Merge pull request #1930 from tsalo/master

[DOC] Add duecredit references for AFNI and FSL.

Author: oesteban

nipype/interfaces/afni/base.py

@@ -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
@@ -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')
@@ -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')

nipype/interfaces/afni/utils.py

@@ -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)
@@ -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):

nipype/interfaces/base.py

@@ -1387,8 +1387,8 @@ 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
+    ----------
     pid : integer
         the process ID of process to profile
     mem_mb : float

nipype/interfaces/fsl/base.py

@@ -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')
 
@@ -157,6 +158,18 @@ class FSLCommand(CommandLine):
     input_spec = FSLCommandInputSpec
     _output_type = None
 
+    references_ = [{'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')