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package ij.plugin;
import ij.*;
import ij.process.*;
import ij.gui.*;
/** This plugin, which concatenates two images or stacks, implements the
Image/Stacks/Tools/Concatenate command.
The images or stacks must have same width, height and data type. */
public class Concatenator implements PlugIn {
ImagePlus imp1, imp2;
static boolean keep;
static String title = "Concatenated Stacks";
public void run(String arg) {
if (!showDialog())
return;
ImagePlus imp3 = null;
if (imp1.isComposite() || imp1.isHyperStack()) {
ImagePlus[] images = new ImagePlus[2];
images[0] = imp1;
images[1] = imp2;
imp3 = concatenate(images, keep);
if (imp3==null)
error();
else
imp3.setTitle(title);
} else
imp3 = concatenate(imp1, imp2, keep);
if (imp3!=null) imp3.show();
}
public ImagePlus concatenate(ImagePlus imp1, ImagePlus imp2, boolean keep) {
if (imp1.getType()!=imp2.getType() || imp1.isHyperStack() || imp2.isHyperStack())
{error(); return null;}
int width = imp1.getWidth();
int height = imp1.getHeight();
if (width!=imp2.getWidth() || height!=imp2.getHeight())
{error(); return null;}
ImageStack stack1 = imp1.getStack();
ImageStack stack2 = imp2.getStack();
int size1 = stack1.getSize();
int size2 = stack2.getSize();
ImageStack stack3 = imp1.createEmptyStack();
int slice = 1;
for (int i=1; i<=size1; i++) {
ImageProcessor ip = stack1.getProcessor(slice);
String label = stack1.getSliceLabel(slice);
if (keep || imp1==imp2) {
ip = ip.duplicate();
slice++;
} else
stack1.deleteSlice(slice);
stack3.addSlice(label, ip);
}
slice = 1;
for (int i=1; i<=size2; i++) {
ImageProcessor ip = stack2.getProcessor(slice);
String label = stack2.getSliceLabel(slice);
if (keep || imp1==imp2) {
ip = ip.duplicate();
slice++;
} else
stack2.deleteSlice(slice);
stack3.addSlice(label, ip);
}
ImagePlus imp3 = new ImagePlus(title, stack3);
imp3.setCalibration(imp1.getCalibration());
if (!keep) {
imp1.changes = false;
imp1.close();
if (imp1!=imp2) {
imp2.changes = false;
imp2.close();
}
}
return imp3;
}
public ImagePlus concatenate(ImagePlus[] images, boolean keepSourceImages) {
int n = images.length;
int width = images[0].getWidth();
int height = images[0].getHeight();
int bitDepth = images[0].getBitDepth();
int channels = images[0].getNChannels();
int slices = images[0].getNSlices();
int frames = images[0].getNFrames();
boolean concatSlices = slices>1 && frames==1;
for (int i=1; i<n; i++) {
if (images[i].getNFrames()>1) concatSlices = false;
if (images[i].getWidth()!=width
|| images[i].getHeight()!=height
|| images[i].getBitDepth()!=bitDepth
|| images[i].getNChannels()!=channels
|| (!concatSlices && images[i].getNSlices()!=slices))
return null;
}
ImageStack stack2 = new ImageStack(width, height);
int slices2=0, frames2=0;
for (int i=0;i<n;i++) {
ImageStack stack = images[i].getStack();
slices = images[i].getNSlices();
if (concatSlices) {
slices = images[i].getNSlices();
slices2 += slices;
frames2 = frames;
} else {
frames = images[i].getNFrames();
frames2 += frames;
slices2 = slices;
}
for (int f=1; f<=frames; f++) {
for (int s=1; s<=slices; s++) {
for (int c=1; c<=channels; c++) {
int index = (f-1)*channels*s + (s-1)*channels + c;
ImageProcessor ip = stack.getProcessor(index);
if (keepSourceImages)
ip = ip.duplicate();
String label = stack.getSliceLabel(index);
stack2.addSlice(label, ip);
}
}
}
}
ImagePlus imp2 = new ImagePlus("Concatenated Images", stack2);
imp2.setDimensions(channels, slices2, frames2);
if (channels>1) {
int mode = 0;
if (images[0].isComposite())
mode = ((CompositeImage)images[0]).getMode();
imp2 = new CompositeImage(imp2, mode);
((CompositeImage)imp2).copyLuts(images[0]);
}
if (channels>1 && frames2>1)
imp2.setOpenAsHyperStack(true);
if (!keepSourceImages) {
for (int i=0; i<n; i++) {
images[i].changes = false;
images[i].close();
}
}
return imp2;
}
int getStackIndex(int channel, int slice, int frame, int nChannels, int nSlices, int nFrames) {
return (frame-1)*nChannels*nSlices + (slice-1)*nChannels + channel;
}
boolean showDialog() {
int[] wList = WindowManager.getIDList();
if (wList==null) {
IJ.noImage();
return false;
}
String[] titles = new String[wList.length];
for (int i=0; i<wList.length; i++) {
ImagePlus imp = WindowManager.getImage(wList[i]);
titles[i] = imp!=null?imp.getTitle():"";
}
GenericDialog gd = new GenericDialog("Concatenator");
gd.addChoice("Stack1:", titles, titles[0]);
gd.addChoice("Stack2:", titles, wList.length>1?titles[1]:titles[0]);
gd.addStringField("Title:", title, 16);
gd.addCheckbox("Keep Source Stacks", keep);
gd.showDialog();
if (gd.wasCanceled())
return false;
int[] index = new int[3];
int index1 = gd.getNextChoiceIndex();
int index2 = gd.getNextChoiceIndex();
title = gd.getNextString();
keep = gd.getNextBoolean();
imp1 = WindowManager.getImage(wList[index1]);
imp2 = WindowManager.getImage(wList[index2]);
return true;
}
void error() {
IJ.showMessage("Concatenator", "This command requires two images with\n"+
"the same dimesions and data type.");
}
}
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