Exemplo n.º 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();
 }
Exemplo n.º 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;
 }
Exemplo n.º 3
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);
      }
    }
  }