From 8c69d1bb1bc698632888cc24a297a99b3e92a3ee Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 20 Aug 2021 16:05:12 +0100
Subject: [PATCH] MNT: Improve imglob performance by avoiding expensive imports
(numpy/nibabel/etc)
---
fsl/scripts/imglob.py | 27 +++++++++++++++++----------
fsl/utils/path.py | 3 +--
2 files changed, 18 insertions(+), 12 deletions(-)
diff --git a/fsl/scripts/imglob.py b/fsl/scripts/imglob.py
index 9aafce906..8c8c631e2 100644
--- a/fsl/scripts/imglob.py
+++ b/fsl/scripts/imglob.py
@@ -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
diff --git a/fsl/utils/path.py b/fsl/utils/path.py
index 09546f4b2..bbaaa206f 100644
--- a/fsl/utils/path.py
+++ b/fsl/utils/path.py
@@ -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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