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[FIX] Define ANTSPATH for ants.BrainExtraction automatically #1986

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Merged
merged 3 commits into from
May 3, 2017
Merged

[FIX] Define ANTSPATH for ants.BrainExtraction automatically #1986

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a28c7a2
[FIX] Define ANTSPATH for ants.BrainExtraction automatically
oesteban May 1, 2017
76cbf0f
automatically set ANTSPATH when possible
oesteban May 1, 2017
3b78740
update check
oesteban May 3, 2017
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32 changes: 31 additions & 1 deletion nipype/interfaces/ants/segmentation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,8 @@
import os
from ...external.due import BibTeX
from ...utils.filemanip import split_filename, copyfile
from ..base import TraitedSpec, File, traits, InputMultiPath, OutputMultiPath, isdefined
from ..base import (TraitedSpec, File, traits, InputMultiPath, OutputMultiPath, isdefined,
_exists_in_path)
from .base import ANTSCommand, ANTSCommandInputSpec


Expand Down Expand Up @@ -692,6 +693,35 @@ class BrainExtraction(ANTSCommand):
output_spec = BrainExtractionOutputSpec
_cmd = 'antsBrainExtraction.sh'

def _run_interface(self, runtime, correct_return_codes=(0,)):
# antsBrainExtraction.sh requires ANTSPATH to be defined
out_environ = self._get_environ()
if out_environ.get('ANTSPATH') is None:
runtime.environ.update(out_environ)
executable_name = self.cmd.split()[0]
exist_val, cmd_path = _exists_in_path(executable_name, runtime.environ)
if not exist_val:
raise IOError("command '%s' could not be found on host %s" %
(self.cmd.split()[0], runtime.hostname))

# Set the environment variable if found
runtime.environ.update({'ANTSPATH': os.path.dirname(cmd_path)})
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i believe ANTSPATH requires a trailing /. could you confirm this and make sure we adjust for it?

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Most of the scripts don't need the trailing /. Particularly, the antsBrainExtraction.sh doesn't need it.

But I can add it anyways if you want.

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then not necessary.


runtime = super(BrainExtraction, self)._run_interface(runtime)

# Still, double-check if it didn't found N4
if 'we cant find the N4 program' in runtime.stdout:
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since the script can be in a different location than the N4 executable, can we not do this check before running in this particular case?

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Sorry I'm lost here. Which check would you remove?

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i meant to put the N4 check before calling _run_interface instead of checking the output.

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Judging from this: https://github.com/stnava/ANTs/blob/646459bf297a50cdf608ea7d39cb79b44906ad22/Scripts/antsBrainExtraction.sh#L5-L20, I think we just parse the output for "we cant find" and raise the message for the missing tool.

For next release we can decouple or, as @blakedewey suggested, replicate antsBrainExtraction in pure nipype.

errmsg = ('antsBrainExtraction.sh requires the environment variable '
'ANTSPATH to be defined')
if runtime.stderr is None:
runtime.stderr = errmsg
else:
runtime.stderr += '\n' + errmsg
runtime.returncode = 1
self.raise_exception(runtime)

return runtime

def _list_outputs(self):
outputs = self._outputs().get()
outputs['BrainExtractionMask'] = os.path.join(os.getcwd(),
Expand Down