Update main wtih dev changes

.github/workflows/test_and_deploy.yml

@@ -49,6 +49,23 @@ jobs:
         with:
           qt: true
 
+      # cache atlases needed by the tests
+      - name: Cache Atlases
+        id: atlas-cache
+        uses: actions/cache@v3
+        with:
+          path: | # ensure we don't cache any interrupted atlas download and extraction!
+            ~/.brainglobe/*
+            !~/.brainglobe/atlas.tar.gz
+          key: ${{ runner.os }}-cached-atlases
+          enableCrossOsArchive: false # ~ and $HOME evaluate to different places across OSs!
+
+      - if: ${{ steps.atlas-cache.outputs.cache-hit == 'true' }}
+        name: List files in brainglobe data folder # good to be able to sanity check that user data is as expected
+        run: |
+          ls -af ~/.brainglobe/
+
+
       # Run tests
       - uses: neuroinformatics-unit/actions/test@v2
         with:

.gitignore

@@ -82,3 +82,6 @@ venv/
 
 # written by setuptools_scm
 **/_version.py
+
+# Elastix related files
+/Logs/

brainglobe_registration/elastix/register.py

@@ -1,7 +1,8 @@
-from typing import List
+from typing import List, Tuple
 
 import itk
 import numpy as np
+import numpy.typing as npt
 from brainglobe_atlasapi import BrainGlobeAtlas
 
 
@@ -28,28 +29,30 @@ def run_registration(
     atlas_image,
     moving_image,
     annotation_image,
-    parameter_lists: List[tuple[str, dict]],
-) -> tuple[np.ndarray, itk.ParameterObject, np.ndarray]:
+    parameter_lists: List[Tuple[str, dict]],
+) -> Tuple[npt.NDArray, itk.ParameterObject, npt.NDArray]:
     """
     Run the registration process on the given images.
 
     Parameters
     ----------
-    atlas_image : np.ndarray
+    atlas_image : npt.NDArray
         The atlas image.
-    moving_image : np.ndarray
+    moving_image : npt.NDArray
         The moving image.
-    annotation_image : np.ndarray
+    annotation_image : npt.NDArray
         The annotation image.
     parameter_lists : List[tuple[str, dict]], optional
         The list of parameter lists, by default None
 
     Returns
     -------
-    np.ndarray
+    npt.NDArray
         The result image.
     itk.ParameterObject
         The result transform parameters.
+    npt.NDArray
+        The transformed annotation image.
     """
     # convert to ITK, view only
     atlas_image = itk.GetImageViewFromArray(atlas_image).astype(itk.F)