From 23abdcca41b5c30368a409cd1caa66ef4e5287af Mon Sep 17 00:00:00 2001
From: Adam Tyson <code@adamltyson.com>
Date: Wed, 15 May 2024 14:28:12 +0100
Subject: [PATCH] Update use of brainio to brainglobe-utils (#288)

---
 .../atlas_generation/atlas_scripts/humanatlas.py          | 8 +++-----
 .../atlas_generation/atlas_scripts/kim_mouse.py           | 2 --
 .../atlas_generation/atlas_scripts/perens_lsfm_mouse.py   | 1 -
 3 files changed, 3 insertions(+), 8 deletions(-)

diff --git a/brainglobe_atlasapi/atlas_generation/atlas_scripts/humanatlas.py b/brainglobe_atlasapi/atlas_generation/atlas_scripts/humanatlas.py
index a575bfa3..6f6a54bd 100644
--- 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
index 0482f4fb..93d8b60e 100644
--- 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
index 21d49777..cb70c5ee 100644
--- 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,