def create_trackmate(imp, results_table): """ Creates a TrackMate instance configured to operated on the specified ImagePlus imp with cell analysis stored in the specified ResultsTable results_table. """ cal = imp.getCalibration() # TrackMate. # Model. model = Model() model.setLogger(Logger.IJ_LOGGER) model.setPhysicalUnits(cal.getUnit(), cal.getTimeUnit()) # Settings. settings = Settings() settings.setFrom(imp) # Create the TrackMate instance. trackmate = TrackMate(model, settings) # Add ALL the feature analyzers known to TrackMate, via # providers. # They offer automatic analyzer detection, so all the # available feature analyzers will be added. # Some won't make sense on the binary image (e.g. contrast) # but nevermind. spotAnalyzerProvider = SpotAnalyzerProvider() for key in spotAnalyzerProvider.getKeys(): print(key) settings.addSpotAnalyzerFactory(spotAnalyzerProvider.getFactory(key)) edgeAnalyzerProvider = EdgeAnalyzerProvider() for key in edgeAnalyzerProvider.getKeys(): print(key) settings.addEdgeAnalyzer(edgeAnalyzerProvider.getFactory(key)) trackAnalyzerProvider = TrackAnalyzerProvider() for key in trackAnalyzerProvider.getKeys(): print(key) settings.addTrackAnalyzer(trackAnalyzerProvider.getFactory(key)) trackmate.getModel().getLogger().log( settings.toStringFeatureAnalyzersInfo()) trackmate.computeSpotFeatures(True) trackmate.computeEdgeFeatures(True) trackmate.computeTrackFeatures(True) # Skip detection and get spots from results table. spots = spots_from_results_table(results_table, cal.frameInterval) model.setSpots(spots, False) # Configure detector. We put nothing here, since we already have the spots # from previous step. settings.detectorFactory = ManualDetectorFactory() settings.detectorSettings = {} settings.detectorSettings['RADIUS'] = 1. # Configure tracker settings.trackerFactory = SparseLAPTrackerFactory() settings.trackerSettings = LAPUtils.getDefaultLAPSettingsMap() settings.trackerSettings['LINKING_MAX_DISTANCE'] = 20.0 settings.trackerSettings['GAP_CLOSING_MAX_DISTANCE'] = 20.0 settings.trackerSettings['MAX_FRAME_GAP'] = 3 settings.initialSpotFilterValue = -1. return trackmate
def create_trackmate( imp, results_table ): """ Creates a TrackMate instance configured to operated on the specified ImagePlus imp with cell analysis stored in the specified ResultsTable results_table. """ cal = imp.getCalibration() # TrackMate. # Model. model = Model() model.setLogger( Logger.IJ_LOGGER ) model.setPhysicalUnits( cal.getUnit(), cal.getTimeUnit() ) # Settings. settings = Settings() settings.setFrom( imp ) # Create the TrackMate instance. trackmate = TrackMate( model, settings ) # Add ALL the feature analyzers known to TrackMate, via # providers. # They offer automatic analyzer detection, so all the # available feature analyzers will be added. # Some won't make sense on the binary image (e.g. contrast) # but nevermind. spotAnalyzerProvider = SpotAnalyzerProvider() for key in spotAnalyzerProvider.getKeys(): print( key ) settings.addSpotAnalyzerFactory( spotAnalyzerProvider.getFactory( key ) ) edgeAnalyzerProvider = EdgeAnalyzerProvider() for key in edgeAnalyzerProvider.getKeys(): print( key ) settings.addEdgeAnalyzer( edgeAnalyzerProvider.getFactory( key ) ) trackAnalyzerProvider = TrackAnalyzerProvider() for key in trackAnalyzerProvider.getKeys(): print( key ) settings.addTrackAnalyzer( trackAnalyzerProvider.getFactory( key ) ) trackmate.getModel().getLogger().log( settings.toStringFeatureAnalyzersInfo() ) trackmate.computeSpotFeatures( True ) trackmate.computeEdgeFeatures( True ) trackmate.computeTrackFeatures( True ) # Skip detection and get spots from results table. spots = spots_from_results_table( results_table, cal.frameInterval ) model.setSpots( spots, False ) # Configure detector. We put nothing here, since we already have the spots # from previous step. settings.detectorFactory = ManualDetectorFactory() settings.detectorSettings = {} settings.detectorSettings[ 'RADIUS' ] = 1. # Configure tracker settings.trackerFactory = SparseLAPTrackerFactory() settings.trackerSettings = LAPUtils.getDefaultLAPSettingsMap() settings.trackerSettings[ 'LINKING_MAX_DISTANCE' ] = 10.0 settings.trackerSettings[ 'GAP_CLOSING_MAX_DISTANCE' ] = 15.0 settings.trackerSettings[ 'MAX_FRAME_GAP' ] = 3 settings.trackerSettings[ 'ALLOW_TRACK_SPLITTING' ] = True settings.trackerSettings[ 'SPLITTING_MAX_DISTANCE' ] = 7.0 settings.trackerSettings settings.initialSpotFilterValue = -1. ### print(model.getFeatureModel().getTrackFeatureNames()) # TRACK_START: Track start, # TRACK_INDEX: Track index, # NUMBER_MERGES: Number of merge events, # TRACK_STD_SPEED: Velocity standard deviation, # TRACK_ID: Track ID, # TRACK_MEDIAN_QUALITY: Median quality, # TRACK_STD_QUALITY: Quality standard deviation, # TRACK_X_LOCATION: X Location (mean), # TRACK_MEDIAN_SPEED: Median velocity, # NUMBER_SPOTS: Number of spots in track, # TRACK_MIN_SPEED: Minimal velocity, # NUMBER_GAPS: Number of gaps, # TRACK_Z_LOCATION: Z Location (mean), # TRACK_STOP: Track stop, # TRACK_MEAN_SPEED: Mean velocity, # NUMBER_SPLITS: Number of split events, # TRACK_MAX_SPEED: Maximal velocity, # TRACK_Y_LOCATION: Y Location (mean), # TRACK_DISPLACEMENT: Track displacement, # NUMBER_COMPLEX: Complex points, # TRACK_MEAN_QUALITY: Mean quality, # TRACK_DURATION: Duration of track, # TRACK_MAX_QUALITY: Maximal quality, # LONGEST_GAP: Longest gap, # TRACK_MIN_QUALITY: Minimal quality settings.addTrackFilter(FeatureFilter('NUMBER_SPLITS', 0.9, True)) return trackmate
csvReader = BufferedReader(FileReader(input_path)) header = csvReader.readLine().split(",") row = csvReader.readLine() spots = SpotCollection() while row is not None: data = {col: val for col, val in zip(header, row.split(","))} spot = Spot(float(data['j']), float(data['i']), 0, math.sqrt(float(data['area']) / math.pi), 1, data['cell']) spots.add(spot, int(data['frame'])) row = csvReader.readLine() csvReader.close() model.setSpots(spots, False) # Set up dummy detector settings.detectorFactory = ManualDetectorFactory() settings.detectorSettings = {} settings.detectorSettings['RADIUS'] = 1. # Configure tracker - We want to allow merges and fusions settings.trackerFactory = SparseLAPTrackerFactory() settings.trackerSettings = LAPUtils.getDefaultLAPSettingsMap() # format for json conversion tracker_settings = tracker_settings.replace('{', '{"').replace(':', '":').replace( ', ', ', "') tracker_settings = json.loads(tracker_settings)