public void generateTestSet() {
List<ImageDisplay> displays = imageDisplayService.getImageDisplays();
imgDatasets = new ArrayList<>(displays.size());
List<Dataset> labeledDs = new ArrayList<>(displays.size());
List<List<Overlay>> overlaySet = new ArrayList<>();
displays
.stream()
.forEach(
id -> {
imgDatasets.add(imageDisplayService.getActiveDataset(id));
overlaySet.add(overlayService.getOverlays(id));
});
List<List<Point2D>> seeds = seeding();
int numProfiles = 0;
for (int ds = 0; ds < imgDatasets.size(); ds++) {
List<Point2D> centers = seeds.get(ds);
ProfilesSet profiles = new DefaultProfilesSet(centers, searchRadius.getValue(), context);
numProfiles += profiles.size();
testData.add(profiles);
}
eventService.publish(new ProfileEvent(ProfileType.TEST, numProfiles));
}
public List<List<Point2D>> seeding() {
// TODO seeding algorithm. Temp manual alternative
List<List<Point2D>> seeds = new ArrayList();
List<ImageDisplay> displays = imageDisplayService.getImageDisplays();
imgDatasets = new ArrayList<>(displays.size());
List<List<Overlay>> overlaySet = new ArrayList<>();
displays
.stream()
.forEach(
id -> {
imgDatasets.add(imageDisplayService.getActiveDataset(id));
overlaySet.add(overlayService.getOverlays(id));
});
for (int ds = 0; ds < imgDatasets.size(); ds++) {
List<Point2D> currSeeds = new ArrayList();
for (Overlay o : overlaySet.get(ds)) {
if (o instanceof PointOverlay) {
double[] point = ((PointOverlay) o).getPoints().get(0);
Point2D point2D = new Point2D(point[0], point[1]);
currSeeds.add(point2D);
}
}
seeds.add(currSeeds);
}
return seeds;
}
/** Generate the different intensity profiles from drawn objects for each ImageDisplay */
public void generateTrainingSet() {
double maxDiameter = 0.0;
List<ImageDisplay> displays = imageDisplayService.getImageDisplays();
imgDatasets = new ArrayList<>(displays.size());
List<Dataset> labeledDs = new ArrayList<>(displays.size());
List<List<Overlay>> overlaySet = new ArrayList<>();
displays
.stream()
.forEach(
id -> {
imgDatasets.add(imageDisplayService.getActiveDataset(id));
overlaySet.add(overlayService.getOverlays(id));
});
int numProfiles = 0;
for (int ds = 0; ds < imgDatasets.size(); ds++) {
labeledDs.add(imagePlaneService.createEmptyPlaneDataset(imgDatasets.get(ds)));
ArrayList<Point2D> centers = new ArrayList<>();
for (Overlay o : overlaySet.get(ds)) {
OverlayShapeStatistics stats = overlayStatService.getShapeStatistics(o);
centers.add(stats.getCenterOfGravity());
if (stats.getFeretDiameter() > maxDiameter) maxDiameter = stats.getFeretDiameter();
overlayDrawingService.drawOverlay(
o, OverlayDrawingService.OUTLINER, labeledDs.get(ds), COLOR);
}
// uis.show(labeledDs.get(ds));
ProfilesSet profiles = new DefaultProfilesSet(centers, (int) maxDiameter, context);
generateConfirmationSet(profiles, labeledDs.get(ds));
numProfiles += profiles.size();
trainingData.add(profiles);
}
eventService.publish(new ProfileEvent(ProfileType.TRAIN, numProfiles));
}
/**
* @param imageDisplay
* @param firstPosition
* @param secondPosition
* @param imageDisplayPane
*/
public void selectPosition(
ImageDisplay imageDisplay,
long[] firstPosition,
long[] secondPosition,
ImageDisplayPane imageDisplayPane) {
workflowModel.setPosition(firstPosition, imageDisplay);
imageDisplayService.getActiveDatasetView(imageDisplay).setColorMode(ColorMode.COLOR);
Dataset datasetFirstSlide = datasetUtillsService.extractPlane(imageDisplay);
workflowModel.setPosition(secondPosition, imageDisplay);
Dataset datasetSecondSlide = datasetUtillsService.extractPlane(imageDisplay);
workflowModel.extractAndMerge(
new Dataset[] {datasetFirstSlide, datasetSecondSlide}, imageDisplayPane);
}