Refactor to use ImageIOLoadException from brainglobe_utils (#186)

* refactor to use ImageIOLoadException from brainglobe_utils

* update brainglobe-utils version

Author: K-Meech

brainreg/core/exceptions.py

@@ -6,10 +6,6 @@
 from brainglobe_utils.image_io import load_any
 
 from brainreg.core.backend.niftyreg.run import run_niftyreg
-from brainreg.core.exceptions import (
-    LoadFileException,
-    path_is_folder_with_one_tiff,
-)
 from brainreg.core.utils.boundaries import boundaries
 from brainreg.core.utils.volume import calculate_volumes
 
@@ -31,9 +27,6 @@ def main(
     save_original_orientation=False,
     brain_geometry="full",
 ):
-    if path_is_folder_with_one_tiff(target_brain_path):
-        raise LoadFileException("single_tiff")
-
     atlas = BrainGlobeAtlas(atlas)
     source_space = bg.AnatomicalSpace(data_orientation)
 
@@ -54,18 +47,15 @@ def main(
 
     logging.info("Loading raw image data")
 
-    try:
-        target_brain = load_any(
-            target_brain_path,
-            scaling[1],
-            scaling[2],
-            scaling[0],
-            load_parallel=load_parallel,
-            sort_input_file=sort_input_file,
-            n_free_cpus=n_free_cpus,
-        )
-    except ValueError as error:
-        raise LoadFileException(None, error) from None
+    target_brain = load_any(
+        target_brain_path,
+        scaling[1],
+        scaling[2],
+        scaling[0],
+        load_parallel=load_parallel,
+        sort_input_file=sort_input_file,
+        n_free_cpus=n_free_cpus,
+    )
 
     target_brain = bg.map_stack_to(
         data_orientation, atlas.metadata["orientation"], target_brain

brainreg/core/main.py

@@ -21,7 +21,7 @@ requires-python = ">=3.9"
 dependencies = [
     "brainglobe-atlasapi>=2.0.1",
     "brainglobe-space>=1.0.0",
-    "brainglobe-utils>=0.4.0",
+    "brainglobe-utils>=0.4.2",
     "fancylog",
     "numpy",
     "scikit-image",

pyproject.toml

@@ -2,9 +2,9 @@
 from pathlib import Path
 
 import pytest
+from brainglobe_utils.image_io.utils import ImageIOLoadException
 
 from brainreg.core.cli import main as brainreg_run
-from brainreg.core.exceptions import LoadFileException
 
 test_data_dir = Path(__file__).parent.parent.parent / "data"
 one_tiff_data_dir = test_data_dir / "input" / "exceptions" / "one_tiff"
@@ -45,13 +45,13 @@ def test_mismatched_dims_error(test_output_dir):
     )
     sys.argv = brainreg_args
 
-    with pytest.raises(LoadFileException) as e:
+    with pytest.raises(ImageIOLoadException) as e:
         brainreg_run()
 
     assert (
-        "File failed to load with brainglobe_utils.image_io. "
-        "Ensure all image files contain the "
-        "same number of pixels. Full traceback above." in e.value.message
+        "Attempted to load an image sequence where individual 2D "
+        "images did not have the same shape. Please ensure all image "
+        "files contain the same number of pixels." in e.value.message
     )
 
 
@@ -60,7 +60,7 @@ def test_one_tiff_data_dir(test_output_dir):
     Test case in which a single 2D image is in the folder,
     which is not supported.
 
-    Some tiffs load as a zero-size array, wheras others
+    Some tiffs load as a zero-size array, whereas others
     load as a 2D array (well, 3D array with a singleton).
     Test both cases here.
     """
@@ -70,7 +70,7 @@ def test_one_tiff_data_dir(test_output_dir):
 
     sys.argv = brainreg_args
 
-    with pytest.raises(LoadFileException) as e:
+    with pytest.raises(ImageIOLoadException) as e:
         brainreg_run()
 
     assert (