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[DOC] Add duecredit references for AFNI and FSL. #1930

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Merged
merged 7 commits into from
Apr 5, 2017
Merged

[DOC] Add duecredit references for AFNI and FSL. #1930

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d9779eb
Merge remote-tracking branch 'nipy/master'
tsalo Mar 29, 2017
d496b3f
Merge remote-tracking branch 'nipy/master'
tsalo Mar 31, 2017
75c65f1
Merge remote-tracking branch 'nipy/master'
tsalo Apr 2, 2017
dbac36d
Add duecredit citations for FSL, AFNI, 3dFWHMx.
tsalo Apr 2, 2017
8fde7e2
Fix typo for Sphinx.
tsalo Apr 5, 2017
381e8c6
Only include 2012 FSL paper in refs.
tsalo Apr 5, 2017
81367a0
Merge remote-tracking branch 'nipy/master'
tsalo Apr 5, 2017
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29 changes: 28 additions & 1 deletion nipype/interfaces/afni/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""Provide interface to AFNI commands."""
from __future__ import print_function, division, unicode_literals, absolute_import
from builtins import object, str, bytes
from builtins import object, str
from future.utils import raise_from

import os
Expand All @@ -13,6 +13,7 @@
from ...utils.filemanip import split_filename
from ..base import (
CommandLine, traits, CommandLineInputSpec, isdefined, File, TraitedSpec)
from ...external.due import BibTeX

# Use nipype's logging system
IFLOGGER = logging.getLogger('interface')
Expand Down Expand Up @@ -148,6 +149,32 @@ class AFNICommand(AFNICommandBase):
input_spec = AFNICommandInputSpec
_outputtype = None

references_ = [{'entry': BibTeX('@article{Cox1996,'
'author={R.W. Cox},'
'title={AFNI: software for analysis and '
'visualization of functional magnetic '
'resonance neuroimages},'
'journal={Computers and Biomedical research},'
'volume={29},'
'number={3},'
'pages={162-173},'
'year={1996},'
'}'),
'tags': ['implementation'],
},
{'entry': BibTeX('@article{CoxHyde1997,'
'author={R.W. Cox and J.S. Hyde},'
'title={Software tools for analysis and '
'visualization of fMRI data},'
'journal={NMR in Biomedicine},'
'volume={10},'
'number={45},'
'pages={171-178},'
'year={1997},'
'}'),
'tags': ['implementation'],
}]

def __init__(self, **inputs):
super(AFNICommand, self).__init__(**inputs)
self.inputs.on_trait_change(self._output_update, 'outputtype')
Expand Down
11 changes: 11 additions & 0 deletions nipype/interfaces/afni/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@
from ..base import (
CommandLineInputSpec, CommandLine, Directory, TraitedSpec,
traits, isdefined, File, InputMultiPath, Undefined, Str)
from ...external.due import BibTeX

from .base import (
AFNICommandBase, AFNICommand, AFNICommandInputSpec, AFNICommandOutputSpec)
Expand Down Expand Up @@ -694,6 +695,16 @@ class FWHMx(AFNICommandBase):
_cmd = '3dFWHMx'
input_spec = FWHMxInputSpec
output_spec = FWHMxOutputSpec

references_ = [{'entry': BibTeX('@article{CoxReynoldsTaylor2016,'
'author={R.W. Cox, R.C. Reynolds, and P.A. Taylor},'
'title={AFNI and clustering: false positive rates redux},'
'journal={bioRxiv},'
'year={2016},'
'}'),
'tags': ['method'],
},
]
_acf = True

def _parse_inputs(self, skip=None):
Expand Down
2 changes: 1 addition & 1 deletion nipype/interfaces/base.py
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Expand Up @@ -1387,7 +1387,7 @@ def _get_ram_mb(pid, pyfunc=False):
def get_max_resources_used(pid, mem_mb, num_threads, pyfunc=False):
"""Function to get the RAM and threads usage of a process

Paramters
Parameters
---------
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Just a tiny change: can you add a hyphen so sphinx does not raise a warning?

pid : integer
the process ID of process to profile
Expand Down
43 changes: 43 additions & 0 deletions nipype/interfaces/fsl/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@
from ... import logging
from ...utils.filemanip import fname_presuffix
from ..base import traits, isdefined, CommandLine, CommandLineInputSpec
from ...external.due import BibTeX

LOGGER = logging.getLogger('interface')

Expand Down Expand Up @@ -157,6 +158,48 @@ class FSLCommand(CommandLine):
input_spec = FSLCommandInputSpec
_output_type = None

references_ = [{'entry': BibTeX('@article{WoolrichJbabdiPatenaudeChappellMakniBehrens'
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I'd say we should place only the Neuroimage 2012 reference at the top level, and then have the specific references with the corresponding interfaces.

'BeckmannJenkinsonSmith2009,'
'author={M.W. Woolrich, S. Jbabdi, B. Patenaude, M. Chappell, '
'S. Makni, T. Behrens, C. Beckmann, M. Jenkinson, and S.M. Smith},'
'title={Bayesian analysis of neuroimaging data in FSL},'
'journal={NeuroImage},'
'volume={45},'
'number={1},'
'pages={S173-186},'
'year={2009},'
'}'),
'tags': ['implementation'],
},
{'entry': BibTeX('@article{SmithJenkinsonWoolrichBeckmannBehrensJohansen'
'BergBannisterDeLucaDrobnjakFlitneyNiazySaundersVickers'
'ZhangDeStefanoBradyMatthews2004,'
'author={S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, '
'T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, '
'I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, '
'Y. Zhang, N. De Stefano, J.M. Brady, and P.M. Matthews},'
'title={Advances in functional and structural MR image analysis '
'and implementation as FSL},'
'journal={NeuroImage},'
'volume={23},'
'number={S1},'
'pages={208-219},'
'year={2004},'
'}'),
'tags': ['implementation'],
},
{'entry': BibTeX('@article{JenkinsonBeckmannBehrensWoolrichSmith2012,'
'author={M. Jenkinson, C.F. Beckmann, T.E. Behrens, '
'M.W. Woolrich, and S.M. Smith},'
'title={FSL},'
'journal={NeuroImage},'
'volume={62},'
'pages={782-790},'
'year={2012},'
'}'),
'tags': ['implementation'],
}]

def __init__(self, **inputs):
super(FSLCommand, self).__init__(**inputs)
self.inputs.on_trait_change(self._output_update, 'output_type')
Expand Down