// at the very end - show output image (if the is a separate one)
private void showOutput() {
if (interrupted) return;
if (outStack != null) {
outImp = new ImagePlus(TITLE_PREFIX[processType] + imp.getShortTitle(), outStack);
int[] d = imp.getDimensions();
outImp.setDimensions(d[2], d[3], d[4]);
for (int i = 1; i <= imp.getStackSize(); i++)
outStack.setSliceLabel(imp.getStack().getSliceLabel(i), i);
}
if (outImageType != BYTE_OVERWRITE) {
ImageProcessor ip = outImp.getProcessor();
if (!Prefs.blackBackground) ip.invertLut();
ip.resetMinAndMax();
outImp.show();
}
}
void addImage() {
ImagePlus imp = IJ.getImage();
int[] wList = WindowManager.getIDList();
if (wList == null || wList.length < 2) {
IJ.error("Add Image...", "The command requires at least two open images.");
return;
}
String[] titles = new String[wList.length];
for (int i = 0; i < wList.length; i++) {
ImagePlus imp2 = WindowManager.getImage(wList[i]);
titles[i] = imp2 != null ? imp2.getTitle() : "";
}
int x = 0, y = 0;
Roi roi = imp.getRoi();
if (roi != null && roi.isArea()) {
Rectangle r = roi.getBounds();
x = r.x;
y = r.y;
}
int index = 0;
if (wList.length == 2) {
ImagePlus i1 = WindowManager.getImage(wList[0]);
ImagePlus i2 = WindowManager.getImage(wList[1]);
if (i2.getWidth() < i1.getWidth() && i2.getHeight() < i1.getHeight()) index = 1;
} else if (imp.getID() == wList[0]) index = 1;
GenericDialog gd = new GenericDialog("Add Image...");
gd.addChoice("Image to add:", titles, titles[index]);
gd.addNumericField("X location:", x, 0);
gd.addNumericField("Y location:", y, 0);
gd.addNumericField("Opacity (0-100%):", 100, 0);
gd.addCheckbox("Create image selection", createImageRoi);
gd.showDialog();
if (gd.wasCanceled()) return;
index = gd.getNextChoiceIndex();
x = (int) gd.getNextNumber();
y = (int) gd.getNextNumber();
double opacity = gd.getNextNumber() / 100.0;
createImageRoi = gd.getNextBoolean();
ImagePlus overlay = WindowManager.getImage(wList[index]);
if (wList.length == 2) {
ImagePlus i1 = WindowManager.getImage(wList[0]);
ImagePlus i2 = WindowManager.getImage(wList[1]);
if (i2.getWidth() < i1.getWidth() && i2.getHeight() < i1.getHeight()) {
imp = i1;
overlay = i2;
}
}
if (overlay == imp) {
IJ.error(
"Add Image...", "Image to be added cannot be the same as\n\"" + imp.getTitle() + "\".");
return;
}
if (overlay.getWidth() > imp.getWidth() && overlay.getHeight() > imp.getHeight()) {
IJ.error(
"Add Image...", "Image to be added cannnot be larger than\n\"" + imp.getTitle() + "\".");
return;
}
if (createImageRoi && x == 0 && y == 0) {
x = imp.getWidth() / 2 - overlay.getWidth() / 2;
y = imp.getHeight() / 2 - overlay.getHeight() / 2;
}
roi = new ImageRoi(x, y, overlay.getProcessor());
roi.setName(overlay.getShortTitle());
if (opacity != 1.0) ((ImageRoi) roi).setOpacity(opacity);
if (createImageRoi) imp.setRoi(roi);
else {
Overlay overlayList = imp.getOverlay();
if (overlayList == null) overlayList = new Overlay();
overlayList.add(roi);
imp.setOverlay(overlayList);
overlay2 = overlayList;
Undo.setup(Undo.OVERLAY_ADDITION, imp);
}
}
/** Called by the PlugInFilterRunner to process the image or one frame of a stack */
public void run(ImageProcessor ip) {
if (interrupted) return;
int width = ip.getWidth();
int height = ip.getHeight();
int backgroundValue =
(processType == VORONOI)
? (background255 ? 0 : (byte) 255)
: // Voronoi needs EDM of the background
(background255 ? (byte) 255 : 0); // all others do EDM of the foreground
if (USES_WATERSHED[processType]) nPasses = 0; // watershed has its own progress bar
FloatProcessor floatEdm = makeFloatEDM(ip, backgroundValue, false);
ByteProcessor maxIp = null;
if (USES_MAX_FINDER[processType]) {
if (processType == VORONOI) floatEdm.multiply(-1); // Voronoi starts from minima of EDM
int maxOutputType =
USES_WATERSHED[processType] ? MaximumFinder.SEGMENTED : MaximumFinder.SINGLE_POINTS;
boolean isEDM = processType != VORONOI;
maxIp =
maxFinder.findMaxima(
floatEdm,
MAXFINDER_TOLERANCE,
ImageProcessor.NO_THRESHOLD,
maxOutputType,
false,
isEDM);
if (maxIp == null) { // segmentation cancelled by user?
interrupted = true;
return;
} else if (processType != WATERSHED) {
if (processType == VORONOI) floatEdm.multiply(-1);
resetMasked(floatEdm, maxIp, processType == VORONOI ? -1 : 0);
}
}
ImageProcessor outIp = null;
if (processType == WATERSHED) {
if (background255) maxIp.invert();
ip.copyBits(maxIp, 0, 0, Blitter.COPY);
ip.setBinaryThreshold();
} else
switch (outImageType) { // for all these, output contains the values of the EDM
case FLOAT:
outIp = floatEdm;
break;
case SHORT:
floatEdm.setMinAndMax(0., 65535.);
outIp = floatEdm.convertToShort(true);
break;
case BYTE:
floatEdm.setMinAndMax(0., 255.);
outIp = floatEdm.convertToByte(true);
break;
case BYTE_OVERWRITE:
ip.setPixels(0, floatEdm);
if (floatEdm.getMax() > 255.) ip.resetMinAndMax(); // otherwise we have max of floatEdm
}
if (outImageType != BYTE_OVERWRITE) { // new output image
if (outStack == null) {
outImp = new ImagePlus(TITLE_PREFIX[processType] + imp.getShortTitle(), outIp);
} else outStack.setPixels(outIp.getPixels(), pfr.getSliceNumber());
}
} // public void run