void scale(ImageProcessor ip) {
if (newWindow) {
Rectangle r = ip.getRoi();
ImagePlus imp2 = imp.createImagePlus();
imp2.setProcessor(title, ip.resize(newWidth, newHeight));
Calibration cal = imp2.getCalibration();
if (cal.scaled()) {
cal.pixelWidth *= 1.0 / xscale;
cal.pixelHeight *= 1.0 / yscale;
}
imp2.show();
imp.trimProcessor();
imp2.trimProcessor();
imp2.changes = true;
} else {
if (processStack && imp.getStackSize() > 1) {
Undo.reset();
StackProcessor sp = new StackProcessor(imp.getStack(), ip);
sp.scale(xscale, yscale, bgValue);
} else {
ip.snapshot();
Undo.setup(Undo.FILTER, imp);
ip.setSnapshotCopyMode(true);
ip.scale(xscale, yscale);
ip.setSnapshotCopyMode(false);
}
imp.killRoi();
imp.updateAndDraw();
imp.changes = true;
}
}
protected void hideRois() {
if (currentImage == null) return;
currentImage.killRoi();
if (currentImage.isVisible()) {
currentImage.updateAndDraw();
ImageUtils.removeScrollListener(currentImage, this, this);
}
currentImage = null;
}
protected void updateRoi() {
// System.out.println("image:"+currentImage.getTitle()+ " slice:"+currentImage.getSlice());
Roi r = currentROIs.get(currentImage.getSlice());
if (r != null) {
currentImage.setRoi(r);
} else {
currentImage.killRoi();
}
currentImage.updateAndDraw();
}
public void run() {
while (!done) {
synchronized (this) {
try {
wait();
} catch (InterruptedException e) {
}
reset(imp, ip); // GL
apply(imp, ip); // GL
imp.updateAndDraw(); // GL
}
}
}
public void actionPerformed(ActionEvent e) {
Button b = (Button) e.getSource();
if (b == null) return;
boolean imageThere = checkImage();
if (imageThere) {
if (b == originalB) {
reset(imp, ip);
filteredB.setEnabled(true);
} else if (b == filteredB) {
apply(imp, ip);
} else if (b == sampleB) {
reset(imp, ip);
sample();
apply(imp, ip);
} else if (b == stackB) {
applyStack();
} else if (b == helpB) {
IJ.showMessage(
"Help",
"Threshold Colour v1.0\n \n"
+ "Modification of Bob Dougherty's BandPass2 plugin by G.Landini to\n"
+ "threshold 24 bit RGB images based on Hue, Saturation and Brightness\n"
+ "or Red, Green and Blue components.\n \n"
+ "Pass: Band-pass filter (anything within range is displayed).\n \n"
+ "Stop: Band-reject filter (anything within range is NOT displayed).\n \n"
+ "Original: Shows the original image and updates the buffer when\n"
+ " switching to another image.\n \n"
+ "Filtered: Shows the filtered image.\n \n"
+ "Stack: Processes the rest of the slices in the stack (if any)\n"
+ " using the current settings.\n \n"
+ "Threshold: Shows the object/background in the foreground and\n"
+ " background colours selected in the ImageJ toolbar.\n \n"
+ "Invert: Swaps the fore/background colours.\n \n"
+ "Sample: (experimental) Sets the ranges of the filters based on the\n"
+ " pixel value componentd in a rectangular, user-defined, ROI.\n \n"
+ "HSB RGB: Selects HSB or RGB space and resets all the filters.\n \n"
+ "Note that the \'thresholded\' image is RGB, not 8 bit grey.");
}
updatePlot();
updateLabels();
imp.updateAndDraw();
} else {
IJ.beep();
IJ.showStatus("No Image");
}
notify();
}
void setStackDisplayRange(ImagePlus imp) {
ImageStack stack = imp.getStack();
double min = Double.MAX_VALUE;
double max = -Double.MAX_VALUE;
int n = stack.getSize();
for (int i = 1; i <= n; i++) {
if (!silentMode) IJ.showStatus("Calculating stack min and max: " + i + "/" + n);
ImageProcessor ip = stack.getProcessor(i);
ip.resetMinAndMax();
if (ip.getMin() < min) min = ip.getMin();
if (ip.getMax() > max) max = ip.getMax();
}
imp.getProcessor().setMinAndMax(min, max);
imp.updateAndDraw();
}
protected void registerActiveImage() {
ImagePlus activeImage = WindowManager.getCurrentImage();
if (activeImage != null
&& activeImage.getProcessor() != null) { // && activeImage.getImageStackSize() > 1
if (currentImage != null && currentImage.getWindow() != null && currentImage != activeImage) {
// System.out.println("remove listener:"+currentImage.getTitle());
ImageUtils.removeScrollListener(currentImage, this, this);
currentImage.killRoi();
currentImage.updateAndDraw();
currentImage = null;
}
if (currentImage != activeImage) {
// System.out.println("add listener:"+activeImage.getTitle());
ImageUtils.addScrollListener(activeImage, this, this);
this.currentImage = activeImage;
}
}
}
public void mergeSelectedObjects() {
this.populatingObjects = true;
HashMap<Integer, ArrayList<Object3DGui>> allObjects = getSplitSelection();
for (int channelIdx : allObjects.keySet()) {
ArrayList<Object3DGui> objects = allObjects.get(channelIdx);
if (objects != null && objects.size() >= 2) {
Collections.sort(objects);
Object3DGui o1 = objects.get(0);
for (int i = objects.size() - 1; i > 0; i--) {
Object3DGui o2 = objects.get(i);
o1.merge(o2);
listModel.removeElement(o2);
// IJ.log("merge:"+o1.getName()+ "::"+objects.get(i).getName()+ " channel:"+channelIdx);
}
o1.getChannel().createObjects();
if (autoSave) o1.getChannel().saveOutput();
ImagePlus img = o1.getChannel().getSegmented().getImagePlus();
if (img.isVisible()) {
img.updateAndDraw();
}
}
}
this.populatingObjects = false;
}
public void deleteSelectedObjects() {
populatingObjects = true;
try {
boolean[] modif = new boolean[currentChannels.length];
for (Object o : this.list.getSelectedValues()) {
listModel.removeElement(o);
modif[getChannelRank(((Object3DGui) o).getChannel())] = true;
((Object3DGui) o).delete(true);
}
for (int i = 0; i < currentChannels.length; i++) {
if (modif[i]) {
ImagePlus img = currentChannels[i].getSegmented().getImagePlus();
if (img.isVisible()) {
img.updateAndDraw();
}
currentChannels[i].createObjects();
if (autoSave) currentChannels[i].saveOutput();
}
}
} catch (Exception e) {
exceptionPrinter.print(e, "", Core.GUIMode);
}
populatingObjects = false;
}
ImageProcessor setup(ImagePlus imp) {
ImageProcessor ip;
int type = imp.getType();
if (type != ImagePlus.COLOR_RGB) return null;
ip = imp.getProcessor();
int id = imp.getID();
int slice = imp.getCurrentSlice();
if ((id != previousImageID) | (slice != previousSlice) | (flag)) {
flag = false; // if true, flags a change from HSB to RGB or viceversa
numSlices = imp.getStackSize();
stack = imp.getStack();
width = stack.getWidth();
height = stack.getHeight();
numPixels = width * height;
hSource = new byte[numPixels];
sSource = new byte[numPixels];
bSource = new byte[numPixels];
// restore = (int[])ip.getPixelsCopy(); //This runs into trouble sometimes, so do it the
// long way:
int[] temp = (int[]) ip.getPixels();
restore = new int[numPixels];
for (int i = 0; i < numPixels; i++) restore[i] = temp[i];
fillMask = new int[numPixels];
// Get hsb or rgb from image.
ColorProcessor cp = (ColorProcessor) ip;
IJ.showStatus("Gathering data");
if (isRGB) cp.getRGB(hSource, sSource, bSource);
else cp.getHSB(hSource, sSource, bSource);
IJ.showStatus("done");
// Create a spectrum ColorModel for the Hue histogram plot.
Color c;
byte[] reds = new byte[256];
byte[] greens = new byte[256];
byte[] blues = new byte[256];
for (int i = 0; i < 256; i++) {
c = Color.getHSBColor(i / 255f, 1f, 1f);
reds[i] = (byte) c.getRed();
greens[i] = (byte) c.getGreen();
blues[i] = (byte) c.getBlue();
}
ColorModel cm = new IndexColorModel(8, 256, reds, greens, blues);
// Make an image with just the hue from the RGB image and the spectrum LUT.
// This is just for a hue histogram for the plot. Do not show it.
// ByteProcessor bpHue = new ByteProcessor(width,height,h,cm);
ByteProcessor bpHue = new ByteProcessor(width, height, hSource, cm);
ImagePlus impHue = new ImagePlus("Hue", bpHue);
// impHue.show();
ByteProcessor bpSat = new ByteProcessor(width, height, sSource, cm);
ImagePlus impSat = new ImagePlus("Sat", bpSat);
// impSat.show();
ByteProcessor bpBri = new ByteProcessor(width, height, bSource, cm);
ImagePlus impBri = new ImagePlus("Bri", bpBri);
// impBri.show();
plot.setHistogram(impHue, 0);
splot.setHistogram(impSat, 1);
bplot.setHistogram(impBri, 2);
updateLabels();
updatePlot();
updateScrollBars();
imp.updateAndDraw();
}
previousImageID = id;
previousSlice = slice;
return ip;
}
