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/**
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* MRI MS2 QUANT PRE-PROCESSING
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*
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* Do the preprocessing for MS2Quant
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* - concatenate stacks
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* - measure and report the mean intensity in a 3D background region
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* - crop 4D cells and save them in separate files
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* - allow to outline and save transcription sites, nuclei and control regions as input to ms2quant
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*
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* written 2013-14 by Volker Baecker (INSERM) at Montpellier RIO Imaging (www.mri.cnrs.fr)
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*/
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var _SLICES = 12;
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var _FRAMES = 304;
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var sourceDir = "";
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var _COUNTER = 0;
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var _CELL_FOLDER;
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var _CELL_NAME;
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var _ENHANCE_CONTRAST = 1;
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var _MARK = "PST";
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var _IS_FOR_BATCH = false;
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var helpURL = "http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/MS2Quant_Pre-Processing";
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macro "run tests [f12]" {
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runTests();
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}
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macro "MS2 Quant PP Help [f1]" {
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showHelp();
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}
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macro "MS2 Quant PP concatenate stacks [f2]" {
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ms2quantPPConcatenateStacks();
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}
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macro "MS2 Quant PP measure background [f3]" {
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ms2quantPPMeasureMeanBackground();
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}
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macro "MS2 Quant PP crop and save cell [f4]" {
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ms2quantPPCropAndSave();
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}
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macro "MS2 Quant PP add selection [f5]" {
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ms2quantPPAddRoi();
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}
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macro "MS2 Quant PP add selections [f6]" {
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ms2quantPPAddRois();
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}
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macro "MS2 Quant PP save selections [f7]" {
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ms2quantPPSaveRois();
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}
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macro "Unused Tool - C037" { }
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macro "MS2 Quant PP Help (f1) Action Tool - C037T0d08MT8d08STed082"{
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showHelp();
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}
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macro 'MS2 Quant PP Help (f1) Action Tool Options...' {
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Dialog.create("MS2QuantPP Options");
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Dialog.addNumber("z-slices: ", _SLICES);
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Dialog.addNumber("time-frames: ", _FRAMES);
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Dialog.addNumber("enhance contrast (%saturated): ", _ENHANCE_CONTRAST);
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Dialog.addString("mark: ", _MARK);
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Dialog.addCheckbox("is for batch: ", _IS_FOR_BATCH);
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Dialog.show();
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_SLICES = Dialog.getNumber();
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_FRAMES = Dialog.getNumber();
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_ENHANCE_CONTRAST = Dialog.getNumber();
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_MARK = Dialog.getString();
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_IS_FOR_BATCH = Dialog.getCheckbox();
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}
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macro "concatenate stacks (f2) Action Tool - C037T0d14cTad14s" {
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ms2quantPPConcatenateStacks();
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}
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macro "measure background (f3) Action Tool - C037T0d14mTcd14b" {
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ms2quantPPMeasureMeanBackground();
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}
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macro "crop and save cell (f4) Action Tool - C037T0d09cT5d09rT8d09oTdd09p" {
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ms2quantPPCropAndSave();
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}
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macro "add selection (f5) Action Tool - C037T0d09+T6d09rTad09oTfd09i" {
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ms2quantPPAddRoi();
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}
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macro "add selections (f6) Action Tool - C037T0d09rT5d09oTbd09iTdd09s" {
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ms2quantPPAddRois();
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}
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macro "save selections (f7) Action Tool - C037T0d09sT5d09aTbd09vTdd09e" {
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ms2quantPPSaveRois();
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}
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function showHelp() {
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run('URL...', 'url='+helpURL);
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}
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function ms2quantPPAddRoi() {
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count = roiManager("count");
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if (count==3) roiManager("reset");
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count = roiManager("count");
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name = "T";
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if (count == 1) name = "N";
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if (count == 2) name = "C";
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roiManager("Add");
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roiManager("Deselect");
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roiManager("Show None");
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roiManager("Show All");
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run("Select None");
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roiManager("Select", count);
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roiManager("Rename", name);
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roiManager("Deselect");
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roiManager("Show None");
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roiManager("Show All");
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if (count == 2) {
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roiManager("Save", _CELL_FOLDER + "/RoiSet.zip");
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title = _CELL_NAME + ".tif";
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closeImageAndProjections(title);
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run("Add Selection...");
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}
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}
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function ms2quantPPAddRois() {
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count = roiManager("count");
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if ((count % 3) == 0) name = "T";
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if ((count % 3) == 1) name = "N";
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if ((count % 3) == 2) name = "C";
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name = name + "_" + floor(count / 3) + 1;
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roiManager("Add");
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roiManager("Deselect");
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roiManager("Show None");
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roiManager("Show All");
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run("Select None");
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roiManager("Select", count);
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roiManager("Rename", name);
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roiManager("Deselect");
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roiManager("Show None");
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roiManager("Show All");
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}
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function closeImageAndProjections(title) {
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selectImage(title);
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close();
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selectImage("MAX_"+title);
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close();
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selectImage("MAX_MAX_"+title);
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close();
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}
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function ms2quantPPSaveRois() {
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roiManager("Save", sourceDir + "/" + "MAX_" + _CELL_NAME +"_RoiSet.zip");
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title = _CELL_NAME + ".tif";
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selectImage("MAX_" + title);
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save(sourceDir + "/" + "MAX_" + title);
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closeImageAndProjections(title);
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}
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function ms2quantPPCropAndSave() {
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sourceDir = getDirectory("image");
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title = getTitle();
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parts = split(title, ".");
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cellNumber = getCellNumber(sourceDir, parts[0]);
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_CELL_NAME = parts[0];
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if (!_IS_FOR_BATCH) _CELL_NAME = _CELL_NAME + "_c" + cellNumber;
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newTitle = _CELL_NAME + ".tif";
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run("Duplicate...", "title="+newTitle+" duplicate range=1-" + nSlices);
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run("Select None");
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run("Remove Overlay");
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if (!_IS_FOR_BATCH) {
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if (!File.exists(sourceDir + newTitle)) File.makeDirectory(sourceDir + _CELL_NAME);
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_CELL_FOLDER = sourceDir + _CELL_NAME;
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save(_CELL_FOLDER + "/" + newTitle);
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}
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showHyperstackAndProjections();
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roiManager("Reset");
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}
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function showHyperstackAndProjections() {
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run("Stack to Hyperstack...", "order=xyczt(default) channels=1 slices="+_SLICES+" frames="+_FRAMES+" display=Color");
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run("Enhance Contrast", "saturated=" + _ENHANCE_CONTRAST);
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getDimensions(width, height, channels, slices, frames);
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run("Z Project...", "start=1 stop="+slices+" projection=[Max Intensity] all");
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run("Enhance Contrast", "saturated=" + _ENHANCE_CONTRAST);
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run("Z Project...", "start=1 stop="+frames+" projection=[Max Intensity]");
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run("Enhance Contrast", "saturated=" + _ENHANCE_CONTRAST);
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run("Tile");
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setTool("freehand");
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}
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function ms2quantPPMeasureMeanBackground() {
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setBatchMode(true);
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sourceDir = getDirectory("Choose the source directory");
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files = getFileList(sourceDir);
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images = filterTifFiles(files);
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_COUNTER = 0
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logStart("MEASURE BACKGROUND");
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for(i=0; i<images.length; i++) {
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logUpdate(i, images);
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measureBackgoundOnStack(images[i]);
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}
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if (isOpen("Background")) {
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print("Saving measurements");
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selectWindow("Background");
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saveAs("Text", sourceDir + "Background.xls");
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}
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setBatchMode("exit and display");
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logEnd("MEASURE BACKGROUND");
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}
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function ms2quantPPConcatenateStacks() {
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print("\\Clear");
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setBatchMode(true);
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sourceDir = getDirectory("Choose the source directory");
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files = getFileList(sourceDir);
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files = filterFiles(files);
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run("Clear Results");
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logStart("CONCATENATE STACKS");
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for(i=0; i<files.length; i++) {
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logUpdate(i, files);
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handleStack(files[i]);
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}
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setBatchMode("exit and display");
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logEnd("CONCATENATE STACKS");
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}
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function getCellNumber(sourceDir, name) {
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counter = 0;
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files = getFileList(sourceDir);
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for (i=0; i<files.length; i++) {
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file = files[i];
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if (File.isDirectory(sourceDir+ file) && startsWith(file, name + "_c")) counter++;
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}
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return counter + 1;
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}
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function measureBackgoundOnStack(file) {
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open(file);
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id = getImageID();
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loadRois(file);
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numberOfRois = roiManager("count");
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if (numberOfRois != 1) {
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print ("No selection for: " + file);
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selectImage(id);
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close();
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return;
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}
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roiManager("Select", 0);
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run("Clear Results");
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if (!isOpen("Background")) {
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run("Table...", "name=Background width=350 height=250");
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print("[Background]", "\\Headings:n\timage\tmean background");
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}
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title = getTitle();
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run("Set Measurements...", " mean display redirect=None decimal=3");
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run("Plot Z-axis Profile");
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run("Summarize");
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res = getResult("Mean", nResults-4);
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title = getTitle();
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selectWindow(title);
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close();
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_COUNTER++;
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print("[Background]", _COUNTER + "\t" + file + "\t"+ res);
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selectImage(id);
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close();
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}
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function handleStack(file) {
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otherFile = otherStackFor(file);
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open(file);
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title1 = getTitle();
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open(otherFile);
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title2 = getTitle();
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resultTitle = title1;
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run("Concatenate...", " title=" + resultTitle + " image1=" + title1 + " image2=" + title2 + " image3=[-- None --]");
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imageID = getImageID();
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if (!File.exists(sourceDir+"STACKS")) File.makeDirectory(sourceDir+"STACKS");
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saveAs("Tiff", sourceDir+"STACKS/" + resultTitle);
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selectImage(imageID);
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close();
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}
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function otherStackFor(file) {
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preFix =beforeMajorNumber(file);
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postFix = afterMajorNumber(file);
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majorNumber = getMajorNumber(file);
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nextMajorNumber = substring(majorNumber, 0, 2) + "2";
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return "" + preFix + nextMajorNumber + postFix;
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}
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function filterFiles(files) {
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count = countInterestingFiles(files);
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filteredFiles = newArray(count);
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counter = 0;
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for(i=0; i<files.length; i++) {
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if (isInteresting(files[i])) {
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filteredFiles[counter] = files[i];
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counter++;
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}
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}
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return filteredFiles;
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}
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function filterTifFiles(files) {
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count = 0;
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for (i=0; i<files.length; i++) {
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if (isTifFile(files[i])) count = count + 1;
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}
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images = newArray(count);
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count = 0;
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for (i=0; i<files.length; i++) {
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if (isTifFile(files[i])) {
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images[count] = files[i];
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count = count + 1;
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}
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}
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return images;
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}
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function countInterestingFiles(files) {
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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 (isInteresting(file)) counter++;
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}
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return counter;
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}
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function isInteresting(file) {
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if (!isImageFile(file)) return false;
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majorNumber = getMajorNumber(file);
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if (!endsWith(majorNumber, "1") ) return false;
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otherStack = otherStackFor(file);
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fullPath = "" + sourceDir + otherStack;
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if (!File.exists(fullPath)) return false;
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return true;
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}
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function isImageFile(file) {
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extensions = imageFileExtensions();
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for (i=0; i<extensions.length; i++) {
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extension = extensions[i];
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if (endsWith(file, extension)) return true;
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}
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return false;
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}
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function isTifFile(file) {
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extensions = newArray(".tif", ".TIF", ".tiff", ".TIFF");
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for (i=0; i<extensions.length; i++) {
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extension = extensions[i];
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if (endsWith(file, extension)) return true;
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}
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return false;
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}
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function imageFileExtensions() {
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exts = newArray(".dv");
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return exts;
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}
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function afterMajorNumber(file) {
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index = lastIndexOf(file, "_"+_MARK+"_");
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result = substring(file, index + 5 + 3, lengthOf(file));
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return result;
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}
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function beforeMajorNumber(file) {
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index = lastIndexOf(file, "_"+_MARK+"_");
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result = substring(file, 0, index+5);
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return result;
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}
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function getMajorNumber(file) {
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index = lastIndexOf(file, "_"+_MARK+"_");
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number = substring(file, index+5, index + 5 + 3);
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return number;
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}
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function logStart(nameOfMacro) {
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print("\\Clear");
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getDateAndTime(year, month, dayOfWeek, dayOfMonth, hour, minute, second, msec);
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print("" + dayOfMonth + "-" + (month+1) + "-" + year + " " + hour + ":" + minute + ":" + second + "." + msec + " " + nameOfMacro + " STARTED");
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}
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function logUpdate(i, files) {
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print("\\Update1:Processing image " + (i+1) +" of "+ files.length);
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print(files[i]);
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}
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function logEnd(nameOfMacro) {
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print("FINISHED " + nameOfMacro);
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getDateAndTime(year, month, dayOfWeek, dayOfMonth, hour, minute, second, msec);
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print("" + dayOfMonth + "-" + (month+1) + "-" + year + " " + hour + ":" + minute + ":" + second + "." + msec);
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}
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function loadRois(file) {
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roiFile = sourceDir + file + ".zip";
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roiManager("Reset");
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if (File.exists(roiFile)) {
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roiManager("Open", roiFile);
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roiManager("Show None");
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roiManager("Show All");
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}
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}
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// Unit tests
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function runTests() {
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sourceDir = "/media/donnees/mri/in/tantale/1-2-3/";
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print("START OF TESTRUN");
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result = "failed";
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if (testGetMajorNumber()) result = "ok";
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print ("testGetMajorNumber - " + result);
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result = "failed";
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if (testOtherStackFor()) result = "ok";
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print ("testOtherStackFor - " + result);
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result = "failed";
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if (testAfterMajorNumber()) result = "ok";
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print ("testAfterMajorNumber - " + result);
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result = "failed";
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if (testBeforeMajorNumber()) result = "ok";
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print ("testBeforeMajorNumber - " + result);
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result = "failed";
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if (testIsImageFile()) result = "ok";
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print ("testIsImageFile - " + result);
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result = "failed";
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if (testIsInteresting()) result = "ok";
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print ("testIsInteresting - " + result);
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result = "failed";
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if (testFilterFiles()) result = "ok";
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print ("testFilterFiles - " + result);
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result = "failed";
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if (testIsTifFile()) result = "ok";
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print ("testIsTifFile - " + result);
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print("END OF TESTRUN");
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}
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function testGetMajorNumber() {
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result = true;
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majorNumber = getMajorNumber("20130816_100x_Movie_Calibration_RI510_128_PST_002_3.dv");
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result = result && (majorNumber == "002");
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return result;
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}
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function testOtherStackFor() {
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result = true;
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other = otherStackFor("20130816_100x_Movie_Calibration_RI510_128_PST_001_pt_2.dv");
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result = result && (other == "20130816_100x_Movie_Calibration_RI510_128_PST_002_pt_2.dv");
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return result;
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}
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function testAfterMajorNumber() {
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result = true;
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after = afterMajorNumber("20130816_100x_Movie_Calibration_RI510_128_PST_001_pt_2.dv");
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result = result && (after=="_pt_2.dv");
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return result;
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}
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function testBeforeMajorNumber() {
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result = true;
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before = beforeMajorNumber("20130816_100x_Movie_Calibration_RI510_128_PST_001_pt_2.dv");
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result = result && (before=="20130816_100x_Movie_Calibration_RI510_128_PST_");
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return result;
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}
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function testIsImageFile() {
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result = true;
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result = result && (!isImageFile("20130816_100x_Movie_Calibration_RI510_128_PST_001.log"));
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result = result && (isImageFile("20130816_100x_Movie_Calibration_RI510_128_PST_001_pt_2.dv"));
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return result;
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}
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function testIsInteresting() {
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result = true;
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result = result && (isInteresting("20130816_100x_Movie_Calibration_RI510_128_PST_001_pt_2.dv"));
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result = result && (!isInteresting("20130816_100x_Movie_Calibration_RI510_128_PST_001_pt_2_PRJ.dv"));
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return result;
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}
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function testIsTifFile() {
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result = true;
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result = result && (isTifFile("20130816_100x_Movie_Calibration_RI510_128_PST_001_pt_2.tif"));
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result = result && (!isTifFile("20130816_100x_Movie_Calibration_RI510_128_PST_001_pt_2.tif.zip"));
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return result;
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}
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function testFilterFiles() {
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files = newArray("20130816_100x_Movie_Calibration_RI510_128_PST_001.log",
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"20130816_100x_Movie_Calibration_RI510_128_PST_001_pt_2.dv",
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"20130816_100x_Movie_Calibration_RI510_128_PST_001_pt_2_PRJ.dv",
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"20130816_100x_Movie_Calibration_RI510_128_PST_001_pt_2_task.sh.joblog",
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|
"20130816_100x_Movie_Calibration_RI510_128_PST_001_pt_3.dv",
|
|
"20130816_100x_Movie_Calibration_RI510_128_PST_002_pt_2.dv");
|
|
filtered = filterFiles(files);
|
|
result = true;
|
|
result = result && (filtered.length == 2);
|
|
result = result && (filtered[0] == "20130816_100x_Movie_Calibration_RI510_128_PST_001_pt_2.dv");
|
|
return result;
|
|
}
|
|
|