public void run(String arg) {
ImagePlus imp = WindowManager.getCurrentImage();
if (imp == null) {
IJ.noImage();
return;
}
ImageStack stack1 = imp.getStack();
String fileName = imp.getTitle();
int endslice = stack1.getSize();
ImagePlus imp2 = duplicateStack(imp);
imp2.show();
String duplicateName = imp2.getTitle();
// IJ.showMessage("Box",fileName);
ImageStack stack2 = imp2.getStack();
stack1.deleteSlice(1);
stack2.deleteSlice(endslice);
String calculatorstring =
("image1='"
+ fileName
+ "' operation=Subtract image2="
+ imp2.getTitle()
+ " create stack");
IJ.run("Image Calculator...", calculatorstring);
ImagePlus imp3 = WindowManager.getCurrentImage();
imp3.setTitle(fileName + " DeltaF up");
imp2.getWindow().close();
imp.getWindow().close();
}
public void run(ImageProcessor ip) {
dimz = stack.getSize();
dimy = stack.getWidth();
dimx = stack.getHeight();
SaveDialog sd = new SaveDialog("Save Measurements as Text...", "res", ".dat");
String name = sd.getFileName();
if (name == null) return;
String directory = sd.getDirectory();
nb = calculnb(stack); // -1;
IJ.showStatus("Measure parameters for the " + nb + " objects ...");
if (nb < 1) {
IJ.showMessage("volume must be labeled");
} else {
double[] volume_m = new double[nb];
int[] volume_p = new int[nb];
double[] surface = new double[nb];
double[] surfacenb = new double[nb];
double[][][] I = new double[3][3][nb];
double[][] J = new double[3][nb];
double[][][] dir = new double[3][3][nb];
double[] xg = new double[nb];
double[] yg = new double[nb];
double[] zg = new double[nb];
byte[] bord = new byte[nb];
// double[] a = new double[nb];
// double[] b = new double[nb];
// double[] c = new double[nb];
// double[] Fab = new double[nb];
// double[] Fac = new double[nb];
// double[] Fbc = new double[nb];
// double[] sp = new double[nb];
double[][] lmin = new double[nb][3];
double[][] lmax = new double[nb][3];
IJ.showStatus("Measure surfaces ...");
calculmarchsurfstack(stack, nb, surface, volume_m);
calculmarchsurfstacknb(stack, nb, surfacenb);
// calculvolumestack(stack,nb,volume_p);
IJ.showStatus("Measure volumes and inertia ...");
calculcgstack(stack, nb, volume_p, xg, yg, zg);
calculinertiestack(stack, nb, xg, yg, zg, I);
inertie(nb, I, J, dir);
IJ.showStatus("Measure bounding boxes ...");
boitestack(stack, nb, xg, yg, zg, dir, lmin, lmax);
borderstack(stack, nb, bord);
IJ.showStatus("Save results ...");
sauvegarde(
volume_p, volume_m, surface, surfacenb, xg, yg, zg, J, dir, nb, bord, lmin, lmax,
directory, name);
volume_m = null;
volume_p = null;
surface = null;
xg = null;
yg = null;
zg = null;
}
}
/**
* 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;
}
/**
* 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);
}
/**
* 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);
}
void addScrollbars(ImagePlus imp) {
ImageStack s = imp.getStack();
int stackSize = s.getSize();
nSlices = stackSize;
hyperStack = imp.getOpenAsHyperStack();
// imp.setOpenAsHyperStack(false);
int[] dim = imp.getDimensions();
int nDimensions = 2 + (dim[2] > 1 ? 1 : 0) + (dim[3] > 1 ? 1 : 0) + (dim[4] > 1 ? 1 : 0);
if (nDimensions <= 3 && dim[2] != nSlices) hyperStack = false;
if (hyperStack) {
nChannels = dim[2];
nSlices = dim[3];
nFrames = dim[4];
}
// IJ.log("StackWindow: "+hyperStack+" "+nChannels+" "+nSlices+" "+nFrames);
if (nSlices == stackSize) hyperStack = false;
if (nChannels * nSlices * nFrames != stackSize) hyperStack = false;
if (cSelector != null || zSelector != null || tSelector != null) removeScrollbars();
ImageJ ij = IJ.getInstance();
if (nChannels > 1) {
cSelector = new ScrollbarWithLabel(this, 1, 1, 1, nChannels + 1, 'c');
add(cSelector);
if (ij != null) cSelector.addKeyListener(ij);
cSelector.addAdjustmentListener(this);
cSelector.setFocusable(false); // prevents scroll bar from blinking on Windows
cSelector.setUnitIncrement(1);
cSelector.setBlockIncrement(1);
}
if (nSlices > 1) {
char label = nChannels > 1 || nFrames > 1 ? 'z' : 't';
if (stackSize == dim[2] && imp.isComposite()) label = 'c';
zSelector = new ScrollbarWithLabel(this, 1, 1, 1, nSlices + 1, label);
if (label == 't') animationSelector = zSelector;
add(zSelector);
if (ij != null) zSelector.addKeyListener(ij);
zSelector.addAdjustmentListener(this);
zSelector.setFocusable(false);
int blockIncrement = nSlices / 10;
if (blockIncrement < 1) blockIncrement = 1;
zSelector.setUnitIncrement(1);
zSelector.setBlockIncrement(blockIncrement);
sliceSelector = zSelector.bar;
}
if (nFrames > 1) {
animationSelector = tSelector = new ScrollbarWithLabel(this, 1, 1, 1, nFrames + 1, 't');
add(tSelector);
if (ij != null) tSelector.addKeyListener(ij);
tSelector.addAdjustmentListener(this);
tSelector.setFocusable(false);
int blockIncrement = nFrames / 10;
if (blockIncrement < 1) blockIncrement = 1;
tSelector.setUnitIncrement(1);
tSelector.setBlockIncrement(blockIncrement);
}
}
@Test
public final void testRegionalMaxima_CubicMeshC26() {
// load the reference image, and get its size
ImageStack image = createCubicMeshImage();
int sizeX = image.getWidth();
int sizeY = image.getHeight();
int sizeZ = image.getSize();
// create test image: add a band with value 127 in the middle
int zMid = sizeZ / 2;
for (int y = 0; y < sizeY; y++) {
for (int x = 0; x < sizeX; x++) {
double val = image.getVoxel(x, y, zMid);
if (val == 255) image.setVoxel(x, y, zMid, 127);
}
}
ImageStack maxima = MinimaAndMaxima3D.regionalMaxima(image, 26);
for (int z = 0; z < sizeZ; z++) {
for (int y = 0; y < sizeY; y++) {
for (int x = 0; x < sizeX; x++) {
int v0 = (int) image.getVoxel(x, y, z);
int v = (int) maxima.getVoxel(x, y, z);
if (v0 == 255) assertEquals(255, v);
else assertEquals(0, v);
}
}
}
}
public void run(String arg) {
int[] wList = WindowManager.getIDList();
if (wList == null) {
IJ.error("No images are open.");
return;
}
double thalf = 0.5;
boolean keep;
GenericDialog gd = new GenericDialog("Bleach correction");
gd.addNumericField("t½:", thalf, 1);
gd.addCheckbox("Keep source stack:", true);
gd.showDialog();
if (gd.wasCanceled()) return;
long start = System.currentTimeMillis();
thalf = gd.getNextNumber();
keep = gd.getNextBoolean();
if (keep) IJ.run("Duplicate...", "title='Bleach corrected' duplicate");
ImagePlus imp1 = WindowManager.getCurrentImage();
int d1 = imp1.getStackSize();
double v1, v2;
int width = imp1.getWidth();
int height = imp1.getHeight();
ImageProcessor ip1, ip2, ip3;
int slices = imp1.getStackSize();
ImageStack stack1 = imp1.getStack();
ImageStack stack2 = imp1.getStack();
int currentSlice = imp1.getCurrentSlice();
for (int n = 1; n <= slices; n++) {
ip1 = stack1.getProcessor(n);
ip3 = stack1.getProcessor(1);
ip2 = stack2.getProcessor(n);
for (int x = 0; x < width; x++) {
for (int y = 0; y < height; y++) {
v1 = ip1.getPixelValue(x, y);
v2 = ip3.getPixelValue(x, y);
// =B8/(EXP(-C$7*A8))
v1 = (v1 / Math.exp(-n * thalf));
ip2.putPixelValue(x, y, v1);
}
}
IJ.showProgress((double) n / slices);
IJ.showStatus(n + "/" + slices);
}
// stack2.show();
imp1.updateAndDraw();
}
/** Performs actual projection using specified method. */
public void doProjection() {
if (imp == null) return;
sliceCount = 0;
if (method < AVG_METHOD || method > MEDIAN_METHOD) method = AVG_METHOD;
for (int slice = startSlice; slice <= stopSlice; slice += increment) sliceCount++;
if (method == MEDIAN_METHOD) {
projImage = doMedianProjection();
return;
}
// Create new float processor for projected pixels.
FloatProcessor fp = new FloatProcessor(imp.getWidth(), imp.getHeight());
ImageStack stack = imp.getStack();
RayFunction rayFunc = getRayFunction(method, fp);
if (IJ.debugMode == true) {
IJ.log("\nProjecting stack from: " + startSlice + " to: " + stopSlice);
}
// Determine type of input image. Explicit determination of
// processor type is required for subsequent pixel
// manipulation. This approach is more efficient than the
// more general use of ImageProcessor's getPixelValue and
// putPixel methods.
int ptype;
if (stack.getProcessor(1) instanceof ByteProcessor) ptype = BYTE_TYPE;
else if (stack.getProcessor(1) instanceof ShortProcessor) ptype = SHORT_TYPE;
else if (stack.getProcessor(1) instanceof FloatProcessor) ptype = FLOAT_TYPE;
else {
IJ.error("Z Project", "Non-RGB stack required");
return;
}
// Do the projection.
for (int n = startSlice; n <= stopSlice; n += increment) {
IJ.showStatus("ZProjection " + color + ": " + n + "/" + stopSlice);
IJ.showProgress(n - startSlice, stopSlice - startSlice);
projectSlice(stack.getPixels(n), rayFunc, ptype);
}
// Finish up projection.
if (method == SUM_METHOD) {
fp.resetMinAndMax();
projImage = new ImagePlus(makeTitle(), fp);
} else if (method == SD_METHOD) {
rayFunc.postProcess();
fp.resetMinAndMax();
projImage = new ImagePlus(makeTitle(), fp);
} else {
rayFunc.postProcess();
projImage = makeOutputImage(imp, fp, ptype);
}
if (projImage == null) IJ.error("Z Project", "Error computing projection.");
}
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;
}
/**
* Resizes the current array to the given dimensions.
*
* @param input the array to resize
* @param lenX the desired length in x-direction (with, horizontal length)
* @param lenY the desired length in y-direction (height, vertical length)
* @return a new 2d float array with the specified dimensions, and values interpolated from the
* input array.
*/
public static float[][] resize(float[][] input, int lenX, int lenY) {
float[] linearized = linearize2DArray(input);
ImageStack is = ImageStack.create(input.length, input[0].length, 1, 32);
is.setPixels(linearized, 1);
ImageProcessor ip = new ImagePlus("", is).getProcessor();
ip.setInterpolationMethod(ImageProcessor.BICUBIC);
float[] resized = (float[]) ip.resize(lenX, lenY).getPixels();
return linearizedArrayTo2D(resized, lenX, lenY);
}
private ImageStack createLeveledCubeGraphImage() {
ImageStack stack = createCubeGraphImage();
stack.setVoxel(5, 1, 1, 224);
stack.setVoxel(9, 5, 1, 192);
stack.setVoxel(9, 9, 5, 160);
stack.setVoxel(9, 5, 9, 128);
stack.setVoxel(5, 1, 9, 96);
stack.setVoxel(1, 5, 9, 64);
stack.setVoxel(1, 9, 5, 32);
return stack;
}
private final void invertGray8Stack(ImageStack image) {
int sizeX = image.getWidth();
int sizeY = image.getHeight();
int sizeZ = image.getSize();
for (int z = 0; z < sizeZ; z++) {
for (int y = 0; y < sizeY; y++) {
for (int x = 0; x < sizeX; x++) {
image.setVoxel(x, y, z, 255 - image.getVoxel(x, y, z));
}
}
}
}
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);
}
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);
}
}
@Test
public final void testDilationThinCubicMeshC26() {
ImageStack mask = createThinCubicMeshImage();
ImageStack marker = ImageStack.create(5, 5, 5, 8);
marker.setVoxel(0, 0, 0, 255);
GeodesicReconstruction3DHybrid0Gray8 algo = new GeodesicReconstruction3DHybrid0Gray8();
algo.setConnectivity(26);
ImageStack result = algo.applyTo(marker, mask);
assertEquals(255, result.getVoxel(0, 4, 0), .01);
}
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);
}
}
private ImageStack loadImages() {
String fileNameNumberRef = new String();
String fileNameNumberCorr = new String();
if (numOfIteration < 9) {
fileNameNumberRef = "000" + numOfIteration;
fileNameNumberCorr = "000" + (numOfIteration + 1);
}
if (numOfIteration == 9) {
fileNameNumberRef = "0009";
fileNameNumberCorr = "0010";
}
if (numOfIteration >= 10 && numOfIteration < 99) {
fileNameNumberRef = "00" + numOfIteration;
fileNameNumberCorr = "00" + (numOfIteration + 1);
}
if (numOfIteration == 99) {
fileNameNumberRef = "0099";
fileNameNumberCorr = "0100";
}
if (numOfIteration >= 100 && numOfIteration < 999) {
fileNameNumberRef = "0" + numOfIteration;
fileNameNumberCorr = "0" + (numOfIteration + 1);
}
if (numOfIteration == 999) {
fileNameNumberRef = "0999";
fileNameNumberCorr = "1000";
}
if (numOfIteration >= 1000) {
fileNameNumberRef = String.valueOf(numOfIteration);
fileNameNumberCorr = String.valueOf(numOfIteration + 1);
}
ImagePlus ref = new ImagePlus(dir + name + fileNameNumberRef + format);
ImagePlus corr = new ImagePlus(dir + name + (fileNameNumberCorr) + format);
ImageStack tmp = ImageStack.create(ref.getWidth(), ref.getHeight(), 2, ref.getBitDepth());
tmp.setPixels(ref.getProcessor().getPixels(), 1);
tmp.setPixels(corr.getProcessor().getPixels(), 2);
return tmp;
}
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));
}
void setStackDisplayRange(ImagePlus imp) {
ImageStack stack = imp.getStack();
double min = Double.MAX_VALUE;
double max = -Double.MAX_VALUE;
int n = stack.getSize();
for (int i = 1; i <= n; i++) {
if (!silentMode) IJ.showStatus("Calculating stack min and max: " + i + "/" + n);
ImageProcessor ip = stack.getProcessor(i);
ip.resetMinAndMax();
if (ip.getMin() < min) min = ip.getMin();
if (ip.getMax() > max) max = ip.getMax();
}
imp.getProcessor().setMinAndMax(min, max);
imp.updateAndDraw();
}
public void resetDisplayRanges() {
int channels = getNChannels();
if (lut == null) setupLuts(channels);
ImageStack stack2 = getImageStack();
if (lut == null
|| channels != lut.length
|| channels > stack2.getSize()
|| channels > MAX_CHANNELS) return;
for (int i = 0; i < channels; ++i) {
ImageProcessor ip2 = stack2.getProcessor(i + 1);
ip2.resetMinAndMax();
lut[i].min = ip2.getMin();
lut[i].max = ip2.getMax();
}
}
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;
}
void borderstack(final ImageStack stack1, int nb, byte[] b) {
final AtomicInteger ai = new AtomicInteger(0);
final int dimX = stack1.getWidth();
final int dimY = stack1.getHeight();
final int dimZ = stack1.getSize();
final byte[][] bord = new byte[dimZ][nb];
for (int ithread = 0; ithread < threads.length; ithread++) {
// Concurrently run in as many threads as CPUs
threads[ithread] =
new Thread() {
public void run() {
for (int superi = ai.getAndIncrement();
superi < dimZ;
superi = ai.getAndIncrement()) {
int k = superi;
ImageProcessor ip = stack1.getProcessor(k + 1);
for (int j = 0; j < dimY; j++) {
for (int i = 0; i < dimX; i++) {
int val = (int) (ip.getPixelValue(i, j));
if ((val != 0)
&& (i == 0
|| j == 0
|| k == 0
|| i == dimX - 1
|| j == dimY - 1
|| k == dimZ - 1))
// bord[k][val-2]=1;
bord[k][val - 1] = 1;
}
}
}
}
};
}
startAndJoin(threads);
for (int i = 0; i < dimZ; i++) {
for (int j = 0; j < nb; j++) {
b[j] *= (1 - bord[i][j]);
}
}
for (int j = 0; j < nb; j++) {
b[j] = (byte) (1 - b[j]);
}
}
public void run(String arg) {
imp = WindowManager.getCurrentImage();
if (imp == null) {
IJ.noImage();
return;
}
ImageStack stack = imp.getStack();
int size = stack.getSize();
if (size == 1 || (imp.getNChannels() == size && imp.isComposite())) {
IJ.error("Stack or hyperstack required");
return;
}
if (!showDialog(stack)) return;
if (hyperstack) reduceHyperstack(imp, factor, reduceSlices);
else reduceStack(imp, factor);
}
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;
}
/**
* Combination of {@link ImageJInterpolation#crop(float[][], float, float, float, float)} and
* {@link ImageJInterpolation#resize(float[][], int, int)}. Crops and resizes the input array into
* a new output array.
*
* @param input the array to work on
* @param lenX the desired length in x-direction (with, horizontal length)
* @param lenY the desired length in y-direction (height, vertical length)
* @param minX the lower index in x-direction
* @param minY the lower index in y-direction
* @param maxX the higher index in x-direction
* @param maxY the higher index in y-direction
* @return a new cropped and resized version of the input array
*/
public static float[][] cropAndResize(
float[][] input, int lenX, int lenY, float minX, float minY, float maxX, float maxY) {
float[] linearized = linearize2DArray(input);
ImageStack is = ImageStack.create(input[0].length, input.length, 1, 32);
is.setPixels(linearized, 1);
ImageProcessor ip = new ImagePlus("", is).getProcessor();
ip.setInterpolationMethod(ImageProcessor.BICUBIC);
ip.setRoi((int) minX, (int) minY, (int) Math.ceil(maxX - minX), (int) Math.ceil(maxY - minY));
float[] resized = (float[]) ip.crop().resize(lenX, lenY).getPixels();
return linearizedArrayTo2D(resized, lenX, lenY);
}
void showResults() {
int count = rt.getCounter();
// if (count==0) return;
boolean lastSlice = !processStack || slice == imp.getStackSize();
if ((showChoice == OVERLAY_OUTLINES || showChoice == OVERLAY_MASKS) && slice == 1 && count > 0)
imp.setOverlay(overlay);
else if (outlines != null && lastSlice) {
String title = imp != null ? imp.getTitle() : "Outlines";
String prefix;
if (showChoice == MASKS) prefix = "Mask of ";
else if (showChoice == ROI_MASKS) prefix = "Count Masks of ";
else prefix = "Drawing of ";
outlines.update(drawIP);
outputImage = new ImagePlus(prefix + title, outlines);
if (inSituShow) {
if (imp.getStackSize() == 1) Undo.setup(Undo.TRANSFORM, imp);
imp.setStack(null, outputImage.getStack());
} else if (!hideOutputImage) outputImage.show();
}
if (showResults && !processStack) {
TextPanel tp = IJ.getTextPanel();
if (beginningCount > 0 && tp != null && tp.getLineCount() != count) rt.show("Results");
Analyzer.firstParticle = beginningCount;
Analyzer.lastParticle = Analyzer.getCounter() - 1;
} else Analyzer.firstParticle = Analyzer.lastParticle = 0;
}
/**
* 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;
}