Apply suggestions from code review

Co-authored-by: Alessandro Felder <[email protected]>

cellfinder/core/detect/filters/plane/classical_filter.py

@@ -14,7 +14,7 @@ def normalize(
 ) -> None:
     """
     Normalizes the 3d tensor so each z-plane is independently scaled to be
-    in the [0, clipping_value] range.
+    in the [0, clipping_value] range (if upscale is `True`) or in the [0,1] (if `upscale` is `False`).
 
     It is done to filtered_planes inplace.
     """

cellfinder/core/detect/filters/plane/plane_filter.py

@@ -148,7 +148,7 @@ def _threshold_planes(
     threshold_value: int,
 ) -> None:
     """
-    Thresholds peaks to those above the mean/std.
+    Sets each plane (in-place) to threshold_value, where the corresponding enhanced_plane > mean + n_sds_above_mean_thresh*std. Each plane will be set to zero elsewhere.
     """
     planes_1d = enhanced_planes.view(enhanced_planes.shape[0], -1)
 

cellfinder/core/tools/threading.py

@@ -1,6 +1,6 @@
 """
 Provides classes that can run a function in another thread or process and
-allows passing data to and from them. It also passes on any exceptions that
+allow passing data to and from the threads/processes. It also passes on any exceptions that
 occur in the secondary thread/sub-process in the main thread or when it
 exits.
 
@@ -36,6 +36,7 @@ def worker(thread: ThreadWithException, power: float):
             # just send the id back
             thread.send_msg_to_mainthread(tensor_id)
 
+	    # we can also handle errors here, which will be re-raised in the main process
             if tensor_id == 7:
                 raise ValueError("I fell asleep")
 

tests/core/test_integration/test_detection.py

@@ -282,10 +282,7 @@ def test_detection_cluster_splitting(
 
 def test_detection_cell_too_large(synthetic_spot_clusters, no_free_cpus):
     """
-    Test cluster splitting for overlapping cells.
-
-    Test filtering/detection on cpu and cuda. Because splitting is only on cpu
-    so make sure if detection is on cuda, splitting still works.
+    Test we detect one big artifact if the signal has a too large foreground structure.
     """
     # max_cell_volume is volume of soma * spread sphere. For values below
     # radius is 7 pixels. So volume is ~1500 pixels