/**
* Constructor
*
* @param image The intensity image to be labeled
* @param scale the minimum distance between maxima of objects. Less technically, this should be
* the diameter of the smallest object.
* @param sigma1 the standard deviation for the larger smoothing. The difference between sigma1
* and sigma2 should be roughly the width of the desired edge in the DoG image. A larger
* difference will obscure small, faint edges.
* @param sigma2 the standard deviation for the smaller smoothing. This should be on the order of
* the largest insignificant feature in the image.
* @param names - an iterator that generates names of type L for the labels. The iterator will
* waste the last name taken on the background label. You can use
* AllConnectedComponents.getIntegerNames() as your name generator if you don't care about
* names.
*/
public GradientWatershed(
Image<T> input, double[] scale, double[] sigma1, double[] sigma2, Iterator<L> names) {
this.input = input;
this.scale = scale;
this.sigma1 = sigma1;
this.sigma2 = sigma2;
structuringElement = AllConnectedComponents.getStructuringElement(input.getNumDimensions());
this.names = names;
labelingFactory =
new ImageFactory<LabelingType<L>>(new LabelingType<L>(), input.getContainerFactory());
}
/**
* Return a difference of gaussian image that measures the gradient at a scale defined by the two
* sigmas of the gaussians.
*
* @param image
* @param sigma1
* @param sigma2
* @return
*/
public Image<FloatType> getGradientImage() {
/*
* Create the DoG kernel.
*/
double[][] kernels1d1 = new double[input.getNumDimensions()][];
double[][] kernels1d2 = new double[input.getNumDimensions()][];
int[] kernelDimensions = input.createPositionArray();
int[] offset = input.createPositionArray();
for (int i = 0; i < kernels1d1.length; i++) {
kernels1d1[i] = Util.createGaussianKernel1DDouble(sigma1[i], true);
kernels1d2[i] = Util.createGaussianKernel1DDouble(sigma2[i], true);
kernelDimensions[i] = kernels1d1[i].length;
offset[i] = (kernels1d1[i].length - kernels1d2[i].length) / 2;
}
Image<FloatType> kernel = getFloatFactory().createImage(kernelDimensions);
LocalizableCursor<FloatType> kc = kernel.createLocalizableCursor();
int[] position = input.createPositionArray();
for (FloatType t : kc) {
kc.getPosition(position);
double value1 = 1;
double value2 = 1;
for (int i = 0; i < kernels1d1.length; i++) {
value1 *= kernels1d1[i][position[i]];
int position2 = position[i] - offset[i];
if ((position2 >= 0) && (position2 < kernels1d2[i].length)) {
value2 *= kernels1d2[i][position2];
} else {
value2 = 0;
}
}
t.setReal(value1 - value2);
}
kc.close();
/*
* Apply the kernel to the image.
*/
FourierConvolution<FloatType, FloatType> convolution =
new FourierConvolution<FloatType, FloatType>(getFloatImage(), kernel);
if (!convolution.process()) return null;
Image<FloatType> result = convolution.getResult();
/*
* Quantize the image.
*/
ComputeMinMax<FloatType> computeMinMax = new ComputeMinMax<FloatType>(result);
computeMinMax.process();
final float min = computeMinMax.getMin().get();
final float max = computeMinMax.getMax().get();
if (max == min) return result;
ImageConverter<FloatType, FloatType> quantizer =
new ImageConverter<FloatType, FloatType>(
result,
result.getImageFactory(),
new Converter<FloatType, FloatType>() {
@Override
public void convert(FloatType input, FloatType output) {
float value = (input.get() - min) / (max - min);
value = Math.round(value * 100);
output.set(value);
}
});
quantizer.process();
return quantizer.getResult();
}
protected boolean checkDimensions(double[] array) {
return array.length == input.getNumDimensions();
}
@Override
public int getNumDimensions() {
return image.getNumDimensions();
}
/**
* Fuse one slice/volume (one channel)
*
* @param output - same the type of the ImagePlus input
* @param input - FloatType, because of Interpolation that needs to be done
* @param transform - the transformation
*/
public static <T extends RealType<T>> void fuseChannel(
final Image<T> output,
final Image<FloatType> input,
final float[] offset,
final InvertibleCoordinateTransform transform,
final InterpolatorFactory<FloatType> factory) {
final int dims = output.getNumDimensions();
long imageSize = output.getDimension(0);
for (int d = 1; d < output.getNumDimensions(); ++d) imageSize *= output.getDimension(d);
// run multithreaded
final AtomicInteger ai = new AtomicInteger(0);
final Thread[] threads = SimpleMultiThreading.newThreads();
final Vector<Chunk> threadChunks =
SimpleMultiThreading.divideIntoChunks(imageSize, threads.length);
for (int ithread = 0; ithread < threads.length; ++ithread)
threads[ithread] =
new Thread(
new Runnable() {
public void run() {
// Thread ID
final int myNumber = ai.getAndIncrement();
// get chunk of pixels to process
final Chunk myChunk = threadChunks.get(myNumber);
final long startPos = myChunk.getStartPosition();
final long loopSize = myChunk.getLoopSize();
final LocalizableCursor<T> out = output.createLocalizableCursor();
final Interpolator<FloatType> in = input.createInterpolator(factory);
final float[] tmp = new float[input.getNumDimensions()];
try {
// move to the starting position of the current thread
out.fwd(startPos);
// do as many pixels as wanted by this thread
for (long j = 0; j < loopSize; ++j) {
out.fwd();
for (int d = 0; d < dims; ++d) tmp[d] = out.getPosition(d) + offset[d];
transform.applyInverseInPlace(tmp);
in.setPosition(tmp);
out.getType().setReal(in.getType().get());
}
} catch (NoninvertibleModelException e) {
IJ.log("Cannot invert model, qutting.");
return;
}
}
});
SimpleMultiThreading.startAndJoin(threads);
/*
final LocalizableCursor<T> out = output.createLocalizableCursor();
final Interpolator<FloatType> in = input.createInterpolator( factory );
final float[] tmp = new float[ input.getNumDimensions() ];
try
{
while ( out.hasNext() )
{
out.fwd();
for ( int d = 0; d < dims; ++d )
tmp[ d ] = out.getPosition( d ) + offset[ d ];
transform.applyInverseInPlace( tmp );
in.setPosition( tmp );
out.getType().setReal( in.getType().get() );
}
}
catch (NoninvertibleModelException e)
{
IJ.log( "Cannot invert model, qutting." );
return;
}
*/
}