/**
* Assigns the data values of a {@link Dataset} from a paired {@link ImagePlus}. Assumes the
* Dataset and ImagePlus have compatible dimensions and that the data planes are not directly
* mapped. Gets values via {@link ImageProcessor}::getf(). In cases where there is a narrowing of
* data into modern ImageJ types the data is range clamped. Does not change the Dataset's
* metadata.
*/
@Override
public void updateDataset(final Dataset ds, final ImagePlus imp) {
final RealType<?> type = ds.getType();
final double typeMin = type.getMinValue();
final double typeMax = type.getMaxValue();
final boolean signed16BitData = type instanceof ShortType;
final RandomAccess<? extends RealType<?>> accessor = ds.getImgPlus().randomAccess();
final long[] dims = ds.getDims();
final AxisType[] axes = ds.getAxes();
final int xIndex = ds.getAxisIndex(Axes.X);
final int yIndex = ds.getAxisIndex(Axes.Y);
final int zIndex = ds.getAxisIndex(Axes.Z);
final int tIndex = ds.getAxisIndex(Axes.TIME);
final int xSize = imp.getWidth();
final int ySize = imp.getHeight();
final int zSize = imp.getNSlices();
final int tSize = imp.getNFrames();
final int cSize = imp.getNChannels();
final ImageStack stack = imp.getStack();
int planeNum = 1;
final long[] pos = new long[dims.length];
for (int t = 0; t < tSize; t++) {
if (tIndex >= 0) pos[tIndex] = t;
for (int z = 0; z < zSize; z++) {
if (zIndex >= 0) pos[zIndex] = z;
for (int c = 0; c < cSize; c++) {
LegacyUtils.fillChannelIndices(dims, axes, c, pos);
final ImageProcessor proc = stack.getProcessor(planeNum++);
for (int x = 0; x < xSize; x++) {
if (xIndex >= 0) pos[xIndex] = x;
for (int y = 0; y < ySize; y++) {
if (yIndex >= 0) pos[yIndex] = y;
accessor.setPosition(pos);
double value = proc.getf(x, y);
if (signed16BitData) value -= 32768.0;
if (value < typeMin) value = typeMin;
else if (value > typeMax) value = typeMax;
accessor.get().setReal(value);
}
}
}
}
}
ds.update();
}
@Override
public void compute1(
final IterableInterval<RealType<?>> input, final IterableInterval<RealType<?>> output) {
Cursor<RealType<?>> inputCursor = input.cursor();
Cursor<RealType<?>> outputCursor = output.cursor();
double tmp = 0.0d;
while (outputCursor.hasNext()) {
RealType<?> inputValue = inputCursor.next();
RealType<?> outputValue = outputCursor.next();
// Compute inputValue^order
tmp += inputValue.getRealDouble();
outputValue.setReal(tmp);
}
}
@SuppressWarnings({"rawtypes", "unchecked"})
private static final NumericType<?> withValue(
final Img<? extends NumericType<?>> img, final NumericType<?> type, final Number val) {
final NumericType t = img.firstElement().createVariable();
if (ARGBType.class.isAssignableFrom(t.getClass())) {
int i = val.intValue();
t.set(new ARGBType(i));
} else {
((RealType) t).setReal(val.doubleValue());
}
return t;
}
@Override
public RealType<?> compute(ComplexType<?> input, RealType<?> output) {
output.setReal(input.getRealDouble());
return output;
}