コード例 #1
0
ファイル: PolygonRoi.java プロジェクト: oeway/Eva-ImageJ
 void handleMouseMove(int sx, int sy) {
   // Do rubber banding
   int tool = Toolbar.getToolId();
   if (!(tool == Toolbar.POLYGON || tool == Toolbar.POLYLINE || tool == Toolbar.ANGLE)) {
     imp.deleteRoi();
     imp.draw();
     return;
   }
   drawRubberBand(sx, sy);
   degrees = Double.NaN;
   double len = -1;
   if (nPoints > 1) {
     double x1, y1, x2, y2;
     if (xpf != null) {
       x1 = xpf[nPoints - 2];
       y1 = ypf[nPoints - 2];
       x2 = xpf[nPoints - 1];
       y2 = ypf[nPoints - 1];
     } else {
       x1 = xp[nPoints - 2];
       y1 = yp[nPoints - 2];
       x2 = xp[nPoints - 1];
       y2 = yp[nPoints - 1];
     }
     degrees =
         getAngle(
             (int) Math.round(x1),
             (int) Math.round(y1),
             (int) Math.round(x2),
             (int) Math.round(y2));
     if (tool != Toolbar.ANGLE) {
       Calibration cal = imp.getCalibration();
       double pw = cal.pixelWidth, ph = cal.pixelHeight;
       if (IJ.altKeyDown()) {
         pw = 1.0;
         ph = 1.0;
       }
       len = Math.sqrt((x2 - x1) * pw * (x2 - x1) * pw + (y2 - y1) * ph * (y2 - y1) * ph);
     }
   }
   if (tool == Toolbar.ANGLE) {
     if (nPoints == 2) angle1 = degrees;
     else if (nPoints == 3) {
       double angle2 = getAngle(xp[1], yp[1], xp[2], yp[2]);
       degrees = Math.abs(180 - Math.abs(angle1 - angle2));
       if (degrees > 180.0) degrees = 360.0 - degrees;
     }
   }
   String length = len != -1 ? ", length=" + IJ.d2s(len) : "";
   double degrees2 =
       tool == Toolbar.ANGLE && nPoints == 3 && Prefs.reflexAngle ? 360.0 - degrees : degrees;
   String angle = !Double.isNaN(degrees) ? ", angle=" + IJ.d2s(degrees2) : "";
   int ox = ic != null ? ic.offScreenX(sx) : sx;
   int oy = ic != null ? ic.offScreenY(sy) : sy;
   IJ.showStatus(imp.getLocationAsString(ox, oy) + length + angle);
 }
コード例 #2
0
ファイル: Opener.java プロジェクト: kkkkxu/BioImage
 public static String getLoadRate(double time, ImagePlus imp) {
   time = (System.currentTimeMillis() - time) / 1000.0;
   double mb = imp.getWidth() * imp.getHeight() * imp.getStackSize();
   int bits = imp.getBitDepth();
   if (bits == 16) mb *= 2;
   else if (bits == 24 || bits == 32) mb *= 4;
   mb /= 1024 * 1024;
   double rate = mb / time;
   int digits = rate < 100.0 ? 1 : 0;
   return "" + IJ.d2s(time, 2) + " seconds (" + IJ.d2s(mb / time, digits) + " MB/sec)";
 }
コード例 #3
0
ファイル: Info.java プロジェクト: boron1111/ij
 private String displayRanges(ImagePlus imp) {
   LUT[] luts = imp.getLuts();
   if (luts == null) return "";
   String s = "Display ranges\n";
   int n = luts.length;
   if (n > 7) n = 7;
   for (int i = 0; i < n; i++) {
     double min = luts[i].min;
     double max = luts[i].max;
     int digits = (int) min == min && (int) max == max ? 0 : 2;
     s += "  " + (i + 1) + ": " + IJ.d2s(min, digits) + "-" + IJ.d2s(max, digits) + "\n";
   }
   return s;
 }
コード例 #4
0
ファイル: Wand.java プロジェクト: AlexJoz/docuensj
 /* Are we tracing a one pixel wide line? Makes Legacy mode 8-connected instead of 4-connected */
 private boolean isLine(int xs, int ys) {
   int r = 5;
   int xmin = xs;
   int xmax = xs + 2 * r;
   if (xmax >= width) xmax = width - 1;
   int ymin = ys - r;
   if (ymin < 0) ymin = 0;
   int ymax = ys + r;
   if (ymax >= height) ymax = height - 1;
   int area = 0;
   int insideCount = 0;
   for (int x = xmin; (x <= xmax); x++)
     for (int y = ymin; y <= ymax; y++) {
       area++;
       if (inside(x, y)) insideCount++;
     }
   if (IJ.debugMode)
     IJ.log(
         (((double) insideCount) / area < 0.25 ? "line " : "blob ")
             + insideCount
             + " "
             + area
             + " "
             + IJ.d2s(((double) insideCount) / area));
   return ((double) insideCount) / area < 0.25;
 }
コード例 #5
0
 byte[] getJar(String address) {
   // System.out.println("getJar: "+address);
   byte[] data;
   try {
     URL url = new URL(address);
     IJ.showStatus("Connecting to " + IJ.URL);
     URLConnection uc = url.openConnection();
     int len = uc.getContentLength();
     if (IJ.debugMode) IJ.log("Updater (url): " + address + " " + len);
     if (len <= 0) return null;
     String name = address.contains("wsr") ? "daily build (" : "ij.jar (";
     IJ.showStatus("Downloading " + name + IJ.d2s((double) len / 1048576, 1) + "MB)");
     InputStream in = uc.getInputStream();
     data = new byte[len];
     int n = 0;
     while (n < len) {
       int count = in.read(data, n, len - n);
       if (count < 0) throw new EOFException();
       n += count;
       IJ.showProgress(n, len);
     }
     in.close();
   } catch (IOException e) {
     if (IJ.debugMode) IJ.log("" + e);
     return null;
   }
   if (IJ.debugMode) IJ.wait(6000);
   return data;
 }
コード例 #6
0
ファイル: GenericDialog.java プロジェクト: aschain/ImageJA
 public synchronized void adjustmentValueChanged(AdjustmentEvent e) {
   Object source = e.getSource();
   for (int i = 0; i < slider.size(); i++) {
     if (source == slider.elementAt(i)) {
       Scrollbar sb = (Scrollbar) source;
       TextField tf = (TextField) numberField.elementAt(sliderIndexes[i]);
       int digits = sliderScales[i] == 1.0 ? 0 : 2;
       tf.setText("" + IJ.d2s(sb.getValue() / sliderScales[i], digits));
     }
   }
 }
コード例 #7
0
ファイル: Options.java プロジェクト: kkkkxu/BioImage
 // Conversion Options
 void conversions() {
   double[] weights = ColorProcessor.getWeightingFactors();
   boolean weighted = !(weights[0] == 1d / 3d && weights[1] == 1d / 3d && weights[2] == 1d / 3d);
   // boolean weighted = !(Math.abs(weights[0]-1d/3d)<0.0001 && Math.abs(weights[1]-1d/3d)<0.0001
   // && Math.abs(weights[2]-1d/3d)<0.0001);
   GenericDialog gd = new GenericDialog("Conversion Options");
   gd.addCheckbox("Scale when converting", ImageConverter.getDoScaling());
   String prompt = "Weighted RGB conversions";
   if (weighted)
     prompt +=
         " (" + IJ.d2s(weights[0]) + "," + IJ.d2s(weights[1]) + "," + IJ.d2s(weights[2]) + ")";
   gd.addCheckbox(prompt, weighted);
   gd.showDialog();
   if (gd.wasCanceled()) return;
   ImageConverter.setDoScaling(gd.getNextBoolean());
   Prefs.weightedColor = gd.getNextBoolean();
   if (!Prefs.weightedColor) ColorProcessor.setWeightingFactors(1d / 3d, 1d / 3d, 1d / 3d);
   else if (Prefs.weightedColor && !weighted)
     ColorProcessor.setWeightingFactors(0.299, 0.587, 0.114);
   return;
 }
コード例 #8
0
ファイル: GenericDialog.java プロジェクト: aschain/ImageJA
 /**
  * Adds a numeric field. The first word of the label must be unique or command recording will not
  * work.
  *
  * @param label the label
  * @param defaultValue value to be initially displayed
  * @param digits number of digits to right of decimal point
  * @param columns width of field in characters
  * @param units a string displayed to the right of the field
  */
 public void addNumericField(
     String label, double defaultValue, int digits, int columns, String units) {
   String label2 = label;
   if (label2.indexOf('_') != -1) label2 = label2.replace('_', ' ');
   Label theLabel = makeLabel(label2);
   c.gridx = 0;
   c.gridy = y;
   c.anchor = GridBagConstraints.EAST;
   c.gridwidth = 1;
   if (firstNumericField) c.insets = getInsets(5, 0, 3, 0);
   else c.insets = getInsets(0, 0, 3, 0);
   grid.setConstraints(theLabel, c);
   add(theLabel);
   if (numberField == null) {
     numberField = new Vector(5);
     defaultValues = new Vector(5);
     defaultText = new Vector(5);
   }
   if (IJ.isWindows()) columns -= 2;
   if (columns < 1) columns = 1;
   String defaultString = IJ.d2s(defaultValue, digits);
   if (Double.isNaN(defaultValue)) defaultString = "";
   TextField tf = new TextField(defaultString, columns);
   if (IJ.isLinux()) tf.setBackground(Color.white);
   tf.addActionListener(this);
   tf.addTextListener(this);
   tf.addFocusListener(this);
   tf.addKeyListener(this);
   numberField.addElement(tf);
   defaultValues.addElement(new Double(defaultValue));
   defaultText.addElement(tf.getText());
   c.gridx = 1;
   c.gridy = y;
   c.anchor = GridBagConstraints.WEST;
   tf.setEditable(true);
   // if (firstNumericField) tf.selectAll();
   firstNumericField = false;
   if (units == null || units.equals("")) {
     grid.setConstraints(tf, c);
     add(tf);
   } else {
     Panel panel = new Panel();
     panel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
     panel.add(tf);
     panel.add(new Label(" " + units));
     grid.setConstraints(panel, c);
     add(panel);
   }
   if (Recorder.record || macro) saveLabel(tf, label);
   y++;
 }
コード例 #9
0
  private void drawGraph(
      final double[] params, final double[] boxSizes, final double[] boxCountSums) {

    final int samples = 100;
    final float[] px = new float[samples];
    final float[] py = new float[samples];
    double[] a = Tools.getMinMax(boxSizes);
    final double xmin = a[0], xmax = a[1];

    a = Tools.getMinMax(boxCountSums);
    double ymin = a[0], ymax = a[1];
    final double inc = (xmax - xmin) / ((double) samples - 1);
    double tmp = xmin;

    for (int i = 0; i < samples; i++) {
      px[i] = (float) tmp;
      tmp += inc;
    }
    for (int i = 0; i < samples; i++) {
      py[i] = (float) CurveFitter.f(CurveFitter.STRAIGHT_LINE, params, px[i]);
    }
    a = Tools.getMinMax(py);
    ymin = Math.min(ymin, a[0]);
    ymax = Math.max(ymax, a[1]);
    final Plot plot = new Plot("Plot", "-log(box size)", "log(box count)", px, py);
    plot.setLimits(xmin, xmax * 0.9, ymin, ymax * 1.1);
    plot.draw();
    plot.addPoints(boxSizes, boxCountSums, Plot.CIRCLE);
    plot.addPoints(px, py, Plot.LINE);
    final CurveFitter cf = new CurveFitter(boxSizes, boxCountSums);
    cf.doFit(CurveFitter.STRAIGHT_LINE);
    plot.addLabel(
        0.1, 0.1, "Slope: " + IJ.d2s(params[1], 4) + "\n" + "R²: " + IJ.d2s(cf.getRSquared(), 4));
    final ImagePlus plotImage = new ImagePlus("Plot", plot.getProcessor());
    plotImage.show();
    return;
  }
コード例 #10
0
ファイル: PolygonRoi.java プロジェクト: oeway/Eva-ImageJ
 String getAngleAsString() {
   double angle1 = 0.0;
   double angle2 = 0.0;
   if (xpf != null) {
     angle1 = getFloatAngle(xpf[0], ypf[0], xpf[1], ypf[1]);
     angle2 = getFloatAngle(xpf[1], ypf[1], xpf[2], ypf[2]);
   } else {
     angle1 = getFloatAngle(xp[0], yp[0], xp[1], yp[1]);
     angle2 = getFloatAngle(xp[1], yp[1], xp[2], yp[2]);
   }
   degrees = Math.abs(180 - Math.abs(angle1 - angle2));
   if (degrees > 180.0) degrees = 360.0 - degrees;
   double degrees2 = Prefs.reflexAngle && type == ANGLE ? 360.0 - degrees : degrees;
   return ", angle=" + IJ.d2s(degrees2);
 }
コード例 #11
0
ファイル: ImageJ_Updater.java プロジェクト: AlexJoz/docuensj
 byte[] getJar(String address) {
   byte[] data;
   boolean gte133 = version().compareTo("1.33u") >= 0;
   try {
     URL url = new URL(address);
     URLConnection uc = url.openConnection();
     int len = uc.getContentLength();
     String name = address.endsWith("ij/ij.jar") ? "daily build" : "ij.jar";
     IJ.showStatus("Downloading ij.jar (" + IJ.d2s((double) len / 1048576, 1) + "MB)");
     InputStream in = uc.getInputStream();
     data = new byte[len];
     int n = 0;
     while (n < len) {
       int count = in.read(data, n, len - n);
       if (count < 0) throw new EOFException();
       n += count;
       if (gte133) IJ.showProgress(n, len);
     }
     in.close();
   } catch (IOException e) {
     return null;
   }
   return data;
 }
コード例 #12
0
  // TODO split run method into more sensible methods
  public void run(final String arg) {
    if (!ImageCheck.checkEnvironment()) return;
    final ImagePlus imp = IJ.getImage();
    if (null == imp) {
      IJ.noImage();
      return;
    }
    final ImageCheck ic = new ImageCheck();
    if (!ImageCheck.isBinary(imp)) {
      IJ.showMessage("Fractal Count requires a binary image.");
      return;
    }
    if (noGo) return;
    final ImagePlus surfaceImp = findSurfaceVoxels(imp);
    try {
      // Fetch data
      final int width = imp.getWidth();
      final int height = imp.getHeight();
      final int depth = imp.getStackSize();

      if (autoParam) {
        maxBox = Math.max(width, Math.max(height, depth)) / autoDiv;
        if (verboseOutput) {
          IJ.log("Automatic max box size " + maxBox + " selected");
        }
      }

      // Create variables we need and set them
      long bestCount; // keep track of best count so far
      long count = 0; // current count
      final ArrayList<Double> xList = new ArrayList<Double>();
      final ArrayList<Double> yList = new ArrayList<Double>();
      int xPos, yPos, zPos, yPart;
      int xGrid, yGrid, zGrid;
      int xStart, yStart, zStart;
      int xEnd, yEnd, zEnd;

      // Start timer
      final long startTime = System.currentTimeMillis();

      for (int boxSize = maxBox; boxSize >= minBox; boxSize /= divBox) {
        if (verboseOutput) {
          IJ.showStatus("Estimating dimension, box size: " + boxSize);
        }

        bestCount = Long.MAX_VALUE; // init count for this boxSize

        final int increment = Math.max(1, boxSize / numOffsets);

        for (int gridOffsetX = 0;
            (gridOffsetX < boxSize) && (gridOffsetX < width);
            gridOffsetX += increment) {

          for (int gridOffsetY = 0;
              (gridOffsetY < boxSize) && (gridOffsetY < height);
              gridOffsetY += increment) {

            for (int gridOffsetZ = 0;
                (gridOffsetZ < boxSize) && (gridOffsetZ < depth);
                gridOffsetZ += increment) {

              count = 0;

              final int iMax = width + gridOffsetX;
              final int jMax = height + gridOffsetY;
              final int kMax = depth + gridOffsetZ;

              // Iterate over box-grid
              for (int i = 0; i <= iMax; i += boxSize) {
                xGrid = -gridOffsetX + i;
                for (int j = 0; j <= jMax; j += boxSize) {
                  yGrid = -gridOffsetY + j;
                  for (int k = 0; k <= kMax; k += boxSize) {
                    zGrid = -gridOffsetZ + k;

                    xStart = 0;
                    if (xGrid < 0) {
                      xStart = -xGrid;
                    }
                    if ((boxSize + xGrid) >= width) {
                      xEnd = Math.min(width, (width - xGrid));
                    } else {
                      xEnd = boxSize;
                    }

                    yStart = 0;
                    if (yGrid < 0) {
                      yStart = -yGrid;
                    }
                    if ((boxSize + yGrid) >= height) {
                      yEnd = Math.min(height, (height - yGrid));
                    } else {
                      yEnd = boxSize;
                    }

                    zStart = 0;
                    if (zGrid < 0) {
                      zStart = -zGrid;
                    }
                    if ((boxSize + zGrid) >= depth) {
                      zEnd = Math.min(depth, (depth - zGrid));
                    } else {
                      zEnd = boxSize;
                    }

                    for (int x = xStart; x < xEnd; x++) {
                      xPos = x + xGrid;

                      for (int y = yStart; y < yEnd; y++) {
                        yPos = (y + yGrid);
                        yPart = yPos * width;

                        for (int z = zStart; z < zEnd; z++) {
                          zPos = z + zGrid;

                          // If pixel inside region,
                          // count it

                          if ((0xff
                                  & ((byte[]) surfaceImp.getStack().getPixels(zPos + 1))
                                      [xPos + yPart])
                              >= threshold) {
                            count++;
                            z = x = y = boxSize; // stops
                            // things
                          }
                        }
                      }
                    }
                  }
                }
              }
              if (count < bestCount) {
                bestCount = count;
              }
            }
          }
        }
        xList.add(new Double(boxSize));
        yList.add(new Double(bestCount));
      }

      if (verboseOutput) {
        IJ.log("\nDuration: " + (System.currentTimeMillis() - startTime) / 1000.0 + " seconds\n");
      }

      final double[] boxSizes = new double[xList.size()];
      final double[] boxCountSums = new double[yList.size()];
      for (int i = 0; i < boxSizes.length; i++) {
        boxSizes[i] = -Math.log((xList.get(i)).doubleValue());
        boxCountSums[i] = Math.log((yList.get(i)).doubleValue());
      }

      if (verboseOutput) {
        IJ.log(
            "Used " + boxSizes.length + " different box sizes, from " + maxBox + " to " + minBox);
        IJ.log(
            "with a reduction rate of "
                + divBox
                + " and "
                + numOffsets
                + " translations of each box.");
      }

      if (boxSizes.length == 0) {
        IJ.error(
            "\nError: No boxes!\n"
                + "Make sure that starting and ending box size and"
                + "reduction rate allow for at least one"
                + " box size to exist!");
        return;
      }

      final CurveFitter cf = new CurveFitter(boxSizes, boxCountSums);
      cf.doFit(CurveFitter.STRAIGHT_LINE);
      final double[] p = cf.getParams();
      final double RSq = cf.getRSquared();

      if (verboseOutput) {
        IJ.log(
            imp.getTitle()
                + ": Dimension estimate: "
                + IJ.d2s(p[1], 4)
                + ": R²: "
                + RSq
                + ": Settings: "
                + maxBox
                + ":"
                + minBox
                + ":"
                + divBox
                + ":"
                + numOffsets);
      }

      if (verboseOutput) {
        IJ.log("Box Size    Box Count");
        for (int i = 0; i < boxSizes.length; i++) {
          IJ.log(IJ.d2s(xList.get(i), 0) + "            " + IJ.d2s(yList.get(i), 0));
        }
      }

      final ResultInserter ri = ResultInserter.getInstance();
      ri.setResultInRow(imp, "Fractal Dimension", p[1]);
      ri.setResultInRow(imp, "R²", RSq);
      ri.updateTable();

      if (plotGraph && !Interpreter.isBatchMode()) {
        drawGraph(p, boxSizes, boxCountSums);
      }
    } catch (final Exception e) {
      e.printStackTrace();
    }
    UsageReporter.reportEvent(this).send();
  }
コード例 #13
0
ファイル: Info.java プロジェクト: boron1111/ij
 String d2s(double n) {
   return n == (int) n ? Integer.toString((int) n) : IJ.d2s(n);
 }
コード例 #14
0
ファイル: SpecifyROI.java プロジェクト: dannyZhou/imagej
  public boolean dialogItemChanged(GenericDialog gd, AWTEvent e) {
    if (IJ.isMacOSX()) IJ.wait(50);
    Calibration cal = imp.getCalibration();
    width = gd.getNextNumber();
    height = gd.getNextNumber();
    xRoi = gd.getNextNumber();
    yRoi = gd.getNextNumber();
    if (stackSize > 1) iSlice = (int) gd.getNextNumber();
    oval = gd.getNextBoolean();
    square = gd.getNextBoolean();
    centered = gd.getNextBoolean();
    if (cal.scaled()) scaledUnits = gd.getNextBoolean();
    if (gd.invalidNumber() || width <= 0 || height <= 0) return false;
    //
    Vector numFields = gd.getNumericFields();
    Vector checkboxes = gd.getCheckboxes();
    boolean newWidth = false, newHeight = false, newXY = false;
    if (e != null && e.getSource() == checkboxes.get(SQUARE) && square) {
      width = 0.5 * (width + height); // make square: same width&height
      height = width;
      newWidth = true;
      newHeight = true;
    }
    if (e != null && e.getSource() == checkboxes.get(CENTERED)) {
      double shiftBy = centered ? 0.5 : -0.5; // 'centered' changed:
      xRoi += shiftBy * width; // shift x, y to keep roi the same
      yRoi += shiftBy * height;
      newXY = true;
    }
    if (square && width != height && e != null) { // in 'square' mode, synchronize width&height
      if (e.getSource() == numFields.get(WIDTH)) {
        height = width;
        newHeight = true;
      } else if (e.getSource() == numFields.get(HEIGHT)) {
        width = height;
        newWidth = true;
      }
    }
    if (e != null && cal.scaled() && e.getSource() == checkboxes.get(SCALED_UNITS)) {
      double xFactor = scaledUnits ? cal.pixelWidth : 1. / cal.pixelWidth;
      double yFactor = scaledUnits ? cal.pixelHeight : 1. / cal.pixelHeight;
      width *= xFactor; // transform everything to keep roi the same
      height *= yFactor;
      xRoi *= xFactor;
      yRoi *= yFactor;
      newWidth = true;
      newHeight = true;
      newXY = true;
    }
    int digits = (scaledUnits || (int) width != width) ? 2 : 0;
    if (newWidth) ((TextField) (numFields.get(WIDTH))).setText(IJ.d2s(width, digits));
    if (newHeight) ((TextField) (numFields.get(HEIGHT))).setText(IJ.d2s(height, digits));
    digits = (scaledUnits || (int) xRoi != xRoi || (int) yRoi != yRoi) ? 2 : 0;
    if (newXY) {
      ((TextField) (numFields.get(X_ROI))).setText(IJ.d2s(xRoi, digits));
      ((TextField) (numFields.get(Y_ROI))).setText(IJ.d2s(yRoi, digits));
    }

    if (stackSize > 1 && iSlice > 0 && iSlice <= stackSize) imp.setSlice(iSlice);
    if (!newWidth && !newHeight && !newXY) // don't draw if an update will come immediately
    drawRoi();
    return true;
  }
コード例 #15
0
 private String d2s(double n) {
   return IJ.d2s(n, Tools.getDecimalPlaces(n));
 }
コード例 #16
0
ファイル: Thickness.java プロジェクト: kmiller324/BoneJ
  public void run(String arg) {
    ImageCheck ic = new ImageCheck();
    if (!ImageCheck.checkEnvironment()) return;
    ImagePlus imp = IJ.getImage();
    if (!ic.isBinary(imp)) {
      IJ.error("8-bit binary (black and white only) image required.");
      return;
    }

    if (!ic.isVoxelIsotropic(imp, 1E-3)) {
      if (IJ.showMessageWithCancel(
          "Anisotropic voxels",
          "This image contains anisotropic voxels, which will\n"
              + "result in incorrect thickness calculation.\n\n"
              + "Consider rescaling your data so that voxels are isotropic\n"
              + "(Image > Scale...).\n\n"
              + "Continue anyway?")) {
      } else return;
    }
    GenericDialog gd = new GenericDialog("Options");
    gd.addCheckbox("Thickness", true);
    gd.addCheckbox("Spacing", false);
    gd.addCheckbox("Graphic Result", true);
    gd.addCheckbox("Use_ROI_Manager", false);
    gd.addCheckbox("Mask thickness map", true);
    gd.addHelp("http://bonej.org/thickness");
    gd.showDialog();
    if (gd.wasCanceled()) {
      return;
    }
    boolean doThickness = gd.getNextBoolean();
    boolean doSpacing = gd.getNextBoolean();
    boolean doGraphic = gd.getNextBoolean();
    boolean doRoi = gd.getNextBoolean();
    boolean doMask = gd.getNextBoolean();

    long startTime = System.currentTimeMillis();
    String title = stripExtension(imp.getTitle());

    RoiManager roiMan = RoiManager.getInstance();
    // calculate trabecular thickness (Tb.Th)
    if (doThickness) {
      boolean inverse = false;
      ImagePlus impLTC = new ImagePlus();
      if (doRoi && roiMan != null) {
        ImageStack stack = RoiMan.cropStack(roiMan, imp.getStack(), true, 0, 1);
        ImagePlus crop = new ImagePlus(imp.getTitle(), stack);
        crop.setCalibration(imp.getCalibration());
        impLTC = getLocalThickness(crop, inverse, doMask);
      } else impLTC = getLocalThickness(imp, inverse, doMask);
      impLTC.setTitle(title + "_Tb.Th");
      impLTC.setCalibration(imp.getCalibration());
      double[] stats = StackStats.meanStdDev(impLTC);
      insertResults(imp, stats, inverse);
      if (doGraphic && !Interpreter.isBatchMode()) {
        impLTC.show();
        impLTC.setSlice(1);
        impLTC.getProcessor().setMinAndMax(0, stats[2]);
        IJ.run("Fire");
      }
    }
    if (doSpacing) {
      boolean inverse = true;
      ImagePlus impLTCi = new ImagePlus();
      if (doRoi && roiMan != null) {
        ImageStack stack = RoiMan.cropStack(roiMan, imp.getStack(), true, 255, 1);
        ImagePlus crop = new ImagePlus(imp.getTitle(), stack);
        crop.setCalibration(imp.getCalibration());
        impLTCi = getLocalThickness(crop, inverse, doMask);
      } else impLTCi = getLocalThickness(imp, inverse, doMask);
      // check marrow cavity size (i.e. trabcular separation, Tb.Sp)
      impLTCi.setTitle(title + "_Tb.Sp");
      impLTCi.setCalibration(imp.getCalibration());
      double[] stats = StackStats.meanStdDev(impLTCi);
      insertResults(imp, stats, inverse);
      if (doGraphic && !Interpreter.isBatchMode()) {
        impLTCi.show();
        impLTCi.setSlice(1);
        impLTCi.getProcessor().setMinAndMax(0, stats[2]);
        IJ.run("Fire");
      }
    }
    IJ.showProgress(1.0);
    IJ.showStatus("Done");
    double duration = ((double) System.currentTimeMillis() - (double) startTime) / (double) 1000;
    IJ.log("Duration = " + IJ.d2s(duration, 3) + " s");
    UsageReporter.reportEvent(this).send();
    return;
  }
コード例 #17
0
	public void run(String arg) {

  int[] wList = WindowManager.getIDList();
        if (wList==null) {
            IJ.error("No images are open.");
            return;
        }
	double kernel=3;
	double kernelsum = 0;
	double kernelvarsum =0;
	double kernalvar = 0;
	double sigmawidth = 2;
	int kernelindex, minpixnumber;
	String[] kernelsize =  { "3�,"5�, "7�, "9�};

	GenericDialog gd = new GenericDialog("Sigma Filter");
	gd.addChoice("Kernel size", kernelsize, kernelsize[0]);
	gd.addNumericField("Sigma width",sigmawidth , 2);
	gd.addNumericField("Minimum number of pixels", 1, 0);

	gd.addCheckbox("Keep source:",true);
	gd.addCheckbox("Do all stack:",true);
	gd.addCheckbox("Modified Lee's FIlter:",true);
	       	
	gd.showDialog();
       	if (gd.wasCanceled()) return ;
	kernelindex =  gd.getNextChoiceIndex();
          	sigmawidth = gd.getNextNumber();
          	minpixnumber = ((int)gd.getNextNumber());
          	boolean keep = gd.getNextBoolean();
	boolean doallstack = gd.getNextBoolean();
	boolean modified = gd.getNextBoolean();
	if (kernelindex==0) kernel = 3;
	if (kernelindex==1) kernel = 5;
	if (kernelindex==2) kernel = 7;
	if (kernelindex==3) kernel = 9;
    	long start = System.currentTimeMillis();
	
if (minpixnumber> (kernel*kernel)){
	      IJ.showMessage("Sigma filter", "There must be more pixels in the kernel than+\n" + "the minimum number to be included");
            return;
        }
	double v, midintensity;
	int   x, y, ix, iy;
	double sum = 0;
	double backupsum =0;
	int count = 0;
	int n = 0;
	if (keep) {IJ.run("Select All"); IJ.run("Duplicate...", "title='Sigma filtered' duplicate");}

	int radius = (int)(kernel-1)/2;
	ImagePlus imp = WindowManager.getCurrentImage();
	ImageStack stack1 = imp.getStack();
	int width = imp.getWidth();
	int height = imp.getHeight();
	int nslices = stack1.getSize();
	int cslice = imp.getCurrentSlice();
	double status = width*height*nslices;
	
	ImageProcessor  ip = imp.getProcessor();
	int sstart = 1;
	if (!doallstack) {sstart = cslice; nslices=sstart;status = status/nslices;};

 for (int i=sstart; i<=nslices; i++) {
                imp.setSlice(i);
                    
for (x=radius;x<width+radius;x++)	{
		for (y=radius;y<height+radius;y++)	{
			
			midintensity = ip.getPixelValue(x,y);
			count = 0;
			sum = 0;
			kernelsum =0;
			kernalvar =0;
			kernelvarsum =0;
			backupsum = 0;

		//calculate mean of kernel value
			for (ix=0;ix<kernel;ix++)	{
					for (iy=0;iy<kernel;iy++)	{
							v = ip.getPixelValue(x+ix-radius,y+iy-radius);
							kernelsum = kernelsum+v;
								}
						}
			double sigmacalcmean = (kernelsum/(kernel*kernel));

		//calculate variance of kernel
			for (ix=0;ix<kernel;ix++)	{
					for (iy=0;iy<kernel;iy++)	{
							v = ip.getPixelValue(x+ix-radius,y+iy-radius);
							kernalvar = (v-sigmacalcmean)*(v-sigmacalcmean);
							kernelvarsum = kernelvarsum + kernalvar;
								}
						}
			//double variance = kernelvarsum/kernel;
			double sigmacalcvar = kernelvarsum/((kernel*kernel)-1);

			//calcuate sigma range = sqrt(variance/(mean^2)) � sigmawidth
			double sigmarange  = sigmawidth*(Math.sqrt((sigmacalcvar) /(sigmacalcmean*sigmacalcmean)));
			//calulate sigma top value and bottom value
			double sigmatop = midintensity*(1+sigmarange);
			double sigmabottom = midintensity*(1-sigmarange);
			//calculate mean of values that differ are in sigma range.
			for (ix=0;ix<kernel;ix++)	{
					for (iy=0;iy<kernel;iy++)	{
							v = ip.getPixelValue(x+ix-radius,y+iy-radius);
							if ((v>=sigmabottom)&&(v<=sigmatop)){
								sum = sum+v;
								count = count+1;   }
								backupsum = v+ backupsum;
										}		
						}
//if there are too few pixels in the kernal that are within sigma range, the 
//mean of the entire kernal is taken. My modification of Lee's filter is to exclude the central value 
//from the calculation of the mean as I assume it to be spuriously high or low 
			if (!(count>(minpixnumber)))
				{sum = (backupsum-midintensity);
				count = (int)((kernel*kernel)-1);
				if (!modified)
					{sum = (backupsum);
					count  = (int)(kernel*kernel);}
				}
			
			double val =  (sum/count);
			ip.putPixelValue(x,y, val);
			n = n+1;
	double percentage = (((double)n/status)*100);
			 IJ.showStatus(IJ.d2s(percentage,0) +"% done");		
			
}

	//		IJ.showProgress(i, status);
					}}
			imp.updateAndDraw();
 			IJ.showStatus(IJ.d2s((System.currentTimeMillis()-start)/1000.0, 2)+" seconds");        }      
コード例 #18
0
ファイル: Info.java プロジェクト: boron1111/ij
  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;
  }
コード例 #19
0
ファイル: GenericDialog.java プロジェクト: aschain/ImageJA
  /**
   * Adds a slider (scroll bar) to the dialog box. Floating point values will be used if
   * (maxValue-minValue)<=5.0 and either minValue or maxValue are non-integer.
   *
   * @param label the label
   * @param minValue the minimum value of the slider
   * @param maxValue the maximum value of the slider
   * @param defaultValue the initial value of the slider
   */
  public void addSlider(String label, double minValue, double maxValue, double defaultValue) {
    if (defaultValue < minValue) defaultValue = minValue;
    if (defaultValue > maxValue) defaultValue = maxValue;
    int columns = 4;
    int digits = 0;
    double scale = 1.0;
    if ((maxValue - minValue) <= 5.0
        && (minValue != (int) minValue
            || maxValue != (int) maxValue
            || defaultValue != (int) defaultValue)) {
      scale = 20.0;
      minValue *= scale;
      maxValue *= scale;
      defaultValue *= scale;
      digits = 2;
    }
    String label2 = label;
    if (label2.indexOf('_') != -1) label2 = label2.replace('_', ' ');
    Label theLabel = makeLabel(label2);
    c.gridx = 0;
    c.gridy = y;
    c.anchor = GridBagConstraints.EAST;
    c.gridwidth = 1;
    c.insets = new Insets(0, 0, 3, 0);
    grid.setConstraints(theLabel, c);
    add(theLabel);

    if (slider == null) {
      slider = new Vector(5);
      sliderIndexes = new int[MAX_SLIDERS];
      sliderScales = new double[MAX_SLIDERS];
    }
    Scrollbar s =
        new Scrollbar(
            Scrollbar.HORIZONTAL, (int) defaultValue, 1, (int) minValue, (int) maxValue + 1);
    GUI.fix(s);
    slider.addElement(s);
    s.addAdjustmentListener(this);
    s.setUnitIncrement(1);

    if (numberField == null) {
      numberField = new Vector(5);
      defaultValues = new Vector(5);
      defaultText = new Vector(5);
    }
    if (IJ.isWindows()) columns -= 2;
    if (columns < 1) columns = 1;
    TextField tf = new TextField(IJ.d2s(defaultValue / scale, digits), columns);
    if (IJ.isLinux()) tf.setBackground(Color.white);
    tf.addActionListener(this);
    tf.addTextListener(this);
    tf.addFocusListener(this);
    tf.addKeyListener(this);
    numberField.addElement(tf);
    sliderIndexes[slider.size() - 1] = numberField.size() - 1;
    sliderScales[slider.size() - 1] = scale;
    defaultValues.addElement(new Double(defaultValue / scale));
    defaultText.addElement(tf.getText());
    tf.setEditable(true);
    firstSlider = false;

    Panel panel = new Panel();
    GridBagLayout pgrid = new GridBagLayout();
    GridBagConstraints pc = new GridBagConstraints();
    panel.setLayout(pgrid);
    pc.gridx = 0;
    pc.gridy = 0;
    pc.gridwidth = 1;
    pc.ipadx = 85;
    pc.anchor = GridBagConstraints.WEST;
    pgrid.setConstraints(s, pc);
    panel.add(s);
    pc.ipadx = 0; // reset
    // text field
    pc.gridx = 1;
    pc.insets = new Insets(5, 5, 0, 0);
    pc.anchor = GridBagConstraints.EAST;
    pgrid.setConstraints(tf, pc);
    panel.add(tf);

    grid.setConstraints(panel, c);
    c.gridx = 1;
    c.gridy = y;
    c.gridwidth = 1;
    c.anchor = GridBagConstraints.WEST;
    c.insets = new Insets(0, 0, 0, 0);
    grid.setConstraints(panel, c);
    add(panel);
    y++;
    if (Recorder.record || macro) saveLabel(tf, label);
  }
コード例 #20
0
  /** 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;
  }
コード例 #21
0
ファイル: Selection.java プロジェクト: dscho/ImageJA
  /*
  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
      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.killRoi();
      int d = (int) Math.round(2.0 * r);
      IJ.makeOval(
          (int) Math.round(stats.xCentroid - r), (int) Math.round(stats.yCentroid - r), d, d);
      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;
    imp.killRoi();
    IJ.makeOval(
        (int) Math.round(CenterX - radius),
        (int) Math.round(CenterY - radius),
        (int) Math.round(2 * radius),
        (int) Math.round(2 * radius));
  }
コード例 #22
0
ファイル: ZProjector.java プロジェクト: halirutan/imagej1
  public void run(String arg) {
    imp = IJ.getImage();
    int stackSize = imp.getStackSize();
    if (imp == null) {
      IJ.noImage();
      return;
    }

    //  Make sure input image is a stack.
    if (stackSize == 1) {
      IJ.error("Z Project", "Stack required");
      return;
    }

    //  Check for inverting LUT.
    if (imp.getProcessor().isInvertedLut()) {
      if (!IJ.showMessageWithCancel("ZProjection", lutMessage)) return;
    }

    // Set default bounds.
    int channels = imp.getNChannels();
    int frames = imp.getNFrames();
    int slices = imp.getNSlices();
    isHyperstack =
        imp.isHyperStack()
            || (ij.macro.Interpreter.isBatchMode()
                && ((frames > 1 && frames < stackSize) || (slices > 1 && slices < stackSize)));
    boolean simpleComposite = channels == stackSize;
    if (simpleComposite) isHyperstack = false;
    startSlice = 1;
    if (isHyperstack) {
      int nSlices = imp.getNSlices();
      if (nSlices > 1) stopSlice = nSlices;
      else stopSlice = imp.getNFrames();
    } else stopSlice = stackSize;

    // Build control dialog
    GenericDialog gd = buildControlDialog(startSlice, stopSlice);
    gd.showDialog();
    if (gd.wasCanceled()) return;

    if (!imp.lock()) return; // exit if in use
    long tstart = System.currentTimeMillis();
    setStartSlice((int) gd.getNextNumber());
    setStopSlice((int) gd.getNextNumber());
    method = gd.getNextChoiceIndex();
    Prefs.set(METHOD_KEY, method);
    if (isHyperstack) {
      allTimeFrames = imp.getNFrames() > 1 && imp.getNSlices() > 1 ? gd.getNextBoolean() : false;
      doHyperStackProjection(allTimeFrames);
    } else if (imp.getType() == ImagePlus.COLOR_RGB) doRGBProjection(true);
    else doProjection(true);

    if (arg.equals("") && projImage != null) {
      long tstop = System.currentTimeMillis();
      projImage.setCalibration(imp.getCalibration());
      if (simpleComposite) IJ.run(projImage, "Grays", "");
      projImage.show("ZProjector: " + IJ.d2s((tstop - tstart) / 1000.0, 2) + " seconds");
    }

    imp.unlock();
    IJ.register(ZProjector.class);
    return;
  }