/**
* 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();
}
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;
}
/** 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;
}