private IDataset getToggledData(IImageTrace image, IProgressMonitor monitor) {
if (image.getData() == trans) {
return orig;
} else {
this.orig = image.getData();
Object[] oa;
try {
oa = filter.filter(orig, null);
this.trans = (IDataset) oa[0];
return trans;
} catch (Exception e) {
e.printStackTrace();
return orig;
}
}
}
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;
}
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;
}