Expose max_distance in cli

weigertlab · Jul 4, 2024 · db86a54 · db86a54
1 parent 2918a7b
commit db86a54
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Showing 2 changed files with 9 additions and 1 deletion.
diff --git a/trackastra/cli.py b/trackastra/cli.py
@@ -68,6 +68,13 @@ def cli():
             " https://github.com/weigertlab/trackastra#installation."
         ),
     )
+    p_track.add_argument(
+        "--max-distance",
+        type=float,
+        default=128,
+        help="Maximum distance for linking cells.",
+    )
+
     p_track.add_argument(
         "--device",
         choices=["cuda", "mps", "cpu", "automatic"],
@@ -110,6 +117,7 @@ def _track_from_disk(args):
         args.imgs,
         args.masks,
         mode=args.mode,
+        max_distance=args.max_distance
     )
 
     if args.output_ctc:

diff --git a/trackastra/data/wrfeat.py b/trackastra/data/wrfeat.py
@@ -458,7 +458,7 @@ def get_features(
     imgs = _check_dimensions(imgs, ndim)
     logger.info(f"Extracting features from {len(detections)} detections")
     if n_workers > 0:
-        features = joblib.Parallel(n_jobs=n_workers, backend="multiprocessing")(
+        features = joblib.Parallel(n_jobs=n_workers)(
             joblib.delayed(WRFeatures.from_mask_img)(
                 # New axis for time component
                 mask=mask[np.newaxis, ...],