Warning, /geant4/examples/advanced/dna/cellularPhantom/ImageJ/phantom.ijm is written in an unsupported language. File is not indexed.
0001 // Created by
0002 // - Ph. Barberet, J. Bordes
0003 // Bordeaux U., France
0004 // E-mail: barberet@lp2ib.in2p3.fr
0005 // - L. Morelli
0006 // Politecnico di Milano, Italy
0007
0008 // Show progress
0009 showProgress(0);
0010
0011 // The phantom file will be saved in the directory chosen by the user
0012 dir = getDirectory("Choose the output directory");
0013
0014 // Get voxel size and image dimensions
0015 getVoxelSize(voxelWidth, voxelHeight, depth, unit);
0016 getDimensions(imgWidth, imgHeight, channels, slices, frames);
0017
0018 // User settings dialog
0019 title = "Phantom settings";
0020 threshold1 = 0;
0021 threshold2 = 0;
0022 threshold3 = 0;
0023 Dialog.createNonBlocking(title);
0024 Dialog.addString("Output file name (.dat):", "phantom");
0025 Dialog.addNumber("Threshold red [0:255]:", 30);
0026 Dialog.addNumber("Threshold green [0:255]:", 30);
0027 Dialog.addNumber("Threshold blue [0:255]:", 30);
0028
0029 numberSlices = 0;
0030 items = newArray("RGB", "RBG", "BRG", "BGR", "GRB", "GBR"); //Definition of color priority order (1st color priority, 2nd color priority, 3rd color priority)
0031 Dialog.addChoice("Priority", items);
0032 Dialog.show();
0033
0034 // Read dialog parameters
0035 filename = Dialog.getString();
0036 threshold1 = Dialog.getNumber();
0037 threshold2 = Dialog.getNumber();
0038 threshold3 = Dialog.getNumber();
0039 priority = Dialog.getChoice();
0040
0041 // Print output directory
0042 print(dir);
0043
0044 // Generate file path
0045 path2file = dir + filename + ".dat";
0046
0047 for (num = 0; File.exists(path2file); num++) {
0048 newfilename = filename + "_" + num;
0049 path2file = dir + newfilename + ".dat";
0050 }
0051
0052 // Open temporary file for writing
0053 tempF = File.open(dir + "_temp.dat");
0054
0055 // Display file parameters
0056 W = getWidth(); // Image width in voxels
0057 H = getHeight(); // Image height in voxels
0058
0059 print("Voxel size : ", voxelWidth, " ", voxelHeight, " ", depth, " ", unit);
0060 print("Number of slices : ", slices);
0061 print("Definition : ", W, "*", H);
0062 print("Thresholds : ", threshold1, threshold2, threshold3);
0063
0064 // Display number of voxels
0065 showStatus("Voxels count");
0066
0067
0068 // Initialize voxel counters
0069 numberVoxels1 = 0;
0070 numberVoxels2 = 0;
0071 numberVoxels3 = 0;
0072
0073
0074 // Initialize a string to store lines of data
0075 linesToWrite = "";
0076 linesArray = newArray("");
0077
0078 // Loop through the image to write voxel coordinates and material in the phantom file
0079 for(k=0; k< nSlices; k++)
0080 {
0081 showProgress(k/(nSlices));
0082 setSlice(k+1);
0083
0084 for(j=0; j<H; j++)
0085 {
0086 for(i=0; i< W; i++)
0087 {
0088
0089 v=getPixel(i,j);
0090 red = (v>>16)&0xff; //Extracting red color data - bits 23-16
0091 green = (v>>8)&0xff; //Extracting green color data - bits 15-8
0092 blue = v&0xff; //Extracting blue color data - bits 7-0
0093
0094 //voxel coordinates (real units)
0095 x=i*voxelWidth;
0096 y=j*voxelWidth;
0097 z=k*depth;
0098
0099
material = 0;
0100 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.
0101 {
0102 if (red>=threshold1) {
0103 numberVoxels1 +=1;
0104 material = 1;}
0105 else if (green>=threshold2) {
0106 numberVoxels2 +=1;
0107 material = 2;}
0108 else if (blue>=threshold3) {
0109 numberVoxels3 +=1;
0110 material = 3;}
0111
0112
0113 }
0114
0115 else if (priority=="RBG")
0116 {
0117 if (red>=threshold1) {
0118 numberVoxels1 +=1;
0119 material = 1;}
0120 else if (blue>=threshold3) {
0121 numberVoxels3 +=1;
0122 material = 3}
0123 else if (green>=threshold2) {
0124 numberVoxels2 +=1;
0125 material = 2;}
0126 }
0127
0128 else if (priority=="BRG")
0129 {
0130 if (blue>=threshold3) {
0131 numberVoxels3 +=1;
0132 material = 3;}
0133 else if (red>=threshold1) {
0134 numberVoxels1 +=1;
0135 material = 1;}
0136 else if (green>=threshold2) {
0137 numberVoxels2 +=1;
0138 material = 2;}
0139 }
0140
0141 else if (priority=="BGR")
0142 {
0143 if (blue>=threshold3) {
0144 numberVoxels3 +=1;
0145 material = 3;}
0146 else if (green>=threshold2) {
0147 numberVoxels2 +=1;
0148 material = 2;}
0149 else if (red>=threshold1) {
0150 numberVoxels1 +=1;
0151 material = 1;}
0152 }
0153
0154 else if (priority=="GBR")
0155 {
0156 if (green>=threshold2) {
0157 numberVoxels2 +=1;
0158 material = 2;}
0159 else if (blue>=threshold3) {
0160 numberVoxels3 +=1;
0161 material = 3;}
0162 else if (red>=threshold1) {
0163 numberVoxels1 +=1;
0164 material = 1;}
0165 }
0166
0167 else if (priority=="GRB")
0168 {
0169 if (green>=threshold2) {
0170 numberVoxels2 +=1;
0171 material = 2;}
0172 else if (red>=threshold1) {
0173 numberVoxels1 +=1;
0174 material = 1;}
0175 else if (blue>=threshold3) {
0176 numberVoxels3 +=1;
0177 material = 3;}
0178 }
0179
0180 // Append the line to the list of lines to write
0181 if (material != 0){
0182 print(tempF, d2s(x,4) + " \t" + d2s(y,4) + " \t" + d2s(z,4) + " \t" + material + "\n");
0183 }
0184
0185 }
0186 }
0187 }
0188
0189 numberVoxels=numberVoxels1+numberVoxels2+numberVoxels3;
0190
0191 // Close temporary file
0192 File.close(tempF);
0193
0194 // Open main file for writing
0195 F = File.open(path2file);
0196
0197 // Write header in main file
0198 print(F, numberVoxels + "\t" + numberVoxels1 + "\t" + numberVoxels2 + "\t" + numberVoxels3 + "\n");
0199 print(F, imgWidth * voxelWidth + "\t" + imgHeight * voxelWidth + "\t" + slices * depth + "\t" + unit + "\n");
0200 print(F, voxelWidth + "\t" + voxelWidth + "\t" + depth + "\t" + unit + "\n");
0201
0202 // Read data from temporary file and write to main file
0203 data = File.openAsString(dir + "_temp.dat");
0204 print(F, data);
0205
0206 // Close main file
0207 File.close(F);
0208
0209 // Delete temporary file
0210 File.delete(dir + "_temp.dat");
0211
0212 // Show completion messages
0213 showProgress(1)
0214
0215 if (num > 0) {
0216 showMessage("WARNING: '" + filename + ".dat' file already exists.\nNew file: '" + newfilename + ".dat'");
0217 }
0218 showStatus("Completed");
0219 showMessage("Completed");
