@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; }