def trackmate(self): calibration = self.imp.getCalibration() model = Model() model.setLogger(Logger.IJ_LOGGER) settings = Settings() settings.setFrom(self.imp) # Configure detector - We use the Strings for the keys settings.detectorFactory = LogDetectorFactory() settings.detectorSettings = { 'DO_SUBPIXEL_LOCALIZATION': True, 'RADIUS': calibration.getX(self.trackmateSize), 'TARGET_CHANNEL': 1, 'THRESHOLD': self.trackmateThreashold, 'DO_MEDIAN_FILTERING': True, } # Configure spot filters - Classical filter on quality filter1 = FeatureFilter('QUALITY', 0.01, True) settings.addSpotFilter(filter1) settings.addSpotAnalyzerFactory(SpotIntensityMultiCAnalyzerFactory()) settings.initialSpotFilterValue = 1 # Configure tracker - We want to allow merges and fusions settings.trackerFactory = SparseLAPTrackerFactory() settings.trackerSettings = LAPUtils.getDefaultLAPSettingsMap() trackmate = TrackMate(model, settings) #-------- # Process #-------- ok = trackmate.checkInput() if not ok: print("NOT OK") ok = trackmate.process() if not ok: print("NOT OK") #---------------- # Display results #---------------- #selectionModel = SelectionModel(model) #displayer = HyperStackDisplayer(model, selectionModel, self.imp) #displayer.render() #displayer.refresh() # Echo results with the logger we set at start: spots = model.getSpots() return spots.iterable(True)
def detection(imp, c): cal = imp.getCalibration() model = Model() settings = Settings() settings.setFrom(imp) # Configure detector - Manually determined as best settings.detectorFactory = LogDetectorFactory() settings.detectorSettings = { 'DO_SUBPIXEL_LOCALIZATION': True, 'RADIUS': 2.0, 'TARGET_CHANNEL': c, 'THRESHOLD': 20.0, 'DO_MEDIAN_FILTERING': False, } settings.addSpotAnalyzerFactory(SpotIntensityAnalyzerFactory()) settings.addSpotAnalyzerFactory(SpotContrastAndSNRAnalyzerFactory()) settings.trackerFactory = SparseLAPTrackerFactory() settings.trackerSettings = LAPUtils.getDefaultLAPSettingsMap() trackmate = TrackMate(model, settings) ok = trackmate.checkInput() if not ok: sys.exit(str(trackmate.getErrorMessage())) try: ok = trackmate.process() except: IJ.log("Nothing detected") IJ.selectWindow('test') IJ.run('Close') else: selectionModel = SelectionModel(model) displayer = HyperStackDisplayer(model, selectionModel, imp) displayer.render() displayer.refresh() # Get spots information spots = model.getSpots() spotIt = spots.iterator(0, False) # Loop through spots and save into files # Fetch spot features directly from spot sid = [] x = [] y = [] q = [] r = [] spotID = 0 for spot in spotIt: spotID = spotID + 1 sid.append(spotID) x.append(spot.getFeature('POSITION_X')) y.append(spot.getFeature('POSITION_Y')) q.append(spot.getFeature('QUALITY')) r.append(spot.getFeature('RADIUS')) data = zip(sid, x, y, q, r) return data
def runTrackMate(imp, targetChannel, dt, radius, threshold, frameGap, linkingMax, closingMax): # Get the number of channels nChannels = imp.getNChannels() IJ.log("->Detection threshold used: " + str(threshold)) IJ.log("->Number of frames is: " + str(imp.getStackSize())) IJ.log("->Target channel is: " + str(targetChannel)) IJ.log('->Number of channels to measure %d' % nChannels) # Setup settings for TrackMate settings = Settings() settings.setFrom(imp) settings.dt = dt # Spot analyzer: we want the multi-C intensity analyzer. settings.addSpotAnalyzerFactory(SpotMultiChannelIntensityAnalyzerFactory()) # Spot detector. settings.detectorFactory = LogDetectorFactory() settings.detectorSettings = settings.detectorFactory.getDefaultSettings() settings.detectorSettings['RADIUS'] = radius settings.detectorSettings['THRESHOLD'] = threshold settings.detectorSettings['TARGET_CHANNEL'] = targetChannel # Spot tracker. #settings.trackerFactory = SparseLAPTrackerFactory() settings.trackerFactory = LAPTrackerFactory() settings.trackerSettings = LAPUtils.getDefaultLAPSettingsMap() settings.trackerSettings['MAX_FRAME_GAP'] = frameGap settings.trackerSettings['LINKING_MAX_DISTANCE'] = linkingMax settings.trackerSettings['GAP_CLOSING_MAX_DISTANCE'] = closingMax settings.trackerSettings['ALLOW_TRACK_MERGING'] = False settings.trackerSettings['ALLOW_GAP_CLOSING'] = False settings.trackerSettings['ALLOW_TRACK_SPLITTING'] = False settings.trackerSettings['ALLOW_TRACK_MERGING'] = False settings.trackerSettings['ALTERNATIVE_LINKING_COST_FACTOR'] = 0.5 settings.trackerSettings['BLOCKING_VALUE'] = 1.0 settings.trackerSettings['CUTOFF_PERCENTILE'] = 1.0 #settings.trackerSettings['SPLITTING_MAX_DISTANCE'] = 16.0 # Run TrackMate and store data into Model. model = Model() trackmate = TrackMate(model, settings) if not trackmate.checkInput() or not trackmate.process(): IJ.log('Could not execute TrackMate: ' + str(trackmate.getErrorMessage())) else: return model, nChannels
str_name_fil = root + '/' + files [z] print(str_name_fil) imp = IJ.openImage(str_name_fil) #imp.show() dims = imp.getDimensions() imp.setDimensions( dims[ 2 ], dims[ 4 ], dims[ 3 ] ) #---------------------------- # Create the model object now #---------------------------- # Some of the parameters we configure below need to have # a reference to the model at creation. So we create an # empty model now. model = Model() # Send all messages to ImageJ log window. model.setLogger(Logger.IJ_LOGGER) #------------------------ # Prepare settings object #------------------------ settings = Settings() settings.setFrom(imp) # Configure detector - We use the Strings for the keys settings.detectorFactory = LogDetectorFactory()
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
else: print 'track', 'load' imp = ij.IJ.openImage(path + gg.replace('original', 'filter')) # open Golgi image imp.show() lx, ly, lc, lz, lt = imp.getDimensions() # get image dimensions lz, lt = min(lz, lt), max(lz, lt) ij.IJ.run( 'Properties...', 'channels=1 slices=' + str(lz) + ' frames=' + str(lt) + ' unit=pixel pixel_width=1.0000 pixel_height=1.0000 voxel_depth=' + str(depth) ) # set number of z-slices and frames and spacing between z-slices print 'track', 'setup' model = Model() # set tracking model factories settings = Settings() settings.setFrom(imp) settings.detectorFactory = DogDetectorFactory() settings.detectorSettings[ 'DO_SUBPIXEL_LOCALIZATION'] = True # do subpixel localization settings.detectorSettings['RADIUS'] = radius # set blob radius settings.detectorSettings['TARGET_CHANNEL'] = 1 # set target channel settings.detectorSettings[ 'THRESHOLD'] = 1.0 # set detection threshold to one to exclude region outside mask settings.detectorSettings[ 'DO_MEDIAN_FILTERING'] = True # do median filtering settings.addSpotAnalyzerFactory(SpotIntensityAnalyzerFactory()) settings.addSpotAnalyzerFactory(SpotRadiusEstimatorFactory()) settings.addSpotAnalyzerFactory(SpotContrastAndSNRAnalyzerFactory()) settings.initialSpotFilterValue = quality
#5. Configure LAP Tracker #6. Run trackmate #7. Get spot or track features #8. Save log as a parsable data set #1. #Opening data and determing auto quality number the_input = getArgument() the_list = the_input.rpartition(" ") image = the_list[0] imp = IJ.openImage(image) imp.show() subtraction = float(the_list[2]) model = Model() settings = Settings() settings.setFrom(imp) settings.detectorFactory = DogDetectorFactory() settings.detectorSettings = { 'DO_SUBPIXEL_LOCALIZATION': True, 'RADIUS': 0.350, 'TARGET_CHANNEL': 1, 'THRESHOLD': 0.0, 'DO_MEDIAN_FILTERING': True, } settings.addSpotAnalyzerFactory(SpotIntensityAnalyzerFactory()) settings.trackerSettings['LINKING_MAX_DISTANCE'] = 1.000 settings.trackerSettings['GAP_CLOSING_MAX_DISTANCE'] = 1.000 settings.trackerSettings['MAX_FRAME_GAP'] = 3
import fiji.plugin.trackmate.features.spot.SpotIntensityAnalyzerFactory as SpotIntensityAnalyzerFactory import fiji.plugin.trackmate.features.track.TrackSpeedStatisticsAnalyzer as TrackSpeedStatisticsAnalyzer import fiji.plugin.trackmate.util.TMUtils as TMUtils # Get currently selected image #imp = WindowManager.getCurrentImage() imp = IJ.openImage('http://fiji.sc/samples/FakeTracks.tif') #imp.show() #------------------------- # Instantiate model object #------------------------- model = Model() # Set logger model.setLogger(Logger.IJ_LOGGER) #------------------------ # Prepare settings object #------------------------ settings = Settings() settings.setFrom(imp) # Configure detector settings.detectorFactory = DogDetectorFactory() settings.detectorSettings = { DetectorKeys.KEY_DO_SUBPIXEL_LOCALIZATION : True,
import fiji.plugin.trackmate.features.spot.SpotIntensityAnalyzerFactory as SpotIntensityAnalyzerFactory import fiji.plugin.trackmate.features.track.TrackSpeedStatisticsAnalyzer as TrackSpeedStatisticsAnalyzer import fiji.plugin.trackmate.features.track.TrackDurationAnalyzer as TrackDurationAnalyzer import fiji.plugin.trackmate.util.TMUtils as TMUtils # Get currently selected image #imp = WindowManager.getCurrentImage() imp = IJ.openImage('{target_file}') #imp = IJ.openImage('/home/ubuntu/data/RED_nPEG_37C_pH72_S1_1_1_2.tif') #imp.show() #------------------------- # Instantiate model object #------------------------- model = Model() # Set logger model.setLogger(Logger.IJ_LOGGER) #------------------------ # Prepare settings object #------------------------ settings = Settings() settings.setFrom(imp) # Configure detector settings.detectorFactory = DogDetectorFactory() settings.detectorSettings = {{ DetectorKeys.KEY_DO_SUBPIXEL_LOCALIZATION: True,
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
def run_trackmate(imp, path, filename, params, batch_mode=False): # initialize trackmate model model = Model() # Set logger - use to see outputs, not needed in batch mode model.setLogger(Logger.IJ_LOGGER) # Create setting object from image settings = Settings() settings.setFrom(imp) cal = imp.getCalibration() model.setPhysicalUnits("micron", "sec") # Configure detector settings.detectorFactory = LogDetectorFactory() # settings.detectorFactory = DogDetectorFactory() settings.detectorSettings = { 'DO_SUBPIXEL_LOCALIZATION': params.do_subpixel_localization, 'RADIUS': params.radius, 'TARGET_CHANNEL': 0, 'THRESHOLD': params.threshold, 'DO_MEDIAN_FILTERING': params.do_median_filtering, } # print(params) # Add spot filters filter_quality = FeatureFilter('QUALITY', params.quality, True) settings.addSpotFilter(filter_quality) filter_snr = FeatureFilter('SNR', params.snr, True) settings.addSpotFilter(filter_snr) # Compute spot features settings.addSpotAnalyzerFactory(SpotIntensityAnalyzerFactory()) settings.addSpotAnalyzerFactory(SpotContrastAndSNRAnalyzerFactory()) # Compute track features settings.addTrackAnalyzer(TrackBranchingAnalyzer()) settings.addTrackAnalyzer(TrackDurationAnalyzer()) settings.addTrackAnalyzer(TrackIndexAnalyzer()) settings.addTrackAnalyzer(TrackLocationAnalyzer()) settings.addTrackAnalyzer(TrackSpeedStatisticsAnalyzer()) settings.addTrackAnalyzer(TrackSpotQualityFeatureAnalyzer()) # Update model ModelFeatureUpdater(model, settings) # Configure tracker settings.trackerFactory = SparseLAPTrackerFactory() settings.trackerSettings = LAPUtils.getDefaultLAPSettingsMap() settings.trackerSettings[ 'LINKING_MAX_DISTANCE'] = params.linking_max_distance settings.trackerSettings[ 'GAP_CLOSING_MAX_DISTANCE'] = params.gap_closing_max_distance settings.trackerSettings['MAX_FRAME_GAP'] = params.max_frame_gap # Add track filters filter_T1 = FeatureFilter('TRACK_DURATION', params.track_duration, True) filter_MTD = FeatureFilter('TRACK_DISPLACEMENT', params.track_displacement, True) settings.addTrackFilter(filter_T1) settings.addTrackFilter(filter_MTD) # Instantiate trackmate trackmate = TrackMate(model, settings) # Execute all ok = trackmate.checkInput() if not ok: IJ.showMessage("No spots found... Adjust detection parameter.\n" + str(trackmate.getErrorMessage())) sys.exit(str(trackmate.getErrorMessage())) ok = trackmate.process() if not ok: IJ.showMessage("No spots found... Adjust detection parameter.\n" + str(trackmate.getErrorMessage())) sys.exit(str(trackmate.getErrorMessage())) filename = os.path.splitext(filename)[0] #filename without extension outFile = File(os.path.join(path, filename + "_Tracks.xml")) ExportTracksToXML.export(model, settings, outFile) #imp.close() tm_writer = TmXmlWriter(File(os.path.join(path, filename + "_TM.xml"))) tm_writer.appendModel(model) tm_writer.appendSettings(settings) tm_writer.writeToFile() if not batch_mode: selectionModel = SelectionModel(model) displayer = HyperStackDisplayer(model, selectionModel, imp) displayer.render() displayer.refresh() # Echo results with the logger we set at start: model.getLogger().log(str(model))
" autoscale color_mode=Default rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT" )) imp = WindowManager.getCurrentImage() IJ.run(imp, "Subtract Background...", "rolling=50 sliding disable stack") dx = imp.getCalibration().pixelWidth dy = imp.getCalibration().pixelHeight #---------------------------- # Create the model object now #---------------------------- # Some of the parameters we configure below need to have # a reference to the model at creation. So we create an # empty model now. model = Model() # Send all messages to ImageJ log window. model.setLogger(Logger.IJ_LOGGER) #------------------------ # Prepare settings object #------------------------ settings = Settings() model.getLogger().log('') model.getLogger().log('Filename' + file1 + "TEST:" + str(file1.endswith("*R3D_PRJ.dv"))) settings.setFrom(imp) # Configure detector - We use the Strings for the keys
for movie in list_of_movies: id = path_to_movies + movie options = ImporterOptions() options.setId(id) options.setAutoscale(False) bf_imp = BF.openImagePlus(options) imp = bf_imp[0] #------------------------- # Instantiate model object #------------------------- model = Model() # Set logger model.setLogger(Logger.IJ_LOGGER) #------------------------ # Prepare settings object #------------------------ settings = Settings() settings.setFrom(imp) # Configure detector settings.detectorFactory = LogDetectorFactory() settings.detectorSettings = { 'DO_SUBPIXEL_LOCALIZATION' : True,
def nucleus_detection(infile, nucleus_channel, stacksize, animation): # Detect nucleus with 3d log filters fullpath = infile infile = filename(infile) IJ.log("Start Segmentation " + str(infile)) # First get Nb Stacks reader = ImageReader() omeMeta = MetadataTools.createOMEXMLMetadata() reader.setMetadataStore(omeMeta) reader.setId(fullpath) default_options = "stack_order=XYCZT color_mode=Composite view=Hyperstack specify_range c_begin=" + \ str(nucleus_channel) + " c_end=" + str(nucleus_channel) + \ " c_step=1 open=[" + fullpath + "]" NbStack = reader.getSizeZ() reader.close() output = re.sub('.ids', '.csv', infile) with open(os.path.join(folder5, output), 'wb') as outfile: DETECTwriter = csv.writer(outfile, delimiter=',') DETECTwriter.writerow( ['spotID', 'roundID', 'X', 'Y', 'Z', 'QUALITY', 'SNR', 'INTENSITY']) rounds = NbStack // stacksize spotID = 1 for roundid in xrange(1, rounds + 2): # Process stacksize by stacksize otherwise crash because too many spots Zstart = (stacksize * roundid - stacksize + 1) Zend = (stacksize * roundid) if(Zend > NbStack): Zend = NbStack % stacksize + (roundid - 1) * stacksize IJ.log("Round:" + str(roundid) + ' Zstart=' + str(Zstart) + ' Zend=' + str(Zend) + ' out of ' + str(NbStack)) IJ.run("Bio-Formats Importer", default_options + " z_begin=" + str(Zstart) + " z_end=" + str(Zend) + " z_step=1") imp = IJ.getImage() imp.show() cal = imp.getCalibration() model = Model() settings = Settings() settings.setFrom(imp) # Configure detector - Manually determined as best settings.detectorFactory = LogDetectorFactory() settings.detectorSettings = { 'DO_SUBPIXEL_LOCALIZATION': True, 'RADIUS': 5.5, 'TARGET_CHANNEL': 1, 'THRESHOLD': 50.0, 'DO_MEDIAN_FILTERING': False, } filter1 = FeatureFilter('QUALITY', 1, True) settings.addSpotFilter(filter1) settings.addSpotAnalyzerFactory(SpotIntensityAnalyzerFactory()) settings.addSpotAnalyzerFactory(SpotContrastAndSNRAnalyzerFactory()) settings.trackerFactory = SparseLAPTrackerFactory() settings.trackerSettings = LAPUtils.getDefaultLAPSettingsMap() trackmate = TrackMate(model, settings) ok = trackmate.checkInput() if not ok: sys.exit(str(trackmate.getErrorMessage())) try: ok = trackmate.process() except: IJ.log("Nothing detected, Round:" + str(roundid) + ' Zstart=' + str(Zstart) + ' Zend=' + str(Zend) + ' out of ' + str(NbStack)) IJ.selectWindow(infile) IJ.run('Close') continue else: if animation: # For plotting purpose only imp.setPosition(1, 1, imp.getNFrames()) imp.getProcessor().setMinAndMax(0, 4000) selectionModel = SelectionModel(model) displayer = HyperStackDisplayer(model, selectionModel, imp) displayer.render() displayer.refresh() for i in xrange(1, imp.getNSlices() + 1): imp.setSlice(i) time.sleep(0.05) IJ.selectWindow(infile) IJ.run('Close') spots = model.getSpots() spotIt = spots.iterator(0, False) sid = [] sroundid = [] x = [] y = [] z = [] q = [] snr = [] intensity = [] for spot in spotIt: sid.append(spotID) spotID = spotID + 1 sroundid.append(roundid) x.append(spot.getFeature('POSITION_X')) y.append(spot.getFeature('POSITION_Y')) q.append(spot.getFeature('QUALITY')) snr.append(spot.getFeature('SNR')) intensity.append(spot.getFeature('MEAN_INTENSITY')) # Correct Z position correct_z = spot.getFeature( 'POSITION_Z') + (roundid - 1) * float(stacksize) * cal.pixelDepth z.append(correct_z) with open(os.path.join(folder5, output), 'ab') as outfile: DETECTwriter = csv.writer(outfile, delimiter=',') Sdata = zip(sid, sroundid, x, y, z, q, snr, intensity) for Srow in Sdata: DETECTwriter.writerow(Srow)
files.append(file) for file in files: # Get currently selected image imp = IJ.openImage(dir_input + file) imp.show() #---------------------------- # Create the model object now #---------------------------- # Some of the parameters we configure below need to have # a reference to the model at creation. So we create an # empty model now. model = Model() # Send all messages to ImageJ log window. model.setLogger(Logger.IJ_LOGGER) #------------------------ # Prepare settings object #------------------------ settings = Settings() settings.setFrom(imp) # Configure detector - We use the Strings for the keys settings.detectorFactory = LogDetectorFactory() settings.detectorSettings = { 'DO_SUBPIXEL_LOCALIZATION': True,
import fiji.plugin.trackmate.features.ModelFeatureUpdater as ModelFeatureUpdater import fiji.plugin.trackmate.util.TMUtils as TMUtils batchmode = True # Get currently selected image imp = WindowManager.getCurrentImage() #imp = IJ.openImage('http://fiji.sc/samples/FakeTracks.tif') #imp.show() #------------------------- # Instantiate model object #------------------------- model = Model() model.setPhysicalUnits(imp.getCalibration().getUnits(), imp.getCalibration().getTimeUnit()) # Set logger model.setLogger(Logger.IJ_LOGGER) #------------------------ # Prepare settings object #------------------------ settings = Settings() settings.setFrom(imp) settings.tstart = 2 settings.tend = settings.tend - 5
def track_cells(folder_w, filename, imp, correction): #imp = IJ.openImage(os.path.join(folder,filename)) #imp.show() #get image dimensions, set ROI remove part of flouresncent ring x_size = ImagePlus.getDimensions(imp)[0] y_size = ImagePlus.getDimensions(imp)[1] x_start = 0 y_start = 0 #calculate alternative ROI if crop_ring: x_start = 170 / 2 y_start = 170 / 2 x_size = x_size - 170 y_size = y_size - 170 print( str(x_start) + ", " + str(y_start) + ", " + str(x_size) + ", " + str(y_size)) imp.setRoi(OvalRoi(x_start, y_start, x_size, y_size)) #imp_dup = imp.duplicate() #imp_dup.show() #red_corrected_img.show() IJ.run(imp, "Make Inverse", "") IJ.setForegroundColor(0, 0, 0) IJ.run(imp, "Fill", "stack") imp.killRoi() #imp.show() #sys.exit() #img_filename = filename+"_corrected_red_stack.tif" #folder_filename= os.path.join(well_folder,img_filename) #IJ.save(imp, folder_filename) #---------------------------- # Create the model object now #---------------------------- # Some of the parameters we configure below need to have # a reference to the model at creation. So we create an # empty model now. model = Model() # Send all messages to ImageJ log window. model.setLogger(Logger.IJ_LOGGER) #------------------------ # Prepare settings object #------------------------ settings = Settings() settings.setFrom(imp) # Configure detector - We use the Strings for the keys settings.detectorFactory = LogDetectorFactory() settings.detectorSettings = { 'DO_SUBPIXEL_LOCALIZATION': SUBPIXEL_LOCALIZATION, 'RADIUS': RADIUS, 'TARGET_CHANNEL': TARGET_CHANNEL, 'THRESHOLD': THRESHOLD, 'DO_MEDIAN_FILTERING': MEDIAN_FILTERING, } # Configure spot filters - Classical filter on quality settings.initialSpotFilterValue = SPOT_FILTER settings.addSpotAnalyzerFactory(SpotIntensityAnalyzerFactory()) settings.addSpotAnalyzerFactory(SpotContrastAndSNRAnalyzerFactory()) settings.addSpotAnalyzerFactory(SpotMorphologyAnalyzerFactory()) settings.addSpotAnalyzerFactory(SpotRadiusEstimatorFactory()) filter1 = FeatureFilter('QUALITY', QUALITY, True) filter2 = FeatureFilter('CONTRAST', CONTRAST, True) filter2a = FeatureFilter('ESTIMATED_DIAMETER', MAX_ESTIMATED_DIAMETER, False) filter2b = FeatureFilter('MEDIAN_INTENSITY', MAX_MEDIAN_INTENSITY, False) settings.addSpotFilter(filter1) settings.addSpotFilter(filter2) settings.addSpotFilter(filter2a) settings.addSpotFilter(filter2b) print(settings.spotFilters) # Configure tracker - We want to allow merges and fusions settings.trackerFactory = SparseLAPTrackerFactory() settings.trackerSettings = LAPUtils.getDefaultLAPSettingsMap( ) # almost good enough ##adapted from https://forum.image.sc/t/trackmate-scripting-automatically-exporting-spots-in-tracks-links-in-tracks-tracks-statistics-and-branching-analysis-to-csv/6256 #linking settings settings.trackerSettings['LINKING_MAX_DISTANCE'] = LINKING_MAX_DISTANCE if LINKING_FEATURE_PENALTIES == True: settings.trackerSettings['LINKING_FEATURE_PENALTIES'] = { LINKING_FEATURE_PENALTIES_TYPE: LINKING_FEATURE_PENALTIES_VALUE } else: settings.trackerSettings['LINKING_FEATURE_PENALTIES'] = {} #gap closing settings settings.trackerSettings['ALLOW_GAP_CLOSING'] = ALLOW_GAP_CLOSING if ALLOW_GAP_CLOSING == True: settings.trackerSettings[ 'GAP_CLOSING_MAX_DISTANCE'] = GAP_CLOSING_MAX_DISTANCE settings.trackerSettings['MAX_FRAME_GAP'] = MAX_FRAME_GAP if GAP_CLOSING_FEATURE_PENALTIES == True: settings.trackerSettings['GAP_CLOSING_FEATURE_PENALTIES'] = { GAP_CLOSING_FEATURE_PENALTIES_TYPE: GAP_CLOSING_FEATURE_PENALTIES_VALUE } else: settings.trackerSettings['GAP_CLOSING_FEATURE_PENALTIES'] = {} #splitting settings settings.trackerSettings['ALLOW_TRACK_SPLITTING'] = ALLOW_TRACK_SPLITTING if ALLOW_TRACK_SPLITTING == True: settings.trackerSettings[ 'SPLITTING_MAX_DISTANCE'] = SPLITTING_MAX_DISTANCE if SPLITTING_FEATURE_PENALTIES == True: settings.trackerSettings['SPLITTING_FEATURE_PENALTIES'] = { SPLITTING_FEATURE_PENALTIES_TYPE: SPLITTING_FEATURE_PENALTIES_VALUE } else: settings.trackerSettings['SPLITTING_FEATURE_PENALTIES'] = {} #merging settings settings.trackerSettings['ALLOW_TRACK_MERGING'] = ALLOW_TRACK_MERGING if ALLOW_TRACK_MERGING == True: settings.trackerSettings['MERGING_MAX_DISTANCE'] = MERGING_MAX_DISTANCE if MERGING_FEATURE_PENALTIES == True: settings.trackerSettings['MERGING_FEATURE_PENALTIES'] = { MERGING_FEATURE_PENALTIES_TYPE: MERGING_FEATURE_PENALTIES_VALUE } else: settings.trackerSettings['MERGING_FEATURE_PENALTIES'] = {} print(settings.trackerSettings) # Configure track analyzers - Later on we want to filter out tracks # based on their displacement, so we need to state that we want # track displacement to be calculated. By default, out of the GUI, # not features are calculated. # The displacement feature is provided by the TrackDurationAnalyzer. settings.addTrackAnalyzer(TrackDurationAnalyzer()) settings.addTrackAnalyzer(TrackSpotQualityFeatureAnalyzer()) # Configure track filters - We want to get rid of the two immobile spots at # the bottom right of the image. Track displacement must be above 10 pixels. filter3 = FeatureFilter('TRACK_DISPLACEMENT', TRACK_DISPLACEMENT, True) filter4 = FeatureFilter('TRACK_START', TRACK_START, False) #filter5 = FeatureFilter('TRACK_STOP', float(imp.getStack().getSize())-1.1, True) settings.addTrackFilter(filter3) settings.addTrackFilter(filter4) #settings.addTrackFilter(filter5) #------------------- # Instantiate plugin #------------------- trackmate = TrackMate(model, settings) #-------- # Process #-------- ok = trackmate.checkInput() if not ok: sys.exit(str(trackmate.getErrorMessage())) ok = trackmate.process() # if not ok: #sys.exit(str(trackmate.getErrorMessage())) #---------------- # Display results #---------------- #Set output folder and filename and create output folder well_folder = os.path.join(folder_w, filename) output_folder = os.path.join(well_folder, "Tracking") create_folder(output_folder) xml_file_name = filename + "_" + correction + "_trackmate_analysis.xml" folder_filename_xml = os.path.join(output_folder, xml_file_name) #ExportTracksToXML.export(model, settings, File(folder_filename_xml)) outfile = TmXmlWriter(File(folder_filename_xml)) outfile.appendSettings(settings) outfile.appendModel(model) outfile.writeToFile() # Echo results with the logger we set at start: #model.getLogger().log(str(model)) #create araray of timepoint length with filled 0 cell_counts = zerolistmaker(imp.getStack().getSize()) if ok: for id in model.getTrackModel().trackIDs(True): # Fetch the track feature from the feature model. track = model.getTrackModel().trackSpots(id) for spot in track: # Fetch spot features directly from spot. t = spot.getFeature('FRAME') print(t) cell_counts[int(t)] = cell_counts[int(t)] + 1 else: print("No spots detected!") if HEADLESS == False: selectionModel = SelectionModel(model) displayer = HyperStackDisplayer(model, selectionModel, imp) displayer.render() displayer.refresh() del imp return (cell_counts + [len(model.getTrackModel().trackIDs(True))])
def run_process(input_path, output_path): IJ.run("Image Sequence...", "open=[" + input_path + "] convert sort") imp = WindowManager.getCurrentImage() dims = imp.getDimensions() imp.setDimensions(dims[2], dims[4], dims[3]) dims = imp.getDimensions() ImageConverter(imp).convertToGray8() model = Model() model.setLogger(Logger.IJ_LOGGER) settings = Settings() settings.setFrom(imp) settings.detectorFactory = LogDetectorFactory() settings.detectorSettings = { 'DO_SUBPIXEL_LOCALIZATION': True, 'RADIUS': float(11.0), 'THRESHOLD': float(0.0), 'DO_MEDIAN_FILTERING': True } # Configure spot filters - Classical filter on quality # filter1 = FeatureFilter('QUALITY', 30, True) # settings.addSpotFilter(filter1) settings.trackerFactory = SparseLAPTrackerFactory() settings.trackerSettings = LAPUtils.getDefaultLAPSettingsMap( ) #this sets tens of madatory settings settings.trackerSettings['LINKING_MAX_DISTANCE'] = 15.0 settings.trackerSettings['GAP_CLOSING_MAX_DISTANCE'] = 15.0 settings.trackerSettings['MAX_FRAME_GAP'] = 2 # print(LAPUtils.getDefaultLAPSettingsMap()) # # settings.trackerFactory = SimpleLAPTrackerFactory() ## settings.trackerSettings = LAPUtils.SimpleLAPTrackerFactory() #this sets tens of madatory settings # settings.trackerSettings['LINKING_MAX_DISTANCE'] = 15.0 # settings.trackerSettings['GAP_CLOSING_MAX_DISTANCE']=15.0 # settings.trackerSettings['MAX_FRAME_GAP']= 2 # settings.trackerSettings['ALLOW_GAP_CLOSING']= True # settings.trackerSettings['ALLOW_TRACK_SPLITTING']= False # settings.trackerSettings['ALLOW_TRACK_MERGING']= False # settings.trackerSettings['SPLITTING_MAX_DISTANCE']= 1000.0 # settings.trackerSettings['MERGING_MAX_DISTANCE']= 1000.0 # settings.trackerSettings['ALTERNATIVE_LINKING_COST_FACTOR']= 1000.0 # # ? # settings.trackerSettings['CUTOFF_PERCENTILE']= 1000.0 # settings.trackerSettings['BLOCKING_VALUE']= 1000.0 # # filter2 = FeatureFilter('NUMBER_OF_SPOTS_IN_TRACK', 6.86, True) # settings.addTrackFilter(filter2) trackmate = TrackMate(model, settings) ok = trackmate.checkInput() if not ok: sys.exit(str(trackmate.getErrorMessage())) raise Exception("trackmate: checkInput failed") # if ok: # print("Input ok") ok = trackmate.process() if not ok: raise Exception("trackmate: process failed") # if ok: # print("Process ok") #---------------- # Display results #---------------- model.getLogger().log('Found ' + str(model.getTrackModel().nTracks(True)) + ' tracks.') selectionModel = SelectionModel(model) displayer = HyperStackDisplayer(model, selectionModel, imp) # displayer.render() # The feature model, that stores edge and track features. fm = model.getFeatureModel() # print(fm) labels_row = [ 'id', 'spot_id', 'x', 'y', 'frame', 'quality', 'type', 'length' ] #'qualitiy','visability', 'track_length'] #rows = [] track_ids = model.getTrackModel().trackIDs(True) with open(output_path, 'w') as file: writer = csv.writer(file) writer.writerow(labels_row) for id in track_ids: # Fetch the track feature from the feature model. # model.getLogger().log('') # model.getLogger().log('Track ' + str(id) + ': mean velocity = ' + str(v) + ' ' + model.getSpaceUnits() + '/' + model.getTimeUnits()) track = model.getTrackModel().trackSpots(id) num_spots = track.size() for spot in track: # print(spot.getFeatures()) row = [] row.append(id) sid = spot.ID() row.append(sid) # Fetch spot features directly from spot. x = spot.getFeature('POSITION_X') row.append(x) y = spot.getFeature('POSITION_Y') row.append(y) t = spot.getFeature('FRAME') row.append(int(t)) # print("x: {} y: {} t: {}".format(x, y, t)) q = spot.getFeature('QUALITY') row.append(q) # snr=spot.getFeature('SNR') # row.append(snr) # mean=spot.getFeature('MEAN_INTENSITY') # row.append(mean) # visibility=spot.getFeature('VISIBILITY') # print(visibility) # break # row.append(visability) # model.getLogger().log('\tspot ID = ' + str(sid) + ': x='+str(x)+', y='+str(y)+', t='+str(t)+', q='+str(q) + ', snr='+str(snr) + ', mean = ' + str(mean)) row.append(1) row.append(num_spots) writer.writerow(row) # rows.append(row) file.close() return IJ
def analyze(tempFile): # Get currently selected image #imp = WindowManager.getCurrentImage() imp = IJ.openImage(tempFile) imp.show() dims = imp.getDimensions(); imp.setDimensions(dims[2], dims[4], dims[3]); #---------------------------- # Create the model object now #---------------------------- # Some of the parameters we configure below need to have # a reference to the model at creation. So we create an # empty model now. model = Model() # Send all messages to ImageJ log window. model.setLogger(Logger.IJ_LOGGER) #------------------------ # Prepare settings object #------------------------ settings = Settings() settings.setFrom(imp) print(settings.imageFileName) # Configure detector - We use the Strings for the keys settings.detectorFactory = LogDetectorFactory() settings.detectorSettings = { 'DO_SUBPIXEL_LOCALIZATION' : False, 'RADIUS' : 20., 'TARGET_CHANNEL' : 1, 'THRESHOLD' : 0.95, 'DO_MEDIAN_FILTERING' : True, } # Configure spot filters - Classical filter on quality #filter1 = FeatureFilter('QUALITY', 0.5, True) #settings.addSpotFilter(filter1) # Configure tracker - We want to allow merges and fusions settings.trackerFactory = SimpleSparseLAPTrackerFactory() settings.trackerSettings = LAPUtils.getDefaultLAPSettingsMap() #probably good enough #settings.trackerSettings['ALLOW_TRACK_SPLITTING'] = False #settings.trackerSettings['ALLOW_TRACK_MERGING'] = False settings.trackerSettings['LINKING_MAX_DISTANCE'] = 35.0 settings.trackerSettings['GAP_CLOSING_MAX_DISTANCE']= 60.0 settings.trackerSettings['MAX_FRAME_GAP']= 2 # Configure track analyzers - Later on we want to filter out tracks # based on their displacement, so we need to state that we want # track displacement to be calculated. By default, out of the GUI, # not features are calculated. # The displacement feature is provided by the TrackDurationAnalyzer. settings.addTrackAnalyzer(TrackDurationAnalyzer()) #------------------- # Instantiate plugin #------------------- trackmate = TrackMate(model, settings) ok = trackmate.process() if not ok: sys.exit(str(trackmate.getErrorMessage())) #---------------- # Display results #---------------- selectionModel = SelectionModel(model) displayer = HyperStackDisplayer(model, selectionModel, imp) displayer.render() displayer.refresh() # Echo results with the logger we set at start: model.getLogger().log(str(model)) print(str(settings)) filename = os.path.splitext(settings.imageFileName) pathname = settings.imageFolder + "" + filename[0] + "tracks.xml" guicontroller = TrackMateGUIController(trackmate) newFile = File(pathname) ExportTracksToXML(guicontroller).export(model, settings, newFile) actionObject = CaptureOverlayAction() actionObject.execute(trackmate) imp = WindowManager.getCurrentImage() fileSaver = FileSaver(imp) fileSaver.saveAsTiffStack(settings.imageFolder + "" + filename[0] + "overlay.tif") WindowManager.closeAllWindows() guicontroller.quit() selectionModel.clearSelection(); model.clearTracks(1)
def processImages(cfg, wellName, wellPath, images): firstImage = IJ.openImage(images[0][0][0][0]) imgWidth = firstImage.getWidth() imgHeight = firstImage.getHeight() for c in range(0, cfg.getValue(ELMConfig.numChannels)): chanName = cfg.getValue(ELMConfig.chanLabel)[c] if cfg.getValue(ELMConfig.chanLabel)[c] in cfg.getValue( ELMConfig.chansToSkip): continue imColorSeq = ImageStack(imgWidth, imgHeight) imSeq = ImageStack(imgWidth, imgHeight) totalHist = [] for z in range(0, cfg.getValue(ELMConfig.numZ)): for t in range(0, cfg.getValue(ELMConfig.numT)): currIP = IJ.openImage(images[c][z][t][0]) imColorSeq.addSlice(currIP.duplicate().getProcessor()) currIP = ELMImageUtils.getGrayScaleImage( currIP, c, chanName, cfg) imSeq.addSlice(currIP.getProcessor()) imgStats = currIP.getStatistics() currHist = imgStats.getHistogram() if not totalHist: for i in range(len(currHist)): totalHist.append(currHist[i]) else: for i in range(len(currHist)): totalHist[i] += currHist[i] if cfg.hasValue(ELMConfig.thresholdFromWholeRange) and cfg.getValue( ELMConfig.thresholdFromWholeRange) == True: threshMethod = "Otsu" # Default works very poorly for this data if cfg.hasValue(ELMConfig.thresholdMethod): threshMethod = cfg.getValue(ELMConfig.thresholdMethod) thresholder = AutoThresholder() computedThresh = thresholder.getThreshold(threshMethod, totalHist) cfg.setValue(ELMConfig.imageThreshold, computedThresh) print("\tComputed threshold from total hist (" + threshMethod + "): " + str(computedThresh)) print() else: print("\tUsing threshold computed on individual images!") print() computedThresh = 0 chanName = cfg.getValue(ELMConfig.chanLabel)[c] imp = ImagePlus() imp.setStack(imSeq) imp.setDimensions(1, 1, cfg.getValue(ELMConfig.numT)) imp.setTitle(wellName + ", channel " + str(c)) impColor = ImagePlus() impColor.setStack(imColorSeq) impColor.setDimensions(1, 1, cfg.getValue(ELMConfig.numT)) impColor.setTitle(wellName + ", channel " + str(c) + " (Color)") #---------------------------- # Create the model object now #---------------------------- # Some of the parameters we configure below need to have # a reference to the model at creation. So we create an # empty model now. model = Model() # Send all messages to ImageJ log window. model.setLogger(Logger.IJ_LOGGER) pa_features = [ "Area", "PercentArea", "Mean", "StdDev", "Mode", "Min", "Max", "X", "Y", "XM", "YM", "Perim.", "BX", "BY", "Width", "Height", "Major", "Minor", "Angle", "Circ.", "Feret", "IntDen", "Median", "Skew", "Kurt", "RawIntDen", "FeretX", "FeretY", "FeretAngle", "MinFeret", "AR", "Round", "Solidity" ] featureNames = {} featureShortNames = {} featureDimensions = {} isInt = {} for feature in pa_features: featureNames[feature] = feature featureShortNames[feature] = feature featureDimensions[feature] = Dimension.STRING isInt[feature] = False model.getFeatureModel().declareSpotFeatures(pa_features, featureNames, featureShortNames, featureDimensions, isInt) #------------------------ # Prepare settings object #------------------------ settings = Settings() settings.setFrom(imp) dbgPath = os.path.join(wellPath, 'debugImages_' + chanName) if not os.path.exists(dbgPath): os.makedirs(dbgPath) if cfg.hasValue(ELMConfig.thresholdMethod): threshMethod = cfg.getValue(ELMConfig.thresholdMethod) else: threshMethod = "Default" # Configure detector - We use the Strings for the keys settings.detectorFactory = ThresholdDetectorFactory() settings.detectorSettings = { 'THRESHOLD': computedThresh, 'ABOVE': True, 'DEBUG_MODE': True, 'DEBUG_OUTPATH': dbgPath, 'THRESHOLD_METHOD': threshMethod } #settings.detectorFactory = LocalThresholdDetectorFactory() #settings.detectorSettings = { # 'THRESHOLD' : computedThresh, # 'DEBUG_MODE' : True, # 'DEBUG_OUTPATH' : dbgPath #} # Configure spot filters - Classical filter on quality filter1 = FeatureFilter('QUALITY', 150, True) settings.addSpotFilter(filter1) # Configure tracker - We want to allow merges and fusions settings.trackerFactory = SparseLAPTrackerFactory() settings.trackerSettings = LAPUtils.getDefaultLAPSettingsMap( ) # almost good enough # Linking settings.trackerSettings[TrackerKeys.KEY_LINKING_MAX_DISTANCE] = 220.0 # in pixels linkFeaturePenalties = HashMap() linkFeaturePenalties['Area'] = 1.0 linkFeaturePenalties['POSITION_X'] = 1.0 linkFeaturePenalties['POSITION_Y'] = 1.0 #linkFeaturePenalties['Circ.'] = 1.0 #linkFeaturePenalties['Mean'] = 1.0 settings.trackerSettings[ TrackerKeys.KEY_LINKING_FEATURE_PENALTIES] = linkFeaturePenalties # Gap closing settings.trackerSettings[TrackerKeys.KEY_ALLOW_GAP_CLOSING] = True settings.trackerSettings[TrackerKeys.KEY_GAP_CLOSING_MAX_FRAME_GAP] = 8 settings.trackerSettings[ TrackerKeys.KEY_GAP_CLOSING_MAX_DISTANCE] = 120.0 # in pixels #settings.trackerSettings[TrackerKeys.KEY_GAP_CLOSING_FEATURE_PENALTIES] = new HashMap<>(DEFAULT_GAP_CLOSING_FEATURE_PENALTIES)); # Track splitting settings.trackerSettings[TrackerKeys.KEY_ALLOW_TRACK_SPLITTING] = False settings.trackerSettings[TrackerKeys.KEY_SPLITTING_MAX_DISTANCE] = 45.0 # in pixels #settings.trackerSettings[TrackerKeys.KEY_SPLITTING_FEATURE_PENALTIES] = new HashMap<>(DEFAULT_SPLITTING_FEATURE_PENALTIES)); # Track merging settings.trackerSettings[TrackerKeys.KEY_ALLOW_TRACK_MERGING] = True settings.trackerSettings[TrackerKeys.KEY_MERGING_MAX_DISTANCE] = 45.0 # in pixels #settings.trackerSettings[TrackerKeys.KEY_MERGING_FEATURE_PENALTIES] = new HashMap<>(DEFAULT_MERGING_FEATURE_PENALTIES)); # Others settings.trackerSettings[TrackerKeys.KEY_BLOCKING_VALUE] = float("inf") settings.trackerSettings[ TrackerKeys.KEY_ALTERNATIVE_LINKING_COST_FACTOR] = 1.05 settings.trackerSettings[TrackerKeys.KEY_CUTOFF_PERCENTILE] = 0.9 # Configure track analyzers - Later on we want to filter out tracks # based on their displacement, so we need to state that we want # track displacement to be calculated. By default, out of the GUI, # no features are calculated. # The displacement feature is provided by the TrackDurationAnalyzer. settings.addTrackAnalyzer(TrackDurationAnalyzer()) settings.addTrackAnalyzer(TrackBranchingAnalyzer()) settings.addTrackAnalyzer(TrackIndexAnalyzer()) settings.addTrackAnalyzer(TrackLocationAnalyzer()) settings.addTrackAnalyzer(TrackSpeedStatisticsAnalyzer()) settings.addSpotAnalyzerFactory(SpotIntensityAnalyzerFactory()) settings.addSpotAnalyzerFactory(SpotContrastAndSNRAnalyzerFactory()) # Configure track filters - We want to get rid of the two immobile spots at # the bottom right of the image. Track displacement must be above 10 pixels. #filter2 = FeatureFilter('TRACK_DISPLACEMENT', 1, True) #settings.addTrackFilter(filter2) #filter2 = FeatureFilter('TRACK_DISPLACEMENT', 1, True) #settings.addTrackFilter(filter2) #print("Spot feature analyzers: " + settings.toStringFeatureAnalyzersInfo()) #------------------- # Instantiate plugin #------------------- trackmate = TrackMate(model, settings) trackmate.setNumThreads(1) #-------- # Process #-------- ok = trackmate.checkInput() if not ok: sys.exit(str(trackmate.getErrorMessage())) print("Processing " + chanName + "...") ok = trackmate.process() if not ok: sys.exit(str(trackmate.getErrorMessage())) #---------------- # Display results #---------------- print("Rendering...") # Set spot names based on track IDs # This allows track IDs to be displayed in the rendered video for tId in model.getTrackModel().trackIDs(True): trackSpots = model.getTrackModel().trackSpots(tId) for spot in trackSpots: spot.setName(str(tId)) # Determine sub-tracks within a track # Since tracks can merge, we want to keep track of which track a spot is # in prior to the merge spotToSubTrackMap = {} spotIt = model.getSpots().iterator(False) trackModel = model.getTrackModel() subTrackCount = {} while spotIt.hasNext(): spot = spotIt.next() spotEdges = trackModel.edgesOf(spot) # Find merge points within a track: ignore spots with fewer than 2 edges if (len(spotEdges) < 2): continue # We have a merge if we have multiple incoming edges incomingEdges = 0 edgeIt = spotEdges.iterator() ancestorSpots = [] while edgeIt.hasNext(): edge = edgeIt.next() src = trackModel.getEdgeSource(edge) dst = trackModel.getEdgeTarget(edge) if dst.ID() == spot.ID(): ancestorSpots.append(src) incomingEdges += 1 # Ignore non-merges if incomingEdges < 2: continue trackId = trackModel.trackIDOf(spot) if trackId in subTrackCount: subTrackId = subTrackCount[trackId] else: subTrackId = 1 for ancestorSpot in ancestorSpots: labelSubTrackAncestors(trackModel, spotToSubTrackMap, ancestorSpot, subTrackId, trackId, False) subTrackId += 1 subTrackCount[trackId] = subTrackId # Spots after the last merge still need to be labeled for tId in trackModel.trackIDs(True): trackSpots = trackModel.trackSpots(tId) spotIt = trackSpots.iterator() lastSpot = None while spotIt.hasNext(): spot = spotIt.next() outgoingEdges = 0 spotEdges = trackModel.edgesOf(spot) edgeIt = spotEdges.iterator() while edgeIt.hasNext(): edge = edgeIt.next() src = trackModel.getEdgeSource(edge) dst = trackModel.getEdgeTarget(edge) if src.ID() == spot.ID(): outgoingEdges += 1 if outgoingEdges == 0 and len(spotEdges) > 0: lastSpot = spot if tId in subTrackCount: subTrackId = subTrackCount[tId] else: subTrackId = 1 if not lastSpot == None: labelSubTrackAncestors(trackModel, spotToSubTrackMap, lastSpot, subTrackId, tId, True) # Create output file trackOut = os.path.join(wellPath, chanName + "_spotToTrackMap.csv") trackFile = open(trackOut, 'w') # Fetch the track feature from the feature model. trackFile.write('Spot Id, Track Sub Id, Track Id, Frame \n') for spotId in spotToSubTrackMap: trackFile.write( str(spotId) + ', ' + ','.join(spotToSubTrackMap[spotId]) + '\n') trackFile.close() # Write Edge Set trackOut = os.path.join(wellPath, chanName + "_mergeEdgeSet.csv") trackFile = open(trackOut, 'w') trackFile.write('Track Id, Spot Id, Spot Id \n') edgeIt = trackModel.edgeSet().iterator() while edgeIt.hasNext(): edge = edgeIt.next() src = trackModel.getEdgeSource(edge) dst = trackModel.getEdgeTarget(edge) trackId = trackModel.trackIDOf(edge) srcSubTrack = spotToSubTrackMap[src.ID()][0] dstSubTrack = spotToSubTrackMap[dst.ID()][0] if not srcSubTrack == dstSubTrack: trackFile.write( str(trackId) + ', ' + str(src.ID()) + ', ' + str(dst.ID()) + '\n') trackFile.close() selectionModel = SelectionModel(model) displayer = HyperStackDisplayer(model, selectionModel, impColor) displayer.setDisplaySettings( TrackMateModelView.KEY_TRACK_COLORING, PerTrackFeatureColorGenerator(model, TrackIndexAnalyzer.TRACK_INDEX)) displayer.setDisplaySettings( TrackMateModelView.KEY_SPOT_COLORING, SpotColorGeneratorPerTrackFeature(model, TrackIndexAnalyzer.TRACK_INDEX)) displayer.setDisplaySettings(TrackMateModelView.KEY_DISPLAY_SPOT_NAMES, True) displayer.setDisplaySettings( TrackMateModelView.KEY_TRACK_DISPLAY_MODE, TrackMateModelView.TRACK_DISPLAY_MODE_LOCAL_BACKWARD_QUICK) displayer.setDisplaySettings( TrackMateModelView.KEY_TRACK_DISPLAY_DEPTH, 2) displayer.render() displayer.refresh() trackmate.getSettings().imp = impColor coa = CaptureOverlayAction(None) coa.execute(trackmate) WindowManager.setTempCurrentImage(coa.getCapture()) IJ.saveAs('avi', os.path.join(wellPath, chanName + "_out.avi")) imp.close() impColor.close() displayer.clear() displayer.getImp().hide() displayer.getImp().close() coa.getCapture().hide() coa.getCapture().close() # Echo results with the logger we set at start: model.getLogger().log(str(model)) # The feature model, that stores edge and track features. fm = model.getFeatureModel() # Write output for tracks numTracks = model.getTrackModel().trackIDs(True).size() print "Writing track data for " + str(numTracks) + " tracks." trackDat = {} for tId in model.getTrackModel().trackIDs(True): track = model.getTrackModel().trackSpots(tId) # Ensure track spots dir exists trackOut = os.path.join(wellPath, chanName + "_track_spots") if not os.path.exists(trackOut): os.makedirs(trackOut) # Create output file trackOut = os.path.join(trackOut, "track_" + str(tId) + ".csv") trackFile = open(trackOut, 'w') # Write Header header = 'Name, ID, Frame, ' for feature in track.toArray()[0].getFeatures().keySet(): if feature == 'Frame': continue header += feature + ", " header = header[0:len(header) - 2] header += '\n' trackFile.write(header) # Write spot data avgTotalIntensity = 0 for spot in track: #print spot.echo() data = [ spot.getName(), str(spot.ID()), str(spot.getFeature('FRAME')) ] for feature in spot.getFeatures(): if feature == 'Frame': continue elif feature == 'TOTAL_INTENSITY': avgTotalIntensity += spot.getFeature(feature) data.append(str(spot.getFeature(feature))) trackFile.write(','.join(data) + '\n') trackFile.close() avgTotalIntensity /= len(track) # Write out track stats # Make sure dir exists trackOut = os.path.join(wellPath, chanName + "_tracks") if not os.path.exists(trackOut): os.makedirs(trackOut) # Create output file trackOut = os.path.join(trackOut, "track_" + str(tId) + ".csv") trackFile = open(trackOut, 'w') # Fetch the track feature from the feature model. header = '' for featName in fm.getTrackFeatureNames(): header += featName + ", " header = header[0:len(header) - 2] header += '\n' trackFile.write(header) features = '' for featName in fm.getTrackFeatureNames(): features += str(fm.getTrackFeature(tId, featName)) + ', ' features = features[0:len(features) - 2] features += '\n' trackFile.write(features) trackFile.write('\n') trackFile.close() trackDat[tId] = [ str(tId), str(fm.getTrackFeature(tId, 'TRACK_DURATION')), str(avgTotalIntensity), str(fm.getTrackFeature(tId, 'TRACK_START')), str(fm.getTrackFeature(tId, 'TRACK_STOP')) ] # Create output file trackOut = os.path.join(wellPath, chanName + "_trackSummary.csv") trackFile = open(trackOut, 'w') # Fetch the track feature from the feature model. trackFile.write( 'Track Id, Duration, Avg Total Intensity, Start Frame, Stop Frame \n' ) for track in trackDat: trackFile.write(','.join(trackDat[track]) + '\n') trackFile.close() trackOut = os.path.join(wellPath, chanName + "_trackModel.xml") trackFile = File(trackOut) writer = TmXmlWriter(trackFile, model.getLogger()) #writer.appendLog( logPanel.getTextContent() ); writer.appendModel(trackmate.getModel()) writer.appendSettings(trackmate.getSettings()) #writer.appendGUIState( controller.getGuimodel() ); writer.writeToFile() model.clearSpots(True) model.clearTracks(True) return trackDat
# Spot detector. settings.detectorFactory = LogDetectorFactory() settings.detectorSettings = settings.detectorFactory.getDefaultSettings() settings.detectorSettings['RADIUS'] = radius settings.detectorSettings['THRESHOLD'] = threshold # Spot tracker. settings.trackerFactory = SparseLAPTrackerFactory() settings.trackerSettings = LAPUtils.getDefaultLAPSettingsMap() settings.trackerSettings['MAX_FRAME_GAP'] = frameGap settings.trackerSettings['LINKING_MAX_DISTANCE'] = linkingMax settings.trackerSettings['GAP_CLOSING_MAX_DISTANCE'] = closingMax # Run TrackMate and store data into Model. model = Model() trackmate = TrackMate(model, settings) if not trackmate.checkInput() or not trackmate.process(): IJ.log('Could not execute TrackMate: ' + str( trackmate.getErrorMessage() ) ) else: IJ.log('TrackMate completed successfully.' ) IJ.log( 'Found %d spots in %d tracks.' % ( model.getSpots().getNSpots( True ) , model.getTrackModel().nTracks( True ) ) ) # Print results in the console. headerStr = '%10s %10s %10s %10s %10s %10s' % ( 'Spot_ID', 'Track_ID', 'Frame', 'X', 'Y', 'Z' ) rowStr = '%10d %10d %10d %10.1f %10.1f %10.1f' for i in range( nChannels ): headerStr += ( ' %10s' % ( 'C' + str(i+1) ) ) rowStr += ( ' %10.1f' )
import fiji.plugin.trackmate.Model as Model import fiji.plugin.trackmate.Logger as Logger import fiji.plugin.trackmate.Spot as Spot import fiji.plugin.trackmate.SelectionModel as SelectionModel import fiji.plugin.trackmate.TrackMate as TrackMate import fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayer as HyperStackDisplayer import fiji.plugin.trackmate.visualization.trackscheme.TrackScheme as TrackScheme import fiji.plugin.trackmate.visualization.PerTrackFeatureColorGenerator as PerTrackFeatureColorGenerator import fiji.plugin.trackmate.features.ModelFeatureUpdater as ModelFeatureUpdater import fiji.plugin.trackmate.features.track.TrackIndexAnalyzer as TrackIndexAnalyzer import ij.plugin.Animator as Animator import math # We just need a model for this script. Nothing else, since # we will do everything manually. model = Model() model.setLogger(Logger.IJ_LOGGER) # Well actually, we still need a bit: # We want to color-code the tracks by their feature, for instance # with the track index. But for this, we need to compute the # features themselves. # # Manuall, this is done by declaring what features interest you # in a settings object, and creating a ModelFeatureUpdater that # will listen to changes in the model, and compute the feautures # on the fly. settings = Settings() settings.addTrackAnalyzer( TrackIndexAnalyzer() ) # If you want more, add more analyzers.
def runTrackMate(imp): import fiji.plugin.trackmate.Settings as Settings import fiji.plugin.trackmate.Model as Model import fiji.plugin.trackmate.SelectionModel as SelectionModel import fiji.plugin.trackmate.TrackMate as TrackMate import fiji.plugin.trackmate.Logger as Logger import fiji.plugin.trackmate.detection.DetectorKeys as DetectorKeys import fiji.plugin.trackmate.detection.DogDetectorFactory as DogDetectorFactory import fiji.plugin.trackmate.tracking.sparselap.SparseLAPTrackerFactory as SparseLAPTrackerFactory import fiji.plugin.trackmate.tracking.LAPUtils as LAPUtils import fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayer as HyperStackDisplayer import fiji.plugin.trackmate.features.FeatureFilter as FeatureFilter import fiji.plugin.trackmate.features.FeatureAnalyzer as FeatureAnalyzer import fiji.plugin.trackmate.features.spot.SpotContrastAndSNRAnalyzerFactory as SpotContrastAndSNRAnalyzerFactory import fiji.plugin.trackmate.action.ExportStatsToIJAction as ExportStatsToIJAction import fiji.plugin.trackmate.io.TmXmlReader as TmXmlReader import fiji.plugin.trackmate.action.ExportTracksToXML as ExportTracksToXML import fiji.plugin.trackmate.io.TmXmlWriter as TmXmlWriter import fiji.plugin.trackmate.features.ModelFeatureUpdater as ModelFeatureUpdater import fiji.plugin.trackmate.features.SpotFeatureCalculator as SpotFeatureCalculator import fiji.plugin.trackmate.features.spot.SpotContrastAndSNRAnalyzer as SpotContrastAndSNRAnalyzer import fiji.plugin.trackmate.features.spot.SpotIntensityAnalyzerFactory as SpotIntensityAnalyzerFactory import fiji.plugin.trackmate.features.track.TrackSpeedStatisticsAnalyzer as TrackSpeedStatisticsAnalyzer import fiji.plugin.trackmate.util.TMUtils as TMUtils import fiji.plugin.trackmate.visualization.trackscheme.TrackScheme as TrackScheme import fiji.plugin.trackmate.visualization.PerTrackFeatureColorGenerator as PerTrackFeatureColorGenerator #------------------------- # Instantiate model object #------------------------- nFrames = imp.getNFrames() model = Model() # Set logger #model.setLogger(Logger.IJ_LOGGER) #------------------------ # Prepare settings object #------------------------ settings = Settings() settings.setFrom(imp) # Configure detector settings.detectorFactory = DogDetectorFactory() settings.detectorSettings = { DetectorKeys.KEY_DO_SUBPIXEL_LOCALIZATION: True, DetectorKeys.KEY_RADIUS: 12.30, DetectorKeys.KEY_TARGET_CHANNEL: 1, DetectorKeys.KEY_THRESHOLD: 100., DetectorKeys.KEY_DO_MEDIAN_FILTERING: False, } # Configure tracker settings.trackerFactory = SparseLAPTrackerFactory() settings.trackerSettings = LAPUtils.getDefaultLAPSettingsMap() settings.trackerSettings['LINKING_MAX_DISTANCE'] = 10.0 settings.trackerSettings['GAP_CLOSING_MAX_DISTANCE'] = 10.0 settings.trackerSettings['MAX_FRAME_GAP'] = 3 # Add the analyzers for some spot features. # You need to configure TrackMate with analyzers that will generate # the data you need. # Here we just add two analyzers for spot, one that computes generic # pixel intensity statistics (mean, max, etc...) and one that computes # an estimate of each spot's SNR. # The trick here is that the second one requires the first one to be in # place. Be aware of this kind of gotchas, and read the docs. settings.addSpotAnalyzerFactory(SpotIntensityAnalyzerFactory()) settings.addSpotAnalyzerFactory(SpotContrastAndSNRAnalyzerFactory()) # Add an analyzer for some track features, such as the track mean speed. settings.addTrackAnalyzer(TrackSpeedStatisticsAnalyzer()) settings.initialSpotFilterValue = 1 print(str(settings)) #---------------------- # Instantiate trackmate #---------------------- trackmate = TrackMate(model, settings) #------------ # Execute all #------------ ok = trackmate.checkInput() if not ok: sys.exit(str(trackmate.getErrorMessage())) ok = trackmate.process() if not ok: sys.exit(str(trackmate.getErrorMessage())) #---------------- # Display results #---------------- selectionModel = SelectionModel(model) displayer = HyperStackDisplayer(model, selectionModel, imp) displayer.render() displayer.refresh() #--------------------- # Select correct spots #--------------------- # Prepare display. sm = SelectionModel(model) color = PerTrackFeatureColorGenerator(model, 'TRACK_INDEX') # launch TrackScheme to select spots and tracks trackscheme = TrackScheme(model, sm) trackscheme.setDisplaySettings('TrackColoring', color) trackscheme.render() # Update image with TrackScheme commands view = HyperStackDisplayer(model, sm, imp) view.setDisplaySettings('TrackColoring', color) view.render() # Wait for the user to select correct spots and tracks before collecting data dialog = WaitForUserDialog( "Spots", "Delete incorrect spots and edit tracks if necessary. (Press ESC to cancel analysis)" ) dialog.show() if dialog.escPressed(): IJ.run("Remove Overlay", "") imp.close() return ([], nFrames) # The feature model, that stores edge and track features. #model.getLogger().log('Found ' + str(model.getTrackModel().nTracks(True)) + ' tracks.') fm = model.getFeatureModel() crds_perSpot = [] for id in model.getTrackModel().trackIDs(True): # Fetch the track feature from the feature model.(remove """ to enable) """v = fm.getTrackFeature(id, 'TRACK_MEAN_SPEED') model.getLogger().log('') model.getLogger().log('Track ' + str(id) + ': mean velocity = ' + str(v) + ' ' + model.getSpaceUnits() + '/' + model.getTimeUnits())""" trackID = str(id) track = model.getTrackModel().trackSpots(id) spot_track = {} for spot in track: sid = spot.ID() # Fetch spot features directly from spot. x = spot.getFeature('POSITION_X') y = spot.getFeature('POSITION_Y') t = spot.getFeature('FRAME') q = spot.getFeature('QUALITY') snr = spot.getFeature('SNR') mean = spot.getFeature('MEAN_INTENSITY') #model.getLogger().log('\tspot ID = ' + str(sid) + ', x='+str(x)+', y='+str(y)+', t='+str(t)+', q='+str(q) + ', snr='+str(snr) + ', mean = ' + str(mean)) spot_track[t] = (x, y) crds_perSpot.append(spot_track) #print ("Spot", crds_perSpot.index(spot_track),"has the following coordinates:", crds_perSpot[crds_perSpot.index(spot_track)]) return (crds_perSpot, nFrames)
import fiji.plugin.trackmate.features.spot.SpotMorphologyAnalyzerFactory as SpotMorphologyAnalyzerFactory import fiji.plugin.trackmate.features.spot.SpotMorphologyAnalyzer as SpotMorphologyAnalyzer import fiji.plugin.trackmate.features.edges.EdgeTargetAnalyzer as EdgeTargetAnalyzer import fiji.plugin.trackmate.features.edges.EdgeTimeLocationAnalyzer as EdgeTimeLocationAnalyzer import fiji.plugin.trackmate.features.edges.EdgeVelocityAnalyzer as EdgeVelocityAnalyzer import fiji.plugin.trackmate.features.track.TrackDurationAnalyzer as TrackDurationAnalyzer import fiji.plugin.trackmate.features.track.TrackIndexAnalyzer as TrackIndexAnalyzer import fiji.plugin.trackmate.features.track.TrackLocationAnalyzer as TrackLocationAnalyzer import fiji.plugin.trackmate.features.track.TrackSpeedStatisticsAnalyzer as TrackSpeedStatisticsAnalyzer import fiji.plugin.trackmate.features.track.TrackSpotFeatureAnalyzer as TrackSpotFeatureAnalyzer trackmate = TrackMate() settings = Settings() model = Model() # Get currently selected image imp = WindowManager.getCurrentImage() GuiUtils.userCheckImpDimensions(imp) #------------------------- # Instantiate model object #------------------------- model.setPhysicalUnits(imp.getCalibration().getUnits(), imp.getCalibration().getTimeUnit()) # Set logger model.setLogger(Logger.IJ_LOGGER) #------------------------
imp.show() cal = Calibration() cal.setUnit('micron') cal.pixelHeight = resolution cal.pixelWidth = resolution cal.pixelDepth = 2**16 cal.fps = 10 cal.frameInterval = 1 imp.setCalibration(cal) #------------------------- # Instantiate model object #------------------------- model = Model() model.setPhysicalUnits('micron', 'frames') # Set logger model.setLogger(Logger.IJ_LOGGER) #------------------------ # Prepare settings object #------------------------ settings = Settings() settings.setFrom(imp) # Configure detector - We use the Strings for the keys settings.detectorFactory = LogDetectorFactory() settings.detectorSettings = {
def track_single_batch(path, filename): # Get currently selected image imp = WindowManager.getCurrentImage() # imp = IJ.openImage('https://fiji.sc/samples/FakeTracks.tif') imp.show() #---------------------------- # Create the model object now #---------------------------- # Some of the parameters we configure below need to have # a reference to the model at creation. So we create an # empty model now. model = Model() # Send all messages to ImageJ log window. model.setLogger(Logger.IJ_LOGGER) #------------------------ # Prepare settings object #------------------------ settings = Settings() settings.setFrom(imp) # Configure detector - We use the Strings for the keys #settings.detectorFactory = LogDetectorFactory() settings.detectorFactory = BlockLogDetectorFactory() print settings.detectorSettings = { 'DO_SUBPIXEL_LOCALIZATION': True, 'RADIUS': 7.5, 'TARGET_CHANNEL': 1, 'THRESHOLD': 0.25, 'DO_MEDIAN_FILTERING': False, 'NSPLIT': 3, } # Configure spot filters - Classical filter on quality filter1 = FeatureFilter('QUALITY', 0.1, True) # in higher SNR; settings.addSpotFilter(filter1) # Configure tracker - We want to allow merges and fusions settings.trackerFactory = SparseLAPTrackerFactory() #settings.trackerFactory = LAPTrackerFactory() settings.trackerSettings = LAPUtils.getDefaultLAPSettingsMap( ) # almost good enough settings.trackerSettings['ALLOW_TRACK_SPLITTING'] = True settings.trackerSettings['ALLOW_TRACK_MERGING'] = True settings.trackerSettings['LINKING_MAX_DISTANCE'] = 15.0 settings.trackerSettings['GAP_CLOSING_MAX_DISTANCE'] = 15.0 settings.trackerSettings['MAX_FRAME_GAP'] = 5 # feature 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)) #filter2 = FeatureFilter('TRACK_DISPLACEMENT', 3, True) #settings.addTrackFilter(filter2) # processing trackmate = TrackMate(model, settings) ok = trackmate.checkInput() if not ok: sys.exit(str(trackmate.getErrorMessage())) try: ok = trackmate.process() except: IJ.log("Nothing detected") else: selectionModel = SelectionModel(model) displayer = HyperStackDisplayer(model, selectionModel, imp) displayer.render() displayer.refresh() # Echo results with the logger we set at start: model.getLogger().log(str(model)) save_path = os.path.join(path, 'result') if not os.path.exists(save_path): os.mkdir(save_path, 0755) outFile = File(save_path, filename) ExportTracksToXML.export(model, settings, outFile) imp.close()
# Spot detector. settings.detectorFactory = LogDetectorFactory() settings.detectorSettings = settings.detectorFactory.getDefaultSettings() settings.detectorSettings['RADIUS'] = radius settings.detectorSettings['THRESHOLD'] = threshold # Spot tracker. settings.trackerFactory = SparseLAPTrackerFactory() settings.trackerSettings = LAPUtils.getDefaultLAPSettingsMap() settings.trackerSettings['MAX_FRAME_GAP'] = frameGap settings.trackerSettings['LINKING_MAX_DISTANCE'] = linkingMax settings.trackerSettings['GAP_CLOSING_MAX_DISTANCE'] = closingMax # Run TrackMate and store data into Model. model = Model() trackmate = TrackMate(model, settings) if not trackmate.checkInput() or not trackmate.process(): IJ.log('Could not execute TrackMate: ' + str(trackmate.getErrorMessage())) else: IJ.log('TrackMate completed successfully.') IJ.log( 'Found %d spots in %d tracks.' % (model.getSpots().getNSpots(True), model.getTrackModel().nTracks(True))) # Print results in the console. headerStr = '%10s %10s %10s %10s %10s %10s' % ('Spot_ID', 'Track_ID', 'Frame', 'X', 'Y', 'Z') rowStr = '%10d %10d %10d %10.1f %10.1f %10.1f' for i in range(nChannels):
print(ROI_list[ROI_idx]); rm = RoiManager(); rm = RoiManager.getInstance(); rm.runCommand("Open", Roi_File); total_rois = rm.getCount(); for idx in range(total_rois): #---------------------------- # Create the model object now #---------------------------- # Some of the parameters we configure below need to have # a reference to the model at creation. So we create an # empty model now. model = Model(); # Send all messages to ImageJ log window. model.setLogger(Logger.IJ_LOGGER); model.setPhysicalUnits(Calib.getUnit(), Calib.getTimeUnit()); #------------------------ # Prepare settings object #------------------------ settings = Settings(); rm.select(imp,idx); actual_roi = rm.getRoi(idx); imp.setRoi(actual_roi); settings.setFrom(imp); settings.tstart = Initial_frames; settings.tend = imp.getNFrames() - Final_frames -1;
settings.detectorSettings['RADIUS'] = radius settings.detectorSettings['THRESHOLD'] = threshold println settings.detectorSettings settings.trackerFactory = new SparseLAPTrackerFactory() settings.trackerSettings = LAPUtils.getDefaultLAPSettingsMap() settings.trackerSettings['MAX_FRAME_GAP'] = frameGap settings.trackerSettings['LINKING_MAX_DISTANCE'] = linkingMax settings.trackerSettings['GAP_CLOSING_MAX_DISTANCE'] = closingMax // Run TrackMate and store data into Model model = new Model() trackmate = new TrackMate(model, settings) println trackmate.checkInput() println trackmate.process() println trackmate.getErrorMessage() println model.getSpots().getNSpots(true) println model.getTrackModel().nTracks(true) // Save tracks as XML if (!filename.endsWith(".xml")) { filename += ".xml" } outFile = new File(outputFolder, filename) ExportTracksToXML.export(model, settings, outFile)
OUTFILE = os.path.join(root, filename + ".txt") # This is a weird dimension swap that seems to be useful for some TIFF stacks where dimensions get mis-ordered. # Swap Z and T dimensions if T=1 dims = imp.getDimensions() # default order: XYCZT if (dims[4] == 1): imp.setDimensions(dims[2, 4, 3]) # Get the number of channels. # IMPORTANT: This code assumes that the H2B channel is Channel 2 and ErkKTR is Channel 1 nChannels = imp.getNChannels() #---------------------------- # Create the model object now #---------------------------- model = Model() # Send all messages to ImageJ log window. model.setLogger(Logger.IJ_LOGGER) #------------------------ # Prepare settings object #------------------------ settings = Settings() settings.setFrom(imp) # Use the spot analyzer for assessing fluorescence intensities in each channel settings.addSpotAnalyzerFactory( SpotMultiChannelIntensityAnalyzerFactory()) # Configure the detector for finding nuclei
log_info += 'height: ' + str(imp.getHeight()) + '\n' cal = Calibration() cal.setUnit('micron') cal.pixelHeight = resolution cal.pixelWidth = resolution cal.pixelDepth = 0. cal.fps = 1 cal.frameInterval = 1 imp.setCalibration(cal) #------------------------- # Instantiate model object #------------------------- model = Model() model.setPhysicalUnits('micron', 'frames') # Set logger model.setLogger(Logger.IJ_LOGGER) #------------------------ # Prepare settings object #------------------------ settings = Settings() settings.setFrom(imp) # Configure detector - We use the Strings for the keys settings.detectorFactory = LogDetectorFactory() settings.detectorSettings = {
def run_trackmate( imp, path_out="./", detector="log", radius=2.5, threshold=0.0, median_filter=False ): """Log Trackmate detection run with given parameters. Saves spots in a csv file in the given path_out with encoded parameters. Args: imp: ImagePlus to be processed path_out: Output directory to save files. detector: Type of detection method. Options are 'log', 'dog'. radius: Radius of spots in pixels. threshold: Threshold value to filter spots. median_filter: True if median_filtering should be used. """ if imp.dimensions[2] != 1: raise ValueError( "Imp's dimensions must be [n, n, 1] but are " + imp.dimensions[2] ) # Create the model object now model = Model() model.setLogger(Logger.VOID_LOGGER) # Prepare settings object settings = Settings() settings.setFrom(imp) # Configure detector settings.detectorFactory = ( DogDetectorFactory() if detector == "dog" else LogDetectorFactory() ) settings.detectorSettings = { "DO_SUBPIXEL_LOCALIZATION": True, "RADIUS": radius, "TARGET_CHANNEL": 1, "THRESHOLD": threshold, "DO_MEDIAN_FILTERING": median_filter, } # Instantiate plugin trackmate = TrackMate(model, settings) # Process # output = trackmate.process() output = trackmate.execDetection() if not output: print("error process") return None # Get output from a single image fname = str(imp.title) spots = [["fname", "detector", "radius", "threshold", "median", "x", "y", "q"]] for spot in model.spots.iterator(0): x = spot.getFeature("POSITION_X") y = spot.getFeature("POSITION_Y") q = spot.getFeature("QUALITY") spots.append([fname, detector, radius, threshold, median_filter, x, y, q]) # Save output outname = os.path.splitext(os.path.basename(fname))[0] + "_" + str(radius) + ".csv" with open(os.path.join(path_out, outname), "wb") as f: wr = csv.writer(f) for row in spots: wr.writerow(row)
for inputFile, outputFile in data: # Get currently selected image #imp = WindowManager.getCurrentImage() imp = IJ.openImage(inputFile) #imp.show() #---------------------------- # Create the model object now #---------------------------- # Some of the parameters we configure below need to have # a reference to the model at creation. So we create an # empty model now. model = Model() # Send all messages to ImageJ log window. model.setLogger(Logger.IJ_LOGGER) #------------------------ # Prepare settings object #------------------------ settings = Settings() settings.setFrom(imp) # Configure detector - We use the Strings for the keys settings.detectorFactory = DogDetectorFactory() settings.detectorSettings = { 'DO_SUBPIXEL_LOCALIZATION': True,
IJ.run("Close All", ""); imp = IJ.run("Bio-Formats Importer", ("open=" + filename + " autoscale color_mode=Default rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT")) imp = WindowManager.getCurrentImage() IJ.run(imp, "Subtract Background...", "rolling=50 sliding disable stack"); dx = imp.getCalibration().pixelWidth dy = imp.getCalibration().pixelHeight #---------------------------- # Create the model object now #---------------------------- # Some of the parameters we configure below need to have # a reference to the model at creation. So we create an # empty model now. model = Model() # Send all messages to ImageJ log window. model.setLogger(Logger.IJ_LOGGER) #------------------------ # Prepare settings object #------------------------ settings = Settings() model.getLogger().log('') model.getLogger().log('Filename' + file1 + "TEST:" + str(file1.endswith("*R3D_PRJ.dv"))) settings.setFrom(imp) # Configure detector - We use the Strings for the keys settings.detectorFactory = LogDetectorFactory()
def track(): imp = IJ.getImage() nChannels = imp.getNChannels() # Get the number of channels orgtitle = imp.getTitle() IJ.run("Subtract Background...", "rolling=50 sliding stack") IJ.run("Enhance Contrast...", "saturated=0.3") IJ.run("Multiply...", "value=10 stack") IJ.run("Subtract Background...", "rolling=50 sliding stack") IJ.run("Set Scale...", "distance=0") channels = ChannelSplitter.split(imp) imp_GFP = channels[0] imp_RFP = channels[1] IJ.selectWindow(orgtitle) IJ.run("Close") ic = ImageCalculator() imp_merge = ic.run("Add create stack", imp_GFP, imp_RFP) imp_merge.setTitle("add_channels") imp_merge.show() imp_RFP.show() imp_GFP.show() imp5 = ImagePlus() IJ.run(imp5, "Merge Channels...", "c1=[" + imp_merge.title + "] c2=" + imp_GFP.title + ' c3=' + imp_RFP.title + " create") print("c1=[" + imp_merge.title + "] c2=" + imp_GFP.title + ' c3=' + imp_RFP.title + " create") imp5.show() imp5 = IJ.getImage() nChannels = imp5.getNChannels() # Setup settings for TrackMate settings = Settings() settings.setFrom(imp5) # Spot analyzer: we want the multi-C intensity analyzer. settings.addSpotAnalyzerFactory(SpotMultiChannelIntensityAnalyzerFactory()) # Spot detector. settings.detectorFactory = LogDetectorFactory() settings.detectorSettings = settings.detectorFactory.getDefaultSettings() settings.detectorSettings['TARGET_CHANNEL'] = 1 settings.detectorSettings['RADIUS'] = 24.0 settings.detectorSettings['THRESHOLD'] = 0.0 # Spot tracker. # Configure tracker - We don't want to allow merges or splits settings.trackerFactory = SparseLAPTrackerFactory() settings.trackerSettings = LAPUtils.getDefaultLAPSettingsMap() # almost good enough settings.trackerSettings['ALLOW_TRACK_SPLITTING'] = False settings.trackerSettings['ALLOW_TRACK_MERGING'] = False settings.trackerSettings['LINKING_MAX_DISTANCE'] = 8.0 settings.trackerSettings['GAP_CLOSING_MAX_DISTANCE'] = 8.0 settings.trackerSettings['MAX_FRAME_GAP'] = 1 # Configure track filters settings.addTrackAnalyzer(TrackDurationAnalyzer()) settings.addTrackAnalyzer(TrackSpotQualityFeatureAnalyzer()) filter1 = FeatureFilter('TRACK_DURATION', 20, True) settings.addTrackFilter(filter1) # Run TrackMate and store data into Model. model = Model() trackmate = TrackMate(model, settings) ok = trackmate.checkInput() if not ok: sys.exit(str(trackmate.getErrorMessage())) ok = trackmate.process() if not ok: sys.exit(str(trackmate.getErrorMessage())) selectionModel = SelectionModel(model) displayer = HyperStackDisplayer(model, selectionModel, imp5) displayer.render() displayer.refresh() IJ.log('TrackMate completed successfully.') IJ.log('Found %d spots in %d tracks.' % (model.getSpots().getNSpots(True) , model.getTrackModel().nTracks(True))) # Print results in the console. headerStr = '%10s %10s %10s %10s %10s %10s' % ('Spot_ID', 'Track_ID', 'Frame', 'X', 'Y', 'Z') rowStr = '%10d %10d %10d %10.1f %10.1f %10.1f' for i in range( nChannels ): headerStr += (' %10s' % ( 'C' + str(i+1) ) ) rowStr += ( ' %10.1f' ) #open a file to save results myfile = open('/home/rickettsia/Desktop/data/Clamydial_Image_Analysis/EMS_BMECBMELVA_20X_01122019/data/'+orgtitle.split('.')[0]+'.csv', 'wb') wr = csv.writer(myfile, quoting=csv.QUOTE_ALL) wr.writerow(['Spot_ID', 'Track_ID', 'Frame', 'X', 'Y', 'Z', 'Channel_1', 'Channel_2']) IJ.log('\n') IJ.log(headerStr) tm = model.getTrackModel() trackIDs = tm.trackIDs(True) for trackID in trackIDs: spots = tm.trackSpots(trackID) # Let's sort them by frame. ls = ArrayList(spots) for spot in ls: values = [spot.ID(), trackID, spot.getFeature('FRAME'), \ spot.getFeature('POSITION_X'), spot.getFeature('POSITION_Y'), spot.getFeature('POSITION_Z')] for i in range(nChannels): values.append(spot.getFeature('MEAN_INTENSITY%02d' % (i+1))) IJ.log(rowStr % tuple(values)) l1 = (values[0], values[1], values[2], values[3], values[4], values[5], values[7], values[8]) wr.writerow(l1) myfile.close() IJ.selectWindow("Merged") IJ.run("Close")
def process(srcDir, dstDir, currentDir, fileName, keepDirectories): print "Processing:" # Opening the image print "Open image file", fileName imp = IJ.openImage(os.path.join(currentDir, fileName)) #Here we make sure the calibration are correct units = "pixel" TimeUnit = "unit" newCal = Calibration() newCal.pixelWidth = 1 newCal.pixelHeight = 1 newCal.frameInterval = 1 newCal.setXUnit(units) newCal.setYUnit(units) newCal.setTimeUnit(TimeUnit) imp.setCalibration(newCal) cal = imp.getCalibration() dims = imp.getDimensions() # default order: XYCZT if (dims[4] == 1): imp.setDimensions(1, 1, dims[3]) # Start the tracking model = Model() #Read the image calibration model.setPhysicalUnits(cal.getUnit(), cal.getTimeUnit()) # Send all messages to ImageJ log window. model.setLogger(Logger.IJ_LOGGER) settings = Settings() settings.setFrom(imp) # Configure detector - We use the Strings for the keys # Configure detector - We use the Strings for the keys settings.detectorFactory = DownsampleLogDetectorFactory() settings.detectorSettings = { DetectorKeys.KEY_RADIUS: 2., DetectorKeys.KEY_DOWNSAMPLE_FACTOR: 2, DetectorKeys.KEY_THRESHOLD: 1., } print(settings.detectorSettings) # Configure spot filters - Classical filter on quality filter1 = FeatureFilter('QUALITY', 0, True) settings.addSpotFilter(filter1) # Configure tracker - We want to allow merges and fusions settings.trackerFactory = SparseLAPTrackerFactory() settings.trackerSettings = LAPUtils.getDefaultLAPSettingsMap( ) # almost good enough settings.trackerSettings['LINKING_MAX_DISTANCE'] = LINKING_MAX_DISTANCE settings.trackerSettings['ALLOW_TRACK_SPLITTING'] = ALLOW_TRACK_SPLITTING settings.trackerSettings['SPLITTING_MAX_DISTANCE'] = SPLITTING_MAX_DISTANCE settings.trackerSettings['ALLOW_TRACK_MERGING'] = ALLOW_TRACK_MERGING settings.trackerSettings['MERGING_MAX_DISTANCE'] = MERGING_MAX_DISTANCE settings.trackerSettings[ 'GAP_CLOSING_MAX_DISTANCE'] = GAP_CLOSING_MAX_DISTANCE settings.trackerSettings['MAX_FRAME_GAP'] = MAX_FRAME_GAP # Configure track analyzers - Later on we want to filter out tracks # based on their displacement, so we need to state that we want # track displacement to be calculated. By default, out of the GUI, # not features are calculated. # The displacement feature is provided by the TrackDurationAnalyzer. settings.addTrackAnalyzer(TrackDurationAnalyzer()) settings.addTrackAnalyzer(TrackSpeedStatisticsAnalyzer()) filter2 = FeatureFilter('TRACK_DISPLACEMENT', 10, True) settings.addTrackFilter(filter2) #------------------- # Instantiate plugin #------------------- trackmate = TrackMate(model, settings) #-------- # Process #-------- ok = trackmate.checkInput() if not ok: sys.exit(str(trackmate.getErrorMessage())) ok = trackmate.process() if not ok: sys.exit(str(trackmate.getErrorMessage())) #---------------- # Display results #---------------- if showtracks: model.getLogger().log('Found ' + str(model.getTrackModel().nTracks(True)) + ' tracks.') selectionModel = SelectionModel(model) displayer = HyperStackDisplayer(model, selectionModel, imp) displayer.render() displayer.refresh() # The feature model, that stores edge and track features. fm = model.getFeatureModel() with open(dstDir + fileName + 'tracks_properties.csv', "w") as file: writer1 = csv.writer(file) writer1.writerow([ "track #", "TRACK_MEAN_SPEED (micrometer.secs)", "TRACK_MAX_SPEED (micrometer.secs)", "NUMBER_SPLITS", "TRACK_DURATION (secs)", "TRACK_DISPLACEMENT (micrometer)" ]) with open(dstDir + fileName + 'spots_properties.csv', "w") as trackfile: writer2 = csv.writer(trackfile) #writer2.writerow(["spot ID","POSITION_X","POSITION_Y","Track ID", "FRAME"]) writer2.writerow( ["Tracking ID", "Timepoint", "Time (secs)", "X pos", "Y pos"]) for id in model.getTrackModel().trackIDs(True): # Fetch the track feature from the feature model. v = (fm.getTrackFeature(id, 'TRACK_MEAN_SPEED') * Pixel_calibration) / Time_interval ms = (fm.getTrackFeature(id, 'TRACK_MAX_SPEED') * Pixel_calibration) / Time_interval s = fm.getTrackFeature(id, 'NUMBER_SPLITS') d = fm.getTrackFeature(id, 'TRACK_DURATION') * Time_interval e = fm.getTrackFeature( id, 'TRACK_DISPLACEMENT') * Pixel_calibration model.getLogger().log('') model.getLogger().log('Track ' + str(id) + ': mean velocity = ' + str(v) + ' ' + model.getSpaceUnits() + '/' + model.getTimeUnits()) track = model.getTrackModel().trackSpots(id) writer1.writerow( [str(id), str(v), str(ms), str(s), str(d), str(e)]) for spot in track: sid = spot.ID() x = spot.getFeature('POSITION_X') y = spot.getFeature('POSITION_Y') z = spot.getFeature('TRACK_ID') t = spot.getFeature('FRAME') time = int(t) * int(Time_interval) writer2.writerow( [str(id), str(t), str(time), str(x), str(y)])
def track(imp): from fiji.plugin.trackmate import Model from fiji.plugin.trackmate import Settings from fiji.plugin.trackmate import TrackMate from fiji.plugin.trackmate import SelectionModel from fiji.plugin.trackmate import Logger from fiji.plugin.trackmate.detection import LogDetectorFactory from fiji.plugin.trackmate.tracking.sparselap import SparseLAPTrackerFactory from fiji.plugin.trackmate.tracking import LAPUtils from ij import IJ import fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayer as HyperStackDisplayer import fiji.plugin.trackmate.features.FeatureFilter as FeatureFilter import sys import fiji.plugin.trackmate.features.track.TrackDurationAnalyzer as TrackDurationAnalyzer # Get currently selected image #imp = WindowManager.getCurrentImage() #imp = IJ.openImage('http://fiji.sc/samples/FakeTracks.tif') #imp.show() #---------------------------- # Create the model object now #---------------------------- # Some of the parameters we configure below need to have # a reference to the model at creation. So we create an # empty model now. model = Model() # Send all messages to ImageJ log window. model.setLogger(Logger.IJ_LOGGER) #------------------------ # Prepare settings object #------------------------ settings = Settings() settings.setFrom(imp) # Configure detector - We use the Strings for the keys settings.detectorFactory = LogDetectorFactory() settings.detectorSettings = { 'DO_SUBPIXEL_LOCALIZATION': True, 'RADIUS': 3.0, 'TARGET_CHANNEL': 1, 'THRESHOLD': 1., 'DO_MEDIAN_FILTERING': False, } # Configure spot filters - Classical filter on quality filter1 = FeatureFilter('QUALITY', 30, True) settings.addSpotFilter(filter1) # Configure tracker - We want to allow merges and fusions settings.trackerFactory = SparseLAPTrackerFactory() settings.trackerSettings = LAPUtils.getDefaultLAPSettingsMap( ) # almost good enough settings.trackerSettings['ALLOW_TRACK_SPLITTING'] = True settings.trackerSettings['ALLOW_TRACK_MERGING'] = True # Configure track analyzers - Later on we want to filter out tracks # based on their displacement, so we need to state that we want # track displacement to be calculated. By default, out of the GUI, # not features are calculated. # The displacement feature is provided by the TrackDurationAnalyzer. settings.addTrackAnalyzer(TrackDurationAnalyzer()) #------------------- # Instantiate plugin #------------------- trackmate = TrackMate(model, settings) #-------- # Process #-------- ok = trackmate.checkInput() if not ok: sys.exit(str(trackmate.getErrorMessage())) ok = trackmate.process() if not ok: sys.exit(str(trackmate.getErrorMessage())) #---------------- # Display results #---------------- selectionModel = SelectionModel(model) displayer = HyperStackDisplayer(model, selectionModel, imp) displayer.render() displayer.refresh() # Echo results with the logger we set at start: #model.getLogger().log(str(model)) fm = model.getFeatureModel() norm_x = [] norm_y = [] for id in model.getTrackModel().trackIDs(True): track = model.getTrackModel().trackSpots(id) for spot in track: t = spot.getFeature('FRAME') if (t == 0.0): min_x = spot.getFeature('POSITION_X') min_y = spot.getFeature('POSITION_Y') for spot in track: norm_x.append(spot.getFeature('POSITION_X') - min_x) norm_y.append(spot.getFeature('POSITION_Y') - min_y) max_x = abs(max(norm_x, key=abs)) max_y = abs(max(norm_y, key=abs)) return max_x, max_y
# NanoJ: 59.2s: Estimated Gain=8.971858 Offset=493.7476 with Readout-Sigma=59.08754 print("number of frames is: "+str(imp.getStackSize())) print("first channel is: "+str(imp. getChannel())) #imp.show() IJ.run(imp, "Properties...", "channels=1 slices=1 frames="+str(imp.getStackSize())+" unit=pixel pixel_width=1.0000 pixel_height=1.0000 voxel_depth=5.0000") IJ.run(imp, "Maximum 3D...", "x=2 y=2 z=2") IJ.run(imp, "Median 3D...", "x=1 y=1 z=1") #imp.show() #------------------------- # Instantiate model object #------------------------- model = Model() # Set logger model.setLogger(Logger.IJ_LOGGER) #------------------------ # Prepare settings object #------------------------ settings = Settings() settings.setFrom(imp) # Configure detector settings.detectorFactory = LogDetectorFactory() settings.detectorSettings = { DetectorKeys.KEY_DO_SUBPIXEL_LOCALIZATION : True,
# Get currently selected image #imp = WindowManager.getCurrentImage() imp = IJ.openImage( 'D:\\uni\\TFG\\TrackingImageJInfo\\ScriptingWithPy\\1-paralelo-1.tif') imp.show() #---------------------------- # Create the model object now #---------------------------- # Some of the parameters we configure below need to have # a reference to the model at creation. So we create an # empty model now. model = Model() # Send all messages to ImageJ log window. model.setLogger(Logger.IJ_LOGGER) #------------------------ # Prepare settings object #------------------------ settings = Settings() settings.setFrom(imp) #Take the rest of the settings from a xml file. file = File( "D:\\uni\\TFG\\TrackingImageJInfo\\ScriptingWithPy\\TrackFilterAfter.xml")
# Get currently selected image #imp = WindowManager.getCurrentImage() imp = IJ.openImage('http://fiji.sc/samples/FakeTracks.tif') imp.show() #---------------------------- # Create the model object now #---------------------------- # Some of the parameters we configure below need to have # a reference to the model at creation. So we create an # empty model now. model = Model() # Send all messages to ImageJ log window. model.setLogger(Logger.IJ_LOGGER) #------------------------ # Prepare settings object #------------------------ settings = Settings() settings.setFrom(imp) # Configure detector - We use the Strings for the keys settings.detectorFactory = LogDetectorFactory()