protected void updateRoi() {
// System.out.println("image:"+currentImage.getTitle()+ " slice:"+currentImage.getSlice());
Roi r = currentROIs.get(currentImage.getSlice());
if (r != null) {
currentImage.setRoi(r);
} else {
currentImage.killRoi();
}
currentImage.updateAndDraw();
}
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 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();
}
