Example #1
0
  /** Performs actual projection using specified method. */
  public void doProjection() {
    if (imp == null) return;
    sliceCount = 0;
    if (method < AVG_METHOD || method > MEDIAN_METHOD) method = AVG_METHOD;
    for (int slice = startSlice; slice <= stopSlice; slice += increment) sliceCount++;
    if (method == MEDIAN_METHOD) {
      projImage = doMedianProjection();
      return;
    }

    // Create new float processor for projected pixels.
    FloatProcessor fp = new FloatProcessor(imp.getWidth(), imp.getHeight());
    ImageStack stack = imp.getStack();
    RayFunction rayFunc = getRayFunction(method, fp);
    if (IJ.debugMode == true) {
      IJ.log("\nProjecting stack from: " + startSlice + " to: " + stopSlice);
    }

    // Determine type of input image. Explicit determination of
    // processor type is required for subsequent pixel
    // manipulation.  This approach is more efficient than the
    // more general use of ImageProcessor's getPixelValue and
    // putPixel methods.
    int ptype;
    if (stack.getProcessor(1) instanceof ByteProcessor) ptype = BYTE_TYPE;
    else if (stack.getProcessor(1) instanceof ShortProcessor) ptype = SHORT_TYPE;
    else if (stack.getProcessor(1) instanceof FloatProcessor) ptype = FLOAT_TYPE;
    else {
      IJ.error("Z Project", "Non-RGB stack required");
      return;
    }

    // Do the projection.
    for (int n = startSlice; n <= stopSlice; n += increment) {
      IJ.showStatus("ZProjection " + color + ": " + n + "/" + stopSlice);
      IJ.showProgress(n - startSlice, stopSlice - startSlice);
      projectSlice(stack.getPixels(n), rayFunc, ptype);
    }

    // Finish up projection.
    if (method == SUM_METHOD) {
      fp.resetMinAndMax();
      projImage = new ImagePlus(makeTitle(), fp);
    } else if (method == SD_METHOD) {
      rayFunc.postProcess();
      fp.resetMinAndMax();
      projImage = new ImagePlus(makeTitle(), fp);
    } else {
      rayFunc.postProcess();
      projImage = makeOutputImage(imp, fp, ptype);
    }

    if (projImage == null) IJ.error("Z Project", "Error computing projection.");
  }
Example #2
0
 public StandardDeviation(FloatProcessor fp, int num) {
   result = (float[]) fp.getPixels();
   len = result.length;
   this.num = num;
   sum = new double[len];
   sum2 = new double[len];
 }
Example #3
0
  /** Generate output image whose type is same as input image. */
  private ImagePlus makeOutputImage(ImagePlus imp, FloatProcessor fp, int ptype) {
    int width = imp.getWidth();
    int height = imp.getHeight();
    float[] pixels = (float[]) fp.getPixels();
    ImageProcessor oip = null;

    // Create output image consistent w/ type of input image.
    int size = pixels.length;
    switch (ptype) {
      case BYTE_TYPE:
        oip = imp.getProcessor().createProcessor(width, height);
        byte[] pixels8 = (byte[]) oip.getPixels();
        for (int i = 0; i < size; i++) pixels8[i] = (byte) pixels[i];
        break;
      case SHORT_TYPE:
        oip = imp.getProcessor().createProcessor(width, height);
        short[] pixels16 = (short[]) oip.getPixels();
        for (int i = 0; i < size; i++) pixels16[i] = (short) pixels[i];
        break;
      case FLOAT_TYPE:
        oip = new FloatProcessor(width, height, pixels, null);
        break;
    }

    // Adjust for display.
    // Calling this on non-ByteProcessors ensures image
    // processor is set up to correctly display image.
    oip.resetMinAndMax();

    // Create new image plus object. Don't use
    // ImagePlus.createImagePlus here because there may be
    // attributes of input image that are not appropriate for
    // projection.
    return new ImagePlus(makeTitle(), oip);
  }
Example #4
0
 /** Simple constructor since no preprocessing is necessary. */
 public MinIntensity(FloatProcessor fp) {
   fpixels = (float[]) fp.getPixels();
   len = fpixels.length;
   for (int i = 0; i < len; i++) fpixels[i] = Float.MAX_VALUE;
 }
Example #5
0
 /**
  * Constructor requires number of slices to be projected. This is used to determine average at
  * each pixel.
  */
 public AverageIntensity(FloatProcessor fp, int num) {
   fpixels = (float[]) fp.getPixels();
   len = fpixels.length;
   this.num = num;
 }