@Override
public void run(final String arg0) {
final GenericDialogPlus dialog = new GenericDialogPlus("Inverse Compositional Image Alignment");
dialog.addImageChoice("template", null);
dialog.addImageChoice("image to align", null);
dialog.addNumericField("max iterations", 50, 0);
dialog.addNumericField("min parameter change", 0.001, 4);
dialog.showDialog();
if (dialog.wasCanceled()) return;
ImagePlus impTemplate = dialog.getNextImage();
ImagePlus impImage = dialog.getNextImage();
int maxIterations = (int) dialog.getNextNumber();
double minParameterChange = dialog.getNextNumber();
if (impTemplate == null || impImage == null) {
IJ.showMessage("Please select two images.");
return;
}
RandomAccessibleInterval<FloatType> template = ImageJFunctions.convertFloat(impTemplate);
RandomAccessibleInterval<FloatType> image = ImageJFunctions.convertFloat(impImage);
if (image == null || template == null) {
IJ.showMessage("Image type not supported.");
return;
}
Align<FloatType> align = new Align<>(template, new ArrayImgFactory<>());
AffineTransform transform = align.align(image, maxIterations, minParameterChange);
// TODO:
// 1.) Use ImageJFunctions.wrapRGBA(), wrapByte(), etc. to get a Img<T> wrapping impImage
// with T according to the type of the ImagePlus.
// 2.) Show the transformed Img<T>. Maybe put this functionality into a generic method to
// avoid having to re-implement each case.
switch (impTemplate.getType()) {
case ImagePlus.GRAY8:
// TODO
break;
case ImagePlus.GRAY16:
// TODO
break;
case ImagePlus.GRAY32:
// TODO
break;
case ImagePlus.COLOR_RGB:
// TODO
break;
default:
IJ.showMessage("Image type not supported.");
}
}
public <T extends RealType<T>> void process(Img<T> img) {
// compute the gradient on the image
Img<FloatType> gradient = gradient(img);
// show the new Img that contains the gradient
ImageJFunctions.show(gradient);
}
public Example1c() {
// create the ImgFactory based on cells (cellsize = 5x5x5...x5) that will
// instantiate the Img
final ImgFactory<FloatType> imgFactory = new CellImgFactory<FloatType>(5);
// create an 3d-Img with dimensions 20x30x40 (here cellsize is 5x5x5)Ø
final Img<FloatType> img1 = imgFactory.create(new long[] {20, 30, 40}, new FloatType());
// create another image with the same size
// note that the input provides the size for the new image as it implements
// the Interval interface
final Img<FloatType> img2 = imgFactory.create(img1, img1.firstElement());
// display both (but they are empty)
ImageJFunctions.show(img1);
ImageJFunctions.show(img2);
}
public Example6a1() throws ImgIOException {
// open with ImgOpener as a FloatType
Img<FloatType> image = new ImgOpener().openImg("DrosophilaWing.tif", new FloatType());
// perform gaussian convolution with float precision
double[] sigma = new double[image.numDimensions()];
for (int d = 0; d < image.numDimensions(); ++d) sigma[d] = 8;
// convolve & display
ImageJFunctions.show(Gauss.toFloat(sigma, image));
}
public void run(String arg0) {
// get the current ImageJ ImagePlus
ImagePlus imp = WindowManager.getCurrentImage();
// test if an image is open
if (imp == null) {
IJ.log("No image open");
return;
}
// wrap it into an ImgLib2 Img (no copying)
Img<RealType> img = ImageJFunctions.wrapReal(imp);
// test if it could be wrapped
if (img == null) {
IJ.log("Cannot wrap image");
return;
}
// process wrapped image with ImgLib2
process(img);
}
public static void main(final String[] args) {
final int N_BLOBS = 20;
final double RADIUS = 5; // µm
final Random RAN = new Random();
final double WIDTH = 100; // µm
final double HEIGHT = 100; // µm
final double DEPTH = 50; // µm
final double[] CALIBRATION = new double[] {0.5f, 0.5f, 1};
final AxisType[] AXES = new AxisType[] {Axes.X, Axes.Y, Axes.Z};
// Create 3D image
final Img<UnsignedByteType> source =
new ArrayImgFactory<UnsignedByteType>()
.create(
new int[] {
(int) (WIDTH / CALIBRATION[0]),
(int) (HEIGHT / CALIBRATION[1]),
(int) (DEPTH / CALIBRATION[2])
},
new UnsignedByteType());
final ImgPlus<UnsignedByteType> img =
new ImgPlus<UnsignedByteType>(source, "Test", AXES, CALIBRATION);
// Random blobs
final double[] radiuses = new double[N_BLOBS];
final ArrayList<double[]> centers = new ArrayList<double[]>(N_BLOBS);
final int[] intensities = new int[N_BLOBS];
double x, y, z;
for (int i = 0; i < N_BLOBS; i++) {
radiuses[i] = RADIUS + RAN.nextGaussian();
x = WIDTH * RAN.nextFloat();
y = HEIGHT * RAN.nextFloat();
z = DEPTH * RAN.nextFloat();
centers.add(i, new double[] {x, y, z});
intensities[i] = RAN.nextInt(100) + 100;
}
// Put the blobs in the image
for (int i = 0; i < N_BLOBS; i++) {
final Spot tmpSpot =
new Spot(centers.get(i)[0], centers.get(i)[1], centers.get(i)[2], radiuses[i], -1d);
tmpSpot.putFeature(Spot.RADIUS, radiuses[i]);
final SpotNeighborhood<UnsignedByteType> sphere =
new SpotNeighborhood<UnsignedByteType>(tmpSpot, img);
for (final UnsignedByteType pixel : sphere) {
pixel.set(intensities[i]);
}
}
// Instantiate detector
final LogDetector<UnsignedByteType> detector =
new LogDetector<UnsignedByteType>(
img, img, TMUtils.getSpatialCalibration(img), RADIUS, 0, true, false);
// Segment
final long start = System.currentTimeMillis();
if (!detector.checkInput() || !detector.process()) {
System.out.println(detector.getErrorMessage());
return;
}
final Collection<Spot> spots = detector.getResult();
final long end = System.currentTimeMillis();
// Display image
ImageJFunctions.show(img);
// Display results
final int spot_found = spots.size();
System.out.println("Segmentation took " + (end - start) + " ms.");
System.out.println("Found " + spot_found + " blobs.\n");
Point3d p1, p2;
double dist, min_dist;
int best_index = 0;
double[] best_match;
final ArrayList<Spot> spot_list = new ArrayList<Spot>(spots);
Spot best_spot = null;
final double[] coords = new double[3];
final String[] posFeats = Spot.POSITION_FEATURES;
while (!spot_list.isEmpty() && !centers.isEmpty()) {
min_dist = Float.POSITIVE_INFINITY;
for (final Spot s : spot_list) {
int index = 0;
for (final String pf : posFeats) {
coords[index++] = s.getFeature(pf).doubleValue();
}
p1 = new Point3d(coords);
for (int j = 0; j < centers.size(); j++) {
p2 = new Point3d(centers.get(j));
dist = p1.distance(p2);
if (dist < min_dist) {
min_dist = dist;
best_index = j;
best_spot = s;
}
}
}
spot_list.remove(best_spot);
best_match = centers.remove(best_index);
int index = 0;
for (final String pf : posFeats) {
coords[index++] = best_spot.getFeature(pf).doubleValue();
}
System.out.println("Blob coordinates: " + Util.printCoordinates(coords));
System.out.println(
String.format(
" Best matching center at distance %.1f with coords: "
+ Util.printCoordinates(best_match),
min_dist));
}
System.out.println();
System.out.println("Unmatched centers:");
for (int i = 0; i < centers.size(); i++)
System.out.println("Center " + i + " at position: " + Util.printCoordinates(centers.get(i)));
}
public static void main(final String[] args) {
// TEST 2D case
// Parameters
final int size_x = 200;
final int size_y = 200;
final long a = 10;
final long b = 5;
final double phi_r = Math.toRadians(30);
final long max_radius = Math.max(a, b);
final double[] calibration = new double[] {1, 1};
// Create blank image
final Img<UnsignedByteType> img =
new ArrayImgFactory<UnsignedByteType>()
.create(new int[] {200, 200}, new UnsignedByteType());
final ImgPlus<UnsignedByteType> imgplus = new ImgPlus<UnsignedByteType>(img);
for (int d = 0; d < imgplus.numDimensions(); d++) {
imgplus.setAxis(new DefaultLinearAxis(imgplus.axis(d).type(), calibration[d]), d);
}
final byte on = (byte) 255;
// Create an ellipse
long start = System.currentTimeMillis();
System.out.println(String.format("Creating an ellipse with a = %d, b = %d", a, b));
System.out.println(String.format("phi = %.1f", Math.toDegrees(phi_r)));
final long[] center = new long[] {size_x / 2, size_y / 2};
final long[] radiuses = new long[] {max_radius, max_radius};
final EllipseNeighborhood<UnsignedByteType> disc =
new EllipseNeighborhood<UnsignedByteType>(img, center, radiuses);
final EllipseCursor<UnsignedByteType> sc = disc.cursor();
double r2, phi, term;
double cosphi, sinphi;
while (sc.hasNext()) {
sc.fwd();
r2 = sc.getDistanceSquared();
phi = sc.getPhi();
cosphi = Math.cos(phi - phi_r);
sinphi = Math.sin(phi - phi_r);
term = r2 * cosphi * cosphi / a / a + r2 * sinphi * sinphi / b / b;
if (term <= 1) sc.get().set(on);
}
final long end = System.currentTimeMillis();
System.out.println("Ellipse creation done in " + (end - start) + " ms.");
System.out.println();
ij.ImageJ.main(args);
ImageJFunctions.show(imgplus);
start = System.currentTimeMillis();
final Spot spot = new Spot(center[0], center[1], 0d, max_radius, -1d);
final SpotMorphologyAnalyzer<UnsignedByteType> bm =
new SpotMorphologyAnalyzer<UnsignedByteType>(imgplus, null);
bm.process(spot);
System.out.println("Blob morphology analyzed in " + (end - start) + " ms.");
double phiv, thetav, lv;
for (int j = 0; j < 2; j++) {
lv = spot.getFeature(featurelist_sa[j]);
phiv = spot.getFeature(featurelist_phi[j]);
thetav = spot.getFeature(featurelist_theta[j]);
System.out.println(
String.format(
"For axis of semi-length %.1f, orientation is phi = %.1f°, theta = %.1f°",
lv, Math.toDegrees(phiv), Math.toDegrees(thetav)));
}
System.out.println(spot.echo());
// TEST 3D case
/*
*
* // Parameters int size_x = 200; int size_y = 200; int size_z = 200;
*
* double a = 5.5f; double b = 4.9f; double c = 5; double theta_r =
* (double) Math.toRadians(0); // I am unable to have it working for
* theta_r != 0 double phi_r = (double) Math.toRadians(45);
*
* double max_radius = Math.max(a, Math.max(b, c)); double[] calibration
* = new double[] {1, 1, 1};
*
* // Create blank image Image<UnsignedByteType> img = new
* ImageFactory<UnsignedByteType>( new UnsignedByteType(), new
* ArrayContainerFactory() ).createImage(new int[] {200, 200, 200});
* final byte on = (byte) 255;
*
* // Create an ellipse long start = System.currentTimeMillis();
* System.out.println(String.format(
* "Creating an ellipse with a = %.1f, b = %.1f, c = %.1f", a, b, c));
* System.out.println(String.format("phi = %.1f and theta = %.1f",
* Math.toDegrees(phi_r), Math.toDegrees(theta_r))); double[] center =
* new double[] { size_x/2, size_y/2, size_z/2 };
* SphereCursor<UnsignedByteType> sc = new
* SphereCursor<UnsignedByteType>(img, center, max_radius, calibration);
* double r2, theta, phi, term; double cosphi, sinphi, costheta,
* sintheta; while (sc.hasNext()) { sc.fwd(); r2 =
* sc.getDistanceSquared(); phi = sc.getPhi(); theta = sc.getTheta();
* cosphi = Math.cos(phi-phi_r); sinphi = Math.sin(phi-phi_r); costheta
* = Math.cos(theta-theta_r); sintheta = Math.sin(theta-theta_r); term =
* r2*cosphi*cosphi*sintheta*sintheta/a/a +
* r2*sinphi*sinphi*sintheta*sintheta/b/b + r2*costheta*costheta/c/c; if
* (term <= 1) sc.getType().set(on); } sc.close(); long end =
* System.currentTimeMillis();
* System.out.println("Ellipse creation done in " + (end-start) +
* " ms."); System.out.println();
*
* ij.ImageJ.main(args); img.getDisplay().setMinMax();
* ImageJFunctions.copyToImagePlus(img).show();
*
* start = System.currentTimeMillis(); BlobMorphology<UnsignedByteType>
* bm = new BlobMorphology<UnsignedByteType>(img, calibration); SpotImp
* spot = new SpotImp(center); spot.putFeature(Feature.RADIUS,
* max_radius); bm.process(spot); end = System.currentTimeMillis();
* System.out.println("Blob morphology analyzed in " + (end-start) +
* " ms."); double phiv, thetav, lv; for (int j = 0; j < 3; j++) { lv =
* spot.getFeature(featurelist_sa[j]); phiv =
* spot.getFeature(featurelist_phi[j]); thetav =
* spot.getFeature(featurelist_theta[j]);
* System.out.println(String.format(
* "For axis of semi-length %.1f, orientation is phi = %.1f°, theta = %.1f°"
* , lv, Math.toDegrees(phiv), Math.toDegrees(thetav))); }
* System.out.println(spot.echo());
*/
}
/**
* Fuses one stack, i.e. all angles/illuminations for one timepoint and channel
*
* @param timepoint
* @param channel
* @return
*/
public boolean fuseStacksAndGetPSFs(
final TimePoint timepoint,
final Channel channel,
final ImgFactory<FloatType> imgFactory,
final int osemIndex,
double osemspeedup,
WeightType weightType,
final HashMap<Channel, ChannelPSF> extractPSFLabels,
final long[] psfSize,
final HashMap<Channel, ArrayList<Pair<Pair<Angle, Illumination>, String>>> psfFiles,
final boolean transformLoadedPSFs) {
// TODO: get rid of this hack
if (files != null) {
weightType = WeightType.LOAD_WEIGHTS;
IOFunctions.println("WARNING: LOADING WEIGHTS FROM IMAGES, files.length()=" + files.length);
}
// get all views that are fused for this timepoint & channel
this.viewDescriptions =
FusionHelper.assembleInputData(spimData, timepoint, channel, viewIdsToProcess);
if (this.viewDescriptions.size() == 0) return false;
this.imgs = new HashMap<ViewId, RandomAccessibleInterval<FloatType>>();
this.weights = new HashMap<ViewId, RandomAccessibleInterval<FloatType>>();
final Img<FloatType> overlapImg;
if (weightType == WeightType.WEIGHTS_ONLY)
overlapImg = imgFactory.create(bb.getDimensions(), new FloatType());
else overlapImg = null;
final boolean extractPSFs =
(extractPSFLabels != null) && (extractPSFLabels.get(channel).getLabel() != null);
final boolean loadPSFs = (psfFiles != null);
if (extractPSFs) ePSF = new ExtractPSF<FloatType>();
else if (loadPSFs) ePSF = loadPSFs(channel, viewDescriptions, psfFiles, transformLoadedPSFs);
else {
ePSF = assignOtherChannel(channel, extractPSFLabels);
}
if (ePSF == null) return false;
// remember the extracted or loaded PSFs
extractPSFLabels.get(channel).setExtractPSFInstance(ePSF);
// we will need to run some batches until all is fused
for (int i = 0; i < viewDescriptions.size(); ++i) {
final ViewDescription vd = viewDescriptions.get(i);
IOFunctions.println(
"Transforming view "
+ i
+ " of "
+ (viewDescriptions.size() - 1)
+ " (viewsetup="
+ vd.getViewSetupId()
+ ", tp="
+ vd.getTimePointId()
+ ")");
IOFunctions.println(
"("
+ new Date(System.currentTimeMillis())
+ "): Reserving memory for transformed & weight image.");
// creating the output
RandomAccessibleInterval<FloatType> transformedImg; // might be null if WEIGHTS_ONLY
final RandomAccessibleInterval<FloatType>
weightImg; // never null (except LOAD_WEIGHTS which is not implemented yet)
if (weightType == WeightType.WEIGHTS_ONLY) transformedImg = overlapImg;
else transformedImg = imgFactory.create(bb.getDimensions(), new FloatType());
IOFunctions.println(
"("
+ new Date(System.currentTimeMillis())
+ "): Transformed image factory: "
+ imgFactory.getClass().getSimpleName());
// loading the input if necessary
final RandomAccessibleInterval<FloatType> img;
if (weightType == WeightType.WEIGHTS_ONLY && !extractPSFs) {
img = null;
} else {
IOFunctions.println("(" + new Date(System.currentTimeMillis()) + "): Loading image.");
img = ProcessFusion.getImage(new FloatType(), spimData, vd, true);
if (Img.class.isInstance(img))
IOFunctions.println(
"("
+ new Date(System.currentTimeMillis())
+ "): Input image factory: "
+ ((Img<FloatType>) img).factory().getClass().getSimpleName());
}
// initializing weights
IOFunctions.println(
"("
+ new Date(System.currentTimeMillis())
+ "): Initializing transformation & weights: "
+ weightType.name());
spimData.getViewRegistrations().getViewRegistration(vd).updateModel();
final AffineTransform3D transform =
spimData.getViewRegistrations().getViewRegistration(vd).getModel();
final long[] offset = new long[] {bb.min(0), bb.min(1), bb.min(2)};
if (weightType == WeightType.PRECOMPUTED_WEIGHTS || weightType == WeightType.WEIGHTS_ONLY)
weightImg = imgFactory.create(bb.getDimensions(), new FloatType());
else if (weightType == WeightType.NO_WEIGHTS)
weightImg =
Views.interval(
new ConstantRandomAccessible<FloatType>(
new FloatType(1), transformedImg.numDimensions()),
transformedImg);
else if (weightType == WeightType.VIRTUAL_WEIGHTS) {
final Blending blending = getBlending(img, blendingBorder, blendingRange, vd);
weightImg =
new TransformedRealRandomAccessibleInterval<FloatType>(
blending, new FloatType(), transformedImg, transform, offset);
} else // if ( processType == ProcessType.LOAD_WEIGHTS )
{
IOFunctions.println("WARNING: LOADING WEIGHTS FROM: '" + new File(files[i]) + "'");
ImagePlus imp = StackImgLoaderIJ.open(new File(files[i]));
weightImg = imgFactory.create(bb.getDimensions(), new FloatType());
StackImgLoaderIJ.imagePlus2ImgLib2Img(imp, (Img<FloatType>) weightImg, false);
imp.close();
if (debugImport) {
imp = ImageJFunctions.show(weightImg);
imp.setTitle("ViewSetup " + vd.getViewSetupId() + " Timepoint " + vd.getTimePointId());
}
}
// split up into many parts for multithreading
final Vector<ImagePortion> portions =
FusionHelper.divideIntoPortions(
Views.iterable(transformedImg).size(), Threads.numThreads() * 4);
// set up executor service
final ExecutorService taskExecutor = Executors.newFixedThreadPool(Threads.numThreads());
final ArrayList<Callable<String>> tasks = new ArrayList<Callable<String>>();
IOFunctions.println(
"("
+ new Date(System.currentTimeMillis())
+ "): Transforming image & computing weights.");
for (final ImagePortion portion : portions) {
if (weightType == WeightType.WEIGHTS_ONLY) {
final Interval imgInterval =
new FinalInterval(
ViewSetupUtils.getSizeOrLoad(
vd.getViewSetup(),
vd.getTimePoint(),
spimData.getSequenceDescription().getImgLoader()));
final Blending blending = getBlending(imgInterval, blendingBorder, blendingRange, vd);
tasks.add(
new TransformWeights(
portion, imgInterval, blending, transform, overlapImg, weightImg, offset));
} else if (weightType == WeightType.PRECOMPUTED_WEIGHTS) {
final Blending blending = getBlending(img, blendingBorder, blendingRange, vd);
tasks.add(
new TransformInputAndWeights(
portion, img, blending, transform, transformedImg, weightImg, offset));
} else if (weightType == WeightType.NO_WEIGHTS
|| weightType == WeightType.VIRTUAL_WEIGHTS
|| weightType == WeightType.LOAD_WEIGHTS) {
tasks.add(new TransformInput(portion, img, transform, transformedImg, offset));
} else {
throw new RuntimeException(weightType.name() + " not implemented yet.");
}
}
try {
// invokeAll() returns when all tasks are complete
taskExecutor.invokeAll(tasks);
} catch (final InterruptedException e) {
IOFunctions.println("Failed to compute fusion: " + e);
e.printStackTrace();
return false;
}
taskExecutor.shutdown();
// extract PSFs if wanted
if (extractPSFs) {
final ArrayList<double[]> llist =
getLocationsOfCorrespondingBeads(
timepoint, vd, extractPSFLabels.get(channel).getLabel());
IOFunctions.println(
"("
+ new Date(System.currentTimeMillis())
+ "): Extracting PSF for viewsetup "
+ vd.getViewSetupId()
+ " using label '"
+ extractPSFLabels.get(channel).getLabel()
+ "'"
+ " ("
+ llist.size()
+ " corresponding detections available)");
ePSF.extractNextImg(img, vd, transform, llist, psfSize);
}
if (weightType != WeightType.WEIGHTS_ONLY) imgs.put(vd, transformedImg);
weights.put(vd, weightImg);
}
// normalize the weights
final ArrayList<RandomAccessibleInterval<FloatType>> weightsSorted =
new ArrayList<RandomAccessibleInterval<FloatType>>();
for (final ViewDescription vd : viewDescriptions) weightsSorted.add(weights.get(vd));
IOFunctions.println(
"("
+ new Date(System.currentTimeMillis())
+ "): Computing weight normalization for deconvolution.");
final WeightNormalizer wn;
if (weightType == WeightType.WEIGHTS_ONLY
|| weightType == WeightType.PRECOMPUTED_WEIGHTS
|| weightType == WeightType.LOAD_WEIGHTS) wn = new WeightNormalizer(weightsSorted);
else if (weightType == WeightType.VIRTUAL_WEIGHTS)
wn = new WeightNormalizer(weightsSorted, imgFactory);
else // if ( processType == ProcessType.NO_WEIGHTS )
wn = null;
if (wn != null && !wn.process()) return false;
// put the potentially modified weights back
for (int i = 0; i < viewDescriptions.size(); ++i)
weights.put(viewDescriptions.get(i), weightsSorted.get(i));
this.minOverlappingViews = wn.getMinOverlappingViews();
this.avgOverlappingViews = wn.getAvgOverlappingViews();
IOFunctions.println(
"("
+ new Date(System.currentTimeMillis())
+ "): Minimal number of overlapping views: "
+ getMinOverlappingViews()
+ ", using "
+ (this.minOverlappingViews = Math.max(1, this.minOverlappingViews)));
IOFunctions.println(
"("
+ new Date(System.currentTimeMillis())
+ "): Average number of overlapping views: "
+ getAvgOverlappingViews()
+ ", using "
+ (this.avgOverlappingViews = Math.max(1, this.avgOverlappingViews)));
if (osemIndex == 1) osemspeedup = getMinOverlappingViews();
else if (osemIndex == 2) osemspeedup = getAvgOverlappingViews();
IOFunctions.println(
"("
+ new Date(System.currentTimeMillis())
+ "): Adjusting for OSEM speedup = "
+ osemspeedup);
if (weightType == WeightType.WEIGHTS_ONLY)
displayWeights(osemspeedup, weightsSorted, overlapImg, imgFactory);
else adjustForOSEM(weights, weightType, osemspeedup);
IOFunctions.println(
"("
+ new Date(System.currentTimeMillis())
+ "): Finished precomputations for deconvolution.");
return true;
}
/** Saves image using imageJ */
public void saveImage(final String file) {
ImagePlus ips = ImageJFunctions.show(getImage());
FileSaver fs = new FileSaver(ips);
fs.saveAsTiff(file);
}
/** Shows image using fiji */
public void showImage(final String title) {
ImageJFunctions.show(getImage()).setTitle(title);
}