/**
* Reduce error in thickness quantitation by trimming the one pixel overhang in the thickness map
*
* @param imp Binary input image
* @param impLTC Thickness map
* @param inv true if calculating thickness of background, false for foreground
* @return Thickness map with pixels masked by input image
*/
private ImagePlus trimOverhang(ImagePlus imp, ImagePlus impLTC, boolean inv) {
final int w = imp.getWidth();
final int h = imp.getHeight();
final int d = imp.getImageStackSize();
final ImageStack stack = imp.getImageStack();
final ImageStack mapStack = impLTC.getImageStack();
final int keepValue = inv ? 0 : 255;
ImageProcessor ip = new ByteProcessor(w, h);
ImageProcessor map = new FloatProcessor(w, h);
for (int z = 1; z <= d; z++) {
IJ.showStatus("Masking thickness map...");
IJ.showProgress(z, d);
ip = stack.getProcessor(z);
map = mapStack.getProcessor(z);
for (int y = 0; y < h; y++) {
for (int x = 0; x < w; x++) {
if (ip.get(x, y) != keepValue) map.set(x, y, 0);
}
}
}
return impLTC;
}
public CompositeImage(ImagePlus imp, int mode) {
if (mode < COMPOSITE || mode > GRAYSCALE) mode = COLOR;
this.mode = mode;
int channels = imp.getNChannels();
bitDepth = getBitDepth();
if (IJ.debugMode) IJ.log("CompositeImage: " + imp + " " + mode + " " + channels);
ImageStack stack2;
boolean isRGB = imp.getBitDepth() == 24;
if (isRGB) {
if (imp.getImageStackSize() > 1)
throw new IllegalArgumentException("RGB stacks not supported");
stack2 = getRGBStack(imp);
} else stack2 = imp.getImageStack();
int stackSize = stack2.getSize();
if (channels == 1 && isRGB) channels = 3;
if (channels == 1 && stackSize <= MAX_CHANNELS && !imp.dimensionsSet) channels = stackSize;
if (channels < 1 || (stackSize % channels) != 0)
throw new IllegalArgumentException("stacksize not multiple of channels");
if (mode == COMPOSITE && channels > MAX_CHANNELS) this.mode = COLOR;
compositeImage = true;
int z = imp.getNSlices();
int t = imp.getNFrames();
if (channels == stackSize || channels * z * t != stackSize)
setDimensions(channels, stackSize / channels, 1);
else setDimensions(channels, z, t);
setStack(imp.getTitle(), stack2);
setCalibration(imp.getCalibration());
FileInfo fi = imp.getOriginalFileInfo();
if (fi != null) {
displayRanges = fi.displayRanges;
channelLuts = fi.channelLuts;
}
setFileInfo(fi);
Object info = imp.getProperty("Info");
if (info != null) setProperty("Info", imp.getProperty("Info"));
if (mode == COMPOSITE) {
for (int i = 0; i < MAX_CHANNELS; i++) active[i] = true;
} else active[0] = true;
// if (!(channels==3&&stackSize==3))
setRoi(imp.getRoi());
setOverlay(imp.getOverlay());
if (channels != stackSize) setOpenAsHyperStack(true);
}
