예제 #1
0
 void interpolate() {
   Roi roi = imp.getRoi();
   if (roi == null) {
     noRoi("Interpolate");
     return;
   }
   if (roi.getType() == Roi.POINT) return;
   if (IJ.isMacro() && Macro.getOptions() == null) Macro.setOptions("interval=1");
   GenericDialog gd = new GenericDialog("Interpolate");
   gd.addNumericField("Interval:", 1.0, 1, 4, "pixel");
   gd.addCheckbox("Smooth", IJ.isMacro() ? false : smooth);
   gd.showDialog();
   if (gd.wasCanceled()) return;
   double interval = gd.getNextNumber();
   smooth = gd.getNextBoolean();
   Undo.setup(Undo.ROI, imp);
   FloatPolygon poly = roi.getInterpolatedPolygon(interval, smooth);
   int t = roi.getType();
   int type = roi.isLine() ? Roi.FREELINE : Roi.FREEROI;
   if (t == Roi.POLYGON && interval > 1.0) type = Roi.POLYGON;
   if ((t == Roi.RECTANGLE || t == Roi.OVAL || t == Roi.FREEROI) && interval >= 5.0)
     type = Roi.POLYGON;
   if ((t == Roi.LINE || t == Roi.FREELINE) && interval >= 5.0) type = Roi.POLYLINE;
   if (t == Roi.POLYLINE && interval >= 1.0) type = Roi.POLYLINE;
   ImageCanvas ic = imp.getCanvas();
   if (poly.npoints <= 150 && ic != null && ic.getMagnification() >= 12.0)
     type = roi.isLine() ? Roi.POLYLINE : Roi.POLYGON;
   Roi p = new PolygonRoi(poly, type);
   if (roi.getStroke() != null) p.setStrokeWidth(roi.getStrokeWidth());
   p.setStrokeColor(roi.getStrokeColor());
   p.setName(roi.getName());
   transferProperties(roi, p);
   imp.setRoi(p);
 }
예제 #2
0
 void fitSpline() {
   Roi roi = imp.getRoi();
   if (roi == null) {
     noRoi("Spline");
     return;
   }
   int type = roi.getType();
   boolean segmentedSelection = type == Roi.POLYGON || type == Roi.POLYLINE;
   if (!(segmentedSelection
       || type == Roi.FREEROI
       || type == Roi.TRACED_ROI
       || type == Roi.FREELINE)) {
     IJ.error("Spline", "Polygon or polyline selection required");
     return;
   }
   if (roi instanceof EllipseRoi) return;
   PolygonRoi p = (PolygonRoi) roi;
   if (!segmentedSelection) {
     if (p.subPixelResolution()) p = trimFloatPolygon(p, p.getUncalibratedLength());
     else p = trimPolygon(p, p.getUncalibratedLength());
   }
   String options = Macro.getOptions();
   if (options != null && options.indexOf("straighten") != -1) p.fitSplineForStraightening();
   else if (options != null && options.indexOf("remove") != -1) p.removeSplineFit();
   else p.fitSpline();
   imp.draw();
   LineWidthAdjuster.update();
 }
예제 #3
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));
 }
예제 #4
0
 void lineToArea(ImagePlus imp) {
   Roi roi = imp.getRoi();
   if (roi == null || !roi.isLine()) {
     IJ.error("Line to Area", "Line selection required");
     return;
   }
   Undo.setup(Undo.ROI, imp);
   Roi roi2 = null;
   if (roi.getType() == Roi.LINE) {
     double width = roi.getStrokeWidth();
     if (width <= 1.0) roi.setStrokeWidth(1.0000001);
     FloatPolygon p = roi.getFloatPolygon();
     roi.setStrokeWidth(width);
     roi2 = new PolygonRoi(p, Roi.POLYGON);
     roi2.setDrawOffset(roi.getDrawOffset());
   } else {
     ImageProcessor ip2 = new ByteProcessor(imp.getWidth(), imp.getHeight());
     ip2.setColor(255);
     roi.drawPixels(ip2);
     // new ImagePlus("ip2", ip2.duplicate()).show();
     ip2.setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE);
     ThresholdToSelection tts = new ThresholdToSelection();
     roi2 = tts.convert(ip2);
   }
   transferProperties(roi, roi2);
   roi2.setStrokeWidth(0);
   Color c = roi2.getStrokeColor();
   if (c != null) // remove any transparency
   roi2.setStrokeColor(new Color(c.getRed(), c.getGreen(), c.getBlue()));
   imp.setRoi(roi2);
   Roi.previousRoi = (Roi) roi.clone();
 }
예제 #5
0
 void lineToArea(ImagePlus imp) {
   Roi roi = imp.getRoi();
   if (roi == null || !roi.isLine()) {
     IJ.error("Line to Area", "Line selection required");
     return;
   }
   if (roi.getType() == Roi.LINE && roi.getStrokeWidth() == 1) {
     IJ.error("Line to Area", "Straight line width must be > 1");
     return;
   }
   ImageProcessor ip2 = new ByteProcessor(imp.getWidth(), imp.getHeight());
   ip2.setColor(255);
   if (roi.getType() == Roi.LINE) ip2.fillPolygon(roi.getPolygon());
   else {
     roi.drawPixels(ip2);
     // BufferedImage bi = new BufferedImage(imp.getWidth(), imp.getHeight(),
     // BufferedImage.TYPE_BYTE_GRAY);
     // Graphics g = bi.getGraphics();
     // Roi roi2 = (Roi)roi.clone();
     // roi2.setStrokeColor(Color.white);
     // roi2.drawOverlay(g);
     // ip2 = new ByteProcessor(bi);
   }
   // new ImagePlus("ip2", ip2.duplicate()).show();
   ip2.setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE);
   ThresholdToSelection tts = new ThresholdToSelection();
   Roi roi2 = tts.convert(ip2);
   imp.setRoi(roi2);
   Roi.previousRoi = (Roi) roi.clone();
 }
예제 #6
0
 void toBoundingBox(ImagePlus imp) {
   Roi roi = imp.getRoi();
   if (roi == null) {
     noRoi("To Bounding Box");
     return;
   }
   Rectangle r = roi.getBounds();
   imp.killRoi();
   imp.setRoi(new Roi(r.x, r.y, r.width, r.height));
 }
예제 #7
0
 private boolean ignoreArrowKeys(ImagePlus imp) {
   Frame frame = WindowManager.getFrontWindow();
   String title = frame.getTitle();
   if (title != null && title.equals("ROI Manager")) return true;
   // Control Panel?
   if (frame != null && frame instanceof javax.swing.JFrame) return true;
   ImageWindow win = imp.getWindow();
   // LOCI Data Browser window?
   if (imp.getStackSize() > 1 && win != null && win.getClass().getName().startsWith("loci"))
     return true;
   return false;
 }
예제 #8
0
 void invert(ImagePlus imp) {
   Roi roi = imp.getRoi();
   if (roi == null || !roi.isArea()) {
     IJ.error("Inverse", "Area selection required");
     return;
   }
   ShapeRoi s1, s2;
   if (roi instanceof ShapeRoi) s1 = (ShapeRoi) roi;
   else s1 = new ShapeRoi(roi);
   s2 = new ShapeRoi(new Roi(0, 0, imp.getWidth(), imp.getHeight()));
   imp.setRoi(s1.xor(s2));
 }
예제 #9
0
 void toBoundingBox(ImagePlus imp) {
   Roi roi = imp.getRoi();
   if (roi == null) {
     noRoi("To Bounding Box");
     return;
   }
   Undo.setup(Undo.ROI, imp);
   Rectangle r = roi.getBounds();
   imp.deleteRoi();
   Roi roi2 = new Roi(r.x, r.y, r.width, r.height);
   transferProperties(roi, roi2);
   imp.setRoi(roi2);
 }
예제 #10
0
 void createMaskFromThreshold(ImagePlus imp) {
   ImageProcessor ip = imp.getProcessor();
   if (ip.getMinThreshold() == ImageProcessor.NO_THRESHOLD) {
     IJ.error("Create Mask", "Area selection or thresholded image required");
     return;
   }
   double t1 = ip.getMinThreshold();
   double t2 = ip.getMaxThreshold();
   IJ.run("Duplicate...", "title=mask");
   ImagePlus imp2 = WindowManager.getCurrentImage();
   ImageProcessor ip2 = imp2.getProcessor();
   ip2.setThreshold(t1, t2, ImageProcessor.NO_LUT_UPDATE);
   IJ.run("Convert to Mask");
 }
예제 #11
0
 void convexHull(ImagePlus imp) {
   Roi roi = imp.getRoi();
   int type = roi != null ? roi.getType() : -1;
   if (!(type == Roi.FREEROI
       || type == Roi.TRACED_ROI
       || type == Roi.POLYGON
       || type == Roi.POINT)) {
     IJ.error("Convex Hull", "Polygonal or point selection required");
     return;
   }
   if (roi instanceof EllipseRoi) return;
   Polygon p = roi.getConvexHull();
   if (p != null) imp.setRoi(new PolygonRoi(p.xpoints, p.ypoints, p.npoints, roi.POLYGON));
 }
예제 #12
0
 void addToRoiManager(ImagePlus imp) {
   if (IJ.macroRunning() && Interpreter.isBatchModeRoiManager())
     IJ.error("run(\"Add to Manager\") may not work in batch mode macros");
   Frame frame = WindowManager.getFrame("ROI Manager");
   if (frame == null) IJ.run("ROI Manager...");
   if (imp == null) return;
   Roi roi = imp.getRoi();
   if (roi == null) return;
   frame = WindowManager.getFrame("ROI Manager");
   if (frame == null || !(frame instanceof RoiManager)) IJ.error("ROI Manager not found");
   RoiManager rm = (RoiManager) frame;
   boolean altDown = IJ.altKeyDown();
   IJ.setKeyUp(IJ.ALL_KEYS);
   if (altDown && !IJ.macroRunning()) IJ.setKeyDown(KeyEvent.VK_SHIFT);
   if (roi.getState() == Roi.CONSTRUCTING) { // wait (up to 2 sec.) until ROI finished
     long start = System.currentTimeMillis();
     while (true) {
       IJ.wait(10);
       if (roi.getState() != Roi.CONSTRUCTING) break;
       if ((System.currentTimeMillis() - start) > 2000) {
         IJ.beep();
         IJ.error("Add to Manager", "Selection is not complete");
         return;
       }
     }
   }
   rm.runCommand("add");
   IJ.setKeyUp(IJ.ALL_KEYS);
 }
예제 #13
0
 void runMacro(String arg) {
   Roi roi = imp.getRoi();
   if (IJ.macroRunning()) {
     String options = Macro.getOptions();
     if (options != null
         && (options.indexOf("grid=") != -1 || options.indexOf("interpolat") != -1)) {
       IJ.run("Rotate... ", options); // run Image>Transform>Rotate
       return;
     }
   }
   if (roi == null) {
     noRoi("Rotate>Selection");
     return;
   }
   roi = (Roi) roi.clone();
   if (arg.equals("rotate")) {
     double d = Tools.parseDouble(angle);
     if (Double.isNaN(d)) angle = "15";
     String value = IJ.runMacroFile("ij.jar:RotateSelection", angle);
     if (value != null) angle = value;
   } else if (arg.equals("enlarge")) {
     String value = IJ.runMacroFile("ij.jar:EnlargeSelection", enlarge);
     if (value != null) enlarge = value;
     Roi.previousRoi = roi;
   }
 }
예제 #14
0
 void lineToArea(ImagePlus imp) {
   Roi roi = imp.getRoi();
   if (roi == null || !roi.isLine()) {
     IJ.error("Line to Area", "Line selection required");
     return;
   }
   ImageProcessor ip2 = new ByteProcessor(imp.getWidth(), imp.getHeight());
   ip2.setColor(255);
   if (roi.getType() == Roi.LINE && roi.getStrokeWidth() > 1) ip2.fillPolygon(roi.getPolygon());
   else roi.drawPixels(ip2);
   // new ImagePlus("ip2", ip2.duplicate()).show();
   ip2.setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE);
   ThresholdToSelection tts = new ThresholdToSelection();
   Roi roi2 = tts.convert(ip2);
   imp.setRoi(roi2);
   Roi.previousRoi = (Roi) roi.clone();
 }
예제 #15
0
 private void enlarge(ImagePlus imp) {
   Roi roi = imp.getRoi();
   if (roi != null) {
     Undo.setup(Undo.ROI, imp);
     roi = (Roi) roi.clone();
     (new RoiEnlarger()).run("");
   } else noRoi("Enlarge");
 }
예제 #16
0
 void createMask(ImagePlus imp) {
   Roi roi = imp.getRoi();
   boolean useInvertingLut = Prefs.useInvertingLut;
   Prefs.useInvertingLut = false;
   if (roi == null || !(roi.isArea() || roi.getType() == Roi.POINT)) {
     createMaskFromThreshold(imp);
     Prefs.useInvertingLut = useInvertingLut;
     return;
   }
   ImagePlus maskImp = null;
   Frame frame = WindowManager.getFrame("Mask");
   if (frame != null && (frame instanceof ImageWindow))
     maskImp = ((ImageWindow) frame).getImagePlus();
   if (maskImp == null) {
     ImageProcessor ip = new ByteProcessor(imp.getWidth(), imp.getHeight());
     if (!Prefs.blackBackground) ip.invertLut();
     maskImp = new ImagePlus("Mask", ip);
     maskImp.show();
   }
   ImageProcessor ip = maskImp.getProcessor();
   ip.setRoi(roi);
   ip.setValue(255);
   ip.fill(ip.getMask());
   maskImp.updateAndDraw();
   Prefs.useInvertingLut = useInvertingLut;
 }
예제 #17
0
 public void run(String arg) {
   imp = WindowManager.getCurrentImage();
   if (arg.equals("add")) {
     addToRoiManager(imp);
     return;
   }
   if (imp == null) {
     IJ.noImage();
     return;
   }
   if (arg.equals("all")) imp.setRoi(0, 0, imp.getWidth(), imp.getHeight());
   else if (arg.equals("none")) imp.killRoi();
   else if (arg.equals("restore")) imp.restoreRoi();
   else if (arg.equals("spline")) fitSpline();
   else if (arg.equals("circle")) fitCircle(imp);
   else if (arg.equals("ellipse")) createEllipse(imp);
   else if (arg.equals("hull")) convexHull(imp);
   else if (arg.equals("mask")) createMask(imp);
   else if (arg.equals("from")) createSelectionFromMask(imp);
   else if (arg.equals("inverse")) invert(imp);
   else if (arg.equals("toarea")) lineToArea(imp);
   else if (arg.equals("toline")) areaToLine(imp);
   else if (arg.equals("properties")) {
     setProperties("Properties ", imp.getRoi());
     imp.draw();
   } else if (arg.equals("band")) makeBand(imp);
   else if (arg.equals("tobox")) toBoundingBox(imp);
   else runMacro(arg);
 }
예제 #18
0
 // Finds the index of the upper right point that is guaranteed to be on convex hull
 int findFirstPoint(int[] xCoordinates, int[] yCoordinates, int n, ImagePlus imp) {
   int smallestY = imp.getHeight();
   int x, y;
   for (int i = 0; i < n; i++) {
     y = yCoordinates[i];
     if (y < smallestY) smallestY = y;
   }
   int smallestX = imp.getWidth();
   int p1 = 0;
   for (int i = 0; i < n; i++) {
     x = xCoordinates[i];
     y = yCoordinates[i];
     if (y == smallestY && x < smallestX) {
       smallestX = x;
       p1 = i;
     }
   }
   return p1;
 }
예제 #19
0
 public void run(String arg) {
   ImagePlus imp = WindowManager.getImage(id);
   if (imp != null && imp.getWindow() != null) {
     imp.getWindow().toFront();
     return;
   }
   int colorWidth = 22;
   int colorHeight = 16;
   int columns = 5;
   int rows = 20;
   int width = columns * colorWidth;
   int height = rows * colorHeight;
   ColorGenerator cg = new ColorGenerator(width, height, new int[width * height], this);
   cg.drawColors(colorWidth, colorHeight, columns, rows);
   setProcessor("CP", cg);
   id = getID();
   show();
   IJ.register(ColorPicker.class);
 }
예제 #20
0
  private boolean showDialog() {
    String[] types = {"RAW", "JPEG", "ZLIB"};
    GenericDialog gd = new GenericDialog("Generate Bricks");
    gd.addChoice("FileType", types, filetype);
    gd.addNumericField("JPEG quality", jpeg_quality, 0);
    gd.addNumericField("Max file size (MB)", bdsizelimit, 0);

    int[] wlist = WindowManager.getIDList();
    if (wlist == null) return false;

    String[] titles = new String[wlist.length];
    for (int i = 0; i < wlist.length; i++) titles[i] = "";

    int tnum = 0;
    for (int i = 0; i < wlist.length; i++) {
      ImagePlus imp = WindowManager.getImage(wlist[i]);
      if (imp != null) {
        titles[tnum] = imp.getTitle();
        tnum++;
      }
    }
    gd.addChoice("Source image: ", titles, titles[0]);

    gd.showDialog();
    if (gd.wasCanceled()) return false;

    filetype = types[gd.getNextChoiceIndex()];
    jpeg_quality = (int) gd.getNextNumber();
    if (jpeg_quality > 100) jpeg_quality = 100;
    if (jpeg_quality < 0) jpeg_quality = 0;
    bdsizelimit = (int) gd.getNextNumber();

    int id = gd.getNextChoiceIndex();
    lvImgTitle = new ArrayList<String>();
    lvImgTitle.add(titles[id]);

    Prefs.set("filetype.string", filetype);
    Prefs.set("jpeg_quality.int", jpeg_quality);
    Prefs.set("bdsizelimit.int", bdsizelimit);

    return true;
  }
예제 #21
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;
 }
예제 #22
0
 public void refreshBackground() {
   // Boundary for Background Selection
   setColor(0x444444);
   drawRect((w * 2) - 12, 276, (w * 2) + 4, (h * 2) + 4);
   setColor(0x999999);
   drawRect((w * 2) - 11, 277, (w * 2) + 2, (h * 2) + 2);
   setRoi((w * 2) - 10, 278, w * 2, h * 2); // Paints the Background Color
   setColor(Toolbar.getBackgroundColor());
   fill();
   imp.updateAndDraw();
 }
예제 #23
0
 public void refreshForeground() {
   // Boundary for Foreground Selection
   setColor(0x444444);
   drawRect(8, 266, (w * 2) + 4, (h * 2) + 4);
   setColor(0x999999);
   drawRect(9, 267, (w * 2) + 2, (h * 2) + 2);
   setRoi(10, 268, w * 2, h * 2); // Paints the Foreground Color
   setColor(Toolbar.getForegroundColor());
   fill();
   imp.updateAndDraw();
 }
예제 #24
0
 void areaToLine(ImagePlus imp) {
   Roi roi = imp.getRoi();
   if (roi == null || !roi.isArea()) {
     IJ.error("Area to Line", "Area selection required");
     return;
   }
   Polygon p = roi.getPolygon();
   if (p == null) return;
   int type1 = roi.getType();
   if (type1 == Roi.COMPOSITE) {
     IJ.error("Area to Line", "Composite selections cannot be converted to lines.");
     return;
   }
   int type2 = Roi.POLYLINE;
   if (type1 == Roi.OVAL
       || type1 == Roi.FREEROI
       || type1 == Roi.TRACED_ROI
       || ((roi instanceof PolygonRoi) && ((PolygonRoi) roi).isSplineFit())) type2 = Roi.FREELINE;
   Roi roi2 = new PolygonRoi(p.xpoints, p.ypoints, p.npoints, type2);
   imp.setRoi(roi2);
 }
예제 #25
0
 private void rotate(ImagePlus imp) {
   Roi roi = imp.getRoi();
   if (IJ.macroRunning()) {
     String options = Macro.getOptions();
     if (options != null
         && (options.indexOf("grid=") != -1 || options.indexOf("interpolat") != -1)) {
       IJ.run("Rotate... ", options); // run Image>Transform>Rotate
       return;
     }
   }
   (new RoiRotator()).run("");
 }
예제 #26
0
 void abortPluginOrMacro(ImagePlus imp) {
   if (imp != null) {
     ImageWindow win = imp.getWindow();
     if (win != null) {
       win.running = false;
       win.running2 = false;
     }
   }
   Macro.abort();
   Interpreter.abort();
   if (Interpreter.getInstance() != null) IJ.beep();
 }
예제 #27
0
  public boolean beadCalibration3d() {
    imp = IJ.getImage();
    if (imp == null) {
      IJ.noImage();
      return false;
    } else if (imp.getStackSize() == 1) {
      IJ.error("Stack required");
      return false;
    } else if (imp.getType() != ImagePlus.GRAY8 && imp.getType() != ImagePlus.GRAY16) {
      // In order to support 32bit images, pict[] must be changed to float[], and  getPixel(x, y);
      // requires a Float.intBitsToFloat() conversion
      IJ.error("8 or 16 bit greyscale image required");
      return false;
    }
    width = imp.getWidth();
    height = imp.getHeight();
    nslices = imp.getStackSize();
    imtitle = imp.getTitle();

    models[0] = "*None*";
    models[1] = "line";
    models[2] = "2nd degree polynomial";
    models[3] = "3rd degree polynomial";
    models[4] = "4th degree polynomial";

    GenericDialog gd = new GenericDialog("3D PALM calibration");
    gd.addNumericField("Maximum FWHM (in px)", prefs.get("QuickPALM.3Dcal_fwhm", 20), 0);
    gd.addNumericField(
        "Particle local threshold (% maximum intensity)", prefs.get("QuickPALM.pthrsh", 20), 0);
    gd.addNumericField("Z-spacing (nm)", prefs.get("QuickPALM.z-step", 10), 2);
    gd.addNumericField("Calibration Z-smoothing (radius)", prefs.get("QuickPALM.window", 1), 0);
    gd.addChoice("Model", models, prefs.get("QuickPALM.model", models[3]));
    gd.addCheckbox(
        "Show divergence of bead positions against model",
        prefs.get("QuickPALM.3Dcal_showDivergence", false));
    gd.addCheckbox("Show extra particle info", prefs.get("QuickPALM.3Dcal_showExtraInfo", false));
    gd.addMessage("\n\nDon't forget to save the table in the end...");
    gd.showDialog();
    if (gd.wasCanceled()) return false;
    fwhm = gd.getNextNumber();
    prefs.set("QuickPALM.QuickPALM.3Dcal_fwhm", fwhm);
    pthrsh = gd.getNextNumber() / 100;
    prefs.set("QuickPALM.pthrsh", pthrsh * 100);
    cal_z = gd.getNextNumber();
    prefs.set("QuickPALM.z-step", cal_z);
    window = (int) gd.getNextNumber();
    prefs.set("QuickPALM.window", window);
    model = gd.getNextChoice();
    prefs.set("QuickPALM.model", model);
    part_divergence = gd.getNextBoolean();
    prefs.set("QuickPALM.3Dcal_showDivergence", part_divergence);
    part_extrainfo = gd.getNextBoolean();
    prefs.set("QuickPALM.3Dcal_showExtraInfo", part_extrainfo);
    return true;
  }
예제 #28
0
 public void run() {
   while (!done) {
     synchronized (this) {
       try {
         wait();
       } catch (InterruptedException e) {
       }
       reset(imp, ip); // GL
       apply(imp, ip); // GL
       imp.updateAndDraw(); // GL
     }
   }
 }
예제 #29
0
 void runMacro(String arg, ImagePlus imp) {
   boolean rotate = arg.equals("rotate");
   Roi roi = imp.getRoi();
   if (rotate && IJ.macroRunning()) {
     String options = Macro.getOptions();
     if (options != null
         && (options.indexOf("grid=") != -1 || options.indexOf("interpolat") != -1)) {
       IJ.run("Rotate... ", options); // run Image>Transform>Rotate
       return;
     }
   }
   if (roi == null) {
     noRoi(rotate ? "Rotate" : "Enlarge");
     return;
   }
   double dangle = Tools.parseDouble(angle);
   if (Double.isNaN(dangle)) {
     dangle = 15;
     angle = "" + dangle;
   }
   if (rotate && (roi instanceof ImageRoi)) {
     dangle = IJ.getNumber("Angle (degrees):", dangle);
     ((ImageRoi) roi).rotate(dangle);
     imp.draw();
     angle = "" + dangle;
     return;
   }
   Undo.setup(Undo.ROI, imp);
   roi = (Roi) roi.clone();
   if (rotate) {
     String value = IJ.runMacroFile("ij.jar:RotateSelection", angle);
     Roi roi2 = imp.getRoi();
     transferProperties(roi, roi2);
     imp.setRoi(roi2);
     if (value != null) angle = value;
   } else if (arg.equals("enlarge")) (new RoiEnlarger()).run("");
 }
예제 #30
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();
    }