1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88
|
# 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):
if type(nargout) != int or nargout < 0:
print("Usage: bart(<nargout>, <command>, <arguements...>)")
return None
try:
bart_path = os.environ['TOOLBOX_PATH'] + '/bart '
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 TOOLBOX_PATH is not set.')
name = tmp.NamedTemporaryFile().name
nargin = len(args)
infiles = [name + 'in' + str(idx) for idx in range(nargin)]
in_str = ' '.join(infiles)
for idx in range(nargin):
cfl.writecfl(infiles[idx], args[idx])
outfiles = [name + 'out' + str(idx) for idx in range(nargout)]
out_str = ' '.join(outfiles)
if os.name =='nt':
if isWSL:
#For WSL and modify paths
cmdWSL = PathCorrection(cmd)
in_strWSL = PathCorrection(in_str)
out_strWSL = PathCorrection(out_str)
ERR = os.system('wsl bart ' + cmdWSL + ' ' + in_strWSL + ' ' + out_strWSL)
else:
#For cygwin use bash and modify paths
ERR = os.system('bash.exe --login -c ' + bart_path + '"/bart ' + cmd.replace(os.path.sep, '/') + ' ' + in_str.replace(os.path.sep, '/') + ' ' + out_str.replace(os.path.sep, '/') + '"')
#TODO: Test with cygwin, this is just translation from matlab code
else:
ERR = os.system(bart_path + '/bart ' + cmd + ' ' + in_str + ' ' + out_str)
for elm in infiles:
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:
raise Exception("Command exited with an error.")
if nargout == 1:
output = output[0]
return output
|