Exemplo n.º 1
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;
 }
Exemplo n.º 2
0
 public void dragOver(DropTargetDragEvent e) {
   if (IJ.debugMode) IJ.log("DragOver: " + e.getLocation());
   Point loc = e.getLocation();
   int buttonSize = Toolbar.getButtonSize();
   int width = IJ.getInstance().getSize().width;
   openAsVirtualStack = width - loc.x <= buttonSize;
   if (openAsVirtualStack) IJ.showStatus("<<Open as Virtual Stack>>");
   else IJ.showStatus("<<Drag and Drop>>");
 }
Exemplo n.º 3
0
 public void mouseMoved(MouseEvent e) {
   // if (ij==null) return;
   int sx = e.getX();
   int sy = e.getY();
   int ox = offScreenX(sx);
   int oy = offScreenY(sy);
   flags = e.getModifiers();
   setCursor(sx, sy, ox, oy);
   IJ.setInputEvent(e);
   Roi roi = imp.getRoi();
   if (roi != null
       && (roi.getType() == Roi.POLYGON
           || roi.getType() == Roi.POLYLINE
           || roi.getType() == Roi.ANGLE)
       && roi.getState() == roi.CONSTRUCTING) {
     PolygonRoi pRoi = (PolygonRoi) roi;
     pRoi.handleMouseMove(ox, oy);
   } else {
     if (ox < imageWidth && oy < imageHeight) {
       ImageWindow win = imp.getWindow();
       // Cursor must move at least 12 pixels before text
       // displayed using IJ.showStatus() is overwritten.
       if ((sx - sx2) * (sx - sx2) + (sy - sy2) * (sy - sy2) > 144) showCursorStatus = true;
       if (win != null && showCursorStatus) win.mouseMoved(ox, oy);
     } else IJ.showStatus("");
   }
 }
Exemplo n.º 4
0
    public synchronized void adjustmentValueChanged(AdjustmentEvent e) {

      if (!checkImage()) {
        IJ.beep();
        IJ.showStatus("No Image");
        return;
      }

      if (e.getSource() == minSlider) {
        adjustMinHue((int) minSlider.getValue());
      } else if (e.getSource() == maxSlider) {
        adjustMaxHue((int) maxSlider.getValue());
      } else if (e.getSource() == minSlider2) {
        adjustMinSat((int) minSlider2.getValue());
      } else if (e.getSource() == maxSlider2) {
        adjustMaxSat((int) maxSlider2.getValue());
      } else if (e.getSource() == minSlider3) {
        adjustMinBri((int) minSlider3.getValue());
      } else if (e.getSource() == maxSlider3) {
        adjustMaxBri((int) maxSlider3.getValue());
      }
      originalB.setEnabled(true);
      updateLabels();
      updatePlot();
      notify();
    }
Exemplo n.º 5
0
 public void mouseExited(MouseEvent e) {
   // autoScroll(e);
   ImageWindow win = imp.getWindow();
   if (win != null) setCursor(defaultCursor);
   IJ.showStatus("");
   mouseExited = true;
 }
 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;
 }
Exemplo n.º 7
0
 private boolean checkImage() {
   imp = WindowManager.getCurrentImage();
   if (imp == null) {
     IJ.beep();
     IJ.showStatus("No image");
     return false;
   }
   ip = setup(imp);
   if (ip == null) return false;
   return true;
 }
Exemplo n.º 8
0
 String[] openUrlAsList(String address) {
   IJ.showStatus("Connecting to " + IJ.URL);
   Vector v = new Vector();
   try {
     URL url = new URL(address);
     InputStream in = url.openStream();
     BufferedReader br = new BufferedReader(new InputStreamReader(in));
     String line;
     while (true) {
       line = br.readLine();
       if (line == null) break;
       if (!line.equals("")) v.addElement(line);
     }
     br.close();
   } catch (Exception e) {
   }
   String[] lines = new String[v.size()];
   v.copyInto((String[]) lines);
   IJ.showStatus("");
   return lines;
 }
Exemplo n.º 9
0
    public void actionPerformed(ActionEvent e) {
      Button b = (Button) e.getSource();
      if (b == null) return;

      boolean imageThere = checkImage();

      if (imageThere) {
        if (b == originalB) {
          reset(imp, ip);
          filteredB.setEnabled(true);
        } else if (b == filteredB) {
          apply(imp, ip);
        } else if (b == sampleB) {
          reset(imp, ip);
          sample();
          apply(imp, ip);
        } else if (b == stackB) {
          applyStack();
        } else if (b == helpB) {
          IJ.showMessage(
              "Help",
              "Threshold Colour  v1.0\n \n"
                  + "Modification of Bob Dougherty's BandPass2 plugin by G.Landini to\n"
                  + "threshold 24 bit RGB images based on Hue, Saturation and Brightness\n"
                  + "or Red, Green and Blue components.\n \n"
                  + "Pass: Band-pass filter (anything within range is displayed).\n \n"
                  + "Stop: Band-reject filter (anything within range is NOT displayed).\n \n"
                  + "Original: Shows the original image and updates the buffer when\n"
                  + " switching to another image.\n \n"
                  + "Filtered: Shows the filtered image.\n \n"
                  + "Stack: Processes the rest of the slices in the stack (if any)\n"
                  + " using the current settings.\n \n"
                  + "Threshold: Shows the object/background in the foreground and\n"
                  + " background colours selected in the ImageJ toolbar.\n \n"
                  + "Invert: Swaps the fore/background colours.\n \n"
                  + "Sample: (experimental) Sets the ranges of the filters based on the\n"
                  + " pixel value componentd in a rectangular, user-defined, ROI.\n \n"
                  + "HSB RGB: Selects HSB or RGB space and resets all the filters.\n \n"
                  + "Note that the \'thresholded\' image is RGB, not 8 bit grey.");
        }
        updatePlot();
        updateLabels();
        imp.updateAndDraw();
      } else {
        IJ.beep();
        IJ.showStatus("No Image");
      }
      notify();
    }
Exemplo n.º 10
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 11
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 12
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;
   }
 }
Exemplo n.º 13
0
 void applyStack() {
   // int minKeepH = minHue, maxKeepH = maxHue; //GL not needed?
   // int minKeepS = minSat, maxKeepS = maxSat;
   // int minKeepB = minBri, maxKeepB = maxBri;
   for (int i = 1; i <= numSlices; i++) {
     imp.setSlice(i);
     if (!checkImage()) {
       IJ.beep();
       IJ.showStatus("No Image");
       return;
     }
     //	minHue = minKeepH;
     //	maxHue = maxKeepH;
     //	minSat = minKeepS;
     //	maxSat = maxKeepS;
     //	minBri = minKeepB;
     //	maxBri = maxKeepB;
     apply(imp, ip);
   }
 }
Exemplo n.º 14
0
 protected void setDrawingColor(int ox, int oy, boolean setBackground) {
   // IJ.log("setDrawingColor: "+setBackground+this);
   int type = imp.getType();
   int[] v = imp.getPixel(ox, oy);
   switch (type) {
     case ImagePlus.GRAY8:
       {
         if (setBackground) setBackgroundColor(getColor(v[0]));
         else setForegroundColor(getColor(v[0]));
         break;
       }
     case ImagePlus.GRAY16:
     case ImagePlus.GRAY32:
       {
         double min = imp.getProcessor().getMin();
         double max = imp.getProcessor().getMax();
         double value = (type == ImagePlus.GRAY32) ? Float.intBitsToFloat(v[0]) : v[0];
         int index = (int) (255.0 * ((value - min) / (max - min)));
         if (index < 0) index = 0;
         if (index > 255) index = 255;
         if (setBackground) setBackgroundColor(getColor(index));
         else setForegroundColor(getColor(index));
         break;
       }
     case ImagePlus.COLOR_RGB:
     case ImagePlus.COLOR_256:
       {
         Color c = new Color(v[0], v[1], v[2]);
         if (setBackground) setBackgroundColor(c);
         else setForegroundColor(c);
         break;
       }
   }
   Color c;
   if (setBackground) c = Toolbar.getBackgroundColor();
   else {
     c = Toolbar.getForegroundColor();
     imp.setColor(c);
   }
   IJ.showStatus("(" + c.getRed() + ", " + c.getGreen() + ", " + c.getBlue() + ")");
 }
Exemplo n.º 15
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;
 }
Exemplo n.º 16
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;
 }
Exemplo n.º 17
0
  public boolean dialogItemChanged(GenericDialog gd, AWTEvent e) {
    int width = imp.getWidth();
    int height = imp.getHeight();
    type = gd.getNextChoice();
    areaPerPoint = gd.getNextNumber();
    color = gd.getNextChoice();
    randomOffset = gd.getNextBoolean();

    double minArea = (width * height) / 50000.0;
    if (type.equals(types[1]) && minArea < 144.0) minArea = 144.0;
    else if (minArea < 16) minArea = 16.0;
    if (areaPerPoint / (pixelWidth * pixelHeight) < minArea) {
      String err = "\"Area per Point\" too small";
      if (gd.wasOKed()) IJ.error("Grid", err);
      else IJ.showStatus(err);
      return true;
    }
    double tileSize = Math.sqrt(areaPerPoint);
    tileWidth = tileSize / pixelWidth;
    tileHeight = tileSize / pixelHeight;
    if (randomOffset) {
      xstart = (int) (random.nextDouble() * tileWidth);
      ystart = (int) (random.nextDouble() * tileHeight);
    } else {
      xstart = (int) (tileWidth / 2.0 + 0.5);
      ystart = (int) (tileHeight / 2.0 + 0.5);
    }
    linesV = (int) ((width - xstart) / tileWidth) + 1;
    linesH = (int) ((height - ystart) / tileHeight) + 1;
    if (gd.invalidNumber()) return true;
    if (type.equals(types[0])) drawLines();
    else if (type.equals(types[1])) drawCrosses();
    else if (type.equals(types[2])) drawPoints();
    else showGrid(null);
    return true;
  }
Exemplo n.º 18
0
  /** Restores original disk or network version of image. */
  public void revertToSaved(ImagePlus imp) {
    Image img;
    ProgressBar pb = IJ.getInstance().getProgressBar();
    ImageProcessor ip;
    String path = fi.directory + fi.fileName;

    if (fi.fileFormat == fi.GIF_OR_JPG) {
      // restore gif or jpg
      img = Toolkit.getDefaultToolkit().createImage(path);
      imp.setImage(img);
      if (imp.getType() == ImagePlus.COLOR_RGB) Opener.convertGrayJpegTo8Bits(imp);
      return;
    }

    if (fi.fileFormat == fi.DICOM) {
      // restore DICOM
      ImagePlus imp2 = (ImagePlus) IJ.runPlugIn("ij.plugin.DICOM", path);
      if (imp2 != null) imp.setProcessor(null, imp2.getProcessor());
      return;
    }

    if (fi.fileFormat == fi.BMP) {
      // restore BMP
      ImagePlus imp2 = (ImagePlus) IJ.runPlugIn("ij.plugin.BMP_Reader", path);
      if (imp2 != null) imp.setProcessor(null, imp2.getProcessor());
      return;
    }

    if (fi.fileFormat == fi.PGM) {
      // restore PGM
      ImagePlus imp2 = (ImagePlus) IJ.runPlugIn("ij.plugin.PGM_Reader", path);
      if (imp2 != null) imp.setProcessor(null, imp2.getProcessor());
      return;
    }

    if (fi.fileFormat == fi.ZIP_ARCHIVE) {
      // restore ".zip" file
      ImagePlus imp2 = (new Opener()).openZip(path);
      if (imp2 != null) imp.setProcessor(null, imp2.getProcessor());
      return;
    }

    // restore PNG or another image opened using ImageIO
    if (fi.fileFormat == fi.IMAGEIO) {
      ImagePlus imp2 = (new Opener()).openUsingImageIO(path);
      if (imp2 != null) imp.setProcessor(null, imp2.getProcessor());
      return;
    }

    if (fi.nImages > 1) return;

    ColorModel cm;
    if (fi.url == null || fi.url.equals("")) IJ.showStatus("Loading: " + path);
    else IJ.showStatus("Loading: " + fi.url + fi.fileName);
    Object pixels = readPixels(fi);
    if (pixels == null) return;
    cm = createColorModel(fi);
    switch (fi.fileType) {
      case FileInfo.GRAY8:
      case FileInfo.COLOR8:
      case FileInfo.BITMAP:
        ip = new ByteProcessor(width, height, (byte[]) pixels, cm);
        imp.setProcessor(null, ip);
        break;
      case FileInfo.GRAY16_SIGNED:
      case FileInfo.GRAY16_UNSIGNED:
      case FileInfo.GRAY12_UNSIGNED:
        ip = new ShortProcessor(width, height, (short[]) pixels, cm);
        imp.setProcessor(null, ip);
        break;
      case FileInfo.GRAY32_INT:
      case FileInfo.GRAY32_FLOAT:
        ip = new FloatProcessor(width, height, (float[]) pixels, cm);
        imp.setProcessor(null, ip);
        break;
      case FileInfo.RGB:
      case FileInfo.BGR:
      case FileInfo.ARGB:
      case FileInfo.ABGR:
      case FileInfo.RGB_PLANAR:
        img =
            Toolkit.getDefaultToolkit()
                .createImage(new MemoryImageSource(width, height, (int[]) pixels, 0, width));
        imp.setImage(img);
        break;
    }
  }
Exemplo n.º 19
0
 public void focusGained(FocusEvent e) {
   if (!checkImage()) {
     IJ.beep();
     IJ.showStatus("No Image");
   }
 }
Exemplo n.º 20
0
    ImageProcessor setup(ImagePlus imp) {

      ImageProcessor ip;
      int type = imp.getType();
      if (type != ImagePlus.COLOR_RGB) return null;
      ip = imp.getProcessor();
      int id = imp.getID();
      int slice = imp.getCurrentSlice();

      if ((id != previousImageID) | (slice != previousSlice) | (flag)) {
        flag = false; // if true, flags a change from HSB to RGB or viceversa
        numSlices = imp.getStackSize();
        stack = imp.getStack();
        width = stack.getWidth();
        height = stack.getHeight();
        numPixels = width * height;

        hSource = new byte[numPixels];
        sSource = new byte[numPixels];
        bSource = new byte[numPixels];

        // restore = (int[])ip.getPixelsCopy(); //This runs into trouble sometimes, so do it the
        // long way:
        int[] temp = (int[]) ip.getPixels();
        restore = new int[numPixels];
        for (int i = 0; i < numPixels; i++) restore[i] = temp[i];

        fillMask = new int[numPixels];

        // Get hsb or rgb from image.
        ColorProcessor cp = (ColorProcessor) ip;
        IJ.showStatus("Gathering data");

        if (isRGB) cp.getRGB(hSource, sSource, bSource);
        else cp.getHSB(hSource, sSource, bSource);

        IJ.showStatus("done");

        // Create a spectrum ColorModel for the Hue histogram plot.
        Color c;
        byte[] reds = new byte[256];
        byte[] greens = new byte[256];
        byte[] blues = new byte[256];
        for (int i = 0; i < 256; i++) {
          c = Color.getHSBColor(i / 255f, 1f, 1f);

          reds[i] = (byte) c.getRed();
          greens[i] = (byte) c.getGreen();
          blues[i] = (byte) c.getBlue();
        }
        ColorModel cm = new IndexColorModel(8, 256, reds, greens, blues);

        // Make an image with just the hue from the RGB image and the spectrum LUT.
        // This is just for a hue histogram for the plot.  Do not show it.
        // ByteProcessor bpHue = new ByteProcessor(width,height,h,cm);
        ByteProcessor bpHue = new ByteProcessor(width, height, hSource, cm);
        ImagePlus impHue = new ImagePlus("Hue", bpHue);
        // impHue.show();

        ByteProcessor bpSat = new ByteProcessor(width, height, sSource, cm);
        ImagePlus impSat = new ImagePlus("Sat", bpSat);
        // impSat.show();

        ByteProcessor bpBri = new ByteProcessor(width, height, bSource, cm);
        ImagePlus impBri = new ImagePlus("Bri", bpBri);
        // impBri.show();

        plot.setHistogram(impHue, 0);
        splot.setHistogram(impSat, 1);
        bplot.setHistogram(impBri, 2);

        updateLabels();
        updatePlot();
        updateScrollBars();
        imp.updateAndDraw();
      }
      previousImageID = id;
      previousSlice = slice;
      return ip;
    }
Exemplo n.º 21
0
    public BandAdjuster() {

      super("Threshold Colour");
      if (instance != null) {
        instance.toFront();
        return;
      }
      imp = WindowManager.getCurrentImage();
      if (imp == null) {
        IJ.beep();
        IJ.showStatus("No image");
        return;
      }
      IJ.run("Select None");
      thread = new Thread(this, "BandAdjuster");
      WindowManager.addWindow(this);
      instance = this;
      IJ.register(PasteController.class);

      ij = IJ.getInstance();
      Font font = new Font("SansSerif", Font.PLAIN, 10);
      GridBagLayout gridbag = new GridBagLayout();
      GridBagConstraints c = new GridBagConstraints();
      setLayout(gridbag);

      int y = 0;
      c.gridx = 0;
      c.gridy = y;
      c.gridwidth = 1;
      c.weightx = 0;
      c.insets = new Insets(5, 0, 0, 0);
      labelh = new Label("Hue", Label.CENTER);
      add(labelh, c);

      c.gridx = 1;
      c.gridy = y++;
      c.gridwidth = 1;
      c.weightx = 0;
      c.insets = new Insets(7, 0, 0, 0);
      labelf = new Label("Filter type", Label.RIGHT);
      add(labelf, c);

      // plot
      c.gridx = 0;
      c.gridy = y;
      c.gridwidth = 1;
      c.fill = c.BOTH;
      c.anchor = c.CENTER;
      c.insets = new Insets(0, 5, 0, 0);
      add(plot, c);

      // checkboxes
      panelh = new Panel();
      filterTypeH = new CheckboxGroup();
      bandPassH = new Checkbox("Pass");
      bandPassH.setCheckboxGroup(filterTypeH);
      bandPassH.addItemListener(this);
      panelh.add(bandPassH);
      bandStopH = new Checkbox("Stop");
      bandStopH.setCheckboxGroup(filterTypeH);
      bandStopH.addItemListener(this);
      panelh.add(bandStopH);
      bandPassH.setState(true);
      c.gridx = 1;
      c.gridy = y++;
      c.gridwidth = 2;
      c.insets = new Insets(5, 0, 0, 0);
      add(panelh, c);

      // minHue slider
      minSlider = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
      c.gridx = 0;
      c.gridy = y++;
      c.gridwidth = 1;
      c.weightx = IJ.isMacintosh() ? 90 : 100;
      c.fill = c.HORIZONTAL;
      c.insets = new Insets(5, 5, 0, 0);

      add(minSlider, c);
      minSlider.addAdjustmentListener(this);
      minSlider.setUnitIncrement(1);

      // minHue slider label
      c.gridx = 1;
      c.gridwidth = 1;
      c.weightx = IJ.isMacintosh() ? 10 : 0;
      c.insets = new Insets(5, 0, 0, 0);
      label1 = new Label("       ", Label.LEFT);
      label1.setFont(font);
      add(label1, c);

      // maxHue sliderHue
      maxSlider = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
      c.gridx = 0;
      c.gridy = y;
      c.gridwidth = 1;
      c.weightx = 100;
      c.insets = new Insets(5, 5, 0, 0);
      add(maxSlider, c);
      maxSlider.addAdjustmentListener(this);
      maxSlider.setUnitIncrement(1);

      // maxHue slider label
      c.gridx = 1;
      c.gridwidth = 1;
      c.gridy = y++;
      c.weightx = 0;
      c.insets = new Insets(5, 0, 0, 0);
      label2 = new Label("       ", Label.LEFT);
      label2.setFont(font);
      add(label2, c);

      // =====
      c.gridx = 0;
      c.gridy = y++;
      c.gridwidth = 1;
      c.weightx = 0;
      c.insets = new Insets(10, 0, 0, 0);
      labels = new Label("Saturation", Label.CENTER);
      add(labels, c);

      // plot
      c.gridx = 0;
      c.gridy = y;
      c.gridwidth = 1;
      c.fill = c.BOTH;
      c.anchor = c.CENTER;
      c.insets = new Insets(0, 5, 0, 0);
      add(splot, c);

      // checkboxes
      panels = new Panel();
      filterTypeS = new CheckboxGroup();
      bandPassS = new Checkbox("Pass");
      bandPassS.setCheckboxGroup(filterTypeS);
      bandPassS.addItemListener(this);
      panels.add(bandPassS);
      bandStopS = new Checkbox("Stop");
      bandStopS.setCheckboxGroup(filterTypeS);
      bandStopS.addItemListener(this);
      panels.add(bandStopS);
      bandPassS.setState(true);
      c.gridx = 1;
      c.gridy = y++;
      c.gridwidth = 2;
      c.insets = new Insets(5, 0, 0, 0);
      add(panels, c);

      // minSat slider
      minSlider2 = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
      c.gridx = 0;
      c.gridy = y++;
      c.gridwidth = 1;
      c.weightx = IJ.isMacintosh() ? 90 : 100;
      c.fill = c.HORIZONTAL;
      c.insets = new Insets(5, 5, 0, 0);
      add(minSlider2, c);
      minSlider2.addAdjustmentListener(this);
      minSlider2.setUnitIncrement(1);

      // minSat slider label
      c.gridx = 1;
      c.gridwidth = 1;
      c.weightx = IJ.isMacintosh() ? 10 : 0;
      c.insets = new Insets(5, 0, 0, 0);
      label3 = new Label("       ", Label.LEFT);
      label3.setFont(font);
      add(label3, c);

      // maxSat slider
      maxSlider2 = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
      c.gridx = 0;
      c.gridy = y++;
      c.gridwidth = 1;
      c.weightx = 100;
      c.insets = new Insets(5, 5, 0, 0);
      add(maxSlider2, c);
      maxSlider2.addAdjustmentListener(this);
      maxSlider2.setUnitIncrement(1);

      // maxSat slider label
      c.gridx = 1;
      c.gridwidth = 1;
      c.weightx = 0;
      c.insets = new Insets(5, 0, 0, 0);
      label4 = new Label("       ", Label.LEFT);
      label4.setFont(font);
      add(label4, c);

      // =====
      c.gridx = 0;
      c.gridwidth = 1;
      c.gridy = y++;
      c.weightx = 0;
      c.insets = new Insets(10, 0, 0, 0);
      labelb = new Label("Brightness", Label.CENTER);
      add(labelb, c);

      c.gridx = 0;
      c.gridwidth = 1;
      c.gridy = y;
      c.fill = c.BOTH;
      c.anchor = c.CENTER;
      c.insets = new Insets(0, 5, 0, 0);
      add(bplot, c);

      // checkboxes
      panelb = new Panel();
      filterTypeB = new CheckboxGroup();
      bandPassB = new Checkbox("Pass");
      bandPassB.setCheckboxGroup(filterTypeB);
      bandPassB.addItemListener(this);
      panelb.add(bandPassB);
      bandStopB = new Checkbox("Stop");
      bandStopB.setCheckboxGroup(filterTypeB);
      bandStopB.addItemListener(this);
      panelb.add(bandStopB);
      bandPassB.setState(true);
      c.gridx = 1;
      c.gridy = y++;
      c.gridwidth = 2;
      c.insets = new Insets(5, 0, 0, 0);
      add(panelb, c);

      // minBri slider
      minSlider3 = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
      c.gridx = 0;
      c.gridy = y++;
      c.gridwidth = 1;
      c.weightx = IJ.isMacintosh() ? 90 : 100;
      c.fill = c.HORIZONTAL;
      c.insets = new Insets(5, 5, 0, 0);
      add(minSlider3, c);
      minSlider3.addAdjustmentListener(this);
      minSlider3.setUnitIncrement(1);

      // minBri slider label
      c.gridx = 1;
      c.gridwidth = 1;
      c.weightx = IJ.isMacintosh() ? 10 : 0;
      c.insets = new Insets(5, 0, 0, 0);
      label5 = new Label("       ", Label.LEFT);
      label5.setFont(font);
      add(label5, c);

      // maxBri slider
      maxSlider3 = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
      c.gridx = 0;
      c.gridy = y++;
      c.gridwidth = 1;
      c.weightx = 100;
      c.insets = new Insets(5, 5, 0, 0);
      add(maxSlider3, c);
      maxSlider3.addAdjustmentListener(this);
      maxSlider3.setUnitIncrement(1);

      // maxBri slider label
      c.gridx = 1;
      c.gridwidth = 1;
      c.weightx = 0;
      c.insets = new Insets(5, 0, 0, 0);
      label6 = new Label("       ", Label.LEFT);
      label6.setFont(font);
      add(label6, c);

      // =====
      panelt = new Panel();
      threshold = new Checkbox("Threshold");
      threshold.addItemListener(this);
      panelt.add(threshold);

      invert = new Checkbox("Invert");
      invert.addItemListener(this);
      panelt.add(invert);

      c.gridx = 0;
      c.gridy = y++;
      c.gridwidth = 2;
      c.insets = new Insets(0, 0, 0, 0);
      add(panelt, c);

      // buttons
      panel = new Panel();
      // panel.setLayout(new GridLayout(2, 2, 0, 0));
      originalB = new Button("Original");
      originalB.setEnabled(false);
      originalB.addActionListener(this);
      originalB.addKeyListener(ij);
      panel.add(originalB);

      filteredB = new Button("Filtered");
      filteredB.setEnabled(false);
      filteredB.addActionListener(this);
      filteredB.addKeyListener(ij);
      panel.add(filteredB);

      stackB = new Button("Stack");
      stackB.addActionListener(this);
      stackB.addKeyListener(ij);
      panel.add(stackB);

      helpB = new Button("Help");
      helpB.addActionListener(this);
      helpB.addKeyListener(ij);
      panel.add(helpB);

      c.gridx = 0;
      c.gridy = y++;
      c.gridwidth = 2;
      c.insets = new Insets(0, 0, 0, 0);
      add(panel, c);

      panelMode = new Panel();

      sampleB = new Button("Sample");
      sampleB.addActionListener(this);
      sampleB.addKeyListener(ij);
      panelMode.add(sampleB);

      colourMode = new CheckboxGroup();
      hsb = new Checkbox("HSB");
      hsb.setCheckboxGroup(colourMode);
      hsb.addItemListener(this);
      panelMode.add(hsb);
      hsb.setState(true);
      rgb = new Checkbox("RGB");
      rgb.setCheckboxGroup(colourMode);
      rgb.addItemListener(this);
      panelMode.add(rgb);

      c.gridx = 0;
      c.gridy = y++;
      c.gridwidth = 2;
      c.insets = new Insets(0, 0, 0, 0);
      add(panelMode, c);

      addKeyListener(ij); // ImageJ handles keyboard shortcuts
      pack();
      GUI.center(this);
      setVisible(true);

      ip = setup(imp);
      if (ip == null) {
        imp.unlock();
        IJ.beep();
        IJ.showStatus("RGB image cannot be thresholded");
        return;
      }
      thread.start();
    }
 void install() {
   subMenus.clear();
   if (text != null) {
     Tokenizer tok = new Tokenizer();
     pgm = tok.tokenize(text);
   }
   if (macrosMenu != null) IJ.showStatus("");
   int[] code = pgm.getCode();
   Symbol[] symbolTable = pgm.getSymbolTable();
   int count = 0, token, nextToken, address;
   String name;
   Symbol symbol;
   shortcutsInUse = null;
   inUseCount = 0;
   nShortcuts = 0;
   toolCount = 0;
   macroStarts = new int[MAX_MACROS];
   macroNames = new String[MAX_MACROS];
   boolean isPluginsMacrosMenu = false;
   if (macrosMenu != null) {
     int itemCount = macrosMenu.getItemCount();
     isPluginsMacrosMenu = macrosMenu == Menus.getMacrosMenu();
     int baseCount = isPluginsMacrosMenu ? MACROS_MENU_COMMANDS : Editor.MACROS_MENU_ITEMS;
     if (itemCount > baseCount) {
       for (int i = itemCount - 1; i >= baseCount; i--) macrosMenu.remove(i);
     }
   }
   if (pgm.hasVars() && pgm.macroCount() > 0 && pgm.getGlobals() == null)
     new Interpreter().saveGlobals(pgm);
   ArrayList tools = new ArrayList();
   for (int i = 0; i < code.length; i++) {
     token = code[i] & TOK_MASK;
     if (token == MACRO) {
       nextToken = code[i + 1] & TOK_MASK;
       if (nextToken == STRING_CONSTANT) {
         if (count == MAX_MACROS) {
           if (isPluginsMacrosMenu)
             IJ.error("Macro Installer", "Macro sets are limited to " + MAX_MACROS + " macros.");
           break;
         }
         address = code[i + 1] >> TOK_SHIFT;
         symbol = symbolTable[address];
         name = symbol.str;
         macroStarts[count] = i + 2;
         macroNames[count] = name;
         if (name.indexOf('-') != -1
             && (name.indexOf("Tool") != -1 || name.indexOf("tool") != -1)) {
           tools.add(name);
           toolCount++;
         } else if (name.startsWith("AutoRun")) {
           if (autoRunCount == 0 && !openingStartupMacrosInEditor) {
             new MacroRunner(pgm, macroStarts[count], name, (String) null);
             if (name.equals("AutoRunAndHide")) autoRunAndHideCount++;
           }
           autoRunCount++;
           count--;
         } else if (name.equals("Popup Menu")) installPopupMenu(name, pgm);
         else if (!name.endsWith("Tool Selected")) {
           if (macrosMenu != null) {
             addShortcut(name);
             int pos = name.indexOf(">");
             boolean inSubMenu = name.startsWith("<") && (pos > 1);
             if (inSubMenu) {
               Menu parent = macrosMenu;
               Menu subMenu = null;
               String parentStr = name.substring(1, pos).trim();
               String childStr = name.substring(pos + 1).trim();
               MenuItem mnuItem = new MenuItem();
               mnuItem.setActionCommand(name);
               mnuItem.setLabel(childStr);
               for (int jj = 0; jj < subMenus.size(); jj++) {
                 String aName = subMenus.get(jj).getName();
                 if (aName.equals(parentStr)) subMenu = subMenus.get(jj);
               }
               if (subMenu == null) {
                 subMenu = new Menu(parentStr);
                 subMenu.setName(parentStr);
                 subMenu.addActionListener(this);
                 subMenus.add(subMenu);
                 parent.add(subMenu);
               }
               subMenu.add(mnuItem);
             } else macrosMenu.add(new MenuItem(name));
           }
         }
         // IJ.log(count+" "+name+" "+macroStarts[count]);
         count++;
       }
     } else if (token == EOF) break;
   }
   nMacros = count;
   if (toolCount > 0 && (isPluginsMacrosMenu || macrosMenu == null) && installTools) {
     Toolbar tb = Toolbar.getInstance();
     if (toolCount == 1) tb.addMacroTool((String) tools.get(0), this);
     else {
       for (int i = 0; i < tools.size(); i++) {
         String toolName = (String) tools.get(i);
         if (toolName.startsWith("Abort Macro or Plugin") && toolCount > 6)
           toolName = "Unused " + toolName;
         tb.addMacroTool(toolName, this, i);
       }
     }
     if (toolCount > 1 && Toolbar.getToolId() >= Toolbar.CUSTOM1) tb.setTool(Toolbar.RECTANGLE);
     tb.repaint();
   }
   if (macrosMenu != null) this.instance = this;
   if (shortcutsInUse != null && text != null)
     IJ.showMessage(
         "Install Macros",
         (inUseCount == 1 ? "This keyboard shortcut is" : "These keyboard shortcuts are")
             + " already in use:"
             + shortcutsInUse);
   if (nMacros == 0 && fileName != null) {
     if (text == null || text.length() == 0) return;
     int dotIndex = fileName.lastIndexOf('.');
     if (dotIndex > 0) anonymousName = fileName.substring(0, dotIndex);
     else anonymousName = fileName;
     if (macrosMenu != null) macrosMenu.add(new MenuItem(anonymousName));
     macroNames[0] = anonymousName;
     nMacros = 1;
   }
   String word = nMacros == 1 ? " macro" : " macros";
   if (isPluginsMacrosMenu) IJ.showStatus(nMacros + word + " installed");
 }
Exemplo n.º 23
0
 public void mousePressed(MouseEvent e) {
   Undo.reset();
   if (!Prefs.noClickToGC) System.gc();
   IJ.showStatus(version() + IJ.freeMemory());
   if (IJ.debugMode) IJ.log("Windows: " + WindowManager.getWindowCount());
 }
Exemplo n.º 24
0
  /**
   * If 'applet' is not null, creates a new ImageJ frame that runs as an applet. If 'mode' is
   * ImageJ.EMBEDDED and 'applet is null, creates an embedded (non-standalone) version of ImageJ.
   */
  public ImageJ(java.applet.Applet applet, int mode) {
    super("ImageJ");
    if ((mode & DEBUG) != 0) IJ.setDebugMode(true);
    mode = mode & 255;
    if (IJ.debugMode) IJ.log("ImageJ starting in debug mode: " + mode);
    embedded = applet == null && (mode == EMBEDDED || mode == NO_SHOW);
    this.applet = applet;
    String err1 = Prefs.load(this, applet);
    setBackground(backgroundColor);
    Menus m = new Menus(this, applet);
    String err2 = m.addMenuBar();
    m.installPopupMenu(this);
    setLayout(new BorderLayout());

    // Tool bar
    toolbar = new Toolbar();
    toolbar.addKeyListener(this);
    add("Center", toolbar);

    // Status bar
    statusBar = new Panel();
    statusBar.setLayout(new BorderLayout());
    statusBar.setForeground(Color.black);
    statusBar.setBackground(backgroundColor);
    statusLine = new JLabel();
    statusLine.setFont(new Font("SansSerif", Font.PLAIN, 13));
    statusLine.addKeyListener(this);
    statusLine.addMouseListener(this);
    statusBar.add("Center", statusLine);
    progressBar = new ProgressBar(120, 20);
    progressBar.addKeyListener(this);
    progressBar.addMouseListener(this);
    statusBar.add("East", progressBar);
    add("South", statusBar);

    IJ.init(this, applet);
    addKeyListener(this);
    addWindowListener(this);
    setFocusTraversalKeysEnabled(false);
    m.installStartupMacroSet(); // add custom tools
    runStartupMacro();

    Point loc = getPreferredLocation();
    Dimension tbSize = toolbar.getPreferredSize();
    setCursor(Cursor.getDefaultCursor()); // work-around for JDK 1.1.8 bug
    if (mode != NO_SHOW) {
      if (IJ.isWindows())
        try {
          setIcon();
        } catch (Exception e) {
        }
      setLocation(loc.x, loc.y);
      setResizable(!IJ.isMacOSX());
      pack();
      setVisible(true);
    }
    if (err1 != null) IJ.error(err1);
    if (err2 != null) {
      IJ.error(err2);
      IJ.runPlugIn("ij.plugin.ClassChecker", "");
    }
    if (IJ.isMacintosh() && applet == null) {
      Object qh = null;
      qh = IJ.runPlugIn("MacAdapter", "");
      if (qh == null) IJ.runPlugIn("QuitHandler", "");
    }
    if (applet == null) IJ.runPlugIn("ij.plugin.DragAndDrop", "");
    String str = m.getMacroCount() == 1 ? " macro" : " macros";
    IJ.showStatus(version() + m.getPluginCount() + " commands; " + m.getMacroCount() + str);
    configureProxy();
    if (applet == null) loadCursors();
  }
Exemplo n.º 25
0
  /**
   * If 'applet' is not null, creates a new ImageJ frame that runs as an applet. If 'mode' is
   * ImageJ.EMBEDDED and 'applet is null, creates an embedded (non-standalone) version of ImageJ.
   */
  public ImageJ(java.applet.Applet applet, int mode) {
    super("ImageJ");
    embedded = applet == null && (mode == EMBEDDED || mode == NO_SHOW);
    this.applet = applet;
    String err1 = Prefs.load(this, applet);
    if (IJ.isLinux()) {
      backgroundColor = new Color(240, 240, 240);
      setBackground(backgroundColor);
    }
    Menus m = new Menus(this, applet);
    String err2 = m.addMenuBar();
    m.installPopupMenu(this);
    setLayout(new GridLayout(2, 1));

    // Tool bar
    toolbar = new Toolbar();
    toolbar.addKeyListener(this);
    add(toolbar);

    // Status bar
    statusBar = new Panel();
    statusBar.setLayout(new BorderLayout());
    statusBar.setForeground(Color.black);
    statusBar.setBackground(backgroundColor);
    statusLine = new Label();
    statusLine.setFont(SansSerif12);
    statusLine.addKeyListener(this);
    statusLine.addMouseListener(this);
    statusBar.add("Center", statusLine);
    progressBar = new ProgressBar(120, 20);
    progressBar.addKeyListener(this);
    progressBar.addMouseListener(this);
    statusBar.add("East", progressBar);
    statusBar.setSize(toolbar.getPreferredSize());
    add(statusBar);

    IJ.init(this, applet);
    addKeyListener(this);
    addWindowListener(this);
    setFocusTraversalKeysEnabled(false);

    Point loc = getPreferredLocation();
    Dimension tbSize = toolbar.getPreferredSize();
    int ijWidth = tbSize.width + 10;
    int ijHeight = 100;
    setCursor(Cursor.getDefaultCursor()); // work-around for JDK 1.1.8 bug
    if (mode != NO_SHOW) {
      if (IJ.isWindows())
        try {
          setIcon();
        } catch (Exception e) {
        }
      setBounds(loc.x, loc.y, ijWidth, ijHeight); // needed for pack to work
      setLocation(loc.x, loc.y);
      pack();
      setResizable(!(IJ.isMacintosh() || IJ.isWindows())); // make resizable on Linux
      show();
    }
    if (err1 != null) IJ.error(err1);
    if (err2 != null) {
      IJ.error(err2);
      IJ.runPlugIn("ij.plugin.ClassChecker", "");
    }
    m.installStartupMacroSet();
    if (IJ.isMacintosh() && applet == null) {
      Object qh = null;
      qh = IJ.runPlugIn("MacAdapter", "");
      if (qh == null) IJ.runPlugIn("QuitHandler", "");
    }
    if (applet == null) IJ.runPlugIn("ij.plugin.DragAndDrop", "");
    String str = m.getMacroCount() == 1 ? " macro" : " macros";
    IJ.showStatus(version() + m.getPluginCount() + " commands; " + m.getMacroCount() + str);
    // if (applet==null && !embedded && Prefs.runSocketListener)
    //	new SocketListener();
    configureProxy();
    if (applet == null) loadCursors();
  }
Exemplo n.º 26
0
 public void dragExit(DropTargetEvent e) {
   IJ.showStatus("");
 }
Exemplo n.º 27
0
 public void dragEnter(DropTargetDragEvent e) {
   IJ.showStatus("<<Drag and Drop>>");
   if (IJ.debugMode) IJ.log("DragEnter: " + e.getLocation());
   e.acceptDrag(DnDConstants.ACTION_COPY);
   openAsVirtualStack = false;
 }