Beispiel #1
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 #2
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 #3
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;
  }