var helpURL = "http://dev.mri.cnrs.fr/wiki/imagej-macros/Count_Segments"

var subtractRadius = 10;
var filterRadius = 3;
var minSize = 60;

macro "Unused Tool - C037" { }

macro "Count Segments Help Action Tool - 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"{
	run('URL...', 'url='+helpURL);
}

macro "Options Action Tool- C000T4b12o" {
    Dialog.create("Count Segments Options");
    Dialog.addNumber("subtract radius", subtractRadius);
    Dialog.addNumber("filter radius", filterRadius);
    Dialog.addNumber("min. size", minSize);
    Dialog.show();
    subtractRadius = Dialog.getNumber();
    filterRadius = Dialog.getNumber();
    minSize = Dialog.getNumber();
}

macro "Count Segments Action Tool- C000T4b12c" {
      filename = getInfo("image.filename");
      path = getInfo("image.directory");
      title = getTitle();
      setBatchMode(true);
      number = countSegmentsOnCurrentImage(title);
      print(filename + "," + number + "," + path); 
      setBatchMode(false);
      run("Enhance Contrast", "saturated=0.35");
      updateDisplay();
}

macro "Count Segments Batch Action Tool- C000T4b12b" {

    progressTitle = "[Progress]";
    run("Text Window...", "name="+ progressTitle +" width=25 height=2 monospaced");

    IJ.log("\\Clear");
    print("subtractRadius=" + subtractRadius  + ",filterRadius=" + filterRadius + ",minSize=" + minSize);
    print("file,count,path"); 

    call("fr.cnrs.mri.macro.io.IOSettings.resetFileLists");
    call("fr.cnrs.mri.macro.io.IOSettings.show");
    waitForUser("Please select the input files using the IOSettings dialog and press ok");

    list = call("fr.cnrs.mri.macro.io.IOSettings.getFileList");
    files = split(list, ",");
    if (list=="none") {
       IJ.log("No files selected! Macro stopped.");
       return;
    }
    setBatchMode(true);
    length = files.length;
    for (i=0; i<length; i++) {
        print(progressTitle, "\\Update:"+i+"/"+length+" ("+(i*100)/length+"%)\n"+getBar(i, length));
        file = files[i];
        open(file);
        filename = getInfo("image.filename");
        path = getInfo("image.directory");
        title = getTitle();
        number = countSegmentsOnCurrentImage(title);
        inFolder = File.getParent(file);
        outFolder = inFolder + "/control/";
        if (!File.exists(outFolder)) File.makeDirectory(outFolder);
        saveAs("tiff", outFolder + title);
        close();
        print(filename + "," + number + "," + path); 
    }
    selectWindow("Log");
    timeStamp = getTimeStamp();
    saveAs("Text", inFolder + "/Results " + timeStamp + ".xls");
    setBatchMode(false);
    print(progressTitle, "\\Close");
    print("FINISHED");
}

function getTimeStamp() {
	getDateAndTime(year, month, dayOfWeek, dayOfMonth, hour, minute, second, msec);
	timeString = "" + year + "-" + ( month+1) + "-" + dayOfMonth + " " + hour +"-" +  minute +"-" + second + "-" +msec;
	return timeString;
}

function getBar(p1, p2) {
        n = 20;
        bar1 = "--------------------";
        bar2 = "********************";
        index = round(n*(p1/p2));
        if (index<1) index = 1;
        if (index>n-1) index = n-1;
        return substring(bar2, 0, index) + substring(bar1, index+1, n);
  }

function countSegmentsOnCurrentImage(title) {
        run("Set Scale...", "distance=0 known=0 pixel=1 unit=pixel");
        run("8-bit");
        run("Red");
        run("Duplicate...", "title=tmp");
        run("Gaussian Blur...", "sigma=" + subtractRadius);
        imageCalculator("Subtract create", title, "tmp");
        rename("tmp2");
        selectImage("tmp");
        close();
        selectImage("tmp2");
        run("Gaussian Blur...", "sigma=" + filterRadius);
        setAutoThreshold("IsoData dark");
        run("Convert to Mask");
        run("Skeletonize");
        run("Analyze Particles...", "size="+minSize+"-Infinity circularity=0.00-1.00 show=Masks in_situ");
        if (isOpen("Results")) { 
	selectWindow("Results");
	run("Close");
        }
        selectImage("tmp2");

        // find skeleton endpoints
        w = getWidth();
        h = getHeight();
        setKeyDown("shift");
        number = 0;
        showStatus("detecting skeleton end-points");
        for (x=0; x < w; x++) {
          for (y=0; y < h; y++) {
             showProgress((x*h + y) / (w*h));
             if (getPixel(x,y) == 255) {
                    count = getPixel(x-1,y-1) +
	     getPixel(x,y-1) +
	     getPixel(x+1,y-1) +
	     getPixel(x-1,y) +
	     getPixel(x+1,y) +
	     getPixel(x-1,y+1) +
	     getPixel(x,y+1) +
	     getPixel(x+1,y+1);
                   if (count==255) {
                       setKeyDown("shift");
                       makePoint(x,y);
                       number++;
               }
             }
          }
        }
        setKeyDown("none");
        selectImage(title);
        run("Restore Selection");
        selectImage("tmp2");
        close();
        result = round(number / 2);
        showStatus("");
        return result;
}