Beispiel #1
0
 public void reduceHyperstack(ImagePlus imp, int factor, boolean reduceSlices) {
   int channels = imp.getNChannels();
   int slices = imp.getNSlices();
   int frames = imp.getNFrames();
   int zfactor = reduceSlices ? factor : 1;
   int tfactor = reduceSlices ? 1 : factor;
   ImageStack stack = imp.getStack();
   ImageStack stack2 = new ImageStack(imp.getWidth(), imp.getHeight());
   boolean virtual = stack.isVirtual();
   int slices2 = slices / zfactor + ((slices % zfactor) != 0 ? 1 : 0);
   int frames2 = frames / tfactor + ((frames % tfactor) != 0 ? 1 : 0);
   int n = channels * slices2 * frames2;
   int count = 1;
   for (int t = 1; t <= frames; t += tfactor) {
     for (int z = 1; z <= slices; z += zfactor) {
       for (int c = 1; c <= channels; c++) {
         int i = imp.getStackIndex(c, z, t);
         IJ.showProgress(i, n);
         ImageProcessor ip = stack.getProcessor(imp.getStackIndex(c, z, t));
         // IJ.log(count++ +"  "+i+" "+c+" "+z+" "+t);
         stack2.addSlice(stack.getSliceLabel(i), ip);
       }
     }
   }
   imp.setStack(stack2, channels, slices2, frames2);
   Calibration cal = imp.getCalibration();
   if (cal.scaled()) cal.pixelDepth *= zfactor;
   if (virtual) imp.setTitle(imp.getTitle());
   IJ.showProgress(1.0);
 }
Beispiel #2
0
 byte[] getJar(String address) {
   // System.out.println("getJar: "+address);
   byte[] data;
   try {
     URL url = new URL(address);
     IJ.showStatus("Connecting to " + IJ.URL);
     URLConnection uc = url.openConnection();
     int len = uc.getContentLength();
     if (IJ.debugMode) IJ.log("Updater (url): " + address + " " + len);
     if (len <= 0) return null;
     String name = address.contains("wsr") ? "daily build (" : "ij.jar (";
     IJ.showStatus("Downloading " + name + IJ.d2s((double) len / 1048576, 1) + "MB)");
     InputStream in = uc.getInputStream();
     data = new byte[len];
     int n = 0;
     while (n < len) {
       int count = in.read(data, n, len - n);
       if (count < 0) throw new EOFException();
       n += count;
       IJ.showProgress(n, len);
     }
     in.close();
   } catch (IOException e) {
     if (IJ.debugMode) IJ.log("" + e);
     return null;
   }
   if (IJ.debugMode) IJ.wait(6000);
   return data;
 }
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
 void write16BitStack(OutputStream out, Object[] stack) throws IOException {
   showProgressBar = false;
   for (int i = 0; i < fi.nImages; i++) {
     IJ.showStatus("Writing: " + (i + 1) + "/" + fi.nImages);
     write16BitImage(out, (short[]) stack[i]);
     IJ.showProgress((double) (i + 1) / fi.nImages);
   }
 }
Beispiel #5
0
 public void reduceStack(ImagePlus imp, int factor) {
   ImageStack stack = imp.getStack();
   boolean virtual = stack.isVirtual();
   int n = stack.getSize();
   ImageStack stack2 = new ImageStack(stack.getWidth(), stack.getHeight());
   for (int i = 1; i <= n; i += factor) {
     if (virtual) IJ.showProgress(i, n);
     stack2.addSlice(stack.getSliceLabel(i), stack.getProcessor(i));
   }
   imp.setStack(null, stack2);
   if (virtual) {
     IJ.showProgress(1.0);
     imp.setTitle(imp.getTitle());
   }
   Calibration cal = imp.getCalibration();
   if (cal.scaled()) cal.pixelDepth *= factor;
 }
Beispiel #6
0
 void createNewStack(ImagePlus imp, ImageProcessor ip) {
   int nSlices = imp.getStackSize();
   int w = imp.getWidth(), h = imp.getHeight();
   ImagePlus imp2 = imp.createImagePlus();
   Rectangle r = ip.getRoi();
   boolean crop = r.width != imp.getWidth() || r.height != imp.getHeight();
   ImageStack stack1 = imp.getStack();
   ImageStack stack2 = new ImageStack(newWidth, newHeight);
   ImageProcessor ip1, ip2;
   int method = interpolationMethod;
   if (w == 1 || h == 1) method = ImageProcessor.NONE;
   for (int i = 1; i <= nSlices; i++) {
     IJ.showStatus("Scale: " + i + "/" + nSlices);
     ip1 = stack1.getProcessor(i);
     String label = stack1.getSliceLabel(i);
     if (crop) {
       ip1.setRoi(r);
       ip1 = ip1.crop();
     }
     ip1.setInterpolationMethod(method);
     ip2 = ip1.resize(newWidth, newHeight, averageWhenDownsizing);
     if (ip2 != null) stack2.addSlice(label, ip2);
     IJ.showProgress(i, nSlices);
   }
   imp2.setStack(title, stack2);
   Calibration cal = imp2.getCalibration();
   if (cal.scaled()) {
     cal.pixelWidth *= 1.0 / xscale;
     cal.pixelHeight *= 1.0 / yscale;
   }
   IJ.showProgress(1.0);
   int[] dim = imp.getDimensions();
   imp2.setDimensions(dim[2], dim[3], dim[4]);
   if (imp.isComposite()) {
     imp2 = new CompositeImage(imp2, ((CompositeImage) imp).getMode());
     ((CompositeImage) imp2).copyLuts(imp);
   }
   if (imp.isHyperStack()) imp2.setOpenAsHyperStack(true);
   if (newDepth > 0 && newDepth != oldDepth)
     imp2 = (new Resizer()).zScale(imp2, newDepth, interpolationMethod);
   if (imp2 != null) {
     imp2.show();
     imp2.changes = true;
   }
 }
Beispiel #7
0
    public void run() {
      final int width = this.w;
      final int height = this.h;
      final int depth = this.d;
      final byte[][] daTa = this.data;
      final boolean inverse = inv;
      int zStart, zStop, zBegin, zEnd;
      // float[] sk;
      int n = width;
      if (height > n) n = height;
      if (depth > n) n = depth;
      int noResult = 3 * (n + 1) * (n + 1);
      int[] tempInt = new int[n];
      int[] tempS = new int[n];
      boolean nonempty;
      int test, min, delta;
      for (int j = thread; j < height; j += nThreads) {
        final int wj = width * j;
        IJ.showProgress(j / (1. * height));
        for (int i = 0; i < width; i++) {
          nonempty = false;
          for (int k = 0; k < depth; k++) {
            tempS[k] = (int) s[k][i + wj];
            if (tempS[k] > 0) nonempty = true;
          }
          if (nonempty) {
            zStart = 0;
            while ((zStart < (depth - 1)) && (tempS[zStart] == 0)) zStart++;
            if (zStart > 0) zStart--;
            zStop = depth - 1;
            while ((zStop > 0) && (tempS[zStop] == 0)) zStop--;
            if (zStop < (depth - 1)) zStop++;

            for (int k = 0; k < depth; k++) {
              // Limit to the non-background to save time,
              if (((daTa[k][i + wj] & 255) >= 128) ^ inverse) {
                min = noResult;
                zBegin = zStart;
                zEnd = zStop;
                if (zBegin > k) zBegin = k;
                if (zEnd < k) zEnd = k;
                delta = k - zBegin;
                for (int z = zBegin; z <= zEnd; z++) {
                  test = tempS[z] + delta * delta--;
                  if (test < min) min = test;
                  // min = (test < min) ? test : min;
                }
                tempInt[k] = min;
              }
            }
            for (int k = 0; k < depth; k++) {
              s[k][i + wj] = tempInt[k];
            }
          }
        }
      }
    }
 public static byte[] download(String urlString, String name) {
   int maxLength = 52428800; // 50MB
   URL url = null;
   boolean unknownLength = false;
   byte[] data = null;
   ;
   int n = 0;
   try {
     url = new URL(urlString);
     if (IJ.debugMode) IJ.log("PluginInstaller: " + urlString + "  " + url);
     if (url == null) return null;
     URLConnection uc = url.openConnection();
     int len = uc.getContentLength();
     unknownLength = len < 0;
     if (unknownLength) len = maxLength;
     if (name != null) IJ.showStatus("Downloading " + url.getFile());
     InputStream in = uc.getInputStream();
     data = new byte[len];
     int lenk = len / 1024;
     while (n < len) {
       int count = in.read(data, n, len - n);
       if (count < 0) break;
       n += count;
       if (name != null)
         IJ.showStatus("Downloading " + name + " (" + (n / 1024) + "/" + lenk + "k)");
       IJ.showProgress(n, len);
     }
     in.close();
   } catch (Exception e) {
     String msg = "" + e;
     if (!msg.contains("://")) msg += "\n   " + urlString;
     IJ.error("Plugin Installer", msg);
     return null;
   } finally {
     IJ.showProgress(1.0);
   }
   if (name != null) IJ.showStatus("");
   if (unknownLength) {
     byte[] data2 = data;
     data = new byte[n];
     for (int i = 0; i < n; i++) data[i] = data2[i];
   }
   return data;
 }
Beispiel #9
0
  public void run(String arg) {
    int[] wList = WindowManager.getIDList();
    if (wList == null) {
      IJ.error("No images are open.");
      return;
    }

    double thalf = 0.5;
    boolean keep;

    GenericDialog gd = new GenericDialog("Bleach correction");

    gd.addNumericField("t½:", thalf, 1);
    gd.addCheckbox("Keep source stack:", true);
    gd.showDialog();
    if (gd.wasCanceled()) return;

    long start = System.currentTimeMillis();
    thalf = gd.getNextNumber();
    keep = gd.getNextBoolean();
    if (keep) IJ.run("Duplicate...", "title='Bleach corrected' duplicate");
    ImagePlus imp1 = WindowManager.getCurrentImage();
    int d1 = imp1.getStackSize();
    double v1, v2;
    int width = imp1.getWidth();
    int height = imp1.getHeight();
    ImageProcessor ip1, ip2, ip3;

    int slices = imp1.getStackSize();
    ImageStack stack1 = imp1.getStack();
    ImageStack stack2 = imp1.getStack();
    int currentSlice = imp1.getCurrentSlice();

    for (int n = 1; n <= slices; n++) {
      ip1 = stack1.getProcessor(n);
      ip3 = stack1.getProcessor(1);
      ip2 = stack2.getProcessor(n);
      for (int x = 0; x < width; x++) {
        for (int y = 0; y < height; y++) {
          v1 = ip1.getPixelValue(x, y);
          v2 = ip3.getPixelValue(x, y);

          // =B8/(EXP(-C$7*A8))
          v1 = (v1 / Math.exp(-n * thalf));
          ip2.putPixelValue(x, y, v1);
        }
      }
      IJ.showProgress((double) n / slices);
      IJ.showStatus(n + "/" + slices);
    }

    // stack2.show();
    imp1.updateAndDraw();
  }
Beispiel #10
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.");
  }
Beispiel #11
0
 void write16BitVirtualStack(OutputStream out, VirtualStack virtualStack) throws IOException {
   showProgressBar = false;
   boolean flip = "FlipTheseImages".equals(fi.fileName);
   for (int i = 1; i <= fi.nImages; i++) {
     IJ.showStatus("Writing: " + i + "/" + fi.nImages);
     ImageProcessor ip = virtualStack.getProcessor(i);
     if (flip) ip.flipVertical();
     short[] pixels = (short[]) ip.getPixels();
     write16BitImage(out, pixels);
     IJ.showProgress((double) i / fi.nImages);
   }
 }
Beispiel #12
0
 void createNewStack(ImagePlus imp, ImageProcessor ip) {
   Rectangle r = ip.getRoi();
   boolean crop = r.width != imp.getWidth() || r.height != imp.getHeight();
   int nSlices = imp.getStackSize();
   ImageStack stack1 = imp.getStack();
   ImageStack stack2 = new ImageStack(newWidth, newHeight);
   ImageProcessor ip1, ip2;
   boolean interp = interpolate;
   if (imp.getWidth() == 1 || imp.getHeight() == 1) interp = false;
   for (int i = 1; i <= nSlices; i++) {
     IJ.showStatus("Scale: " + i + "/" + nSlices);
     ip1 = stack1.getProcessor(i);
     String label = stack1.getSliceLabel(i);
     if (crop) {
       ip1.setRoi(r);
       ip1 = ip1.crop();
     }
     ip1.setInterpolate(interp);
     ip2 = ip1.resize(newWidth, newHeight);
     if (ip2 != null) stack2.addSlice(label, ip2);
     IJ.showProgress(i, nSlices);
   }
   ImagePlus imp2 = imp.createImagePlus();
   imp2.setStack(title, stack2);
   Calibration cal = imp2.getCalibration();
   if (cal.scaled()) {
     cal.pixelWidth *= 1.0 / xscale;
     cal.pixelHeight *= 1.0 / yscale;
   }
   int[] dim = imp.getDimensions();
   imp2.setDimensions(dim[2], dim[3], dim[4]);
   IJ.showProgress(1.0);
   if (imp.isComposite()) {
     imp2 = new CompositeImage(imp2, 0);
     ((CompositeImage) imp2).copyLuts(imp);
   }
   if (imp.isHyperStack()) imp2.setOpenAsHyperStack(true);
   imp2.show();
   imp2.changes = true;
 }
Beispiel #13
0
 ImagePlus doMedianProjection() {
   IJ.showStatus("Calculating median...");
   ImageStack stack = imp.getStack();
   ImageProcessor[] slices = new ImageProcessor[sliceCount];
   int index = 0;
   for (int slice = startSlice; slice <= stopSlice; slice += increment)
     slices[index++] = stack.getProcessor(slice);
   ImageProcessor ip2 = slices[0].duplicate();
   ip2 = ip2.convertToFloat();
   float[] values = new float[sliceCount];
   int width = ip2.getWidth();
   int height = ip2.getHeight();
   int inc = Math.max(height / 30, 1);
   for (int y = 0; y < height; y++) {
     if (y % inc == 0) IJ.showProgress(y, height - 1);
     for (int x = 0; x < width; x++) {
       for (int i = 0; i < sliceCount; i++) values[i] = slices[i].getPixelValue(x, y);
       ip2.putPixelValue(x, y, median(values));
     }
   }
   if (imp.getBitDepth() == 8) ip2 = ip2.convertToByte(false);
   IJ.showProgress(1, 1);
   return new ImagePlus(makeTitle(), ip2);
 }
Beispiel #14
0
 public void run(String arg) {
   imp = IJ.getImage();
   Roi roi = imp.getRoi();
   if (roi != null && !roi.isArea()) imp.killRoi(); // ignore any line selection
   ImageProcessor ip = imp.getProcessor();
   if (!showDialog(ip)) return;
   if (ip.getWidth() > 1 && ip.getHeight() > 1) ip.setInterpolate(interpolate);
   else ip.setInterpolate(false);
   ip.setBackgroundValue(bgValue);
   imp.startTiming();
   try {
     if (newWindow && imp.getStackSize() > 1 && processStack) createNewStack(imp, ip);
     else scale(ip);
   } catch (OutOfMemoryError o) {
     IJ.outOfMemory("Scale");
   }
   IJ.showProgress(1.0);
 }
Beispiel #15
0
 public void run() {
   final int width = this.w;
   final int height = this.h;
   final int depth = this.d;
   final boolean inverse = inv;
   float[] sk;
   int n = width;
   if (height > n) n = height;
   if (depth > n) n = depth;
   int noResult = 3 * (n + 1) * (n + 1);
   boolean[] background = new boolean[n];
   int test, min;
   for (int k = thread; k < depth; k += nThreads) {
     IJ.showProgress(k / (1. * depth));
     sk = s[k];
     final byte[] dk = data[k];
     for (int j = 0; j < height; j++) {
       final int wj = width * j;
       for (int i = 0; i < width; i++) {
         background[i] = ((dk[i + wj] & 255) < 128) ^ inverse;
       }
       for (int i = 0; i < width; i++) {
         min = noResult;
         for (int x = i; x < width; x++) {
           if (background[x]) {
             test = i - x;
             test *= test;
             min = test;
             break;
           }
         }
         for (int x = i - 1; x >= 0; x--) {
           if (background[x]) {
             test = i - x;
             test *= test;
             if (test < min) min = test;
             break;
           }
         }
         sk[i + wj] = min;
       }
     }
   }
 } // run
Beispiel #16
0
 public void doHyperStackProjection(boolean allTimeFrames) {
   int start = startSlice;
   int stop = stopSlice;
   int firstFrame = 1;
   int lastFrame = imp.getNFrames();
   if (!allTimeFrames) firstFrame = lastFrame = imp.getFrame();
   ImageStack stack = new ImageStack(imp.getWidth(), imp.getHeight());
   int channels = imp.getNChannels();
   int slices = imp.getNSlices();
   if (slices == 1) {
     slices = imp.getNFrames();
     firstFrame = lastFrame = 1;
   }
   int frames = lastFrame - firstFrame + 1;
   increment = channels;
   boolean rgb = imp.getBitDepth() == 24;
   for (int frame = firstFrame; frame <= lastFrame; frame++) {
     for (int channel = 1; channel <= channels; channel++) {
       startSlice = (frame - 1) * channels * slices + (start - 1) * channels + channel;
       stopSlice = (frame - 1) * channels * slices + (stop - 1) * channels + channel;
       if (rgb) doHSRGBProjection(imp);
       else doProjection();
       stack.addSlice(null, projImage.getProcessor());
     }
   }
   projImage = new ImagePlus(makeTitle(), stack);
   projImage.setDimensions(channels, 1, frames);
   if (channels > 1) {
     projImage = new CompositeImage(projImage, 0);
     ((CompositeImage) projImage).copyLuts(imp);
     if (method == SUM_METHOD || method == SD_METHOD)
       ((CompositeImage) projImage).resetDisplayRanges();
   }
   if (frames > 1) projImage.setOpenAsHyperStack(true);
   Overlay overlay = imp.getOverlay();
   if (overlay != null) {
     startSlice = start;
     stopSlice = stop;
     if (imp.getType() == ImagePlus.COLOR_RGB)
       projImage.setOverlay(projectRGBHyperStackRois(overlay));
     else projImage.setOverlay(projectHyperStackRois(overlay));
   }
   IJ.showProgress(1, 1);
 }
  public ImageStack expandStack(ImageStack stackOld, int wNew, int hNew, int xOff, int yOff) {
    int nFrames = stackOld.getSize();
    ImageProcessor ipOld = stackOld.getProcessor(1);
    java.awt.Color colorBack = Toolbar.getBackgroundColor();

    ImageStack stackNew = new ImageStack(wNew, hNew, stackOld.getColorModel());
    ImageProcessor ipNew;

    for (int i = 1; i <= nFrames; i++) {
      IJ.showProgress((double) i / nFrames);
      ipNew = ipOld.createProcessor(wNew, hNew);
      if (zeroFill) ipNew.setValue(0.0);
      else ipNew.setColor(colorBack);
      ipNew.fill();
      ipNew.insert(stackOld.getProcessor(i), xOff, yOff);
      stackNew.addSlice(stackOld.getSliceLabel(i), ipNew);
    }
    return stackNew;
  }
Beispiel #18
0
 public void run() {
   final int width = this.w;
   final int height = this.h;
   final int depth = this.d;
   float[] sk;
   int n = width;
   if (height > n) n = height;
   if (depth > n) n = depth;
   int noResult = 3 * (n + 1) * (n + 1);
   int[] tempInt = new int[n];
   int[] tempS = new int[n];
   boolean nonempty;
   int test, min, delta;
   for (int k = thread; k < depth; k += nThreads) {
     IJ.showProgress(k / (1. * depth));
     sk = s[k];
     for (int i = 0; i < width; i++) {
       nonempty = false;
       for (int j = 0; j < height; j++) {
         tempS[j] = (int) sk[i + width * j];
         if (tempS[j] > 0) nonempty = true;
       }
       if (nonempty) {
         for (int j = 0; j < height; j++) {
           min = noResult;
           delta = j;
           for (int y = 0; y < height; y++) {
             test = tempS[y] + delta * delta--;
             if (test < min) min = test;
           }
           tempInt[j] = min;
         }
         for (int j = 0; j < height; j++) {
           sk[i + width * j] = tempInt[j];
         }
       }
     }
   }
 } // run
Beispiel #19
0
 byte[] getJar(String address) {
   byte[] data;
   boolean gte133 = version().compareTo("1.33u") >= 0;
   try {
     URL url = new URL(address);
     URLConnection uc = url.openConnection();
     int len = uc.getContentLength();
     String name = address.endsWith("ij/ij.jar") ? "daily build" : "ij.jar";
     IJ.showStatus("Downloading ij.jar (" + IJ.d2s((double) len / 1048576, 1) + "MB)");
     InputStream in = uc.getInputStream();
     data = new byte[len];
     int n = 0;
     while (n < len) {
       int count = in.read(data, n, len - n);
       if (count < 0) throw new EOFException();
       n += count;
       if (gte133) IJ.showProgress(n, len);
     }
     in.close();
   } catch (IOException e) {
     return null;
   }
   return data;
 }
Beispiel #20
0
  /**
   * Reduce error in thickness quantitation by trimming the one pixel overhang in the thickness map
   *
   * @param imp Binary input image
   * @param impLTC Thickness map
   * @param inv true if calculating thickness of background, false for foreground
   * @return Thickness map with pixels masked by input image
   */
  private ImagePlus trimOverhang(ImagePlus imp, ImagePlus impLTC, boolean inv) {
    final int w = imp.getWidth();
    final int h = imp.getHeight();
    final int d = imp.getImageStackSize();

    final ImageStack stack = imp.getImageStack();
    final ImageStack mapStack = impLTC.getImageStack();

    final int keepValue = inv ? 0 : 255;
    ImageProcessor ip = new ByteProcessor(w, h);
    ImageProcessor map = new FloatProcessor(w, h);
    for (int z = 1; z <= d; z++) {
      IJ.showStatus("Masking thickness map...");
      IJ.showProgress(z, d);
      ip = stack.getProcessor(z);
      map = mapStack.getProcessor(z);
      for (int y = 0; y < h; y++) {
        for (int x = 0; x < w; x++) {
          if (ip.get(x, y) != keepValue) map.set(x, y, 0);
        }
      }
    }
    return impLTC;
  }
  public void build_bricks() {

    ImagePlus imp;
    ImagePlus orgimp;
    ImageStack stack;
    FileInfo finfo;

    if (lvImgTitle.isEmpty()) return;
    orgimp = WindowManager.getImage(lvImgTitle.get(0));
    imp = orgimp;

    finfo = imp.getFileInfo();
    if (finfo == null) return;

    int[] dims = imp.getDimensions();
    int imageW = dims[0];
    int imageH = dims[1];
    int nCh = dims[2];
    int imageD = dims[3];
    int nFrame = dims[4];
    int bdepth = imp.getBitDepth();
    double xspc = finfo.pixelWidth;
    double yspc = finfo.pixelHeight;
    double zspc = finfo.pixelDepth;
    double z_aspect = Math.max(xspc, yspc) / zspc;

    int orgW = imageW;
    int orgH = imageH;
    int orgD = imageD;
    double orgxspc = xspc;
    double orgyspc = yspc;
    double orgzspc = zspc;

    lv = lvImgTitle.size();
    if (filetype == "JPEG") {
      for (int l = 0; l < lv; l++) {
        if (WindowManager.getImage(lvImgTitle.get(l)).getBitDepth() != 8) {
          IJ.error("A SOURCE IMAGE MUST BE 8BIT GLAYSCALE");
          return;
        }
      }
    }

    // calculate levels
    /*		int baseXY = 256;
    		int baseZ = 256;

    		if (z_aspect < 0.5) baseZ = 128;
    		if (z_aspect > 2.0) baseXY = 128;
    		if (z_aspect >= 0.5 && z_aspect < 1.0) baseZ = (int)(baseZ*z_aspect);
    		if (z_aspect > 1.0 && z_aspect <= 2.0) baseXY = (int)(baseXY/z_aspect);

    		IJ.log("Z_aspect: " + z_aspect);
    		IJ.log("BaseXY: " + baseXY);
    		IJ.log("BaseZ: " + baseZ);
    */

    int baseXY = 256;
    int baseZ = 128;
    int dbXY = Math.max(orgW, orgH) / baseXY;
    if (Math.max(orgW, orgH) % baseXY > 0) dbXY *= 2;
    int dbZ = orgD / baseZ;
    if (orgD % baseZ > 0) dbZ *= 2;
    lv = Math.max(log2(dbXY), log2(dbZ)) + 1;

    int ww = orgW;
    int hh = orgH;
    int dd = orgD;
    for (int l = 0; l < lv; l++) {
      int bwnum = ww / baseXY;
      if (ww % baseXY > 0) bwnum++;
      int bhnum = hh / baseXY;
      if (hh % baseXY > 0) bhnum++;
      int bdnum = dd / baseZ;
      if (dd % baseZ > 0) bdnum++;

      if (bwnum % 2 == 0) bwnum++;
      if (bhnum % 2 == 0) bhnum++;
      if (bdnum % 2 == 0) bdnum++;

      int bw = (bwnum <= 1) ? ww : ww / bwnum + 1 + (ww % bwnum > 0 ? 1 : 0);
      int bh = (bhnum <= 1) ? hh : hh / bhnum + 1 + (hh % bhnum > 0 ? 1 : 0);
      int bd = (bdnum <= 1) ? dd : dd / bdnum + 1 + (dd % bdnum > 0 ? 1 : 0);

      bwlist.add(bw);
      bhlist.add(bh);
      bdlist.add(bd);

      IJ.log("LEVEL: " + l);
      IJ.log("  width: " + ww);
      IJ.log("  hight: " + hh);
      IJ.log("  depth: " + dd);
      IJ.log("  bw: " + bw);
      IJ.log("  bh: " + bh);
      IJ.log("  bd: " + bd);

      int xyl2 = Math.max(ww, hh) / baseXY;
      if (Math.max(ww, hh) % baseXY > 0) xyl2 *= 2;
      if (lv - 1 - log2(xyl2) <= l) {
        ww /= 2;
        hh /= 2;
      }
      IJ.log("  xyl2: " + (lv - 1 - log2(xyl2)));

      int zl2 = dd / baseZ;
      if (dd % baseZ > 0) zl2 *= 2;
      if (lv - 1 - log2(zl2) <= l) dd /= 2;
      IJ.log("  zl2: " + (lv - 1 - log2(zl2)));

      if (l < lv - 1) {
        lvImgTitle.add(lvImgTitle.get(0) + "_level" + (l + 1));
        IJ.selectWindow(lvImgTitle.get(0));
        IJ.run(
            "Scale...",
            "x=- y=- z=- width="
                + ww
                + " height="
                + hh
                + " depth="
                + dd
                + " interpolation=Bicubic average process create title="
                + lvImgTitle.get(l + 1));
      }
    }

    for (int l = 0; l < lv; l++) {
      IJ.log(lvImgTitle.get(l));
    }

    Document doc = newXMLDocument();
    Element root = doc.createElement("BRK");
    root.setAttribute("version", "1.0");
    root.setAttribute("nLevel", String.valueOf(lv));
    root.setAttribute("nChannel", String.valueOf(nCh));
    root.setAttribute("nFrame", String.valueOf(nFrame));
    doc.appendChild(root);

    for (int l = 0; l < lv; l++) {
      IJ.showProgress(0.0);

      int[] dims2 = imp.getDimensions();
      IJ.log(
          "W: "
              + String.valueOf(dims2[0])
              + " H: "
              + String.valueOf(dims2[1])
              + " C: "
              + String.valueOf(dims2[2])
              + " D: "
              + String.valueOf(dims2[3])
              + " T: "
              + String.valueOf(dims2[4])
              + " b: "
              + String.valueOf(bdepth));

      bw = bwlist.get(l).intValue();
      bh = bhlist.get(l).intValue();
      bd = bdlist.get(l).intValue();

      boolean force_pow2 = false;
      /*			if(IsPowerOf2(bw) && IsPowerOf2(bh) && IsPowerOf2(bd)) force_pow2 = true;

      			if(force_pow2){
      				//force pow2
      				if(Pow2(bw) > bw) bw = Pow2(bw)/2;
      				if(Pow2(bh) > bh) bh = Pow2(bh)/2;
      				if(Pow2(bd) > bd) bd = Pow2(bd)/2;
      			}

      			if(bw > imageW) bw = (Pow2(imageW) == imageW) ? imageW : Pow2(imageW)/2;
      			if(bh > imageH) bh = (Pow2(imageH) == imageH) ? imageH : Pow2(imageH)/2;
      			if(bd > imageD) bd = (Pow2(imageD) == imageD) ? imageD : Pow2(imageD)/2;

      */
      if (bw > imageW) bw = imageW;
      if (bh > imageH) bh = imageH;
      if (bd > imageD) bd = imageD;

      if (bw <= 1 || bh <= 1 || bd <= 1) break;

      if (filetype == "JPEG" && (bw < 8 || bh < 8)) break;

      Element lvnode = doc.createElement("Level");
      lvnode.setAttribute("lv", String.valueOf(l));
      lvnode.setAttribute("imageW", String.valueOf(imageW));
      lvnode.setAttribute("imageH", String.valueOf(imageH));
      lvnode.setAttribute("imageD", String.valueOf(imageD));
      lvnode.setAttribute("xspc", String.valueOf(xspc));
      lvnode.setAttribute("yspc", String.valueOf(yspc));
      lvnode.setAttribute("zspc", String.valueOf(zspc));
      lvnode.setAttribute("bitDepth", String.valueOf(bdepth));
      root.appendChild(lvnode);

      Element brksnode = doc.createElement("Bricks");
      brksnode.setAttribute("brick_baseW", String.valueOf(bw));
      brksnode.setAttribute("brick_baseH", String.valueOf(bh));
      brksnode.setAttribute("brick_baseD", String.valueOf(bd));
      lvnode.appendChild(brksnode);

      ArrayList<Brick> bricks = new ArrayList<Brick>();
      int mw, mh, md, mw2, mh2, md2;
      double tx0, ty0, tz0, tx1, ty1, tz1;
      double bx0, by0, bz0, bx1, by1, bz1;
      for (int k = 0; k < imageD; k += bd) {
        if (k > 0) k--;
        for (int j = 0; j < imageH; j += bh) {
          if (j > 0) j--;
          for (int i = 0; i < imageW; i += bw) {
            if (i > 0) i--;
            mw = Math.min(bw, imageW - i);
            mh = Math.min(bh, imageH - j);
            md = Math.min(bd, imageD - k);

            if (force_pow2) {
              mw2 = Pow2(mw);
              mh2 = Pow2(mh);
              md2 = Pow2(md);
            } else {
              mw2 = mw;
              mh2 = mh;
              md2 = md;
            }

            if (filetype == "JPEG") {
              if (mw2 < 8) mw2 = 8;
              if (mh2 < 8) mh2 = 8;
            }

            tx0 = i == 0 ? 0.0d : ((mw2 - mw + 0.5d) / mw2);
            ty0 = j == 0 ? 0.0d : ((mh2 - mh + 0.5d) / mh2);
            tz0 = k == 0 ? 0.0d : ((md2 - md + 0.5d) / md2);

            tx1 = 1.0d - 0.5d / mw2;
            if (mw < bw) tx1 = 1.0d;
            if (imageW - i == bw) tx1 = 1.0d;

            ty1 = 1.0d - 0.5d / mh2;
            if (mh < bh) ty1 = 1.0d;
            if (imageH - j == bh) ty1 = 1.0d;

            tz1 = 1.0d - 0.5d / md2;
            if (md < bd) tz1 = 1.0d;
            if (imageD - k == bd) tz1 = 1.0d;

            bx0 = i == 0 ? 0.0d : (i + 0.5d) / (double) imageW;
            by0 = j == 0 ? 0.0d : (j + 0.5d) / (double) imageH;
            bz0 = k == 0 ? 0.0d : (k + 0.5d) / (double) imageD;

            bx1 = Math.min((i + bw - 0.5d) / (double) imageW, 1.0d);
            if (imageW - i == bw) bx1 = 1.0d;

            by1 = Math.min((j + bh - 0.5d) / (double) imageH, 1.0d);
            if (imageH - j == bh) by1 = 1.0d;

            bz1 = Math.min((k + bd - 0.5d) / (double) imageD, 1.0d);
            if (imageD - k == bd) bz1 = 1.0d;

            int x, y, z;
            x = i - (mw2 - mw);
            y = j - (mh2 - mh);
            z = k - (md2 - md);
            bricks.add(
                new Brick(
                    x, y, z, mw2, mh2, md2, 0, 0, tx0, ty0, tz0, tx1, ty1, tz1, bx0, by0, bz0, bx1,
                    by1, bz1));
          }
        }
      }

      Element fsnode = doc.createElement("Files");
      lvnode.appendChild(fsnode);

      stack = imp.getStack();

      int totalbricknum = nFrame * nCh * bricks.size();
      int curbricknum = 0;
      for (int f = 0; f < nFrame; f++) {
        for (int ch = 0; ch < nCh; ch++) {
          int sizelimit = bdsizelimit * 1024 * 1024;
          int bytecount = 0;
          int filecount = 0;
          int pd_bufsize = Math.max(sizelimit, bw * bh * bd * bdepth / 8);
          byte[] packed_data = new byte[pd_bufsize];
          String base_dataname =
              basename
                  + "_Lv"
                  + String.valueOf(l)
                  + "_Ch"
                  + String.valueOf(ch)
                  + "_Fr"
                  + String.valueOf(f);
          String current_dataname = base_dataname + "_data" + filecount;

          Brick b_first = bricks.get(0);
          if (b_first.z_ != 0) IJ.log("warning");
          int st_z = b_first.z_;
          int ed_z = b_first.z_ + b_first.d_;
          LinkedList<ImageProcessor> iplist = new LinkedList<ImageProcessor>();
          for (int s = st_z; s < ed_z; s++)
            iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));

          //					ImagePlus test;
          //					ImageStack tsst;
          //					test = NewImage.createByteImage("test", imageW, imageH, imageD,
          // NewImage.FILL_BLACK);
          //					tsst = test.getStack();
          for (int i = 0; i < bricks.size(); i++) {
            Brick b = bricks.get(i);

            if (ed_z > b.z_ || st_z < b.z_ + b.d_) {
              if (b.z_ > st_z) {
                for (int s = 0; s < b.z_ - st_z; s++) iplist.pollFirst();
                st_z = b.z_;
              } else if (b.z_ < st_z) {
                IJ.log("warning");
                for (int s = st_z - 1; s > b.z_; s--)
                  iplist.addFirst(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
                st_z = b.z_;
              }

              if (b.z_ + b.d_ > ed_z) {
                for (int s = ed_z; s < b.z_ + b.d_; s++)
                  iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
                ed_z = b.z_ + b.d_;
              } else if (b.z_ + b.d_ < ed_z) {
                IJ.log("warning");
                for (int s = 0; s < ed_z - (b.z_ + b.d_); s++) iplist.pollLast();
                ed_z = b.z_ + b.d_;
              }
            } else {
              IJ.log("warning");
              iplist.clear();
              st_z = b.z_;
              ed_z = b.z_ + b.d_;
              for (int s = st_z; s < ed_z; s++)
                iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
            }

            if (iplist.size() != b.d_) {
              IJ.log("Stack Error");
              return;
            }

            //						int zz = st_z;

            int bsize = 0;
            byte[] bdata = new byte[b.w_ * b.h_ * b.d_ * bdepth / 8];
            Iterator<ImageProcessor> ipite = iplist.iterator();
            while (ipite.hasNext()) {

              //							ImageProcessor tsip = tsst.getProcessor(zz+1);

              ImageProcessor ip = ipite.next();
              ip.setRoi(b.x_, b.y_, b.w_, b.h_);
              if (bdepth == 8) {
                byte[] data = (byte[]) ip.crop().getPixels();
                System.arraycopy(data, 0, bdata, bsize, data.length);
                bsize += data.length;
              } else if (bdepth == 16) {
                ByteBuffer buffer = ByteBuffer.allocate(b.w_ * b.h_ * bdepth / 8);
                buffer.order(ByteOrder.LITTLE_ENDIAN);
                short[] data = (short[]) ip.crop().getPixels();
                for (short e : data) buffer.putShort(e);
                System.arraycopy(buffer.array(), 0, bdata, bsize, buffer.array().length);
                bsize += buffer.array().length;
              } else if (bdepth == 32) {
                ByteBuffer buffer = ByteBuffer.allocate(b.w_ * b.h_ * bdepth / 8);
                buffer.order(ByteOrder.LITTLE_ENDIAN);
                float[] data = (float[]) ip.crop().getPixels();
                for (float e : data) buffer.putFloat(e);
                System.arraycopy(buffer.array(), 0, bdata, bsize, buffer.array().length);
                bsize += buffer.array().length;
              }
            }

            String filename =
                basename
                    + "_Lv"
                    + String.valueOf(l)
                    + "_Ch"
                    + String.valueOf(ch)
                    + "_Fr"
                    + String.valueOf(f)
                    + "_ID"
                    + String.valueOf(i);

            int offset = bytecount;
            int datasize = bdata.length;

            if (filetype == "RAW") {
              int dummy = -1;
              // do nothing
            }
            if (filetype == "JPEG" && bdepth == 8) {
              try {
                DataBufferByte db = new DataBufferByte(bdata, datasize);
                Raster raster = Raster.createPackedRaster(db, b.w_, b.h_ * b.d_, 8, null);
                BufferedImage img =
                    new BufferedImage(b.w_, b.h_ * b.d_, BufferedImage.TYPE_BYTE_GRAY);
                img.setData(raster);
                ByteArrayOutputStream baos = new ByteArrayOutputStream();
                ImageOutputStream ios = ImageIO.createImageOutputStream(baos);
                String format = "jpg";
                Iterator<javax.imageio.ImageWriter> iter =
                    ImageIO.getImageWritersByFormatName("jpeg");
                javax.imageio.ImageWriter writer = iter.next();
                ImageWriteParam iwp = writer.getDefaultWriteParam();
                iwp.setCompressionMode(ImageWriteParam.MODE_EXPLICIT);
                iwp.setCompressionQuality((float) jpeg_quality * 0.01f);
                writer.setOutput(ios);
                writer.write(null, new IIOImage(img, null, null), iwp);
                // ImageIO.write(img, format, baos);
                bdata = baos.toByteArray();
                datasize = bdata.length;
              } catch (IOException e) {
                e.printStackTrace();
                return;
              }
            }
            if (filetype == "ZLIB") {
              byte[] tmpdata = new byte[b.w_ * b.h_ * b.d_ * bdepth / 8];
              Deflater compresser = new Deflater();
              compresser.setInput(bdata);
              compresser.setLevel(Deflater.DEFAULT_COMPRESSION);
              compresser.setStrategy(Deflater.DEFAULT_STRATEGY);
              compresser.finish();
              datasize = compresser.deflate(tmpdata);
              bdata = tmpdata;
              compresser.end();
            }

            if (bytecount + datasize > sizelimit && bytecount > 0) {
              BufferedOutputStream fis = null;
              try {
                File file = new File(directory + current_dataname);
                fis = new BufferedOutputStream(new FileOutputStream(file));
                fis.write(packed_data, 0, bytecount);
              } catch (IOException e) {
                e.printStackTrace();
                return;
              } finally {
                try {
                  if (fis != null) fis.close();
                } catch (IOException e) {
                  e.printStackTrace();
                  return;
                }
              }
              filecount++;
              current_dataname = base_dataname + "_data" + filecount;
              bytecount = 0;
              offset = 0;
              System.arraycopy(bdata, 0, packed_data, bytecount, datasize);
              bytecount += datasize;
            } else {
              System.arraycopy(bdata, 0, packed_data, bytecount, datasize);
              bytecount += datasize;
            }

            Element filenode = doc.createElement("File");
            filenode.setAttribute("filename", current_dataname);
            filenode.setAttribute("channel", String.valueOf(ch));
            filenode.setAttribute("frame", String.valueOf(f));
            filenode.setAttribute("brickID", String.valueOf(i));
            filenode.setAttribute("offset", String.valueOf(offset));
            filenode.setAttribute("datasize", String.valueOf(datasize));
            filenode.setAttribute("filetype", String.valueOf(filetype));

            fsnode.appendChild(filenode);

            curbricknum++;
            IJ.showProgress((double) (curbricknum) / (double) (totalbricknum));
          }
          if (bytecount > 0) {
            BufferedOutputStream fis = null;
            try {
              File file = new File(directory + current_dataname);
              fis = new BufferedOutputStream(new FileOutputStream(file));
              fis.write(packed_data, 0, bytecount);
            } catch (IOException e) {
              e.printStackTrace();
              return;
            } finally {
              try {
                if (fis != null) fis.close();
              } catch (IOException e) {
                e.printStackTrace();
                return;
              }
            }
          }
        }
      }

      for (int i = 0; i < bricks.size(); i++) {
        Brick b = bricks.get(i);
        Element bricknode = doc.createElement("Brick");
        bricknode.setAttribute("id", String.valueOf(i));
        bricknode.setAttribute("st_x", String.valueOf(b.x_));
        bricknode.setAttribute("st_y", String.valueOf(b.y_));
        bricknode.setAttribute("st_z", String.valueOf(b.z_));
        bricknode.setAttribute("width", String.valueOf(b.w_));
        bricknode.setAttribute("height", String.valueOf(b.h_));
        bricknode.setAttribute("depth", String.valueOf(b.d_));
        brksnode.appendChild(bricknode);

        Element tboxnode = doc.createElement("tbox");
        tboxnode.setAttribute("x0", String.valueOf(b.tx0_));
        tboxnode.setAttribute("y0", String.valueOf(b.ty0_));
        tboxnode.setAttribute("z0", String.valueOf(b.tz0_));
        tboxnode.setAttribute("x1", String.valueOf(b.tx1_));
        tboxnode.setAttribute("y1", String.valueOf(b.ty1_));
        tboxnode.setAttribute("z1", String.valueOf(b.tz1_));
        bricknode.appendChild(tboxnode);

        Element bboxnode = doc.createElement("bbox");
        bboxnode.setAttribute("x0", String.valueOf(b.bx0_));
        bboxnode.setAttribute("y0", String.valueOf(b.by0_));
        bboxnode.setAttribute("z0", String.valueOf(b.bz0_));
        bboxnode.setAttribute("x1", String.valueOf(b.bx1_));
        bboxnode.setAttribute("y1", String.valueOf(b.by1_));
        bboxnode.setAttribute("z1", String.valueOf(b.bz1_));
        bricknode.appendChild(bboxnode);
      }

      if (l < lv - 1) {
        imp = WindowManager.getImage(lvImgTitle.get(l + 1));
        int[] newdims = imp.getDimensions();
        imageW = newdims[0];
        imageH = newdims[1];
        imageD = newdims[3];
        xspc = orgxspc * ((double) orgW / (double) imageW);
        yspc = orgyspc * ((double) orgH / (double) imageH);
        zspc = orgzspc * ((double) orgD / (double) imageD);
        bdepth = imp.getBitDepth();
      }
    }

    File newXMLfile = new File(directory + basename + ".vvd");
    writeXML(newXMLfile, doc);

    for (int l = 1; l < lv; l++) {
      imp = WindowManager.getImage(lvImgTitle.get(l));
      imp.changes = false;
      imp.close();
    }
  }
Beispiel #22
0
  public void run(String arg) {
    ImageCheck ic = new ImageCheck();
    if (!ImageCheck.checkEnvironment()) return;
    ImagePlus imp = IJ.getImage();
    if (!ic.isBinary(imp)) {
      IJ.error("8-bit binary (black and white only) image required.");
      return;
    }

    if (!ic.isVoxelIsotropic(imp, 1E-3)) {
      if (IJ.showMessageWithCancel(
          "Anisotropic voxels",
          "This image contains anisotropic voxels, which will\n"
              + "result in incorrect thickness calculation.\n\n"
              + "Consider rescaling your data so that voxels are isotropic\n"
              + "(Image > Scale...).\n\n"
              + "Continue anyway?")) {
      } else return;
    }
    GenericDialog gd = new GenericDialog("Options");
    gd.addCheckbox("Thickness", true);
    gd.addCheckbox("Spacing", false);
    gd.addCheckbox("Graphic Result", true);
    gd.addCheckbox("Use_ROI_Manager", false);
    gd.addCheckbox("Mask thickness map", true);
    gd.addHelp("http://bonej.org/thickness");
    gd.showDialog();
    if (gd.wasCanceled()) {
      return;
    }
    boolean doThickness = gd.getNextBoolean();
    boolean doSpacing = gd.getNextBoolean();
    boolean doGraphic = gd.getNextBoolean();
    boolean doRoi = gd.getNextBoolean();
    boolean doMask = gd.getNextBoolean();

    long startTime = System.currentTimeMillis();
    String title = stripExtension(imp.getTitle());

    RoiManager roiMan = RoiManager.getInstance();
    // calculate trabecular thickness (Tb.Th)
    if (doThickness) {
      boolean inverse = false;
      ImagePlus impLTC = new ImagePlus();
      if (doRoi && roiMan != null) {
        ImageStack stack = RoiMan.cropStack(roiMan, imp.getStack(), true, 0, 1);
        ImagePlus crop = new ImagePlus(imp.getTitle(), stack);
        crop.setCalibration(imp.getCalibration());
        impLTC = getLocalThickness(crop, inverse, doMask);
      } else impLTC = getLocalThickness(imp, inverse, doMask);
      impLTC.setTitle(title + "_Tb.Th");
      impLTC.setCalibration(imp.getCalibration());
      double[] stats = StackStats.meanStdDev(impLTC);
      insertResults(imp, stats, inverse);
      if (doGraphic && !Interpreter.isBatchMode()) {
        impLTC.show();
        impLTC.setSlice(1);
        impLTC.getProcessor().setMinAndMax(0, stats[2]);
        IJ.run("Fire");
      }
    }
    if (doSpacing) {
      boolean inverse = true;
      ImagePlus impLTCi = new ImagePlus();
      if (doRoi && roiMan != null) {
        ImageStack stack = RoiMan.cropStack(roiMan, imp.getStack(), true, 255, 1);
        ImagePlus crop = new ImagePlus(imp.getTitle(), stack);
        crop.setCalibration(imp.getCalibration());
        impLTCi = getLocalThickness(crop, inverse, doMask);
      } else impLTCi = getLocalThickness(imp, inverse, doMask);
      // check marrow cavity size (i.e. trabcular separation, Tb.Sp)
      impLTCi.setTitle(title + "_Tb.Sp");
      impLTCi.setCalibration(imp.getCalibration());
      double[] stats = StackStats.meanStdDev(impLTCi);
      insertResults(imp, stats, inverse);
      if (doGraphic && !Interpreter.isBatchMode()) {
        impLTCi.show();
        impLTCi.setSlice(1);
        impLTCi.getProcessor().setMinAndMax(0, stats[2]);
        IJ.run("Fire");
      }
    }
    IJ.showProgress(1.0);
    IJ.showStatus("Done");
    double duration = ((double) System.currentTimeMillis() - (double) startTime) / (double) 1000;
    IJ.log("Duration = " + IJ.d2s(duration, 3) + " s");
    UsageReporter.reportEvent(this).send();
    return;
  }
Beispiel #23
0
 private void showProgress(int current, int last) {
   if (showProgressBar && (System.currentTimeMillis() - startTime) > 500L)
     IJ.showProgress(current, last);
 }
Beispiel #24
0
 /** add work done in the meanwhile and show progress */
 private void addProgress(double deltaProgress) {
   if (nPasses == 0) return;
   progressDone += deltaProgress;
   IJ.showProgress(progressDone / nPasses);
 }
Beispiel #25
0
 private void showProgress(double progress) {
   if (showProgressBar) IJ.showProgress(progress);
 }
  void Otsu(ImagePlus imp, int radius, double par1, double par2, boolean doIwhite) {
    // Otsu's threshold algorithm
    // C++ code by Jordan Bevik <*****@*****.**>
    // ported to ImageJ plugin by G.Landini. Same algorithm as in Auto_Threshold, this time on local
    // circular regions
    int[] data;
    int w = imp.getWidth();
    int h = imp.getHeight();
    int position;
    int radiusx2 = radius * 2;
    ImageProcessor ip = imp.getProcessor();
    byte[] pixels = (byte[]) ip.getPixels();
    byte[] pixelsOut =
        new byte
            [pixels.length]; // need this to avoid changing the image data (and further histograms)
    byte object;
    byte backg;

    if (doIwhite) {
      object = (byte) 0xff;
      backg = (byte) 0;
    } else {
      object = (byte) 0;
      backg = (byte) 0xff;
    }

    int k, kStar; // k = the current threshold; kStar = optimal threshold
    int N1, N; // N1 = # points with intensity <=k; N = total number of points
    double BCV, BCVmax; // The current Between Class Variance and maximum BCV
    double num, denom; // temporary bookeeping
    int Sk; // The total intensity for all histogram points <=k
    int S,
        L =
            256; // The total intensity of the image. Need to hange here if modifying for >8 bits
                 // images
    int roiy;

    Roi roi = new OvalRoi(0, 0, radiusx2, radiusx2);
    // ip.setRoi(roi);
    for (int y = 0; y < h; y++) {
      IJ.showProgress(
          (double) (y) / (h - 1)); // this method is slow, so let's show the progress bar
      roiy = y - radius;
      for (int x = 0; x < w; x++) {
        roi.setLocation(x - radius, roiy);
        ip.setRoi(roi);
        // ip.setRoi(new OvalRoi(x-radius, roiy, radiusx2, radiusx2));
        position = x + y * w;
        data = ip.getHistogram();

        // Initialize values:
        S = N = 0;
        for (k = 0; k < L; k++) {
          S += k * data[k]; // Total histogram intensity
          N += data[k]; // Total number of data points
        }

        Sk = 0;
        N1 = data[0]; // The entry for zero intensity
        BCV = 0;
        BCVmax = 0;
        kStar = 0;

        // Look at each possible threshold value,
        // calculate the between-class variance, and decide if it's a max
        for (k = 1; k < L - 1; k++) { // No need to check endpoints k = 0 or k = L-1
          Sk += k * data[k];
          N1 += data[k];

          // The float casting here is to avoid compiler warning about loss of precision and
          // will prevent overflow in the case of large saturated images
          denom = (double) (N1) * (N - N1); // Maximum value of denom is (N^2)/4 =  approx. 3E10

          if (denom != 0) {
            // Float here is to avoid loss of precision when dividing
            num = ((double) N1 / N) * S - Sk; // Maximum value of num =  255*N = approx 8E7
            BCV = (num * num) / denom;
          } else BCV = 0;

          if (BCV >= BCVmax) { // Assign the best threshold found so far
            BCVmax = BCV;
            kStar = k;
          }
        }
        // kStar += 1;	// Use QTI convention that intensity -> 1 if intensity >= k
        // (the algorithm was developed for I-> 1 if I <= k.)
        // return kStar;
        pixelsOut[position] = ((int) (pixels[position] & 0xff) > kStar) ? object : backg;
      }
    }
    for (position = 0; position < w * h; position++)
      pixels[position] = pixelsOut[position]; // update with thresholded pixels
  }
  /**
   * Performs particle analysis on the specified ImagePlus and ImageProcessor. Returns false if
   * there is an error.
   */
  public boolean analyze(ImagePlus imp, ImageProcessor ip) {
    if (this.imp == null) this.imp = imp;
    showResults = (options & SHOW_RESULTS) != 0;
    excludeEdgeParticles = (options & EXCLUDE_EDGE_PARTICLES) != 0;
    resetCounter = (options & CLEAR_WORKSHEET) != 0;
    showProgress = (options & SHOW_PROGRESS) != 0;
    floodFill = (options & INCLUDE_HOLES) == 0;
    recordStarts = (options & RECORD_STARTS) != 0;
    addToManager = (options & ADD_TO_MANAGER) != 0;
    displaySummary = (options & DISPLAY_SUMMARY) != 0;
    inSituShow = (options & IN_SITU_SHOW) != 0;
    outputImage = null;
    ip.snapshot();
    ip.setProgressBar(null);
    if (Analyzer.isRedirectImage()) {
      redirectImp = Analyzer.getRedirectImage(imp);
      if (redirectImp == null) return false;
      int depth = redirectImp.getStackSize();
      if (depth > 1 && depth == imp.getStackSize()) {
        ImageStack redirectStack = redirectImp.getStack();
        redirectIP = redirectStack.getProcessor(imp.getCurrentSlice());
      } else redirectIP = redirectImp.getProcessor();
    } else if (imp.getType() == ImagePlus.COLOR_RGB) {
      ImagePlus original = (ImagePlus) imp.getProperty("OriginalImage");
      if (original != null
          && original.getWidth() == imp.getWidth()
          && original.getHeight() == imp.getHeight()) {
        redirectImp = original;
        redirectIP = original.getProcessor();
      }
    }
    if (!setThresholdLevels(imp, ip)) return false;
    width = ip.getWidth();
    height = ip.getHeight();
    if (!(showChoice == NOTHING || showChoice == OVERLAY_OUTLINES || showChoice == OVERLAY_MASKS)) {
      blackBackground = Prefs.blackBackground && inSituShow;
      if (slice == 1) outlines = new ImageStack(width, height);
      if (showChoice == ROI_MASKS) drawIP = new ShortProcessor(width, height);
      else drawIP = new ByteProcessor(width, height);
      drawIP.setLineWidth(lineWidth);
      if (showChoice == ROI_MASKS) {
      } // Place holder for now...
      else if (showChoice == MASKS && !blackBackground) drawIP.invertLut();
      else if (showChoice == OUTLINES) {
        if (!inSituShow) {
          if (customLut == null) makeCustomLut();
          drawIP.setColorModel(customLut);
        }
        drawIP.setFont(new Font("SansSerif", Font.PLAIN, fontSize));
        if (fontSize > 12 && inSituShow) drawIP.setAntialiasedText(true);
      }
      outlines.addSlice(null, drawIP);

      if (showChoice == ROI_MASKS || blackBackground) {
        drawIP.setColor(Color.black);
        drawIP.fill();
        drawIP.setColor(Color.white);
      } else {
        drawIP.setColor(Color.white);
        drawIP.fill();
        drawIP.setColor(Color.black);
      }
    }
    calibration = redirectImp != null ? redirectImp.getCalibration() : imp.getCalibration();

    if (rt == null) {
      rt = Analyzer.getResultsTable();
      analyzer = new Analyzer(imp);
    } else analyzer = new Analyzer(imp, measurements, rt);
    if (resetCounter && slice == 1) {
      if (!Analyzer.resetCounter()) return false;
    }
    beginningCount = Analyzer.getCounter();

    byte[] pixels = null;
    if (ip instanceof ByteProcessor) pixels = (byte[]) ip.getPixels();
    if (r == null) {
      r = ip.getRoi();
      mask = ip.getMask();
      if (displaySummary) {
        if (mask != null) totalArea = ImageStatistics.getStatistics(ip, AREA, calibration).area;
        else totalArea = r.width * calibration.pixelWidth * r.height * calibration.pixelHeight;
      }
    }
    minX = r.x;
    maxX = r.x + r.width;
    minY = r.y;
    maxY = r.y + r.height;
    if (r.width < width || r.height < height || mask != null) {
      if (!eraseOutsideRoi(ip, r, mask)) return false;
    }
    int offset;
    double value;
    int inc = Math.max(r.height / 25, 1);
    int mi = 0;
    ImageWindow win = imp.getWindow();
    if (win != null) win.running = true;
    if (measurements == 0) measurements = Analyzer.getMeasurements();
    if (showChoice == ELLIPSES) measurements |= ELLIPSE;
    measurements &= ~LIMIT; // ignore "Limit to Threshold"
    roiNeedsImage =
        (measurements & PERIMETER) != 0
            || (measurements & SHAPE_DESCRIPTORS) != 0
            || (measurements & FERET) != 0;
    particleCount = 0;
    wand = new Wand(ip);
    pf = new PolygonFiller();
    if (floodFill) {
      ImageProcessor ipf = ip.duplicate();
      ipf.setValue(fillColor);
      ff = new FloodFiller(ipf);
    }
    roiType = Wand.allPoints() ? Roi.FREEROI : Roi.TRACED_ROI;

    for (int y = r.y; y < (r.y + r.height); y++) {
      offset = y * width;
      for (int x = r.x; x < (r.x + r.width); x++) {
        if (pixels != null) value = pixels[offset + x] & 255;
        else if (imageType == SHORT) value = ip.getPixel(x, y);
        else value = ip.getPixelValue(x, y);
        if (value >= level1 && value <= level2) analyzeParticle(x, y, imp, ip);
      }
      if (showProgress && ((y % inc) == 0)) IJ.showProgress((double) (y - r.y) / r.height);
      if (win != null) canceled = !win.running;
      if (canceled) {
        Macro.abort();
        break;
      }
    }
    if (showProgress) IJ.showProgress(1.0);
    if (showResults) rt.updateResults();
    imp.killRoi();
    ip.resetRoi();
    ip.reset();
    if (displaySummary && IJ.getInstance() != null) updateSliceSummary();
    if (addToManager && roiManager != null) roiManager.setEditMode(imp, true);
    maxParticleCount = (particleCount > maxParticleCount) ? particleCount : maxParticleCount;
    totalCount += particleCount;
    if (!canceled) showResults();
    return true;
  }
Beispiel #28
0
  /**
   * Saito-Toriwaki algorithm for Euclidian Distance Transformation. Direct application of Algorithm
   * 1. Bob Dougherty 8/8/2006
   *
   * <ul>
   *   <li>Version S1A: lower memory usage.
   *   <li>Version S1A.1 A fixed indexing bug for 666-bin data set
   *   <li>Version S1A.2 Aug. 9, 2006. Changed noResult value.
   *   <li>Version S1B Aug. 9, 2006. Faster.
   *   <li>Version S1B.1 Sept. 6, 2006. Changed comments.
   *   <li>Version S1C Oct. 1, 2006. Option for inverse case. <br>
   *       Fixed inverse behavior in y and z directions.
   *   <li>Version D July 30, 2007. Multithread processing for step 2.
   * </ul>
   *
   * <p>This version assumes the input stack is already in memory, 8-bit, and outputs to a new
   * 32-bit stack. Versions that are more stingy with memory may be forthcoming.
   *
   * @param imp 8-bit (binary) ImagePlus
   */
  private float[][] geometryToDistanceMap(ImagePlus imp, boolean inv) {
    final int w = imp.getWidth();
    final int h = imp.getHeight();
    final int d = imp.getStackSize();
    int nThreads = Runtime.getRuntime().availableProcessors();

    // Create references to input data
    ImageStack stack = imp.getStack();
    byte[][] data = new byte[d][];
    for (int k = 0; k < d; k++) data[k] = (byte[]) stack.getPixels(k + 1);

    // Create 32 bit floating point stack for output, s. Will also use it
    // for g in Transformation 1.
    float[][] s = new float[d][];
    for (int k = 0; k < d; k++) {
      ImageProcessor ipk = new FloatProcessor(w, h);
      s[k] = (float[]) ipk.getPixels();
    }
    float[] sk;
    // Transformation 1. Use s to store g.
    IJ.showStatus("EDT transformation 1/3");
    Step1Thread[] s1t = new Step1Thread[nThreads];
    for (int thread = 0; thread < nThreads; thread++) {
      s1t[thread] = new Step1Thread(thread, nThreads, w, h, d, inv, s, data);
      s1t[thread].start();
    }
    try {
      for (int thread = 0; thread < nThreads; thread++) {
        s1t[thread].join();
      }
    } catch (InterruptedException ie) {
      IJ.error("A thread was interrupted in step 1 .");
    }
    // Transformation 2. g (in s) -> h (in s)
    IJ.showStatus("EDT transformation 2/3");
    Step2Thread[] s2t = new Step2Thread[nThreads];
    for (int thread = 0; thread < nThreads; thread++) {
      s2t[thread] = new Step2Thread(thread, nThreads, w, h, d, s);
      s2t[thread].start();
    }
    try {
      for (int thread = 0; thread < nThreads; thread++) {
        s2t[thread].join();
      }
    } catch (InterruptedException ie) {
      IJ.error("A thread was interrupted in step 2 .");
    }
    // Transformation 3. h (in s) -> s
    IJ.showStatus("EDT transformation 3/3");
    Step3Thread[] s3t = new Step3Thread[nThreads];
    for (int thread = 0; thread < nThreads; thread++) {
      s3t[thread] = new Step3Thread(thread, nThreads, w, h, d, inv, s, data);
      s3t[thread].start();
    }
    try {
      for (int thread = 0; thread < nThreads; thread++) {
        s3t[thread].join();
      }
    } catch (InterruptedException ie) {
      IJ.error("A thread was interrupted in step 3 .");
    }
    // Find the largest distance for scaling
    // Also fill in the background values.
    float distMax = 0;
    final int wh = w * h;
    float dist;
    for (int k = 0; k < d; k++) {
      sk = s[k];
      for (int ind = 0; ind < wh; ind++) {
        if (((data[k][ind] & 255) < 128) ^ inv) {
          sk[ind] = 0;
        } else {
          dist = (float) Math.sqrt(sk[ind]);
          sk[ind] = dist;
          distMax = (dist > distMax) ? dist : distMax;
        }
      }
    }
    IJ.showProgress(1.0);
    IJ.showStatus("Done");
    return s;
  }