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/**
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* MRI NDPI Tools
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*
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* written 2011-2012 by Volker Baecker (INSERM) at Montpellier RIO Imaging (www.mri.cnrs.fr)
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*/
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var helpURL = "http://dev.mri.cnrs.fr/wiki/imagej-macros/NDPI_Tools"
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var rows =1;
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var columns = 4;
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var lowerThreshold = 0;
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var upperThreshold = 249;
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var splitCommand="/"+getDirectory("macros")+"bin"+"\\"+"ndpisplit";
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var CLOSE_SESSION_AFTER_CONVERT = false;
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var CLOSE_SESSION_AFTER_SPLIT = false;
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var LOG_OFF_COMMAND = "shutdown /l /f";
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macro "Unused Tool - C037" { }
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macro "MRI Skin Tools Help Action Tool -C000T4b12?"{
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run('URL...', 'url='+helpURL);
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}
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macro "Convert NDPI Images Action Tool - C000T4b12c" {
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print ("Convert NDPI Images started");
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dir = getDirectory("Choose a Directory");
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files = getFileList(dir);
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first = true;
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nrOfImages = lengthOf(files);
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for (i=0; i<nrOfImages; i++) {
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file = files[i];
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path = dir + file;
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if (endsWith(file, ".ndpi")) {
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if (first) {
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print("Reading dimensions of available images, please wait...");
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first = false;
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resolutions = call("loci.formats.in.NDPIReader.getResolutionString", path);
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Dialog.create("Select a resolution");
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choices = split(resolutions, "\n");
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Dialog.addChoice("resolution", choices, choices[2]);
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Dialog.show();
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resolution = Dialog.getChoice();
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components = split(resolution, ":");
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resolutionIndex = components[0];
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}
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out = dir + "tif";
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if (!File.exists(out)) {
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File.makeDirectory(out);
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}
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print("\\Update:converting image " + (i+1) + "/" + nrOfImages);
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res = call("loci.formats.in.NDPIExporter.exportAsTif", path, out, resolutionIndex);
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}
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}
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print ("Convert NDPI Images finished");
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if (CLOSE_SESSION_AFTER_CONVERT) exec(LOG_OFF_COMMAND);
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}
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macro "Convert NDPI Images Action Tool Options" {
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Dialog.create("Convert NDPI Images tool options");
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Dialog.addCheckbox("close session when finished", CLOSE_SESSION_AFTER_CONVERT);
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Dialog.show();
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CLOSE_SESSION_AFTER_CONVERT = Dialog.getCheckbox();
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}
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macro "Select cuts Action Tool - C000T4b12s" {
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width = getWidth();
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height = getHeight();
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deltaX = height / (2*rows);
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deltaY = width / (2*columns);
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roiManager("Reset");
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run("8-bit");
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setThreshold(lowerThreshold,upperThreshold);
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for (row = 1; row<=rows; row++) {
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for (column=1; column<=columns; column++) {
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y = ((2 * row) - 1) * deltaX;
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x = ((2*column) -1) * deltaY;
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v = getPixel(x,y);
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print("v="+v);
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while(v>upperThreshold || v<lowerThreshold) {
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x--;
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v = getPixel(x,y);
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print("left");
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}
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print("x="+x+", y="+y);
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doWand(x, y);
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roiManager("Add");
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}
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}
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resetThreshold();
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}
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macro "Select cuts Action Tool Options" {
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Dialog.create("Select cuts tool options");
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Dialog.addNumber("rows", rows);
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Dialog.addNumber("columns", columns);
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Dialog.show();
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rows = Dialog.getNumber();
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columns= Dialog.getNumber();
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}
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macro "Export Selections Action Tool - C000T4b12e" {
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dir = getInfo("image.directory");
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file = getInfo("image.filename");
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path = dir+file;
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outPath = dir + "cut/";
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if (!File.exists(outPath)) {
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File.makeDirectory(outPath);
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}
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comp = split(file, ".");
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titleWithoutExt = comp[0];
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ext = comp[1];
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numberOfROIs = roiManager("count");
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for (i=0; i<numberOfROIs; i++) {
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roiManager("Select", i);
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title = titleWithoutExt + "-" + (i+1) + ext;
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run("Duplicate...", "title=" + title);
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run("Select None");
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saveAs("Tiff", outPath + title);
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close();
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}
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}
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macro "Unused Tool - C037" { }
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macro "Split NDPI Images Batch Action Tool - C000T4b12s" {
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print ("Split NDPI Images started");
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dir = getDirectory("Choose a Directory");
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files = getFileList(dir);
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first = true;
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nrOfImages = lengthOf(files);
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for (i=0; i<nrOfImages; i++) {
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file = files[i];
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path = dir + file;
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if (endsWith(file, ".ndpi")) {
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out = dir + "tif";
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if (!File.exists(out)) {
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File.makeDirectory(out);
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}
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print("\\Update:splitting image " + (i+1) + "/" + nrOfImages);
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exec (splitCommand, "-mn", "\""+path+"\"");
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}
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}
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print ("Split NDPI Images finished");
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if (CLOSE_SESSION_AFTER_SPLIT) exec(LOG_OFF_COMMAND);
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}
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macro "Split NDPI Images Batch Action Tool Options" {
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Dialog.create("Split NDPI Images Batch tool options");
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Dialog.addCheckbox("close session when finished", CLOSE_SESSION_AFTER_SPLIT);
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Dialog.show();
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CLOSE_SESSION_AFTER_SPLIT = Dialog.getCheckbox();
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}
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macro "NDPI selection export Action Tool - C000T4b12n" {
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MAGNIFICATION = "20";
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Z = "0";
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dir = getInfo("image.directory");
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parentDir = File.getParent(dir);
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name =File.nameWithoutExtension;
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mosaic = getMosaicImages(name, parentDir, MAGNIFICATION, Z);
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getSelectionBounds(roiX, roiY, roiWidth, roiHeight);
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imageWidth = getWidth();
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imageHeight = getHeight();
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for (i=0; i<mosaic.length; i++) {
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print(mosaic[i]);
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}
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}
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function getMosaicImages(name, dir, magnification, z) {
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files = getFileList(dir);
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filter = name+"_x"+magnification+"_z"+z+"_";
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hits = 0;
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for (i=0; i<files.length; i++) {
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file = files[i];
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if (startsWith(file, filter)) hits++;
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}
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resultFiles = newArray(hits);
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counter = 0;
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for (i=0; i<files.length; i++) {
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file = files[i];
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if (startsWith(file, filter)) {
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resultFiles[counter]=file;
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counter++;
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}
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}
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return resultFiles;
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}
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