Exemple #1
0
 private String displayRanges(ImagePlus imp) {
   LUT[] luts = imp.getLuts();
   if (luts == null) return "";
   String s = "Display ranges\n";
   int n = luts.length;
   if (n > 7) n = 7;
   for (int i = 0; i < n; i++) {
     double min = luts[i].min;
     double max = luts[i].max;
     int digits = (int) min == min && (int) max == max ? 0 : 2;
     s += "  " + (i + 1) + ": " + IJ.d2s(min, digits) + "-" + IJ.d2s(max, digits) + "\n";
   }
   return s;
 }
 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;
 }
Exemple #3
0
 public synchronized void adjustmentValueChanged(AdjustmentEvent e) {
   Object source = e.getSource();
   for (int i = 0; i < slider.size(); i++) {
     if (source == slider.elementAt(i)) {
       Scrollbar sb = (Scrollbar) source;
       TextField tf = (TextField) numberField.elementAt(sliderIndexes[i]);
       int digits = sliderScales[i] == 1.0 ? 0 : 2;
       tf.setText("" + IJ.d2s(sb.getValue() / sliderScales[i], digits));
     }
   }
 }
Exemple #4
0
 /**
  * Adds a numeric field. The first word of the label must be unique or command recording will not
  * work.
  *
  * @param label the label
  * @param defaultValue value to be initially displayed
  * @param digits number of digits to right of decimal point
  * @param columns width of field in characters
  * @param units a string displayed to the right of the field
  */
 public void addNumericField(
     String label, double defaultValue, int digits, int columns, String units) {
   String label2 = label;
   if (label2.indexOf('_') != -1) label2 = label2.replace('_', ' ');
   Label theLabel = makeLabel(label2);
   c.gridx = 0;
   c.gridy = y;
   c.anchor = GridBagConstraints.EAST;
   c.gridwidth = 1;
   if (firstNumericField) c.insets = getInsets(5, 0, 3, 0);
   else c.insets = getInsets(0, 0, 3, 0);
   grid.setConstraints(theLabel, c);
   add(theLabel);
   if (numberField == null) {
     numberField = new Vector(5);
     defaultValues = new Vector(5);
     defaultText = new Vector(5);
   }
   if (IJ.isWindows()) columns -= 2;
   if (columns < 1) columns = 1;
   String defaultString = IJ.d2s(defaultValue, digits);
   if (Double.isNaN(defaultValue)) defaultString = "";
   TextField tf = new TextField(defaultString, columns);
   if (IJ.isLinux()) tf.setBackground(Color.white);
   tf.addActionListener(this);
   tf.addTextListener(this);
   tf.addFocusListener(this);
   tf.addKeyListener(this);
   numberField.addElement(tf);
   defaultValues.addElement(new Double(defaultValue));
   defaultText.addElement(tf.getText());
   c.gridx = 1;
   c.gridy = y;
   c.anchor = GridBagConstraints.WEST;
   tf.setEditable(true);
   // if (firstNumericField) tf.selectAll();
   firstNumericField = false;
   if (units == null || units.equals("")) {
     grid.setConstraints(tf, c);
     add(tf);
   } else {
     Panel panel = new Panel();
     panel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
     panel.add(tf);
     panel.add(new Label(" " + units));
     grid.setConstraints(panel, c);
     add(panel);
   }
   if (Recorder.record || macro) saveLabel(tf, label);
   y++;
 }
Exemple #5
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;
 }
Exemple #6
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 #7
0
 String d2s(double n) {
   return n == (int) n ? Integer.toString((int) n) : IJ.d2s(n);
 }
Exemple #8
0
  /**
   * Adds a slider (scroll bar) to the dialog box. Floating point values will be used if
   * (maxValue-minValue)<=5.0 and either minValue or maxValue are non-integer.
   *
   * @param label the label
   * @param minValue the minimum value of the slider
   * @param maxValue the maximum value of the slider
   * @param defaultValue the initial value of the slider
   */
  public void addSlider(String label, double minValue, double maxValue, double defaultValue) {
    if (defaultValue < minValue) defaultValue = minValue;
    if (defaultValue > maxValue) defaultValue = maxValue;
    int columns = 4;
    int digits = 0;
    double scale = 1.0;
    if ((maxValue - minValue) <= 5.0
        && (minValue != (int) minValue
            || maxValue != (int) maxValue
            || defaultValue != (int) defaultValue)) {
      scale = 20.0;
      minValue *= scale;
      maxValue *= scale;
      defaultValue *= scale;
      digits = 2;
    }
    String label2 = label;
    if (label2.indexOf('_') != -1) label2 = label2.replace('_', ' ');
    Label theLabel = makeLabel(label2);
    c.gridx = 0;
    c.gridy = y;
    c.anchor = GridBagConstraints.EAST;
    c.gridwidth = 1;
    c.insets = new Insets(0, 0, 3, 0);
    grid.setConstraints(theLabel, c);
    add(theLabel);

    if (slider == null) {
      slider = new Vector(5);
      sliderIndexes = new int[MAX_SLIDERS];
      sliderScales = new double[MAX_SLIDERS];
    }
    Scrollbar s =
        new Scrollbar(
            Scrollbar.HORIZONTAL, (int) defaultValue, 1, (int) minValue, (int) maxValue + 1);
    GUI.fix(s);
    slider.addElement(s);
    s.addAdjustmentListener(this);
    s.setUnitIncrement(1);

    if (numberField == null) {
      numberField = new Vector(5);
      defaultValues = new Vector(5);
      defaultText = new Vector(5);
    }
    if (IJ.isWindows()) columns -= 2;
    if (columns < 1) columns = 1;
    TextField tf = new TextField(IJ.d2s(defaultValue / scale, digits), columns);
    if (IJ.isLinux()) tf.setBackground(Color.white);
    tf.addActionListener(this);
    tf.addTextListener(this);
    tf.addFocusListener(this);
    tf.addKeyListener(this);
    numberField.addElement(tf);
    sliderIndexes[slider.size() - 1] = numberField.size() - 1;
    sliderScales[slider.size() - 1] = scale;
    defaultValues.addElement(new Double(defaultValue / scale));
    defaultText.addElement(tf.getText());
    tf.setEditable(true);
    firstSlider = false;

    Panel panel = new Panel();
    GridBagLayout pgrid = new GridBagLayout();
    GridBagConstraints pc = new GridBagConstraints();
    panel.setLayout(pgrid);
    pc.gridx = 0;
    pc.gridy = 0;
    pc.gridwidth = 1;
    pc.ipadx = 85;
    pc.anchor = GridBagConstraints.WEST;
    pgrid.setConstraints(s, pc);
    panel.add(s);
    pc.ipadx = 0; // reset
    // text field
    pc.gridx = 1;
    pc.insets = new Insets(5, 5, 0, 0);
    pc.anchor = GridBagConstraints.EAST;
    pgrid.setConstraints(tf, pc);
    panel.add(tf);

    grid.setConstraints(panel, c);
    c.gridx = 1;
    c.gridy = y;
    c.gridwidth = 1;
    c.anchor = GridBagConstraints.WEST;
    c.insets = new Insets(0, 0, 0, 0);
    grid.setConstraints(panel, c);
    add(panel);
    y++;
    if (Recorder.record || macro) saveLabel(tf, label);
  }
 private String d2s(double n) {
   return IJ.d2s(n, Tools.getDecimalPlaces(n));
 }
Exemple #10
0
  public boolean dialogItemChanged(GenericDialog gd, AWTEvent e) {
    if (IJ.isMacOSX()) IJ.wait(50);
    Calibration cal = imp.getCalibration();
    width = gd.getNextNumber();
    height = gd.getNextNumber();
    xRoi = gd.getNextNumber();
    yRoi = gd.getNextNumber();
    if (stackSize > 1) iSlice = (int) gd.getNextNumber();
    oval = gd.getNextBoolean();
    square = gd.getNextBoolean();
    centered = gd.getNextBoolean();
    if (cal.scaled()) scaledUnits = gd.getNextBoolean();
    if (gd.invalidNumber() || width <= 0 || height <= 0) return false;
    //
    Vector numFields = gd.getNumericFields();
    Vector checkboxes = gd.getCheckboxes();
    boolean newWidth = false, newHeight = false, newXY = false;
    if (e != null && e.getSource() == checkboxes.get(SQUARE) && square) {
      width = 0.5 * (width + height); // make square: same width&height
      height = width;
      newWidth = true;
      newHeight = true;
    }
    if (e != null && e.getSource() == checkboxes.get(CENTERED)) {
      double shiftBy = centered ? 0.5 : -0.5; // 'centered' changed:
      xRoi += shiftBy * width; // shift x, y to keep roi the same
      yRoi += shiftBy * height;
      newXY = true;
    }
    if (square && width != height && e != null) { // in 'square' mode, synchronize width&height
      if (e.getSource() == numFields.get(WIDTH)) {
        height = width;
        newHeight = true;
      } else if (e.getSource() == numFields.get(HEIGHT)) {
        width = height;
        newWidth = true;
      }
    }
    if (e != null && cal.scaled() && e.getSource() == checkboxes.get(SCALED_UNITS)) {
      double xFactor = scaledUnits ? cal.pixelWidth : 1. / cal.pixelWidth;
      double yFactor = scaledUnits ? cal.pixelHeight : 1. / cal.pixelHeight;
      width *= xFactor; // transform everything to keep roi the same
      height *= yFactor;
      xRoi *= xFactor;
      yRoi *= yFactor;
      newWidth = true;
      newHeight = true;
      newXY = true;
    }
    int digits = (scaledUnits || (int) width != width) ? 2 : 0;
    if (newWidth) ((TextField) (numFields.get(WIDTH))).setText(IJ.d2s(width, digits));
    if (newHeight) ((TextField) (numFields.get(HEIGHT))).setText(IJ.d2s(height, digits));
    digits = (scaledUnits || (int) xRoi != xRoi || (int) yRoi != yRoi) ? 2 : 0;
    if (newXY) {
      ((TextField) (numFields.get(X_ROI))).setText(IJ.d2s(xRoi, digits));
      ((TextField) (numFields.get(Y_ROI))).setText(IJ.d2s(yRoi, digits));
    }

    if (stackSize > 1 && iSlice > 0 && iSlice <= stackSize) imp.setSlice(iSlice);
    if (!newWidth && !newHeight && !newXY) // don't draw if an update will come immediately
    drawRoi();
    return true;
  }