void addToRoiManager(ImagePlus imp) {
if (IJ.macroRunning() && Interpreter.isBatchModeRoiManager())
IJ.error("run(\"Add to Manager\") may not work in batch mode macros");
Frame frame = WindowManager.getFrame("ROI Manager");
if (frame == null) IJ.run("ROI Manager...");
if (imp == null) return;
Roi roi = imp.getRoi();
if (roi == null) return;
frame = WindowManager.getFrame("ROI Manager");
if (frame == null || !(frame instanceof RoiManager)) IJ.error("ROI Manager not found");
RoiManager rm = (RoiManager) frame;
boolean altDown = IJ.altKeyDown();
IJ.setKeyUp(IJ.ALL_KEYS);
if (altDown && !IJ.macroRunning()) IJ.setKeyDown(KeyEvent.VK_SHIFT);
if (roi.getState() == Roi.CONSTRUCTING) { // wait (up to 2 sec.) until ROI finished
long start = System.currentTimeMillis();
while (true) {
IJ.wait(10);
if (roi.getState() != Roi.CONSTRUCTING) break;
if ((System.currentTimeMillis() - start) > 2000) {
IJ.beep();
IJ.error("Add to Manager", "Selection is not complete");
return;
}
}
}
rm.runCommand("add");
IJ.setKeyUp(IJ.ALL_KEYS);
}
/**
* 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();
}
void createMask(ImagePlus imp) {
Roi roi = imp.getRoi();
boolean useInvertingLut = Prefs.useInvertingLut;
Prefs.useInvertingLut = false;
if (roi == null || !(roi.isArea() || roi.getType() == Roi.POINT)) {
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());
maskImp.updateAndDraw();
Prefs.useInvertingLut = useInvertingLut;
}
void updateSliceSummary() {
int slices = imp.getStackSize();
float[] areas = rt.getColumn(ResultsTable.AREA);
if (areas == null) areas = new float[0];
String label = imp.getTitle();
if (slices > 1) {
label = imp.getStack().getShortSliceLabel(slice);
label = label != null && !label.equals("") ? label : "" + slice;
}
String aLine = null;
double sum = 0.0;
int start = areas.length - particleCount;
if (start < 0) return;
for (int i = start; i < areas.length; i++) sum += areas[i];
int places = Analyzer.getPrecision();
Calibration cal = imp.getCalibration();
String total = "\t" + ResultsTable.d2s(sum, places);
String average = "\t" + ResultsTable.d2s(sum / particleCount, places);
String fraction = "\t" + ResultsTable.d2s(sum * 100.0 / totalArea, 1);
aLine = label + "\t" + particleCount + total + average + fraction;
aLine = addMeans(aLine, areas.length > 0 ? start : -1);
if (slices == 1) {
Frame frame = WindowManager.getFrame("Summary");
if (frame != null && (frame instanceof TextWindow) && summaryHdr.equals(prevHdr))
tw = (TextWindow) frame;
}
if (tw == null) {
String title = slices == 1 ? "Summary" : "Summary of " + imp.getTitle();
tw = new TextWindow(title, summaryHdr, aLine, 450, 300);
prevHdr = summaryHdr;
} else tw.append(aLine);
}
void addToRoiManager(ImagePlus imp) {
if (IJ.macroRunning() && Interpreter.isBatchModeRoiManager())
IJ.error("run(\"Add to Manager\") may not work in batch mode macros");
Frame frame = WindowManager.getFrame("ROI Manager");
if (frame == null) IJ.run("ROI Manager...");
if (imp == null) return;
Roi roi = imp.getRoi();
if (roi == null) return;
frame = WindowManager.getFrame("ROI Manager");
if (frame == null || !(frame instanceof RoiManager)) IJ.error("ROI Manager not found");
RoiManager rm = (RoiManager) frame;
boolean altDown = IJ.altKeyDown();
IJ.setKeyUp(IJ.ALL_KEYS);
if (altDown && !IJ.macroRunning()) IJ.setKeyDown(KeyEvent.VK_SHIFT);
rm.runCommand("add");
IJ.setKeyUp(IJ.ALL_KEYS);
}
void saveWindowLocations() {
Frame frame = WindowManager.getFrame("B&C");
if (frame != null) Prefs.saveLocation(ContrastAdjuster.LOC_KEY, frame.getLocation());
frame = WindowManager.getFrame("Threshold");
if (frame != null) Prefs.saveLocation(ThresholdAdjuster.LOC_KEY, frame.getLocation());
frame = WindowManager.getFrame("Results");
if (frame != null) {
Prefs.saveLocation(TextWindow.LOC_KEY, frame.getLocation());
Dimension d = frame.getSize();
Prefs.set(TextWindow.WIDTH_KEY, d.width);
Prefs.set(TextWindow.HEIGHT_KEY, d.height);
}
frame = WindowManager.getFrame("Log");
if (frame != null) {
Prefs.saveLocation(TextWindow.LOG_LOC_KEY, frame.getLocation());
Dimension d = frame.getSize();
Prefs.set(TextWindow.LOG_WIDTH_KEY, d.width);
Prefs.set(TextWindow.LOG_HEIGHT_KEY, d.height);
}
}
void toRoiManager() {
ImagePlus imp = IJ.getImage();
Overlay overlay = imp.getOverlay();
if (overlay == null) {
IJ.error("Overlay required");
return;
}
RoiManager rm = RoiManager.getInstance();
if (rm == null) {
if (Macro.getOptions() != null && Interpreter.isBatchMode())
rm = Interpreter.getBatchModeRoiManager();
if (rm == 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)) return;
rm = (RoiManager) frame;
}
}
rm.runCommand("reset");
for (int i = 0; i < overlay.size(); i++) rm.add(imp, overlay.get(i), i);
rm.setEditMode(imp, true);
if (rm.getCount() == overlay.size()) imp.setOverlay(null);
}
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;
}