package ij.plugin;
import ij.*;
import ij.process.*;
import ij.gui.*;
import java.awt.*;
import java.awt.image.*;
public class RGBStackMerge implements PlugIn {
private static boolean staticCreateComposite = true;
private static boolean staticKeep;
private static boolean staticIgnoreLuts;
private ImagePlus imp;
private byte[] blank;
private boolean ignoreLuts;
public void run(String arg) {
imp = WindowManager.getCurrentImage();
mergeStacks();
}
public static ImagePlus mergeChannels(ImagePlus[] images, boolean keepSourceImages) {
RGBStackMerge rgbsm = new RGBStackMerge();
return rgbsm.mergeHyperstacks(images, keepSourceImages);
}
/** Combines three grayscale stacks into one RGB stack. */
public void mergeStacks() {
int[] wList = WindowManager.getIDList();
if (wList==null) {
error("No images are open.");
return;
}
String[] titles = new String[wList.length+1];
for (int i=0; i<wList.length; i++) {
ImagePlus imp = WindowManager.getImage(wList[i]);
titles[i] = imp!=null?imp.getTitle():"";
}
String none = "*None*";
titles[wList.length] = none;
boolean createComposite = staticCreateComposite;
boolean keep = staticKeep;
ignoreLuts = staticIgnoreLuts;
if (IJ.isMacro())
createComposite = keep = ignoreLuts = false;
GenericDialog gd = new GenericDialog("Color Merge");
gd.addChoice("Red:", titles, titles[0]);
gd.addChoice("Green:", titles, titles[1]);
String title3 = titles.length>2&&!IJ.macroRunning()?titles[2]:none;
gd.addChoice("Blue:", titles, title3);
String title4 = titles.length>3&&!IJ.macroRunning()?titles[3]:none;
gd.addChoice("Gray:", titles, title4);
gd.addCheckbox("Create composite", createComposite);
gd.addCheckbox("Keep source images", keep);
gd.addCheckbox("Ignore source LUTs", ignoreLuts);
gd.showDialog();
if (gd.wasCanceled())
return;
int[] index = new int[4];
index[0] = gd.getNextChoiceIndex();
index[1] = gd.getNextChoiceIndex();
index[2] = gd.getNextChoiceIndex();
index[3] = gd.getNextChoiceIndex();
createComposite = gd.getNextBoolean();
keep = gd.getNextBoolean();
ignoreLuts = gd.getNextBoolean();
if (!IJ.isMacro()) {
staticCreateComposite = createComposite;
staticKeep = keep;
staticIgnoreLuts = ignoreLuts;
}
ImagePlus[] images = new ImagePlus[4];
int stackSize = 0;
int width = 0;
int height = 0;
int bitDepth = 0;
int slices = 0;
int frames = 0;
for (int i=0; i<4; i++) {
//IJ.log(i+" "+index[i]+" "+titles[index[i]]+" "+wList.length);
if (index[i]<wList.length) {
images[i] = WindowManager.getImage(wList[index[i]]);
if (width==0) {
width = images[i].getWidth();
height = images[i].getHeight();
stackSize = images[i].getStackSize();
bitDepth = images[i].getBitDepth();
slices = images[i].getNSlices();
frames = images[i].getNFrames();
}
}
}
if (width==0) {
error("There must be at least one source image or stack.");
return;
}
boolean mergeHyperstacks = false;
for (int i=0; i<4; i++) {
ImagePlus img = images[i];
if (img==null) continue;
if (img.getStackSize()!=stackSize) {
error("The source stacks must have the same number of images.");
return;
}
if (img.isHyperStack()) {
if (img.isComposite()) {
CompositeImage ci = (CompositeImage)img;
if (ci.getMode()!=CompositeImage.COMPOSITE) {
ci.setMode(CompositeImage.COMPOSITE);
img.updateAndDraw();
if (!IJ.isMacro()) IJ.run("Channels Tool...");
return;
}
}
if (bitDepth==24) {
error("Source hyperstacks cannot be RGB.");
return;
}
if (img.getNChannels()>1) {
error("Source hyperstacks cannot have more than 1 channel.");
return;
}
if (img.getNSlices()!=slices || img.getNFrames()!=frames) {
error("Source hyperstacks must have the same dimensions.");
return;
}
mergeHyperstacks = true;
} // isHyperStack
if (img.getWidth()!=width || images[i].getHeight()!=height) {
error("The source images or stacks must have the same width and height.");
return;
}
//if (createComposite) {
// for (int j=0; j<4; j++) {
// if (j!=i && images[j]!=null && img==images[j])
// createComposite = false;
// }
//}
if (createComposite && img.getBitDepth()!=bitDepth) {
error("The source images must have the same bit depth.");
return;
}
}
ImageStack[] stacks = new ImageStack[4];
stacks[0] = images[0]!=null?images[0].getStack():null;
stacks[1] = images[1]!=null?images[1].getStack():null;
stacks[2] = images[2]!=null?images[2].getStack():null;
stacks[3] = images[3]!=null?images[3].getStack():null;
String macroOptions = Macro.getOptions();
if (macroOptions!=null && macroOptions.indexOf("gray=")==-1)
stacks[3] = null; // ensure compatibility with old macros
ImagePlus imp2;
boolean fourChannelRGB = !createComposite && stacks[3]!=null;
if (fourChannelRGB)
createComposite = true;
if (stacks[3]!=null)
createComposite = true;
for (int i=0; i<4; i++) {
if (images[i]!=null && images[i].getBitDepth()==24)
createComposite = false;
}
if (createComposite || mergeHyperstacks) {
imp2 = mergeHyperstacks(images, keep);
if (imp2==null) return;
} else {
ImageStack rgb = mergeStacks(width, height, stackSize, stacks[0], stacks[1], stacks[2], keep);
imp2 = new ImagePlus("RGB", rgb);
}
if (images[0]!=null)
imp2.setCalibration(images[0].getCalibration());
if (!keep) {
for (int i=0; i<4; i++) {
if (images[i]!=null && images[i].getWindow()!=null) {
images[i].changes = false;
images[i].close();
}
}
}
if (fourChannelRGB) {
if (imp2.getStackSize()==1) {
imp2 = imp2.flatten();
imp2.setTitle("RGB");
} else {
imp2.setTitle("RGB");
IJ.run(imp2, "RGB Color", "slices");
}
}
imp2.show();
}
public ImagePlus mergeHyperstacks(ImagePlus[] images, boolean keep) {
int n = images.length;
int channels = 0;
for (int i=0; i<n; i++) {
if (images[i]!=null) channels++;
}
if (channels<2) return null;
ImagePlus[] images2 = new ImagePlus[channels];
Color[] defaultColors = {Color.red, Color.green, Color.blue, Color.white};
Color[] colors = new Color[channels];
int j = 0;
for (int i=0; i<n; i++) {
if (images[i]!=null) {
images2[j] = images[i];
if (i<defaultColors.length)
colors[j] = defaultColors[i];
j++;
}
}
images = images2;
ImageStack[] stacks = new ImageStack[channels];
for (int i=0; i<channels; i++) {
ImagePlus imp2 = images[i];
if (isDuplicate(i,images))
imp2 = imp2.duplicate();
stacks[i] = imp2.getStack();
}
ImagePlus imp = images[0];
int w = imp.getWidth();
int h = imp.getHeight();
int slices = imp.getNSlices();
int frames = imp.getNFrames();
ImageStack stack2 = new ImageStack(w, h);
//IJ.log("mergeHyperstacks: "+w+" "+h+" "+channels+" "+slices+" "+frames);
int[] index = new int[channels];
for (int t=0; t<frames; t++) {
for (int z=0; z<slices; z++) {
for (int c=0; c<channels; c++) {
ImageProcessor ip = stacks[c].getProcessor(index[c]+1);
if (keep)
ip = ip.duplicate();
stack2.addSlice(null, ip);
if (keep)
index[c]++;
else
stacks[c].deleteSlice(1);
}
}
}
String title = imp.getTitle();
if (title.startsWith("C1-"))
title = title.substring(3);
else
title = frames>1?"Merged":"Composite";
ImagePlus imp2 = new ImagePlus(title, stack2);
imp2.setDimensions(channels, slices, frames);
imp2 = new CompositeImage(imp2, CompositeImage.COMPOSITE);
for (int c=0; c<channels; c++) {
ImageProcessor ip = images[c].getProcessor();
IndexColorModel cm = (IndexColorModel)ip.getColorModel();
LUT lut = null;
if (c<colors.length && colors[c]!=null && (ignoreLuts||!ip.isColorLut())) {
lut = LUT.createLutFromColor(colors[c]);
lut.min = ip.getMin();
lut.max = ip.getMax();
} else
lut = new LUT(cm, ip.getMin(), ip.getMax());
((CompositeImage)imp2).setChannelLut(lut, c+1);
}
imp2.setOpenAsHyperStack(true);
return imp2;
}
private boolean isDuplicate(int index, ImagePlus[] images) {
int count = 0;
for (int i=0; i<index; i++) {
if (images[index]==images[i])
return true;
}
return false;
}
/** Deprecated; replaced by mergeChannels(). */
public ImagePlus createComposite(int w, int h, int d, ImageStack[] stacks, boolean keep) {
ImagePlus[] images = new ImagePlus[stacks.length];
for (int i=0; i<stacks.length; i++)
images[i] = new ImagePlus(""+i, stacks[i]);
return mergeHyperstacks(images, keep);
}
public ImageStack mergeStacks(int w, int h, int d, ImageStack red, ImageStack green, ImageStack blue, boolean keep) {
ImageStack rgb = new ImageStack(w, h);
int inc = d/10;
if (inc<1) inc = 1;
ColorProcessor cp;
int slice = 1;
blank = new byte[w*h];
byte[] redPixels, greenPixels, bluePixels;
boolean invertedRed = red!=null?red.getProcessor(1).isInvertedLut():false;
boolean invertedGreen = green!=null?green.getProcessor(1).isInvertedLut():false;
boolean invertedBlue = blue!=null?blue.getProcessor(1).isInvertedLut():false;
try {
for (int i=1; i<=d; i++) {
cp = new ColorProcessor(w, h);
redPixels = getPixels(red, slice, 0);
greenPixels = getPixels(green, slice, 1);
bluePixels = getPixels(blue, slice, 2);
if (invertedRed) redPixels = invert(redPixels);
if (invertedGreen) greenPixels = invert(greenPixels);
if (invertedBlue) bluePixels = invert(bluePixels);
cp.setRGB(redPixels, greenPixels, bluePixels);
if (keep) {
slice++;
} else {
if (red!=null) red.deleteSlice(1);
if (green!=null &&green!=red) green.deleteSlice(1);
if (blue!=null&&blue!=red && blue!=green) blue.deleteSlice(1);
}
rgb.addSlice(null, cp);
if ((i%inc) == 0) IJ.showProgress((double)i/d);
}
IJ.showProgress(1.0);
} catch(OutOfMemoryError o) {
IJ.outOfMemory("Merge Stacks");
IJ.showProgress(1.0);
}
return rgb;
}
byte[] getPixels(ImageStack stack, int slice, int color) {
if (stack==null)
return blank;
Object pixels = stack.getPixels(slice);
if (!(pixels instanceof int[])) {
if (pixels instanceof byte[])
return (byte[])pixels;
else {
ImageProcessor ip = stack.getProcessor(slice);
ip = ip.convertToByte(true);
return (byte[])ip.getPixels();
}
} else { //RGB
byte[] r,g,b;
int size = stack.getWidth()*stack.getHeight();
r = new byte[size];
g = new byte[size];
b = new byte[size];
ColorProcessor cp = (ColorProcessor)stack.getProcessor(slice);
cp.getRGB(r, g, b);
switch (color) {
case 0: return r;
case 1: return g;
case 2: return b;
}
}
return null;
}
byte[] invert(byte[] pixels) {
byte[] pixels2 = new byte[pixels.length];
System.arraycopy(pixels, 0, pixels2, 0, pixels.length);
for (int i=0; i<pixels2.length; i++)
pixels2[i] = (byte)(255-pixels2[i]&255);
return pixels2;
}
void error(String msg) {
IJ.error("Merge Channels", msg);
}
}