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# Copyright 2016. The Regents of the University of California.
# All rights reserved. Use of this source code is governed by
# a BSD-style license which can be found in the LICENSE file.
#
# Authors:
# 2016 Siddharth Iyer <sid8795@gmail.com>
# 2018 Soumick Chatterjee <soumick.chatterjee@ovgu.de> , WSL Support
import subprocess as sp
import tempfile as tmp
import cfl
import os
from wslsupport import PathCorrection
def bart(nargout, cmd, *args, **kwargs):
if type(nargout) != int or nargout < 0:
print("Usage: bart(<nargout>, <command>, <arguments...>)")
return
try:
bart_path = os.environ['BART_TOOLBOX_PATH']
except:
bart_path = None
# support old environment variable:
if bart_path is None:
try:
bart_path = os.environ['TOOLBOX_PATH']
except:
bart_path = None
isWSL = False
if not bart_path:
if os.path.isfile('/usr/local/bin/bart'):
bart_path = '/usr/local/bin'
elif os.path.isfile('/usr/bin/bart'):
bart_path = '/usr/bin'
else:
bartstatus = os.system('wsl bart version -V')
if bartstatus==0:
bart_path = '/usr/bin'
isWSL = True
else:
raise Exception('Environment variable BART_TOOLBOX_PATH is not set.')
name = tmp.NamedTemporaryFile().name
nargin = len(args)
infiles = [name + 'in' + str(idx) for idx in range(nargin)]
for idx in range(nargin):
cfl.writecfl(infiles[idx], args[idx])
args_kw = [("--" if len(kw)>1 else "-") + kw for kw in kwargs]
infiles_kw = [name + 'in' + kw for kw in kwargs]
for idx, kw in enumerate(kwargs):
cfl.writecfl(infiles_kw[idx], kwargs[kw])
outfiles = [name + 'out' + str(idx) for idx in range(nargout)]
cmd = cmd.split(" ")
if os.name =='nt':
if isWSL:
#For WSL and modify paths
infiles = [PathCorrection(item) for item in infiles]
infiles_kw = [PathCorrection(item) for item in infiles_kw]
outfiles = [PathCorrection(item) for item in outfiles]
cmd = [PathCorrection(item) for item in cmd]
args_infiles_kw = [item for pair in zip(args_kw, infiles_kw) for item in pair]
shell_cmd = ['wsl', 'bart', *cmd, *args_infiles_kw, *infiles, *outfiles]
else:
#For cygwin use bash and modify paths
infiles = [item.replace(os.path.sep, '/') for item in infiles]
infiles_kw = [item.replace(os.path.sep, '/') for item in infiles_kw]
outfiles = [item.replace(os.path.sep, '/') for item in outfiles]
cmd = [item.replace(os.path.sep, '/') for item in cmd]
args_infiles_kw = [item for pair in zip(args_kw, infiles_kw) for item in pair]
shell_cmd = ['bash.exe', '--login', '-c', os.path.join(bart_path, 'bart'), *cmd, *args_infiles_kw, *infiles, *outfiles]
#TODO: Test with cygwin, this is just translation from matlab code
else:
args_infiles_kw = [item for pair in zip(args_kw, infiles_kw) for item in pair]
shell_cmd = [os.path.join(bart_path, 'bart'), *cmd, *args_infiles_kw, *infiles, *outfiles]
# run bart command
ERR, stdout, stderr = execute_cmd(shell_cmd)
# store error code, stdout and stderr in function attributes for outside access
# this makes it possible to access these variables from outside the function (e.g "print(bart.ERR)")
bart.ERR, bart.stdout, bart.stderr = ERR, stdout, stderr
for elm in infiles:
if os.path.isfile(elm + '.cfl'):
os.remove(elm + '.cfl')
if os.path.isfile(elm + '.hdr'):
os.remove(elm + '.hdr')
for elm in infiles_kw:
if os.path.isfile(elm + '.cfl'):
os.remove(elm + '.cfl')
if os.path.isfile(elm + '.hdr'):
os.remove(elm + '.hdr')
output = []
for idx in range(nargout):
elm = outfiles[idx]
if not ERR:
output.append(cfl.readcfl(elm))
if os.path.isfile(elm + '.cfl'):
os.remove(elm + '.cfl')
if os.path.isfile(elm + '.hdr'):
os.remove(elm + '.hdr')
if ERR:
print(f"Command exited with error code {ERR}.")
return
if nargout == 0:
return
elif nargout == 1:
return output[0]
else:
return output
def execute_cmd(cmd):
"""
Execute a command in a shell.
Print and catch the output.
"""
errcode = 0
stdout = ""
stderr = ""
# remove empty strings from cmd
cmd = [item for item in cmd if len(item)]
# execute cmd
proc = sp.Popen(cmd, stdout=sp.PIPE, stderr=sp.PIPE, universal_newlines=True)
# print to stdout
for stdout_line in iter(proc.stdout.readline, ""):
stdout += stdout_line
print(stdout_line, end="")
proc.stdout.close()
# in case of error, print to stderr
errcode = proc.wait()
if errcode:
stderr = "".join(proc.stderr.readlines())
print(stderr)
proc.stderr.close()
return errcode, stdout, stderr
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