copilot and robert address

Author: Hendrik-code

TPTBox/core/np_utils.py

@@ -462,10 +462,11 @@ def np_dilate_msk_euclid(arr: np.ndarray, n_pixel: int = 3, use_crop=True, label
 
     Assigns each newly covered voxel to the nearest existing label.
     """
+    arr_bin = arr.copy()
+    if labels is not None:
+        arr_bin[np_isin(arr_bin, labels, invert=True)] = 0
+
     if use_crop:
-        arr_bin = arr.copy()
-        if labels is not None:
-            arr_bin[np_isin(arr_bin, labels, invert=True)] = 0
         crop = np_bbox_binary(arr_bin, px_dist=1 + n_pixel, raise_error=False)
         arrc = arr[crop]
     else:

TPTBox/core/poi.py

@@ -1304,9 +1304,9 @@ def calc_centroids(
         coords = tqdm(coords)
     for i, out_coord in coords:
         if second_stage == -1:
-            ctd_list[first_stage, i] = out_coord
+            ctd_list[first_stage, int(i)] = out_coord
         else:
-            ctd_list[i, second_stage] = out_coord
+            ctd_list[int(i), second_stage] = out_coord
     return POI(ctd_list, **msk_nii._extract_affine(), **args)
 
 

TPTBox/tests/speedtests/speedtest.py

@@ -54,6 +54,7 @@ def speed_test(
     functions: list[Callable],
     repeats: int = 20,
     assert_equal_function: Callable | None = None,
+    print_first_speed_output: bool = False,
     *args,
     **kwargs,
 ):
@@ -72,7 +73,7 @@ def speed_test(
             *args,
             functions=functions,
             assert_equal_function=assert_equal_function,
-            print_output=repeat_idx == 0,
+            print_output=repeat_idx == 0 if print_first_speed_output else False,
             **kwargs,
         )
         for k, v in time_measures.items():

TPTBox/tests/speedtests/speedtest_bids_filter.py

@@ -10,7 +10,7 @@
     # build N real BIDS_FILE candidates once (touches a tempdir; not part of the timed comparison)
     tmp = Path(tempfile.mkdtemp())
     formats = ["T1w", "T2w", "ct", "msk", "dixon"]
-    N = 2000
+    N = 100
     CANDIDATES = []
     for i in range(N):
         fmt = formats[i % len(formats)]
@@ -37,7 +37,7 @@ def get_input():
 
     print(f"\n=== Searchquery.filter flatten mode ({N} candidates, keep {keep}) ===")
     speed_test(
-        repeats=12,
+        repeats=25,
         get_input_func=get_input,
         functions=[old_filter, new_filter],
         assert_equal_function=lambda x, y: [f.BIDS_key for f in x] == [f.BIDS_key for f in y],