From c3245f023d757d2afcb240fb53f0a0f61ac8e722 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 20 Aug 2021 16:13:08 +0100
Subject: [PATCH] MNT: Apply same minor optimisations to other im* scripts -
avoid expensive imports
---
fsl/scripts/imglob.py | 3 +--
fsl/scripts/imln.py | 31 +++++++++++++++++--------------
fsl/scripts/imrm.py | 20 ++++++++++----------
fsl/scripts/imtest.py | 26 +++++++++++++++-----------
fsl/scripts/remove_ext.py | 20 ++++++++++----------
5 files changed, 53 insertions(+), 47 deletions(-)
diff --git a/fsl/scripts/imglob.py b/fsl/scripts/imglob.py
index 8c8c631e2..87314e8fb 100644
--- a/fsl/scripts/imglob.py
+++ b/fsl/scripts/imglob.py
@@ -11,7 +11,6 @@ NIFTI/ANALYZE image files.
import sys
import glob
-import itertools as it
import fsl.utils.path as fslpath
@@ -30,7 +29,7 @@ exts = ['.nii.gz', '.nii', '.img', '.hdr', '.img.gz', '.hdr.gz']
"""List of supported image file extensions. """
-groups = [('.hdr', '.img'), ('.hdr.gz', '.img.gz')]
+groups = [('.hdr', '.img'), ('.hdr.gz', '.img.gz')]
"""List of known image file groups (image/header file pairs). """
diff --git a/fsl/scripts/imln.py b/fsl/scripts/imln.py
index 88955f3cb..74bcaf395 100644
--- a/fsl/scripts/imln.py
+++ b/fsl/scripts/imln.py
@@ -17,19 +17,22 @@ to NIFTI image files.
import os.path as op
import os
import sys
-import warnings
-
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
-
+# 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',
+ '.mnc', '.mnc.gz']
+"""List of file extensions that are supported by ``imtest``.
+"""
-ALLOWED_EXTENSIONS = fslimage.ALLOWED_EXTENSIONS + ['.mnc', '.mnc.gz']
-"""List of file extensions that are supported by ``imln``. """
+groups = [('.hdr', '.img'), ('.hdr.gz', '.img.gz')]
+"""List of known image file groups (image/header file pairs). """
usage = """
@@ -50,8 +53,8 @@ def main(argv=None):
return 1
target, linkbase = argv
- target = fslpath.removeExt(target, ALLOWED_EXTENSIONS)
- linkbase = fslpath.removeExt(linkbase, ALLOWED_EXTENSIONS)
+ target = fslpath.removeExt(target, exts)
+ linkbase = fslpath.removeExt(linkbase, exts)
# Target must exist, so we can
# infer the correct extension(s).
@@ -59,8 +62,8 @@ def main(argv=None):
# (e.g. a.img without a.hdr).
try:
targets = fslpath.getFileGroup(target,
- allowedExts=ALLOWED_EXTENSIONS,
- fileGroups=fslimage.FILE_GROUPS,
+ allowedExts=exts,
+ fileGroups=groups,
unambiguous=True)
except Exception as e:
print(f'Error: {e}')
@@ -70,7 +73,7 @@ def main(argv=None):
if not op.exists(target):
continue
- ext = fslpath.getExt(target, ALLOWED_EXTENSIONS)
+ ext = fslpath.getExt(target, exts)
link = f'{linkbase}{ext}'
try:
diff --git a/fsl/scripts/imrm.py b/fsl/scripts/imrm.py
index bd8110332..7d8287b6e 100644
--- a/fsl/scripts/imrm.py
+++ b/fsl/scripts/imrm.py
@@ -13,22 +13,22 @@ import itertools as it
import os.path as op
import os
import sys
-import warnings
-
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: imrm <list of image names to remove>
NB: filenames can be basenames or not
""".strip()
-ALLOWED_EXTENSIONS = fslimage.ALLOWED_EXTENSIONS + ['.mnc', '.mnc.gz']
+# This list is 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',
+ '.mnc', '.mnc.gz']
"""List of file extensions that are removed by ``imrm``. """
@@ -42,9 +42,9 @@ def main(argv=None):
print(usage)
return 1
- prefixes = [fslpath.removeExt(p, ALLOWED_EXTENSIONS) for p in argv]
+ prefixes = [fslpath.removeExt(p, exts) for p in argv]
- for prefix, ext in it.product(prefixes, ALLOWED_EXTENSIONS):
+ for prefix, ext in it.product(prefixes, exts):
path = f'{prefix}{ext}'
diff --git a/fsl/scripts/imtest.py b/fsl/scripts/imtest.py
index f03c28442..b0fed7c27 100644
--- a/fsl/scripts/imtest.py
+++ b/fsl/scripts/imtest.py
@@ -11,18 +11,22 @@ not, without having to know the file suffix (.nii, .nii.gz, etc).
import os.path as op
import sys
-import warnings
-
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
+# 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',
+ '.mnc', '.mnc.gz']
+"""List of file extensions that are supported by ``imtest``.
+"""
-ALLOWED_EXTENSIONS = fslimage.ALLOWED_EXTENSIONS + ['.mnc', '.mnc.gz']
-"""List of file extensions that are supported by ``imln``. """
+groups = [('.hdr', '.img'), ('.hdr.gz', '.img.gz')]
+"""List of known image file groups (image/header file pairs). """
def main(argv=None):
@@ -38,7 +42,7 @@ def main(argv=None):
print('0')
return 0
- path = fslpath.removeExt(argv[0], ALLOWED_EXTENSIONS)
+ path = fslpath.removeExt(argv[0], exts)
path = op.realpath(path)
# getFileGroup will raise an error
@@ -47,8 +51,8 @@ def main(argv=None):
# image) does not exist
try:
fslpath.getFileGroup(path,
- allowedExts=ALLOWED_EXTENSIONS,
- fileGroups=fslimage.FILE_GROUPS,
+ allowedExts=exts,
+ fileGroups=groups,
unambiguous=True)
print('1')
except fslpath.PathError:
diff --git a/fsl/scripts/remove_ext.py b/fsl/scripts/remove_ext.py
index fc21094ff..54e62f573 100644
--- a/fsl/scripts/remove_ext.py
+++ b/fsl/scripts/remove_ext.py
@@ -6,22 +6,22 @@
#
-import sys
-import warnings
-
+import sys
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: remove_ext <list of image paths to remove extension from>
""".strip()
-ALLOWED_EXTENSIONS = fslimage.ALLOWED_EXTENSIONS + ['.mnc', '.mnc.gz']
+# This list is 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',
+ '.mnc', '.mnc.gz']
"""List of file extensions that are removed by ``remove_ext``. """
@@ -40,7 +40,7 @@ def main(argv=None):
removed = []
for path in argv:
- removed.append(fslpath.removeExt(path, ALLOWED_EXTENSIONS))
+ removed.append(fslpath.removeExt(path, exts))
print(' '.join(removed))
--
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