private void processPlane(
final Position planePos, final long rx, final long ry, final long rw, final long rh) {
final long[] inputPosition = new long[planePos.numDimensions() + 2];
final long[] outputPosition = new long[planePos.numDimensions() + 2];
for (int i = 2; i < inputPosition.length; i++)
inputPosition[i] = planePos.getLongPosition(i - 2);
for (long y = ry; y < ry + rh; y++) {
inputPosition[1] = y;
for (long x = rx; x < rx + rw; x++) {
inputPosition[0] = x;
flipper.calcOutputPosition(inputDimensions, inputPosition, outputPosition);
inputAccessor.setPosition(inputPosition);
outputAccessor.setPosition(outputPosition);
final double value = inputAccessor.get().getRealDouble();
outputAccessor.get().setReal(value);
}
}
}
/*
* Makes sure calculation of IJ1 channels is correctly invertible
*/
@Test
public void testRasterization() {
final long[][] dimsList = {{1, 1, 1}, {1, 2, 3}, {2, 3, 4}, {5, 4, 3}, {4, 2, 7}};
final AxisType[] axes = {Axes.CHANNEL, SCIFIOAxes.SPECTRA, SCIFIOAxes.FREQUENCY};
for (long[] dims : dimsList) {
// setup
long numChannels = 1;
for (long dim : dims) numChannels *= dim;
// test from long index back to long index
for (long channel = 0; channel < numChannels; channel++) {
long[] channelPositions = new long[dims.length];
LegacyUtils.fillChannelIndices(dims, axes, channel, channelPositions);
long ij1Pos = LegacyUtils.calcIJ1ChannelPos(dims, axes, channelPositions);
assertEquals(channel, ij1Pos);
}
// test from long[] index back to long[] index
long[] channelPositions1 = new long[dims.length];
long[] channelPositions2 = new long[dims.length];
Extents extents = new Extents(dims);
Position pos = extents.createPosition();
while (pos.hasNext()) {
pos.fwd();
pos.localize(channelPositions1);
long ij1Channel = LegacyUtils.calcIJ1ChannelPos(dims, axes, channelPositions1);
LegacyUtils.fillChannelIndices(dims, axes, ij1Channel, channelPositions2);
for (int i = 0; i < channelPositions1.length; i++)
assertEquals(channelPositions1[i], channelPositions2[i]);
}
}
}
/** Fills the output image from the input image doing coordinate transformations as needed */
@Override
public boolean process() {
final Img<? extends RealType<?>> inputImage = dataset.getImgPlus();
inputAccessor = inputImage.randomAccess();
outputAccessor = outputImage.randomAccess();
final long width = inputDimensions[0];
final long height = inputDimensions[1];
long rx, ry, rw, rh;
if (flipper.isShapePreserving() && (bounds.width > 0) && (bounds.height > 0)) {
rx = (long) bounds.x;
ry = (long) bounds.y;
rw = (long) bounds.width;
rh = (long) bounds.height;
} else {
rx = 0;
ry = 0;
rw = width;
rh = height;
}
final long[] planeDims = new long[inputImage.numDimensions() - 2];
for (int i = 0; i < planeDims.length; i++) planeDims[i] = inputDimensions[i + 2];
final Extents extents = new Extents(planeDims);
final Position planePos = extents.createPosition();
if (planeDims.length == 0) { // 2d Dataset
processPlane(planePos, rx, ry, rw, rh);
} else { // more than two dimensions
while (planePos.hasNext()) {
planePos.fwd();
processPlane(planePos, rx, ry, rw, rh);
}
}
return true;
}