diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 63d17059ddb8552813c9a62504aa555b385a692b..56ce3f6b90c9afe77eabd6b0ea60d5cfad824f5f 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -2,8 +2,8 @@ This document contains the ``fslpy`` release history in reverse chronological
order.
-3.7.0 (Under development)
--------------------------
+3.7.0 (Friday 20th August 2021)
+-------------------------------
Added
@@ -17,6 +17,10 @@ Added
Changed
^^^^^^^
+
+* Performance of the :mod:`.imglob`, :mod:`.imln`, :mod:`imtest`, :mod:`.imrm`
+ and :mod:`.remove_ext` scripts has been improved, by re-organising them to
+ avoid unnecessary and expensive imports such as ``numpy``.
* The default behaviour of the :func:`fsl.utils.run.run` function (and hence
that of all :mod:`fsl.wrappers` functions) has been changed so that the
standard output and error of the called command is now forwarded to the
diff --git a/fsl/scripts/imglob.py b/fsl/scripts/imglob.py
index 1e756dee6f79d5e3f4a5f087ba355c5a795771bd..87314e8fb65eab271ac10a4dd3fe206f016e034c 100644
--- a/fsl/scripts/imglob.py
+++ b/fsl/scripts/imglob.py
@@ -10,14 +10,9 @@ NIFTI/ANALYZE image files.
import sys
-import warnings
+import glob
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 +20,17 @@ 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):
@@ -59,12 +63,27 @@ def imglob(paths, output=None):
imgfiles = []
+ # Expand any wildcard paths if provided.
+ # Depending on the way that imglob is
+ # invoked, this may not get done by the
+ # calling shell.
+ expanded = []
+ for path in paths:
+ if any(c in path for c in '*?[]'):
+ expanded.extend(glob.glob(path))
+ else:
+ expanded.append(path)
+
+ paths = expanded
+
# Build a list of all image files (both
# 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/scripts/imln.py b/fsl/scripts/imln.py
index 88955f3cb36300853f58f276f6e4dedb6ffda18e..74bcaf395cfc46f20fac9e8fcbca74eb306b3cf0 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 bd81103325b6d8dea25f0b88f02c3bbb40555f6c..7d8287b6e937c55f2e95a6f287d3c597c22abf97 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 f03c28442b52ed79f535b12aae444e310cf83bc3..b0fed7c275e547b18e048397c2601f8292cfcc30 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 fc21094ff113576cc808f25fc3dbde1b7f38ff4f..54e62f5732681fd32d33926b2561cf3e4d092af5 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))
diff --git a/fsl/utils/path.py b/fsl/utils/path.py
index 09546f4b2cdf2660e234e49a7b09814232fac83e..bbaaa206f8c995181b139b3d668e0d201d331964 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:
diff --git a/fsl/utils/platform.py b/fsl/utils/platform.py
index 1a49221ad455cfbfe2dace57d483010c2e89f019..3620ef9ade1b8dd8f90da0cb3225a87514e75c17 100644
--- a/fsl/utils/platform.py
+++ b/fsl/utils/platform.py
@@ -111,26 +111,15 @@ class Platform(notifier.Notifier):
self.WX_MAC_CARBON = WX_MAC_CARBON
self.WX_GTK = WX_GTK
- self.__inSSHSession = False
- self.__inVNCSession = False
+ # initialise fsldir - see fsldir.setter
+ self.fsldir = self.fsldir
+
+ # These are all initialised on first access
self.__glVersion = None
self.__glRenderer = None
self.__glIsSoftware = None
self.__fslVersion = None
-
- # initialise fsldir - see fsldir.setter
- self.fsldir = self.fsldir
-
- # Determine if a display is available. We do
- # this once at init (instead of on-demand in
- # the canHaveGui method) because calling the
- # IsDisplayAvailable function will cause the
- # application to steal focus under OSX!
- try:
- import wx
- self.__canHaveGui = wx.App.IsDisplayAvailable()
- except ImportError:
- self.__canHaveGui = False
+ self.__canHaveGui = None
# If one of the SSH_/VNC environment
# variables is set, then we're probably
@@ -177,7 +166,7 @@ class Platform(notifier.Notifier):
the event loop is called periodically, and so is not always running.
"""
try:
- import wx
+ import wx # pylint: disable=import-outside-toplevel
app = wx.GetApp()
# TODO Previously this conditional
@@ -216,6 +205,17 @@ class Platform(notifier.Notifier):
'Equivalent functionality is available in fsleyes-widgets.')
def canHaveGui(self):
"""``True`` if it is possible to create a GUI, ``False`` otherwise. """
+
+ # Determine if a display is available. Note that
+ # calling the IsDisplayAvailable function will
+ # cause the application to steal focus under OSX!
+ if self.__canHaveGui is None:
+ try:
+ import wx # pylint: disable=import-outside-toplevel
+ self.__canHaveGui = wx.App.IsDisplayAvailable()
+ except ImportError:
+ self.__canHaveGui = False
+
return self.__canHaveGui
@@ -261,14 +261,14 @@ class Platform(notifier.Notifier):
if not self.canHaveGui:
return WX_UNKNOWN
- import wx
+ import wx # pylint: disable=import-outside-toplevel
pi = [t.lower() for t in wx.PlatformInfo]
- if any(['cocoa' in p for p in pi]): plat = WX_MAC_COCOA
- elif any(['carbon' in p for p in pi]): plat = WX_MAC_CARBON
- elif any(['gtk' in p for p in pi]): plat = WX_GTK
- else: plat = WX_UNKNOWN
+ if any('cocoa' in p for p in pi): plat = WX_MAC_COCOA
+ elif any('carbon' in p for p in pi): plat = WX_MAC_CARBON
+ elif any('gtk' in p for p in pi): plat = WX_GTK
+ else: plat = WX_UNKNOWN
if plat is WX_UNKNOWN:
log.warning('Could not determine wx platform from '
@@ -290,7 +290,7 @@ class Platform(notifier.Notifier):
if not self.canHaveGui:
return WX_UNKNOWN
- import wx
+ import wx # pylint: disable=import-outside-toplevel
pi = [t.lower() for t in wx.PlatformInfo]
isPhoenix = False
@@ -323,7 +323,9 @@ class Platform(notifier.Notifier):
@property
def fslwsl(self):
- """Boolean flag indicating whether FSL is installed in Windows Subsystem for Linux """
+ """Boolean flag indicating whether FSL is installed in Windows
+ Subsystem for Linux
+ """
return self.fsldir is not None and self.fsldir.startswith("\\\\wsl$")
@@ -352,8 +354,9 @@ class Platform(notifier.Notifier):
if op.exists(versionFile):
with open(versionFile, 'rt') as f:
# split string at colon for new hash style versions
- # first object in list is the non-hashed version string (e.g. 6.0.2)
- # if no ":hash:" then standard FSL version string is still returned
+ # first object in list is the non-hashed version string
+ # (e.g. 6.0.2) if no ":hash:" then standard FSL version
+ # string is still returned
self.__fslVersion = f.read().strip().split(":")[0]
self.notify(value=value)
diff --git a/fsl/version.py b/fsl/version.py
index ca8bdbc31a907847967a09a4498143f6caaeb049..9030805603613b6397c11d7fce25d31341d03a42 100644
--- a/fsl/version.py
+++ b/fsl/version.py
@@ -47,7 +47,7 @@ import re
import string
-__version__ = '3.7.0.dev0'
+__version__ = '3.8.0.dev0'
"""Current version number, as a string. """
diff --git a/tests/test_scripts/test_imglob.py b/tests/test_scripts/test_imglob.py
index 5ce2c2bc517dfcc00fa5c4be69886fd360de570e..d1b261544990bc37cbb7ab6bd4f0754113ff57f4 100644
--- a/tests/test_scripts/test_imglob.py
+++ b/tests/test_scripts/test_imglob.py
@@ -100,6 +100,9 @@ def test_imglob_shouldPass2():
('file1.hdr file1.img file2.nii', 'file1 file2', 'primary', 'file1.hdr file2.nii'),
('file1.hdr file1.img file2.nii', 'file1 file2', 'all', 'file1.hdr file1.img file2.nii'),
+ # muiltiple files, given wildcard
+ ('file1.nii file2.nii', 'file*', 'prefix', 'file1 file2'),
+
# no file
('file.nii', 'bag', 'prefix', ''),
('file.nii', 'bag', 'primary', ''),