Import Geant4 11.3.0 source tree
This commit is contained in:
Gabriele Cosmo
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// Created by
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// - Ph. Barberet, J. Bordes
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// Bordeaux U., France
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// E-mail: barberet@lp2ib.in2p3.fr
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// - L. Morelli
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// Politecnico di Milano, Italy
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// Show progress
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showProgress(0);
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// The phantom file will be saved in the directory chosen by the user
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dir = getDirectory("Choose the output directory");
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// Get voxel size and image dimensions
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getVoxelSize(voxelWidth, voxelHeight, depth, unit);
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getDimensions(imgWidth, imgHeight, channels, slices, frames);
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// User settings dialog
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title = "Phantom settings";
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threshold1 = 0;
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threshold2 = 0;
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threshold3 = 0;
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Dialog.createNonBlocking(title);
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Dialog.addString("Output file name (.dat):", "phantom");
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Dialog.addNumber("Threshold red [0:255]:", 30);
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Dialog.addNumber("Threshold green [0:255]:", 30);
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Dialog.addNumber("Threshold blue [0:255]:", 30);
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numberSlices = 0;
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items = newArray("RGB", "RBG", "BRG", "BGR", "GRB", "GBR"); //Definition of color priority order (1st color priority, 2nd color priority, 3rd color priority)
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Dialog.addChoice("Priority", items);
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Dialog.show();
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// Read dialog parameters
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filename = Dialog.getString();
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threshold1 = Dialog.getNumber();
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threshold2 = Dialog.getNumber();
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threshold3 = Dialog.getNumber();
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priority = Dialog.getChoice();
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// Print output directory
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print(dir);
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// Generate file path
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path2file = dir + filename + ".dat";
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for (num = 0; File.exists(path2file); num++) {
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newfilename = filename + "_" + num;
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path2file = dir + newfilename + ".dat";
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}
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// Open temporary file for writing
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tempF = File.open(dir + "_temp.dat");
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// Display file parameters
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W = getWidth(); // Image width in voxels
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H = getHeight(); // Image height in voxels
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print("Voxel size : ", voxelWidth, " ", voxelHeight, " ", depth, " ", unit);
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print("Number of slices : ", slices);
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print("Definition : ", W, "*", H);
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print("Thresholds : ", threshold1, threshold2, threshold3);
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// Display number of voxels
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showStatus("Voxels count");
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// Initialize voxel counters
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numberVoxels1 = 0;
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numberVoxels2 = 0;
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numberVoxels3 = 0;
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// Initialize a string to store lines of data
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linesToWrite = "";
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linesArray = newArray("");
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// Loop through the image to write voxel coordinates and material in the phantom file
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for(k=0; k< nSlices; k++)
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{
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showProgress(k/(nSlices));
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setSlice(k+1);
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for(j=0; j<H; j++)
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{
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for(i=0; i< W; i++)
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{
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v=getPixel(i,j);
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red = (v>>16)&0xff; //Extracting red color data - bits 23-16
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green = (v>>8)&0xff; //Extracting green color data - bits 15-8
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blue = v&0xff; //Extracting blue color data - bits 7-0
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//voxel coordinates (real units)
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x=i*voxelWidth;
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y=j*voxelWidth;
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z=k*depth;
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␍ material = 0;
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if (priority=="RGB") //Red has priority over blue, which has priority over green, if 2 or 3 of these colors are greater than their threshold.
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{
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if (red>=threshold1) {
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numberVoxels1 +=1;
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material = 1;}
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else if (green>=threshold2) {
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numberVoxels2 +=1;
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material = 2;}
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else if (blue>=threshold3) {
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numberVoxels3 +=1;
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material = 3;}
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}
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else if (priority=="RBG")
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{
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if (red>=threshold1) {
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numberVoxels1 +=1;
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material = 1;}
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else if (blue>=threshold3) {
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numberVoxels3 +=1;
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material = 3}
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else if (green>=threshold2) {
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numberVoxels2 +=1;
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material = 2;}
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}
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else if (priority=="BRG")
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{
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if (blue>=threshold3) {
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numberVoxels3 +=1;
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material = 3;}
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else if (red>=threshold1) {
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numberVoxels1 +=1;
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material = 1;}
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else if (green>=threshold2) {
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numberVoxels2 +=1;
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material = 2;}
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}
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else if (priority=="BGR")
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{
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if (blue>=threshold3) {
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numberVoxels3 +=1;
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material = 3;}
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else if (green>=threshold2) {
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numberVoxels2 +=1;
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material = 2;}
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else if (red>=threshold1) {
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numberVoxels1 +=1;
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material = 1;}
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}
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else if (priority=="GBR")
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{
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if (green>=threshold2) {
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numberVoxels2 +=1;
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material = 2;}
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else if (blue>=threshold3) {
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numberVoxels3 +=1;
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material = 3;}
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else if (red>=threshold1) {
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numberVoxels1 +=1;
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material = 1;}
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}
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else if (priority=="GRB")
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{
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if (green>=threshold2) {
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numberVoxels2 +=1;
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material = 2;}
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else if (red>=threshold1) {
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numberVoxels1 +=1;
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material = 1;}
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else if (blue>=threshold3) {
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numberVoxels3 +=1;
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material = 3;}
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}
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// Append the line to the list of lines to write
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if (material != 0){
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print(tempF, d2s(x,4) + " \t" + d2s(y,4) + " \t" + d2s(z,4) + " \t" + material + "\n");
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}
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}
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}
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}
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numberVoxels=numberVoxels1+numberVoxels2+numberVoxels3;
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// Close temporary file
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File.close(tempF);
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// Open main file for writing
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F = File.open(path2file);
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// Write header in main file
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print(F, numberVoxels + "\t" + numberVoxels1 + "\t" + numberVoxels2 + "\t" + numberVoxels3 + "\n");
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print(F, imgWidth * voxelWidth + "\t" + imgHeight * voxelWidth + "\t" + slices * depth + "\t" + unit + "\n");
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print(F, voxelWidth + "\t" + voxelWidth + "\t" + depth + "\t" + unit + "\n");
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// Read data from temporary file and write to main file
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data = File.openAsString(dir + "_temp.dat");
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print(F, data);
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// Close main file
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File.close(F);
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// Delete temporary file
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File.delete(dir + "_temp.dat");
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// Show completion messages
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showProgress(1)
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if (num > 0) {
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showMessage("WARNING: '" + filename + ".dat' file already exists.\nNew file: '" + newfilename + ".dat'");
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}
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showStatus("Completed");
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showMessage("Completed");
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