public static void main(final String args[]) {
final File file =
new File(AppUtils.getBaseDirectory(TrackMate.class), "samples/FakeTracks.xml");
// 1 - Load test spots
System.out.println("Opening file: " + file.getAbsolutePath());
final TmXmlReader reader = new TmXmlReader(file);
final Model model = reader.getModel();
final Settings gs = new Settings();
reader.readSettings(gs, null, null, null, null, null);
System.out.println("Spots: " + model.getSpots());
System.out.println("Found " + model.getTrackModel().nTracks(false) + " tracks in the file:");
System.out.println("Track features: ");
System.out.println();
// 2 - Track the test spots
final long start = System.currentTimeMillis();
final Map<String, Object> settings = new HashMap<String, Object>();
settings.put(KEY_LINKING_MAX_DISTANCE, 15d);
final NearestNeighborTracker tracker = new NearestNeighborTracker(model.getSpots(), settings);
tracker.setLogger(Logger.DEFAULT_LOGGER);
if (!tracker.checkInput())
System.err.println("Error checking input: " + tracker.getErrorMessage());
if (!tracker.process()) System.err.println("Error in process: " + tracker.getErrorMessage());
final long end = System.currentTimeMillis();
model.setTracks(tracker.getResult(), true);
// 3 - Print out results for testing
System.out.println();
System.out.println();
System.out.println();
System.out.println("Found " + model.getTrackModel().nTracks(false) + " final tracks.");
System.out.println("Whole tracking done in " + (end - start) + " ms.");
System.out.println();
// 5 - Display tracks
// Load Image
ij.ImageJ.main(args);
final ImagePlus imp = gs.imp;
final TrackMateModelView sd2d = new HyperStackDisplayer(model, new SelectionModel(model), imp);
sd2d.render();
sd2d.setDisplaySettings(
TrackMateModelView.KEY_TRACK_DISPLAY_MODE, TrackMateModelView.TRACK_DISPLAY_MODE_WHOLE);
}
/**
* Links all the spots in the selection, in time-forward order.
*
* @param model the model to modify.
* @param selectionModel the selection that contains the spots to link.
*/
public static void linkSpots(final Model model, final SelectionModel selectionModel) {
/*
* Configure tracker
*/
final TrackableObjectCollection<Spot> spots =
new DefaultTOCollection<Spot>(selectionModel.getSpotSelection());
final Map<String, Object> settings = new HashMap<String, Object>(1);
settings.put(KEY_LINKING_MAX_DISTANCE, Double.POSITIVE_INFINITY);
final NearestNeighborTracker<Spot> tracker = new NearestNeighborTracker<Spot>(spots, settings);
tracker.setNumThreads(1);
/*
* Execute tracking
*/
if (!tracker.checkInput() || !tracker.process()) {
System.err.println("Problem while computing spot links: " + tracker.getErrorMessage());
return;
}
final SimpleWeightedGraph<Spot, DefaultWeightedEdge> graph = tracker.getResult();
/*
* Copy found links in source model
*/
model.beginUpdate();
try {
for (final DefaultWeightedEdge edge : graph.edgeSet()) {
final Spot source = graph.getEdgeSource(edge);
final Spot target = graph.getEdgeTarget(edge);
model.addEdge(source, target, graph.getEdgeWeight(edge));
}
} finally {
model.endUpdate();
}
}
/**
* Check the validity of the given settings map for the target {@link SpotDetector} set in this
* provider. The validity check is strict: we check that all needed parameters are here and are of
* the right class, and that there is no extra unwanted parameters.
*
* @return true if the settings map can be used with the target factory. If not, check {@link
* #getErrorMessage()}
*/
public boolean checkSettingsValidity(final Map<String, Object> settings) {
if (null == settings) {
errorMessage = "Settings map is null.\n";
return false;
}
final StringBuilder str = new StringBuilder();
boolean ok = true;
if (currentKey.equals(FastLAPTracker.TRACKER_KEY)
|| currentKey.equals(SimpleFastLAPTracker.TRACKER_KEY)) {
ok = LAPUtils.checkSettingsValidity(settings, str);
if (!ok) {
errorMessage = str.toString();
}
return ok;
} else if (currentKey.equals(NearestNeighborTracker.TRACKER_KEY)) {
ok = NearestNeighborTracker.checkInput(settings, str);
if (!ok) {
errorMessage = str.toString();
}
return ok;
} else if (currentKey.equals(ManualTracker.TRACKER_KEY)) {
return true;
} else {
errorMessage = "Unknow detector factory key: " + currentKey + ".\n";
return false;
}
}