Beispiel #1
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;
   Undo.setup(Undo.ROI, imp);
   if (!segmentedSelection && p.getNCoordinates() > 3) {
     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();
 }
Beispiel #2
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();
 }
Beispiel #3
0
 void scale(ImageProcessor ip) {
   if (newWindow) {
     Rectangle r = ip.getRoi();
     ImagePlus imp2 = imp.createImagePlus();
     imp2.setProcessor(title, ip.resize(newWidth, newHeight));
     Calibration cal = imp2.getCalibration();
     if (cal.scaled()) {
       cal.pixelWidth *= 1.0 / xscale;
       cal.pixelHeight *= 1.0 / yscale;
     }
     imp2.show();
     imp.trimProcessor();
     imp2.trimProcessor();
     imp2.changes = true;
   } else {
     if (processStack && imp.getStackSize() > 1) {
       Undo.reset();
       StackProcessor sp = new StackProcessor(imp.getStack(), ip);
       sp.scale(xscale, yscale, bgValue);
     } else {
       ip.snapshot();
       Undo.setup(Undo.FILTER, imp);
       ip.setSnapshotCopyMode(true);
       ip.scale(xscale, yscale);
       ip.setSnapshotCopyMode(false);
     }
     imp.killRoi();
     imp.updateAndDraw();
     imp.changes = true;
   }
 }
Beispiel #4
0
 public void run(ImageProcessor ip) {
   if (enlarge && gd.wasOKed())
     synchronized (this) {
       if (!isEnlarged) {
         enlargeCanvas();
         isEnlarged = true;
       }
     }
   if (isEnlarged) { // enlarging may have made the ImageProcessor invalid, also for the parallel
                     // threads
     int slice = pfr.getSliceNumber();
     if (imp.getStackSize() == 1) ip = imp.getProcessor();
     else ip = imp.getStack().getProcessor(slice);
   }
   ip.setInterpolationMethod(interpolationMethod);
   if (fillWithBackground) {
     Color bgc = Toolbar.getBackgroundColor();
     if (bitDepth == 8) ip.setBackgroundValue(ip.getBestIndex(bgc));
     else if (bitDepth == 24) ip.setBackgroundValue(bgc.getRGB());
   } else ip.setBackgroundValue(0);
   ip.rotate(angle);
   if (!gd.wasOKed()) drawGridLines(gridLines);
   if (isEnlarged && imp.getStackSize() == 1) {
     imp.changes = true;
     imp.updateAndDraw();
     Undo.setup(Undo.COMPOUND_FILTER_DONE, imp);
   }
 }
 void showResults() {
   int count = rt.getCounter();
   // if (count==0) return;
   boolean lastSlice = !processStack || slice == imp.getStackSize();
   if ((showChoice == OVERLAY_OUTLINES || showChoice == OVERLAY_MASKS) && slice == 1 && count > 0)
     imp.setOverlay(overlay);
   else if (outlines != null && lastSlice) {
     String title = imp != null ? imp.getTitle() : "Outlines";
     String prefix;
     if (showChoice == MASKS) prefix = "Mask of ";
     else if (showChoice == ROI_MASKS) prefix = "Count Masks of ";
     else prefix = "Drawing of ";
     outlines.update(drawIP);
     outputImage = new ImagePlus(prefix + title, outlines);
     if (inSituShow) {
       if (imp.getStackSize() == 1) Undo.setup(Undo.TRANSFORM, imp);
       imp.setStack(null, outputImage.getStack());
     } else if (!hideOutputImage) outputImage.show();
   }
   if (showResults && !processStack) {
     TextPanel tp = IJ.getTextPanel();
     if (beginningCount > 0 && tp != null && tp.getLineCount() != count) rt.show("Results");
     Analyzer.firstParticle = beginningCount;
     Analyzer.lastParticle = Analyzer.getCounter() - 1;
   } else Analyzer.firstParticle = Analyzer.lastParticle = 0;
 }
Beispiel #6
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;
   Undo.setup(Undo.ROI, imp);
   imp.deleteRoi();
   Roi roi2 = new EllipseRoi(x1, y1, x2, y2, aspectRatio);
   transferProperties(roi, roi2);
   imp.setRoi(roi2);
 }
 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);
 }
Beispiel #8
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");
 }
Beispiel #9
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()));
   Undo.setup(Undo.ROI, imp);
   imp.setRoi(s1.xor(s2));
 }
Beispiel #10
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);
 }
Beispiel #11
0
 void addSelection() {
   ImagePlus imp = IJ.getImage();
   String macroOptions = Macro.getOptions();
   if (macroOptions != null && IJ.macroRunning() && macroOptions.indexOf("remove") != -1) {
     imp.setOverlay(null);
     return;
   }
   Roi roi = imp.getRoi();
   if (roi == null && imp.getOverlay() != null) {
     GenericDialog gd = new GenericDialog("No Selection");
     gd.addMessage("\"Overlay>Add\" requires a selection.");
     gd.setInsets(15, 40, 0);
     gd.addCheckbox("Remove existing overlay", false);
     gd.showDialog();
     if (gd.wasCanceled()) return;
     if (gd.getNextBoolean()) imp.setOverlay(null);
     return;
   }
   if (roi == null) {
     IJ.error("This command requires a selection.");
     return;
   }
   roi = (Roi) roi.clone();
   if (roi.getStrokeColor() == null) roi.setStrokeColor(Toolbar.getForegroundColor());
   int width = Line.getWidth();
   Rectangle bounds = roi.getBounds();
   boolean tooWide = width > Math.max(bounds.width, bounds.height) / 3.0;
   if (roi.getStroke() == null && width > 1 && !tooWide) roi.setStrokeWidth(Line.getWidth());
   Overlay overlay = imp.getOverlay();
   if (overlay != null && overlay.size() > 0 && !roi.isDrawingTool()) {
     Roi roi2 = overlay.get(overlay.size() - 1);
     if (roi.getStroke() == null) roi.setStrokeWidth(roi2.getStrokeWidth());
     if (roi.getFillColor() == null) roi.setFillColor(roi2.getFillColor());
   }
   boolean points = roi instanceof PointRoi && ((PolygonRoi) roi).getNCoordinates() > 1;
   if (points) roi.setStrokeColor(Color.red);
   if (!IJ.altKeyDown() && !(roi instanceof Arrow)) {
     RoiProperties rp = new RoiProperties("Add to Overlay", roi);
     if (!rp.showDialog()) return;
   }
   String name = roi.getName();
   boolean newOverlay = name != null && name.equals("new-overlay");
   if (overlay == null || newOverlay) overlay = new Overlay();
   overlay.add(roi);
   imp.setOverlay(overlay);
   overlay2 = overlay;
   if (points || (roi instanceof ImageRoi) || (roi instanceof Arrow)) imp.killRoi();
   Undo.setup(Undo.OVERLAY_ADDITION, imp);
 }
  /**
   * 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};
  }
Beispiel #13
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...");
 }
Beispiel #14
0
 void areaToLine(ImagePlus imp) {
   Roi roi = imp.getRoi();
   if (roi == null || !roi.isArea()) {
     IJ.error("Area to Line", "Area selection required");
     return;
   }
   Undo.setup(Undo.ROI, imp);
   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);
   transferProperties(roi, roi2);
   imp.setRoi(roi2);
 }
Beispiel #15
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("");
 }
Beispiel #16
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;
   // if (roi.subPixelResolution() && roi instanceof PolygonRoi) {
   //	FloatPolygon p = ((PolygonRoi)roi).getFloatConvexHull();
   //	if (p!=null)
   //		imp.setRoi(new PolygonRoi(p.xpoints, p.ypoints, p.npoints, roi.POLYGON));
   // } else {
   Polygon p = roi.getConvexHull();
   if (p != null) {
     Undo.setup(Undo.ROI, imp);
     Roi roi2 = new PolygonRoi(p.xpoints, p.ypoints, p.npoints, roi.POLYGON);
     transferProperties(roi, roi2);
     imp.setRoi(roi2);
   }
 }
Beispiel #17
0
  void addImage() {
    ImagePlus imp = IJ.getImage();
    int[] wList = WindowManager.getIDList();
    if (wList == null || wList.length < 2) {
      IJ.error("Add Image...", "The command requires at least two open images.");
      return;
    }
    String[] titles = new String[wList.length];
    for (int i = 0; i < wList.length; i++) {
      ImagePlus imp2 = WindowManager.getImage(wList[i]);
      titles[i] = imp2 != null ? imp2.getTitle() : "";
    }
    int x = 0, y = 0;
    Roi roi = imp.getRoi();
    if (roi != null && roi.isArea()) {
      Rectangle r = roi.getBounds();
      x = r.x;
      y = r.y;
    }
    int index = 0;
    if (wList.length == 2) {
      ImagePlus i1 = WindowManager.getImage(wList[0]);
      ImagePlus i2 = WindowManager.getImage(wList[1]);
      if (i2.getWidth() < i1.getWidth() && i2.getHeight() < i1.getHeight()) index = 1;
    } else if (imp.getID() == wList[0]) index = 1;

    GenericDialog gd = new GenericDialog("Add Image...");
    gd.addChoice("Image to add:", titles, titles[index]);
    gd.addNumericField("X location:", x, 0);
    gd.addNumericField("Y location:", y, 0);
    gd.addNumericField("Opacity (0-100%):", 100, 0);
    gd.addCheckbox("Create image selection", createImageRoi);
    gd.showDialog();
    if (gd.wasCanceled()) return;
    index = gd.getNextChoiceIndex();
    x = (int) gd.getNextNumber();
    y = (int) gd.getNextNumber();
    double opacity = gd.getNextNumber() / 100.0;
    createImageRoi = gd.getNextBoolean();
    ImagePlus overlay = WindowManager.getImage(wList[index]);
    if (wList.length == 2) {
      ImagePlus i1 = WindowManager.getImage(wList[0]);
      ImagePlus i2 = WindowManager.getImage(wList[1]);
      if (i2.getWidth() < i1.getWidth() && i2.getHeight() < i1.getHeight()) {
        imp = i1;
        overlay = i2;
      }
    }
    if (overlay == imp) {
      IJ.error(
          "Add Image...", "Image to be added cannot be the same as\n\"" + imp.getTitle() + "\".");
      return;
    }
    if (overlay.getWidth() > imp.getWidth() && overlay.getHeight() > imp.getHeight()) {
      IJ.error(
          "Add Image...", "Image to be added cannnot be larger than\n\"" + imp.getTitle() + "\".");
      return;
    }
    if (createImageRoi && x == 0 && y == 0) {
      x = imp.getWidth() / 2 - overlay.getWidth() / 2;
      y = imp.getHeight() / 2 - overlay.getHeight() / 2;
    }
    roi = new ImageRoi(x, y, overlay.getProcessor());
    roi.setName(overlay.getShortTitle());
    if (opacity != 1.0) ((ImageRoi) roi).setOpacity(opacity);
    if (createImageRoi) imp.setRoi(roi);
    else {
      Overlay overlayList = imp.getOverlay();
      if (overlayList == null) overlayList = new Overlay();
      overlayList.add(roi);
      imp.setOverlay(overlayList);
      overlay2 = overlayList;
      Undo.setup(Undo.OVERLAY_ADDITION, imp);
    }
  }
  public void run(String arg) {
    int wOld, hOld, wNew, hNew;
    boolean fIsStack = false;

    ImagePlus imp = IJ.getImage();
    wOld = imp.getWidth();
    hOld = imp.getHeight();

    ImageStack stackOld = imp.getStack();
    if ((stackOld != null) && (stackOld.getSize() > 1)) fIsStack = true;

    String[] sPositions = {
      "Top-Left", "Top-Center", "Top-Right",
      "Center-Left", "Center", "Center-Right",
      "Bottom-Left", "Bottom-Center", "Bottom-Right"
    };

    String strTitle = fIsStack ? "Resize Stack Canvas" : "Resize Image Canvas";
    GenericDialog gd = new GenericDialog(strTitle);
    gd.addNumericField("Width:", wOld, 0, 5, "pixels");
    gd.addNumericField("Height:", hOld, 0, 5, "pixels");
    gd.addChoice("Position:", sPositions, sPositions[4]);
    gd.addCheckbox("Zero Fill", zeroFill);
    gd.showDialog();
    if (gd.wasCanceled()) return;

    wNew = (int) gd.getNextNumber();
    hNew = (int) gd.getNextNumber();
    int iPos = gd.getNextChoiceIndex();
    zeroFill = gd.getNextBoolean();
    Prefs.set("resizer.zero", zeroFill);

    int xOff, yOff;
    int xC = (wNew - wOld) / 2; // offset for centered
    int xR = (wNew - wOld); // offset for right
    int yC = (hNew - hOld) / 2; // offset for centered
    int yB = (hNew - hOld); // offset for bottom

    switch (iPos) {
      case 0: // TL
        xOff = 0;
        yOff = 0;
        break;
      case 1: // TC
        xOff = xC;
        yOff = 0;
        break;
      case 2: // TR
        xOff = xR;
        yOff = 0;
        break;
      case 3: // CL
        xOff = 0;
        yOff = yC;
        break;
      case 4: // C
        xOff = xC;
        yOff = yC;
        break;
      case 5: // CR
        xOff = xR;
        yOff = yC;
        break;
      case 6: // BL
        xOff = 0;
        yOff = yB;
        break;
      case 7: // BC
        xOff = xC;
        yOff = yB;
        break;
      case 8: // BR
        xOff = xR;
        yOff = yB;
        break;
      default: // center
        xOff = xC;
        yOff = yC;
        break;
    }

    if (fIsStack) {
      ImageStack stackNew = expandStack(stackOld, wNew, hNew, xOff, yOff);
      imp.setStack(null, stackNew);
    } else {
      if (!IJ.macroRunning()) Undo.setup(Undo.COMPOUND_FILTER, imp);
      ImageWindow win = imp.getWindow();
      if (win != null && (win instanceof PlotWindow)) ((PlotWindow) win).getPlot().setFrozen(true);
      ImageProcessor newIP = expandImage(imp.getProcessor(), wNew, hNew, xOff, yOff);
      imp.setProcessor(null, newIP);
      if (!IJ.macroRunning()) Undo.setup(Undo.COMPOUND_FILTER_DONE, imp);
    }
    Overlay overlay = imp.getOverlay();
    if (overlay != null) overlay.translate(xOff, yOff);
  }
Beispiel #19
0
  /*
  if selection is closed shape, create a circle with the same area and centroid, otherwise use<br>
  the Pratt method to fit a circle to the points that define the line or multi-point selection.<br>
  Reference: Pratt V., Direct least-squares fitting of algebraic surfaces", Computer Graphics, Vol. 21, pages 145-152 (1987).<br>
  Original code: Nikolai Chernov's MATLAB script for Newton-based Pratt fit.<br>
  (http://www.math.uab.edu/~chernov/cl/MATLABcircle.html)<br>
  Java version: https://github.com/mdoube/BoneJ/blob/master/src/org/doube/geometry/FitCircle.java<br>
  Authors: Nikolai Chernov, Michael Doube, Ved Sharma
  */
  void fitCircle(ImagePlus imp) {
    Roi roi = imp.getRoi();
    if (roi == null) {
      noRoi("Fit Circle");
      return;
    }

    if (roi.isArea()) { // create circle with the same area and centroid
      Undo.setup(Undo.ROI, imp);
      ImageProcessor ip = imp.getProcessor();
      ip.setRoi(roi);
      ImageStatistics stats =
          ImageStatistics.getStatistics(ip, Measurements.AREA + Measurements.CENTROID, null);
      double r = Math.sqrt(stats.pixelCount / Math.PI);
      imp.deleteRoi();
      int d = (int) Math.round(2.0 * r);
      Roi roi2 =
          new OvalRoi(
              (int) Math.round(stats.xCentroid - r), (int) Math.round(stats.yCentroid - r), d, d);
      transferProperties(roi, roi2);
      imp.setRoi(roi2);
      return;
    }

    Polygon poly = roi.getPolygon();
    int n = poly.npoints;
    int[] x = poly.xpoints;
    int[] y = poly.ypoints;
    if (n < 3) {
      IJ.error("Fit Circle", "At least 3 points are required to fit a circle.");
      return;
    }

    // calculate point centroid
    double sumx = 0, sumy = 0;
    for (int i = 0; i < n; i++) {
      sumx = sumx + poly.xpoints[i];
      sumy = sumy + poly.ypoints[i];
    }
    double meanx = sumx / n;
    double meany = sumy / n;

    // calculate moments
    double[] X = new double[n], Y = new double[n];
    double Mxx = 0, Myy = 0, Mxy = 0, Mxz = 0, Myz = 0, Mzz = 0;
    for (int i = 0; i < n; i++) {
      X[i] = x[i] - meanx;
      Y[i] = y[i] - meany;
      double Zi = X[i] * X[i] + Y[i] * Y[i];
      Mxy = Mxy + X[i] * Y[i];
      Mxx = Mxx + X[i] * X[i];
      Myy = Myy + Y[i] * Y[i];
      Mxz = Mxz + X[i] * Zi;
      Myz = Myz + Y[i] * Zi;
      Mzz = Mzz + Zi * Zi;
    }
    Mxx = Mxx / n;
    Myy = Myy / n;
    Mxy = Mxy / n;
    Mxz = Mxz / n;
    Myz = Myz / n;
    Mzz = Mzz / n;

    // calculate the coefficients of the characteristic polynomial
    double Mz = Mxx + Myy;
    double Cov_xy = Mxx * Myy - Mxy * Mxy;
    double Mxz2 = Mxz * Mxz;
    double Myz2 = Myz * Myz;
    double A2 = 4 * Cov_xy - 3 * Mz * Mz - Mzz;
    double A1 = Mzz * Mz + 4 * Cov_xy * Mz - Mxz2 - Myz2 - Mz * Mz * Mz;
    double A0 = Mxz2 * Myy + Myz2 * Mxx - Mzz * Cov_xy - 2 * Mxz * Myz * Mxy + Mz * Mz * Cov_xy;
    double A22 = A2 + A2;
    double epsilon = 1e-12;
    double ynew = 1e+20;
    int IterMax = 20;
    double xnew = 0;
    int iterations = 0;

    // Newton's method starting at x=0
    for (int iter = 1; iter <= IterMax; iter++) {
      iterations = iter;
      double yold = ynew;
      ynew = A0 + xnew * (A1 + xnew * (A2 + 4. * xnew * xnew));
      if (Math.abs(ynew) > Math.abs(yold)) {
        if (IJ.debugMode) IJ.log("Fit Circle: wrong direction: |ynew| > |yold|");
        xnew = 0;
        break;
      }
      double Dy = A1 + xnew * (A22 + 16 * xnew * xnew);
      double xold = xnew;
      xnew = xold - ynew / Dy;
      if (Math.abs((xnew - xold) / xnew) < epsilon) break;
      if (iter >= IterMax) {
        if (IJ.debugMode) IJ.log("Fit Circle: will not converge");
        xnew = 0;
      }
      if (xnew < 0) {
        if (IJ.debugMode) IJ.log("Fit Circle: negative root:  x = " + xnew);
        xnew = 0;
      }
    }
    if (IJ.debugMode)
      IJ.log("Fit Circle: n=" + n + ", xnew=" + IJ.d2s(xnew, 2) + ", iterations=" + iterations);

    // calculate the circle parameters
    double DET = xnew * xnew - xnew * Mz + Cov_xy;
    double CenterX = (Mxz * (Myy - xnew) - Myz * Mxy) / (2 * DET);
    double CenterY = (Myz * (Mxx - xnew) - Mxz * Mxy) / (2 * DET);
    double radius = Math.sqrt(CenterX * CenterX + CenterY * CenterY + Mz + 2 * xnew);
    if (Double.isNaN(radius)) {
      IJ.error("Fit Circle", "Points are collinear.");
      return;
    }
    CenterX = CenterX + meanx;
    CenterY = CenterY + meany;
    Undo.setup(Undo.ROI, imp);
    imp.deleteRoi();
    IJ.makeOval(
        (int) Math.round(CenterX - radius),
        (int) Math.round(CenterY - radius),
        (int) Math.round(2 * radius),
        (int) Math.round(2 * radius));
  }
Beispiel #20
0
 private void makeBand(ImagePlus imp) {
   Roi roi = imp.getRoi();
   if (roi == null) {
     noRoi("Make Band");
     return;
   }
   Roi roiOrig = roi;
   if (!roi.isArea()) {
     IJ.error("Make Band", "Area selection required");
     return;
   }
   Calibration cal = imp.getCalibration();
   double pixels = bandSize;
   double size = pixels * cal.pixelWidth;
   int decimalPlaces = 0;
   if ((int) size != size) decimalPlaces = 2;
   GenericDialog gd = new GenericDialog("Make Band");
   gd.addNumericField("Band Size:", size, decimalPlaces, 4, cal.getUnits());
   gd.showDialog();
   if (gd.wasCanceled()) return;
   size = gd.getNextNumber();
   if (Double.isNaN(size)) {
     IJ.error("Make Band", "invalid number");
     return;
   }
   int n = (int) Math.round(size / cal.pixelWidth);
   if (n > 255) {
     IJ.error("Make Band", "Cannot make bands wider that 255 pixels");
     return;
   }
   int width = imp.getWidth();
   int height = imp.getHeight();
   Rectangle r = roi.getBounds();
   ImageProcessor ip = roi.getMask();
   if (ip == null) {
     ip = new ByteProcessor(r.width, r.height);
     ip.invert();
   }
   ImageProcessor mask = new ByteProcessor(width, height);
   mask.insert(ip, r.x, r.y);
   ImagePlus edm = new ImagePlus("mask", mask);
   boolean saveBlackBackground = Prefs.blackBackground;
   Prefs.blackBackground = false;
   int saveType = EDM.getOutputType();
   EDM.setOutputType(EDM.BYTE_OVERWRITE);
   IJ.run(edm, "Distance Map", "");
   EDM.setOutputType(saveType);
   Prefs.blackBackground = saveBlackBackground;
   ip = edm.getProcessor();
   ip.setThreshold(0, n, ImageProcessor.NO_LUT_UPDATE);
   int xx = -1, yy = -1;
   for (int x = r.x; x < r.x + r.width; x++) {
     for (int y = r.y; y < r.y + r.height; y++) {
       if (ip.getPixel(x, y) < n) {
         xx = x;
         yy = y;
         break;
       }
     }
     if (xx >= 0 || yy >= 0) break;
   }
   int count = IJ.doWand(edm, xx, yy, 0, null);
   if (count <= 0) {
     IJ.error("Make Band", "Unable to make band");
     return;
   }
   ShapeRoi roi2 = new ShapeRoi(edm.getRoi());
   if (!(roi instanceof ShapeRoi)) roi = new ShapeRoi(roi);
   ShapeRoi roi1 = (ShapeRoi) roi;
   roi2 = roi2.not(roi1);
   Undo.setup(Undo.ROI, imp);
   transferProperties(roiOrig, roi2);
   imp.setRoi(roi2);
   bandSize = n;
 }