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package ij.plugin;
import ij.*;
import ij.process.*;
import ij.gui.*;
import ij.measure.Calibration;
import ij.plugin.HyperStackReducer;
import java.awt.*;
import java.util.Vector;
/** This plugin implements the Image/Color/Split Channels command. */
public class ChannelSplitter implements PlugIn {
public void run(String arg) {
ImagePlus imp = IJ.getImage();
if (imp.isComposite()) {
int z = imp.getSlice();
int t = imp.getFrame();
ImagePlus[] channels = split(imp);
imp.changes = false;
imp.setIgnoreFlush(true);
imp.close();
for (int i=0; i<channels.length; i++) {
channels[i].setIJMenuBar(i==channels.length-1);
channels[i].show();
if (z>1 || t>1)
channels[i].setPosition(1, z, t);
}
} else if (imp.getType()==ImagePlus.COLOR_RGB)
splitRGB(imp);
else
IJ.error("Split Channels", "Multichannel image required");
}
private void splitRGB(ImagePlus imp) {
boolean keepSource = IJ.altKeyDown();
String title = imp.getTitle();
Calibration cal = imp.getCalibration();
int pos = imp.getCurrentSlice();
ImageStack[] channels = splitRGB(imp.getStack(), keepSource);
if (!keepSource)
{imp.unlock(); imp.changes=false; imp.close();}
ImagePlus rImp = new ImagePlus(title+" (red)", channels[0]);
rImp.setCalibration(cal);
rImp.setIJMenuBar(false);
rImp.show();
rImp.setSlice(pos);
if (IJ.isMacOSX()) IJ.wait(500);
ImagePlus gImp = new ImagePlus(title+" (green)", channels[1]);
gImp.setCalibration(cal);
gImp.setIJMenuBar(false);
gImp.show();
gImp.setSlice(pos);
if (IJ.isMacOSX()) IJ.wait(500);
ImagePlus bImp = new ImagePlus(title+" (blue)", channels[2]);
bImp.setCalibration(cal);
bImp.show();
bImp.setSlice(pos);
}
/** Splits the specified image into separate channels. */
public static ImagePlus[] split(ImagePlus imp) {
if (imp.getType()==ImagePlus.COLOR_RGB) {
ImageStack[] stacks = splitRGB(imp.getStack(), true);
ImagePlus[] images = new ImagePlus[3];
images[0] = new ImagePlus("red", stacks[0]);
images[1] = new ImagePlus("green", stacks[1]);
images[2] = new ImagePlus("blue", stacks[2]);
return images;
}
int width = imp.getWidth();
int height = imp.getHeight();
int channels = imp.getNChannels();
int slices = imp.getNSlices();
int frames = imp.getNFrames();
int bitDepth = imp.getBitDepth();
int size = slices*frames;
Vector images = new Vector();
HyperStackReducer reducer = new HyperStackReducer(imp);
for (int c=1; c<=channels; c++) {
ImageStack stack2 = new ImageStack(width, height, size); // create empty stack
stack2.setPixels(imp.getProcessor().getPixels(), 1); // can't create ImagePlus will null 1st image
ImagePlus imp2 = new ImagePlus("C"+c+"-"+imp.getTitle(), stack2);
stack2.setPixels(null, 1);
imp.setPosition(c, 1, 1);
imp2.setDimensions(1, slices, frames);
imp2.setCalibration(imp.getCalibration());
reducer.reduce(imp2);
if (imp.isComposite() && ((CompositeImage)imp).getMode()==IJ.GRAYSCALE)
IJ.run(imp2, "Grays", "");
if (imp2.getNDimensions()>3)
imp2.setOpenAsHyperStack(true);
images.add(imp2);
}
ImagePlus[] array = new ImagePlus[images.size()];
return (ImagePlus[])images.toArray(array);
}
/** Returns, as an ImageStack, the specified channel, where 'c' must be greater
than zero and less than or equal to the number of channels in the image. */
public static ImageStack getChannel(ImagePlus imp, int c) {
if (imp.getBitDepth()==24) { // RGB?
if (c<1 || c>3)
throw new IllegalArgumentException("Channel must be 1,2 or 3");
ImageStack[] channels = splitRGB(imp.getStack(), true);
return channels[c-1];
}
if (c<1 || c>imp.getNChannels())
throw new IllegalArgumentException("Channel less than 1 or greater than "+imp.getNChannels());
ImageStack stack1 = imp.getStack();
ImageStack stack2 = new ImageStack(imp.getWidth(), imp.getHeight());
for (int t=1; t<=imp.getNFrames(); t++) {
for (int z=1; z<=imp.getNSlices(); z++) {
int n = imp.getStackIndex(c, z, t);
stack2.addSlice(stack1.getProcessor(n));
}
}
return stack2;
}
/** Splits the specified RGB stack into three 8-bit grayscale stacks.
Deletes the source stack if keepSource is false. */
public static ImageStack[] splitRGB(ImageStack rgb, boolean keepSource) {
int w = rgb.getWidth();
int h = rgb.getHeight();
ImageStack[] channels = new ImageStack[3];
for (int i=0; i<3; i++)
channels[i] = new ImageStack(w,h);
byte[] r,g,b;
ColorProcessor cp;
int slice = 1;
int inc = keepSource?1:0;
int n = rgb.getSize();
for (int i=1; i<=n; i++) {
IJ.showStatus(i+"/"+n);
r = new byte[w*h];
g = new byte[w*h];
b = new byte[w*h];
cp = (ColorProcessor)rgb.getProcessor(slice);
slice += inc;
cp.getRGB(r,g,b);
if (!keepSource)
rgb.deleteSlice(1);
channels[0].addSlice(null,r);
channels[1].addSlice(null,g);
channels[2].addSlice(null,b);
IJ.showProgress((double)i/n);
}
return channels;
}
}
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