@Override
protected OperationData process(IDataset input, IMonitor monitor) {
RectangularROI box = model.getBox();
Dataset in1 =
BoxSlicerRodScanUtils.rOIBox(input, monitor, box.getIntLengths(), box.getIntPoint());
if (g2 == null) g2 = new Polynomial2D(model.getFitPower());
if ((int) Math.pow(model.getFitPower() + 1, 2) != g2.getNoOfParameters())
g2 = new Polynomial2D(model.getFitPower());
Dataset[] fittingBackground =
BoxSlicerRodScanUtils.LeftRightTopBottomBoxes(
input, monitor, box.getIntLengths(), box.getIntPoint(), model.getBoundaryBox());
Dataset offset = DatasetFactory.ones(fittingBackground[2].getShape(), Dataset.FLOAT64);
Dataset intermediateFitTest = Maths.add(offset, fittingBackground[2]);
Dataset matrix =
LinearLeastSquaresServicesForSXRD.polynomial2DLinearLeastSquaresMatrixGenerator(
model.getFitPower(), fittingBackground[0], fittingBackground[1]);
DoubleDataset test = (DoubleDataset) LinearAlgebra.solveSVD(matrix, intermediateFitTest);
double[] params = test.getData();
DoubleDataset in1Background =
g2.getOutputValues0(
params, box.getIntLengths(), model.getBoundaryBox(), model.getFitPower());
IndexIterator it = in1Background.getIterator();
while (it.hasNext()) {
double v = in1Background.getElementDoubleAbs(it.index);
if (v < 0) in1Background.setObjectAbs(it.index, 0);
}
Dataset pBackgroundSubtracted = Maths.subtract(in1, in1Background, null);
pBackgroundSubtracted.setName("pBackgroundSubtracted");
IndexIterator it1 = pBackgroundSubtracted.getIterator();
while (it1.hasNext()) {
double q = pBackgroundSubtracted.getElementDoubleAbs(it1.index);
if (q < 0) pBackgroundSubtracted.setObjectAbs(it1.index, 0);
}
Dataset output = DatasetUtils.cast(pBackgroundSubtracted, Dataset.FLOAT64);
output.setName("Region of Interest, polynomial background removed");
return new OperationData(output);
}
/**
* Get the logged image value.
*
* @param bean
* @return a dataset that can be absolute, if complex, and also be logged according to bean
* Package private for testing
*/
/* package */ Dataset getImageLoggedDataCalc(ImageServiceBean bean) {
Dataset ret = DatasetUtils.convertToDataset(bean.getImage());
if (ret.isComplex()) {
ret = Maths.abs(ret);
}
if (bean.isLogColorScale()) {
double offset = bean.getLogOffset();
if (!Double.isNaN(offset) && !Double.isInfinite(offset)) {
ret = Maths.subtract(ret, offset);
}
ret = Maths.log10(ret);
}
return ret;
}
