protected OperationData process(IDataset input, IMonitor monitor) throws OperationException {
double d = (2 * Math.PI) / model.getqValue();
double p = (2 * Math.PI) / (model.getqValue() + model.getqDelta());
double m = (2 * Math.PI) / (model.getqValue() - model.getqDelta());
IDiffractionMetadata dm = getFirstDiffractionMetadata(input);
if (dm == null) throw new OperationException(this, "No calibration information!");
IParametricROI[] inOut = new IParametricROI[2];
IParametricROI conic =
(IParametricROI)
DSpacing.conicFromDSpacing(
dm.getDetector2DProperties(), dm.getDiffractionCrystalEnvironment(), d);
inOut[0] =
(IParametricROI)
DSpacing.conicFromDSpacing(
dm.getDetector2DProperties(), dm.getDiffractionCrystalEnvironment(), m);
inOut[1] =
(IParametricROI)
DSpacing.conicFromDSpacing(
dm.getDetector2DProperties(), dm.getDiffractionCrystalEnvironment(), p);
PolylineROI points =
PeakFittingEllipseFinder.findPointsOnConic(
DatasetUtils.convertToDataset(input), null, conic, inOut, 256, null);
double rms = -1;
double[] semi = new double[2];
double[] point = new double[2];
double ang = 0;
if (points != null && points.getNumberOfPoints() < 3) {
EllipticalFitROI efroi = PowderRingsUtils.fitAndTrimOutliers(null, points, 2, false);
rms = efroi.getRMS();
semi = efroi.getSemiAxes();
point = efroi.getPoint();
ang = efroi.getAngleDegrees();
}
Dataset r = DatasetFactory.createFromObject(new double[] {rms});
r.setName("rms");
Dataset ax = DatasetFactory.createFromObject(semi);
ax.setName("semi-axes");
Dataset po = DatasetFactory.createFromObject(point);
po.setName("centre");
Dataset a = DatasetFactory.createFromObject(new double[] {ang});
a.setName("angle");
return new OperationData(input, new Serializable[] {r, ax, po, a});
}
@Test
public void testPolylineROIBeanConversionToPolylineROI() throws Exception {
// PolylineROI
ROIBean rbean = new PolylineROIBean();
double[] point0 = {102, 102}, point1 = {105, 105};
List<double[]> points = new ArrayList<double[]>();
// points.add(startPoint);
points.add(point0);
points.add(point1);
((PolylineROIBean) rbean).setName("Polyline");
((PolylineROIBean) rbean).setPoints(points);
((PolylineROIBean) rbean).setStartPoint(startPoint);
((PolylineROIBean) rbean).setType("PolylineROI");
PolylineROI proi = (PolylineROI) ROIBeanFactory.decapsulate(rbean);
assertArrayEquals(startPoint, proi.getPoint(), 0);
assertArrayEquals(point0, proi.getPoint(1).getPoint(), 0);
assertArrayEquals(point1, proi.getPoint(2).getPoint(), 0);
}
public static IROI runConicPeakFit(
final IProgressMonitor monitor,
Display display,
final IPlottingSystem plotter,
IImageTrace t,
IParametricROI roi,
IParametricROI[] innerOuter,
int nPoints) {
if (roi == null) return null;
final ProgressMonitorWrapper mon = new ProgressMonitorWrapper(monitor);
monitor.subTask("Find POIs near initial ellipse");
Dataset image = (Dataset) t.getData();
BooleanDataset mask = (BooleanDataset) t.getMask();
PolylineROI points;
monitor.subTask("Fit POIs");
points = PeakFittingEllipseFinder.findPointsOnConic(image, mask, roi, innerOuter, nPoints, mon);
if (monitor.isCanceled()) return null;
if (points == null) return null;
if (roi instanceof EllipticalROI) {
if (points.getNumberOfPoints() < 3) {
throw new IllegalArgumentException("Could not find enough points to trim");
}
monitor.subTask("Trim POIs");
EllipticalFitROI efroi = PowderRingsUtils.fitAndTrimOutliers(mon, points, 5, false);
logger.debug("Found {}...", efroi);
monitor.subTask("");
return efroi;
}
return points;
}