protected HashMap<Integer, ArrayList<Integer>> getSplitSelectionIndexes() {
HashMap<Integer, ArrayList<Object3DGui>> splitSelection = getSplitSelection();
HashMap<Integer, ArrayList<Integer>> res =
new HashMap<Integer, ArrayList<Integer>>(splitSelection.size());
for (Map.Entry<Integer, ArrayList<Object3DGui>> e : splitSelection.entrySet()) {
ArrayList<Integer> idxs = new ArrayList<Integer>(e.getValue().size());
for (Object3DGui o : e.getValue()) idxs.add(o.getLabel());
res.put(e.getKey(), idxs);
}
return res;
}
protected HashMap<Integer, ArrayList<Object3DGui>> getSplitSelection() {
System.out.println(
"get split selection: currenChannels==null?" + (this.currentChannels == null));
if (this.currentChannels == null) return new HashMap<Integer, ArrayList<Object3DGui>>(0);
HashMap<Integer, ArrayList<Object3DGui>> res =
new HashMap<Integer, ArrayList<Object3DGui>>(this.currentChannels.length);
for (ObjectStructure ass : currentChannels) res.put(ass.getIdx(), new ArrayList<Object3DGui>());
for (Object o : list.getSelectedValues()) {
Object3DGui o3D = (Object3DGui) (o);
int idx = o3D.getChannel().getIdx();
res.get(idx).add(o3D);
}
return res;
}
private void sort(String key, Object3DGui[] objectsGui, int structureIdx) {
Object3DGui.setAscendingOrger(((ObjectManagerLayout) layout).getAscendingOrder());
HashMap<Integer, BasicDBObject> objects =
Core.getExperiment().getConnector().getObjects(currentNucId, structureIdx);
boolean notFound = false;
for (Object3DGui o : objectsGui) {
BasicDBObject dbo = objects.get(o.getLabel());
if (dbo != null) {
if (dbo.containsField(key)) o.setValue(dbo.getDouble(key));
else {
o.setValue(-1);
notFound = true;
}
}
}
if (notFound)
ij.IJ.log("Warning measurement: " + key + " not found for one or several objects");
Arrays.sort(objectsGui);
}
public void populateObjects() {
try {
this.listModel.removeAllElements();
if (currentChannels == null) {
return;
}
this.populatingObjects = true;
ArrayList<Integer> selection = null;
if (showSelection != null && showSelection.isSelected()) selection = new ArrayList<Integer>();
int currentIdx = 0;
for (ObjectStructure ass : currentChannels) {
Object3D[] os = ass.getObjects();
if (os != null) {
Object3DGui[] osg = new Object3DGui[os.length];
for (int i = 0; i < os.length; i++) osg[i] = new Object3DGui(os[i], ass);
if (layout instanceof ObjectManagerLayout
&& currentChannels.length == 1
&& !((ObjectManagerLayout) layout).getSortKey().equals("idx"))
this.sort(((ObjectManagerLayout) layout).getSortKey(), osg, ass.getIdx());
// System.out.println("populating objects.. nb objects:"+os.length);
for (Object3DGui o3D : osg) {
this.listModel.addElement(o3D);
if (selection != null && o3D.isInSelection()) selection.add(currentIdx);
currentIdx++;
}
// if (selection!=null) System.out.println("populating objects.. selection
// size:"+selection.size());
} // else System.out.println("no objects int channel:"+ass.getChannelName());
}
if (selection != null && !selection.isEmpty()) {
int[] sel = new int[selection.size()];
int i = 0;
for (int idx : selection) sel[i++] = idx;
list.setSelectedIndices(sel);
}
} catch (Exception e) {
exceptionPrinter.print(e, "", Core.GUIMode);
}
this.populatingObjects = false;
}
public void showRois3D() {
registerActiveImage();
if (currentImage == null) return;
// verifier que l'image active a les memes dimentions
Object[] os = this.list.getSelectedValues();
if (os.length == 1) {
mcib3d.geom.Object3D o = ((Object3DGui) os[0]).getObject3D();
currentImage.setSlice((o.getZmax() + o.getZmin()) / 2 + 1);
}
int nSlices = currentImage.getNSlices();
currentROIs = new HashMap<Integer, Roi>(nSlices);
// stores the roi mask to save memory..
if (roiMask == null || !roiMask.sameDimentions(currentImage)) {
roiMask = new ImageByte("mask", currentImage.getWidth(), currentImage.getHeight(), nSlices);
} else {
roiMask.erase();
}
ImageStack maskStack = roiMask.getImageStack();
Object3DGui obj;
for (Object o : os) {
obj = (Object3DGui) o;
obj.getObject3D().draw(maskStack, 255);
}
// roiMask.show();
for (int i = 1; i <= nSlices; i++) {
ImagePlus im = new ImagePlus("mask", maskStack.getProcessor(i));
im.getProcessor().setThreshold(1, 255, ImageProcessor.NO_LUT_UPDATE);
ThresholdToSelection tts = new ThresholdToSelection();
tts.setup("", im);
tts.run(im.getProcessor());
Roi r = im.getRoi();
if (r != null) currentROIs.put(i, r);
}
updateRoi();
}
public void mergeSelectedObjects() {
this.populatingObjects = true;
HashMap<Integer, ArrayList<Object3DGui>> allObjects = getSplitSelection();
for (int channelIdx : allObjects.keySet()) {
ArrayList<Object3DGui> objects = allObjects.get(channelIdx);
if (objects != null && objects.size() >= 2) {
Collections.sort(objects);
Object3DGui o1 = objects.get(0);
for (int i = objects.size() - 1; i > 0; i--) {
Object3DGui o2 = objects.get(i);
o1.merge(o2);
listModel.removeElement(o2);
// IJ.log("merge:"+o1.getName()+ "::"+objects.get(i).getName()+ " channel:"+channelIdx);
}
o1.getChannel().createObjects();
if (autoSave) o1.getChannel().saveOutput();
ImagePlus img = o1.getChannel().getSegmented().getImagePlus();
if (img.isVisible()) {
img.updateAndDraw();
}
}
}
this.populatingObjects = false;
}
public void deleteSelectedObjects() {
populatingObjects = true;
try {
boolean[] modif = new boolean[currentChannels.length];
for (Object o : this.list.getSelectedValues()) {
listModel.removeElement(o);
modif[getChannelRank(((Object3DGui) o).getChannel())] = true;
((Object3DGui) o).delete(true);
}
for (int i = 0; i < currentChannels.length; i++) {
if (modif[i]) {
ImagePlus img = currentChannels[i].getSegmented().getImagePlus();
if (img.isVisible()) {
img.updateAndDraw();
}
currentChannels[i].createObjects();
if (autoSave) currentChannels[i].saveOutput();
}
}
} catch (Exception e) {
exceptionPrinter.print(e, "", Core.GUIMode);
}
populatingObjects = false;
}
protected boolean split(Object3DGui og) {
if (!(this instanceof NucleusManager) && og.getChannel() instanceof Nucleus) {
if (Core.GUIMode) ij.IJ.log("Cannont split nucleus!");
return false;
}
Object3DGui[] newObjects = og.split(splitRad.getFloatValue(2), splitDist.getFloatValue(5));
if (newObjects.length == 0) {
if (Core.GUIMode) ij.IJ.log("Object couldn't be split");
return false;
}
Object3D[] objs = og.getChannel().getObjects();
int nextLabel = objs[objs.length - 1].getValue() + 1;
for (Object3DGui o : newObjects) {
o.changeLabel(nextLabel);
this.listModel.addElement(o); // TODO le mettre a la fin des objets du channel..
nextLabel++;
}
og.getChannel().getSegmented().updateDisplay();
return true;
}