From dab1d3984d31ff1c3d3f4d4e1b4105481def7e82 Mon Sep 17 00:00:00 2001
From: Martin Craig <martin.craig@eng.ox.ac.uk>
Date: Tue, 25 Feb 2020 14:26:20 +0000
Subject: [PATCH] Moved fsl command code out of main run function for clarity
---
fsl/utils/run.py | 55 ++++++++++++++++++++++++++++++++----------------
1 file changed, 37 insertions(+), 18 deletions(-)
diff --git a/fsl/utils/run.py b/fsl/utils/run.py
index 6d4b33ee3..abba42f0e 100644
--- a/fsl/utils/run.py
+++ b/fsl/utils/run.py
@@ -362,24 +362,9 @@ def runfsl(*args, **kwargs):
for prefix in prefixes:
cmdpath = op.join(prefix, args[0])
if fslplatform.fslwsl:
- # We want to run the command from FSL installed in the Windows Subsystem for Linux
- # First we check it exists in WSL (translating Windows path separators to Unix)
- # Then we convert any Windows paths in the arguments (e.g. temp files) to the
- # corresponding WSL Unix paths (C:/ -> /mnt/c)
- # Then we prepend important environment variables - note that it seems we cannot
- # use WSLENV for this due to its insistance on path mapping.
- # Finally we append the command and its arguments
- cmdpath = cmdpath.replace("\\", "/")
- retcode = sp.call(["wsl", "test", "-x", cmdpath])
- if retcode == 0:
- args[0] = cmdpath
- args = [wslpath(arg) for arg in args]
- args = [
- "wsl",
- "PATH=$PATH:%s/bin" % fslplatform.fsldir,
- "FSLDIR=%s" % fslplatform.fsldir,
- "FSLOUTPUTTYPE=%s" % os.environ.get("FSLOUTPUTTYPE", "NIFTI_GZ")
- ] + args
+ wslargs = wslcmd(cmdpath, *args)
+ if wslargs is not None:
+ args = wslargs
break
elif op.isfile(cmdpath):
args[0] = cmdpath
@@ -393,6 +378,40 @@ def runfsl(*args, **kwargs):
return run(*args, **kwargs)
+def wslcmd(cmdpath, *args):
+ """
+ Convert a command + arguments into an equivalent set of arguments that will run the command
+ under Windows Subsystem for Linux
+
+ :param cmdpath: Fully qualified path to the command. This is essentially a WSL path not a Windows
+ one since FSLDIR is specified as a WSL path, however it may have backslashes
+ as path separators due to previous use of ``os.path.join``
+ :param args: Sequence of command arguments (the first of which is the unqualified command name)
+
+ :return: If ``cmdpath`` exists and is executable in WSL, return a sequence of command arguments
+ which when executed will run the command in WSL. Windows paths in the argument list will
+ be converted to WSL paths. If ``cmdpath`` was not executable in WSL, returns None
+ """
+ # Check if command exists in WSL (translating Windows path separators to Unix as os.path.join
+ # may have inserted some backslashes)
+ cmdpath = cmdpath.replace("\\", "/")
+ retcode = sp.call(["wsl", "test", "-x", cmdpath])
+ if retcode == 0:
+ # Form a new argument list and convert any Windows paths in it into WSL paths
+ wslargs = [wslpath(arg) for arg in args]
+ wslargs[0] = cmdpath
+ # Prepend important environment variables - note that it seems we cannot
+ # use WSLENV for this due to its insistance on path mapping.
+ return [
+ "wsl",
+ "PATH=$PATH:%s/bin" % fslplatform.fsldir,
+ "FSLDIR=%s" % fslplatform.fsldir,
+ "FSLOUTPUTTYPE=%s" % os.environ.get("FSLOUTPUTTYPE", "NIFTI_GZ")
+ ] + wslargs
+ else:
+ # Command was not found in WSL with this path
+ return None
+
def wslpath(patharg):
"""
Convert a command line argument containing a Windows path to the equivalent WSL path (e.g. ``c:\\Users`` -> ``/mnt/c/Users``)
--
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