Merge branch 'master' of https://github.com/HenriquesLab/ZeroCostDL4Mic

Tools/.DS_Store

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+

Tools/Automated Tracking.py

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+from fiji.plugin.trackmate import Model
+from ij import WindowManager
+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 DetectorKeys
+from fiji.plugin.trackmate.detection import DownsampleLogDetectorFactory
+from fiji.plugin.trackmate.tracking.sparselap import SparseLAPTrackerFactory
+from ij import IJ, WindowManager
+from fiji.plugin.trackmate.tracking import LAPUtils
+import fiji.plugin.trackmate.visualization.hyperstack.HyperStackDisplayer as HyperStackDisplayer
+import fiji.plugin.trackmate.features.FeatureFilter as FeatureFilter
+import sys
+import csv
+import shutil 
+import os
+import fiji.plugin.trackmate.features.track.TrackDurationAnalyzer as TrackDurationAnalyzer
+import fiji.plugin.trackmate.features.track.TrackSpeedStatisticsAnalyzer as TrackSpeedStatisticsAnalyzer
+
+import os
+from ij import IJ, ImagePlus
+from ij.gui import GenericDialog
+
+def run():
+  srcDir = IJ.getDirectory("Input_directory")
+  if not srcDir:
+    return
+  dstDir = IJ.getDirectory("Output_directory")
+  if not dstDir:
+    return
+  gd = GenericDialog("Process Folder")
+  gd.addStringField("File_extension", ".tif")
+  gd.addStringField("File_name_contains", "")
+  gd.addCheckbox("Keep directory structure when saving", True)
+  gd.addCheckbox("Show tracks", True)
+
+
+  gd.showDialog()
+  if gd.wasCanceled():
+    return
+  ext = gd.getNextString()
+  containString = gd.getNextString()
+  keepDirectories = gd.getNextBoolean()
+  showtracks = gd.getNextBoolean()
+
+  for root, directories, filenames in os.walk(srcDir):
+    for filename in filenames:
+      # Check for file extension
+      if not filename.endswith(ext):
+        continue
+      # Check for file name pattern
+      if containString not in filename:
+        continue
+      process(srcDir, dstDir, root, filename, keepDirectories)
+
+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))
+  cal = imp.getCalibration()
+
+
+
+ # 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'] = 20.0
+  settings.trackerSettings['ALLOW_TRACK_SPLITTING'] = True
+  settings.trackerSettings['SPLITTING_MAX_DISTANCE'] = 20.0
+  settings.trackerSettings['ALLOW_TRACK_MERGING'] = False
+  settings.trackerSettings['MERGING_MAX_DISTANCE'] = 10.0
+
+
+# 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", "TRACK_MAX_SPEED", "NUMBER_SPLITS", "TRACK_DURATION", "TRACK_DISPLACEMENT" ])
+
+  	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"])
+
+  		for id in model.getTrackModel().trackIDs(True):
+
+   	 # Fetch the track feature from the feature model.
+  			v = fm.getTrackFeature(id, 'TRACK_MEAN_SPEED')
+  			ms = fm.getTrackFeature(id, 'TRACK_MAX_SPEED')
+  			s = fm.getTrackFeature(id, 'NUMBER_SPLITS')
+  			d = fm.getTrackFeature(id, 'TRACK_DURATION')
+  			e = fm.getTrackFeature(id, 'TRACK_DISPLACEMENT')
+  			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')
+  				writer2.writerow([str(sid), str(x), str(y), str(id), str(t)])
+run()