Load Channels with . in their name

pyproject.toml

@@ -38,6 +38,7 @@ scikit-image = "0.*"
 xarray = "*"
 xmltodict = "^0.13.0"
 charset-normalizer = "^2.1.1"
+pytest = "^7.4.2"
 
 [tool.poetry.group.test]
 optional = true

src/alpineer/load_utils.py

@@ -121,7 +121,7 @@ def load_imgs_from_tree(
         raise ValueError(f"No fovs found in directory, {data_dir}")
 
     # If the fov provided is a single string (`fov_1` instead of [`fov_1`])
-    if type(fovs) is str:
+    if not isinstance(fovs, list):
         fovs = [fovs]
     if img_sub_folder is None:
         # no img_sub_folder, change to empty string to read directly from base folder
@@ -139,7 +139,9 @@ def load_imgs_from_tree(
     # otherwise, fill channel names with correct file extension
     elif not all([img.endswith(tuple(EXTENSION_TYPES["IMAGE"])) for img in channels]):
         # need this to reorder channels back because list_files may mess up the ordering
-        channels_no_delim = [os.path.splitext(img)[0] for img in channels]
+        # channels_no_delim = [os.path.splitext(img)[0] for img in channels]
+
+        channels_no_delim = io_utils.remove_file_extensions(channels)
 
         all_channels = io_utils.list_files(
             dir_name=os.path.join(data_dir, fovs[0], img_sub_folder),
@@ -148,10 +150,13 @@ def load_imgs_from_tree(
         )
 
         # get the corresponding indices found in channels_no_delim
-        channels_indices = [channels_no_delim.index(chan.split(".")[0]) for chan in all_channels]
+        channels_indices = [
+            channels_no_delim.index(io_utils.remove_file_extensions([chan])[0])
+            for chan in all_channels
+        ]
 
         # verify if channels from user input are present in `all_channels`
-        all_channels_no_delim = [channel.split(".")[0] for channel in all_channels]
+        all_channels_no_delim = io_utils.remove_file_extensions(all_channels)
 
         misc_utils.verify_same_elements(
             all_channels_in_folder=all_channels_no_delim, all_channels_detected=channels_no_delim

tests/load_utils_test.py

@@ -84,6 +84,9 @@ def test_load_imgs_from_tree():
 
         fovs, chans, imgs = test_utils.gen_fov_chan_names(num_fovs=3, num_chans=3, return_imgs=True)
 
+        chans = [f"{chan}.0" for chan in chans]
+        imgs = [img.replace(".tiff", ".0.tiff") for img in imgs]
+
         filelocs, data_xr = test_utils.create_paired_xarray_fovs(
             temp_dir,
             fovs,