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()); } } }