Update use of brainglobe_utils image IO submodule (#199)

Author: adamltyson

brainreg/core/backend/niftyreg/run.py

@@ -7,7 +7,8 @@
 from brainglobe_atlasapi import BrainGlobeAtlas
 from brainglobe_utils.general.system import delete_directory_contents
 from brainglobe_utils.image.scale import scale_and_convert_to_16_bits
-from brainglobe_utils.image_io import load_any, to_tiff
+from brainglobe_utils.IO.image.load import load_any
+from brainglobe_utils.IO.image.save import to_tiff
 
 from brainreg.core.backend.niftyreg.parameters import RegistrationParams
 from brainreg.core.backend.niftyreg.paths import NiftyRegPaths

brainreg/core/backend/niftyreg/utils.py

@@ -1,5 +1,5 @@
 import numpy as np
-from brainglobe_utils.image_io import to_nii
+from brainglobe_utils.IO.image.save import to_nii
 
 
 def save_nii(stack, atlas_pixel_sizes, dest_path):

brainreg/core/main.py

@@ -3,7 +3,7 @@
 import brainglobe_space as bg
 from brainglobe_atlasapi import BrainGlobeAtlas
 from brainglobe_utils.general.system import get_num_processes
-from brainglobe_utils.image_io import load_any
+from brainglobe_utils.IO.image.load import load_any
 
 from brainreg.core.backend.niftyreg.run import run_niftyreg
 from brainreg.core.utils.boundaries import boundaries

brainreg/core/utils/boundaries.py

@@ -1,7 +1,8 @@
 import logging
 
 import numpy as np
-from brainglobe_utils.image_io import load_any, to_tiff
+from brainglobe_utils.IO.image.load import load_any
+from brainglobe_utils.IO.image.save import to_tiff
 from skimage.segmentation import find_boundaries
 
 

brainreg/core/utils/volume.py

@@ -9,7 +9,7 @@
 
 import numpy as np
 import pandas as pd
-from brainglobe_utils.image_io import load_any
+from brainglobe_utils.IO.image.load import load_any
 from brainglobe_utils.pandas.misc import initialise_df, safe_pandas_concat
 
 

pyproject.toml

@@ -21,7 +21,7 @@ requires-python = ">=3.9"
 dependencies = [
     "brainglobe-atlasapi>=2.0.1",
     "brainglobe-space>=1.0.0",
-    "brainglobe-utils>=0.4.3",
+    "brainglobe-utils>=0.5.0",
     "fancylog",
     "numpy",
     "scikit-image",

tests/tests/test_integration/utils.py

@@ -2,7 +2,7 @@
 
 import numpy as np
 import pandas as pd
-from brainglobe_utils.image_io import load_any
+from brainglobe_utils.IO.image.load import load_any
 
 relative_tolerance = 0.01
 absolute_tolerance = 10

tests/tests/test_unit/test_exceptions.py

@@ -2,7 +2,7 @@
 from pathlib import Path
 
 import pytest
-from brainglobe_utils.image_io.utils import ImageIOLoadException
+from brainglobe_utils.IO.image.utils import ImageIOLoadException
 
 from brainreg.core.cli import main as brainreg_run