diff --git a/brainreg/core/backend/niftyreg/run.py b/brainreg/core/backend/niftyreg/run.py index 1c0d970..32d4966 100644 --- a/brainreg/core/backend/niftyreg/run.py +++ b/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 diff --git a/brainreg/core/backend/niftyreg/utils.py b/brainreg/core/backend/niftyreg/utils.py index aef067b..fd5ed15 100644 --- a/brainreg/core/backend/niftyreg/utils.py +++ b/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): diff --git a/brainreg/core/main.py b/brainreg/core/main.py index fe893fc..2f8cab2 100644 --- a/brainreg/core/main.py +++ b/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 diff --git a/brainreg/core/utils/boundaries.py b/brainreg/core/utils/boundaries.py index 6531d2b..88f6426 100644 --- a/brainreg/core/utils/boundaries.py +++ b/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 diff --git a/brainreg/core/utils/volume.py b/brainreg/core/utils/volume.py index cb47e1f..9984de6 100644 --- a/brainreg/core/utils/volume.py +++ b/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 diff --git a/pyproject.toml b/pyproject.toml index a82ca4e..078acf8 100644 --- a/pyproject.toml +++ b/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", diff --git a/tests/tests/test_integration/utils.py b/tests/tests/test_integration/utils.py index a99f5d2..8715e5a 100644 --- a/tests/tests/test_integration/utils.py +++ b/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 diff --git a/tests/tests/test_unit/test_exceptions.py b/tests/tests/test_unit/test_exceptions.py index 651af06..e82545d 100644 --- a/tests/tests/test_unit/test_exceptions.py +++ b/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