/**
* @param img
* @return the inferred mapping
*/
private static int[] getInferredMapping(final ImgPlus<?> img) {
int[] inferredMapping = new int[DEFAULT_IJ1_MAPPING.size()];
Arrays.fill(inferredMapping, -1);
for (int d = 0; d < img.numDimensions(); d++) {
inferredMapping[d] = DEFAULT_IJ1_MAPPING.get(img.axis(d).type());
}
int offset = 0;
for (AxisType type : DEFAULT_IJ1_MAPPING.keySet()) {
boolean contains = false;
for (int d = 0; d < img.numDimensions(); d++) {
if (img.axis(d).type().equals(type)) {
contains = true;
break;
}
}
if (!contains) {
inferredMapping[img.numDimensions() + offset] = DEFAULT_IJ1_MAPPING.get(type);
offset++;
}
}
return inferredMapping;
}
/**
* Check if ImgPlus contains axis which can not be mapped to IJ ImagePlus. Valid axes in ImagePlus
* are X, Y, Channel, Z, Time.
*
* @param img
* @return true if mapping is valid
*/
public static boolean validateMapping(final ImgPlus<?> img) {
for (int d = 0; d < img.numDimensions(); d++) {
if (DEFAULT_IJ1_MAPPING.get(((DefaultTypedAxis) img.axis(d)).type()) == null) {
return false;
}
}
return true;
}
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());
*/
}
