Expose tracking model settings as env variables in settings

vanvalenlab · Jul 30, 2019 · ceecf01 · ceecf01
1 parent 51d9c95
commit ceecf01
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Showing 2 changed files with 24 additions and 10 deletions.
diff --git a/redis_consumer/consumers.py b/redis_consumer/consumers.py
@@ -908,12 +908,12 @@ def _get_tracker(self, redis_hash, hvalues, raw, segmented):
         features = {'appearance', 'distance', 'neighborhood', 'regionprop'}
         tracker = tracking.cell_tracker(raw, segmented,
                                         tracking_model,
-                                        max_distance=50,
-                                        track_length=5,
-                                        division=0.9,
-                                        birth=0.95,
-                                        death=0.95,
-                                        neighborhood_scale_size=30,
+                                        max_distance=settings.MAX_DISTANCE,
+                                        track_length=settings.TRACK_LENGTH,
+                                        division=settings.DIVISION,
+                                        birth=settings.BIRTH,
+                                        death=settings.DEATH,
+                                        neighborhood_scale_size=settings.NEIGHBORHOOD_SCALE_SIZE,
                                         features=features)
 
         self.logger.debug('Created tracker!')
@@ -980,10 +980,10 @@ def _load_data(self, hvalues, subdir, fname):
                     'identity_upload': self.hostname,
                     'input_file_name': upload_file_name,
                     'original_name': segment_fname,
-                    'model_name': 'HeLaS3watershed',
-                    'model_version': 2,
-                    'postprocess_function': 'watershed',
-                    'cuts': 0,
+                    'model_name': settings.MODEL_NAME,
+                    'model_version': settings.MODEL_VERSION,
+                    'postprocess_function': settings.POSTPROCESS_FUNCTION,
+                    'cuts': settings.CUTS,
                     'status': 'new',
                     'created_at': current_timestamp,
                     'updated_at': current_timestamp,

diff --git a/redis_consumer/settings.py b/redis_consumer/settings.py
@@ -124,3 +124,17 @@ def _strip(x):
         'retinanet': processing.retinanet_to_label_image
     },
 }
+
+# Tracking settings
+MODEL_NAME = config('MODEL_NAME', default='HeLaS3watershed')
+MODEL_VERSION = config('MODEL_VERSION', default=2)
+POSTPROCESS_FUNCTION = config('POSTPROCESS_FUNCTION', default='watershed')
+CUTS = config('CUTS', default=0)
+
+# tracking.cell_tracker settings
+MAX_DISTANCE = config('MAX_DISTANCE', default=50)
+TRACK_LENGTH = config('TRACK_LENGTH', default=5)
+DIVISION = config('DIVISION', default=0.9)
+BIRTH = config('BIRTH', default=0.95)
+DEATH = config('DEATH', default=0.95)
+NEIGHBORHOOD_SCALE_SIZE = config('NEIGHBORHOOD_SCALE_SIZE', default=30)