Move to the use of "atlas space" instead of "standard space" (#53)

* move from standard to atlas space naming

* fix typo

README.md

@@ -49,7 +49,7 @@ This is typically only used in other software, but you can enable it yourself:
 * Open napari
 * Navigate to `Plugins` -> `Plugin Call Order`
 * In the `Plugin Sorter` window, select `napari_get_reader` from the `select hook...` dropdown box
-* Drag `brainreg_read_dir_standard_space` (the atlas space viewer plugin) above `brainreg_read_dir` (the normal plugin) to ensure that the atlas space plugin is used preferentially.
+* Drag `brainreg_read_dir_atlas_space` (the atlas space viewer plugin) above `brainreg_read_dir` (the normal plugin) to ensure that the atlas space plugin is used preferentially.
 
 
 ### cellfinder

brainglobe_napari_io/brainreg/reader_dir_standard_space.py → brainglobe_napari_io/brainreg/reader_dir_atlas_space.py

@@ -12,7 +12,7 @@
 PathOrPaths = Union[List[os.PathLike], os.PathLike]
 
 
-def brainreg_read_dir_standard_space(path: PathOrPaths) -> Optional[Callable]:
+def brainreg_read_dir_atlas_space(path: PathOrPaths) -> Optional[Callable]:
     """A basic implementation of the napari_get_reader hook specification.
 
     Parameters
@@ -69,7 +69,7 @@ def reader_function(path: os.PathLike) -> List[LayerDataTuple]:
         path,
         layers,
         search_string="downsampled_standard",
-        exlusion_string="downsampled_standard.tiff",
+        exclusion_string="downsampled_standard.tiff",
     )
     layers.append(
         (

brainglobe_napari_io/brainreg/utils.py

@@ -25,16 +25,16 @@ def load_additional_downsampled_channels(
     layers: List[LayerDataTuple],
     extension: str = ".tiff",
     search_string: str = "downsampled_",
-    exlusion_string: str = "downsampled_standard",
+    exclusion_string: str = "downsampled_standard",
 ) -> List[LayerDataTuple]:
     # Get additional downsampled channels, but not main one, and not those
-    # in standard space
+    # in atlas space
 
     for file in path.iterdir():
         if (
             (file.suffix == extension)
             and file.name.startswith(search_string)
-            and not file.name.startswith(exlusion_string)
+            and not file.name.startswith(exclusion_string)
         ):
             print(
                 f"Found additional downsampled image: {file.name}, "

brainglobe_napari_io/napari.yaml

@@ -6,9 +6,9 @@ contributions:
     title: Brainreg Read Directory
     python_name: brainglobe_napari_io.brainreg.reader_dir:brainreg_read_dir
 
-  - id: brainglobe-napari-io.brainreg_read_dir_standard_space
-    title: Brainreg Read Directory Standard Space
-    python_name: brainglobe_napari_io.brainreg.reader_dir_standard_space:brainreg_read_dir_standard_space
+  - id: brainglobe-napari-io.brainreg_read_dir_atlas_space
+    title: Brainreg Read Directory Atlas Space
+    python_name: brainglobe_napari_io.brainreg.reader_dir_atlas_space:brainreg_read_dir_atlas_space
 
   - id: brainglobe-napari-io.cellfinder_read_dir
     title: Cellfinder Read Directory
@@ -29,7 +29,7 @@ contributions:
     - '*.tiff'
     accepts_directories: true
 
-  - command: brainglobe-napari-io.brainreg_read_dir_standard_space
+  - command: brainglobe-napari-io.brainreg_read_dir_atlas_space
     filename_patterns:
       - '*.tiff'
     accepts_directories: true