예제 #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;
   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 #2
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 #3
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);
 }
 /**
  * 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();
 }
예제 #5
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("");
 }
 boolean updateMacroOptions() {
   String options = Macro.getOptions();
   int index = options.indexOf("maximum=");
   if (index == -1) return false;
   index += 8;
   int len = options.length();
   while (index < len - 1 && options.charAt(index) != ' ') index++;
   if (index == len - 1) return false;
   int min = (int) Tools.parseDouble(Macro.getValue(options, "minimum", "1"));
   int max = (int) Tools.parseDouble(Macro.getValue(options, "maximum", "999999"));
   options = "size=" + min + "-" + max + options.substring(index, len);
   Macro.setOptions(options);
   return true;
 }
예제 #7
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("");
 }
  /** Displays a modal options dialog. */
  public boolean showDialog() {
    Calibration cal = imp != null ? imp.getCalibration() : (new Calibration());
    double unitSquared = cal.pixelWidth * cal.pixelHeight;
    if (pixelUnits) unitSquared = 1.0;
    if (Macro.getOptions() != null) {
      boolean oldMacro = updateMacroOptions();
      if (oldMacro) unitSquared = 1.0;
      staticMinSize = 0.0;
      staticMaxSize = DEFAULT_MAX_SIZE;
      staticMinCircularity = 0.0;
      staticMaxCircularity = 1.0;
      staticShowChoice = NOTHING;
    }
    GenericDialog gd = new GenericDialog("Analyze Particles");
    minSize = staticMinSize;
    maxSize = staticMaxSize;
    minCircularity = staticMinCircularity;
    maxCircularity = staticMaxCircularity;
    showChoice = staticShowChoice;
    if (maxSize == 999999) maxSize = DEFAULT_MAX_SIZE;
    options = staticOptions;
    String unit = cal.getUnit();
    boolean scaled = cal.scaled();
    if (unit.equals("inch")) {
      unit = "pixel";
      unitSquared = 1.0;
      scaled = false;
      pixelUnits = true;
    }
    String units = unit + "^2";
    int places = 0;
    double cmin = minSize * unitSquared;
    if ((int) cmin != cmin) places = 2;
    double cmax = maxSize * unitSquared;
    if ((int) cmax != cmax && cmax != DEFAULT_MAX_SIZE) places = 2;
    String minStr = ResultsTable.d2s(cmin, places);
    if (minStr.indexOf("-") != -1) {
      for (int i = places; i <= 6; i++) {
        minStr = ResultsTable.d2s(cmin, i);
        if (minStr.indexOf("-") == -1) break;
      }
    }
    String maxStr = ResultsTable.d2s(cmax, places);
    if (maxStr.indexOf("-") != -1) {
      for (int i = places; i <= 6; i++) {
        maxStr = ResultsTable.d2s(cmax, i);
        if (maxStr.indexOf("-") == -1) break;
      }
    }
    if (scaled) gd.setInsets(5, 0, 0);
    gd.addStringField("Size (" + units + "):", minStr + "-" + maxStr, 12);
    if (scaled) {
      gd.setInsets(0, 40, 5);
      gd.addCheckbox("Pixel units", pixelUnits);
    }
    gd.addStringField("Circularity:", IJ.d2s(minCircularity) + "-" + IJ.d2s(maxCircularity), 12);
    gd.addChoice("Show:", showStrings, showStrings[showChoice]);
    String[] labels = new String[8];
    boolean[] states = new boolean[8];
    labels[0] = "Display results";
    states[0] = (options & SHOW_RESULTS) != 0;
    labels[1] = "Exclude on edges";
    states[1] = (options & EXCLUDE_EDGE_PARTICLES) != 0;
    labels[2] = "Clear results";
    states[2] = (options & CLEAR_WORKSHEET) != 0;
    labels[3] = "Include holes";
    states[3] = (options & INCLUDE_HOLES) != 0;
    labels[4] = "Summarize";
    states[4] = (options & DISPLAY_SUMMARY) != 0;
    labels[5] = "Record starts";
    states[5] = (options & RECORD_STARTS) != 0;
    labels[6] = "Add to Manager";
    states[6] = (options & ADD_TO_MANAGER) != 0;
    labels[7] = "In_situ Show";
    states[7] = (options & IN_SITU_SHOW) != 0;
    gd.addCheckboxGroup(4, 2, labels, states);
    gd.addHelp(IJ.URL + "/docs/menus/analyze.html#ap");
    gd.showDialog();
    if (gd.wasCanceled()) return false;

    String size = gd.getNextString(); // min-max size
    if (scaled) pixelUnits = gd.getNextBoolean();
    if (pixelUnits) unitSquared = 1.0;
    else unitSquared = cal.pixelWidth * cal.pixelHeight;
    String[] minAndMax = Tools.split(size, " -");
    double mins = gd.parseDouble(minAndMax[0]);
    double maxs = minAndMax.length == 2 ? gd.parseDouble(minAndMax[1]) : Double.NaN;
    minSize = Double.isNaN(mins) ? DEFAULT_MIN_SIZE : mins / unitSquared;
    maxSize = Double.isNaN(maxs) ? DEFAULT_MAX_SIZE : maxs / unitSquared;
    if (minSize < DEFAULT_MIN_SIZE) minSize = DEFAULT_MIN_SIZE;
    if (maxSize < minSize) maxSize = DEFAULT_MAX_SIZE;
    staticMinSize = minSize;
    staticMaxSize = maxSize;

    minAndMax = Tools.split(gd.getNextString(), " -"); // min-max circularity
    double minc = gd.parseDouble(minAndMax[0]);
    double maxc = minAndMax.length == 2 ? gd.parseDouble(minAndMax[1]) : Double.NaN;
    minCircularity = Double.isNaN(minc) ? 0.0 : minc;
    maxCircularity = Double.isNaN(maxc) ? 1.0 : maxc;
    if (minCircularity < 0.0 || minCircularity > 1.0) minCircularity = 0.0;
    if (maxCircularity < minCircularity || maxCircularity > 1.0) maxCircularity = 1.0;
    if (minCircularity == 1.0 && maxCircularity == 1.0) minCircularity = 0.0;
    staticMinCircularity = minCircularity;
    staticMaxCircularity = maxCircularity;

    if (gd.invalidNumber()) {
      IJ.error("Bins invalid.");
      canceled = true;
      return false;
    }
    showChoice = gd.getNextChoiceIndex();
    staticShowChoice = showChoice;
    if (gd.getNextBoolean()) options |= SHOW_RESULTS;
    else options &= ~SHOW_RESULTS;
    if (gd.getNextBoolean()) options |= EXCLUDE_EDGE_PARTICLES;
    else options &= ~EXCLUDE_EDGE_PARTICLES;
    if (gd.getNextBoolean()) options |= CLEAR_WORKSHEET;
    else options &= ~CLEAR_WORKSHEET;
    if (gd.getNextBoolean()) options |= INCLUDE_HOLES;
    else options &= ~INCLUDE_HOLES;
    if (gd.getNextBoolean()) options |= DISPLAY_SUMMARY;
    else options &= ~DISPLAY_SUMMARY;
    if (gd.getNextBoolean()) options |= RECORD_STARTS;
    else options &= ~RECORD_STARTS;
    if (gd.getNextBoolean()) options |= ADD_TO_MANAGER;
    else options &= ~ADD_TO_MANAGER;
    if (gd.getNextBoolean()) options |= IN_SITU_SHOW;
    else options &= ~IN_SITU_SHOW;
    staticOptions = options;
    options |= SHOW_PROGRESS;
    if ((options & DISPLAY_SUMMARY) != 0)
      Analyzer.setMeasurements(Analyzer.getMeasurements() | AREA);
    return true;
  }
예제 #9
0
  boolean showDialog(ImageProcessor ip) {
    String macroOptions = Macro.getOptions();
    if (macroOptions != null) {
      if (macroOptions.indexOf(" interpolate") != -1)
        macroOptions.replaceAll(" interpolate", " interpolation=Bilinear");
      else if (macroOptions.indexOf(" interpolation=") == -1)
        macroOptions = macroOptions + " interpolation=None";
      Macro.setOptions(macroOptions);
    }
    int bitDepth = imp.getBitDepth();
    int stackSize = imp.getStackSize();
    boolean isStack = stackSize > 1;
    oldDepth = stackSize;
    if (isStack) {
      xstr = "1.0";
      ystr = "1.0";
      zstr = "1.0";
    }
    r = ip.getRoi();
    int width = newWidth;
    if (width == 0) width = r.width;
    int height = (int) ((double) width * r.height / r.width);
    xscale = Tools.parseDouble(xstr, 0.0);
    yscale = Tools.parseDouble(ystr, 0.0);
    zscale = 1.0;
    if (xscale != 0.0 && yscale != 0.0) {
      width = (int) (r.width * xscale);
      height = (int) (r.height * yscale);
    } else {
      xstr = "-";
      ystr = "-";
    }
    GenericDialog gd = new GenericDialog("Scale");
    gd.addStringField("X Scale:", xstr);
    gd.addStringField("Y Scale:", ystr);
    if (isStack) gd.addStringField("Z Scale:", zstr);
    gd.setInsets(5, 0, 5);
    gd.addStringField("Width (pixels):", "" + width);
    gd.addStringField("Height (pixels):", "" + height);
    if (isStack) {
      String label = "Depth (images):";
      if (imp.isHyperStack()) {
        int slices = imp.getNSlices();
        int frames = imp.getNFrames();
        if (slices == 1 && frames > 1) {
          label = "Depth (frames):";
          oldDepth = frames;
        } else {
          label = "Depth (slices):";
          oldDepth = slices;
        }
      }
      gd.addStringField(label, "" + oldDepth);
    }
    fields = gd.getStringFields();
    for (int i = 0; i < fields.size(); i++) {
      ((TextField) fields.elementAt(i)).addTextListener(this);
      ((TextField) fields.elementAt(i)).addFocusListener(this);
    }
    xField = (TextField) fields.elementAt(0);
    yField = (TextField) fields.elementAt(1);
    if (isStack) {
      zField = (TextField) fields.elementAt(2);
      widthField = (TextField) fields.elementAt(3);
      heightField = (TextField) fields.elementAt(4);
      depthField = (TextField) fields.elementAt(5);
    } else {
      widthField = (TextField) fields.elementAt(2);
      heightField = (TextField) fields.elementAt(3);
    }
    fieldWithFocus = xField;
    gd.addChoice("Interpolation:", methods, methods[interpolationMethod]);
    if (bitDepth == 8 || bitDepth == 24)
      gd.addCheckbox("Fill with background color", fillWithBackground);
    gd.addCheckbox("Average when downsizing", averageWhenDownsizing);
    boolean hyperstack = imp.isHyperStack() || imp.isComposite();
    if (isStack && !hyperstack) gd.addCheckbox("Process entire stack", processStack);
    gd.addCheckbox("Create new window", newWindow);
    title = WindowManager.getUniqueName(imp.getTitle());
    gd.setInsets(10, 0, 0);
    gd.addStringField("Title:", title, 12);
    gd.showDialog();
    if (gd.wasCanceled()) return false;
    xstr = gd.getNextString();
    ystr = gd.getNextString();
    xscale = Tools.parseDouble(xstr, 0.0);
    yscale = Tools.parseDouble(ystr, 0.0);
    if (isStack) {
      zstr = gd.getNextString();
      zscale = Tools.parseDouble(ystr, 0.0);
    }
    String wstr = gd.getNextString();
    newWidth = (int) Tools.parseDouble(wstr, 0);
    newHeight = (int) Tools.parseDouble(gd.getNextString(), 0);
    if (newHeight != 0 && (wstr.equals("-") || wstr.equals("0")))
      newWidth = (int) (newHeight * (double) r.width / r.height);
    if (newWidth == 0 || newHeight == 0) {
      IJ.error("Scaler", "Width or height is 0");
      return false;
    }
    if (xscale > 0.0 && yscale > 0.0) {
      newWidth = (int) (r.width * xscale);
      newHeight = (int) (r.height * yscale);
    }
    if (isStack) newDepth = (int) Tools.parseDouble(gd.getNextString(), 0);
    interpolationMethod = gd.getNextChoiceIndex();
    if (bitDepth == 8 || bitDepth == 24) fillWithBackground = gd.getNextBoolean();
    averageWhenDownsizing = gd.getNextBoolean();
    if (isStack && !hyperstack) processStack = gd.getNextBoolean();
    if (hyperstack) processStack = true;
    newWindow = gd.getNextBoolean();
    if (xscale == 0.0) {
      xscale = (double) newWidth / r.width;
      yscale = (double) newHeight / r.height;
    }
    title = gd.getNextString();

    if (fillWithBackground) {
      Color bgc = Toolbar.getBackgroundColor();
      if (bitDepth == 8) bgValue = ip.getBestIndex(bgc);
      else if (bitDepth == 24) bgValue = bgc.getRGB();
    } else bgValue = 0.0;
    return true;
  }