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);
     }
   }
 }
 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);
 }
Exemple #3
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));
 }
Exemple #4
0
 public int setup(String arg, ImagePlus imp) {
   this.imp = imp;
   if (imp != null) {
     bitDepth = imp.getBitDepth();
     Roi roi = imp.getRoi();
     Rectangle r = roi != null ? roi.getBounds() : null;
     canEnlarge =
         r == null
             || (r.x == 0 && r.y == 0 && r.width == imp.getWidth() && r.height == imp.getHeight());
   }
   return 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);
 }
Exemple #6
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 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);
 }
Exemple #8
0
 public void run(String arg) {
   imp = IJ.getImage();
   if (imp == null) return;
   stackSize = imp.getStackSize();
   Roi roi = imp.getRoi();
   Calibration cal = imp.getCalibration();
   if (roi != null && roi.getBounds().equals(prevRoi) && cal.pixelWidth == prevPixelWidth)
     roi = null;
   if (roi != null) {
     boolean rectOrOval =
         roi != null && (roi.getType() == Roi.RECTANGLE || roi.getType() == Roi.OVAL);
     oval = rectOrOval && (roi.getType() == Roi.OVAL); // Handle existing oval ROI
     Rectangle r = roi.getBounds();
     width = r.width;
     height = r.height;
     xRoi = r.x;
     yRoi = r.y;
     if (scaledUnits && cal.scaled()) {
       xRoi = xRoi * cal.pixelWidth;
       yRoi = yRoi * cal.pixelHeight;
       width = width * cal.pixelWidth;
       height = height * cal.pixelHeight;
     }
     if (centered) { // Make xRoi and yRoi consistent when centered mode is active
       xRoi += width / 2.0;
       yRoi += height / 2.0;
     }
   } else if (!validDialogValues()) {
     width = imp.getWidth() / 2;
     height = imp.getHeight() / 2;
     xRoi = width / 2;
     yRoi = height / 2;
   }
   iSlice = imp.getCurrentSlice();
   showDialog();
 }
Exemple #9
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...");
 }
 public void mouseReleased(MouseEvent e) {
   flags = e.getModifiers();
   flags &= ~InputEvent.BUTTON1_MASK; // make sure button 1 bit is not set
   flags &= ~InputEvent.BUTTON2_MASK; // make sure button 2 bit is not set
   flags &= ~InputEvent.BUTTON3_MASK; // make sure button 3 bit is not set
   Roi roi = imp.getRoi();
   if (roi != null) {
     Rectangle r = roi.getBounds();
     int type = roi.getType();
     if ((r.width == 0 || r.height == 0)
         && !(type == Roi.POLYGON || type == Roi.POLYLINE || type == Roi.ANGLE || type == Roi.LINE)
         && !(roi instanceof TextRoi)
         && roi.getState() == roi.CONSTRUCTING
         && type != roi.POINT) imp.killRoi();
     else {
       roi.handleMouseUp(e.getX(), e.getY());
       if (roi.getType() == Roi.LINE && roi.getLength() == 0.0) imp.killRoi();
     }
   }
 }
Exemple #11
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;
 }
Exemple #12
0
 void drawRoi() {
   double xPxl = xRoi;
   double yPxl = yRoi;
   if (centered) {
     xPxl -= width / 2;
     yPxl -= height / 2;
   }
   double widthPxl = width;
   double heightPxl = height;
   Calibration cal = imp.getCalibration();
   if (scaledUnits && cal.scaled()) {
     xPxl /= cal.pixelWidth;
     yPxl /= cal.pixelHeight;
     widthPxl /= cal.pixelWidth;
     heightPxl /= cal.pixelHeight;
     prevPixelWidth = cal.pixelWidth;
   }
   Roi roi;
   if (oval) roi = new OvalRoi(xPxl, yPxl, widthPxl, heightPxl);
   else roi = new Roi(xPxl, yPxl, widthPxl, heightPxl);
   imp.setRoi(roi);
   prevRoi = roi.getBounds();
   // prevPixelWidth = cal.pixelWidth;
 }
Exemple #13
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 mousePressed(MouseEvent e) {
    // if (ij==null) return;
    showCursorStatus = true;
    int toolID = Toolbar.getToolId();
    ImageWindow win = imp.getWindow();
    if (win != null && win.running2 && toolID != Toolbar.MAGNIFIER) {
      if (win instanceof StackWindow) ((StackWindow) win).setAnimate(false);
      else win.running2 = false;
      return;
    }

    int x = e.getX();
    int y = e.getY();
    flags = e.getModifiers();
    // IJ.log("Mouse pressed: " + e.isPopupTrigger() + "  " + ij.modifiers(flags));
    // if (toolID!=Toolbar.MAGNIFIER && e.isPopupTrigger()) {
    if (toolID != Toolbar.MAGNIFIER
        && (e.isPopupTrigger() || (!IJ.isMacintosh() && (flags & Event.META_MASK) != 0))) {
      handlePopupMenu(e);
      return;
    }

    int ox = offScreenX(x);
    int oy = offScreenY(y);
    xMouse = ox;
    yMouse = oy;
    if (IJ.spaceBarDown()) {
      // temporarily switch to "hand" tool of space bar down
      setupScroll(ox, oy);
      return;
    }
    if (showAllROIs) {
      Roi roi = imp.getRoi();
      if (!(roi != null && (roi.contains(ox, oy) || roi.isHandle(x, y) >= 0))
          && roiManagerSelect(x, y)) return;
    }
    if (customRoi && overlay != null) return;

    switch (toolID) {
      case Toolbar.MAGNIFIER:
        if (IJ.shiftKeyDown()) zoomToSelection(ox, oy);
        else if ((flags & (Event.ALT_MASK | Event.META_MASK | Event.CTRL_MASK)) != 0) {
          // IJ.run("Out");
          zoomOut(x, y);
          if (getMagnification() < 1.0) imp.repaintWindow();
        } else {
          // IJ.run("In");
          zoomIn(x, y);
          if (getMagnification() <= 1.0) imp.repaintWindow();
        }
        break;
      case Toolbar.HAND:
        setupScroll(ox, oy);
        break;
      case Toolbar.DROPPER:
        setDrawingColor(ox, oy, IJ.altKeyDown());
        break;
      case Toolbar.WAND:
        Roi roi = imp.getRoi();
        if (roi != null && roi.contains(ox, oy)) {
          Rectangle r = roi.getBounds();
          if (r.width == imageWidth && r.height == imageHeight) imp.killRoi();
          else if (!e.isAltDown()) {
            handleRoiMouseDown(e);
            return;
          }
        }
        if (roi != null) {
          int handle = roi.isHandle(x, y);
          if (handle >= 0) {
            roi.mouseDownInHandle(handle, x, y);
            return;
          }
        }
        setRoiModState(e, roi, -1);
        String mode = WandToolOptions.getMode();
        double tolerance = WandToolOptions.getTolerance();
        int npoints = IJ.doWand(ox, oy, tolerance, mode);
        if (Recorder.record && npoints > 0) {
          if (tolerance == 0.0 && mode.equals("Legacy")) Recorder.record("doWand", ox, oy);
          else
            Recorder.recordString(
                "doWand(" + ox + ", " + oy + ", " + tolerance + ", \"" + mode + "\");\n");
        }
        break;
      case Toolbar.OVAL:
        if (Toolbar.getBrushSize() > 0) new RoiBrush();
        else handleRoiMouseDown(e);
        break;
      case Toolbar.SPARE1:
      case Toolbar.SPARE2:
      case Toolbar.SPARE3:
      case Toolbar.SPARE4:
      case Toolbar.SPARE5:
      case Toolbar.SPARE6:
      case Toolbar.SPARE7:
      case Toolbar.SPARE8:
      case Toolbar.SPARE9:
        Toolbar.getInstance().runMacroTool(toolID);
        break;
      default: // selection tool
        handleRoiMouseDown(e);
    }
  }
Exemple #15
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;
  }
 void drawRoiFilledParticle(ImageProcessor ip, Roi roi, ImageProcessor mask, int count) {
   int grayLevel = (count < 65535) ? count : 65535;
   ip.setValue((double) grayLevel);
   ip.setRoi(roi.getBounds());
   ip.fill(mask);
 }
 void drawFilledParticle(ImageProcessor ip, Roi roi, ImageProcessor mask) {
   // IJ.write(roi.getBounds()+" "+mask.length);
   ip.setRoi(roi.getBounds());
   ip.fill(mask);
 }
 void analyzeParticle(int x, int y, ImagePlus imp, ImageProcessor ip) {
   // Wand wand = new Wand(ip);
   ImageProcessor ip2 = redirectIP != null ? redirectIP : ip;
   wand.autoOutline(x, y, level1, level2, wandMode);
   if (wand.npoints == 0) {
     IJ.log("wand error: " + x + " " + y);
     return;
   }
   Roi roi = new PolygonRoi(wand.xpoints, wand.ypoints, wand.npoints, roiType);
   Rectangle r = roi.getBounds();
   if (r.width > 1 && r.height > 1) {
     PolygonRoi proi = (PolygonRoi) roi;
     pf.setPolygon(proi.getXCoordinates(), proi.getYCoordinates(), proi.getNCoordinates());
     ip2.setMask(pf.getMask(r.width, r.height));
     if (floodFill) ff.particleAnalyzerFill(x, y, level1, level2, ip2.getMask(), r);
   }
   ip2.setRoi(r);
   ip.setValue(fillColor);
   ImageStatistics stats = getStatistics(ip2, measurements, calibration);
   boolean include = true;
   if (excludeEdgeParticles) {
     if (r.x == minX || r.y == minY || r.x + r.width == maxX || r.y + r.height == maxY)
       include = false;
     if (polygon != null) {
       Rectangle bounds = roi.getBounds();
       int x1 = bounds.x + wand.xpoints[wand.npoints - 1];
       int y1 = bounds.y + wand.ypoints[wand.npoints - 1];
       int x2, y2;
       for (int i = 0; i < wand.npoints; i++) {
         x2 = bounds.x + wand.xpoints[i];
         y2 = bounds.y + wand.ypoints[i];
         if (!polygon.contains(x2, y2)) {
           include = false;
           break;
         }
         if ((x1 == x2 && ip.getPixel(x1, y1 - 1) == fillColor)
             || (y1 == y2 && ip.getPixel(x1 - 1, y1) == fillColor)) {
           include = false;
           break;
         }
         x1 = x2;
         y1 = y2;
       }
     }
   }
   ImageProcessor mask = ip2.getMask();
   if (minCircularity > 0.0 || maxCircularity < 1.0) {
     double perimeter = roi.getLength();
     double circularity =
         perimeter == 0.0 ? 0.0 : 4.0 * Math.PI * (stats.pixelCount / (perimeter * perimeter));
     if (circularity > 1.0) circularity = 1.0;
     // IJ.log(circularity+"	"+perimeter+"  "+stats.area);
     if (circularity < minCircularity || circularity > maxCircularity) include = false;
   }
   if (stats.pixelCount >= minSize && stats.pixelCount <= maxSize && include) {
     particleCount++;
     if (roiNeedsImage) roi.setImage(imp);
     stats.xstart = x;
     stats.ystart = y;
     saveResults(stats, roi);
     if (showChoice != NOTHING) drawParticle(drawIP, roi, stats, mask);
   }
   if (redirectIP != null) ip.setRoi(r);
   ip.fill(mask);
 }
Exemple #19
0
 private void makeBand(ImagePlus imp) {
   Roi roi = imp.getRoi();
   if (roi == null) {
     noRoi("Make Band");
     return;
   }
   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;
   IJ.run(edm, "Distance Map", "");
   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);
   imp.setRoi(roi2);
   bandSize = n;
 }
 void toBoundingBox(ImagePlus imp) {
   Roi roi = imp.getRoi();
   Rectangle r = roi.getBounds();
   imp.killRoi();
   imp.setRoi(new Roi(r.x, r.y, r.width, r.height));
 }