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)));
}
