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);
}
/**
* Build an ImagePlus from double or float array
*
* @param imi : double or float array
* @param name : name of the image
* @param width
* @param height
* @return ImagePlus object
*/
public static ImagePlus buildImagePlusFromDoubleOrFloatArrays(
Object imi, String name, int width, int height) {
float[][] im;
if (imi instanceof double[][]) im = convertDoublesToFloats((double[][]) imi);
else im = (float[][]) imi;
if (im != null) {
if (im.length == 1) {
float[] tmp = new float[im[0].length];
System.arraycopy(im[0], 0, tmp, 0, im[0].length);
ImagePlus img = new ImagePlus(name, new FloatProcessor(width, height, tmp, null));
return img;
} else { // Stack
ImageStack is = new ImageStack(width, height);
for (int i = 0; i < im.length; i++) {
if (im[i] != null) {
float[] tmp = new float[im[i].length];
System.arraycopy(im[i], 0, tmp, 0, im[i].length);
is.addSlice("lvl " + (i + 1), new FloatProcessor(width, height, tmp, null));
}
}
ImagePlus img = new ImagePlus(name, is);
return img;
}
}
return null;
}
/**
* Read VoxelMatrix file stored in the old format
*
* @param path image file name with complete path
* @param dis input data stream to read from
* @param size1 dimension 1
* @param size2 dimension 2
* @param size3 dimension 3
* @return read image or null if error
* @throws IOException
*/
static ImagePlus readOldFormat(String path, DataInputStream dis, int size1, int size2, int size3)
throws IOException {
// prepare variables
ImageStack stack = new ImageStack(size1, size2);
final int numPixels = size1 * size2;
final int bufferSize = 4 * numPixels;
final byte[] buffer = new byte[bufferSize];
// write pixels
for (int z = 0; z < size3; ++z) {
final float[][] pixels = new float[size1][size2];
int n = dis.read(buffer, 0, bufferSize);
if (n < 0) return null;
for (int j = 0; j < bufferSize; j += 4) {
int tmp =
(int)
((buffer[j]) << 24
| (buffer[j + 1]) << 16
| (buffer[j + 2]) << 8
| (buffer[j + 3]));
int currentPos = j / 4;
int y = currentPos / size2;
int x = currentPos % size2;
pixels[y][x] = (float) (tmp);
}
final FloatProcessor fp = new FloatProcessor(pixels);
stack.addSlice(fp);
}
return new ImagePlus(path, stack);
}
ImageStack getRGBStack(ImagePlus imp) {
ImageProcessor ip = imp.getProcessor();
int w = ip.getWidth();
int h = ip.getHeight();
int size = w * h;
byte[] r = new byte[size];
byte[] g = new byte[size];
byte[] b = new byte[size];
((ColorProcessor) ip).getRGB(r, g, b);
ImageStack stack = new ImageStack(w, h);
stack.addSlice("Red", r);
stack.addSlice("Green", g);
stack.addSlice("Blue", b);
stack.setColorModel(ip.getDefaultColorModel());
return stack;
}
/**
* Returns subset of given hyperstack
*
* @param imp
* @param slices
* @param frames
* @param channels
* @return
*/
public static ImagePlus getSubHyperStack(
ImagePlus imp, int[] slices, int[] frames, int[] channels) {
int sizes[] = imp.getDimensions();
// Zero index --> keep all indices
if (slices.length == 1 && slices[0] == 0) {
slices = Commons.getSequence(1, sizes[3]);
}
if (frames.length == 1 && frames[0] == 0) {
frames = Commons.getSequence(1, sizes[4]);
}
if (channels.length == 1 && channels[0] == 0) {
channels = Commons.getSequence(1, sizes[2]);
}
// Check input arguments
if ((Commons.getMin(slices) < 1) || (Commons.getMax(slices) > sizes[3])) {
System.out.println("Subscripts for slices out of bounds.");
return imp;
}
if ((Commons.getMin(frames) < 1) || (Commons.getMax(frames) > sizes[4])) {
System.out.println("Subscripts for frames out of bounds.");
return imp;
}
if ((Commons.getMin(channels) < 1) || (Commons.getMax(channels) > sizes[2])) {
System.out.println("Subscripts for channels out of bounds.");
return imp;
}
// Convert indices into stack indices
ImageStack ims = imp.getImageStack();
boolean keep[] = new boolean[ims.getSize()];
Arrays.fill(keep, false);
int slicesToKeep = 0;
for (int i = 0; i < slices.length; i++) {
for (int j = 0; j < frames.length; j++) {
for (int k = 0; k < channels.length; k++) {
int test = imp.getStackIndex(channels[k], slices[i], frames[j]);
keep[imp.getStackIndex(channels[k], slices[i], frames[j]) - 1] = true;
slicesToKeep++;
}
}
}
ImageStack resIms = new ImageStack(imp.getWidth(), imp.getHeight());
for (int i = 0; i < ims.getSize(); i++) {
if (keep[i]) {
resIms.addSlice(ims.getProcessor(i + 1));
}
}
ImagePlus resImp = new ImagePlus("SubHyperStack of " + imp.getTitle(), resIms);
resImp.setOpenAsHyperStack(true);
resImp.setDimensions(channels.length, slices.length, frames.length);
return resImp;
}
/**
* Convert VectorProcessor to ImagePlus with FloatProcessor stack.
*
* @return ImagePlus representation of this object.
* @see #toFloatProcessors()
*/
public ImagePlus toFloatStack() {
final ImageStack stack = new ImageStack(width, height);
final FloatProcessor[] fps = toFloatProcessors();
for (int i = 0; i < fps.length; i++) {
stack.addSlice("band " + i, fps[i]);
}
return new ImagePlus("From VectorProcessor", stack);
}
private void doHSRGBProjection(ImagePlus rgbImp) {
ImageStack stack = rgbImp.getStack();
ImageStack stack2 = new ImageStack(stack.getWidth(), stack.getHeight());
for (int i = startSlice; i <= stopSlice; i++) stack2.addSlice(null, stack.getProcessor(i));
startSlice = 1;
stopSlice = stack2.getSize();
doRGBProjection(stack2);
}
@Override
public void run(ImageProcessor ip) {
w = image.getWidth();
h = image.getHeight();
float[] rgb = new float[3];
float[] lab = new float[3];
if (image.getStack().getSize() == 1) {
int[] pixels = (int[]) image.getProcessor().getPixels();
float[] l = new float[w * h];
float[] a = new float[w * h];
float[] b = new float[w * h];
for (int i = 0; i < w * h; i++) {
int v = pixels[i];
CIELAB.int2sRGB(v, rgb);
CIELAB.sRGB2CIELAB(rgb, lab);
l[i] = lab[0];
a[i] = lab[1];
b[i] = lab[2];
}
ImageStack stack = new ImageStack(w, h);
stack.addSlice("L", new FloatProcessor(w, h, l, null));
stack.addSlice("a", new FloatProcessor(w, h, a, null));
stack.addSlice("b", new FloatProcessor(w, h, b, null));
new ImagePlus(image.getTitle() + " Lab", stack).show();
} else {
int[] rgbi = new int[3];
ImageStack stack = image.getStack();
float[] l = (float[]) stack.getProcessor(1).getPixels();
float[] a = (float[]) stack.getProcessor(2).getPixels();
float[] b = (float[]) stack.getProcessor(3).getPixels();
int[] pixels = new int[w * h];
for (int i = 0; i < w * h; i++) {
lab[0] = l[i];
lab[1] = a[i];
lab[2] = b[i];
CIELAB.CIELAB2sRGB(lab, rgb);
pixels[i] = CIELAB.sRGB2int(rgb);
}
ip = new ColorProcessor(w, h, pixels);
new ImagePlus(image.getTitle() + " RGB", ip).show();
}
}
/** Adds the image in 'ip' to the end of the stack. */
public void addSlice(String sliceLabel, ImageProcessor ip) {
if (ip.getWidth() != width || ip.getHeight() != height)
throw new IllegalArgumentException("Dimensions do not match");
if (nSlices == 0) {
cm = ip.getColorModel();
min = ip.getMin();
max = ip.getMax();
}
addSlice(sliceLabel, ip.getPixels());
}
public static ImageStack getChannel(ImagePlus imp, int c) {
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;
}
public static ImagePlus scale(ImagePlus imp, double factor) {
int newWidth = (int) Math.round(imp.getWidth() * factor);
int newHeight = (int) Math.round(imp.getHeight() * factor);
ImageStack is = new ImageStack(newWidth, newHeight);
for (int i = 0; i < imp.getNSlices(); i++) {
imp.setSlice(i);
ImageProcessor ic = imp.getProcessor().resize(newWidth);
is.addSlice(ic);
}
ImagePlus resImp = new ImagePlus(imp.getTitle() + "_scaled", is);
return (resImp);
}
/**
* Adds the image in 'ip' to the stack following slice 'n'. Adds the slice to the beginning of the
* stack if 'n' is zero.
*/
public void addSlice(String sliceLabel, ImageProcessor ip, int n) {
if (n < 0 || n > nSlices) throw new IllegalArgumentException(outOfRange + n);
addSlice(sliceLabel, ip);
Object tempSlice = stack[nSlices - 1];
String tempLabel = label[nSlices - 1];
int first = n > 0 ? n : 1;
for (int i = nSlices - 1; i >= first; i--) {
stack[i] = stack[i - 1];
label[i] = label[i - 1];
}
stack[n] = tempSlice;
label[n] = tempLabel;
}
public void makeTransition(ImagePlus imp, int from, int num) {
ImageStack stack = imp.getStack();
int w = imp.getWidth(), h = imp.getHeight();
ImageProcessor fr = stack.getProcessor(from).duplicate();
ImageProcessor to = stack.getProcessor(from + 1);
int[] row = new int[w];
for (int n = 0; n < num; n++) {
for (int y = n; y < h; y += num) {
to.getRow(0, y, row, w);
fr.putRow(0, y, row, w);
}
stack.addSlice("", fr, from + n);
}
}
public void makeTransition(ImagePlus imp, int from, int num) {
ImageStack stack = imp.getStack();
int w = imp.getWidth(), h = imp.getHeight();
ImageProcessor fr = stack.getProcessor(from).duplicate();
ImageProcessor to = stack.getProcessor(from + 1);
int[] col = new int[h];
for (int n = 0; n < num; n++) {
for (int x = n; x < w; x += num) {
to.getColumn(x, 0, col, h);
fr.putColumn(x, 0, col, h);
}
stack.addSlice("", fr, from + n);
}
}
ImagePlus openDicomStack(ZipInputStream zis, ZipEntry entry) throws IOException {
ImagePlus imp = null;
int count = 0;
ImageStack stack = null;
while (true) {
if (count > 0) entry = zis.getNextEntry();
if (entry == null) break;
String name = entry.getName();
ImagePlus imp2 = null;
if (name.endsWith(".dcm")) {
ByteArrayOutputStream out = new ByteArrayOutputStream();
byte[] buf = new byte[4096];
int len, byteCount = 0, progress = 0;
while (true) {
len = zis.read(buf);
if (len < 0) break;
out.write(buf, 0, len);
byteCount += len;
// IJ.showProgress((double)(byteCount%fileSize)/fileSize);
}
byte[] bytes = out.toByteArray();
out.close();
InputStream is = new ByteArrayInputStream(bytes);
DICOM dcm = new DICOM(is);
dcm.run(name);
imp2 = dcm;
is.close();
}
zis.closeEntry();
if (imp2 == null) continue;
count++;
String label = imp2.getTitle();
String info = (String) imp2.getProperty("Info");
if (info != null) label += "\n" + info;
if (count == 1) {
imp = imp2;
imp.getStack().setSliceLabel(label, 1);
} else {
stack = imp.getStack();
stack.addSlice(label, imp2.getProcessor());
imp.setStack(stack);
}
}
zis.close();
IJ.showProgress(1.0);
if (count == 0)
throw new IOException("This ZIP archive does not appear to contain any .dcm files");
return imp;
}
/*
* This test is illustrative of an issue in IJ1 where the internal stack gets
* deleted in certain cases. If you setProcessor() on an ImagePlus with a
* stack of 1 slice the stack gets deleted. A subsequent call to getStack()
* will hatch a new one using the pixels of the current ImageProcessor.
* Basically to avoid problems the legacy layer should never call
* setProcessor() or if it does it should do a getStack() rather than cache
* calls to previous getStack() calls.
*/
@Test
public void testStackKiller() {
final ImageStack stack = new ImageStack(2, 2);
final byte[] slice = new byte[] {1, 2, 3, 4};
stack.addSlice("one slice", slice);
final ImagePlus imp = new ImagePlus("fred", stack);
assertEquals(stack, imp.getStack());
final byte[] slice2 = new byte[] {5, 6, 7, 8};
final ByteProcessor proc = new ByteProcessor(2, 2, slice2, null);
imp.setProcessor(proc);
final ImageStack secondStack = imp.getStack();
assertNotSame(stack, secondStack);
assertEquals(slice, stack.getPixels(1));
assertEquals(slice2, secondStack.getPixels(1));
}
public ImagePlus record() {
pause();
int s = univ.getStartTime();
int e = univ.getEndTime();
univ.showTimepoint(s);
try {
Thread.sleep(100);
} catch (InterruptedException ex) {
}
ImagePlus imp = univ.takeSnapshot();
ImageStack stack = new ImageStack(imp.getWidth(), imp.getHeight());
stack.addSlice("", imp.getProcessor());
for (int i = s + 1; i <= e; i++) {
univ.showTimepoint(i);
try {
Thread.sleep(100);
} catch (InterruptedException ex) {
}
stack.addSlice("", univ.takeSnapshot().getProcessor());
}
return new ImagePlus("Movie", stack);
}
/**
* Rearranges an ImageJ XYCTZ Hyperstack into XYCZT without wasting memory for processing 3d
* images as a chunk, if it is already XYCTZ it will shuffle it back to XYCZT
*
* @param imp - the input {@link ImagePlus}
* @return - an {@link ImagePlus} which can be the same instance if the image is XYC, XYZ, XYT or
* XY - otherwise a new instance containing the same processors but in the new order XYZCT
*/
public static ImagePlus switchZTinXYCZT(final ImagePlus imp) {
final int numChannels = imp.getNChannels();
final int numTimepoints = imp.getNFrames();
final int numZStacks = imp.getNSlices();
String newTitle;
if (imp.getTitle().startsWith("[XYCTZ]"))
newTitle = imp.getTitle().substring(8, imp.getTitle().length());
else newTitle = "[XYCTZ] " + imp.getTitle();
// there is only one timepoint and one z-stack, i.e. XY(C)
if (numTimepoints == 1 && numZStacks == 1) {
return imp;
}
// there is only one channel XYZ(T) or one z-stack XYC(T)
else if (numTimepoints == 1 || numZStacks == 1) {
// numchannels, z-slices, timepoints
// but of course now reversed...
imp.setDimensions(numChannels, numTimepoints, numZStacks);
imp.setTitle(newTitle);
return imp;
}
// now we have to rearrange
final ImageStack stack = new ImageStack(imp.getWidth(), imp.getHeight());
for (int z = 1; z <= numZStacks; ++z) {
for (int t = 1; t <= numTimepoints; ++t) {
for (int c = 1; c <= numChannels; ++c) {
final int index = imp.getStackIndex(c, z, t);
final ImageProcessor ip = imp.getStack().getProcessor(index);
stack.addSlice(imp.getStack().getSliceLabel(index), ip);
}
}
}
final ImagePlus result = new ImagePlus(newTitle, stack);
// numchannels, z-slices, timepoints
// but of course now reversed...
result.setDimensions(numChannels, numTimepoints, numZStacks);
result.getCalibration().pixelWidth = imp.getCalibration().pixelWidth;
result.getCalibration().pixelHeight = imp.getCalibration().pixelHeight;
result.getCalibration().pixelDepth = imp.getCalibration().pixelDepth;
final CompositeImage composite = new CompositeImage(result);
return composite;
}
/** Opens a stack of images. */
ImagePlus openStack(ColorModel cm, boolean show) {
ImageStack stack = new ImageStack(fi.width, fi.height, cm);
long skip = fi.getOffset();
Object pixels;
try {
ImageReader reader = new ImageReader(fi);
InputStream is = createInputStream(fi);
if (is == null) return null;
IJ.resetEscape();
for (int i = 1; i <= fi.nImages; i++) {
if (!silentMode) IJ.showStatus("Reading: " + i + "/" + fi.nImages);
if (IJ.escapePressed()) {
IJ.beep();
IJ.showProgress(1.0);
silentMode = false;
return null;
}
pixels = reader.readPixels(is, skip);
if (pixels == null) break;
stack.addSlice(null, pixels);
skip = fi.gapBetweenImages;
if (!silentMode) IJ.showProgress(i, fi.nImages);
}
is.close();
} catch (Exception e) {
IJ.log("" + e);
} catch (OutOfMemoryError e) {
IJ.outOfMemory(fi.fileName);
stack.trim();
}
if (!silentMode) IJ.showProgress(1.0);
if (stack.getSize() == 0) return null;
if (fi.sliceLabels != null && fi.sliceLabels.length <= stack.getSize()) {
for (int i = 0; i < fi.sliceLabels.length; i++) stack.setSliceLabel(fi.sliceLabels[i], i + 1);
}
ImagePlus imp = new ImagePlus(fi.fileName, stack);
if (fi.info != null) imp.setProperty("Info", fi.info);
if (show) imp.show();
imp.setFileInfo(fi);
setCalibration(imp);
ImageProcessor ip = imp.getProcessor();
if (ip.getMin() == ip.getMax()) // find stack min and max if first slice is blank
setStackDisplayRange(imp);
if (!silentMode) IJ.showProgress(1.0);
silentMode = false;
return imp;
}
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 makeStack(ImageProcessor ip, int w, int h, int b) {
int stackSize = w * h;
int width = ip.getWidth() / w;
int height = ip.getHeight() / h;
ImageStack stack = new ImageStack(width, height);
for (int y = 0; y < h; y++)
for (int x = 0; x < w; x++) {
ip.setRoi(x * width, y * height, width, height);
stack.addSlice(null, ip.crop());
}
if (b > 0) {
int cropwidth = width - b - b / 2;
int cropheight = height - b - b / 2;
StackProcessor sp = new StackProcessor(stack, ip);
stack = sp.crop(b, b, cropwidth, cropheight);
}
return stack;
}
public void doHyperStackProjection(boolean allTimeFrames) {
int start = startSlice;
int stop = stopSlice;
int firstFrame = 1;
int lastFrame = imp.getNFrames();
if (!allTimeFrames) firstFrame = lastFrame = imp.getFrame();
ImageStack stack = new ImageStack(imp.getWidth(), imp.getHeight());
int channels = imp.getNChannels();
int slices = imp.getNSlices();
if (slices == 1) {
slices = imp.getNFrames();
firstFrame = lastFrame = 1;
}
int frames = lastFrame - firstFrame + 1;
increment = channels;
boolean rgb = imp.getBitDepth() == 24;
for (int frame = firstFrame; frame <= lastFrame; frame++) {
for (int channel = 1; channel <= channels; channel++) {
startSlice = (frame - 1) * channels * slices + (start - 1) * channels + channel;
stopSlice = (frame - 1) * channels * slices + (stop - 1) * channels + channel;
if (rgb) doHSRGBProjection(imp);
else doProjection();
stack.addSlice(null, projImage.getProcessor());
}
}
projImage = new ImagePlus(makeTitle(), stack);
projImage.setDimensions(channels, 1, frames);
if (channels > 1) {
projImage = new CompositeImage(projImage, 0);
((CompositeImage) projImage).copyLuts(imp);
if (method == SUM_METHOD || method == SD_METHOD)
((CompositeImage) projImage).resetDisplayRanges();
}
if (frames > 1) projImage.setOpenAsHyperStack(true);
Overlay overlay = imp.getOverlay();
if (overlay != null) {
startSlice = start;
stopSlice = stop;
if (imp.getType() == ImagePlus.COLOR_RGB)
projImage.setOverlay(projectRGBHyperStackRois(overlay));
else projImage.setOverlay(projectHyperStackRois(overlay));
}
IJ.showProgress(1, 1);
}
// 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;
}
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;
}
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);
}
public static ImagePlus asImagePlus(
String title, double[] data, int width, int height, int nSlices, int nFrames, int nChannels) {
ImageStack imageStack = new ImageStack(width, height);
FloatProcessor ip = null;
for (int i = 0; i < nSlices * nFrames * nChannels; i++) {
ip = new FloatProcessor(width, height);
for (int iX = 0; iX < width; iX++) {
for (int iY = 0; iY < height; iY++) {
ip.putPixelValue(iX, iY, data[i * height * width + iY * width + iX]);
}
}
imageStack.addSlice(ip);
}
ImagePlus resImp = new ImagePlus(title, imageStack);
resImp.setOpenAsHyperStack(true);
resImp.setDimensions(nChannels, nSlices, nFrames);
return resImp;
}
public void runLipschitz(ImageProcessor ip) {
if (IJ.escapePressed()) return;
breaked = false;
Date d1, d2;
d1 = new Date();
IJ.showStatus("Initializing...");
m_stack_out = m_imp.createEmptyStack();
ImagePlus imp2 = null;
for (int i = 0; ((i < m_scount) && (!breaked)); i++) {
if (m_scount > 1) {
ip = m_stack.getProcessor(i + 1);
}
iptmp = ip.createProcessor(ImageWidth, ImageHeight);
iptmp.copyBits(ip, 0, 0, Blitter.COPY);
IJ.showStatus("Filtering " + (i + 1) + "/" + m_scount + " slice.");
Lipschitz2D(iptmp);
m_stack_out.addSlice(m_imp.getShortTitle() + " " + (i + 1) + "/" + m_scount, iptmp);
if (breaked = IJ.escapePressed()) IJ.beep();
}
imp2 =
new ImagePlus(
m_imp.getShortTitle()
+ " Filtered (Lipschitz) Slope:"
+ m_Slope
+ " "
+ ((m_Down) ? " -Down" : " ")
+ " "
+ ((m_TopHat) ? " -TopHat" : " ")
+ ((breaked) ? " -INTERUPTED" : ""),
m_stack_out);
imp2.show();
imp2.updateAndDraw();
IJ.showProgress(1.0);
} // end of 'runLipschitz' method
/* Replaces all sample index in imp with neighbor sample*/
public static ImagePlus ReplaceSlices(ImagePlus imp, ArrayList<Integer> samples) {
ImageStack ims = imp.getStack();
Iterator itr = samples.iterator();
while (itr.hasNext()) {
Integer k = (Integer) itr.next();
if (k == 0) {
continue;
}
ImageProcessor ip_slice = ims.getProcessor(k);
// double value_1 = getMeanOfSlice(ims.getProcessor(k-1));
// double value_2 = getMeanOfSlice(ims.getProcessor(k));
// double value_3 = getMeanOfSlice(ims.getProcessor(k+1));
// double value_4 = getMeanOfSlice(ims.getProcessor(k+2));
// System.out.print("Replacing "+ value_ori+"with " +value_re );
ims.addSlice("", ip_slice, k);
ims.deleteSlice(k + 2);
}
imp.setStack(ims);
return imp;
}
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;
}