protected void computeAdvanced(final long startPos, final long loopSize) {
final LocalizableByDimCursor<S> cursorIn = image.createLocalizableByDimCursor();
final LocalizableCursor<T> cursorOut = output.createLocalizableCursor();
// move to the starting position of the current thread
cursorOut.fwd(startPos);
// do as many pixels as wanted by this thread
for (long j = 0; j < loopSize; ++j) {
cursorOut.fwd();
cursorIn.setPosition(cursorOut);
converter.convert(cursorIn.getType(), cursorOut.getType());
}
cursorIn.close();
cursorOut.close();
}
/**
* 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();
}
@Override
public boolean process() {
// 0. Prepare new dimensions
int downSamplingFactor = settings.downSamplingFactor;
int[] dimensions = new int[img.getNumDimensions()];
int[] dsarr = new int[img.getNumDimensions()];
float[] dwnCalibration = new float[img.getNumDimensions()];
for (int i = 0; i < 2; i++) {
dimensions[i] = img.getDimension(i) / downSamplingFactor;
dsarr[i] = downSamplingFactor;
dwnCalibration[i] = calibration[i] * downSamplingFactor;
}
if (img.getNumDimensions() > 2) {
// 3D
float zratio = calibration[2] / calibration[0]; // Z spacing is how much bigger
int zdownsampling = (int) (downSamplingFactor / zratio); // temper z downsampling
zdownsampling = Math.max(1, zdownsampling); // but at least 1
dimensions[2] = img.getDimension(2) / zdownsampling;
dsarr[2] = zdownsampling;
dwnCalibration[2] = calibration[2] * zdownsampling;
}
// 1. Downsample the image
Image<T> downsampled = img.createNewImage(dimensions);
LocalizableCursor<T> dwnCursor = downsampled.createLocalizableCursor();
LocalizableByDimCursor<T> srcCursor = img.createLocalizableByDimCursor();
int[] pos = dwnCursor.createPositionArray();
while (dwnCursor.hasNext()) {
dwnCursor.fwd();
dwnCursor.getPosition(pos);
// Scale up position
for (int i = 0; i < pos.length; i++) {
pos[i] = pos[i] * dsarr[i];
}
// Pass it to source cursor
srcCursor.setPosition(pos);
// Copy pixel data
dwnCursor.getType().set(srcCursor.getType());
}
dwnCursor.close();
srcCursor.close();
// 2. Segment downsampled image
// 2.1. Create settings object
LogSegmenterSettings logSettings = new LogSegmenterSettings();
logSettings.expectedRadius = settings.expectedRadius;
logSettings.threshold = settings.threshold;
logSettings.doSubPixelLocalization = true;
;
logSettings.useMedianFilter = settings.useMedianFilter;
// 2.2 Instantiate segmenter
LogSegmenter<T> segmenter = new LogSegmenter<T>();
segmenter.setTarget(downsampled, dwnCalibration, logSettings);
// 2.3 Execute segmentation
if (!segmenter.checkInput() || !segmenter.process()) {
errorMessage = BASE_ERROR_MESSAGE + segmenter.getErrorMessage();
return false;
}
// 3. Benefits
spots = segmenter.getResult();
return true;
}