Alphebatize imports and use splitext

caiman/base/movies.py

@@ -34,8 +34,8 @@
 import caiman.base.traces
 import caiman.mmapping
 import caiman.summary_images
-import caiman.utils.visualization
 import caiman.utils.sbx_utils
+import caiman.utils.visualization
 
 try:
     cv2.setNumThreads(0)
@@ -1311,7 +1311,7 @@ def load(file_name: Union[str, list[str]],
         logging.error('movies.py:load(): channel parameter is not supported for single movie input')
 
     if os.path.exists(file_name):
-        _, extension = os.path.splitext(file_name)[:2]
+        basename, extension = os.path.splitext(file_name)
 
         extension = extension.lower()
         if extension == '.mat':
@@ -1576,8 +1576,8 @@ def load(file_name: Union[str, list[str]],
 
         elif extension == '.sbx':
             logging.debug('sbx')
-            meta_data = caiman.utils.sbx_utils.sbx_meta_data(file_name[:-4])
-            input_arr = caiman.utils.sbx_utils.sbxread(file_name[:-4], subindices)
+            meta_data = caiman.utils.sbx_utils.sbx_meta_data(basename)
+            input_arr = caiman.utils.sbx_utils.sbxread(basename, subindices)
             return movie(input_arr, fr=fr,
                          file_name=os.path.split(file_name)[-1],
                          meta_data=meta_data).astype(outtype)

caiman/tests/test_sbx.py

@@ -1,12 +1,12 @@
 #!/usr/bin/env python
 
-import os
-
 import numpy as np
 import numpy.testing as npt
+import os
+
 import caiman as cm
-from caiman.utils import sbx_utils
 from caiman.paths import caiman_datadir
+from caiman.utils import sbx_utils
 
 testdata_path = os.path.join(caiman_datadir(), 'testdata')
 

caiman/utils/sbx_utils.py

@@ -4,13 +4,12 @@
 Utility functions for Neurolabware Scanbox files (.sbx)
 """
 
-import os
 import logging
-from typing import Iterable
-
 import numpy as np
+import os
 import scipy
 import tifffile
+from typing import Iterable
 
 DimSubindices = Iterable[int] | slice
 FileSubindices = DimSubindices | Iterable[DimSubindices]    # can have inds for just frames or also for y, x, z
@@ -98,8 +97,9 @@ def sbx_to_tif(filename: str, fileout: str | None = None, subindices: FileSubind
             how many frames to load into memory at once (None = load the whole thing)
     """
     # Check filenames
-    if '.sbx' in filename:
-        filename = filename[:-4]
+    basename, ext = os.path.splitext(filename)
+    if ext == '.sbx':
+        filename = basename
 
     if fileout is None:
         fileout = filename + '.tif'
@@ -207,9 +207,9 @@ def sbx_shape(filename: str, info: dict | None = None) -> tuple[int, int, int, i
 
     Output: tuple (chans, X, Y, Z, frames) representing shape of scanbox data
     """
-    # Check if contains .sbx and if so just truncate
-    if '.sbx' in filename:
-        filename = filename[:-4]
+    basename, ext = os.path.splitext(filename)
+    if ext == '.sbx':
+        filename = basename    
 
     # Load info
     if info is None:
@@ -288,8 +288,9 @@ def sbx_meta_data(filename: str):
         filename: str
             filename should be full path excluding .sbx
     """
-    if '.sbx' in filename:
-        filename = filename[:-4]
+    basename, ext = os.path.splitext(filename)
+    if ext == '.sbx':
+        filename = basename
 
     info = loadmat_sbx(filename + '.mat')['info']
 
@@ -380,10 +381,9 @@ def _sbxread_helper(filename: str, subindices: FileSubindices = slice(None), cha
         chunk_size: int | None
             how many frames to load into memory at once (None = load the whole thing)
     """
-
-    # Check if contains .sbx and if so just truncate
-    if '.sbx' in filename:
-        filename = filename[:-4]
+    basename, ext = os.path.splitext(filename)
+    if ext == '.sbx':
+        filename = basename
 
     # Normalize so subindices is a list over dimensions
     if isinstance(subindices, slice) or np.isscalar(subindices[0]):