예제 #1
0
 public static void saveTransform(String transform, String path) {
   String[] s = ij.util.Tools.split(transform);
   float[] m = new float[s.length];
   for (int i = 0; i < s.length; i++) {
     m[i] = Float.parseFloat(s[i]);
   }
   new math3d.TransformIO().saveAffineTransform(m);
 }
예제 #2
0
 public static void setTransform(String transform) {
   Image3DUniverse univ = getUniv();
   if (univ != null && univ.getSelected() != null) {
     String[] s = ij.util.Tools.split(transform);
     float[] m = new float[s.length];
     for (int i = 0; i < s.length; i++) {
       m[i] = Float.parseFloat(s[i]);
     }
     univ.getSelected().setTransform(new Transform3D(m));
   }
 }
  /** 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;
  }