// Note this is a bit of a integration test not a strict unit test
@Test
public void testFillingAMoreComplicatedBoundingRectangle() throws Exception {
double xStart = 0.0;
double xStop = 25.5;
double yStart = 0.0;
double yStop = 33.33;
double xStep = 0.4;
double yStep = 0.6;
RectangularROI roi = new RectangularROI();
roi.setPoint(Math.min(xStart, xStop), Math.min(yStart, yStop));
roi.setLengths(Math.abs(xStop - xStart), Math.abs(yStop - yStart));
RasterModel model = new RasterModel();
model.setxStep(xStep);
model.setyStep(yStep);
// Get the point list
IPointGenerator<RasterModel, Point> gen = service.createGenerator(model, roi);
List<Point> pointList = gen.createPoints();
int rows = (int) (Math.floor((xStop - xStart) / xStep) + 1);
int cols = (int) (Math.floor((yStop - yStart) / yStep) + 1);
// Check the list size
assertEquals("Point list size should be correct", rows * cols, pointList.size());
// Check some points
assertEquals(new Point(0, xStart, 0, yStart), pointList.get(0));
assertEquals(xStart + 3 * xStep, pointList.get(3).getX(), 1e-8);
// TODO more
GeneratorUtil.testGeneratorPoints(gen);
}
static Dataset getLabelsFromLabels(Dataset xl, RectangularROI bounds, int axisIndex) {
try {
int fromIndex = (int) bounds.getPoint()[axisIndex];
int toIndex = (int) bounds.getEndPoint()[axisIndex];
int step = toIndex > fromIndex ? 1 : -1;
final Dataset slice =
xl.getSlice(new int[] {fromIndex}, new int[] {toIndex}, new int[] {step});
return slice;
} catch (Exception ne) {
return null;
}
}
@Test
public void testRectangularROIBeanConversionToRectangularROI() throws Exception {
// RectangularROI
ROIBean rbean = new RectangularROIBean();
((RectangularROIBean) rbean).setName("rectangle");
((RectangularROIBean) rbean).setStartPoint(startPoint);
((RectangularROIBean) rbean).setType("RectangularROI");
((RectangularROIBean) rbean).setLengths(lengths);
((RectangularROIBean) rbean).setAngle(0);
RectangularROI rroi = (RectangularROI) ROIBeanFactory.decapsulate(rbean);
assertArrayEquals(startPoint, rroi.getPoint(), 0);
assertArrayEquals(lengths, rroi.getLengths(), 0);
}
@Override
public DataReductionInfo export(DataReductionSlice drslice) throws Exception {
final Collection<IRegion> regions = getPlottingSystem().getRegions();
for (IRegion region : regions) {
if (!isRegionTypeSupported(region.getRegionType())) continue;
final RectangularROI bounds = (RectangularROI) region.getROI();
if (bounds == null) continue;
if (!region.isVisible()) continue;
final int yInc = bounds.getPoint()[1] < bounds.getEndPoint()[1] ? 1 : -1;
final int xInc = bounds.getPoint()[0] < bounds.getEndPoint()[0] ? 1 : -1;
final Dataset slice =
DatasetUtils.convertToDataset(
drslice
.getData()
.getSlice(
new int[] {(int) bounds.getPoint()[1], (int) bounds.getPoint()[0]},
new int[] {(int) bounds.getEndPoint()[1], (int) bounds.getEndPoint()[0]},
new int[] {yInc, xInc}));
slice.setName(region.getName().replace(' ', '_'));
drslice.appendData(slice);
}
return new DataReductionInfo(Status.OK_STATUS);
}
@Override
protected Collection<? extends ITrace> createProfile(
final IImageTrace image,
IRegion region,
IROI rbs,
boolean tryUpdate,
boolean isDrag,
IProgressMonitor monitor) {
if (monitor.isCanceled()) return null;
if (image == null) return null;
if ((region.getRegionType() != RegionType.BOX)
&& (region.getRegionType() != RegionType.PERIMETERBOX)) return null;
Dataset slice = createZoom(image, region, rbs, tryUpdate, isDrag, monitor);
Dataset yData = slice.sum(0);
yData.setName("Intensity");
Dataset xData = slice.sum(1);
xData.setName("Intensity");
final RectangularROI bounds = (RectangularROI) (rbs == null ? region.getROI() : rbs);
final Dataset y_indices =
DatasetFactory.createRange(
bounds.getPoint()[0], bounds.getPoint()[0] + bounds.getLength(0), 1, Dataset.FLOAT);
y_indices.setName("X Location");
topSystem.updatePlot1D(y_indices, Arrays.asList(new IDataset[] {yData}), monitor);
topSystem.repaint();
final Dataset x_indices =
DatasetFactory.createRange(
bounds.getPoint()[1] + bounds.getLength(1), bounds.getPoint()[1], -1, Dataset.FLOAT);
x_indices.setName("Y Location");
final Collection<ITrace> right =
rightSystem.updatePlot1D(xData, Arrays.asList(new IDataset[] {x_indices}), monitor);
rightSystem.repaint();
Display.getDefault()
.syncExec(
new Runnable() {
@Override
public void run() {
topSystem.setTitle("");
rightSystem.setTitle("");
ILineTrace line = (ILineTrace) right.iterator().next();
line.setTraceColor(ColorConstants.red);
}
});
return profilePlottingSystem.getTraces();
}
protected Dataset createZoom(
final IImageTrace image,
IRegion region,
IROI rbs,
boolean tryUpdate,
boolean isDrag,
IProgressMonitor monitor) {
if (!(region.getROI() instanceof RectangularROI)) return null;
final RectangularROI bounds = (RectangularROI) (rbs == null ? region.getROI() : rbs);
if (bounds == null) return null;
if (!region.isVisible()) return null;
if (monitor.isCanceled()) return null;
final int yInc = bounds.getPoint()[1] < bounds.getEndPoint()[1] ? 1 : -1;
final int xInc = bounds.getPoint()[0] < bounds.getEndPoint()[0] ? 1 : -1;
Dataset im = DatasetUtils.convertToDataset(image.getData());
Dataset slice = DatasetUtils.convertToDataset(ToolUtils.getClippedSlice(im, bounds));
slice.setName(region.getName());
// Calculate axes to have real values not size
Dataset yLabels = null;
Dataset xLabels = null;
if (image.getAxes() != null && image.getAxes().size() > 0) {
Dataset xl = DatasetUtils.convertToDataset(image.getAxes().get(0));
if (xl != null) xLabels = ZoomTool.getLabelsFromLabels(xl, bounds, 0);
Dataset yl = DatasetUtils.convertToDataset(image.getAxes().get(1));
if (yl != null) yLabels = ZoomTool.getLabelsFromLabels(yl, bounds, 1);
}
if (yLabels == null)
yLabels =
DatasetFactory.createRange(
IntegerDataset.class, bounds.getPoint()[1], bounds.getEndPoint()[1], yInc);
if (xLabels == null)
xLabels =
DatasetFactory.createRange(
IntegerDataset.class, bounds.getPoint()[0], bounds.getEndPoint()[0], xInc);
final IImageTrace zoom_trace =
(IImageTrace)
profilePlottingSystem.updatePlot2D(
slice, Arrays.asList(new IDataset[] {xLabels, yLabels}), monitor);
registerTraces(region, Arrays.asList(new ITrace[] {zoom_trace}));
Display.getDefault()
.syncExec(
new Runnable() {
public void run() {
zoom_trace.setPaletteData(image.getPaletteData());
}
});
return slice;
}
@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);
}