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package ij.plugin;
import ij.*;
import ij.gui.*;
import ij.process.*;
import ij.measure.Calibration;
import ij.macro.Interpreter;
import ij.io.FileInfo;
import java.awt.image.ColorModel;
/** Implements the "Stack to HyperStack", "RGB to HyperStack"
and "HyperStack to Stack" commands. */
public class HyperStackConverter implements PlugIn {
static final int C=0, Z=1, T=2;
static final int CZT=0, CTZ=1, ZCT=2, ZTC=3, TCZ=4, TZC=5;
static final String[] orders = {"xyczt(default)", "xyctz", "xyzct", "xyztc", "xytcz", "xytzc"};
static int order = CZT;
static boolean splitRGB = true;
public void run(String arg) {
if (arg.equals("new"))
{newHyperStack(); return;}
ImagePlus imp = IJ.getImage();
if (arg.equals("stacktohs"))
convertStackToHS(imp);
else if (arg.equals("hstostack"))
convertHSToStack(imp);
}
/** Displays the current stack in a HyperStack window. Based on the
Stack_to_Image5D class in Joachim Walter's Image5D plugin. */
void convertStackToHS(ImagePlus imp) {
int nChannels = imp.getNChannels();
int nSlices = imp.getNSlices();
int nFrames = imp.getNFrames();
int stackSize = imp.getImageStackSize();
if (stackSize==1) {
IJ.error("Stack to HyperStack", "Stack required");
return;
}
boolean rgb = imp.getBitDepth()==24;
String[] modes = {"Composite", "Color", "Grayscale"};
GenericDialog gd = new GenericDialog("Convert to HyperStack");
gd.addChoice("Order:", orders, orders[order]);
gd.addNumericField("Channels (c):", nChannels, 0);
gd.addNumericField("Slices (z):", nSlices, 0);
gd.addNumericField("Frames (t):", nFrames, 0);
gd.addChoice("Display Mode:", modes, modes[1]);
if (rgb) {
gd.setInsets(15, 0, 0);
gd.addCheckbox("Convert RGB to 3 Channel Hyperstack", splitRGB);
}
gd.showDialog();
if (gd.wasCanceled()) return;
order = gd.getNextChoiceIndex();
nChannels = (int) gd.getNextNumber();
nSlices = (int) gd.getNextNumber();
nFrames = (int) gd.getNextNumber();
int mode = gd.getNextChoiceIndex();
if (rgb)
splitRGB = gd.getNextBoolean();
if (rgb && splitRGB==true) {
new CompositeConverter().run(mode==0?"composite":"color");
return;
}
if (rgb && nChannels>1) {
IJ.error("HyperStack Converter", "RGB stacks are limited to one channel");
return;
}
if (nChannels*nSlices*nFrames!=stackSize) {
IJ.error("HyperStack Converter", "channels x slices x frames <> stack size");
return;
}
imp.setDimensions(nChannels, nSlices, nFrames);
if (order!=CZT && imp.getStack().isVirtual())
IJ.error("HyperStack Converter", "Virtual stacks must by in XYCZT order.");
else {
shuffle(imp, order);
ImagePlus imp2 = imp;
if (nChannels>1 && imp.getBitDepth()!=24) {
LUT[] luts = imp.getLuts();
if (luts!=null && luts.length<nChannels) luts = null;
imp2 = new CompositeImage(imp, mode+1);
if (luts!=null)
((CompositeImage)imp2).setLuts(luts);
} else if (imp.getClass().getName().indexOf("Image5D")!=-1) {
imp2 = imp.createImagePlus();
imp2.setStack(imp.getTitle(), imp.getImageStack());
imp2.setDimensions(imp.getNChannels(), imp.getNSlices(), imp.getNFrames());
imp2.getProcessor().resetMinAndMax();
}
imp2.setOpenAsHyperStack(true);
new StackWindow(imp2);
if (imp!=imp2) {
imp2.setOverlay(imp.getOverlay());
imp.hide();
WindowManager.setCurrentWindow(imp2.getWindow());
}
}
}
/** Changes the dimension order of a 4D or 5D stack from
the specified order (CTZ, ZCT, ZTC, TCZ or TZC) to
the XYCZT order used by ImageJ. */
public void shuffle(ImagePlus imp, int order) {
int nChannels = imp.getNChannels();
int nSlices = imp.getNSlices();
int nFrames = imp.getNFrames();
int first=C, middle=Z, last=T;
int nFirst=nChannels, nMiddle=nSlices, nLast=nFrames;
switch (order) {
case CTZ: first=C; middle=T; last=Z;
nFirst=nChannels; nMiddle=nFrames; nLast=nSlices;
break;
case ZCT: first=Z; middle=C; last=T;
nFirst=nSlices; nMiddle=nChannels; nLast=nFrames;
break;
case ZTC: first=Z; middle=T; last=C;
nFirst=nSlices; nMiddle=nFrames; nLast=nChannels;
break;
case TCZ: first=T; middle=C; last=Z;
nFirst=nFrames; nMiddle=nChannels; nLast=nSlices;
break;
case TZC: first=T; middle=Z; last=C;
nFirst=nFrames; nMiddle=nSlices; nLast=nChannels;
break;
}
if (order!=CZT) {
ImageStack stack = imp.getImageStack();
Object[] images1 = stack.getImageArray();
Object[] images2 = new Object[images1.length];
System.arraycopy(images1, 0, images2, 0, images1.length);
String[] labels1 = stack.getSliceLabels();
String[] labels2 = new String[labels1.length];
System.arraycopy(labels1, 0, labels2, 0, labels1.length);
int[] index = new int[3];
for (index[2]=0; index[2]<nFrames; ++index[2]) {
for (index[1]=0; index[1]<nSlices; ++index[1]) {
for (index[0]=0; index[0]<nChannels; ++index[0]) {
int dstIndex = index[0] + index[1]*nChannels + index[2]*nChannels*nSlices;
int srcIndex = index[first] + index[middle]*nFirst + index[last]*nFirst*nMiddle;
images1[dstIndex] = images2[srcIndex];
labels1[dstIndex] = labels2[srcIndex];
}
}
}
}
}
void convertHSToStack(ImagePlus imp) {
if (!imp.isHyperStack()) return;
ImagePlus imp2 = imp;
if (imp.isComposite()) {
ImageStack stack = imp.getStack();
imp2 = imp.createImagePlus();
imp2.setStack(imp.getTitle(), stack);
int[] dim = imp.getDimensions();
imp2.setDimensions(dim[2], dim[3], dim[4]);
ImageProcessor ip2 = imp2.getProcessor();
ip2.setColorModel(ip2.getDefaultColorModel());
}
imp2.setOpenAsHyperStack(false);
new StackWindow(imp2);
if (imp!=imp2) {
imp2.setOverlay(imp.getOverlay());
imp.hide();
}
}
void newHyperStack() {
IJ.runMacroFile("ij.jar:HyperStackMaker", "");
}
}
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