Merge pull request #82 from brainglobe/pynrrd

Remove nrrd IO

brainglobe_utils/IO/image/load.py

@@ -7,7 +7,6 @@
 from pathlib import Path
 from typing import Tuple
 
-import nrrd
 import numpy as np
 import tifffile
 from dask import array as da
@@ -50,7 +49,7 @@ def load_any(
     Parameters
     ----------
     src_path : str or pathlib.Path
-        Can be the path of a nifty file, nrrd file, tiff file, tiff files
+        Can be the path of a nifty file, tiff file, tiff files
         folder, or text file containing a list of paths.
 
     x_scaling_factor : float, optional
@@ -136,9 +135,6 @@ def load_any(
             z_scaling_factor,
             anti_aliasing=anti_aliasing,
         )
-    elif src_path.suffix == ".nrrd":
-        logging.debug("Data type is: nrrd")
-        img = load_nrrd(src_path)
     elif src_path.suffix in [".nii", ".nii.gz"]:
         logging.debug("Data type is: NifTI")
         img = load_nii(src_path, as_array=True, as_numpy=as_numpy)
@@ -150,27 +146,6 @@ def load_any(
     return img
 
 
-def load_nrrd(src_path):
-    """
-    Load an .nrrd file as a numpy array.
-
-    Parameters
-    ----------
-    src_path : str or pathlib.Path
-        The path of the image to be loaded.
-
-    Returns
-    -------
-    np.ndarray
-        The loaded brain array.
-    """
-    if isinstance(src_path, Path):
-        src_path = str(src_path.resolve())
-
-    stack, _ = nrrd.read(src_path)
-    return stack
-
-
 def load_img_stack(
     stack_path,
     x_scaling_factor,

brainglobe_utils/IO/image/save.py

@@ -1,7 +1,6 @@
 import warnings
 from pathlib import Path
 
-import nrrd
 import numpy as np
 import tifffile
 
@@ -99,24 +98,6 @@ def to_tiffs(img_volume, path_prefix, path_suffix="", extension=".tif"):
         tifffile.imwrite(dest_path, img)
 
 
-def to_nrrd(img_volume, dest_path):
-    """
-    Save the image volume (numpy array) as nrrd.
-
-    Parameters
-    ----------
-    img_volume : np.ndarray
-        The image to be saved.
-
-    dest_path : str or pathlib.Path
-        The file path where to save the nrrd image.
-    """
-    if isinstance(dest_path, Path):
-        dest_path = str(dest_path.resolve())
-
-    nrrd.write(dest_path, img_volume)
-
-
 def save_any(img_volume, dest_path):
     """
     Save the image volume (numpy array) to the given file path, using the save
@@ -130,7 +111,7 @@ def save_any(img_volume, dest_path):
     dest_path : str or pathlib.Path
         The file path to save the image to.
         Supports directories (will save a sequence of tiffs), .tif, .tiff,
-        .nrrd and .nii.
+        and .nii.
     """
     dest_path = Path(dest_path)
 
@@ -140,9 +121,6 @@ def save_any(img_volume, dest_path):
     elif dest_path.suffix in [".tif", ".tiff"]:
         to_tiff(img_volume, dest_path)
 
-    elif dest_path.suffix == ".nrrd":
-        to_nrrd(img_volume, dest_path)
-
     elif dest_path.suffix == ".nii":
         to_nii(img_volume, dest_path)
 

pyproject.toml

@@ -27,7 +27,6 @@ dependencies = [
     "pandas",
     "psutil",
     "pyarrow",
-    "pynrrd",
     "PyYAML",
     "scikit-image",
     "scipy",
@@ -82,20 +81,6 @@ exclude = ["tests", "docs*"]
 
 [tool.pytest.ini_options]
 addopts = "--cov=brainglobe_utils"
-filterwarnings = [
-    "error",
-    # Emitted by scikit-image on import, see https://github.com/scikit-image/scikit-image/issues/6663
-    # This filter should be removed when scikit-image 0.20 is released
-    "ignore:`np.bool8` is a deprecated alias for `np.bool_`",
-    # Emitted by nptyping, see https://github.com/ramonhagenaars/nptyping/issues/102
-    # for upstream issue
-    "ignore:`np.object0` is a deprecated alias for ``np.object0`",
-    "ignore:`np.int0` is a deprecated alias for `np.intp`",
-    "ignore:`np.uint0` is a deprecated alias for `np.uintp`",
-    "ignore:`np.void0` is a deprecated alias for `np.void`",
-    "ignore:`np.bytes0` is a deprecated alias for `np.bytes_`",
-    "ignore:`np.str0` is a deprecated alias for `np.str_`",
-]
 
 [tool.black]
 target-version = ['py39', 'py310', 'py311']
@@ -115,11 +100,6 @@ select = ["I", "E", "F"]
 [tool.mypy]
 ignore_errors = true
 
-# [[tool.mypy.overrides]]
-# module = ["imlib.cells.*"]
-# ignore_errors = false
-# strict = true
-
 [tool.tox]
 legacy_tox_ini = """
 [tox]

tests/tests/test_IO/test_image_io.py

@@ -276,29 +276,12 @@ def test_nii_read_to_numpy(tmp_path, array_3d):
     np.testing.assert_array_equal(reloaded_array, array_3d)
 
 
-@pytest.mark.parametrize("use_path", [True, False], ids=["Path", "String"])
-def test_nrrd_io(tmp_path, array_3d, use_path):
-    """
-    Test that a 3D image can be written and read correctly as nrrd, using both
-    str and pathlib.Path input.
-    """
-    filename = "test_array.nrrd"
-    if use_path:
-        nrrd_path = tmp_path / filename
-    else:
-        nrrd_path = str(tmp_path / filename)
-
-    save.to_nrrd(array_3d, nrrd_path)
-    assert (load.load_nrrd(nrrd_path) == array_3d).all()
-
-
 @pytest.mark.parametrize("use_path", [True, False], ids=["Path", "String"])
 @pytest.mark.parametrize(
     "file_name",
     [
         "test_array.tiff",
         "test_array.tif",
-        "test_array.nrrd",
         "test_array.nii",
         pytest.param("", id="dir of tiffs"),
     ],