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/**
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* MRI Skin Tools
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*
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* The Skin Tools allow to analyse masks of skin
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* tissue that touch the right and left border of the image.
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* The length of the lower border line is measured. For
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* each extremum on the lower border line of the mask the
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* length of a vertical line across the mask is measured.
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*
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* The interdigitation index can be measured using a given number of segments.
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* The thickness is estimated by using random lines across the skin, that are perpendicular
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* to the skin border.
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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/Skin_Tools"
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var minRadius = 15;
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var numberOfSegments = 4;
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var numberOfLines = 10;
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var randomSet = false;
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var removeScale = true;
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var COLOR1_R = 255;
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var COLOR1_G = 255;
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var COLOR1_B = 0;
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var COLOR2_R = 0;
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var COLOR2_G = 255;
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var COLOR2_B = 0;
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var LINE_WIDTH1 = 4;
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var LINE_WIDTH2 = 1;
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var SMOOTH_BORDER = true;
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var SMOOTH_BORDER_RADIUS = 5;
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macro "Unused Tool - C037" { }
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macro "MRI Skin Tools Help Action Tool -C000D00D01D02D03D04D0aD0bD0cD0dD0eD0fD10D11D12D13D14D1aD1bD1cD1dD1eD1fD20D21D22D23D24D2aD2bD2cD2dD2eD2fD30D31D32D33D34D3bD3cD3dD3eD3fD40D41D42D43D4cD4dD4eD4fD50D51D52D5dD5eD5fD60D6eD6fD70D7eD7fD80D8dD8eD8fD90D91D9bD9cD9dD9eD9fDa0Da1Da2DaaDabDacDadDaeDafDb0Db1Db2DbaDbbDbcDbdDbeDbfDc0Dc1Dc2Dc3DcaDcbDccDcdDceDcfDd0Dd1Dd2Dd3DdbDdcDddDdeDdfDe0De1De2De3DebDecDedDeeDefDf0DfcDfdDfeDffCfffD05D06D07D08D09D25D26D27D28D29D35D36D37D38D39D3aD44D45D46D47D48D49D4aD4bD53D54D55D56D57D58D59D5aD5bD5cD61D62D63D64D65D66D67D68D69D6aD6bD6cD6dD81D82D83D84D85D86D87D88D89D8aD8bD8cD92D93D94D95D96D97D98D99D9aDa3Da4Da5Da6Da7Da8Da9Dc4Dc5Dc6Dc7Dc8Dc9Dd4Dd5Dd6Dd7Dd8Dd9DdaDe4De5De6De7De8De9DeaDf1Df2Df3Df4Df5Df6Df7Df8Df9DfaDfbC0ffD15D16D17D18D19D71D72D73D74D75D76D77D78D79D7aD7bD7cD7dDb3Db4Db5Db6Db7Db8Db9"{
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run('URL...', 'url='+helpURL);
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}
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macro "Options Action Tool- C000T4b12o" {
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Dialog.create("MRI Skin Tools Options");
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Dialog.addNumber("minimum radius", minRadius);
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Dialog.addCheckbox("remove scale", removeScale);
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Dialog.addCheckbox("smooth border", SMOOTH_BORDER);
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Dialog.addNumber("smooth border radius", SMOOTH_BORDER_RADIUS);
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Dialog.show();
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minRadius = Dialog.getNumber();
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removeScale = Dialog.getCheckbox();
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SMOOTH_BORDER = Dialog.getCheckbox();
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SMOOTH_BORDER_RADIUS = Dialog.getNumber();
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}
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macro "Measure Filaggrin Thickness (vertical lines) Action Tool- C000T4b12m" {
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run("Set Measurements...", " bounding display redirect=None decimal=3");
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measureOneImage();
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roiManager("Show All");
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roiManager("Measure");
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}
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macro "Measure Interdigitation Index Action Tool- C000T4b12i" {
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lengths = newArray(numberOfSegments);
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distances = newArray(numberOfSegments);
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measureSegments(lengths, distances);
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title1 = "Interdigitation Indices";
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title2 = "["+title1+"]";
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f = title2;
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if (isOpen(title1))
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print(f, "\\Clear");
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else
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run("Table...", "name="+title2+" width=250 height=600");
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print(f, "\\Headings:nr\tlength\tdistance\tinterdigitation index");
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for (i=0; i<numberOfSegments; i++) {
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print(f, (i+1) + "\t" + lengths[i] + "\t" + distances[i] +"\t" + (lengths[i] / distances[i]));
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}
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}
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macro "Measure Interdigitation Index Action Tool Options" {
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Dialog.create("Interdigitation Index Options");
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Dialog.addNumber("segments", numberOfSegments);
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Dialog.show();
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numberOfSegments = Dialog.getNumber();
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}
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macro "Measure Filaggrin Thickness Action Tool- C000T4b12t" {
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prepareImage();
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roiManager("Reset");
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run("Clear Results");
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measureWidthPerpendicularLines();
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run("Clear Results");
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roiManager("Measure");
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run("Summarize");
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}
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macro "Measure Filaggrin Thickness Action Tool Options" {
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Dialog.create("Filaggrin Thickness Options");
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Dialog.addNumber("number of lines", numberOfLines);
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Dialog.show();
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numberOfLines = Dialog.getNumber();
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}
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macro "Measure Advanced Skin Properties Batch Action Tool- C000T4b12bit" {
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roiManager("Reset");
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showStatus("measure advanced skin properties...");
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run("Clear Results");
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setForegroundColor(255, 255, 0);
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run("Set Measurements...", " bounding display redirect=None decimal=3");
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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 IO_Settings dialog and press ok");
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list = call("fr.cnrs.mri.macro.io.IOSettings.getFileList");
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if (list=="none") {IJ.log("No files selected! Macro stopped."); return;}
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files = split(list, ",");
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if (files.length>0) {
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file = files[0];
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folder = File.getParent(file);
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headings = "File\t" + "length of border\t" + "distance\t"+ "segments\t" + "length\t" + "distance\t"
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+ "mean interdigitation index\t" + "stdDev\t" + "min\t" + "max\t"
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+ "vertical lines\t" + "mean width\t" + "stdDev\t" + "min\t" + "max\t"
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+ "perpendicular lines\t" + "mean width\t" + "stdDev\t" + "min\t" + "max\t" + "path\n";
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filenameSummary = folder + "/skin-tools-summary.csv";
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fileSummary = openCSVFile(filenameSummary, headings);
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headings = "file\tn\tlength\tpath\n";
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tableVerticalLines = createTable("vertical-lines", headings);
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tablePerpendicularLines = createTable("perpendicular-lines", headings);
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headings = "file\tn\tlength\tdistance\tindex\tpath\n";
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tableInterdigitationIndex = createTable("interdigitation-index", headings);
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}
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for (fileIndex=0; fileIndex< files.length; fileIndex++) {
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setBatchMode(true);
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file = files[fileIndex];
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path = File.getParent(file);
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open(file);
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prepareImage();
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folder = File.getParent(file);
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// measure length of lower border
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length = measureLengthOfLowerBorder();
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getSelectionCoordinates(x, y);
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xs = x[0];
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ys = y[0];
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xe = x[x.length-1];
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ye = y[y.length-1];
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toScaled(xs, ys);
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toScaled(xe, ye);
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distance = sqrt (((xe - xs) * (xe - xs)) + ((ye - ys) * (ye - ys)));
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// Interdigitation index
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lengths = newArray(numberOfSegments);
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distances = newArray(numberOfSegments);
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measureSegments(lengths, distances);
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index = newArray(distances.length);
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for (i=0; i<distances.length; i++) {
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index[i] = lengths[i] / distances[i];
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}
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Array.getStatistics(lengths, minLength, maxLength, meanLength, stdDevLength);
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Array.getStatistics(distances, minDistance, maxDistance, meanDistance, stdDevDistance);
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Array.getStatistics(index, minIndex, maxIndex, meanIndex, stdDevIndex);
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// Width (perpendicular lines)
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run("Clear Results");
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widths = measureWidthPerpendicularLines();
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Array.getStatistics(widths, minWidth, maxWidth, meanWidth, stdDevWidth);
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// Width (vertical lines)
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run("From ROI Manager");
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widthsVertical = measureWidthVerticalLines();
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Array.getStatistics(widthsVertical, minWidthsVertical, maxWidthsVertical, meanWidthsVertical, stdDevWidthsVertical);
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for (i=0; i<roiManager("count");i++) {
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roiManager("Select", i);
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run("Add Selection...");
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}
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run("To ROI Manager");
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run("Remove Overlay");
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// report
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print(fileSummary, File.name+"\t" +length+"\t"+ distance+"\t"+ distances.length + "\t" + meanLength + "\t" + meanDistance +"\t"
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+ meanIndex +"\t" +stdDevIndex +"\t" + minIndex +"\t"+ maxIndex + "\t"
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+ widthsVertical.length + "\t" + meanWidthsVertical + "\t" + stdDevWidthsVertical + "\t" + minWidthsVertical + "\t" + maxWidthsVertical + "\t"
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+ widths.length +"\t" + meanWidth+ "\t" + stdDevWidth + "\t" + minWidth + "\t" + maxWidth + "\t"
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+ path +"\n");
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saveControlImage(widths, distances);
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roiManager("reset");
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for (i=0; i<widthsVertical.length; i++) {
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print(tableVerticalLines, File.name + "\t" + (i+1) + "\t" + widthsVertical[i] + "\t" + path + "\n");
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}
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for (i=0; i<widths.length; i++) {
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print(tablePerpendicularLines, File.name + "\t" + (i+1) + "\t" + widths[i] + "\t" + path + "\n");
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}
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for (i=0; i<index.length; i++) {
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print(tableInterdigitationIndex, File.name + "\t" + (i+1) + "\t" + lengths[i] + "\t" + distances[i] + "\t" + index[i] + "\t" + path + "\n");
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}
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showProgress(fileIndex/(files.length-1));
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print("\\Clear");
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print("\\Update0:Measuring file " + (fileIndex+1) + " from " + files.length);
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}
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if (files.length>0) {
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File.close(fileSummary);
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selectWindow("vertical-lines");
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saveAs("results", folder + "/" + "vertical-lines" + ".csv");
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run("Close");
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selectWindow("perpendicular-lines");
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saveAs("results", folder + "/" + "perpendicular-lines" + ".csv");
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run("Close");
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selectWindow("interdigitation-index");
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saveAs("results", folder + "/" + "interdigitation-index" + ".csv");
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run("Close");
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selectWindow("Results");
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run("Close");
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}
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print("\\Update1:finished processing");
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setBatchMode("exit and display");
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}
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macro "Measure Advanced Skin Properties Batch Action Tool Options" {
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Dialog.create("Measure Advanced Skin Properties Batch Options");
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Dialog.addNumber("color one red", COLOR1_R);
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Dialog.addNumber("color one green", COLOR1_G);
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Dialog.addNumber("color one blue", COLOR1_B);
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Dialog.addNumber("color two red", COLOR2_R);
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Dialog.addNumber("color two green", COLOR2_G);
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Dialog.addNumber("color two blue", COLOR2_B);
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Dialog.addNumber("line width one", LINE_WIDTH1);
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Dialog.addNumber("line width two", LINE_WIDTH2);
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Dialog.show();
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COLOR1_R = Dialog.getNumber();
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COLOR1_G = Dialog.getNumber();
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COLOR1_B = Dialog.getNumber();
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COLOR2_R = Dialog.getNumber();
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COLOR2_G = Dialog.getNumber();
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COLOR2_B = Dialog.getNumber();
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LINE_WIDTH1 = Dialog.getNumber();
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LINE_WIDTH2 = Dialog.getNumber();
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}
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function measureOneImage() {
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prepareImage();
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selectSkinBorder();
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run("MRI Extrema", minRadius);
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call("roi.RoiConverter.addVerticalLinesToRoiManager");
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}
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function writeResultsTableToFile(filename) {
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if (File.exists(filename)) File.delete(filename);
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f = File.open(filename);
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print(f, "File\t" + "x\t" + "y\t" + "angle\t" + "length\n");
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for (i=0; i<nResults; i++) {
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label = getResultLabel(i);
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BX = getResult("BX", i);
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BY = getResult("BY", i);
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Angle = getResult("Angle", i);
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Length = getResult("Length", i);
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if (Length!=0)
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print(f, label + "\t" + BX + "\t" + BY + "\t" + Angle + "\t" + Length + "\n");
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}
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File.close(f);
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}
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function selectSkinBorder() {
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run("Select None");
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setThreshold(0,224);
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run("Analyze Particles...", "size=500-Infinity circularity=0.00-1.00 show=Nothing add");
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lastIndex = roiManager("count")-1;
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roiManager("Select", lastIndex-1);
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roiManager("Delete");
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roiManager("Select", lastIndex-1);
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roiManager("Delete");
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if (roiManager("count")>0) run("Restore Selection");
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run("MRI Roi Converter");
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}
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function getIndexAt(x, y, value) {
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start = 0;
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for (i=0; i<x.length-1; i++) {
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if (x[i] == value || (x[i]<value && x[i+1]>value)) {
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start = i;
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}
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}
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if (x[x.length-1]==value) start = x.length-1;
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xValue = x[start];
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yValue = y[start];
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index = i;
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for (i=start+1; i<x.length; i++) {
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xValueNew = x[i];
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yValueNew = y[i];
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index = i;
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if (xValueNew!=xValue || ((xValueNew!=xValue) && (yValueNew<=yValue))) return index;
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else {
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xValue = xValueNew;
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yValue = yValueNew;
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}
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}
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return index;
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}
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function findUpperEdgeIndex(x1, y1, x2, y2) {
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dx = x2-x1;
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dy = y2-y1;
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n = round(sqrt(dx*dx + dy*dy));
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xInc = dx / n;
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yInc = dy / n;
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n++;
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rx = x2;
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ry = y2;
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for (i=n-1; i>=0; i--) {
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v = getPixel(rx+0.5,ry+0.5);
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if (v>0) {
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i=-1;
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} else {
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rx = rx - xInc;
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ry = ry - yInc;
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}
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}
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xE = rx+0.5;
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yE = ry+0.5;
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makeLine(x1, y1,xE, yE);
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toScaled(x1, y1);
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toScaled(xE, yE);
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length = sqrt(((xE-x1) * (xE-x1)) + ((yE-y1)*(yE-y1)));
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return length;
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}
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function selectLowerObject() {
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run("Select None");
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setThreshold(0,224);
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run("Analyze Particles...", "size=500-Infinity circularity=0.00-1.00 show=Nothing add");
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lastIndex = roiManager("count")-1;
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roiManager("Select", lastIndex-1);
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roiManager("Delete");
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roiManager("Select", lastIndex-1);
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roiManager("Delete");
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if (roiManager("count")>0) run("Restore Selection");
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roiManager("Add");
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}
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function prepareImage() {
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if (removeScale) run("Set Scale...", "distance=0 known=0 pixel=1 unit=pixel");
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run("8-bit");
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run("Grays");
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resetThreshold();
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setAutoThreshold("Default dark");
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run("Convert to Mask");
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run("Fill Holes");
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run("Invert");
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run("Fill Holes");
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run("Invert");
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if (SMOOTH_BORDER) {
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run("Options...", "iterations="+ SMOOTH_BORDER_RADIUS +" count=1 black edm=Overwrite");
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run("Invert");
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run("Open");
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run("Invert");
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}
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}
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function measureLengthOfLowerBorder() {
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roiManager("Reset");
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selectLowerObject();
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run("MRI Roi Converter");
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roiManager("Add");
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resetThreshold();
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roiManager("Select", 0);
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roiManager("Delete");
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run("Clear Results");
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roiManager("Measure");
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length = getResult("Length", 0);
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return length;
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}
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function measureSegments(lengths, distances) {
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roiManager("Reset");
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selectLowerObject();
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getSelectionCoordinates(x, y);
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Array.getStatistics(x, xMin, xMax);
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Array.getStatistics(y, yMin, yMax);
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length = (xMax-xMin) / numberOfSegments;
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initialLength = length;
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if (numberOfSegments>1) {
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for (i=0; i<numberOfSegments; i++) {
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roiManager("Select", 0);
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length=initialLength-1;
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do {
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roiManager("Select", 0);
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length++;
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currentEndX = xMin+((i+1)*length);
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currentStartX = xMin+(i*length);
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if (i<numberOfSegments-1) {
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setKeyDown("ctrl");
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setKeyDown("alt");
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makeRectangle(currentEndX, 0, xMax, yMax);
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setKeyDown("none");
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}
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if (i>0) {
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setKeyDown("ctrl");
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setKeyDown("alt");
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makeRectangle(0, 0, currentStartX, yMax);
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setKeyDown("none");
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}
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} while (selectionType()>3);
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run("MRI Roi Converter");
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roiManager("Add");
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}
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} else {
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run("MRI Roi Converter");
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roiManager("Add");
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}
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resetThreshold();
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roiManager("Select", 0);
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roiManager("Delete");
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run("Clear Results");
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roiManager("Measure");
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for (i=0; i<numberOfSegments; i++) {
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lengths[i] = getResult("Length", i);
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roiManager("Select", i);
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getSelectionCoordinates(x, y);
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xs = x[0];
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ys = y[0];
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xe = x[x.length-1];
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ye = y[y.length-1];
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toScaled(xs, ys);
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toScaled(xe, ye);
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distances[i] = sqrt (((xe - xs) * (xe - xs)) + ((ye - ys) * (ye - ys)));
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}
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}
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function measureWidthPerpendicularLines() {
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width = getWidth();
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if (!randomSet) {
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random("seed", getTime());
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randomSet = true;
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}
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|
selectSkinBorder();
|
|
run("Fit Spline");
|
|
getSelectionCoordinates(x, y);
|
|
Array.getStatistics(y, yMin);
|
|
numberOfLinesTried = 0;
|
|
numberOfLinesFound = 0;
|
|
maxNumberOfTrials = numberOfLines * 100;
|
|
maxIndex = x.length - 2;
|
|
minIndex = 1;
|
|
widths = newArray(numberOfLines);
|
|
while (numberOfLinesFound<numberOfLines && numberOfLinesTried<maxNumberOfTrials) {
|
|
index =minIndex + round (random * ((maxIndex - minIndex)));
|
|
makeLine(x[index], y[index], x[index+1], y[index+1]);
|
|
run("Rotate...", "angle=90");
|
|
getSelectionCoordinates(xL, yL);
|
|
x1 = xL[0];
|
|
y1 = yL[0];
|
|
x2 = xL[xL.length-1];
|
|
y2 = yL[yL.length-1];
|
|
x0 = x1 - y1 * ((x2-x1) / (y2-y1));
|
|
if (x0>=0 && x0 < width) {
|
|
widths[numberOfLinesFound] = findUpperEdgeIndex(x[index], y[index], x0, 0);
|
|
numberOfLinesFound++;
|
|
roiManager("Add");
|
|
}
|
|
numberOfLinesTried++;
|
|
}
|
|
return widths;
|
|
}
|
|
|
|
function measureWidthVerticalLines() {
|
|
roiManager("Reset");
|
|
selectSkinBorder();
|
|
run("MRI Extrema", minRadius);
|
|
call("roi.RoiConverter.addVerticalLinesToRoiManager");
|
|
run("Select None");
|
|
run("Clear Results");
|
|
roiManager("Measure");
|
|
widths = newArray(nResults);
|
|
for (i=0; i<nResults; i++) {
|
|
widths[i] = getResult("Length", i);
|
|
}
|
|
return widths;
|
|
}
|
|
|
|
function saveControlImage(widths, distances) {
|
|
colorR = newArray(2);
|
|
colorG = newArray(2);
|
|
colorB = newArray(2);
|
|
colorR[0] = COLOR1_R;
|
|
colorG[0] = COLOR1_G;
|
|
colorB[0] = COLOR1_B;
|
|
colorR[1] = COLOR2_R;
|
|
colorG[1] = COLOR2_G;
|
|
colorB[1] = COLOR2_B;
|
|
|
|
run("RGB Color");
|
|
|
|
for (i=0; i<distances.length; i++) {
|
|
setForegroundColor(colorR[i % 2], colorG[i % 2], colorB[i % 2]);
|
|
roiManager("select", i);
|
|
roiManager("Set Line Width", LINE_WIDTH1);
|
|
roiManager("Draw");
|
|
}
|
|
setForegroundColor(colorR[0], colorG[0], colorB[0]);
|
|
for (i=distances.length; i<distances.length + widths.length; i++) {
|
|
roiManager("select", i);
|
|
roiManager("Set Line Width", LINE_WIDTH2);
|
|
roiManager("Draw");
|
|
}
|
|
setForegroundColor(colorR[1], colorG[1], colorB[1]);
|
|
for (i=distances.length+widths.length; i<roiManager("Count"); i++) {
|
|
roiManager("select", i);
|
|
roiManager("Set Line Width", LINE_WIDTH2);
|
|
roiManager("Draw");
|
|
}
|
|
if (!File.exists(folder + "/" + "control/")) File.makeDirectory(folder+ "/" + "control/");
|
|
saveAs("png", folder + "/" + "control/" + File.nameWithoutExtension + ".png");
|
|
close();
|
|
}
|
|
|
|
function openCSVFile(filename, headings) {
|
|
if (File.exists(filename)) File.delete(filename);
|
|
file = File.open(filename);
|
|
print(file, headings);
|
|
return file;
|
|
}
|
|
|
|
function createTable(title, headings) {
|
|
f = "[" + title + "]";
|
|
if (isOpen(title))
|
|
print(f, "\\Clear");
|
|
else
|
|
run("Table...", "name="+f+" width=250 height=600");
|
|
print(f, "\\Headings:"+headings);
|
|
return f;
|
|
}
|
|
|