public void reduceHyperstack(ImagePlus imp, int factor, boolean reduceSlices) {
int channels = imp.getNChannels();
int slices = imp.getNSlices();
int frames = imp.getNFrames();
int zfactor = reduceSlices ? factor : 1;
int tfactor = reduceSlices ? 1 : factor;
ImageStack stack = imp.getStack();
ImageStack stack2 = new ImageStack(imp.getWidth(), imp.getHeight());
boolean virtual = stack.isVirtual();
int slices2 = slices / zfactor + ((slices % zfactor) != 0 ? 1 : 0);
int frames2 = frames / tfactor + ((frames % tfactor) != 0 ? 1 : 0);
int n = channels * slices2 * frames2;
int count = 1;
for (int t = 1; t <= frames; t += tfactor) {
for (int z = 1; z <= slices; z += zfactor) {
for (int c = 1; c <= channels; c++) {
int i = imp.getStackIndex(c, z, t);
IJ.showProgress(i, n);
ImageProcessor ip = stack.getProcessor(imp.getStackIndex(c, z, t));
// IJ.log(count++ +" "+i+" "+c+" "+z+" "+t);
stack2.addSlice(stack.getSliceLabel(i), ip);
}
}
}
imp.setStack(stack2, channels, slices2, frames2);
Calibration cal = imp.getCalibration();
if (cal.scaled()) cal.pixelDepth *= zfactor;
if (virtual) imp.setTitle(imp.getTitle());
IJ.showProgress(1.0);
}
public String getImageInfo(ImagePlus imp, ImageProcessor ip) {
String infoProperty = null;
if (imp.getStackSize() > 1) {
ImageStack stack = imp.getStack();
String label = stack.getSliceLabel(imp.getCurrentSlice());
if (label != null && label.indexOf('\n') > 0) infoProperty = label;
}
if (infoProperty == null) {
infoProperty = (String) imp.getProperty("Info");
if (infoProperty == null) infoProperty = getExifData(imp);
}
String info = getInfo(imp, ip);
if (infoProperty != null) return infoProperty + "\n------------------------\n" + info;
else return info;
}
public void reduceStack(ImagePlus imp, int factor) {
ImageStack stack = imp.getStack();
boolean virtual = stack.isVirtual();
int n = stack.getSize();
ImageStack stack2 = new ImageStack(stack.getWidth(), stack.getHeight());
for (int i = 1; i <= n; i += factor) {
if (virtual) IJ.showProgress(i, n);
stack2.addSlice(stack.getSliceLabel(i), stack.getProcessor(i));
}
imp.setStack(null, stack2);
if (virtual) {
IJ.showProgress(1.0);
imp.setTitle(imp.getTitle());
}
Calibration cal = imp.getCalibration();
if (cal.scaled()) cal.pixelDepth *= factor;
}
void createNewStack(ImagePlus imp, ImageProcessor ip) {
int nSlices = imp.getStackSize();
int w = imp.getWidth(), h = imp.getHeight();
ImagePlus imp2 = imp.createImagePlus();
Rectangle r = ip.getRoi();
boolean crop = r.width != imp.getWidth() || r.height != imp.getHeight();
ImageStack stack1 = imp.getStack();
ImageStack stack2 = new ImageStack(newWidth, newHeight);
ImageProcessor ip1, ip2;
int method = interpolationMethod;
if (w == 1 || h == 1) method = ImageProcessor.NONE;
for (int i = 1; i <= nSlices; i++) {
IJ.showStatus("Scale: " + i + "/" + nSlices);
ip1 = stack1.getProcessor(i);
String label = stack1.getSliceLabel(i);
if (crop) {
ip1.setRoi(r);
ip1 = ip1.crop();
}
ip1.setInterpolationMethod(method);
ip2 = ip1.resize(newWidth, newHeight, averageWhenDownsizing);
if (ip2 != null) stack2.addSlice(label, ip2);
IJ.showProgress(i, nSlices);
}
imp2.setStack(title, stack2);
Calibration cal = imp2.getCalibration();
if (cal.scaled()) {
cal.pixelWidth *= 1.0 / xscale;
cal.pixelHeight *= 1.0 / yscale;
}
IJ.showProgress(1.0);
int[] dim = imp.getDimensions();
imp2.setDimensions(dim[2], dim[3], dim[4]);
if (imp.isComposite()) {
imp2 = new CompositeImage(imp2, ((CompositeImage) imp).getMode());
((CompositeImage) imp2).copyLuts(imp);
}
if (imp.isHyperStack()) imp2.setOpenAsHyperStack(true);
if (newDepth > 0 && newDepth != oldDepth)
imp2 = (new Resizer()).zScale(imp2, newDepth, interpolationMethod);
if (imp2 != null) {
imp2.show();
imp2.changes = true;
}
}
public ImageStack expandStack(ImageStack stackOld, int wNew, int hNew, int xOff, int yOff) {
int nFrames = stackOld.getSize();
ImageProcessor ipOld = stackOld.getProcessor(1);
java.awt.Color colorBack = Toolbar.getBackgroundColor();
ImageStack stackNew = new ImageStack(wNew, hNew, stackOld.getColorModel());
ImageProcessor ipNew;
for (int i = 1; i <= nFrames; i++) {
IJ.showProgress((double) i / nFrames);
ipNew = ipOld.createProcessor(wNew, hNew);
if (zeroFill) ipNew.setValue(0.0);
else ipNew.setColor(colorBack);
ipNew.fill();
ipNew.insert(stackOld.getProcessor(i), xOff, yOff);
stackNew.addSlice(stackOld.getSliceLabel(i), ipNew);
}
return stackNew;
}
// extract range of slices
ImagePlus stackRange(ImagePlus imp, int first, int last, int inc, String title) throws Exception {
ImageStack stack = imp.getStack();
ImageStack stack2 = null;
Roi roi = imp.getRoi();
for (int i = first, j = 0; i <= last; i += inc) {
// IJ.log(first+" "+last+" "+inc+" "+i);
IJ.showProgress(i - first, last - first);
int currSlice = i - j;
ImageProcessor ip2 = stack.getProcessor(currSlice);
// ip2.setRoi(roi);
// ip2 = ip2.crop();
if (stack2 == null) stack2 = new ImageStack(ip2.getWidth(), ip2.getHeight());
stack2.addSlice(stack.getSliceLabel(currSlice), ip2);
}
ImagePlus substack = imp.createImagePlus();
substack.setStack(title, stack2);
substack.setCalibration(imp.getCalibration());
return substack;
}
ImagePlus duplicateStack(ImagePlus img1) {
ImageStack stack1 = img1.getStack();
int width = stack1.getWidth();
int height = stack1.getHeight();
int n = stack1.getSize();
ImageStack stack2 = img1.createEmptyStack();
try {
for (int i = 1; i <= n; i++) {
ImageProcessor ip1 = stack1.getProcessor(i);
ip1.resetRoi();
ImageProcessor ip2 = ip1.crop();
stack2.addSlice(stack1.getSliceLabel(i), ip2);
}
} catch (OutOfMemoryError e) {
stack2.trim();
stack2 = null;
return null;
}
return new ImagePlus("Duplicate", stack2);
}
void createNewStack(ImagePlus imp, ImageProcessor ip) {
Rectangle r = ip.getRoi();
boolean crop = r.width != imp.getWidth() || r.height != imp.getHeight();
int nSlices = imp.getStackSize();
ImageStack stack1 = imp.getStack();
ImageStack stack2 = new ImageStack(newWidth, newHeight);
ImageProcessor ip1, ip2;
boolean interp = interpolate;
if (imp.getWidth() == 1 || imp.getHeight() == 1) interp = false;
for (int i = 1; i <= nSlices; i++) {
IJ.showStatus("Scale: " + i + "/" + nSlices);
ip1 = stack1.getProcessor(i);
String label = stack1.getSliceLabel(i);
if (crop) {
ip1.setRoi(r);
ip1 = ip1.crop();
}
ip1.setInterpolate(interp);
ip2 = ip1.resize(newWidth, newHeight);
if (ip2 != null) stack2.addSlice(label, ip2);
IJ.showProgress(i, nSlices);
}
ImagePlus imp2 = imp.createImagePlus();
imp2.setStack(title, stack2);
Calibration cal = imp2.getCalibration();
if (cal.scaled()) {
cal.pixelWidth *= 1.0 / xscale;
cal.pixelHeight *= 1.0 / yscale;
}
int[] dim = imp.getDimensions();
imp2.setDimensions(dim[2], dim[3], dim[4]);
IJ.showProgress(1.0);
if (imp.isComposite()) {
imp2 = new CompositeImage(imp2, 0);
((CompositeImage) imp2).copyLuts(imp);
}
if (imp.isHyperStack()) imp2.setOpenAsHyperStack(true);
imp2.show();
imp2.changes = true;
}