protected void generateHistogramData(DataContainer<T> container) {
double ch1BinWidth = getXBinWidth(container);
double ch2BinWidth = getYBinWidth(container);
// get the 2 images for the calculation of Pearson's
final RandomAccessibleInterval<T> img1 = getImageCh1(container);
final RandomAccessibleInterval<T> img2 = getImageCh2(container);
final RandomAccessibleInterval<BitType> mask = container.getMask();
// get the cursors for iterating through pixels in images
TwinCursor<T> cursor =
new TwinCursor<T>(
img1.randomAccess(), img2.randomAccess(), Views.iterable(mask).localizingCursor());
// create new image to put the scatter-plot in
final ImgFactory<LongType> scatterFactory = new ArrayImgFactory<LongType>();
plotImage = scatterFactory.create(new int[] {xBins, yBins}, new LongType());
// create access cursors
final RandomAccess<LongType> histogram2DCursor = plotImage.randomAccess();
// iterate over images
long[] pos = new long[plotImage.numDimensions()];
while (cursor.hasNext()) {
cursor.fwd();
double ch1 = cursor.getFirst().getRealDouble();
double ch2 = cursor.getSecond().getRealDouble();
/* Scale values for both channels to fit in the range.
* Moreover mirror the y value on the x axis.
*/
pos[0] = getXValue(ch1, ch1BinWidth, ch2, ch2BinWidth);
pos[1] = getYValue(ch1, ch1BinWidth, ch2, ch2BinWidth);
// set position of input/output cursor
histogram2DCursor.setPosition(pos);
// get current value at position and increment it
long count = histogram2DCursor.get().getIntegerLong();
count++;
histogram2DCursor.get().set(count);
}
xBinWidth = ch1BinWidth;
yBinWidth = ch2BinWidth;
xLabel = getLabelCh1();
yLabel = getLabelCh2();
xMin = getXMin(container);
xMax = getXMax(container);
yMin = getYMin(container);
yMax = getYMax(container);
}
/**
* Gets the minimum of channel two. Takes channel swapping into consideration and will return min
* of channel one if swapped.
*
* @return The minimum of what is seen as channel two.
*/
protected double getMinCh2(DataContainer<T> container) {
return swapChannels ? container.getMinCh1() : container.getMinCh2();
}
/**
* Gets the image of channel two. Takes channel swapping into consideration and will return image
* of channel one if swapped.
*
* @return The image of what is seen as channel two.
*/
protected RandomAccessibleInterval<T> getImageCh2(DataContainer<T> container) {
return swapChannels ? container.getSourceImage1() : container.getSourceImage2();
}
