Ejemplo n.º 1
0
 void createMask(ImagePlus imp) {
   Roi roi = imp.getRoi();
   boolean useInvertingLut = Prefs.useInvertingLut;
   Prefs.useInvertingLut = false;
   if (roi == null || !(roi.isArea() || roi.getType() == Roi.POINT)) {
     createMaskFromThreshold(imp);
     Prefs.useInvertingLut = useInvertingLut;
     return;
   }
   ImagePlus maskImp = null;
   Frame frame = WindowManager.getFrame("Mask");
   if (frame != null && (frame instanceof ImageWindow))
     maskImp = ((ImageWindow) frame).getImagePlus();
   if (maskImp == null) {
     ImageProcessor ip = new ByteProcessor(imp.getWidth(), imp.getHeight());
     if (!Prefs.blackBackground) ip.invertLut();
     maskImp = new ImagePlus("Mask", ip);
     maskImp.show();
   }
   ImageProcessor ip = maskImp.getProcessor();
   ip.setRoi(roi);
   ip.setValue(255);
   ip.fill(ip.getMask());
   maskImp.updateAndDraw();
   Prefs.useInvertingLut = useInvertingLut;
 }
Ejemplo n.º 2
0
 void createMask(ImagePlus imp) {
   Roi roi = imp.getRoi();
   boolean useInvertingLut = Prefs.useInvertingLut;
   Prefs.useInvertingLut = false;
   boolean selectAll =
       roi != null
           && roi.getType() == Roi.RECTANGLE
           && roi.getBounds().width == imp.getWidth()
           && roi.getBounds().height == imp.getHeight()
           && imp.isThreshold();
   if (roi == null || !(roi.isArea() || roi.getType() == Roi.POINT) || selectAll) {
     createMaskFromThreshold(imp);
     Prefs.useInvertingLut = useInvertingLut;
     return;
   }
   ImagePlus maskImp = null;
   Frame frame = WindowManager.getFrame("Mask");
   if (frame != null && (frame instanceof ImageWindow))
     maskImp = ((ImageWindow) frame).getImagePlus();
   if (maskImp == null) {
     ImageProcessor ip = new ByteProcessor(imp.getWidth(), imp.getHeight());
     if (!Prefs.blackBackground) ip.invertLut();
     maskImp = new ImagePlus("Mask", ip);
     maskImp.show();
   }
   ImageProcessor ip = maskImp.getProcessor();
   ip.setRoi(roi);
   ip.setValue(255);
   ip.fill(ip.getMask());
   Calibration cal = imp.getCalibration();
   if (cal.scaled()) {
     Calibration cal2 = maskImp.getCalibration();
     cal2.pixelWidth = cal.pixelWidth;
     cal2.pixelHeight = cal.pixelHeight;
     cal2.setUnit(cal.getUnit());
   }
   maskImp.updateAndRepaintWindow();
   Prefs.useInvertingLut = useInvertingLut;
 }
  public void run(ImageProcessor ip) {
    String[] imageNames = getOpenImageNames();
    if (imageNames[0] == "None") {
      IJ.error("need at least 2 binary open images");
      return;
    }
    double previousMinOverlap = Prefs.get("BVTB.BinaryFeatureExtractor.minOverlap", 0);
    boolean previousCombine = Prefs.get("BVTB.BinaryFeatureExtractor.combine", false);

    GenericDialog gd = new GenericDialog("Binary Feature Extractor");
    gd.addChoice("Objects image", imageNames, imageNames[0]);
    gd.addChoice("Selector image", imageNames, imageNames[1]);
    gd.addNumericField("Object_overlap in % (0=off)", previousMinOverlap, 0, 9, "");
    gd.addCheckbox("Combine objects and selectors", previousCombine);
    gd.addCheckbox("Count output", true);
    gd.addCheckbox("Analysis tables", false);
    gd.showDialog();
    if (gd.wasCanceled()) {
      return;
    }
    String objectsImgTitle = gd.getNextChoice();
    String selectorsImgTitle = gd.getNextChoice();
    double minOverlap = gd.getNextNumber();
    boolean combineImages = gd.getNextBoolean();
    boolean showCountOutput = gd.getNextBoolean();
    boolean showAnalysis = gd.getNextBoolean();
    if (gd.invalidNumber() || minOverlap < 0 || minOverlap > 100) {
      IJ.error("invalid number");
      return;
    }
    Prefs.set("BVTB.BinaryFeatureExtractor.minOverlap", minOverlap);
    Prefs.set("BVTB.BinaryFeatureExtractor.combine", combineImages);

    if (objectsImgTitle.equals(selectorsImgTitle)) {
      IJ.error("images need to be different");
      return;
    }

    ImagePlus objectsImp = WindowManager.getImage(objectsImgTitle);
    ImageProcessor objectsIP = objectsImp.getProcessor();
    ImagePlus selectorsImp = WindowManager.getImage(selectorsImgTitle);
    ImageProcessor selectorsIP = selectorsImp.getProcessor();

    if (!objectsIP.isBinary() || !selectorsIP.isBinary()) {
      IJ.error("works with 8-bit binary images only");
      return;
    }

    if ((objectsImp.getWidth() != selectorsImp.getWidth())
        || objectsImp.getHeight() != selectorsImp.getHeight()) {
      IJ.error("images need to be of the same size");
      return;
    }

    // close any existing RoiManager before instantiating a new one for this analysis
    RoiManager oldRM = RoiManager.getInstance2();
    if (oldRM != null) {
      oldRM.close();
    }

    RoiManager objectsRM = new RoiManager(true);
    ResultsTable objectsRT = new ResultsTable();
    ParticleAnalyzer analyzeObjects =
        new ParticleAnalyzer(analyzerOptions, measurementFlags, objectsRT, 0.0, 999999999.9);
    analyzeObjects.setRoiManager(objectsRM);

    analyzeObjects.analyze(objectsImp);
    objectsRM.runCommand("Show None");
    int objectNumber = objectsRT.getCounter();

    Roi[] objectRoi = objectsRM.getRoisAsArray();

    ResultsTable measureSelectorsRT = new ResultsTable();
    Analyzer overlapAnalyzer = new Analyzer(selectorsImp, measurementFlags, measureSelectorsRT);

    ImagePlus outputImp =
        IJ.createImage("output", "8-bit black", objectsImp.getWidth(), objectsImp.getHeight(), 1);
    ImageProcessor outputIP = outputImp.getProcessor();

    double[] measuredOverlap = new double[objectNumber];

    outputIP.setValue(255.0);
    for (int o = 0; o < objectNumber; o++) {
      selectorsImp.killRoi();
      selectorsImp.setRoi(objectRoi[o]);
      overlapAnalyzer.measure();
      measuredOverlap[o] = measureSelectorsRT.getValue("%Area", o);
      if (minOverlap != 0.0 && measuredOverlap[o] >= minOverlap) {
        outputIP.fill(objectRoi[o]);
        finalCount++;
      } else if (minOverlap == 0.0 && measuredOverlap[o] > 0.0) {
        outputIP.fill(objectRoi[o]);
        finalCount++;
      }
    }
    // measureSelectorsRT.show("Objects");

    selectorsImp.killRoi();
    RoiManager selectorRM = new RoiManager(true);
    ResultsTable selectorRT = new ResultsTable();
    ParticleAnalyzer.setRoiManager(selectorRM);
    ParticleAnalyzer analyzeSelectors =
        new ParticleAnalyzer(analyzerOptions, measurementFlags, selectorRT, 0.0, 999999999.9);
    analyzeSelectors.analyze(selectorsImp);
    selectorRM.runCommand("Show None");
    int selectorNumber = selectorRT.getCounter();

    if (combineImages) {
      outputImp.updateAndDraw();
      Roi[] selectorRoi = selectorRM.getRoisAsArray();

      ResultsTable measureObjectsRT = new ResultsTable();
      Analyzer selectorAnalyzer = new Analyzer(outputImp, measurementFlags, measureObjectsRT);

      double[] selectorOverlap = new double[selectorNumber];
      outputIP.setValue(255.0);
      for (int s = 0; s < selectorNumber; s++) {
        outputImp.killRoi();
        outputImp.setRoi(selectorRoi[s]);
        selectorAnalyzer.measure();
        selectorOverlap[s] = measureObjectsRT.getValue("%Area", s);
        if (selectorOverlap[s] > 0.0d) {
          outputIP.fill(selectorRoi[s]);
        }
      }
      selectorRoi = null;
      selectorAnalyzer = null;
      measureObjectsRT = null;
    }
    // selectorRT.show("Selectors");
    outputImp.killRoi();
    String outputImageTitle = WindowManager.getUniqueName("Extracted_" + objectsImgTitle);
    outputImp.setTitle(outputImageTitle);
    outputImp.show();
    outputImp.changes = true;

    if (showCountOutput) {
      String[] openTextWindows = WindowManager.getNonImageTitles();
      boolean makeNewTable = true;
      for (int w = 0; w < openTextWindows.length; w++) {
        if (openTextWindows[w].equals("BFE_Results")) {
          makeNewTable = false;
        }
      }

      TextWindow existingCountTable = ResultsTable.getResultsWindow();
      if (makeNewTable) {
        countTable = new ResultsTable();
        countTable.setPrecision(0);
        countTable.setValue("Image", 0, outputImageTitle);
        countTable.setValue("Objects", 0, objectNumber);
        countTable.setValue("Selectors", 0, selectorNumber);
        countTable.setValue("Extracted", 0, finalCount);
        countTable.show("BFE_Results");
      } else {
        IJ.renameResults("BFE_Results", "Results");
        countTable = ResultsTable.getResultsTable();
        countTable.setPrecision(0);
        countTable.incrementCounter();
        countTable.addValue("Image", outputImageTitle);
        countTable.addValue("Objects", objectNumber);
        countTable.addValue("Selectors", selectorNumber);
        countTable.addValue("Extracted", finalCount);
        IJ.renameResults("Results", "BFE_Results");
        countTable.show("BFE_Results");
      }
    }

    if (showAnalysis) {
      ResultsTable extractedRT = new ResultsTable();
      ParticleAnalyzer analyzeExtracted =
          new ParticleAnalyzer(
              ParticleAnalyzer.CLEAR_WORKSHEET | ParticleAnalyzer.RECORD_STARTS,
              measurementFlags,
              extractedRT,
              0.0,
              999999999.9);
      analyzeExtracted.analyze(outputImp);
      objectsRT.show("Objects");
      selectorRT.show("Selectors");
      extractedRT.show("Extracted");
    } else {
      objectsRT = null;
      selectorRT = null;
    }

    objectsRM = null;
    measureSelectorsRT = null;
    analyzeObjects = null;
    overlapAnalyzer = null;
    objectRoi = null;
    selectorRM = null;

    objectsImp.killRoi();
    objectsImp.changes = false;
    selectorsImp.changes = false;
  }