Exemple #1
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;
 }
Exemple #2
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);
 }
 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) {
     FloatPolygon p = roi.getFloatPolygon();
     roi2 = new PolygonRoi(p, Roi.POLYGON);
   } 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();
 }
Exemple #4
0
 public void deleteHandle(double ox, double oy) {
   if (imp == null) return;
   if (nPoints <= 1) {
     imp.deleteRoi();
     return;
   }
   boolean splineFit = xSpline != null;
   xSpline = null;
   FloatPolygon points = getFloatPolygon();
   modState = NO_MODS;
   if (previousRoi != null) previousRoi.modState = NO_MODS;
   int pointToDelete = getClosestPoint(ox, oy, points);
   FloatPolygon points2 = new FloatPolygon();
   for (int i = 0; i < points.npoints; i++) {
     if (i != pointToDelete) points2.addPoint(points.xpoints[i], points.ypoints[i]);
   }
   if (type == POINT) imp.setRoi(new PointRoi(points2.xpoints, points2.ypoints, points2.npoints));
   else {
     if (subPixelResolution()) {
       Roi roi2 = new PolygonRoi(points2, type);
       roi2.setDrawOffset(getDrawOffset());
       imp.setRoi(roi2);
     } else
       imp.setRoi(
           new PolygonRoi(toInt(points2.xpoints), toInt(points2.ypoints), points2.npoints, type));
     if (splineFit) ((PolygonRoi) imp.getRoi()).fitSpline(splinePoints);
   }
 }
 /**
  * Saves statistics for one particle in a results table. This is a method subclasses may want to
  * override.
  */
 protected void saveResults(ImageStatistics stats, Roi roi) {
   analyzer.saveResults(stats, roi);
   if (recordStarts) {
     rt.addValue("XStart", stats.xstart);
     rt.addValue("YStart", stats.ystart);
   }
   if (addToManager) {
     if (roiManager == null) {
       if (Macro.getOptions() != null && Interpreter.isBatchMode())
         roiManager = Interpreter.getBatchModeRoiManager();
       if (roiManager == null) {
         Frame frame = WindowManager.getFrame("ROI Manager");
         if (frame == null) IJ.run("ROI Manager...");
         frame = WindowManager.getFrame("ROI Manager");
         if (frame == null || !(frame instanceof RoiManager)) {
           addToManager = false;
           return;
         }
         roiManager = (RoiManager) frame;
       }
       if (resetCounter) roiManager.runCommand("reset");
     }
     if (imp.getStackSize() > 1) roi.setPosition(imp.getCurrentSlice());
     if (lineWidth != 1) roi.setStrokeWidth(lineWidth);
     roiManager.add(imp, roi, rt.getCounter());
   }
   if (showResults) rt.addResults();
 }
 /** Sets the cursor based on the current tool and cursor location. */
 public void setCursor(int sx, int sy, int ox, int oy) {
   xMouse = ox;
   yMouse = oy;
   mouseExited = false;
   Roi roi = imp.getRoi();
   ImageWindow win = imp.getWindow();
   if (win == null) return;
   if (IJ.spaceBarDown()) {
     setCursor(handCursor);
     return;
   }
   int id = Toolbar.getToolId();
   switch (Toolbar.getToolId()) {
     case Toolbar.MAGNIFIER:
       setCursor(moveCursor);
       break;
     case Toolbar.HAND:
       setCursor(handCursor);
       break;
     default: // selection tool
       if (id == Toolbar.SPARE1 || id >= Toolbar.SPARE2) {
         if (Prefs.usePointerCursor) setCursor(defaultCursor);
         else setCursor(crosshairCursor);
       } else if (roi != null && roi.getState() != roi.CONSTRUCTING && roi.isHandle(sx, sy) >= 0)
         setCursor(handCursor);
       else if (Prefs.usePointerCursor
           || (roi != null && roi.getState() != roi.CONSTRUCTING && roi.contains(ox, oy)))
         setCursor(defaultCursor);
       else setCursor(crosshairCursor);
   }
 }
Exemple #7
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();
 }
Exemple #8
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));
 }
 void drawRoiLabel(Graphics g, int index, Roi roi) {
   Rectangle r = roi.getBounds();
   int x = screenX(r.x);
   int y = screenY(r.y);
   double mag = getMagnification();
   int width = (int) (r.width * mag);
   int height = (int) (r.height * mag);
   int size = width > 40 && height > 40 ? 12 : 9;
   if (font != null) {
     g.setFont(font);
     size = font.getSize();
   } else if (size == 12) g.setFont(largeFont);
   else g.setFont(smallFont);
   boolean drawingList = index >= LIST_OFFSET;
   if (drawingList) index -= LIST_OFFSET;
   String label = "" + (index + 1);
   if (drawNames && roi.getName() != null) label = roi.getName();
   FontMetrics metrics = g.getFontMetrics();
   int w = metrics.stringWidth(label);
   x = x + width / 2 - w / 2;
   y = y + height / 2 + Math.max(size / 2, 6);
   int h = metrics.getAscent() + metrics.getDescent();
   if (bgColor != null) {
     g.setColor(bgColor);
     g.fillRoundRect(x - 1, y - h + 2, w + 1, h - 3, 5, 5);
   }
   if (!drawingList && labelRects != null && index < labelRects.length)
     labelRects[index] = new Rectangle(x - 1, y - h + 2, w + 1, h);
   g.setColor(labelColor);
   g.drawString(label, x, y - 2);
   g.setColor(defaultColor);
 }
 public void mouseMoved(MouseEvent e) {
   // if (ij==null) return;
   int sx = e.getX();
   int sy = e.getY();
   int ox = offScreenX(sx);
   int oy = offScreenY(sy);
   flags = e.getModifiers();
   setCursor(sx, sy, ox, oy);
   IJ.setInputEvent(e);
   Roi roi = imp.getRoi();
   if (roi != null
       && (roi.getType() == Roi.POLYGON
           || roi.getType() == Roi.POLYLINE
           || roi.getType() == Roi.ANGLE)
       && roi.getState() == roi.CONSTRUCTING) {
     PolygonRoi pRoi = (PolygonRoi) roi;
     pRoi.handleMouseMove(ox, oy);
   } else {
     if (ox < imageWidth && oy < imageHeight) {
       ImageWindow win = imp.getWindow();
       // Cursor must move at least 12 pixels before text
       // displayed using IJ.showStatus() is overwritten.
       if ((sx - sx2) * (sx - sx2) + (sy - sy2) * (sy - sy2) > 144) showCursorStatus = true;
       if (win != null && showCursorStatus) win.mouseMoved(ox, oy);
     } else IJ.showStatus("");
   }
 }
 public int setup(String arg, ImagePlus imp) {
   this.arg = arg;
   this.imp = imp;
   IJ.register(ParticleAnalyzer.class);
   if (imp == null) {
     IJ.noImage();
     return DONE;
   }
   if (imp.getBitDepth() == 24 && !isThresholdedRGB(imp)) {
     IJ.error(
         "Particle Analyzer",
         "RGB images must be thresholded using\n" + "Image>Adjust>Color Threshold.");
     return DONE;
   }
   if (!showDialog()) return DONE;
   int baseFlags = DOES_ALL + NO_CHANGES + NO_UNDO;
   int flags = IJ.setupDialog(imp, baseFlags);
   processStack = (flags & DOES_STACKS) != 0;
   slice = 0;
   saveRoi = imp.getRoi();
   if (saveRoi != null && saveRoi.getType() != Roi.RECTANGLE && saveRoi.isArea())
     polygon = saveRoi.getPolygon();
   imp.startTiming();
   nextFontSize = defaultFontSize;
   nextLineWidth = 1;
   return flags;
 }
Exemple #12
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;
   }
 }
Exemple #13
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");
 }
Exemple #14
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));
 }
 /** @deprecated replaced by ImagePlus.setOverlay(Shape, Color, BasicStroke) */
 public void setDisplayList(Shape shape, Color color, BasicStroke stroke) {
   if (shape == null) {
     setOverlay(null);
     return;
   }
   Roi roi = new ShapeRoi(shape);
   roi.setStrokeColor(color);
   roi.setStroke(stroke);
   Overlay list = new Overlay();
   list.add(roi);
   setOverlay(list);
 }
Exemple #16
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));
 }
 void setRoiModState(MouseEvent e, Roi roi, int handle) {
   if (roi == null || (handle >= 0 && roi.modState == Roi.NO_MODS)) return;
   if (roi.state == Roi.CONSTRUCTING) return;
   int tool = Toolbar.getToolId();
   if (tool > Toolbar.FREEROI && tool != Toolbar.WAND && tool != Toolbar.POINT) {
     roi.modState = Roi.NO_MODS;
     return;
   }
   if (e.isShiftDown()) roi.modState = Roi.ADD_TO_ROI;
   else if (e.isAltDown()) roi.modState = Roi.SUBTRACT_FROM_ROI;
   else roi.modState = Roi.NO_MODS;
   // IJ.log("setRoiModState: "+roi.modState+" "+ roi.state);
 }
Exemple #18
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);
 }
 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();
 }
Exemple #20
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));
 }
 public void mouseDragged(MouseEvent e) {
   int x = e.getX();
   int y = e.getY();
   xMouse = offScreenX(x);
   yMouse = offScreenY(y);
   flags = e.getModifiers();
   // IJ.log("mouseDragged: "+flags);
   if (flags == 0) // workaround for Mac OS 9 bug
   flags = InputEvent.BUTTON1_MASK;
   if (Toolbar.getToolId() == Toolbar.HAND || IJ.spaceBarDown()) scroll(x, y);
   else {
     IJ.setInputEvent(e);
     Roi roi = imp.getRoi();
     if (roi != null) roi.handleMouseDrag(x, y, flags);
   }
 }
 protected void handleRoiMouseDown(MouseEvent e) {
   int sx = e.getX();
   int sy = e.getY();
   int ox = offScreenX(sx);
   int oy = offScreenY(sy);
   Roi roi = imp.getRoi();
   int handle = roi != null ? roi.isHandle(sx, sy) : -1;
   boolean multiPointMode =
       roi != null
           && (roi instanceof PointRoi)
           && handle == -1
           && Toolbar.getToolId() == Toolbar.POINT
           && Toolbar.getMultiPointMode();
   if (multiPointMode) {
     imp.setRoi(((PointRoi) roi).addPoint(ox, oy));
     return;
   }
   setRoiModState(e, roi, handle);
   if (roi != null) {
     if (handle >= 0) {
       roi.mouseDownInHandle(handle, sx, sy);
       return;
     }
     Rectangle r = roi.getBounds();
     int type = roi.getType();
     if (type == Roi.RECTANGLE
         && r.width == imp.getWidth()
         && r.height == imp.getHeight()
         && roi.getPasteMode() == Roi.NOT_PASTING
         && !(roi instanceof ImageRoi)) {
       imp.killRoi();
       return;
     }
     if (roi.contains(ox, oy)) {
       if (roi.modState == Roi.NO_MODS) roi.handleMouseDown(sx, sy);
       else {
         imp.killRoi();
         imp.createNewRoi(sx, sy);
       }
       return;
     }
     if ((type == Roi.POLYGON || type == Roi.POLYLINE || type == Roi.ANGLE)
         && roi.getState() == roi.CONSTRUCTING) return;
     int tool = Toolbar.getToolId();
     if ((tool == Toolbar.POLYGON || tool == Toolbar.POLYLINE || tool == Toolbar.ANGLE)
         && !(IJ.shiftKeyDown() || IJ.altKeyDown())) {
       imp.killRoi();
       return;
     }
   }
   imp.createNewRoi(sx, sy);
 }
 void drawRoi(Graphics g, Roi roi, int index) {
   int type = roi.getType();
   ImagePlus imp2 = roi.getImage();
   roi.setImage(imp);
   Color saveColor = roi.getStrokeColor();
   if (saveColor == null) roi.setStrokeColor(defaultColor);
   if (roi instanceof TextRoi) ((TextRoi) roi).drawText(g);
   else roi.drawOverlay(g);
   roi.setStrokeColor(saveColor);
   if (index >= 0) {
     if (roi == currentRoi) g.setColor(Roi.getColor());
     else g.setColor(defaultColor);
     drawRoiLabel(g, index, roi);
   }
   if (imp2 != null) roi.setImage(imp2);
   else roi.setImage(null);
 }
Exemple #24
0
 public void run(String arg) {
   imp = IJ.getImage();
   Roi roi = imp.getRoi();
   if (roi != null && !roi.isArea()) imp.killRoi(); // ignore any line selection
   ImageProcessor ip = imp.getProcessor();
   if (!showDialog(ip)) return;
   if (ip.getWidth() > 1 && ip.getHeight() > 1) ip.setInterpolate(interpolate);
   else ip.setInterpolate(false);
   ip.setBackgroundValue(bgValue);
   imp.startTiming();
   try {
     if (newWindow && imp.getStackSize() > 1 && processStack) createNewStack(imp, ip);
     else scale(ip);
   } catch (OutOfMemoryError o) {
     IJ.outOfMemory("Scale");
   }
   IJ.showProgress(1.0);
 }
 void drawAllROIs(Graphics g) {
   RoiManager rm = RoiManager.getInstance();
   if (rm == null) {
     rm = Interpreter.getBatchModeRoiManager();
     if (rm != null && rm.getList().getItemCount() == 0) rm = null;
   }
   if (rm == null) {
     // if (showAllList!=null)
     //	overlay = showAllList;
     showAllROIs = false;
     repaint();
     return;
   }
   initGraphics(g, null, showAllColor);
   Hashtable rois = rm.getROIs();
   java.awt.List list = rm.getList();
   boolean drawLabels = rm.getDrawLabels();
   currentRoi = null;
   int n = list.getItemCount();
   if (IJ.debugMode) IJ.log("paint: drawing " + n + " \"Show All\" ROIs");
   if (labelRects == null || labelRects.length != n) labelRects = new Rectangle[n];
   if (!drawLabels) showAllList = new Overlay();
   else showAllList = null;
   if (imp == null) return;
   int currentImage = imp.getCurrentSlice();
   int channel = 0, slice = 0, frame = 0;
   boolean hyperstack = imp.isHyperStack();
   if (hyperstack) {
     channel = imp.getChannel();
     slice = imp.getSlice();
     frame = imp.getFrame();
   }
   drawNames = Prefs.useNamesAsLabels;
   for (int i = 0; i < n; i++) {
     String label = list.getItem(i);
     Roi roi = (Roi) rois.get(label);
     if (roi == null) continue;
     if (showAllList != null) showAllList.add(roi);
     if (i < 200 && drawLabels && roi == imp.getRoi()) currentRoi = roi;
     if (Prefs.showAllSliceOnly && imp.getStackSize() > 1) {
       if (hyperstack && roi.getPosition() == 0) {
         int c = roi.getCPosition();
         int z = roi.getZPosition();
         int t = roi.getTPosition();
         if ((c == 0 || c == channel) && (z == 0 || z == slice) && (t == 0 || t == frame))
           drawRoi(g, roi, drawLabels ? i : -1);
       } else {
         int position = roi.getPosition();
         if (position == 0) position = getSliceNumber(roi.getName());
         if (position == 0 || position == currentImage) drawRoi(g, roi, drawLabels ? i : -1);
       }
     } else drawRoi(g, roi, drawLabels ? i : -1);
   }
   ((Graphics2D) g).setStroke(Roi.onePixelWide);
   drawNames = false;
 }
Exemple #26
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);
 }
Exemple #27
0
 boolean setProperties(String title, Roi roi) {
   Frame f = WindowManager.getFrontWindow();
   if (f != null && f.getTitle().indexOf("3D Viewer") != -1) return false;
   if (roi == null) {
     IJ.error("This command requires a selection.");
     return false;
   }
   RoiProperties rp = new RoiProperties(title, roi);
   boolean ok = rp.showDialog();
   if (IJ.debugMode) IJ.log(roi.getDebugInfo());
   return ok;
 }
 void drawOutline(ImageProcessor ip, Roi roi, int count) {
   if (showChoice == OVERLAY_OUTLINES || showChoice == OVERLAY_MASKS) {
     if (overlay == null) {
       overlay = new Overlay();
       overlay.drawLabels(true);
       overlay.setLabelFont(new Font("SansSerif", Font.PLAIN, fontSize));
     }
     Roi roi2 = (Roi) roi.clone();
     roi2.setStrokeColor(Color.cyan);
     if (lineWidth != 1) roi2.setStrokeWidth(lineWidth);
     if (showChoice == OVERLAY_MASKS) roi2.setFillColor(Color.cyan);
     overlay.add(roi2);
   } else {
     Rectangle r = roi.getBounds();
     int nPoints = ((PolygonRoi) roi).getNCoordinates();
     int[] xp = ((PolygonRoi) roi).getXCoordinates();
     int[] yp = ((PolygonRoi) roi).getYCoordinates();
     int x = r.x, y = r.y;
     if (!inSituShow) ip.setValue(0.0);
     ip.moveTo(x + xp[0], y + yp[0]);
     for (int i = 1; i < nPoints; i++) ip.lineTo(x + xp[i], y + yp[i]);
     ip.lineTo(x + xp[0], y + yp[0]);
     if (showChoice != BARE_OUTLINES) {
       String s = ResultsTable.d2s(count, 0);
       ip.moveTo(r.x + r.width / 2 - ip.getStringWidth(s) / 2, r.y + r.height / 2 + fontSize / 2);
       if (!inSituShow) ip.setValue(1.0);
       ip.drawString(s);
     }
   }
 }
 protected void handlePopupMenu(MouseEvent e) {
   if (disablePopupMenu) return;
   if (IJ.debugMode) IJ.log("show popup: " + (e.isPopupTrigger() ? "true" : "false"));
   int x = e.getX();
   int y = e.getY();
   Roi roi = imp.getRoi();
   if (roi != null
       && (roi.getType() == Roi.POLYGON
           || roi.getType() == Roi.POLYLINE
           || roi.getType() == Roi.ANGLE)
       && roi.getState() == roi.CONSTRUCTING) {
     roi.handleMouseUp(x, y); // simulate double-click to finalize
     roi.handleMouseUp(x, y); // polygon or polyline selection
     return;
   }
   PopupMenu popup = Menus.getPopupMenu();
   if (popup != null) {
     add(popup);
     if (IJ.isMacOSX()) IJ.wait(10);
     popup.show(this, x, y);
   }
 }
Exemple #30
0
 void createMask(ImagePlus imp) {
   Roi roi = imp.getRoi();
   boolean useInvertingLut = Prefs.useInvertingLut;
   Prefs.useInvertingLut = false;
   boolean selectAll =
       roi != null
           && roi.getType() == Roi.RECTANGLE
           && roi.getBounds().width == imp.getWidth()
           && roi.getBounds().height == imp.getHeight()
           && imp.isThreshold();
   if (roi == null || !(roi.isArea() || roi.getType() == Roi.POINT) || selectAll) {
     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());
   Calibration cal = imp.getCalibration();
   if (cal.scaled()) {
     Calibration cal2 = maskImp.getCalibration();
     cal2.pixelWidth = cal.pixelWidth;
     cal2.pixelHeight = cal.pixelHeight;
     cal2.setUnit(cal.getUnit());
   }
   maskImp.updateAndRepaintWindow();
   Prefs.useInvertingLut = useInvertingLut;
 }