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));
}
/**
* Updates the menu structure to reflect changes in the given module. Does nothing unless the
* module is already in the menu structure.
*
* @return true if the module was successfully updated
*/
public boolean update(final ModuleInfo module) {
final ShadowMenu removed = removeInternal(module);
if (removed == null) return false; // was not in menu structure
final ShadowMenu node = addInternal(module);
if (node == null) return false;
if (es != null) es.publish(new MenusUpdatedEvent(node));
return true;
}
@Override
public void setActiveTool(final Tool activeTool) {
if (this.activeTool == activeTool) return; // nothing to do
assert this.activeTool != null;
if (activeTool == null) {
throw new IllegalArgumentException("Active tool cannot be null");
}
// deactivate old tool
this.activeTool.deactivate();
eventService.publish(new ToolDeactivatedEvent(this.activeTool));
// activate new tool
this.activeTool = activeTool;
activeTool.activate();
eventService.publish(new ToolActivatedEvent(activeTool));
}
@Override
public boolean remove(final Object o) {
if (!(o instanceof ModuleInfo)) return false;
final ModuleInfo info = (ModuleInfo) o;
final ShadowMenu node = removeInternal(info);
if (node == null) return false;
if (es != null) es.publish(new MenusRemovedEvent(node));
return true;
}
/**
* Adds the given module to the menu structure. If the module is not visible (i.e., {@link
* ModuleInfo#isVisible()} returns false), it is ignored.
*
* <p>{@inheritDoc}
*/
@Override
public boolean add(final ModuleInfo o) {
if (!o.isVisible()) return false;
final ShadowMenu node = addInternal(o);
if (node == null) return false;
if (es != null) es.publish(new MenusAddedEvent(node));
return true;
}
/**
* Adds the given modules to the menu structure. If a module is not visible (i.e., {@link
* ModuleInfo#isVisible()} returns false), it is ignored.
*
* <p>{@inheritDoc}
*/
@Override
public boolean addAll(final Collection<? extends ModuleInfo> c) {
final HashSet<ShadowMenu> nodes = new HashSet<>();
for (final ModuleInfo info : c) {
if (!info.isVisible()) continue;
final ShadowMenu node = addInternal(info);
if (node != null) nodes.add(node);
}
if (nodes.isEmpty()) return false;
if (es != null) es.publish(new MenusAddedEvent(nodes));
return true;
}
/**
* Updates the menu structure to reflect changes in the given modules. Does nothing unless at
* least one of the modules is already in the menu structure.
*
* @return true if at least one module was successfully updated
*/
public boolean updateAll(final Collection<? extends ModuleInfo> c) {
final HashSet<ShadowMenu> nodes = new HashSet<>();
for (final ModuleInfo info : c) {
final ShadowMenu removed = removeInternal(info);
if (removed == null) continue; // was not in menu structure
final ShadowMenu node = addInternal(info);
if (node != null) nodes.add(node);
}
if (nodes.isEmpty()) return false;
if (es != null) es.publish(new MenusUpdatedEvent(nodes));
return true;
}
@Override
public boolean removeAll(final Collection<?> c) {
final HashSet<ShadowMenu> nodes = new HashSet<>();
for (final Object o : c) {
if (!(o instanceof ModuleInfo)) continue;
final ModuleInfo info = (ModuleInfo) o;
final ShadowMenu node = removeInternal(info);
if (node != null) nodes.add(node);
}
if (nodes.isEmpty()) return false;
if (es != null) es.publish(new MenusRemovedEvent(nodes));
return true;
}
/** 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));
}
@Override
public void setCurrentTool(Class<? extends FxTool> currentToolCl) {
this.currentTool = getTool(currentToolCl);
eventService.publish(new ToolChangeEvent(currentTool));
}
@Override
public void addModule(final ModuleInfo module) {
if (moduleIndex.add(module)) {
eventService.publish(new ModulesAddedEvent(module));
}
}
@Override
public void removeModules(final Collection<? extends ModuleInfo> modules) {
if (moduleIndex.removeAll(modules)) {
eventService.publish(new ModulesRemovedEvent(modules));
}
}
@Override
public void addModules(final Collection<? extends ModuleInfo> modules) {
if (moduleIndex.addAll(modules)) {
eventService.publish(new ModulesAddedEvent(modules));
}
}
@Override
public void removeModule(final ModuleInfo module) {
if (moduleIndex.remove(module)) {
eventService.publish(new ModulesRemovedEvent(module));
}
}