Exemple #1
0
 // Added by Marcel Boeglin 2013.09.22
 private Overlay projectHyperStackRois(Overlay overlay) {
   if (overlay == null) return null;
   int t1 = imp.getFrame();
   int channels = projImage.getNChannels();
   int slices = 1;
   int frames = projImage.getNFrames();
   Overlay overlay2 = new Overlay();
   Roi roi;
   int c, z, t;
   int size = channels * slices * frames;
   for (Roi r : overlay.toArray()) {
     c = r.getCPosition();
     z = r.getZPosition();
     t = r.getTPosition();
     roi = (Roi) r.clone();
     if (size == channels) { // current time frame
       if (z >= startSlice && z <= stopSlice && t == t1 || c == 0) {
         roi.setPosition(c);
         overlay2.add(roi);
       }
     } else if (size == frames * channels) { // all time frames
       if (z >= startSlice && z <= stopSlice) roi.setPosition(c, 1, t);
       else if (z == 0) roi.setPosition(c, 0, t);
       else continue;
       overlay2.add(roi);
     }
   }
   return overlay2;
 }
 void drawAllROIs(Graphics g) {
   RoiManager rm = RoiManager.getInstance();
   if (rm == null) {
     rm = Interpreter.getBatchModeRoiManager();
     if (rm != null && rm.getList().getItemCount() == 0) rm = null;
   }
   if (rm == null) {
     // if (showAllList!=null)
     //	overlay = showAllList;
     showAllROIs = false;
     repaint();
     return;
   }
   initGraphics(g, null, showAllColor);
   Hashtable rois = rm.getROIs();
   java.awt.List list = rm.getList();
   boolean drawLabels = rm.getDrawLabels();
   currentRoi = null;
   int n = list.getItemCount();
   if (IJ.debugMode) IJ.log("paint: drawing " + n + " \"Show All\" ROIs");
   if (labelRects == null || labelRects.length != n) labelRects = new Rectangle[n];
   if (!drawLabels) showAllList = new Overlay();
   else showAllList = null;
   if (imp == null) return;
   int currentImage = imp.getCurrentSlice();
   int channel = 0, slice = 0, frame = 0;
   boolean hyperstack = imp.isHyperStack();
   if (hyperstack) {
     channel = imp.getChannel();
     slice = imp.getSlice();
     frame = imp.getFrame();
   }
   drawNames = Prefs.useNamesAsLabels;
   for (int i = 0; i < n; i++) {
     String label = list.getItem(i);
     Roi roi = (Roi) rois.get(label);
     if (roi == null) continue;
     if (showAllList != null) showAllList.add(roi);
     if (i < 200 && drawLabels && roi == imp.getRoi()) currentRoi = roi;
     if (Prefs.showAllSliceOnly && imp.getStackSize() > 1) {
       if (hyperstack && roi.getPosition() == 0) {
         int c = roi.getCPosition();
         int z = roi.getZPosition();
         int t = roi.getTPosition();
         if ((c == 0 || c == channel) && (z == 0 || z == slice) && (t == 0 || t == frame))
           drawRoi(g, roi, drawLabels ? i : -1);
       } else {
         int position = roi.getPosition();
         if (position == 0) position = getSliceNumber(roi.getName());
         if (position == 0 || position == currentImage) drawRoi(g, roi, drawLabels ? i : -1);
       }
     } else drawRoi(g, roi, drawLabels ? i : -1);
   }
   ((Graphics2D) g).setStroke(Roi.onePixelWide);
   drawNames = false;
 }
Exemple #3
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 void run(String arg) {
    Toolkit toolkit = Toolkit.getDefaultToolkit();
    Image Image1 = toolkit.getImage(arg);
    imp = new ImagePlus("title", Image1);

    AffineTransform aTran = new AffineTransform();

    if (imp.isComposite()) {
      int z = imp.getSlice();
      int t = imp.getFrame();
      ImagePlus[] channels = split(imp);
      imp.changes = false;
      imp.setIgnoreFlush(true);
      imp.close();
      for (int i = 0; i < channels.length; i++) {
        channels[i].show();
        if (z > 1 || t > 1) channels[i].setPosition(1, z, t);
      }
    } else if (imp.getType() == ImagePlus.COLOR_RGB) splitRGB(imp);
    else IJ.error("Split Channels", "Multichannel image required");
  }
Exemple #5
0
 // Added by Marcel Boeglin 2013.09.22
 private Overlay projectRGBHyperStackRois(Overlay overlay) {
   if (overlay == null) return null;
   int frames = projImage.getNFrames();
   int t1 = imp.getFrame();
   Overlay overlay2 = new Overlay();
   Roi roi;
   int c, z, t;
   for (Roi r : overlay.toArray()) {
     c = r.getCPosition();
     z = r.getZPosition();
     t = r.getTPosition();
     roi = (Roi) r.clone();
     if (z >= startSlice && z <= stopSlice || z == 0 || c == 0 || t == 0) {
       if (frames == 1 && t != t1 && t != 0) // current time frame
       continue;
       roi.setPosition(t);
       overlay2.add(roi);
     }
   }
   return overlay2;
 }
 void drawOverlay(Graphics g) {
   if (imp != null && imp.getHideOverlay()) return;
   Color labelColor = overlay.getLabelColor();
   if (labelColor == null) labelColor = Color.white;
   initGraphics(g, labelColor, Roi.getColor());
   int n = overlay.size();
   if (IJ.debugMode) IJ.log("paint: drawing " + n + " ROI display list");
   int currentImage = imp != null ? imp.getCurrentSlice() : -1;
   if (imp.getStackSize() == 1) currentImage = -1;
   int channel = 0, slice = 0, frame = 0;
   boolean hyperstack = imp.isHyperStack();
   if (hyperstack) {
     channel = imp.getChannel();
     slice = imp.getSlice();
     frame = imp.getFrame();
   }
   drawNames = overlay.getDrawNames();
   boolean drawLabels = drawNames || overlay.getDrawLabels();
   for (int i = 0; i < n; i++) {
     if (overlay == null) break;
     Roi roi = overlay.get(i);
     if (hyperstack && roi.getPosition() == 0) {
       int c = roi.getCPosition();
       int z = roi.getZPosition();
       int t = roi.getTPosition();
       if ((c == 0 || c == channel) && (z == 0 || z == slice) && (t == 0 || t == frame))
         drawRoi(g, roi, drawLabels ? i + LIST_OFFSET : -1);
     } else {
       int position = roi.getPosition();
       if (position == 0 || position == currentImage)
         drawRoi(g, roi, drawLabels ? i + LIST_OFFSET : -1);
     }
   }
   ((Graphics2D) g).setStroke(Roi.onePixelWide);
   drawNames = false;
 }
Exemple #7
0
  String getInfo(ImagePlus imp, ImageProcessor ip) {
    String s = new String("\n");
    s += "Title: " + imp.getTitle() + "\n";
    Calibration cal = imp.getCalibration();
    int stackSize = imp.getStackSize();
    int channels = imp.getNChannels();
    int slices = imp.getNSlices();
    int frames = imp.getNFrames();
    int digits = imp.getBitDepth() == 32 ? 4 : 0;
    if (cal.scaled()) {
      String unit = cal.getUnit();
      String units = cal.getUnits();
      s +=
          "Width:  "
              + IJ.d2s(imp.getWidth() * cal.pixelWidth, 2)
              + " "
              + units
              + " ("
              + imp.getWidth()
              + ")\n";
      s +=
          "Height:  "
              + IJ.d2s(imp.getHeight() * cal.pixelHeight, 2)
              + " "
              + units
              + " ("
              + imp.getHeight()
              + ")\n";
      if (slices > 1)
        s += "Depth:  " + IJ.d2s(slices * cal.pixelDepth, 2) + " " + units + " (" + slices + ")\n";
      double xResolution = 1.0 / cal.pixelWidth;
      double yResolution = 1.0 / cal.pixelHeight;
      int places = Tools.getDecimalPlaces(xResolution, yResolution);
      if (xResolution == yResolution)
        s += "Resolution:  " + IJ.d2s(xResolution, places) + " pixels per " + unit + "\n";
      else {
        s += "X Resolution:  " + IJ.d2s(xResolution, places) + " pixels per " + unit + "\n";
        s += "Y Resolution:  " + IJ.d2s(yResolution, places) + " pixels per " + unit + "\n";
      }
    } else {
      s += "Width:  " + imp.getWidth() + " pixels\n";
      s += "Height:  " + imp.getHeight() + " pixels\n";
      if (stackSize > 1) s += "Depth:  " + slices + " pixels\n";
    }
    if (stackSize > 1)
      s +=
          "Voxel size: "
              + d2s(cal.pixelWidth)
              + "x"
              + d2s(cal.pixelHeight)
              + "x"
              + d2s(cal.pixelDepth)
              + " "
              + cal.getUnit()
              + "\n";
    else
      s +=
          "Pixel size: "
              + d2s(cal.pixelWidth)
              + "x"
              + d2s(cal.pixelHeight)
              + " "
              + cal.getUnit()
              + "\n";

    s += "ID: " + imp.getID() + "\n";
    String zOrigin = stackSize > 1 || cal.zOrigin != 0.0 ? "," + d2s(cal.zOrigin) : "";
    s += "Coordinate origin:  " + d2s(cal.xOrigin) + "," + d2s(cal.yOrigin) + zOrigin + "\n";
    int type = imp.getType();
    switch (type) {
      case ImagePlus.GRAY8:
        s += "Bits per pixel: 8 ";
        String lut = "LUT";
        if (imp.getProcessor().isColorLut()) lut = "color " + lut;
        else lut = "grayscale " + lut;
        if (imp.isInvertedLut()) lut = "inverting " + lut;
        s += "(" + lut + ")\n";
        if (imp.getNChannels() > 1) s += displayRanges(imp);
        else s += "Display range: " + (int) ip.getMin() + "-" + (int) ip.getMax() + "\n";
        break;
      case ImagePlus.GRAY16:
      case ImagePlus.GRAY32:
        if (type == ImagePlus.GRAY16) {
          String sign = cal.isSigned16Bit() ? "signed" : "unsigned";
          s += "Bits per pixel: 16 (" + sign + ")\n";
        } else s += "Bits per pixel: 32 (float)\n";
        if (imp.getNChannels() > 1) s += displayRanges(imp);
        else {
          s += "Display range: ";
          double min = ip.getMin();
          double max = ip.getMax();
          if (cal.calibrated()) {
            min = cal.getCValue((int) min);
            max = cal.getCValue((int) max);
          }
          s += IJ.d2s(min, digits) + " - " + IJ.d2s(max, digits) + "\n";
        }
        break;
      case ImagePlus.COLOR_256:
        s += "Bits per pixel: 8 (color LUT)\n";
        break;
      case ImagePlus.COLOR_RGB:
        s += "Bits per pixel: 32 (RGB)\n";
        break;
    }
    double interval = cal.frameInterval;
    double fps = cal.fps;
    if (stackSize > 1) {
      ImageStack stack = imp.getStack();
      int slice = imp.getCurrentSlice();
      String number = slice + "/" + stackSize;
      String label = stack.getShortSliceLabel(slice);
      if (label != null && label.length() > 0) label = " (" + label + ")";
      else label = "";
      if (interval > 0.0 || fps != 0.0) {
        s += "Frame: " + number + label + "\n";
        if (fps != 0.0) {
          String sRate =
              Math.abs(fps - Math.round(fps)) < 0.00001 ? IJ.d2s(fps, 0) : IJ.d2s(fps, 5);
          s += "Frame rate: " + sRate + " fps\n";
        }
        if (interval != 0.0)
          s +=
              "Frame interval: "
                  + ((int) interval == interval ? IJ.d2s(interval, 0) : IJ.d2s(interval, 5))
                  + " "
                  + cal.getTimeUnit()
                  + "\n";
      } else s += "Image: " + number + label + "\n";
      if (imp.isHyperStack()) {
        if (channels > 1) s += "  Channel: " + imp.getChannel() + "/" + channels + "\n";
        if (slices > 1) s += "  Slice: " + imp.getSlice() + "/" + slices + "\n";
        if (frames > 1) s += "  Frame: " + imp.getFrame() + "/" + frames + "\n";
      }
      if (imp.isComposite()) {
        if (!imp.isHyperStack() && channels > 1) s += "  Channels: " + channels + "\n";
        String mode = ((CompositeImage) imp).getModeAsString();
        s += "  Composite mode: \"" + mode + "\"\n";
      }
    }

    if (ip.getMinThreshold() == ImageProcessor.NO_THRESHOLD) s += "No Threshold\n";
    else {
      double lower = ip.getMinThreshold();
      double upper = ip.getMaxThreshold();
      int dp = digits;
      if (cal.calibrated()) {
        lower = cal.getCValue((int) lower);
        upper = cal.getCValue((int) upper);
        dp = cal.isSigned16Bit() ? 0 : 4;
      }
      s += "Threshold: " + IJ.d2s(lower, dp) + "-" + IJ.d2s(upper, dp) + "\n";
    }
    ImageCanvas ic = imp.getCanvas();
    double mag = ic != null ? ic.getMagnification() : 1.0;
    if (mag != 1.0) s += "Magnification: " + IJ.d2s(mag, 2) + "\n";

    if (cal.calibrated()) {
      s += " \n";
      int curveFit = cal.getFunction();
      s += "Calibration Function: ";
      if (curveFit == Calibration.UNCALIBRATED_OD) s += "Uncalibrated OD\n";
      else if (curveFit == Calibration.CUSTOM) s += "Custom lookup table\n";
      else s += CurveFitter.fList[curveFit] + "\n";
      double[] c = cal.getCoefficients();
      if (c != null) {
        s += "  a: " + IJ.d2s(c[0], 6) + "\n";
        s += "  b: " + IJ.d2s(c[1], 6) + "\n";
        if (c.length >= 3) s += "  c: " + IJ.d2s(c[2], 6) + "\n";
        if (c.length >= 4) s += "  c: " + IJ.d2s(c[3], 6) + "\n";
        if (c.length >= 5) s += "  c: " + IJ.d2s(c[4], 6) + "\n";
      }
      s += "  Unit: \"" + cal.getValueUnit() + "\"\n";
    } else s += "Uncalibrated\n";

    FileInfo fi = imp.getOriginalFileInfo();
    if (fi != null) {
      if (fi.url != null && !fi.url.equals("")) s += "URL: " + fi.url + "\n";
      else if (fi.directory != null && fi.fileName != null)
        s += "Path: " + fi.directory + fi.fileName + "\n";
    }

    ImageWindow win = imp.getWindow();
    if (win != null) {
      Point loc = win.getLocation();
      Dimension screen = IJ.getScreenSize();
      s +=
          "Screen location: "
              + loc.x
              + ","
              + loc.y
              + " ("
              + screen.width
              + "x"
              + screen.height
              + ")\n";
    }

    Overlay overlay = imp.getOverlay();
    if (overlay != null) {
      String hidden = imp.getHideOverlay() ? " (hidden)" : " ";
      int n = overlay.size();
      String elements = n == 1 ? " element" : " elements";
      s += "Overlay: " + n + elements + (imp.getHideOverlay() ? " (hidden)" : "") + "\n";
    } else s += "No Overlay\n";

    Roi roi = imp.getRoi();
    if (roi == null) {
      if (cal.calibrated()) s += " \n";
      s += "No Selection\n";
    } else if (roi instanceof EllipseRoi) {
      s += "\nElliptical Selection\n";
      double[] p = ((EllipseRoi) roi).getParams();
      double dx = p[2] - p[0];
      double dy = p[3] - p[1];
      double major = Math.sqrt(dx * dx + dy * dy);
      s += "  Major: " + IJ.d2s(major, 2) + "\n";
      s += "  Minor: " + IJ.d2s(major * p[4], 2) + "\n";
      s += "  X1: " + IJ.d2s(p[0], 2) + "\n";
      s += "  Y1: " + IJ.d2s(p[1], 2) + "\n";
      s += "  X2: " + IJ.d2s(p[2], 2) + "\n";
      s += "  Y2: " + IJ.d2s(p[3], 2) + "\n";
      s += "  Aspect ratio: " + IJ.d2s(p[4], 2) + "\n";
    } else {
      s += " \n";
      s += roi.getTypeAsString() + " Selection";
      String points = null;
      if (roi instanceof PointRoi) {
        int npoints = ((PolygonRoi) roi).getNCoordinates();
        String suffix = npoints > 1 ? "s)" : ")";
        points = " (" + npoints + " point" + suffix;
      }
      String name = roi.getName();
      if (name != null) {
        s += " (\"" + name + "\")";
        if (points != null) s += "\n " + points;
      } else if (points != null) s += points;
      s += "\n";
      Rectangle r = roi.getBounds();
      if (roi instanceof Line) {
        Line line = (Line) roi;
        s += "  X1: " + IJ.d2s(line.x1d * cal.pixelWidth) + "\n";
        s += "  Y1: " + IJ.d2s(yy(line.y1d, imp) * cal.pixelHeight) + "\n";
        s += "  X2: " + IJ.d2s(line.x2d * cal.pixelWidth) + "\n";
        s += "  Y2: " + IJ.d2s(yy(line.y2d, imp) * cal.pixelHeight) + "\n";
      } else if (cal.scaled()) {
        s += "  X: " + IJ.d2s(cal.getX(r.x)) + " (" + r.x + ")\n";
        s += "  Y: " + IJ.d2s(cal.getY(r.y, imp.getHeight())) + " (" + r.y + ")\n";
        s += "  Width: " + IJ.d2s(r.width * cal.pixelWidth) + " (" + r.width + ")\n";
        s += "  Height: " + IJ.d2s(r.height * cal.pixelHeight) + " (" + r.height + ")\n";
      } else {
        s += "  X: " + r.x + "\n";
        s += "  Y: " + yy(r.y, imp) + "\n";
        s += "  Width: " + r.width + "\n";
        s += "  Height: " + r.height + "\n";
      }
    }

    return s;
  }
Exemple #8
0
 public void itemStateChanged(ItemEvent e) {
   ImagePlus imp = WindowManager.getCurrentImage();
   if (imp == null) return;
   if (!imp.isComposite()) {
     int channels = imp.getNChannels();
     if (channels == 1 && imp.getStackSize() <= 4) channels = imp.getStackSize();
     if (imp.getBitDepth() == 24 || (channels > 1 && channels < CompositeImage.MAX_CHANNELS)) {
       GenericDialog gd = new GenericDialog(imp.getTitle());
       gd.addMessage("Convert to multi-channel composite image?");
       gd.showDialog();
       if (gd.wasCanceled()) return;
       else IJ.doCommand("Make Composite");
     } else {
       IJ.error(
           "Channels",
           "A composite image is required (e.g., "
               + moreLabel
               + " Open HeLa Cells),\nor create one using "
               + moreLabel
               + " Make Composite.");
       return;
     }
   }
   if (!imp.isComposite()) return;
   CompositeImage ci = (CompositeImage) imp;
   Object source = e.getSource();
   if (source == choice) {
     int index = ((Choice) source).getSelectedIndex();
     switch (index) {
       case 0:
         ci.setMode(IJ.COMPOSITE);
         break;
       case 1:
         ci.setMode(IJ.COLOR);
         break;
       case 2:
         ci.setMode(IJ.GRAYSCALE);
         break;
     }
     ci.updateAndDraw();
     if (Recorder.record) {
       String mode = null;
       switch (index) {
         case 0:
           mode = "composite";
           break;
         case 1:
           mode = "color";
           break;
         case 2:
           mode = "grayscale";
           break;
       }
       Recorder.record("Stack.setDisplayMode", mode);
     }
   } else if (source instanceof Checkbox) {
     for (int i = 0; i < checkbox.length; i++) {
       Checkbox cb = (Checkbox) source;
       if (cb == checkbox[i]) {
         if (ci.getMode() == IJ.COMPOSITE) {
           boolean[] active = ci.getActiveChannels();
           active[i] = cb.getState();
           if (Recorder.record) {
             String str = "";
             for (int c = 0; c < ci.getNChannels(); c++) str += active[c] ? "1" : "0";
             Recorder.record("Stack.setActiveChannels", str);
             Recorder.record("//Stack.toggleChannel", imp.getChannel());
           }
         } else {
           imp.setPosition(i + 1, imp.getSlice(), imp.getFrame());
           if (Recorder.record) Recorder.record("Stack.setChannel", i + 1);
         }
         ci.updateAndDraw();
         return;
       }
     }
   }
 }