Пример #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;
 }
Пример #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>>");
 }
Пример #3
0
 void loadParticleResults(String filename, ResultsTable res) {
   try {
     String line;
     FileReader fr = new FileReader(filename);
     BufferedReader br = new BufferedReader(fr);
     java.lang.String header =
         " 	Intensity	X (px)	Y (px)	X (nm)	Y (nm)	Z (nm)	Left-Width(px)	Right-Width (px)	Up-Height (px)	Down-Height (px)	X Symmetry (%)	Y Symmetry (%)	Width minus Height (px)	Frame Number";
     java.lang.String firstline = br.readLine();
     if (!firstline.contains("X (px)	Y (px)	X (nm)	Y (nm)	Z (nm)")) {
       IJ.error("File does not seam to be a Particles Table file");
       IJ.log("Found header: " + firstline);
       IJ.log("Expecting: " + header);
       return;
     }
     res.reset();
     int counter = 1;
     java.util.concurrent.locks.Lock lock = new java.util.concurrent.locks.ReentrantLock();
     ThreadedLoader tloader = new ThreadedLoader();
     // java.lang.String txt = fr.read();
     while ((line = br.readLine()) != null) {
       tloader = new ThreadedLoader();
       tloader.mysetup(res, lock, line);
       tloader.start();
       IJ.showStatus("Loading particle " + counter + "... sit back and relax.");
       counter++;
     }
     try {
       tloader.join();
     } catch (Exception e) {
       IJ.error("" + e);
     }
     if (res.getCounter() < 5000000) {
       IJ.showStatus("Creating particle table, this should take a few seconds...");
       res.show("Results");
     } else
       IJ.showMessage(
           "Warning",
           "Results table has too many particles, they will not be shown but the data still exists within it\nyou can still use all the plugin functionality or save table changes though the 'Save Particle Table' command.");
     fr.close();
     IJ.showStatus("Done loading table...");
   } catch (FileNotFoundException e) {
     IJ.error("File not found exception" + e);
     return;
   } catch (IOException e) {
     IJ.error("IOException exception" + e);
     return;
   } catch (NumberFormatException e) {
     IJ.error("Number format exception" + e);
     return;
   }
 }
Пример #4
0
 void loadTransformation(String filename, ResultsTable res) {
   try {
     String line;
     FileReader fr = new FileReader(filename);
     BufferedReader br = new BufferedReader(fr);
     if (!br.readLine().equals(" 	Z-Step	Raw Width minus Heigh	Calibration Width minus Height")) {
       IJ.error("File does not seam to be an Astigmatism calibration file");
       return;
     }
     // java.lang.String [] elements = new java.lang.String [3];
     java.lang.String[] elements;
     int counter = 1;
     res.reset();
     while ((line = br.readLine()) != null) {
       IJ.showStatus("Loading element " + counter + "... sit back and relax.");
       counter++;
       line.trim();
       elements = line.split("\t");
       res.incrementCounter();
       res.addValue("Z-Step", Double.parseDouble(elements[1]));
       res.addValue("Raw Width minus Heigh", Double.parseDouble(elements[2]));
       res.addValue("Calibration Width minus Height", Double.parseDouble(elements[3]));
     }
     fr.close();
   } catch (FileNotFoundException e) {
     IJ.error("File not found exception" + e);
     return;
   } catch (IOException e) {
     IJ.error("IOException exception" + e);
     return;
   } catch (NumberFormatException e) {
     IJ.error("Number format exception" + e);
     return;
   }
 }
Пример #5
0
 void createEllipse(ImagePlus imp) {
   IJ.showStatus("Fitting ellipse");
   Roi roi = imp.getRoi();
   if (roi == null) {
     noRoi("Fit Ellipse");
     return;
   }
   if (roi.isLine()) {
     IJ.error("Fit Ellipse", "\"Fit Ellipse\" does not work with line selections");
     return;
   }
   ImageProcessor ip = imp.getProcessor();
   ip.setRoi(roi);
   int options = Measurements.CENTROID + Measurements.ELLIPSE;
   ImageStatistics stats = ImageStatistics.getStatistics(ip, options, null);
   double dx = stats.major * Math.cos(stats.angle / 180.0 * Math.PI) / 2.0;
   double dy = -stats.major * Math.sin(stats.angle / 180.0 * Math.PI) / 2.0;
   double x1 = stats.xCentroid - dx;
   double x2 = stats.xCentroid + dx;
   double y1 = stats.yCentroid - dy;
   double y2 = stats.yCentroid + dy;
   double aspectRatio = stats.minor / stats.major;
   imp.killRoi();
   imp.setRoi(new EllipseRoi(x1, y1, x2, y2, aspectRatio));
 }
Пример #6
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();
    }
Пример #7
0
 /** Overrides ImagePlus.show(). * */
 public void show() {
   if (img == null && ip != null) img = ip.createImage();
   ImageWindow.centerNextImage();
   win = new ImageWindow(this, new ColorCanvas(this));
   draw();
   IJ.showStatus("");
 }
Пример #8
0
  /**
   * Execute the plugin functionality: duplicate and scale the given image.
   *
   * @return an Object[] array with the name and the scaled ImagePlus. Does NOT show the new, image;
   *     just returns it.
   */
  public Object[] exec(
      ImagePlus imp, String myMethod, int radius, double par1, double par2, boolean doIwhite) {

    // 0 - Check validity of parameters
    if (null == imp) return null;
    ImageProcessor ip = imp.getProcessor();
    int xe = ip.getWidth();
    int ye = ip.getHeight();

    // int [] data = (ip.getHistogram());

    IJ.showStatus("Thresholding...");
    long startTime = System.currentTimeMillis();
    // 1 Do it
    if (imp.getStackSize() == 1) {
      ip.snapshot();
      Undo.setup(Undo.FILTER, imp);
    }
    // Apply the selected algorithm
    if (myMethod.equals("Bernsen")) {
      Bernsen(imp, radius, par1, par2, doIwhite);
    } else if (myMethod.equals("Contrast")) {
      Contrast(imp, radius, par1, par2, doIwhite);
    } else if (myMethod.equals("Mean")) {
      Mean(imp, radius, par1, par2, doIwhite);
    } else if (myMethod.equals("Median")) {
      Median(imp, radius, par1, par2, doIwhite);
    } else if (myMethod.equals("MidGrey")) {
      MidGrey(imp, radius, par1, par2, doIwhite);
    } else if (myMethod.equals("Niblack")) {
      Niblack(imp, radius, par1, par2, doIwhite);
    } else if (myMethod.equals("Otsu")) {
      Otsu(imp, radius, par1, par2, doIwhite);
    } else if (myMethod.equals("Phansalkar")) {
      Phansalkar(imp, radius, par1, par2, doIwhite);
    } else if (myMethod.equals("Sauvola")) {
      Sauvola(imp, radius, par1, par2, doIwhite);
    }
    // IJ.showProgress((double)(255-i)/255);
    imp.updateAndDraw();
    imp.getProcessor().setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE);
    // 2 - Return the threshold and the image
    IJ.showStatus("\nDone " + (System.currentTimeMillis() - startTime) / 1000.0);
    return new Object[] {imp};
  }
 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;
 }
Пример #10
0
 void enlargeCanvas() {
   imp.unlock();
   if (imp.getStackSize() == 1) Undo.setup(Undo.COMPOUND_FILTER, imp);
   IJ.run("Select All");
   IJ.run("Rotate...", "angle=" + angle);
   Roi roi = imp.getRoi();
   Rectangle r = roi.getBounds();
   if (r.width < imp.getWidth()) r.width = imp.getWidth();
   if (r.height < imp.getHeight()) r.height = imp.getHeight();
   IJ.showStatus("Rotate: Enlarging...");
   IJ.run(
       "Canvas Size...",
       "width="
           + r.width
           + " height="
           + r.height
           + " position=Center "
           + (fillWithBackground ? "" : "zero"));
   IJ.showStatus("Rotating...");
 }
Пример #11
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;
 }
Пример #12
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();
  }
Пример #13
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.");
  }
Пример #14
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;
 }
Пример #15
0
 void doIterations(ImageProcessor ip, String mode) {
   if (escapePressed) return;
   if (!previewing && iterations > 1) IJ.showStatus(arg + "... press ESC to cancel");
   for (int i = 0; i < iterations; i++) {
     if (Thread.currentThread().isInterrupted()) return;
     if (IJ.escapePressed()) {
       escapePressed = true;
       ip.reset();
       return;
     }
     if (mode.equals("erode")) ((ByteProcessor) ip).erode(count, background);
     else ((ByteProcessor) ip).dilate(count, background);
   }
 }
Пример #16
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();
    }
Пример #17
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();
 }
Пример #18
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;
 }
Пример #19
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;
   }
 }
Пример #20
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);
   }
 }
Пример #21
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;
 }
Пример #22
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;
  }
Пример #23
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;
 }
Пример #24
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);
 }
Пример #25
0
  private void fitglobal() {
    int nparams = 11;
    int nsel = 0;
    for (int i = 0; i < ncurves; i++) {
      if (include[i]) {
        nsel++;
      }
    }
    double[][] params = new double[nsel][nparams];
    String[][] tempformulas = new String[nsel][nparams];
    double[][][] constraints = new double[2][nsel][nparams];
    int[][] vflmatrix = new int[nsel][nparams];

    int counter = 0;
    for (int i = 0; i < ncurves; i++) {
      if (include[i]) {
        for (int j = 0; j < nparams; j++) {
          params[counter][j] = globalparams[i][j];
          tempformulas[counter][j] = globalformulas[i][j];
          constraints[0][counter][j] = globalconstraints[0][i][j];
          constraints[1][counter][j] = globalconstraints[1][i][j];
          vflmatrix[counter][j] = globalvflmatrix[i][j];
        }
        counter++;
      }
      for (int j = 0; j < nparams; j++) {
        undoparams[i][j] = globalparams[i][j];
        undoformulas[i][j] = globalformulas[i][j];
        undovflmatrix[i][j] = globalvflmatrix[i][j];
      }
      for (int j = 0; j < xpts; j++) {
        for (int k = 0; k < ypts; k++) {
          undofit[i][j][k] = fit[i][j][k];
        }
      }
      undoc2[i] = c2[i];
    }
    undoglobalc2 = globalc2;
    if (showglobalfitdialog(params, tempformulas, vflmatrix)) {
      counter = 0;
      for (int i = 0; i < ncurves; i++) {
        if (include[i]) {
          for (int j = 0; j < nparams; j++) {
            globalparams[i][j] = params[counter][j];
            globalformulas[i][j] = tempformulas[counter][j];
            globalvflmatrix[i][j] = vflmatrix[counter][j];
          }
          counter++;
        }
      }
      double[] stats = new double[2];
      float[][] tempdata = new float[nsel][xpts * ypts];
      float[][] tempweights = new float[nsel][xpts * ypts];
      counter = 0;
      for (int i = 0; i < ncurves; i++) {
        if (include[i]) {
          for (int j = 0; j < xpts; j++) {
            for (int k = 0; k < ypts; k++) {
              tempdata[counter][j + k * xpts] = (float) ((double) pch[i][j][k] / (double) nmeas[i]);
              tempweights[counter][j + k * xpts] = weights[i][j][k];
            }
          }
          counter++;
        }
      }
      int tempmaxiter = globalfitclass.maxiter;
      if (checkc2) {
        globalfitclass.changemaxiter(0);
      }
      double[] tempc2vals = new double[nsel];
      IJ.showStatus("Fitting Globally");
      float[][] tempfit =
          globalfitclass.fitdata(
              params,
              vflmatrix,
              tempformulas,
              paramsnames,
              constraints,
              tempdata,
              tempweights,
              stats,
              tempc2vals,
              false);
      IJ.showStatus("Fit Complete");
      globalfitclass.changemaxiter(tempmaxiter);
      globalc2 = stats[1];
      globalc2label.setText("Global chi^2 = " + (float) globalc2);
      counter = 0;
      for (int i = 0; i < ncurves; i++) {
        if (include[i]) {
          for (int j = 0; j < xpts; j++) {
            for (int k = 0; k < ypts; k++) {
              fit[i][j][k] = tempfit[counter][j + xpts * k] * (float) nmeas[i];
            }
          }
          if (i == dispcurve) {
            pwfit.updateSeries(fit[dispcurve], 1, true);
          }
          for (int j = 0; j < nparams; j++) {
            globalparams[i][j] = params[counter][j];
          }
          c2[i] = tempc2vals[counter];
          c2array[i].setText("" + (float) c2[i]);
          counter++;
        }
      }
      float[] temp = pwfit.getLimits();
      temp[4] = 1.0f;
      pwfit.setLimits(temp);
    }
  }
Пример #26
0
 public void showresults(String results) {
   IJ.showStatus(results);
   IJ.log(results);
 }
Пример #27
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());
 }
Пример #28
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();
  }
Пример #29
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;
    }
  }
Пример #30
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();
  }