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 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 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);
}
}
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 ImagePlus findSurfaceVoxels(final ImagePlus imp) {
final int w = imp.getWidth();
final int h = imp.getHeight();
final int d = imp.getImageStackSize();
final ImageStack stack = imp.getImageStack();
final ImageStack surfaceStack = new ImageStack(w, h, d);
for (int z = 0; z < d; z++) {
IJ.showStatus("Finding surface voxels");
final byte[] pixels = (byte[]) stack.getPixels(z + 1);
surfaceStack.setPixels(pixels.clone(), z + 1);
final ImageProcessor surfaceIP = surfaceStack.getProcessor(z + 1);
for (int y = 0; y < h; y++) {
checkNeighbours:
for (int x = 0; x < w; x++) {
if (getPixel(stack, x, y, z, w, h, d) == (byte) 0) continue;
for (int nz = -1; nz < 2; nz++) {
final int znz = z + nz;
for (int ny = -1; ny < 2; ny++) {
final int yny = y + ny;
for (int nx = -1; nx < 2; nx++) {
final int xnx = x + nx;
final byte pixel = getPixel(stack, xnx, yny, znz, w, h, d);
if (pixel == (byte) 0) continue checkNeighbours;
}
}
}
// we checked all the neighbours for a 0
// but didn't find one, so this is not a surface voxel
surfaceIP.set(x, y, (byte) 1);
}
}
}
// turn all the 1's into 0's
final int wh = w * h;
for (int z = 0; z < d; z++) {
IJ.showStatus("Finding surface voxels");
final ImageProcessor ip = surfaceStack.getProcessor(z + 1);
for (int i = 0; i < wh; i++) {
if (ip.get(i) == (byte) 1) ip.set(i, (byte) 0);
}
}
final ImagePlus surfaceImp = new ImagePlus("Surface");
surfaceImp.setStack(surfaceStack);
surfaceImp.setCalibration(imp.getCalibration());
return surfaceImp;
}
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);
}
/**
* 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;
}
/**
* 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;
}
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);
}
/**
* 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());
}
@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();
}
}
/** 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 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 void run(String arg0) {
while (numOfIteration <= numberOfImagesToProcess - 1) {
ImageStack cloudStack = loadImages();
ref = cloudStack.getProcessor(1); // Referenzbinärbild
corr = cloudStack.getProcessor(2); // Korrespondenzbinärbild
// An dieser Stelle kommt das Tracking die entstehenden Listen, kannst du ja mit einer
// Konsolenausgabe überprüfen
referenceList = Tracking.startTracking(ref, numOfIteration);
correspondenceList = Tracking.startTracking(corr, numOfIteration);
numOfIteration++;
}
}
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;
}
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 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 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 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();
}
}
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();
}
/**
* Reduce error in thickness quantitation by trimming the one pixel overhang in the thickness map
*
* @param imp Binary input image
* @param impLTC Thickness map
* @param inv true if calculating thickness of background, false for foreground
* @return Thickness map with pixels masked by input image
*/
private ImagePlus trimOverhang(ImagePlus imp, ImagePlus impLTC, boolean inv) {
final int w = imp.getWidth();
final int h = imp.getHeight();
final int d = imp.getImageStackSize();
final ImageStack stack = imp.getImageStack();
final ImageStack mapStack = impLTC.getImageStack();
final int keepValue = inv ? 0 : 255;
ImageProcessor ip = new ByteProcessor(w, h);
ImageProcessor map = new FloatProcessor(w, h);
for (int z = 1; z <= d; z++) {
IJ.showStatus("Masking thickness map...");
IJ.showProgress(z, d);
ip = stack.getProcessor(z);
map = mapStack.getProcessor(z);
for (int y = 0; y < h; y++) {
for (int x = 0; x < w; x++) {
if (ip.get(x, y) != keepValue) map.set(x, y, 0);
}
}
}
return impLTC;
}
public static ImagePlus multiply(ImagePlus a, double[] b) {
Duplicator dp = new Duplicator();
ImagePlus c = dp.run(a);
IJ.run(c, "32-bit", "");
ImageStack ims = c.getStack();
ImagePlus tmpImp;
for (int i = 0; i < c.getNSlices(); i++) {
tmpImp = new ImagePlus("tmp", ims.getProcessor(i + 1));
IJ.run(tmpImp, "Multiply...", "value=" + Double.toString(b[i]));
ims.setProcessor(tmpImp.getProcessor(), i + 1);
}
c = new ImagePlus(a.getTitle() + "_mult", ims);
return (c);
}
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;
}
}
/**
* Assigns the data values of a {@link Dataset} from a paired {@link ImagePlus}. Assumes the
* Dataset and ImagePlus have compatible dimensions and that the data planes are not directly
* mapped. Gets values via {@link ImageProcessor}::getf(). In cases where there is a narrowing of
* data into modern ImageJ types the data is range clamped. Does not change the Dataset's
* metadata.
*/
@Override
public void updateDataset(final Dataset ds, final ImagePlus imp) {
final RealType<?> type = ds.getType();
final double typeMin = type.getMinValue();
final double typeMax = type.getMaxValue();
final boolean signed16BitData = type instanceof ShortType;
final RandomAccess<? extends RealType<?>> accessor = ds.getImgPlus().randomAccess();
final long[] dims = ds.getDims();
final AxisType[] axes = ds.getAxes();
final int xIndex = ds.getAxisIndex(Axes.X);
final int yIndex = ds.getAxisIndex(Axes.Y);
final int zIndex = ds.getAxisIndex(Axes.Z);
final int tIndex = ds.getAxisIndex(Axes.TIME);
final int xSize = imp.getWidth();
final int ySize = imp.getHeight();
final int zSize = imp.getNSlices();
final int tSize = imp.getNFrames();
final int cSize = imp.getNChannels();
final ImageStack stack = imp.getStack();
int planeNum = 1;
final long[] pos = new long[dims.length];
for (int t = 0; t < tSize; t++) {
if (tIndex >= 0) pos[tIndex] = t;
for (int z = 0; z < zSize; z++) {
if (zIndex >= 0) pos[zIndex] = z;
for (int c = 0; c < cSize; c++) {
LegacyUtils.fillChannelIndices(dims, axes, c, pos);
final ImageProcessor proc = stack.getProcessor(planeNum++);
for (int x = 0; x < xSize; x++) {
if (xIndex >= 0) pos[xIndex] = x;
for (int y = 0; y < ySize; y++) {
if (yIndex >= 0) pos[yIndex] = y;
accessor.setPosition(pos);
double value = proc.getf(x, y);
if (signed16BitData) value -= 32768.0;
if (value < typeMin) value = typeMin;
else if (value > typeMax) value = typeMax;
accessor.get().setReal(value);
}
}
}
}
}
ds.update();
}
// extract range of slices
ImagePlus stackRange(ImagePlus imp, int first, int last, int inc, String title) throws Exception {
ImageStack stack = imp.getStack();
ImageStack stack2 = null;
Roi roi = imp.getRoi();
for (int i = first, j = 0; i <= last; i += inc) {
// IJ.log(first+" "+last+" "+inc+" "+i);
IJ.showProgress(i - first, last - first);
int currSlice = i - j;
ImageProcessor ip2 = stack.getProcessor(currSlice);
// ip2.setRoi(roi);
// ip2 = ip2.crop();
if (stack2 == null) stack2 = new ImageStack(ip2.getWidth(), ip2.getHeight());
stack2.addSlice(stack.getSliceLabel(currSlice), ip2);
}
ImagePlus substack = imp.createImagePlus();
substack.setStack(title, stack2);
substack.setCalibration(imp.getCalibration());
return substack;
}
ImagePlus duplicateStack(ImagePlus img1) {
ImageStack stack1 = img1.getStack();
int width = stack1.getWidth();
int height = stack1.getHeight();
int n = stack1.getSize();
ImageStack stack2 = img1.createEmptyStack();
try {
for (int i = 1; i <= n; i++) {
ImageProcessor ip1 = stack1.getProcessor(i);
ip1.resetRoi();
ImageProcessor ip2 = ip1.crop();
stack2.addSlice(stack1.getSliceLabel(i), ip2);
}
} catch (OutOfMemoryError e) {
stack2.trim();
stack2 = null;
return null;
}
return new ImagePlus("Duplicate", stack2);
}