/**
  * Wound Healing Tool
  * Collaborators: 
  *     Nathalie Cahuzac, CNRS, IGMM, SPLICOS THERAPEUTICS; 
  *     Virginie Georget, MRI-CRBM
  *
  * Measure the area of a wound in a cellular tissue on a stack 
  * of images representing a time-series
  *
  * (c) 2010-2017, INSERM
  * written by Volker Baecker at Montpellier RIO Imaging (www.mri.cnrs.fr)
  *
*/


var helpURL = "https://github.com/MontpellierRessourcesImagerie/imagej_macros_and_scripts/wiki/Wound-Healing-Tool"
var VARIANCE_FILTER_RADIUS = 20;
var THRESHOLD = 1;
var RADIUS_CLOSE = 4;
var MINIMAL_SIZE = 999999;
var METHODS = newArray("variance", "find edges");
var METHOD = "variance";
var MEASURE_IN_PIXEL_UNITS = false;

runTests();
exit

macro "Unused Tool - C037" { }

macro "MRI Wound Healing Tool Help Action Tool - C000C111C222D07D08D09D0aD0bD0cD0dD0eD0fD18D19D1aD1bD1cD1dD1eD1fD28D29D2cD2dD2eD2fD38D39D3aD3bD3cD3eD3fD40D49D4aD4bD4cD4dD4eD4fD50D51D52D5aD5bD5cD5dD5eD5fD60D61D62D6aD6bD6cD6dD6eD6fD70D71D72D73D7bD7cD7eD7fD80D81D82D83D8cD8dD8eD8fD90D91D93D94D9cD9dD9eD9fDa0Da1Da2Da3Da4DadDaeDafDb0Db1Db2Db3Db4Db5DbeDbfDc0Dc1Dc2Dc4Dc5DcfDd0Dd2Dd4Dd5DdfDe0De2De3De4De5DefDf0Df1Df2Df3Df4Df5Df6C222C333C444C555C666C777C888C999D2aD2bD3dD7dD92Dc3Dd1Dd3De1C999CaaaCbbbCcccCdddCeeeD00D01D02D03D04D05D06D10D11D12D13D14D15D16D17D20D21D22D23D24D25D26D27D30D31D32D33D34D35D36D37D41D42D43D44D45D46D47D48D53D54D55D56D57D58D59D63D64D65D66D67D68D69D74D75D76D77D78D79D7aD84D85D86D87D88D89D8aD8bD95D96D97D98D99D9aD9bDa5Da6Da7Da8Da9DaaDabDacDb6Db7Db8Db9DbaDbbDbcDbdDc6Dc7Dc8Dc9DcaDcbDccDcdDceDd6Dd7Dd8Dd9DdaDdbDdcDddDdeDe6De7De8De9DeaDebDecDedDeeDf7Df8Df9DfaDfbDfcDfdDfeDff"{
    run('URL...', 'url='+helpURL);
}

macro 'Measure Wound Healing Action Tool - C000T4b12m' {
    measureActiveImage();
}

macro 'Batch Measure Wound Healing Action Tool - C000T4b12b' {
    batchMeasureImages();
}

macro 'Measure Wound Healing Action Tool Options' {
     Dialog.create("Wound Healing Tool Options");
     Dialog.addChoice("method", METHODS, METHOD);
     Dialog.addNumber("variance filter radius", VARIANCE_FILTER_RADIUS);
     Dialog.addNumber("threshol", THRESHOLD);
     Dialog.addNumber("radius close", RADIUS_CLOSE);
     Dialog.addNumber("min. size", MINIMAL_SIZE);
     Dialog.addCheckbox("ignore spatial calibration", MEASURE_IN_PIXEL_UNITS);
     Dialog.show();
     
     METHOD = Dialog.getChoice();
     VARIANCE_FILTER_RADIUS= Dialog.getNumber();
     THRESHOLD= Dialog.getNumber();
     RADIUS_CLOSE = Dialog.getNumber();
     MINIMAL_SIZE = Dialog.getNumber();
     MEASURE_IN_PIXEL_UNITS = Dialog.getCheckbox();
}

function batchMeasureImages() {
    print("\\Clear");
    setBatchMode(true);
    getDateAndTime(year, month, dayOfWeek, dayOfMonth, hour, minute, second, msec);
    print(dayOfMonth + "-" + (month+1) + "-" + year + " " + hour + ":" + minute + ":" + second + "." + msec);
    dir = getDirectory("Select the folder containing the images");
    files = getFileList(dir);
    numberOfImages = 0;
    for (i=0; i<files.length; i++) {
        file = files[i];
        if (isInputImage(file)) {
            numberOfImages++;
        }
    }
    counter = 1;
    for (i=0; i<files.length; i++) {
        file = files[i];
        if (isInputImage(file)) {
            print("\\Update1:Processing file " + (counter) + " of " + numberOfImages);
            open(dir+"/"+file);
            title = getTitle();
            measureActiveImage();
            outDir = dir + "/" + "control-images";
            if (!File.exists(outDir)) {
                File.makeDirectory(outDir);
            }
            save(outDir + "/" + title);
            close();
            selectWindow("Results");
            saveAs("Text", dir + "/scratch_areas_" + title + ".xls");
            counter++;
        }
    }
    print("FINISHED");
    getDateAndTime(year, month, dayOfWeek, dayOfMonth, hour, minute, second, msec);    
    print(dayOfMonth + "-" + (month+1) + "-" + year + " " + hour + ":" + minute + ":" + second + "." + msec);
    setBatchMode("exit and display");    
}

function measureActiveImage() {
    if (MEASURE_IN_PIXEL_UNITS) removeScale;
    initialize();
    createMaskWithGapAsForeground(METHOD, VARIANCE_FILTER_RADIUS, THRESHOLD);
    applyMorphologicalCloseOnTissue(RADIUS_CLOSE);
    createRoisOfGaps(MINIMAL_SIZE);
    closeMask();
    roiManager("Measure"); 
    roiManager("Show All");
}

function removeScale() {
    run("Set Scale...", "distance=0 known=0 pixel=1 unit=pixel");
}

function initialize() {
    roiManager("reset")
    roiManager("Associate", "true");
    run("Clear Results");   
    run("Select None");
}

function createMaskWithGapAsForeground(method, radius, threshold) {
    run("Duplicate...", "duplicate");
    if (method=="variance") 
        thresholdVariance(radius, threshold);
    else 
        thresholdFindEdges();
    run("Convert to Mask", " black");
}

function applyMorphologicalCloseOnTissue(iterations) {
    run("Options...", "iterations="+iterations+" count=1 pad black do=Open stack");
    run("Options...", "iterations=1 count=1 black do=Nothing");
}

function createRoisOfGaps(minimalArea) {
    run("Analyze Particles...", "size="+minimalArea+"-Infinity circularity=0.00-1.00 show=Nothing add stack");
}

function closeMask() {
    close();
}

function isInputImage(name) {
    if (!endsWith(name, ".tif") && !endsWith(name, ".TIF")) return false;
    return true;
}

function thresholdVariance(radius, threshold) {
    run("Variance...", "radius=" + radius + " stack");
    run("8-bit");
    setThreshold(0, threshold);
}

function thresholdFindEdges() {
    run("Find Edges", "stack");
    run("Invert", "stack");
    if (bitDepth==24) run("8-bit");
    setAutoThreshold("Percentile dark");
}

function runTests() {
    print("STARTING TESTS...");
    print("testIsInputImage", testIsInputImage());
    print("testThresholdVariance", testThresholdVariance());
    print("testThresholdFindEdges", testThresholdFindEdges());
    print("testMeasureActiveImageVariance", testMeasureActiveImageVariance());
    print("testMeasureActiveImageFindEdges", testMeasureActiveImageFindEdges());
    print("FINISHED TESTS");
}

function testIsInputImage() {
    image1 = "test.tif";
    result = isInputImage(image1);
    image2 = "test.TIF";
    result = result && isInputImage(image2);
    image3 = "test.png";
    result = result && !isInputImage(image3);
    return result;
}

function testThresholdVariance() {
    setBatchMode(true);
    newImage("Untitled", "8-bit ramp", 16, 16, 1);
    thresholdVariance(1, 50);
    getThreshold(lower, upper);
    variance0x0 = getPixel(0, 0);
    variance7x7 = getPixel(7, 7);
    variance15x15 = getPixel(15, 15);
    result = (upper==50);
    result = result && (variance0x0==57);
    result = result && (variance7x7==171);
    result = result && (variance15x15==57);
    close();
    setBatchMode(false);
    return result;
}

function testThresholdFindEdges() {
    setBatchMode(true);
    newImage("Untitled", "8-bit ramp", 16, 16, 1);
    thresholdFindEdges();
    getThreshold(lower, upper);
    variance0x0 = getPixel(0, 0);
    variance7x7 = getPixel(7, 7);
    variance15x15 = getPixel(15, 15);
    result = (lower==128);
    result = result && (variance0x0==191);
    result = result && (variance7x7==127);
    result = result && (variance15x15==191);
    close();
    setBatchMode(false);
    return result;    
}

function testMeasureActiveImageVariance() {
    setBatchMode(true);
    createTestImage();
    METHOD = "variance";
    VARIANCE_FILTER_RADIUS = 1;
    THRESHOLD = 1;
    RADIUS_CLOSE = 1;
    MINIMAL_SIZE = 50;
    measureActiveImage();
    roiManager("Select", 0);
    getSelectionBounds(x, y, width, height);
    close();
    result = (x==5);
    result = result && (y==0);
    result = result && (width==7);
    result = result && (height==16);
    setBatchMode(false);
    roiManager("reset");
    return result;
}

function testMeasureActiveImageFindEdges() {
    setBatchMode(true);
    createTestImage();
    METHOD = "find edges";
    THRESHOLD = 1;
    RADIUS_CLOSE = 1;
    MINIMAL_SIZE = 50;
    measureActiveImage();
    roiManager("Select", 0);
    getSelectionBounds(x, y, width, height);
    close();
    result = true;
    result = result && (y==0);
    result = result && (height==16);
    setBatchMode(false);
    roiManager("reset");
    return result;
}

function createTestImage() {
    newImage("Untitled", "8-bit black", 16, 16, 1);
    makeRectangle(0, 0, 4, 16);
    run("Add Noise");
    makeRectangle(13, 0, 3, 16);
    run("Add Noise");
    run("Select None");
}