/**
* 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;
}
public static double[] getPixels(ImagePlus imp, int[] slices, int[] frames, int[] channels) {
ImagePlus subImp = AccessImage.getSubHyperStack(imp, slices, frames, channels);
ImageStack imageStack = subImp.getImageStack();
double[] pixels = new double[subImp.getWidth() * subImp.getHeight() * imageStack.getSize()];
for (int i = 0; i < imageStack.getSize(); i++) {
switch (subImp.getType()) {
case ImagePlus.GRAY8:
ByteProcessor byteProcessor = (ByteProcessor) imageStack.getProcessor(i + 1);
for (int iX = 0; iX < subImp.getWidth(); iX++) {
for (int iY = 0; iY < subImp.getHeight(); iY++) {
pixels[i * subImp.getWidth() * subImp.getHeight() + iY * subImp.getWidth() + iX] =
(double) byteProcessor.getPixelValue(iX, iY);
}
}
break;
case ImagePlus.GRAY16:
ShortProcessor shortProcessor = (ShortProcessor) imageStack.getProcessor(i + 1);
for (int iX = 0; iX < subImp.getWidth(); iX++) {
for (int iY = 0; iY < subImp.getHeight(); iY++) {
pixels[i * subImp.getWidth() * subImp.getHeight() + iY * subImp.getWidth() + iX] =
(double) shortProcessor.getPixelValue(iX, iY);
}
}
break;
case ImagePlus.GRAY32:
FloatProcessor floatProcessor = (FloatProcessor) imageStack.getProcessor(i + 1);
for (int iX = 0; iX < subImp.getWidth(); iX++) {
for (int iY = 0; iY < subImp.getHeight(); iY++) {
pixels[i * subImp.getWidth() * subImp.getHeight() + iY * subImp.getWidth() + iX] =
(double) floatProcessor.getPixelValue(iX, iY);
}
}
break;
case ImagePlus.COLOR_RGB:
ColorProcessor colorProcessor = (ColorProcessor) imageStack.getProcessor(i + 1);
int nX = subImp.getWidth();
int nY = subImp.getHeight();
byte[] red = new byte[nX * nY];
byte[] green = new byte[nX * nY];
byte[] blue = new byte[nX * nY];
colorProcessor.getRGB(red, green, blue);
int r, g, b;
for (int j = 0; j < nX * nY; j++) {
r = red[j] << 16;
g = green[j] << 8;
b = blue[j] << 0;
pixels[i * nX * nY + j] = (double) (r + g + b);
}
break;
}
}
return (pixels);
}
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);
}
}
}
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();
}
@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 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);
}
}
}
}
@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);
}
}
}
}
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;
}
@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);
}
}
}
}
@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);
}
}
}
}
/** 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;
}
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 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);
}
}
}
}
/**
* Calculate the Rand index and its derived statistics in 2D between some original labels and the
* corresponding proposed labels. Both images are binarized. We follow the definition of Rand
* index described by William M. Rand \cite{Rand71}.
*
* <p>BibTeX:
*
* <pre>
* @article{Rand71,
* author = {William M. Rand},
* title = {Objective criteria for the evaluation of clustering methods},
* journal = {Journal of the American Statistical Association},
* year = {1971},
* volume = {66},
* number = {336},
* pages = {846--850},
* doi = {10.2307/2284239)
* }
* </pre>
*
* @param binaryThreshold threshold value to binarize proposal (larger than 0 and smaller than 1)
* @return Rand index value and derived satatistics
*/
public ClassificationStatistics getRandIndexStats(double binaryThreshold) {
final ImageStack labelSlices = originalLabels.getImageStack();
final ImageStack proposalSlices = proposedLabels.getImageStack();
double randIndex = 0;
double tp = 0;
double tn = 0;
double fp = 0;
double fn = 0;
// Executor service to produce concurrent threads
final ExecutorService exe =
Executors.newFixedThreadPool(Runtime.getRuntime().availableProcessors());
final ArrayList<Future<ClassificationStatistics>> futures =
new ArrayList<Future<ClassificationStatistics>>();
try {
for (int i = 1; i <= labelSlices.getSize(); i++) {
futures.add(
exe.submit(
getRandIndexStatsConcurrent(
labelSlices.getProcessor(i).convertToFloat(),
proposalSlices.getProcessor(i).convertToFloat(),
binaryThreshold)));
}
// Wait for the jobs to be done
for (Future<ClassificationStatistics> f : futures) {
ClassificationStatistics cs = f.get();
randIndex += cs.metricValue;
tp += cs.truePositives;
tn += cs.trueNegatives;
fp += cs.falsePositives;
fn += cs.falseNegatives;
}
} catch (Exception ex) {
IJ.log("Error when calculating rand error in a concurrent way.");
ex.printStackTrace();
} finally {
exe.shutdown();
}
return new ClassificationStatistics(tp, tn, fp, fn, randIndex / labelSlices.getSize());
}
/** GUI involved test which is run in main function */
public void testAntiDriftController() {
final AntiDriftController ct =
new AntiDriftController(new File("/Users/moon/temp/"), 2, 3, 4, 0, 1, 0);
ct.startNewStack();
final ImageStack stackFirst = impFirst.getImageStack();
for (int k = 1; k <= stackFirst.getSize(); k++) {
ct.addXYSlice(stackFirst.getProcessor(k));
}
ct.finishStack();
ct.startNewStack();
final ImageStack stackSecond = impSecond.getImageStack();
for (int k = 1; k <= stackSecond.getSize(); k++) {
ct.addXYSlice(stackSecond.getProcessor(k));
}
ct.finishStack();
}
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);
}
}
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));
}
}
}
}
/** Test anti drift handler. */
@Test
public void testAntiDrift() {
final DefaultAntiDrift proj = new DefaultAntiDrift();
proj.startNewStack();
final ImageStack stackFirst = impFirst.getImageStack();
for (int k = 1; k <= stackFirst.getSize(); k++) {
proj.addXYSlice(stackFirst.getProcessor(k));
}
proj.finishStack();
proj.startNewStack();
final ImageStack stackSecond = impSecond.getImageStack();
for (int k = 1; k <= stackSecond.getSize(); k++) {
proj.addXYSlice(stackSecond.getProcessor(k));
}
proj.finishStack();
final double DELTA = 1e-5;
final Vector3D correction = proj.getLastCorrection();
Assert.assertEquals(16, correction.getX(), DELTA);
Assert.assertEquals(24, correction.getY(), DELTA);
Assert.assertEquals(32, correction.getZ(), DELTA);
}
/**
* Calculate the Rand error in 2D between some original labels and the corresponding proposed
* labels. Both image are binarized. The Rand error is defined as the 1 - Rand index, as described
* by William M. Rand \cite{Rand71}.
*
* <p>BibTeX:
*
* <pre>
* @article{Rand71,
* author = {William M. Rand},
* title = {Objective criteria for the evaluation of clustering methods},
* journal = {Journal of the American Statistical Association},
* year = {1971},
* volume = {66},
* number = {336},
* pages = {846--850},
* doi = {10.2307/2284239)
* }
* </pre>
*
* @param binaryThreshold threshold value to binarize proposal (larger than 0 and smaller than 1)
* @return Rand error
*/
public double getMetricValue(double binaryThreshold) {
final ImageStack labelSlices = originalLabels.getImageStack();
final ImageStack proposalSlices = proposedLabels.getImageStack();
double randError = 0;
// Executor service to produce concurrent threads
final ExecutorService exe =
Executors.newFixedThreadPool(Runtime.getRuntime().availableProcessors());
final ArrayList<Future<Double>> futures = new ArrayList<Future<Double>>();
try {
for (int i = 1; i <= labelSlices.getSize(); i++) {
futures.add(
exe.submit(
getRandErrorConcurrent(
labelSlices.getProcessor(i).convertToFloat(),
proposalSlices.getProcessor(i).convertToFloat(),
binaryThreshold)));
}
// Wait for the jobs to be done
for (Future<Double> f : futures) {
randError += f.get();
}
} catch (Exception ex) {
IJ.log("Error when calculating rand error in a concurrent way.");
ex.printStackTrace();
} finally {
exe.shutdown();
}
return randError / labelSlices.getSize();
}
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 boolean showDialog(ImageStack stack) {
hyperstack = imp.isHyperStack();
boolean showCheckbox = false;
if (hyperstack && imp.getNSlices() > 1 && imp.getNFrames() > 1) showCheckbox = true;
else if (hyperstack && imp.getNSlices() > 1) reduceSlices = true;
int n = stack.getSize();
GenericDialog gd = new GenericDialog("Reduce Size");
gd.addNumericField("Reduction Factor:", factor, 0);
if (showCheckbox) gd.addCheckbox("Reduce in Z-Dimension", false);
gd.showDialog();
if (gd.wasCanceled()) return false;
factor = (int) gd.getNextNumber();
if (showCheckbox) reduceSlices = gd.getNextBoolean();
return true;
}
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();
}
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);
}
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];
}
}
}
void setup(int channels, ImageStack stack2) {
if (stack2 != null
&& stack2.getSize() > 0
&& (stack2.getProcessor(1) instanceof ColorProcessor)) { // RGB?
cip = null;
lut = null;
return;
}
setupLuts(channels);
if (mode == COMPOSITE) {
cip = new ImageProcessor[channels];
for (int i = 0; i < channels; ++i) {
cip[i] = stack2.getProcessor(i + 1);
cip[i].setLut(lut[i]);
}
currentSlice = currentFrame = 1;
}
}
public CompositeImage(ImagePlus imp, int mode) {
if (mode < COMPOSITE || mode > GRAYSCALE) mode = COLOR;
this.mode = mode;
int channels = imp.getNChannels();
bitDepth = getBitDepth();
if (IJ.debugMode) IJ.log("CompositeImage: " + imp + " " + mode + " " + channels);
ImageStack stack2;
boolean isRGB = imp.getBitDepth() == 24;
if (isRGB) {
if (imp.getImageStackSize() > 1)
throw new IllegalArgumentException("RGB stacks not supported");
stack2 = getRGBStack(imp);
} else stack2 = imp.getImageStack();
int stackSize = stack2.getSize();
if (channels == 1 && isRGB) channels = 3;
if (channels == 1 && stackSize <= MAX_CHANNELS && !imp.dimensionsSet) channels = stackSize;
if (channels < 1 || (stackSize % channels) != 0)
throw new IllegalArgumentException("stacksize not multiple of channels");
if (mode == COMPOSITE && channels > MAX_CHANNELS) this.mode = COLOR;
compositeImage = true;
int z = imp.getNSlices();
int t = imp.getNFrames();
if (channels == stackSize || channels * z * t != stackSize)
setDimensions(channels, stackSize / channels, 1);
else setDimensions(channels, z, t);
setStack(imp.getTitle(), stack2);
setCalibration(imp.getCalibration());
FileInfo fi = imp.getOriginalFileInfo();
if (fi != null) {
displayRanges = fi.displayRanges;
channelLuts = fi.channelLuts;
}
setFileInfo(fi);
Object info = imp.getProperty("Info");
if (info != null) setProperty("Info", imp.getProperty("Info"));
if (mode == COMPOSITE) {
for (int i = 0; i < MAX_CHANNELS; i++) active[i] = true;
} else active[0] = true;
// if (!(channels==3&&stackSize==3))
setRoi(imp.getRoi());
setOverlay(imp.getOverlay());
if (channels != stackSize) setOpenAsHyperStack(true);
}
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;
}