private void highlightEdges(final Collection<DefaultWeightedEdge> edges) {
// Restore previous display settings for previously highlighted edges
if (null != previousEdgeHighlight)
for (final DefaultWeightedEdge edge : previousEdgeHighlight.keySet())
trackNode.setColor(edge, previousEdgeHighlight.get(edge));
// Store current color settings
previousEdgeHighlight = new HashMap<DefaultWeightedEdge, Color>();
for (final DefaultWeightedEdge edge : edges)
previousEdgeHighlight.put(edge, trackNode.getColor(edge));
// Change edge color
final Color highlightColor = (Color) displaySettings.get(KEY_HIGHLIGHT_COLOR);
for (final DefaultWeightedEdge edge : edges) trackNode.setColor(edge, highlightColor);
}
@Override
public void render() {
if (DEBUG) System.out.println("[SpotDisplayer3D] Call to render().");
updateRadiuses();
updateSpotColors();
spotContent.setVisible((Boolean) displaySettings.get(KEY_SPOTS_VISIBLE));
if (null != trackContent) {
trackContent.setVisible((Boolean) displaySettings.get(KEY_TRACKS_VISIBLE));
trackNode.setTrackDisplayMode((Integer) displaySettings.get(KEY_TRACK_DISPLAY_MODE));
trackNode.setTrackDisplayDepth((Integer) displaySettings.get(KEY_TRACK_DISPLAY_DEPTH));
updateTrackColors();
trackNode.refresh();
universe.updateStartAndEndTime(blobs.firstKey(), blobs.lastKey());
universe.updateTimelineGUI();
}
}
private void updateTrackColors() {
final TrackColorGenerator colorGenerator =
(TrackColorGenerator) displaySettings.get(KEY_TRACK_COLORING);
for (final Integer trackID : model.getTrackModel().trackIDs(true)) {
colorGenerator.setCurrentTrackID(trackID);
for (final DefaultWeightedEdge edge : model.getTrackModel().trackEdges(trackID)) {
final Color color = colorGenerator.color(edge);
trackNode.setColor(edge, color);
}
}
}
@Override
public void setDisplaySettings(final String key, final Object value) {
super.setDisplaySettings(key, value);
// Treat change of radius
if (key == KEY_SPOT_RADIUS_RATIO) {
updateRadiuses();
} else if (key == KEY_SPOT_COLORING) {
updateSpotColors();
} else if (key == KEY_TRACK_COLORING) {
updateTrackColors();
} else if (key == KEY_DISPLAY_SPOT_NAMES) {
for (final int frame : blobs.keySet()) {
blobs.get(frame).setShowLabels((Boolean) value);
}
} else if (key == KEY_SPOTS_VISIBLE) {
spotContent.setVisible((Boolean) value);
} else if (key == KEY_TRACKS_VISIBLE && null != trackContent) {
trackContent.setVisible((Boolean) value);
} else if (key == KEY_TRACK_DISPLAY_MODE && null != trackNode) {
trackNode.setTrackDisplayMode((Integer) value);
} else if (key == KEY_TRACK_DISPLAY_DEPTH && null != trackNode) {
trackNode.setTrackDisplayDepth((Integer) value);
}
}
@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());
}
}
}
@Override
public void refresh() {
if (null != trackNode) trackNode.refresh();
}
