OBJ File As ...","Untitled",".obj");
filename=saveDialog.getDirectory()+saveDialog.getFileName();
IJ.log(filename);
}
function createTriangles(probe) {
//IJ.log("key "+probe.key+" "+ probe.x +" "+probe.y+" "+probe.z);
var vertices=[];
var vertex = null;
var edges=triangles[probe.key];
for (var i=0;i<edges.length;i++) {
var index=-1;
var edge = edges[i];
//IJ.log("edge "+edge);
if (probe.edges[edge] != -1) {
// Edge already calculated
index = probe.edges[edge];
}
else {
switch (edge) {
case 0:
if (probe.y != 0) {
probe.edges[edge] = slice.above().edges[2];
index = probe.edges[edge];
}
else {
vertex=interpolate(probe.getVertex(0),probe.getVertex(1) );
mesh.vertices.push(vertex);
index = mesh.vertices.length-1;
probe.edges[edge]= index;
}
break;
case 1:
if (probe.z != 0) {
probe.edges[edge] = slice.back().edges[5];
index = probe.edges[edge];
}
else {
vertex=interpolate(probe.getVertex(1),probe.getVertex(2) );
mesh.vertices.push(vertex);
index = mesh.vertices.length-1;
probe.edges[edge]= index;
}
break;
case 2:
if (probe.z != 0) {
probe.edges[edge] = slice.back().edges[6];
index = probe.edges[edge];
}
else {
vertex=interpolate(probe.getVertex(2),probe.getVertex(3) );
mesh.vertices.push(vertex);
index = mesh.vertices.length-1;
probe.edges[edge]= index;
}
break;
case 3:
if (probe.x != 0) {
probe.edges[edge] = slice.previous().edges[1];
index = probe.edges[edge];
}
else {
vertex=interpolate(probe.getVertex(0),probe.getVertex(3) );
mesh.vertices.push(vertex);
index = mesh.vertices.length-1;
probe.edges[edge]= index;
}
break;
case 4:
if (probe.y != 0) {
probe.edges[edge] = slice.above().edges[6];
index = probe.edges[edge];
}
else {
vertex=interpolate(probe.getVertex(4),probe.getVertex(5) );
mesh.vertices.push(vertex);
index = mesh.vertices.length-1;
probe.edges[edge]= index;
}
break;
case 5:
vertex=interpolate(probe.getVertex(5),probe.getVertex(6) );
mesh.vertices.push(vertex);
index = mesh.vertices.length-1;
probe.edges[edge]= index;
break;
case 6:
vertex=interpolate(probe.getVertex(6),probe.getVertex(7) );
mesh.vertices.push(vertex);
index = mesh.vertices.length-1;
probe.edges[edge]= index;
break;
case 7:
if (probe.x != 0) {
probe.edges[edge] = slice.previous().edges[5];
index = probe.edges[edge];
}
else {
vertex=interpolate(probe.getVertex(4),probe.getVertex(7) );
mesh.vertices.push(vertex);
index = mesh.vertices.length-1;
probe.edges[edge]= index;
}
break;
case 8:
if (probe.x != 0) {
probe.edges[edge] = slice.previous().edges[9];
index = probe.edges[edge];
}
else {
vertex=interpolate(probe.getVertex(0),probe.getVertex(4) );
mesh.vertices.push(vertex);
index = mesh.vertices.length-1;
probe.edges[edge]= index;
}
break;
case 9:
if (probe.y != 0) {
probe.edges[edge] = slice.above().edges[11];
index = probe.edges[edge];
}
else {
vertex=interpolate(probe.getVertex(1),probe.getVertex(5) );
mesh.vertices.push(vertex);
index = mesh.vertices.length-1;
probe.edges[edge]= index;
}
break;
case 10:
if (probe.x != 0) {
probe.edges[edge] = slice.previous().edges[11];
index = probe.edges[edge];
}
else {
vertex = interpolate(probe.getVertex(3),probe.getVertex(7) );
mesh.vertices.push(vertex);
index = mesh.vertices.length-1;
probe.edges[edge]= index;
}
break;
case 11:
vertex=interpolate(probe.getVertex(2),probe.getVertex(6) );
mesh.vertices.push(vertex);
index = mesh.vertices.length-1;
probe.edges[edge]= index;
break;
}
//IJ.log ("faces["+(mesh.faces.length-1)+"]= "+index);
}
mesh.faces.push(index);
}
}
function saveAsOBJ() {
IJ.log("Preparing file ...");
var text='';
// Header
text+="# Marching Cubes\n";
text+="# Jean-Christophe Taveau\n";
text+="# CrazyBioComputing\n";
text+="# WaveFront OBJ File Format\n";
text+="# Vertices: "+mesh.vertices.length+"\n";
text+="\n";
text+="o "+imp.getTitle()+"\n";
text+="\n";
// Write output text in file
var file = new java.io.File(filename);
var printWriter = new java.io.PrintWriter (filename);
IJ.log("Writing header...");
printWriter.println (text);
// Vertices
for (var i=0;i<mesh.vertices.length;i++) {
printWriter.println ("v "+ (mesh.vertices[i].x - center.x)+" "+ (mesh.vertices[i].y - center.y) + " " + (mesh.vertices[i].z - center.z) );
}
IJ.log("Writing vertices...");
printWriter.println (" ");
// Faces (aka lines)
// *Note*: The first vertex in OBJ format has the index 1 (and not 0).
for (var i=0;i<mesh.faces.length;i+=3)
printWriter.println ("f "+(mesh.faces[i]+1) +" "+ (mesh.faces[i+1]+1) +" "+ (mesh.faces[i+2]+1) );
IJ.log("Writing faces...");
// Close file
printWriter.close ();
}
function interpolateNone(v0,v1) {
var x = ( v0.x + v1.x )/2.0;
var y = ( v0.y + v1.y )/2.0;
var z = ( v0.z + v1.z )/2.0;
return {"x":x,"y":y,"z":z};
}
function interpolateBilinear(v0,v1) {
var k = (threshold - v0.voxel)/(v1.voxel - v0.voxel);
var x = v0.x + (v1.x - v0.x) * k;
var y = v0.y + (v1.y - v0.y) * k;
var z = v0.z + (v1.z - v0.z) * k;
return {"x":x,"y":y,"z":z};
}
view raw marchingCubes.js hosted with ❤ by GitHub

+++ End of Script +++

Hope that helps.

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3. Other crazybiocomputing posts

Further readings are available in ...
  • Computer Graphics Series  [Link]
  • Image Processing TOC [Link]

Posted by Jean-Christophe T. at 15:13
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