/**
* 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());
}
protected ImageFactory<FloatType> getFloatFactory() {
if (floatFactory == null) {
floatFactory = new ImageFactory<FloatType>(new FloatType(), input.getContainerFactory());
}
return floatFactory;
}
@Override
public boolean process() {
floatImage = null;
if (output == null) {
output = new Labeling<L>(labelingFactory, input.getDimensions(), null);
} else {
/*
* Initialize the output to all background
*/
LocalizableCursor<LabelingType<L>> c = output.createLocalizableCursor();
List<L> background = c.getType().intern(new ArrayList<L>());
for (LabelingType<L> t : c) {
t.setLabeling(background);
}
c.close();
}
/*
* Get the smoothed image.
*/
Image<FloatType> kernel =
FourierConvolution.createGaussianKernel(input.getContainerFactory(), scale);
FourierConvolution<FloatType, FloatType> convolution =
new FourierConvolution<FloatType, FloatType>(getFloatImage(), kernel);
if (!convolution.process()) return false;
Image<FloatType> smoothed = convolution.getResult();
/*
* Find the local maxima and label them individually.
*/
PickImagePeaks<FloatType> peakPicker = new PickImagePeaks<FloatType>(smoothed);
peakPicker.setSuppression(scale);
peakPicker.process();
Labeling<L> seeds = output.createNewLabeling();
LocalizableByDimCursor<LabelingType<L>> lc = seeds.createLocalizableByDimCursor();
LocalizableByDimCursor<FloatType> imageCursor = smoothed.createLocalizableByDimCursor();
int[] dimensions = input.getDimensions();
for (int[] peak : peakPicker.getPeakList()) {
if (!filterPeak(imageCursor, peak, dimensions, false)) continue;
lc.setPosition(peak);
lc.getType().setLabel(names.next());
}
imageCursor.close();
/*
* Find the local minima and label them all the same.
*/
List<L> background = lc.getType().intern(names.next());
Converter<FloatType, FloatType> invert =
new Converter<FloatType, FloatType>() {
@Override
public void convert(FloatType input, FloatType output) {
output.setReal(-input.getRealFloat());
}
};
ImageConverter<FloatType, FloatType> invSmoothed =
new ImageConverter<FloatType, FloatType>(smoothed, smoothed, invert);
invSmoothed.process();
peakPicker = new PickImagePeaks<FloatType>(smoothed);
peakPicker.setSuppression(scale);
peakPicker.process();
imageCursor = smoothed.createLocalizableByDimCursor();
for (int[] peak : peakPicker.getPeakList()) {
if (!filterPeak(imageCursor, peak, dimensions, true)) continue;
lc.setPosition(peak);
lc.getType().setLabeling(background);
}
lc.close();
imageCursor.close();
smoothed = null;
invSmoothed = null;
Image<FloatType> gradientImage = getGradientImage();
if (gradientImage == null) return false;
/*
* Run the seeded watershed on the image.
*/
Watershed.seededWatershed(gradientImage, seeds, structuringElement, output);
return true;
}