private void doRGBProjection(ImageStack stack) {
ImageStack[] channels = ChannelSplitter.splitRGB(stack, true);
ImagePlus red = new ImagePlus("Red", channels[0]);
ImagePlus green = new ImagePlus("Green", channels[1]);
ImagePlus blue = new ImagePlus("Blue", channels[2]);
imp.unlock();
ImagePlus saveImp = imp;
imp = red;
color = "(red)";
doProjection();
ImagePlus red2 = projImage;
imp = green;
color = "(green)";
doProjection();
ImagePlus green2 = projImage;
imp = blue;
color = "(blue)";
doProjection();
ImagePlus blue2 = projImage;
int w = red2.getWidth(), h = red2.getHeight(), d = red2.getStackSize();
if (method == SD_METHOD) {
ImageProcessor r = red2.getProcessor();
ImageProcessor g = green2.getProcessor();
ImageProcessor b = blue2.getProcessor();
double max = 0;
double rmax = r.getStatistics().max;
if (rmax > max) max = rmax;
double gmax = g.getStatistics().max;
if (gmax > max) max = gmax;
double bmax = b.getStatistics().max;
if (bmax > max) max = bmax;
double scale = 255 / max;
r.multiply(scale);
g.multiply(scale);
b.multiply(scale);
red2.setProcessor(r.convertToByte(false));
green2.setProcessor(g.convertToByte(false));
blue2.setProcessor(b.convertToByte(false));
}
RGBStackMerge merge = new RGBStackMerge();
ImageStack stack2 =
merge.mergeStacks(w, h, d, red2.getStack(), green2.getStack(), blue2.getStack(), true);
imp = saveImp;
projImage = new ImagePlus(makeTitle(), stack2);
}
public BandAdjuster() {
super("Threshold Colour");
if (instance != null) {
instance.toFront();
return;
}
imp = WindowManager.getCurrentImage();
if (imp == null) {
IJ.beep();
IJ.showStatus("No image");
return;
}
IJ.run("Select None");
thread = new Thread(this, "BandAdjuster");
WindowManager.addWindow(this);
instance = this;
IJ.register(PasteController.class);
ij = IJ.getInstance();
Font font = new Font("SansSerif", Font.PLAIN, 10);
GridBagLayout gridbag = new GridBagLayout();
GridBagConstraints c = new GridBagConstraints();
setLayout(gridbag);
int y = 0;
c.gridx = 0;
c.gridy = y;
c.gridwidth = 1;
c.weightx = 0;
c.insets = new Insets(5, 0, 0, 0);
labelh = new Label("Hue", Label.CENTER);
add(labelh, c);
c.gridx = 1;
c.gridy = y++;
c.gridwidth = 1;
c.weightx = 0;
c.insets = new Insets(7, 0, 0, 0);
labelf = new Label("Filter type", Label.RIGHT);
add(labelf, c);
// plot
c.gridx = 0;
c.gridy = y;
c.gridwidth = 1;
c.fill = c.BOTH;
c.anchor = c.CENTER;
c.insets = new Insets(0, 5, 0, 0);
add(plot, c);
// checkboxes
panelh = new Panel();
filterTypeH = new CheckboxGroup();
bandPassH = new Checkbox("Pass");
bandPassH.setCheckboxGroup(filterTypeH);
bandPassH.addItemListener(this);
panelh.add(bandPassH);
bandStopH = new Checkbox("Stop");
bandStopH.setCheckboxGroup(filterTypeH);
bandStopH.addItemListener(this);
panelh.add(bandStopH);
bandPassH.setState(true);
c.gridx = 1;
c.gridy = y++;
c.gridwidth = 2;
c.insets = new Insets(5, 0, 0, 0);
add(panelh, c);
// minHue slider
minSlider = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
c.gridx = 0;
c.gridy = y++;
c.gridwidth = 1;
c.weightx = IJ.isMacintosh() ? 90 : 100;
c.fill = c.HORIZONTAL;
c.insets = new Insets(5, 5, 0, 0);
add(minSlider, c);
minSlider.addAdjustmentListener(this);
minSlider.setUnitIncrement(1);
// minHue slider label
c.gridx = 1;
c.gridwidth = 1;
c.weightx = IJ.isMacintosh() ? 10 : 0;
c.insets = new Insets(5, 0, 0, 0);
label1 = new Label(" ", Label.LEFT);
label1.setFont(font);
add(label1, c);
// maxHue sliderHue
maxSlider = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
c.gridx = 0;
c.gridy = y;
c.gridwidth = 1;
c.weightx = 100;
c.insets = new Insets(5, 5, 0, 0);
add(maxSlider, c);
maxSlider.addAdjustmentListener(this);
maxSlider.setUnitIncrement(1);
// maxHue slider label
c.gridx = 1;
c.gridwidth = 1;
c.gridy = y++;
c.weightx = 0;
c.insets = new Insets(5, 0, 0, 0);
label2 = new Label(" ", Label.LEFT);
label2.setFont(font);
add(label2, c);
// =====
c.gridx = 0;
c.gridy = y++;
c.gridwidth = 1;
c.weightx = 0;
c.insets = new Insets(10, 0, 0, 0);
labels = new Label("Saturation", Label.CENTER);
add(labels, c);
// plot
c.gridx = 0;
c.gridy = y;
c.gridwidth = 1;
c.fill = c.BOTH;
c.anchor = c.CENTER;
c.insets = new Insets(0, 5, 0, 0);
add(splot, c);
// checkboxes
panels = new Panel();
filterTypeS = new CheckboxGroup();
bandPassS = new Checkbox("Pass");
bandPassS.setCheckboxGroup(filterTypeS);
bandPassS.addItemListener(this);
panels.add(bandPassS);
bandStopS = new Checkbox("Stop");
bandStopS.setCheckboxGroup(filterTypeS);
bandStopS.addItemListener(this);
panels.add(bandStopS);
bandPassS.setState(true);
c.gridx = 1;
c.gridy = y++;
c.gridwidth = 2;
c.insets = new Insets(5, 0, 0, 0);
add(panels, c);
// minSat slider
minSlider2 = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
c.gridx = 0;
c.gridy = y++;
c.gridwidth = 1;
c.weightx = IJ.isMacintosh() ? 90 : 100;
c.fill = c.HORIZONTAL;
c.insets = new Insets(5, 5, 0, 0);
add(minSlider2, c);
minSlider2.addAdjustmentListener(this);
minSlider2.setUnitIncrement(1);
// minSat slider label
c.gridx = 1;
c.gridwidth = 1;
c.weightx = IJ.isMacintosh() ? 10 : 0;
c.insets = new Insets(5, 0, 0, 0);
label3 = new Label(" ", Label.LEFT);
label3.setFont(font);
add(label3, c);
// maxSat slider
maxSlider2 = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
c.gridx = 0;
c.gridy = y++;
c.gridwidth = 1;
c.weightx = 100;
c.insets = new Insets(5, 5, 0, 0);
add(maxSlider2, c);
maxSlider2.addAdjustmentListener(this);
maxSlider2.setUnitIncrement(1);
// maxSat slider label
c.gridx = 1;
c.gridwidth = 1;
c.weightx = 0;
c.insets = new Insets(5, 0, 0, 0);
label4 = new Label(" ", Label.LEFT);
label4.setFont(font);
add(label4, c);
// =====
c.gridx = 0;
c.gridwidth = 1;
c.gridy = y++;
c.weightx = 0;
c.insets = new Insets(10, 0, 0, 0);
labelb = new Label("Brightness", Label.CENTER);
add(labelb, c);
c.gridx = 0;
c.gridwidth = 1;
c.gridy = y;
c.fill = c.BOTH;
c.anchor = c.CENTER;
c.insets = new Insets(0, 5, 0, 0);
add(bplot, c);
// checkboxes
panelb = new Panel();
filterTypeB = new CheckboxGroup();
bandPassB = new Checkbox("Pass");
bandPassB.setCheckboxGroup(filterTypeB);
bandPassB.addItemListener(this);
panelb.add(bandPassB);
bandStopB = new Checkbox("Stop");
bandStopB.setCheckboxGroup(filterTypeB);
bandStopB.addItemListener(this);
panelb.add(bandStopB);
bandPassB.setState(true);
c.gridx = 1;
c.gridy = y++;
c.gridwidth = 2;
c.insets = new Insets(5, 0, 0, 0);
add(panelb, c);
// minBri slider
minSlider3 = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
c.gridx = 0;
c.gridy = y++;
c.gridwidth = 1;
c.weightx = IJ.isMacintosh() ? 90 : 100;
c.fill = c.HORIZONTAL;
c.insets = new Insets(5, 5, 0, 0);
add(minSlider3, c);
minSlider3.addAdjustmentListener(this);
minSlider3.setUnitIncrement(1);
// minBri slider label
c.gridx = 1;
c.gridwidth = 1;
c.weightx = IJ.isMacintosh() ? 10 : 0;
c.insets = new Insets(5, 0, 0, 0);
label5 = new Label(" ", Label.LEFT);
label5.setFont(font);
add(label5, c);
// maxBri slider
maxSlider3 = new Scrollbar(Scrollbar.HORIZONTAL, 0, 1, 0, sliderRange);
c.gridx = 0;
c.gridy = y++;
c.gridwidth = 1;
c.weightx = 100;
c.insets = new Insets(5, 5, 0, 0);
add(maxSlider3, c);
maxSlider3.addAdjustmentListener(this);
maxSlider3.setUnitIncrement(1);
// maxBri slider label
c.gridx = 1;
c.gridwidth = 1;
c.weightx = 0;
c.insets = new Insets(5, 0, 0, 0);
label6 = new Label(" ", Label.LEFT);
label6.setFont(font);
add(label6, c);
// =====
panelt = new Panel();
threshold = new Checkbox("Threshold");
threshold.addItemListener(this);
panelt.add(threshold);
invert = new Checkbox("Invert");
invert.addItemListener(this);
panelt.add(invert);
c.gridx = 0;
c.gridy = y++;
c.gridwidth = 2;
c.insets = new Insets(0, 0, 0, 0);
add(panelt, c);
// buttons
panel = new Panel();
// panel.setLayout(new GridLayout(2, 2, 0, 0));
originalB = new Button("Original");
originalB.setEnabled(false);
originalB.addActionListener(this);
originalB.addKeyListener(ij);
panel.add(originalB);
filteredB = new Button("Filtered");
filteredB.setEnabled(false);
filteredB.addActionListener(this);
filteredB.addKeyListener(ij);
panel.add(filteredB);
stackB = new Button("Stack");
stackB.addActionListener(this);
stackB.addKeyListener(ij);
panel.add(stackB);
helpB = new Button("Help");
helpB.addActionListener(this);
helpB.addKeyListener(ij);
panel.add(helpB);
c.gridx = 0;
c.gridy = y++;
c.gridwidth = 2;
c.insets = new Insets(0, 0, 0, 0);
add(panel, c);
panelMode = new Panel();
sampleB = new Button("Sample");
sampleB.addActionListener(this);
sampleB.addKeyListener(ij);
panelMode.add(sampleB);
colourMode = new CheckboxGroup();
hsb = new Checkbox("HSB");
hsb.setCheckboxGroup(colourMode);
hsb.addItemListener(this);
panelMode.add(hsb);
hsb.setState(true);
rgb = new Checkbox("RGB");
rgb.setCheckboxGroup(colourMode);
rgb.addItemListener(this);
panelMode.add(rgb);
c.gridx = 0;
c.gridy = y++;
c.gridwidth = 2;
c.insets = new Insets(0, 0, 0, 0);
add(panelMode, c);
addKeyListener(ij); // ImageJ handles keyboard shortcuts
pack();
GUI.center(this);
setVisible(true);
ip = setup(imp);
if (ip == null) {
imp.unlock();
IJ.beep();
IJ.showStatus("RGB image cannot be thresholded");
return;
}
thread.start();
}
public void run(String arg) {
imp = IJ.getImage();
int stackSize = imp.getStackSize();
if (imp == null) {
IJ.noImage();
return;
}
// Make sure input image is a stack.
if (stackSize == 1) {
IJ.error("Z Project", "Stack required");
return;
}
// Check for inverting LUT.
if (imp.getProcessor().isInvertedLut()) {
if (!IJ.showMessageWithCancel("ZProjection", lutMessage)) return;
}
// Set default bounds.
int channels = imp.getNChannels();
int frames = imp.getNFrames();
int slices = imp.getNSlices();
isHyperstack =
imp.isHyperStack()
|| (ij.macro.Interpreter.isBatchMode()
&& ((frames > 1 && frames < stackSize) || (slices > 1 && slices < stackSize)));
boolean simpleComposite = channels == stackSize;
if (simpleComposite) isHyperstack = false;
startSlice = 1;
if (isHyperstack) {
int nSlices = imp.getNSlices();
if (nSlices > 1) stopSlice = nSlices;
else stopSlice = imp.getNFrames();
} else stopSlice = stackSize;
// Build control dialog
GenericDialog gd = buildControlDialog(startSlice, stopSlice);
gd.showDialog();
if (gd.wasCanceled()) return;
if (!imp.lock()) return; // exit if in use
long tstart = System.currentTimeMillis();
setStartSlice((int) gd.getNextNumber());
setStopSlice((int) gd.getNextNumber());
method = gd.getNextChoiceIndex();
Prefs.set(METHOD_KEY, method);
if (isHyperstack) {
allTimeFrames = imp.getNFrames() > 1 && imp.getNSlices() > 1 ? gd.getNextBoolean() : false;
doHyperStackProjection(allTimeFrames);
} else if (imp.getType() == ImagePlus.COLOR_RGB) doRGBProjection(true);
else doProjection(true);
if (arg.equals("") && projImage != null) {
long tstop = System.currentTimeMillis();
projImage.setCalibration(imp.getCalibration());
if (simpleComposite) IJ.run(projImage, "Grays", "");
projImage.show("ZProjector: " + IJ.d2s((tstop - tstart) / 1000.0, 2) + " seconds");
}
imp.unlock();
IJ.register(ZProjector.class);
return;
}
