/**
* This method exists for the following reason:
*
* <p>The segmenter receives at each frame a cropped image to operate on, depending on the user
* specifying a ROI. It therefore returns spots whose coordinates are with respect to the top-left
* corner of the ROI, not of the original image.
*
* <p>This method modifies the given spots to put them back in the image coordinate system.
* Additionally, is a non-square ROI was specified (e.g. a polygon), it prunes the spots that are
* not within the polygon of the ROI.
*
* @param spotsThisFrame the spot list to inspect
* @param settings the {@link Settings} object that will be used to retrieve the image ROI and
* cropping information
* @return a list of spot. Depending on the presence of a polygon ROI, it might be a new, pruned
* list. Or not.
*/
protected List<Spot> translateAndPruneSpots(
final List<Spot> spotsThisFrame, final Settings settings) {
// Get Roi
final Polygon polygon;
if (null == settings.imp || null == settings.imp.getRoi()) {
polygon = null;
} else {
polygon = settings.imp.getRoi().getPolygon();
}
// Put them back in the right referential
final float[] calibration = settings.getCalibration();
TMUtils.translateSpots(
spotsThisFrame,
settings.xstart * calibration[0],
settings.ystart * calibration[1],
settings.zstart * calibration[2]);
List<Spot> prunedSpots;
// Prune if outside of ROI
if (null != polygon) {
prunedSpots = new ArrayList<Spot>();
for (Spot spot : spotsThisFrame) {
if (polygon.contains(
spot.getFeature(Spot.POSITION_X) / calibration[0],
spot.getFeature(Spot.POSITION_Y) / calibration[1])) prunedSpots.add(spot);
}
} else {
prunedSpots = spotsThisFrame;
}
return prunedSpots;
}
@SuppressWarnings({"unchecked", "rawtypes"})
protected List<Spot> execSingleFrameSegmentation(
final Image<? extends RealType<?>> img, Settings settings, int frameIndex) {
final float[] calibration = settings.getCalibration();
SpotSegmenter segmenter = settings.segmenter.createNewSegmenter();
segmenter.setTarget(img, calibration, settings.segmenterSettings);
if (segmenter.checkInput() && segmenter.process()) {
List<Spot> spotsThisFrame = segmenter.getResult();
return translateAndPruneSpots(spotsThisFrame, settings);
} else {
model.getLogger().error(segmenter.getErrorMessage() + '\n');
return null;
}
}