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added 'tax' switch to ResponseSD interface _cmd to match latest specification of dwi2response #1548

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added 'tax' switch to ResponseSD interface _cmd to match latest specification of dwi2response #1548

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fc17e89
added 'tax' switch to ResponseSD interface _cmd to match latest
Jul 26, 2016
8dcc0f4
edited ResponseSD command line to reflex 'tax' switch
Jul 26, 2016
22df5bd
wrapped error messages within str calls to avoid unicode errors
Sep 21, 2016
4fc519b
Merge branch 'master' of https://github.com/nipy/nipype into mrtrix_d…
Sep 21, 2016
d3053ac
ignore errors on unicode decoding
Sep 21, 2016
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12 changes: 6 additions & 6 deletions nipype/interfaces/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1243,7 +1243,7 @@ def read(self, drain=0):
def _read(self, drain):
"Read from the file descriptor"
fd = self.fileno()
buf = os.read(fd, 4096).decode(self.default_encoding)
buf = os.read(fd, 4096).decode(self.default_encoding, errors='backslashreplace')
if not buf and not self._buf:
return None
if '\n' not in buf:
Expand Down Expand Up @@ -1507,8 +1507,8 @@ def _process(drain=0):
proc.poll()
time.sleep(interval)
stdout, stderr = proc.communicate()
stdout = stdout.decode(default_encoding)
stderr = stderr.decode(default_encoding)
stdout = stdout.decode(default_encoding, errors='backslashreplace')
stderr = stderr.decode(default_encoding, errors='backslashreplace')
result['stdout'] = stdout.split('\n')
result['stderr'] = stderr.split('\n')
result['merged'] = ''
Expand All @@ -1522,8 +1522,8 @@ def _process(drain=0):
ret_code = proc.wait()
stderr.flush()
stdout.flush()
result['stdout'] = [line.decode(default_encoding).strip() for line in open(outfile, 'rb').readlines()]
result['stderr'] = [line.decode(default_encoding).strip() for line in open(errfile, 'rb').readlines()]
result['stdout'] = [line.decode(default_encoding, errors='backslashreplace').strip() for line in open(outfile, 'rb').readlines()]
result['stderr'] = [line.decode(default_encoding, errors='backslashreplace').strip() for line in open(errfile, 'rb').readlines()]
result['merged'] = ''
if output == 'none':
if runtime_profile:
Expand Down Expand Up @@ -1677,7 +1677,7 @@ def cmdline(self):
return ' '.join(allargs)

def raise_exception(self, runtime):
raise RuntimeError(
raise RuntimeError(
('Command:\n{cmdline}\nStandard output:\n{stdout}\n'
'Standard error:\n{stderr}\nReturn code: {returncode}').format(
**runtime.dictcopy()))
Expand Down
3 changes: 1 addition & 2 deletions nipype/interfaces/mrtrix3/preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -97,11 +97,10 @@ class ResponseSD(MRTrix3Base):
>>> resp.inputs.in_mask = 'mask.nii.gz'
>>> resp.inputs.grad_fsl = ('bvecs', 'bvals')
>>> resp.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE
'dwi2response -fslgrad bvecs bvals -mask mask.nii.gz dwi.mif response.txt'
>>> resp.run() # doctest: +SKIP
"""

_cmd = 'dwi2response'
_cmd = 'dwi2response tax'
input_spec = ResponseSDInputSpec
output_spec = ResponseSDOutputSpec

Expand Down