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var subtractRadius = 10;
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var filterRadius = 3;
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var minSize = 60;
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macro "Unused Tool - C037" { }
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macro "Unused Tool - 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"{
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}
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macro "Options Action Tool- C000T4b12o" {
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Dialog.create("Count Segments Options");
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Dialog.addNumber("subtract radius", subtractRadius);
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Dialog.addNumber("filter radius", filterRadius);
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Dialog.addNumber("min. size", minSize);
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Dialog.show();
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subtractRadius = Dialog.getNumber();
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filterRadius = Dialog.getNumber();
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minSize = Dialog.getNumber();
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}
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macro "Count Segments Action Tool- C000T4b12c" {
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filename = getInfo("image.filename");
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path = getInfo("image.directory");
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title = getTitle();
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setBatchMode(true);
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number = countSegmentsOnCurrentImage(title);
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print(filename + "," + number + "," + path);
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setBatchMode(false);
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run("Enhance Contrast", "saturated=0.35");
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updateDisplay();
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}
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macro "Count Segments Batch Action Tool- C000T4b12b" {
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progressTitle = "[Progress]";
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run("Text Window...", "name="+ progressTitle +" width=25 height=2 monospaced");
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IJ.log("\\Clear");
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print("subtractRadius=" + subtractRadius + ",filterRadius=" + filterRadius + ",minSize=" + minSize);
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print("file,count,path");
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call("fr.cnrs.mri.macro.io.IOSettings.resetFileLists");
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call("fr.cnrs.mri.macro.io.IOSettings.show");
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waitForUser("Please select the input files using the IOSettings dialog and press ok");
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list = call("fr.cnrs.mri.macro.io.IOSettings.getFileList");
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files = split(list, ",");
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if (list=="none") {
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IJ.log("No files selected! Macro stopped.");
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return;
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}
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setBatchMode(true);
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length = files.length;
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for (i=0; i<length; i++) {
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print(progressTitle, "\\Update:"+i+"/"+length+" ("+(i*100)/length+"%)\n"+getBar(i, length));
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file = files[i];
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open(file);
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filename = getInfo("image.filename");
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path = getInfo("image.directory");
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title = getTitle();
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number = countSegmentsOnCurrentImage(title);
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inFolder = File.getParent(file);
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outFolder = inFolder + "/control/";
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if (!File.exists(outFolder)) File.makeDirectory(outFolder);
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saveAs("tiff", outFolder + title);
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close();
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print(filename + "," + number + "," + path);
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}
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selectWindow("Log");
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timeStamp = getTimeStamp();
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saveAs("Text", inFolder + "/Results " + timeStamp + ".xls");
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setBatchMode(false);
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print(progressTitle, "\\Close");
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print("FINISHED");
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}
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function getTimeStamp() {
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getDateAndTime(year, month, dayOfWeek, dayOfMonth, hour, minute, second, msec);
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timeString = "" + year + "-" + ( month+1) + "-" + dayOfMonth + " " + hour +"-" + minute +"-" + second + "-" +msec;
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return timeString;
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}
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function getBar(p1, p2) {
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n = 20;
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bar1 = "--------------------";
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bar2 = "********************";
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index = round(n*(p1/p2));
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if (index<1) index = 1;
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if (index>n-1) index = n-1;
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return substring(bar2, 0, index) + substring(bar1, index+1, n);
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}
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function countSegmentsOnCurrentImage(title) {
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run("Set Scale...", "distance=0 known=0 pixel=1 unit=pixel");
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run("8-bit");
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run("Red");
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run("Duplicate...", "title=tmp");
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run("Gaussian Blur...", "sigma=" + subtractRadius);
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imageCalculator("Subtract create", title, "tmp");
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rename("tmp2");
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selectImage("tmp");
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close();
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selectImage("tmp2");
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run("Gaussian Blur...", "sigma=" + filterRadius);
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setAutoThreshold("IsoData dark");
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run("Convert to Mask");
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run("Skeletonize");
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run("Analyze Particles...", "size="+minSize+"-Infinity circularity=0.00-1.00 show=Masks in_situ");
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selectWindow("Results");
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run("Close");
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selectImage("tmp2");
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// find skeleton endpoints
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w = getWidth();
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h = getHeight();
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setKeyDown("shift");
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number = 0;
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showStatus("detecting skeleton end-points");
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for (x=0; x < w; x++) {
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for (y=0; y < h; y++) {
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showProgress((x*h + y) / (w*h));
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if (getPixel(x,y) == 255) {
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count = getPixel(x-1,y-1) +
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getPixel(x,y-1) +
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getPixel(x+1,y-1) +
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getPixel(x-1,y) +
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getPixel(x+1,y) +
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getPixel(x-1,y+1) +
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getPixel(x,y+1) +
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getPixel(x+1,y+1);
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if (count==255) {
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makePoint(x,y);
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number++;
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}
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}
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}
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}
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setKeyDown("none");
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selectImage(title);
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run("Restore Selection");
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selectImage("tmp2");
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close();
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result = round(number / 2);
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showStatus("");
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return result;
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}
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