Example script to run TrackMate on two channels of the same image.

scripts/BatchTrackMateExec.py

@@ -0,0 +1,168 @@
+import os
+
+from java.io import File
+
+from  org.scijava.util import VersionUtils
+
+from ij import IJ
+from ij.plugin.frame import RoiManager
+
+from fiji.plugin.trackmate.io import TmXmlWriter
+from fiji.plugin.trackmate import Settings
+from fiji.plugin.trackmate import TrackMate
+from fiji.plugin.trackmate import Logger
+from fiji.plugin.trackmate.util import TMUtils
+from fiji.plugin.trackmate.features import FeatureFilter
+from fiji.plugin.trackmate.detection import HessianDetectorFactory
+from fiji.plugin.trackmate.tracking.jaqaman import SimpleSparseLAPTrackerFactory
+from fiji.plugin.trackmate.action.closegaps import CloseGapsByDetection
+from fiji.plugin.trackmate.gui.displaysettings import DisplaySettingsIO
+from fiji.plugin.trackmate.gui.wizard.descriptors import ConfigureViewsDescriptor
+
+
+#---------------------------------------------------------------------------------------
+
+LOG_MESSAGE = "Batch tracking with TrackMate v" + VersionUtils.getVersion( TrackMate )
+
+def performTracking(imp, settings):
+	trackmate = TrackMate(settings)
+	if (not trackmate.checkInput()) or (not trackmate.process()):
+		print('Problem with tracking:')
+		print(trackmate.getErrorMessage())
+		print('Skipping')
+		return None
+	return trackmate
+
+def performGapClosing(gapCloser, trackmate):
+	gapCloser.execute(trackmate, Logger.VOID_LOGGER)
+
+def saveTrackMate(trackmate, save_file):
+	writer = TmXmlWriter( File( save_file ), Logger.VOID_LOGGER )
+	writer.appendLog( LOG_MESSAGE + "\n" + TMUtils.getCurrentTimeString() )
+	writer.appendModel( trackmate.getModel() )
+	writer.appendSettings( trackmate.getSettings() )
+	writer.appendGUIState( ConfigureViewsDescriptor.KEY )
+	writer.appendDisplaySettings( DisplaySettingsIO.readUserDefault() )
+	writer.writeToFile()
+
+
+#---------------------------------------------------------------------------------------
+
+# Where the images and the ROI files are.
+source_folder = '/Users/tinevez/Desktop/ForJYT_testBatch'
+# In what subfolder are the ROI files saved.
+roi_sub_folder = 'ROI'
+# Where to save the TrackMate files.
+trackmate_sub_folder = 'Tracking'
+
+# Prepare the settings for tracking.
+# Detection.
+detector_settings_ch1 = {	
+	'TARGET_CHANNEL' : 1,
+	'RADIUS' : 0.5, #  m
+	'RADIUS_Z' : 0.8, #  m
+	'THRESHOLD' : 0.7,
+	'DO_SUBPIXEL_LOCALIZATION' : True,
+	'NORMALIZE' : True,
+}
+detector_settings_ch2 = {	
+	'TARGET_CHANNEL' : 2,
+	'RADIUS' : 0.3, #  m
+	'RADIUS_Z' : 0.5, #  m
+	'THRESHOLD' : 0.8,
+	'DO_SUBPIXEL_LOCALIZATION' : True,
+	'NORMALIZE' : True,
+}
+
+# Tracking.
+tracker_settings_ch1 = SimpleSparseLAPTrackerFactory().getDefaultSettings()
+tracker_settings_ch1['LINKING_MAX_DISTANCE'] = 0.9 # µm
+tracker_settings_ch1['GAP_CLOSING_MAX_DISTANCE'] = 1.4 # µm
+tracker_settings_ch1['MAX_FRAME_GAP'] = 12
+tracker_settings_ch2 = SimpleSparseLAPTrackerFactory().getDefaultSettings()
+tracker_settings_ch2['LINKING_MAX_DISTANCE'] = 0.9 # µm
+tracker_settings_ch2['GAP_CLOSING_MAX_DISTANCE'] = 1.4 # µm
+tracker_settings_ch2['MAX_FRAME_GAP'] = 12
+
+# Filtering.
+min_n_spots_per_track_ch1 = 60
+min_n_spots_per_track_ch2 = 20
+
+# Gap-closing.
+radiusFactor = 2. # In units of the spot radius.
+gapCloser = CloseGapsByDetection()
+gapCloser.getParameters().get(0).value = radiusFactor
+
+# Loop over each TIF files.
+for im_file in os.listdir(source_folder):
+	if not im_file.endswith('.tif'):
+		continue
+
+	im_path = os.path.join(source_folder, im_file)
+	print('\nProcessing %s' % im_path)
+
+	print(' - Loading image.')
+	imp = IJ.openImage(im_path)
+
+	# Look for the corresponding ROIs, stored as a ZIP file.
+	roiManager = RoiManager.getRoiManager()
+	if roiManager:
+		roiManager.close()
+
+	# First ROI syntax: the image name + '.zip'
+	roi_file = os.path.splitext(im_file)[0]+'.zip' 
+	roi_path = os.path.join(source_folder, roi_sub_folder, roi_file)
+	if not os.path.exists(roi_path):
+		# Second ROI syntax: the image name + '_RoiSet.zip'
+		roi_file = os.path.splitext(im_file)[0]+'_RoiSet.zip' 
+		roi_path = os.path.join(source_folder, roi_sub_folder, roi_file)
+		if not os.path.exists(roi_path):	
+			print(' - Could not find matching ROI file "%s". Will process the whole image.' % roi_path)
+		else:
+			print(' - Opened ROI file %s' % roi_path)
+			IJ.open(roi_path)
+	else:
+		print(' - Opened ROI file %s' % roi_path)
+		IJ.open(roi_path)
+
+	# Prepare settings objects.
+	settings_ch1 = Settings(imp)
+	settings_ch1.detectorFactory = HessianDetectorFactory()
+	settings_ch1.detectorSettings = detector_settings_ch1
+	settings_ch1.trackerFactory = SimpleSparseLAPTrackerFactory()
+	settings_ch1.trackerSettings = tracker_settings_ch1
+	settings_ch1.addTrackFilter(FeatureFilter('NUMBER_SPOTS', min_n_spots_per_track_ch1, True))
+
+	settings_ch2 = Settings(imp)
+	settings_ch2.detectorFactory = HessianDetectorFactory()
+	settings_ch2.detectorSettings = detector_settings_ch2
+	settings_ch2.trackerFactory = SimpleSparseLAPTrackerFactory()
+	settings_ch2.trackerSettings = tracker_settings_ch2
+	settings_ch2.addTrackFilter(FeatureFilter('NUMBER_SPOTS', min_n_spots_per_track_ch2, True))
+
+	# Perform tracking and save image for CH1.
+	save_file_ch1 = os.path.join(source_folder, trackmate_sub_folder, os.path.splitext(im_file)[0] + '-ch1.xml')
+	print(' - Executing tracking for channel 1.')	
+	trackmate_ch1 = performTracking(imp, settings_ch1)
+	if not trackmate_ch1:
+		continue
+	performGapClosing(gapCloser, trackmate_ch1)
+	saveTrackMate(trackmate_ch1, save_file_ch1)
+
+	# Perform tracking and save image for CH2.
+	save_file_ch2 = os.path.join(source_folder, trackmate_sub_folder, os.path.splitext(im_file)[0] + '-ch2.xml')
+	print(' - Executing tracking for channel 2.')	
+	trackmate_ch2 = performTracking(imp, settings_ch2)
+	if not trackmate_ch2:
+		continue
+	performGapClosing(gapCloser, trackmate_ch2)
+	saveTrackMate(trackmate_ch2, save_file_ch2)
+
+	print(' - Done.')
+
+	# Force closing the image.
+	imp.flush()
+	imp.changes = False
+	imp.close()
+
+print('\nFinished batch tracking in folder %s' % source_folder)