use of net.imglib2.view.IntervalView in project vcell by virtualcell.
the class DeconstructGeometryCommand method run.
@Override
public void run() {
// Crop to get a z-stack over time (remove channel dimension)
long maxX = fluorData.max(fluorData.dimensionIndex(Axes.X));
long maxY = fluorData.max(fluorData.dimensionIndex(Axes.Y));
long maxZ = fluorData.max(fluorData.dimensionIndex(Axes.Z));
long maxTime = fluorData.max(fluorData.dimensionIndex(Axes.TIME));
Img fluorImg = fluorData.getImgPlus().getImg();
FinalInterval intervals = Intervals.createMinMax(0, 0, 0, 0, 0, maxX, maxY, maxZ, 0, maxTime);
RandomAccessibleInterval fluorImgCropped = ops.transform().crop(fluorImg, intervals, true);
// Calculate scale factors
double[] scaleFactors = { 1, 1, 1, 1 };
for (int i = 0; i < geomData.numDimensions(); i++) {
scaleFactors[i] = geomData.dimension(i) / (double) fluorImgCropped.dimension(i);
}
// Scale the fluorescence dataset to match the geometry
NLinearInterpolatorFactory interpolatorFactory = new NLinearInterpolatorFactory();
RandomAccessibleInterval fluorScaled = ops.transform().scale(fluorImgCropped, scaleFactors, interpolatorFactory);
// Crop out the first slice of each z-stack in time series
intervals = Intervals.createMinMax(0, 0, 0, 0, fluorScaled.dimension(0) - 1, fluorScaled.dimension(1) - 1, 0, fluorScaled.dimension(3) - 1);
IntervalView fluorXYT = (IntervalView) ops.transform().crop(fluorScaled, intervals, true);
// Create a blank image of the same X-Y-Time dimensions
long[] dimensions = { fluorXYT.dimension(0), fluorXYT.dimension(1), fluorXYT.dimension(2) };
Img<DoubleType> result = ops.create().img(dimensions);
// Calculate constant d in TIRF exponential decay function
theta = theta * 2 * Math.PI / 360;
double n1 = 1.52;
double n2 = 1.38;
double d = lambda * Math.pow((Math.pow(n1, 2) * Math.pow(Math.sin(theta), 2) - Math.pow(n2, 2)), -0.5) / (4 * Math.PI);
// Iterate through each time point, using 3D geometry to generate 2D intensities
Cursor<DoubleType> cursor = fluorXYT.localizingCursor();
RandomAccess fluorRA = fluorScaled.randomAccess();
RandomAccess<RealType<?>> geomRA = geomData.randomAccess();
RandomAccess<DoubleType> resultRA = result.randomAccess();
maxZ = geomData.dimension(2) - 1;
while (cursor.hasNext()) {
cursor.fwd();
int[] positionXYZ = { cursor.getIntPosition(0), cursor.getIntPosition(1), (int) maxZ - 1 };
int[] positionXYZT = { cursor.getIntPosition(0), cursor.getIntPosition(1), (int) maxZ - 1, cursor.getIntPosition(2) };
resultRA.setPosition(cursor);
geomRA.setPosition(positionXYZ);
double sum = 0.0;
while (positionXYZ[2] >= 0 && geomRA.get().getRealDouble() != 0.0) {
fluorRA.setPosition(positionXYZT);
geomRA.setPosition(positionXYZ);
sum += geomRA.get().getRealDouble() * Math.exp(-zSpacing * positionXYZ[2] / d);
positionXYZ[2]--;
}
resultRA.get().set(sum);
}
System.out.println("done");
displayService.createDisplay(result);
}
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