atlas utils testing

brainreg_segment/atlas/utils.py

@@ -2,14 +2,33 @@
 
 
 def lateralise_atlas_image(
-    atlas, hemispheres, left_hemisphere_value=1, right_hemisphere_value=2
+    masked_atlas_annotations,
+    hemispheres,
+    left_hemisphere_value=1,
+    right_hemisphere_value=2,
 ):
-    atlas_left = atlas[hemispheres == left_hemisphere_value]
-    atlas_right = atlas[hemispheres == right_hemisphere_value]
-    return atlas_left, atlas_right
+    """
+    :param masked_atlas_annotations: Masked image of atlas annotations
+    :param hemispheres: Hemispheres image
+    :param left_hemisphere_value: Value encoded in hemispheres image
+    :param right_hemisphere_value: Value encoded in hemispheres image
+    :return: Tuple (left, right) of numpy arrays of values within
+    each hemisphere
+    """
+    annotation_left = masked_atlas_annotations[
+        hemispheres == left_hemisphere_value
+    ]
+    annotation_right = masked_atlas_annotations[
+        hemispheres == right_hemisphere_value
+    ]
+    return annotation_left, annotation_right
 
 
 def get_available_atlases():
+    """
+    Get the available brainglobe atlases
+    :return: Dict of available atlases (["name":version])
+    """
     available_atlases = utils.conf_from_url(
         descriptors.remote_url_base.format("last_versions.conf")
     )

tests/tests/test_unit/test_atlas/test_atlas_utils.py

@@ -0,0 +1,35 @@
+import numpy as np
+from brainreg_segment.atlas import utils as atlas_utils
+
+from bg_atlasapi import BrainGlobeAtlas
+
+atlas_name = "allen_mouse_50um"
+
+
+def test_get_available_atlases():
+    atlases = atlas_utils.get_available_atlases()
+
+    # arbitrary selection of atlases
+    assert float(atlases["allen_mouse_10um"]) >= 0.3
+    assert float(atlases["allen_mouse_25um"]) >= 0.3
+    assert float(atlases["allen_mouse_50um"]) >= 0.3
+    assert float(atlases["mpin_zfish_1um"]) >= 0.4
+
+
+def test_lateralise_atlas_image():
+    atlas = BrainGlobeAtlas(atlas_name)
+
+    mask = np.random.random(atlas.annotation.shape) > 0.7
+    masked_annotations = mask * atlas.annotation
+    annotations_left, annotations_right = atlas_utils.lateralise_atlas_image(
+        masked_annotations,
+        atlas.hemispheres,
+        left_hemisphere_value=atlas.left_hemisphere_value,
+        right_hemisphere_value=atlas.right_hemisphere_value,
+    )
+
+    # not the best way to test this is functioning properly
+    total_vals_in = np.prod(mask.shape)
+    total_vals_out = len(annotations_left) + len(annotations_right)
+
+    assert total_vals_in == total_vals_out