Beispiel #1
0
  public void showRois3D() {
    registerActiveImage();
    if (currentImage == null) return;
    // verifier que l'image active a les memes dimentions
    Object[] os = this.list.getSelectedValues();

    if (os.length == 1) {
      mcib3d.geom.Object3D o = ((Object3DGui) os[0]).getObject3D();
      currentImage.setSlice((o.getZmax() + o.getZmin()) / 2 + 1);
    }
    int nSlices = currentImage.getNSlices();

    currentROIs = new HashMap<Integer, Roi>(nSlices);
    // stores the roi mask to save memory..
    if (roiMask == null || !roiMask.sameDimentions(currentImage)) {
      roiMask = new ImageByte("mask", currentImage.getWidth(), currentImage.getHeight(), nSlices);
    } else {
      roiMask.erase();
    }
    ImageStack maskStack = roiMask.getImageStack();
    Object3DGui obj;
    for (Object o : os) {
      obj = (Object3DGui) o;
      obj.getObject3D().draw(maskStack, 255);
    }
    // roiMask.show();

    for (int i = 1; i <= nSlices; i++) {
      ImagePlus im = new ImagePlus("mask", maskStack.getProcessor(i));
      im.getProcessor().setThreshold(1, 255, ImageProcessor.NO_LUT_UPDATE);
      ThresholdToSelection tts = new ThresholdToSelection();
      tts.setup("", im);
      tts.run(im.getProcessor());
      Roi r = im.getRoi();
      if (r != null) currentROIs.put(i, r);
    }
    updateRoi();
  }
Beispiel #2
0
 void setStackDisplayRange(ImagePlus imp) {
   ImageStack stack = imp.getStack();
   double min = Double.MAX_VALUE;
   double max = -Double.MAX_VALUE;
   int n = stack.getSize();
   for (int i = 1; i <= n; i++) {
     if (!silentMode) IJ.showStatus("Calculating stack min and max: " + i + "/" + n);
     ImageProcessor ip = stack.getProcessor(i);
     ip.resetMinAndMax();
     if (ip.getMin() < min) min = ip.getMin();
     if (ip.getMax() > max) max = ip.getMax();
   }
   imp.getProcessor().setMinAndMax(min, max);
   imp.updateAndDraw();
 }
Beispiel #3
0
 /** Opens a stack of images. */
 ImagePlus openStack(ColorModel cm, boolean show) {
   ImageStack stack = new ImageStack(fi.width, fi.height, cm);
   long skip = fi.getOffset();
   Object pixels;
   try {
     ImageReader reader = new ImageReader(fi);
     InputStream is = createInputStream(fi);
     if (is == null) return null;
     IJ.resetEscape();
     for (int i = 1; i <= fi.nImages; i++) {
       if (!silentMode) IJ.showStatus("Reading: " + i + "/" + fi.nImages);
       if (IJ.escapePressed()) {
         IJ.beep();
         IJ.showProgress(1.0);
         silentMode = false;
         return null;
       }
       pixels = reader.readPixels(is, skip);
       if (pixels == null) break;
       stack.addSlice(null, pixels);
       skip = fi.gapBetweenImages;
       if (!silentMode) IJ.showProgress(i, fi.nImages);
     }
     is.close();
   } catch (Exception e) {
     IJ.log("" + e);
   } catch (OutOfMemoryError e) {
     IJ.outOfMemory(fi.fileName);
     stack.trim();
   }
   if (!silentMode) IJ.showProgress(1.0);
   if (stack.getSize() == 0) return null;
   if (fi.sliceLabels != null && fi.sliceLabels.length <= stack.getSize()) {
     for (int i = 0; i < fi.sliceLabels.length; i++) stack.setSliceLabel(fi.sliceLabels[i], i + 1);
   }
   ImagePlus imp = new ImagePlus(fi.fileName, stack);
   if (fi.info != null) imp.setProperty("Info", fi.info);
   if (show) imp.show();
   imp.setFileInfo(fi);
   setCalibration(imp);
   ImageProcessor ip = imp.getProcessor();
   if (ip.getMin() == ip.getMax()) // find stack min and max if first slice is blank
   setStackDisplayRange(imp);
   if (!silentMode) IJ.showProgress(1.0);
   silentMode = false;
   return imp;
 }
Beispiel #4
0
 protected void registerActiveImage() {
   ImagePlus activeImage = WindowManager.getCurrentImage();
   if (activeImage != null
       && activeImage.getProcessor() != null) { // && activeImage.getImageStackSize() > 1
     if (currentImage != null && currentImage.getWindow() != null && currentImage != activeImage) {
       // System.out.println("remove listener:"+currentImage.getTitle());
       ImageUtils.removeScrollListener(currentImage, this, this);
       currentImage.killRoi();
       currentImage.updateAndDraw();
       currentImage = null;
     }
     if (currentImage != activeImage) {
       // System.out.println("add listener:"+activeImage.getTitle());
       ImageUtils.addScrollListener(activeImage, this, this);
       this.currentImage = activeImage;
     }
   }
 }
Beispiel #5
0
  /** Opens the image. Displays it if 'show' is true. Returns an ImagePlus object if successful. */
  public ImagePlus open(boolean show) {
    ImagePlus imp = null;
    Object pixels;
    ProgressBar pb = null;
    ImageProcessor ip;

    ColorModel cm = createColorModel(fi);
    if (fi.nImages > 1) {
      return openStack(cm, show);
    }
    switch (fi.fileType) {
      case FileInfo.GRAY8:
      case FileInfo.COLOR8:
      case FileInfo.BITMAP:
        pixels = readPixels(fi);
        if (pixels == null) return null;
        ip = new ByteProcessor(width, height, (byte[]) pixels, cm);
        imp = new ImagePlus(fi.fileName, ip);
        break;
      case FileInfo.GRAY16_SIGNED:
      case FileInfo.GRAY16_UNSIGNED:
      case FileInfo.GRAY12_UNSIGNED:
        pixels = readPixels(fi);
        if (pixels == null) return null;
        ip = new ShortProcessor(width, height, (short[]) pixels, cm);
        imp = new ImagePlus(fi.fileName, ip);
        break;
      case FileInfo.GRAY32_INT:
      case FileInfo.GRAY32_UNSIGNED:
      case FileInfo.GRAY32_FLOAT:
      case FileInfo.GRAY24_UNSIGNED:
      case FileInfo.GRAY64_FLOAT:
        pixels = readPixels(fi);
        if (pixels == null) return null;
        ip = new FloatProcessor(width, height, (float[]) pixels, cm);
        imp = new ImagePlus(fi.fileName, ip);
        break;
      case FileInfo.RGB:
      case FileInfo.BGR:
      case FileInfo.ARGB:
      case FileInfo.ABGR:
      case FileInfo.BARG:
      case FileInfo.RGB_PLANAR:
        pixels = readPixels(fi);
        if (pixels == null) return null;
        ip = new ColorProcessor(width, height, (int[]) pixels);
        imp = new ImagePlus(fi.fileName, ip);
        break;
      case FileInfo.RGB48:
      case FileInfo.RGB48_PLANAR:
        boolean planar = fi.fileType == FileInfo.RGB48_PLANAR;
        Object[] pixelArray = (Object[]) readPixels(fi);
        if (pixelArray == null) return null;
        ImageStack stack = new ImageStack(width, height);
        stack.addSlice("Red", pixelArray[0]);
        stack.addSlice("Green", pixelArray[1]);
        stack.addSlice("Blue", pixelArray[2]);
        imp = new ImagePlus(fi.fileName, stack);
        imp.setDimensions(3, 1, 1);
        if (planar) imp.getProcessor().resetMinAndMax();
        imp.setFileInfo(fi);
        int mode = CompositeImage.COMPOSITE;
        if (fi.description != null) {
          if (fi.description.indexOf("mode=color") != -1) mode = CompositeImage.COLOR;
          else if (fi.description.indexOf("mode=gray") != -1) mode = CompositeImage.GRAYSCALE;
        }
        imp = new CompositeImage(imp, mode);
        if (!planar && fi.displayRanges == null) {
          for (int c = 1; c <= 3; c++) {
            imp.setPosition(c, 1, 1);
            imp.setDisplayRange(minValue, maxValue);
          }
          imp.setPosition(1, 1, 1);
        }
        break;
    }
    imp.setFileInfo(fi);
    setCalibration(imp);
    if (fi.info != null) imp.setProperty("Info", fi.info);
    if (fi.sliceLabels != null && fi.sliceLabels.length == 1 && fi.sliceLabels[0] != null)
      imp.setProperty("Label", fi.sliceLabels[0]);
    if (show) imp.show();
    return imp;
  }
Beispiel #6
0
  void setCalibration(ImagePlus imp) {
    if (fi.fileType == FileInfo.GRAY16_SIGNED) {
      if (IJ.debugMode) IJ.log("16-bit signed");
      double[] coeff = new double[2];
      coeff[0] = -32768.0;
      coeff[1] = 1.0;
      imp.getLocalCalibration().setFunction(Calibration.STRAIGHT_LINE, coeff, "gray value");
    }

    Properties props = decodeDescriptionString(fi);
    Calibration cal = imp.getCalibration();
    boolean calibrated = false;
    if (fi.pixelWidth > 0.0 && fi.unit != null) {
      cal.pixelWidth = fi.pixelWidth;
      cal.pixelHeight = fi.pixelHeight;
      cal.pixelDepth = fi.pixelDepth;
      cal.setUnit(fi.unit);
      calibrated = true;
    }

    if (fi.valueUnit != null) {
      int f = fi.calibrationFunction;
      if ((f >= Calibration.STRAIGHT_LINE && f <= Calibration.RODBARD2 && fi.coefficients != null)
          || f == Calibration.UNCALIBRATED_OD) {
        boolean zeroClip = props != null && props.getProperty("zeroclip", "false").equals("true");
        cal.setFunction(f, fi.coefficients, fi.valueUnit, zeroClip);
        calibrated = true;
      }
    }

    if (calibrated) checkForCalibrationConflict(imp, cal);

    if (fi.frameInterval != 0.0) cal.frameInterval = fi.frameInterval;

    if (props == null) return;

    cal.xOrigin = getDouble(props, "xorigin");
    cal.yOrigin = getDouble(props, "yorigin");
    cal.zOrigin = getDouble(props, "zorigin");
    cal.info = props.getProperty("info");

    cal.fps = getDouble(props, "fps");
    cal.loop = getBoolean(props, "loop");
    cal.frameInterval = getDouble(props, "finterval");
    cal.setTimeUnit(props.getProperty("tunit", "sec"));

    double displayMin = getDouble(props, "min");
    double displayMax = getDouble(props, "max");
    if (!(displayMin == 0.0 && displayMax == 0.0)) {
      int type = imp.getType();
      ImageProcessor ip = imp.getProcessor();
      if (type == ImagePlus.GRAY8 || type == ImagePlus.COLOR_256)
        ip.setMinAndMax(displayMin, displayMax);
      else if (type == ImagePlus.GRAY16 || type == ImagePlus.GRAY32) {
        if (ip.getMin() != displayMin || ip.getMax() != displayMax)
          ip.setMinAndMax(displayMin, displayMax);
      }
    }

    int stackSize = imp.getStackSize();
    if (stackSize > 1) {
      int channels = (int) getDouble(props, "channels");
      int slices = (int) getDouble(props, "slices");
      int frames = (int) getDouble(props, "frames");
      if (channels == 0) channels = 1;
      if (slices == 0) slices = 1;
      if (frames == 0) frames = 1;
      // IJ.log("setCalibration: "+channels+"  "+slices+"  "+frames);
      if (channels * slices * frames == stackSize) {
        imp.setDimensions(channels, slices, frames);
        if (getBoolean(props, "hyperstack")) imp.setOpenAsHyperStack(true);
      }
    }
  }
Beispiel #7
0
  /** Restores original disk or network version of image. */
  public void revertToSaved(ImagePlus imp) {
    Image img;
    ProgressBar pb = IJ.getInstance().getProgressBar();
    ImageProcessor ip;
    String path = fi.directory + fi.fileName;

    if (fi.fileFormat == fi.GIF_OR_JPG) {
      // restore gif or jpg
      img = Toolkit.getDefaultToolkit().createImage(path);
      imp.setImage(img);
      if (imp.getType() == ImagePlus.COLOR_RGB) Opener.convertGrayJpegTo8Bits(imp);
      return;
    }

    if (fi.fileFormat == fi.DICOM) {
      // restore DICOM
      ImagePlus imp2 = (ImagePlus) IJ.runPlugIn("ij.plugin.DICOM", path);
      if (imp2 != null) imp.setProcessor(null, imp2.getProcessor());
      return;
    }

    if (fi.fileFormat == fi.BMP) {
      // restore BMP
      ImagePlus imp2 = (ImagePlus) IJ.runPlugIn("ij.plugin.BMP_Reader", path);
      if (imp2 != null) imp.setProcessor(null, imp2.getProcessor());
      return;
    }

    if (fi.fileFormat == fi.PGM) {
      // restore PGM
      ImagePlus imp2 = (ImagePlus) IJ.runPlugIn("ij.plugin.PGM_Reader", path);
      if (imp2 != null) imp.setProcessor(null, imp2.getProcessor());
      return;
    }

    if (fi.fileFormat == fi.ZIP_ARCHIVE) {
      // restore ".zip" file
      ImagePlus imp2 = (new Opener()).openZip(path);
      if (imp2 != null) imp.setProcessor(null, imp2.getProcessor());
      return;
    }

    // restore PNG or another image opened using ImageIO
    if (fi.fileFormat == fi.IMAGEIO) {
      ImagePlus imp2 = (new Opener()).openUsingImageIO(path);
      if (imp2 != null) imp.setProcessor(null, imp2.getProcessor());
      return;
    }

    if (fi.nImages > 1) return;

    ColorModel cm;
    if (fi.url == null || fi.url.equals("")) IJ.showStatus("Loading: " + path);
    else IJ.showStatus("Loading: " + fi.url + fi.fileName);
    Object pixels = readPixels(fi);
    if (pixels == null) return;
    cm = createColorModel(fi);
    switch (fi.fileType) {
      case FileInfo.GRAY8:
      case FileInfo.COLOR8:
      case FileInfo.BITMAP:
        ip = new ByteProcessor(width, height, (byte[]) pixels, cm);
        imp.setProcessor(null, ip);
        break;
      case FileInfo.GRAY16_SIGNED:
      case FileInfo.GRAY16_UNSIGNED:
      case FileInfo.GRAY12_UNSIGNED:
        ip = new ShortProcessor(width, height, (short[]) pixels, cm);
        imp.setProcessor(null, ip);
        break;
      case FileInfo.GRAY32_INT:
      case FileInfo.GRAY32_FLOAT:
        ip = new FloatProcessor(width, height, (float[]) pixels, cm);
        imp.setProcessor(null, ip);
        break;
      case FileInfo.RGB:
      case FileInfo.BGR:
      case FileInfo.ARGB:
      case FileInfo.ABGR:
      case FileInfo.RGB_PLANAR:
        img =
            Toolkit.getDefaultToolkit()
                .createImage(new MemoryImageSource(width, height, (int[]) pixels, 0, width));
        imp.setImage(img);
        break;
    }
  }