public static void main(String[] args) { // Load File file = new File(AppUtils.getBaseDirectory(TrackMate.class), "samples/FakeTracks.xml"); TmXmlReader reader = new TmXmlReader(file); // Analyze TrackBranchingAnalyzer analyzer = new TrackBranchingAnalyzer(reader.getModel()); analyzer.process(reader.getModel().getTrackModel().trackIDs(false)); System.out.println("Analysis done in " + analyzer.getProcessingTime() + " ms."); }
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); }