Merge branch 'master' into enh/NewDipyInterfaces

Author: Oscar Esteban

CHANGES

@@ -3,6 +3,8 @@ Next release
 
 * ENH: New interfaces in dipy: RESTORE, EstimateResponseSH, CSD and StreamlineTractography
        (https://github.com/nipy/nipype/pull/1090)
+* ENH: Added interfaces of AFNI (https://github.com/nipy/nipype/pull/1360,
+       https://github.com/nipy/nipype/pull/1361)
 * ENH: Added support for PETPVC (https://github.com/nipy/nipype/pull/1335)
 * ENH: Merge S3DataSink into DataSink, added AWS documentation (https://github.com/nipy/nipype/pull/1316)
 * TST: Cache APT in CircleCI (https://github.com/nipy/nipype/pull/1333)

nipype/interfaces/afni/__init__.py

@@ -12,5 +12,5 @@
                          Fourier, Allineate, Maskave, SkullStrip, TCat, Fim,
                          BlurInMask, Autobox, TCorrMap, Bandpass, Retroicor,
                          TCorrelate, TCorr1D, BrickStat, ROIStats, AutoTcorrelate,
-                         AFNItoNIFTI, Eval, Means)
+                         AFNItoNIFTI, Eval, Means, Hist, FWHMx)
 from .svm import (SVMTest, SVMTrain)

nipype/interfaces/afni/base.py

@@ -2,18 +2,17 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Provide interface to AFNI commands."""
 
-from builtins import object
-
-
 import os
+from sys import platform
+from builtins import object
 
 from ... import logging
 from ...utils.filemanip import split_filename
 from ..base import (
     CommandLine, traits, CommandLineInputSpec, isdefined, File, TraitedSpec)
 
 # Use nipype's logging system
-iflogger = logging.getLogger('interface')
+IFLOGGER = logging.getLogger('interface')
 
 
 class Info(object):
@@ -46,14 +45,14 @@ def version():
             currv = clout.runtime.stdout.split('\n')[1].split('=', 1)[1].strip()
         except IOError:
             # If afni_vcheck is not present, return None
-            iflogger.warn('afni_vcheck executable not found.')
+            IFLOGGER.warn('afni_vcheck executable not found.')
             return None
         except RuntimeError as e:
             # If AFNI is outdated, afni_vcheck throws error.
             # Show new version, but parse current anyways.
             currv = str(e).split('\n')[4].split('=', 1)[1].strip()
             nextv = str(e).split('\n')[6].split('=', 1)[1].strip()
-            iflogger.warn(
+            IFLOGGER.warn(
                 'AFNI is outdated, detected version %s and %s is available.' % (currv, nextv))
 
         if currv.startswith('AFNI_'):
@@ -117,6 +116,17 @@ def standard_image(img_name):
         return os.path.join(basedir, img_name)
 
 
+class AFNICommandBase(CommandLine):
+    """
+    A base class to fix a linking problem in OSX and afni.
+    See http://afni.nimh.nih.gov/afni/community/board/read.php?1,145346,145347#msg-145347
+    """
+    def _run_interface(self, runtime):
+        if platform == 'darwin':
+            runtime.environ['DYLD_FALLBACK_LIBRARY_PATH'] = '/usr/local/afni/'
+        return super(AFNICommandBase, self)._run_interface(runtime)
+
+
 class AFNICommandInputSpec(CommandLineInputSpec):
     outputtype = traits.Enum('AFNI', list(Info.ftypes.keys()),
                              desc='AFNI output filetype')
@@ -130,8 +140,8 @@ class AFNICommandOutputSpec(TraitedSpec):
                     exists=True)
 
 
-class AFNICommand(CommandLine):
-
+class AFNICommand(AFNICommandBase):
+    """Shared options for several AFNI commands """
     input_spec = AFNICommandInputSpec
     _outputtype = None