Exemple #1
0
 private boolean deleteOverlayRoi(ImagePlus imp) {
   if (imp == null) return false;
   Overlay overlay = null;
   ImageCanvas ic = imp.getCanvas();
   if (ic != null) overlay = ic.getShowAllList();
   if (overlay == null) overlay = imp.getOverlay();
   if (overlay == null) return false;
   Roi roi = imp.getRoi();
   for (int i = 0; i < overlay.size(); i++) {
     Roi roi2 = overlay.get(i);
     if (roi2 == roi) {
       overlay.remove(i);
       imp.deleteRoi();
       ic = imp.getCanvas();
       if (ic != null) ic.roiManagerSelect(roi, true);
       return true;
     }
   }
   return false;
 }
Exemple #2
0
  public void keyPressed(KeyEvent e) {
    // if (e.isConsumed()) return;
    int keyCode = e.getKeyCode();
    IJ.setKeyDown(keyCode);
    hotkey = false;
    if (keyCode == KeyEvent.VK_CONTROL || keyCode == KeyEvent.VK_SHIFT) return;
    char keyChar = e.getKeyChar();
    int flags = e.getModifiers();
    if (IJ.debugMode)
      IJ.log(
          "keyPressed: code="
              + keyCode
              + " ("
              + KeyEvent.getKeyText(keyCode)
              + "), char=\""
              + keyChar
              + "\" ("
              + (int) keyChar
              + "), flags="
              + KeyEvent.getKeyModifiersText(flags));
    boolean shift = (flags & KeyEvent.SHIFT_MASK) != 0;
    boolean control = (flags & KeyEvent.CTRL_MASK) != 0;
    boolean alt = (flags & KeyEvent.ALT_MASK) != 0;
    boolean meta = (flags & KeyEvent.META_MASK) != 0;
    String cmd = null;
    ImagePlus imp = WindowManager.getCurrentImage();
    boolean isStack = (imp != null) && (imp.getStackSize() > 1);

    if (imp != null
        && !control
        && ((keyChar >= 32 && keyChar <= 255) || keyChar == '\b' || keyChar == '\n')) {
      Roi roi = imp.getRoi();
      if (roi instanceof TextRoi) {
        if ((flags & KeyEvent.META_MASK) != 0 && IJ.isMacOSX()) return;
        if (alt) {
          switch (keyChar) {
            case 'u':
            case 'm':
              keyChar = IJ.micronSymbol;
              break;
            case 'A':
              keyChar = IJ.angstromSymbol;
              break;
            default:
          }
        }
        ((TextRoi) roi).addChar(keyChar);
        return;
      }
    }

    // Handle one character macro shortcuts
    if (!control && !meta) {
      Hashtable macroShortcuts = Menus.getMacroShortcuts();
      if (macroShortcuts.size() > 0) {
        if (shift) cmd = (String) macroShortcuts.get(new Integer(keyCode + 200));
        else cmd = (String) macroShortcuts.get(new Integer(keyCode));
        if (cmd != null) {
          // MacroInstaller.runMacroCommand(cmd);
          commandName = cmd;
          MacroInstaller.runMacroShortcut(cmd);
          return;
        }
      }
    }

    if ((!Prefs.requireControlKey || control || meta) && keyChar != '+') {
      Hashtable shortcuts = Menus.getShortcuts();
      if (shift) cmd = (String) shortcuts.get(new Integer(keyCode + 200));
      else cmd = (String) shortcuts.get(new Integer(keyCode));
    }

    if (cmd == null) {
      switch (keyChar) {
        case '<':
        case ',':
          if (isStack) cmd = "Previous Slice [<]";
          break;
        case '>':
        case '.':
        case ';':
          if (isStack) cmd = "Next Slice [>]";
          break;
        case '+':
        case '=':
          cmd = "In [+]";
          break;
        case '-':
          cmd = "Out [-]";
          break;
        case '/':
          cmd = "Reslice [/]...";
          break;
        default:
      }
    }

    if (cmd == null) {
      switch (keyCode) {
        case KeyEvent.VK_TAB:
          WindowManager.putBehind();
          return;
        case KeyEvent.VK_BACK_SPACE: // delete
          if (deleteOverlayRoi(imp)) return;
          cmd = "Clear";
          hotkey = true;
          break;
          // case KeyEvent.VK_BACK_SLASH: cmd=IJ.altKeyDown()?"Animation Options...":"Start
          // Animation"; break;
        case KeyEvent.VK_EQUALS:
          cmd = "In [+]";
          break;
        case KeyEvent.VK_MINUS:
          cmd = "Out [-]";
          break;
        case KeyEvent.VK_SLASH:
        case 0xbf:
          cmd = "Reslice [/]...";
          break;
        case KeyEvent.VK_COMMA:
        case 0xbc:
          if (isStack) cmd = "Previous Slice [<]";
          break;
        case KeyEvent.VK_PERIOD:
        case 0xbe:
          if (isStack) cmd = "Next Slice [>]";
          break;
        case KeyEvent.VK_LEFT:
        case KeyEvent.VK_RIGHT:
        case KeyEvent.VK_UP:
        case KeyEvent.VK_DOWN: // arrow keys
          if (imp == null) return;
          Roi roi = imp.getRoi();
          if (IJ.shiftKeyDown() && imp == Orthogonal_Views.getImage()) return;
          boolean stackKey = imp.getStackSize() > 1 && (roi == null || IJ.shiftKeyDown());
          boolean zoomKey = roi == null || IJ.shiftKeyDown() || IJ.controlKeyDown();
          if (stackKey && keyCode == KeyEvent.VK_RIGHT) cmd = "Next Slice [>]";
          else if (stackKey && keyCode == KeyEvent.VK_LEFT) cmd = "Previous Slice [<]";
          else if (zoomKey
              && keyCode == KeyEvent.VK_DOWN
              && !ignoreArrowKeys(imp)
              && Toolbar.getToolId() < Toolbar.SPARE6) cmd = "Out [-]";
          else if (zoomKey
              && keyCode == KeyEvent.VK_UP
              && !ignoreArrowKeys(imp)
              && Toolbar.getToolId() < Toolbar.SPARE6) cmd = "In [+]";
          else if (roi != null) {
            if ((flags & KeyEvent.ALT_MASK) != 0) roi.nudgeCorner(keyCode);
            else roi.nudge(keyCode);
            return;
          }
          break;
        case KeyEvent.VK_ESCAPE:
          abortPluginOrMacro(imp);
          return;
        case KeyEvent.VK_ENTER:
          WindowManager.toFront(this);
          return;
        default:
          break;
      }
    }

    if (cmd != null && !cmd.equals("")) {
      commandName = cmd;
      if (cmd.equals("Fill") || cmd.equals("Draw")) hotkey = true;
      if (cmd.charAt(0) == MacroInstaller.commandPrefix) MacroInstaller.runMacroShortcut(cmd);
      else {
        doCommand(cmd);
        keyPressedTime = System.currentTimeMillis();
        lastKeyCommand = cmd;
      }
    }
  }
  public void run(String arg) {
    ImagePlus imp = WindowManager.getCurrentImage();
    Calibration cal = imp.getCalibration();
    GenericDialog gd = new GenericDialog("Options");
    int subsize = 32;
    gd.addNumericField("Subregion Size (pixels)?", subsize, 0);
    int stepsize = 16;
    gd.addNumericField("Step Size?", stepsize, 0);
    int shift = 3;
    gd.addNumericField("STICS temporal Shift?", shift, 0);
    float xoffset = 0.0f;
    gd.addNumericField("X_Offset", xoffset, 5, 15, null);
    float yoffset = 0.0f;
    gd.addNumericField("Y_Offset", yoffset, 5, 15, null);
    float multiplier = 8.0f;
    gd.addNumericField("Velocity Multiplier", multiplier, 5, 15, null);
    float ftime = 1.0f;
    gd.addNumericField("Frame_Time(min)", ftime, 5, 15, null);
    float scaling = (float) cal.pixelWidth;
    gd.addNumericField("Pixel_Size(um)", scaling, 5, 15, null);
    boolean norm = true;
    gd.addCheckbox("Normalize_Vector_lengths?", norm);
    boolean centered = true;
    gd.addCheckbox("Center_Vectors?", centered);
    float magthresh = 0.0f;
    gd.addNumericField("Magnitude_Threshhold?", magthresh, 5, 15, null);
    int rlength = 10;
    gd.addNumericField("Running_avg_length", rlength, 0);
    int inc = 5;
    gd.addNumericField("Start_frame_increment", inc, 0);
    gd.showDialog();
    if (gd.wasCanceled()) {
      return;
    }
    subsize = (int) gd.getNextNumber();
    stepsize = (int) gd.getNextNumber();
    shift = (int) gd.getNextNumber();
    xoffset = (float) gd.getNextNumber();
    yoffset = (float) gd.getNextNumber();
    multiplier = (float) gd.getNextNumber();
    ftime = (float) gd.getNextNumber();
    scaling = (float) gd.getNextNumber();
    norm = gd.getNextBoolean();
    centered = gd.getNextBoolean();
    magthresh = (float) gd.getNextNumber();
    rlength = (int) gd.getNextNumber();
    inc = (int) gd.getNextNumber();

    int width = imp.getWidth();
    int xregions = 1 + (int) (((float) width - (float) subsize) / (float) stepsize);
    int newwidth = xregions * subsize;
    int height = imp.getHeight();
    int yregions = 1 + (int) (((float) height - (float) subsize) / (float) stepsize);
    int newheight = yregions * subsize;
    ImageStack stack = imp.getStack();
    int slices = imp.getNSlices();
    int channels = imp.getNChannels();
    int frames = imp.getNFrames();
    if (frames == 1) {
      frames = slices;
      slices = 1;
    }

    Roi roi = imp.getRoi();
    if (roi == null) {
      roi = new Roi(0, 0, width, height);
    }

    STICS_map map = new STICS_map(subsize, stepsize);
    Object[] tseries = jutils.get3DTSeries(stack, 0, 0, frames, slices, channels);
    map.update_STICS_map(tseries, width, height, 0, rlength, roi.getPolygon(), shift);
    FloatProcessor fp =
        map.get_map(scaling, ftime, stepsize, centered, norm, multiplier, stepsize, magthresh);
    ImageStack vector_stack = new ImageStack(fp.getWidth(), fp.getHeight());
    vector_stack.addSlice("", fp);
    float[][] vel = map.get_scaled_velocities(scaling, ftime, stepsize);
    ImageStack velstack = new ImageStack(map.xregions, map.yregions);
    velstack.addSlice("", vel[0]);
    velstack.addSlice("", vel[1]);
    int velframes = 2;
    IJ.showStatus("frame " + 0 + " calculated");
    for (int i = inc; i < (frames - rlength); i += inc) {
      map.update_STICS_map(tseries, width, height, i, rlength, roi.getPolygon(), shift);
      FloatProcessor fp2 =
          map.get_map(scaling, ftime, stepsize, centered, norm, multiplier, stepsize, magthresh);
      vector_stack.addSlice("", fp2);
      vel = map.get_scaled_velocities(scaling, ftime, stepsize);
      velstack.addSlice("", vel[0]);
      velstack.addSlice("", vel[1]);
      velframes += 2;
      IJ.showStatus("frame " + i + " calculated");
    }
    (new ImagePlus("STICS Vectors", vector_stack)).show();
    ImagePlus imp3 = new ImagePlus("Velocities", velstack);
    imp3.setOpenAsHyperStack(true);
    imp3.setDimensions(2, 1, velframes / 2);
    new CompositeImage(imp3, CompositeImage.COLOR).show();
  }