Update use of brainio to brainglobe-utils (#288)

brainglobe · May 15, 2024 · 23abdcc · 23abdcc
1 parent 1fd95db
commit 23abdcc
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Showing 3 changed files with 3 additions and 8 deletions.
diff --git a/brainglobe_atlasapi/atlas_generation/atlas_scripts/humanatlas.py b/brainglobe_atlasapi/atlas_generation/atlas_scripts/humanatlas.py
@@ -8,11 +8,9 @@
 import treelib
 import urllib3
 from allensdk.core.structure_tree import StructureTree
-from brainio import brainio
+from brainglobe_utils.IO.image.load import load_any
 from rich.progress import track
 
-# import sys
-# sys.path.append("./")
 from brainglobe_atlasapi.atlas_generation.mesh_utils import (
     Region,
     create_region_mesh,
@@ -99,8 +97,8 @@ def prune_tree(tree):
     # ---------------- #
     #   GET TEMPLATE   #
     # ---------------- #
-    annotation = brainio.load_any(annotations_image)  # shape (394, 466, 378)
-    anatomy = brainio.load_any(anatomy_image)  # shape (394, 466, 378)
+    annotation = load_any(annotations_image)  # shape (394, 466, 378)
+    anatomy = load_any(anatomy_image)  # shape (394, 466, 378)
 
     # Remove weird artefact
     annotation = annotation[:200, :, :]

diff --git a/brainglobe_atlasapi/atlas_generation/atlas_scripts/kim_mouse.py b/brainglobe_atlasapi/atlas_generation/atlas_scripts/kim_mouse.py
@@ -14,8 +14,6 @@
 from rich.progress import track
 from scipy.ndimage import zoom
 
-# import sys
-# sys.path.append("./")
 from brainglobe_atlasapi import utils
 from brainglobe_atlasapi.atlas_generation.mesh_utils import (
     Region,

diff --git a/brainglobe_atlasapi/atlas_generation/atlas_scripts/perens_lsfm_mouse.py b/brainglobe_atlasapi/atlas_generation/atlas_scripts/perens_lsfm_mouse.py
@@ -11,7 +11,6 @@
 import SimpleITK as sitk
 from rich.progress import track
 
-# from allensdk.core.reference_space_cache import ReferenceSpaceCache
 from brainglobe_atlasapi import utils
 from brainglobe_atlasapi.atlas_generation.mesh_utils import (
     Region,