@Test
public final void testErosionCubicMeshC6() {
ImageStack mask = createCubicMeshImage();
invertGray8Stack(mask);
ImageStack marker = ImageStack.create(20, 20, 20, 8);
marker.setVoxel(5, 5, 5, 255);
invertGray8Stack(marker);
GeodesicReconstruction3DHybrid0Gray8 algo = new GeodesicReconstruction3DHybrid0Gray8();
algo.setReconstructionType(GeodesicReconstructionType.BY_EROSION);
algo.setConnectivity(6);
ImageStack result = algo.applyTo(marker, mask);
assertEquals(0, result.getVoxel(5, 15, 5), .01);
assertEquals(255, result.getVoxel(0, 0, 0), .01);
int sizeX = mask.getWidth();
int sizeY = mask.getHeight();
int sizeZ = mask.getSize();
for (int z = 0; z < sizeZ; z++) {
for (int y = 0; y < sizeY; y++) {
for (int x = 0; x < sizeX; x++) {
assertEquals(result.getVoxel(x, y, z), mask.getVoxel(x, y, z), .01);
}
}
}
}
@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(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;
}
}
@Test
public final void testDilationCochleaVolumeC6() {
String fileName = getClass().getResource("/files/bat-cochlea-volume.tif").getFile();
ImagePlus imagePlus = IJ.openImage(fileName);
assertNotNull(imagePlus);
assertTrue(imagePlus.getStackSize() > 0);
ImageStack mask = imagePlus.getStack();
// Ensure regularity of the mask
mask = Morphology.opening(mask, CubeStrel.fromRadius(1));
int width = mask.getWidth();
int height = mask.getHeight();
int depth = mask.getSize();
int bitDepth = mask.getBitDepth();
ImageStack marker = ImageStack.create(width, height, depth, bitDepth);
marker.setVoxel(20, 80, 50, 255);
GeodesicReconstruction3DHybrid0Gray8 algo = new GeodesicReconstruction3DHybrid0Gray8();
algo.setConnectivity(6);
algo.verbose = false;
ImageStack result = algo.applyTo(marker, mask);
for (int z = 0; z < depth; z++) {
for (int y = 0; y < height; y++) {
for (int x = 0; x < width; x++) {
assertEquals(result.getVoxel(x, y, z), mask.getVoxel(x, y, z), .01);
}
}
}
}
/**
* 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;
}
@Test
public final void testDilationHilbertCurveC26() {
String fileName = getClass().getResource("/files/hilbert3d.tif").getFile();
ImagePlus imagePlus = IJ.openImage(fileName);
assertNotNull(imagePlus);
assertTrue(imagePlus.getStackSize() > 0);
ImageStack mask = imagePlus.getStack();
int width = mask.getWidth();
int height = mask.getHeight();
int depth = mask.getSize();
int bitDepth = mask.getBitDepth();
ImageStack marker = ImageStack.create(width, height, depth, bitDepth);
marker.setVoxel(3, 0, 0, 255);
GeodesicReconstruction3DHybrid0Gray8 algo = new GeodesicReconstruction3DHybrid0Gray8();
algo.setConnectivity(26);
algo.verbose = false;
ImageStack result = algo.applyTo(marker, mask);
for (int z = 0; z < depth; z++) {
for (int y = 0; y < height; y++) {
for (int x = 0; x < width; x++) {
assertEquals(result.getVoxel(x, y, z), mask.getVoxel(x, y, z), .01);
}
}
}
}
@Test
public final void testApplyTo() {
GeodesicReconstructionByDilation3DGray8 algo = new GeodesicReconstructionByDilation3DGray8();
String fileName = getClass().getResource("/files/bat-cochlea-volume.tif").getFile();
ImagePlus imagePlus = IJ.openImage(fileName);
assertNotNull(imagePlus);
assertTrue(imagePlus.getStackSize() > 0);
ImageStack mask = imagePlus.getStack();
int width = mask.getWidth();
int height = mask.getHeight();
int depth = mask.getSize();
int bitDepth = mask.getBitDepth();
ImageStack marker = ImageStack.create(width, height, depth, bitDepth);
marker.setVoxel(20, 80, 50, 255);
ImageStack result = algo.applyTo(marker, mask);
for (int z = 0; z < depth; z++) {
for (int y = 0; y < height; y++) {
for (int x = 0; x < width; x++) {
assertEquals(result.getVoxel(x, y, z), mask.getVoxel(x, y, z), .01);
}
}
}
}
private final void assertStackEquals(ImageStack image, ImageStack image2) {
int sizeX = image.getWidth();
int sizeY = image.getHeight();
int sizeZ = image.getSize();
assertEquals(sizeX, image2.getWidth());
assertEquals(sizeY, image2.getHeight());
assertEquals(sizeZ, image2.getSize());
for (int z = 0; z < sizeZ; z++) {
for (int y = 0; y < sizeY; y++) {
for (int x = 0; x < sizeX; x++) {
assertEquals(image.getVoxel(x, y, z), image2.getVoxel(x, y, z), .01);
}
}
}
}
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);
}
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 DataImporter(final String resultsFilePath, final boolean readWeights) {
super();
final ImageStack file = IJ.openImage(resultsFilePath).getImageStack();
slices = file.getSize();
for (int i = 1; i <= file.getSize(); i++) {
for (int y = 0; y < file.getHeight(); y++) {
final float[] point = new float[14];
for (int x = 0; x < file.getWidth(); x++) {
point[x] = file.getProcessor(i).getf(x, y);
}
this.add(point);
}
}
}
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 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;
}
/**
* Constructor that builds up a VectorProcessor froma a stack of {@link FloatProcessor}s This is
* the constructor that is being used in @link{KMeans}
*
* @param stack a stack of {@link FloatProcessor}s.
*/
public VectorProcessor(final ImageStack stack) {
/* Calls the constructor
@link{VectorProcessor(final int width, final int height, final int numberOfValues)}*/
this(stack.getWidth(), stack.getHeight(), stack.getSize());
/* Gets the images in the stack and puts them into an array of Object*/
final Object[] slices = stack.getImageArray();
/* For each image (= component) in the stack */
for (int i = 0; i < numberOfValues; ++i) {
/* get the pixels as an array of float */
final float[] values = (float[]) slices[i];
/* for each pixel */
for (int j = 0; j < values.length; j++) {
/* store the value */
pixels[j][i] = values[j];
}
}
}
private ImageStack createInvertedLeveledCubeGraphImage() {
ImageStack stack = createCubeGraphImage();
for (int z = 0; z < stack.getSize(); z++) {
for (int y = 0; y < stack.getHeight(); y++) {
for (int x = 0; x < stack.getWidth(); x++) {
stack.setVoxel(x, y, z, 255 - stack.getVoxel(x, y, z));
}
}
}
stack.setVoxel(5, 1, 1, 32);
stack.setVoxel(9, 5, 1, 64);
stack.setVoxel(9, 9, 5, 96);
stack.setVoxel(9, 5, 9, 128);
stack.setVoxel(5, 1, 9, 160);
stack.setVoxel(1, 5, 9, 192);
stack.setVoxel(1, 9, 5, 224);
return stack;
}
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);
}
@Test
public final void testErosionCochleaVolumeC26() {
String fileName = getClass().getResource("/files/bat-cochlea-volume.tif").getFile();
ImagePlus imagePlus = IJ.openImage(fileName);
assertNotNull(imagePlus);
assertTrue(imagePlus.getStackSize() > 0);
ImageStack mask = imagePlus.getStack();
// Ensure regularity of the mask
mask = Morphology.opening(mask, CubeStrel.fromRadius(1));
invertGray8Stack(mask);
int width = mask.getWidth();
int height = mask.getHeight();
int depth = mask.getSize();
int bitDepth = mask.getBitDepth();
ImageStack marker = ImageStack.create(width, height, depth, bitDepth);
marker.setVoxel(20, 80, 50, 255);
invertGray8Stack(marker);
GeodesicReconstruction3DHybrid0Gray8 algo =
new GeodesicReconstruction3DHybrid0Gray8(GeodesicReconstructionType.BY_EROSION);
algo.setConnectivity(26);
ImageStack result = algo.applyTo(marker, mask);
for (int z = 0; z < depth; z++) {
for (int y = 0; y < height; y++) {
for (int x = 0; x < width; x++) {
if (Math.abs(result.getVoxel(x, y, z) - mask.getVoxel(x, y, z)) > .1) {
System.out.println("x=" + x + " y=" + y + " z=" + z);
System.out.println(" mask = " + (int) mask.getVoxel(x, y, z));
System.out.println(" res = " + (int) result.getVoxel(x, y, z));
assertTrue(false);
}
}
}
}
}
public int calculnb(final ImageStack stack1) {
final AtomicInteger ai = new AtomicInteger(1);
final int dimX = stack1.getWidth();
final int dimY = stack1.getHeight();
final int dimZ = stack1.getSize();
final int[] value = new int[dimZ];
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 current = superi;
ImageProcessor ip = stack1.getProcessor(current);
for (int j = 0; j < dimY; j++) {
for (int i = 0; i < dimX; i++) {
int val = (int) (ip.getPixelValue(i, j));
if (val > value[current - 1]) value[current - 1] = val;
}
}
}
}
};
}
startAndJoin(threads);
int val = 0;
for (int i = 0; i < dimZ; i++) {
if (val < value[i]) val = value[i];
}
return val;
}
void calculvolumestack(final ImageStack stack1, int nb, int v[]) {
final AtomicInteger ai = new AtomicInteger(1);
final int dimX = stack1.getWidth();
final int dimY = stack1.getHeight();
final int dimZ = stack1.getSize();
final int[][] vol = new int[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 current = superi;
ImageProcessor ip = stack1.getProcessor(current);
for (int j = 0; j < dimY; j++) {
for (int i = 0; i < dimX; i++) {
int val = (int) (ip.getPixelValue(i, j));
// if (val!=0) vol[current-1][val-2]++;
if (val != 0) vol[current - 1][val - 1]++;
}
}
}
}
};
}
startAndJoin(threads);
for (int i = 0; i < dimZ; i++) {
for (int j = 0; j < nb; j++) {
v[j] += vol[i][j];
}
}
}
public void makeTransition(ImagePlus imp, int from, int num) {
if (from > imp.getStackSize()) {
IJ.error("Need a following slice to which to transit.");
return;
}
num++; // so that really num slices are added
ImageStack stack = imp.getStack();
int[] before = (int[]) (stack.getProcessor(from).convertToRGB().getPixels());
int[] after = (int[]) (stack.getProcessor(from + 1).convertToRGB().getPixels());
for (int z = 1; z < num; z++) {
ColorProcessor bp = new ColorProcessor(stack.getWidth(), stack.getHeight());
int[] pixels = (int[]) bp.getPixels();
double dp = z;
double dn = num - z;
for (int i = 0; i < pixels.length; i++) {
pixels[i] = interpolate(before[i], dp, after[i], dn);
}
new ImagePlus("slice + " + z, bp).show();
stack.addSlice("", bp, from + z - 1);
}
}
@Test
public final void testRegionalMaxima_BatCochlea() {
String fileName = getClass().getResource("/files/bat-cochlea-volume.tif").getFile();
ImagePlus imagePlus = IJ.openImage(fileName);
assertNotNull(imagePlus);
assertTrue(imagePlus.getStackSize() > 0);
// load the reference image, and get its size
ImageStack image = imagePlus.getStack();
int sizeX = image.getWidth();
int sizeY = image.getHeight();
int sizeZ = image.getSize();
// create test image:
// use cochlea volume, but 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);
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);
}
}
}
}
ImageProcessor setup(ImagePlus imp) {
ImageProcessor ip;
int type = imp.getType();
if (type != ImagePlus.COLOR_RGB) return null;
ip = imp.getProcessor();
int id = imp.getID();
int slice = imp.getCurrentSlice();
if ((id != previousImageID) | (slice != previousSlice) | (flag)) {
flag = false; // if true, flags a change from HSB to RGB or viceversa
numSlices = imp.getStackSize();
stack = imp.getStack();
width = stack.getWidth();
height = stack.getHeight();
numPixels = width * height;
hSource = new byte[numPixels];
sSource = new byte[numPixels];
bSource = new byte[numPixels];
// restore = (int[])ip.getPixelsCopy(); //This runs into trouble sometimes, so do it the
// long way:
int[] temp = (int[]) ip.getPixels();
restore = new int[numPixels];
for (int i = 0; i < numPixels; i++) restore[i] = temp[i];
fillMask = new int[numPixels];
// Get hsb or rgb from image.
ColorProcessor cp = (ColorProcessor) ip;
IJ.showStatus("Gathering data");
if (isRGB) cp.getRGB(hSource, sSource, bSource);
else cp.getHSB(hSource, sSource, bSource);
IJ.showStatus("done");
// Create a spectrum ColorModel for the Hue histogram plot.
Color c;
byte[] reds = new byte[256];
byte[] greens = new byte[256];
byte[] blues = new byte[256];
for (int i = 0; i < 256; i++) {
c = Color.getHSBColor(i / 255f, 1f, 1f);
reds[i] = (byte) c.getRed();
greens[i] = (byte) c.getGreen();
blues[i] = (byte) c.getBlue();
}
ColorModel cm = new IndexColorModel(8, 256, reds, greens, blues);
// Make an image with just the hue from the RGB image and the spectrum LUT.
// This is just for a hue histogram for the plot. Do not show it.
// ByteProcessor bpHue = new ByteProcessor(width,height,h,cm);
ByteProcessor bpHue = new ByteProcessor(width, height, hSource, cm);
ImagePlus impHue = new ImagePlus("Hue", bpHue);
// impHue.show();
ByteProcessor bpSat = new ByteProcessor(width, height, sSource, cm);
ImagePlus impSat = new ImagePlus("Sat", bpSat);
// impSat.show();
ByteProcessor bpBri = new ByteProcessor(width, height, bSource, cm);
ImagePlus impBri = new ImagePlus("Bri", bpBri);
// impBri.show();
plot.setHistogram(impHue, 0);
splot.setHistogram(impSat, 1);
bplot.setHistogram(impBri, 2);
updateLabels();
updatePlot();
updateScrollBars();
imp.updateAndDraw();
}
previousImageID = id;
previousSlice = slice;
return ip;
}
public static boolean write(ImagePlus imp, String path) {
if (null == imp) return false;
ImageStack stack = imp.getStack();
float pixelWidth = (float) imp.getCalibration().pixelWidth;
float pixelHeight = (float) imp.getCalibration().pixelHeight;
float pixelDepth = (float) imp.getCalibration().pixelDepth;
String unitString = imp.getCalibration().getXUnit();
int size1 = stack.getWidth();
int size2 = stack.getHeight();
int size3 = stack.getSize();
// IJ.log("/"+size1+"/");
File outputFile = new File(path);
try {
// Construct the BufferedOutputStream object
BufferedOutputStream bufferedOutput =
new BufferedOutputStream(new FileOutputStream(outputFile));
DataOutputStream dataOut = new DataOutputStream(bufferedOutput);
// Start writing to the output stream
int zero = 0;
dataOut.writeInt(zero);
dataOut.writeInt(zero);
dataOut.writeInt(zero);
int version = 1;
dataOut.writeInt(reverse(version));
// type of data
// type= 2 - int
// type= 5 - float
int type = 5;
dataOut.writeInt(reverse(type));
dataOut.writeInt(reverse(size1));
dataOut.writeInt(reverse(size2));
dataOut.writeInt(reverse(size3));
// Spatial calibration
dataOut.writeInt(reverse(unitStringToInt(unitString)));
dataOut.writeInt(reverse(Float.floatToIntBits(pixelWidth)));
dataOut.writeInt(reverse(Float.floatToIntBits(pixelHeight)));
dataOut.writeInt(reverse(Float.floatToIntBits(pixelDepth)));
// write pixels
for (int z = 0; z < size3; ++z) {
for (int x = 0; x < size1; ++x) {
for (int y = 0; y < size2; ++y) {
dataOut.writeInt(reverse(Float.floatToIntBits((float) stack.getVoxel(x, y, z))));
}
}
}
// cleanup output stream
dataOut.flush();
dataOut.close();
} catch (Exception e) {
e.printStackTrace();
return false;
}
return true;
}
void boitestack(
final ImageStack stack1,
final int nb,
final double[] xg,
final double[] yg,
final double[] zg,
final double[][][] dir,
double[][] lmin,
double[][] lmax) {
final AtomicInteger ai = new AtomicInteger(0);
final int dimX = stack1.getWidth();
final int dimY = stack1.getHeight();
final int dimZ = stack1.getSize();
final double[][][] lmint = new double[dimZ][nb][3];
final double[][][] lmaxt = new double[dimZ][nb][3];
for (int k = 0; k < nb; k++) {
lmin[k][0] = 100000;
lmin[k][1] = 100000;
lmin[k][2] = 100000;
lmax[k][0] = -100000;
lmax[k][1] = -100000;
lmax[k][2] = -100000;
}
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 l = 0; l < nb; l++) {
lmint[k][l][0] = 100000;
lmint[k][l][1] = 100000;
lmint[k][l][2] = 100000;
lmaxt[k][l][0] = -100000;
lmaxt[k][l][1] = -100000;
lmaxt[k][l][2] = -100000;
}
for (int j = 0; j < dimY; j++) {
for (int i = 0; i < dimX; i++) {
int pix = (int) (ip.getPixelValue(i, j));
if (pix != 0) {
// double v1 =
// (i-xg[pix-2])*dir[0][0][pix-2]+(j-yg[pix-2])*dir[1][0][pix-2]+(k-zg[pix-2])*dir[2][0][pix-2];
// double v2 =
// (i-xg[pix-2])*dir[0][1][pix-2]+(j-yg[pix-2])*dir[1][1][pix-2]+(k-zg[pix-2])*dir[2][1][pix-2];
// double v3 =
// (i-xg[pix-2])*dir[0][2][pix-2]+(j-yg[pix-2])*dir[1][2][pix-2]+(k-zg[pix-2])*dir[2][2][pix-2];
// if (v1<lmint[k][pix-2][0]) lmint[k][pix-2][0]=v1;
// if (v1>lmaxt[k][pix-2][0]) lmaxt[k][pix-2][0]=v1;
// if (v2<lmint[k][pix-2][1]) lmint[k][pix-2][1]=v2;
// if (v2>lmaxt[k][pix-2][1]) lmaxt[k][pix-2][1]=v2;
// if (v3<lmint[k][pix-2][2]) lmint[k][pix-2][2]=v3;
// if (v3>lmaxt[k][pix-2][2]) lmaxt[k][pix-2][2]=v3;
double v1 =
(i - xg[pix - 1]) * dir[0][0][pix - 1]
+ (j - yg[pix - 1]) * dir[1][0][pix - 1]
+ (k - zg[pix - 1]) * dir[2][0][pix - 1];
double v2 =
(i - xg[pix - 1]) * dir[0][1][pix - 1]
+ (j - yg[pix - 1]) * dir[1][1][pix - 1]
+ (k - zg[pix - 1]) * dir[2][1][pix - 1];
double v3 =
(i - xg[pix - 1]) * dir[0][2][pix - 1]
+ (j - yg[pix - 1]) * dir[1][2][pix - 1]
+ (k - zg[pix - 1]) * dir[2][2][pix - 1];
if (v1 < lmint[k][pix - 1][0]) lmint[k][pix - 1][0] = v1;
if (v1 > lmaxt[k][pix - 1][0]) lmaxt[k][pix - 1][0] = v1;
if (v2 < lmint[k][pix - 1][1]) lmint[k][pix - 1][1] = v2;
if (v2 > lmaxt[k][pix - 1][1]) lmaxt[k][pix - 1][1] = v2;
if (v3 < lmint[k][pix - 1][2]) lmint[k][pix - 1][2] = v3;
if (v3 > lmaxt[k][pix - 1][2]) lmaxt[k][pix - 1][2] = v3;
}
}
}
}
}
};
}
startAndJoin(threads);
for (int i = 0; i < dimZ; i++) {
for (int j = 0; j < nb; j++) {
for (int l = 0; l < 3; l++) {
if (lmint[i][j][l] < lmin[j][l]) lmin[j][l] = lmint[i][j][l];
if (lmaxt[i][j][l] > lmax[j][l]) lmax[j][l] = lmaxt[i][j][l];
}
}
lmint[i] = null;
lmaxt[i] = null;
}
}
void calculinertiestack(
final ImageStack stack1,
int nb,
final double[] xg,
final double[] yg,
final double[] zg,
double[][][] I) {
final AtomicInteger ai = new AtomicInteger(0);
final int dimX = stack1.getWidth();
final int dimY = stack1.getHeight();
final int dimZ = stack1.getSize();
final double[][][][] inert = new double[dimZ][nb][3][3];
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 pix = (int) (ip.getPixelValue(i, j));
if (pix != 0) {
//
// inert[k][pix-2][0][0]+=(i-yg[pix-2])*(i-yg[pix-2])+(k-zg[pix-2])*(k-zg[pix-2])+1.0/6.0;
// inert[k][pix-2][0][1]-=(j-xg[pix-2])*(i-yg[pix-2]);
// inert[k][pix-2][0][2]-=(j-xg[pix-2])*(k-zg[pix-2]);
//
// inert[k][pix-2][1][1]+=(j-xg[pix-2])*(j-xg[pix-2])+(k-zg[pix-2])*(k-zg[pix-2])+1.0/6.0;
// inert[k][pix-2][1][2]-=(i-yg[pix-2])*(k-zg[pix-2]);
//
// inert[k][pix-2][2][2]+=(j-xg[pix-2])*(j-xg[pix-2])+(i-yg[pix-2])*(i-yg[pix-2])+1.0/6.0;
inert[k][pix - 1][0][0] +=
(j - yg[pix - 1]) * (j - yg[pix - 1])
+ (k - zg[pix - 1]) * (k - zg[pix - 1])
+ 1.0 / 6.0;
inert[k][pix - 1][0][1] -= (i - xg[pix - 1]) * (j - yg[pix - 1]);
inert[k][pix - 1][0][2] -= (i - xg[pix - 1]) * (k - zg[pix - 1]);
inert[k][pix - 1][1][1] +=
(i - xg[pix - 1]) * (i - xg[pix - 1])
+ (k - zg[pix - 1]) * (k - zg[pix - 1])
+ 1.0 / 6.0;
inert[k][pix - 1][1][2] -= (j - yg[pix - 1]) * (k - zg[pix - 1]);
inert[k][pix - 1][2][2] +=
(i - xg[pix - 1]) * (i - xg[pix - 1])
+ (j - yg[pix - 1]) * (j - yg[pix - 1])
+ 1.0 / 6.0;
}
}
}
}
}
};
}
startAndJoin(threads);
for (int i = 0; i < dimZ; i++) {
for (int j = 0; j < nb; j++) {
for (int l = 0; l < 3; l++) {
for (int m = 0; m <= l; m++) {
I[l][m][j] += inert[i][j][l][m];
}
}
}
inert[i] = null;
}
for (int j = 0; j < nb; j++) {
I[1][0][j] = I[0][1][j];
I[2][0][j] = I[0][2][j];
I[2][1][j] = I[1][2][j];
}
}
void calculcgstack(
final ImageStack stack1,
int nb,
final int[] v,
final double[] xg,
final double[] yg,
final double[] zg) {
final AtomicInteger ai = new AtomicInteger(0);
final int dimX = stack1.getWidth();
final int dimY = stack1.getHeight();
final int dimZ = stack1.getSize();
final int[][] vol = new int[dimZ][nb];
final int[][] tmpxg = new int[dimZ][nb];
final int[][] tmpyg = new int[dimZ][nb];
final int[][] tmpzg = new int[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 pix = (int) (ip.getPixelValue(i, j));
if (pix != 0) {
// tmpxg[k][pix-2] += j;
// tmpyg[k][pix-2] += i;
// tmpzg[k][pix-2] += k;
// vol[k][pix-2]++;
tmpxg[k][pix - 1] += i;
tmpyg[k][pix - 1] += j;
tmpzg[k][pix - 1] += k;
vol[k][pix - 1]++;
}
}
}
}
}
};
}
startAndJoin(threads);
for (int i = 0; i < dimZ; i++) {
for (int j = 0; j < nb; j++) {
v[j] += vol[i][j];
xg[j] += tmpxg[i][j];
yg[j] += tmpyg[i][j];
zg[j] += tmpzg[i][j];
}
}
for (int i = 0; i < nb; i++) {
xg[i] = (1.0 * xg[i] / v[i]);
yg[i] = (1.0 * yg[i] / v[i]);
zg[i] = (1.0 * zg[i] / v[i]);
}
}
void calculsurfacemarch3stack(final ImageStack stack1, int nb, final double[] tri, double[] s2) {
final AtomicInteger ai = new AtomicInteger(0);
final int dimX = stack1.getWidth();
final int dimY = stack1.getHeight();
final int dimZ = stack1.getSize();
final double[][] surf = new double[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 - 1;
superi = ai.getAndIncrement()) {
int k = superi;
ImageProcessor ip1, ip2;
ip1 = stack1.getProcessor(k + 1);
ip2 = stack1.getProcessor(k + 2);
for (int j = 0; j < dimY - 1; j++) {
for (int i = 0; i < dimX - 1; i++) {
int[] p = new int[8];
int p1, p2, p3, p4, p5, p6, p7, p8, ptot;
int[] nontab = new int[8];
ptot = (short) 0;
p[0] = (int) ip1.getPixelValue(i, j);
p[1] = (int) ip1.getPixelValue(i, j + 1);
p[2] = (int) ip2.getPixelValue(i, j);
p[3] = (int) ip2.getPixelValue(i, j + 1);
p[4] = (int) ip1.getPixelValue(i + 1, j);
p[5] = (int) ip1.getPixelValue(i + 1, j + 1);
p[6] = (int) ip2.getPixelValue(i + 1, j);
p[7] = (int) ip2.getPixelValue(i + 1, j + 1);
int pixcoul = 0;
for (int l = 0; l < 8; l++) nontab[l] = 0;
int cpt = 0;
// look for different colors
for (int l = 0; l < 8; l++) {
if (p[l] != 0 && appart(p[l], nontab, 8) == 1) {
nontab[cpt] = p[l];
cpt++;
}
}
for (int mm = 0; mm < cpt; mm++) {
p1 = 0;
p2 = 0;
p3 = 0;
p4 = 0;
p5 = 0;
p6 = 0;
p7 = 0;
p8 = 0;
if (p[0] != 0 && p[0] == nontab[mm]) {
pixcoul = nontab[mm];
p1 = 1;
}
if (p[1] != 0 && p[1] == nontab[mm]) {
pixcoul = nontab[mm];
p2 = 4;
}
if (p[2] != 0 && p[2] == nontab[mm]) {
pixcoul = nontab[mm];
p3 = 2;
}
if (p[3] != 0 && p[3] == nontab[mm]) {
pixcoul = nontab[mm];
p4 = 8;
}
if (p[4] != 0 && p[4] == nontab[mm]) {
pixcoul = nontab[mm];
p5 = 16;
}
if (p[5] != 0 && p[5] == nontab[mm]) {
pixcoul = nontab[mm];
p6 = 64;
}
if (p[6] != 0 && p[6] == nontab[mm]) {
pixcoul = nontab[mm];
p7 = 32;
}
if (p[7] != 0 && p[7] == nontab[mm]) {
pixcoul = nontab[mm];
p8 = 128;
}
ptot = (p1 + p2 + p3 + p4 + p5 + p6 + p7 + p8);
if (pixcoul != 0) {
surf[k][(int) (pixcoul - 1)] += tri[(int) (ptot)];
// surf[k][(int)(pixcoul-2)]+=tri[(int)(ptot)];
}
}
}
}
}
}
};
}
startAndJoin(threads);
for (int i = 0; i < dimZ; i++) {
for (int j = 0; j < nb; j++) {
s2[j] += surf[i][j];
}
}
}