private void updateSpotColors() {
@SuppressWarnings("unchecked")
final FeatureColorGenerator<Spot> spotColorGenerator =
(FeatureColorGenerator<Spot>) displaySettings.get(KEY_SPOT_COLORING);
for (final int frame : blobs.keySet()) {
final SpotGroupNode<Spot> spotGroup = blobs.get(frame);
for (final Iterator<Spot> iterator = model.getSpots().iterator(frame, false);
iterator.hasNext(); ) {
final Spot spot = iterator.next();
spotGroup.setColor(spot, new Color3f(spotColorGenerator.color(spot)));
}
}
}
private void buildFrameContent(
final SpotCollection spots,
final Integer frame,
final double radiusRatio,
final FeatureColorGenerator<Spot> spotColorGenerator) {
final Map<Spot, Point4d> centers = new HashMap<Spot, Point4d>(spots.getNSpots(frame, false));
final Map<Spot, Color4f> colors = new HashMap<Spot, Color4f>(spots.getNSpots(frame, false));
final double[] coords = new double[3];
for (final Iterator<Spot> it = spots.iterator(frame, false); it.hasNext(); ) {
final Spot spot = it.next();
TMUtils.localize(spot, coords);
final Double radius = spot.getFeature(Spot.RADIUS);
final double[] pos = new double[] {coords[0], coords[1], coords[2], radius * radiusRatio};
centers.put(spot, new Point4d(pos));
final Color4f col = new Color4f(spotColorGenerator.color(spot));
col.w = 0f;
colors.put(spot, col);
}
final SpotGroupNode<Spot> blobGroup = new SpotGroupNode<Spot>(centers, colors);
final ContentInstant contentThisFrame = new ContentInstant("Spots_frame_" + frame);
try {
contentThisFrame.display(blobGroup);
} catch (final BadTransformException bte) {
System.err.println(
"Bad content for frame "
+ frame
+ ". Generated an exception:\n"
+ bte.getLocalizedMessage()
+ "\nContent was:\n"
+ blobGroup.toString());
}
// Set visibility:
if (spots.getNSpots(frame, true) > 0) {
blobGroup.setVisible(spots.iterable(frame, true));
}
contentAllFrames.put(frame, contentThisFrame);
blobs.put(frame, blobGroup);
}
@Override
public void modelChanged(final ModelChangeEvent event) {
if (DEBUG) {
System.out.println(
"[SpotDisplayer3D: modelChanged() called with event ID: " + event.getEventID());
System.out.println(event);
}
switch (event.getEventID()) {
case ModelChangeEvent.SPOTS_COMPUTED:
makeSpotContent();
break;
case ModelChangeEvent.SPOTS_FILTERED:
for (final int frame : blobs.keySet()) {
final SpotGroupNode<Spot> frameBlobs = blobs.get(frame);
for (final Iterator<Spot> it = model.getSpots().iterator(frame, false); it.hasNext(); ) {
final Spot spot = it.next();
final boolean visible =
spot.getFeature(SpotCollection.VISIBLITY).compareTo(SpotCollection.ZERO) > 0;
frameBlobs.setVisible(spot, visible);
}
}
break;
case ModelChangeEvent.TRACKS_COMPUTED:
trackContent = makeTrackContent();
universe.removeContent(TRACK_CONTENT_NAME);
universe.addContent(trackContent);
break;
case ModelChangeEvent.TRACKS_VISIBILITY_CHANGED:
updateTrackColors();
trackNode.setTrackVisible(model.getTrackModel().trackIDs(true));
break;
case ModelChangeEvent.MODEL_MODIFIED:
{
/*
* Deal with spots first.
*/
// Useful fields.
@SuppressWarnings("unchecked")
final FeatureColorGenerator<Spot> spotColorGenerator =
(FeatureColorGenerator<Spot>) displaySettings.get(KEY_SPOT_COLORING);
final double radiusRatio = (Double) displaySettings.get(KEY_SPOT_RADIUS_RATIO);
// Iterate each spot of the event.
final Set<Spot> spotsModified = event.getSpots();
for (final Spot spot : spotsModified) {
final int spotFlag = event.getSpotFlag(spot);
final int frame = spot.getFeature(Spot.FRAME).intValue();
final SpotGroupNode<Spot> spotGroupNode = blobs.get(frame);
switch (spotFlag) {
case ModelChangeEvent.FLAG_SPOT_REMOVED:
spotGroupNode.remove(spot);
break;
case ModelChangeEvent.FLAG_SPOT_ADDED:
{
// Sphere location and radius
final double[] coords = new double[3];
TMUtils.localize(spot, coords);
final Double radius = spot.getFeature(Spot.RADIUS);
final double[] pos =
new double[] {coords[0], coords[1], coords[2], radius * radiusRatio};
final Point4d center = new Point4d(pos);
// Sphere color
final Color4f color = new Color4f(spotColorGenerator.color(spot));
color.w = 0;
// Do we have an empty frame?
if (null == spotGroupNode) {
/*
* We then just give up. I dig really hard on an elegant
* way to add a new ContentInstant for a missing frame,
* but found no satisfying way. There is no good way to
* add spots to an empty frame. The way I found is very
* similar to closing the 3D viewer and re-opening it,
* therefore I let the user do it.
*
* So because of this, the SpotDisplayer3D is only a
* partial ModelListener.
*/
System.err.println(
"[SpotDisplayer3D] The TrackMate 3D viewer cannot deal with adding a spot to an empty frame.");
} else {
spotGroupNode.add(spot, center, color);
}
break;
}
case ModelChangeEvent.FLAG_SPOT_FRAME_CHANGED:
{
// Where did it belonged?
Integer targetFrame = -1;
for (final Integer f : blobs.keySet()) {
if (blobs.get(f).centers.containsKey(spot)) {
targetFrame = f;
break;
}
}
if (targetFrame < 0) {
System.err.println(
"[SpotDisplayer3D] Could not find the frame spot " + spot + " belongs to.");
return;
}
blobs.get(targetFrame).remove(spot);
// Sphere location and radius
final double[] coords = new double[3];
TMUtils.localize(spot, coords);
final Double radius = spot.getFeature(Spot.RADIUS);
final double[] pos =
new double[] {coords[0], coords[1], coords[2], radius * radiusRatio};
final Point4d center = new Point4d(pos);
// Sphere color
final Color4f color = new Color4f(spotColorGenerator.color(spot));
color.w = 0;
if (null == spotGroupNode) {
/*
* We then just give up. See above.
*/
System.err.println(
"[SpotDisplayer3D] The TrackMate 3D viewer cannot deal with moving a spot to an empty frame.");
} else {
spotGroupNode.add(spot, center, color);
}
break;
}
case ModelChangeEvent.FLAG_SPOT_MODIFIED:
{
if (null != spotGroupNode) {
spotGroupNode.remove(spot);
// Sphere location and radius
final double[] coords = new double[3];
TMUtils.localize(spot, coords);
final Double radius = spot.getFeature(Spot.RADIUS);
final double[] pos =
new double[] {coords[0], coords[1], coords[2], radius * radiusRatio};
final Point4d center = new Point4d(pos);
// Sphere color
final Color4f color = new Color4f(spotColorGenerator.color(spot));
color.w = 0;
spotGroupNode.add(spot, center, color);
}
break;
}
default:
{
System.err.println("[SpotDisplayer3D] Unknown spot flag ID: " + spotFlag);
}
}
}
/*
* Deal with edges
*/
for (final DefaultWeightedEdge edge : event.getEdges()) {
final int edgeFlag = event.getEdgeFlag(edge);
switch (edgeFlag) {
case ModelChangeEvent.FLAG_EDGE_ADDED:
case ModelChangeEvent.FLAG_EDGE_MODIFIED:
case ModelChangeEvent.FLAG_EDGE_REMOVED:
{
if (null == trackNode) {
trackContent = makeTrackContent();
universe.removeContent(TRACK_CONTENT_NAME);
universe.addContent(trackContent);
} else {
trackNode.makeMeshes();
updateTrackColors();
}
break;
}
default:
{
System.err.println("[SpotDisplayer3D] Unknown edge flag ID: " + edgeFlag);
}
}
}
break;
}
default:
{
System.err.println("[SpotDisplayer3D] Unknown event ID: " + event.getEventID());
}
}
}
