Commit 8c69d1bb authored by Paul McCarthy's avatar Paul McCarthy 🚵
Browse files

MNT: Improve imglob performance by avoiding expensive imports (numpy/nibabel/etc)

parent 2306f558
......@@ -10,14 +10,10 @@ NIFTI/ANALYZE image files.
import sys
import warnings
import glob
import itertools as it
import fsl.utils.path as fslpath
# See atlasq.py for explanation
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=FutureWarning)
import fsl.data.image as fslimage
usage = """
Usage: imglob [-extension/extensions] <list of names>
......@@ -25,8 +21,17 @@ Usage: imglob [-extension/extensions] <list of names>
-extensions for image list with full extensions
""".strip()
exts = fslimage.ALLOWED_EXTENSIONS
groups = fslimage.FILE_GROUPS
# The lists below are defined in the
# fsl.data.image class, but are duplicated
# here for performance (to avoid import of
# nibabel/numpy/etc).
exts = ['.nii.gz', '.nii', '.img', '.hdr', '.img.gz', '.hdr.gz']
"""List of supported image file extensions. """
groups = [('.hdr', '.img'), ('.hdr.gz', '.img.gz')]
"""List of known image file groups (image/header file pairs). """
def imglob(paths, output=None):
......@@ -76,8 +81,10 @@ def imglob(paths, output=None):
# hdr and img and otherwise) that match
for path in paths:
try:
path = fslimage.removeExt(path)
imgfiles.extend(fslimage.addExt(path, unambiguous=False))
path = fslpath.removeExt(path, allowedExts=exts)
imgfiles.extend(fslpath.addExt(path,
allowedExts=exts,
unambiguous=False))
except fslpath.PathError:
continue
......
......@@ -37,8 +37,6 @@ import re
from typing import Sequence, Tuple, Union
from fsl.utils.platform import platform
PathLike = Union[str, pathlib.Path]
......@@ -596,6 +594,7 @@ def winpath(path):
This requires WSL2 which supports the ``\\wsl$\\`` network path.
wslpath is assumed to be an absolute path.
"""
from fsl.utils.platform import platform # pylint: disable=import-outside-toplevel # noqa: E501
if not platform.fslwsl:
return path
else:
......
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