enh: add PETPVC wrapper

circle.yml

@@ -23,8 +23,8 @@ dependencies:
     - pip install -e .
     - pip install matplotlib sphinx ipython boto
     - gem install fakes3
-    - if [[ ! -d ~/examples/data ]]; then wget "http://tcpdiag.dl.sourceforge.net/project/nipy/nipype/nipype-0.2/nipype-tutorial.tar.bz2"; tar jxvf nipype-tutorial.tar.bz2; mkdir ~/examples; mv nipype-tutorial/* ~/examples/; fi
-    - if [[ ! -d ~/examples/fsl_course_data ]]; then wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/fdt1.tar.gz" ; wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/fdt2.tar.gz"; wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/tbss.tar.gz"; mkdir ~/examples/fsl_course_data; tar zxvf fdt1.tar.gz -C ~/examples/fsl_course_data; tar zxvf fdt2.tar.gz -C ~/examples/fsl_course_data; tar zxvf tbss.tar.gz -C ~/examples/fsl_course_data; fi
+    - if [[ ! -d ~/examples/data ]]; then wget "http://tcpdiag.dl.sourceforge.net/project/nipy/nipype/nipype-0.2/nipype-tutorial.tar.bz2" && tar jxvf nipype-tutorial.tar.bz2 && mv nipype-tutorial/* ~/examples/; fi
+    - if [[ ! -d ~/examples/fsl_course_data ]]; then wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/fdt1.tar.gz" && wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/fdt2.tar.gz" && wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/tbss.tar.gz" && mkdir ~/examples/fsl_course_data && tar zxvf fdt1.tar.gz -C ~/examples/fsl_course_data && tar zxvf fdt2.tar.gz -C ~/examples/fsl_course_data && tar zxvf tbss.tar.gz -C ~/examples/fsl_course_data; fi
     - bash ~/nipype/tools/install_spm_mcr.sh
     - mkdir -p ~/.nipype && echo '[logging]' > ~/.nipype/nipype.cfg && echo 'workflow_level = DEBUG' >> ~/.nipype/nipype.cfg && echo 'interface_level = DEBUG' >> ~/.nipype/nipype.cfg && echo 'filemanip_level = DEBUG' >> ~/.nipype/nipype.cfg
 machine:

nipype/interfaces/afni/base.py

@@ -6,13 +6,14 @@
 
 
 import os
-import warnings
 
+from ... import logging
 from ...utils.filemanip import split_filename
 from ..base import (
     CommandLine, traits, CommandLineInputSpec, isdefined, File, TraitedSpec)
 
-warn = warnings.warn
+# Use nipype's logging system
+iflogger = logging.getLogger('interface')
 
 
 class Info(object):
@@ -40,26 +41,29 @@ def version():
         try:
             clout = CommandLine(command='afni_vcheck',
                                 terminal_output='allatonce').run()
+
+            # Try to parse the version number
+            currv = clout.runtime.stdout.split('\n')[1].split('=', 1)[1].strip()
         except IOError:
             # If afni_vcheck is not present, return None
-            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
-            warn('AFNI is outdated')
-            return str(e).split('\n')[4].split('=', 1)[1].strip()
-
-        # Try to parse the version number
-        out = clout.runtime.stdout.split('\n')[1].split('=', 1)[1].strip()
+            # 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(
+                'AFNI is outdated, detected version %s and %s is available.' % (currv, nextv))
 
-        if out.startswith('AFNI_'):
-            out = out[5:]
+        if currv.startswith('AFNI_'):
+            currv = currv[5:]
 
-        v = out.split('.')
+        v = currv.split('.')
         try:
             v = [int(n) for n in v]
         except ValueError:
-            return out
+            return currv
         return tuple(v)
 
     @classmethod

nipype/interfaces/afni/preprocess.py

@@ -8,10 +8,10 @@
     >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
     >>> os.chdir(datadir)
 """
-import warnings
 
 import os
 import re
+from warnings import warn
 
 from .base import AFNICommand, AFNICommandInputSpec, AFNICommandOutputSpec
 from ..base import CommandLineInputSpec, CommandLine, OutputMultiPath
@@ -20,8 +20,6 @@
 from ...utils.filemanip import (load_json, save_json, split_filename)
 from ...utils.filemanip import fname_presuffix
 
-warn = warnings.warn
-
 
 class To3DInputSpec(AFNICommandInputSpec):
     out_file = File(name_template="%s", desc='output image file name',

nipype/interfaces/dipy/preprocess.py

@@ -23,9 +23,6 @@
     package_check('dipy', version='0.6.0')
 except Exception as e:
     have_dipy = False
-else:
-    from dipy.align.aniso2iso import resample
-    from dipy.core.gradients import GradientTable
 
 
 class ResampleInputSpec(TraitedSpec):
@@ -172,6 +169,7 @@ def resample_proxy(in_file, order=3, new_zooms=None, out_file=None):
     """
     Performs regridding of an image to set isotropic voxel sizes using dipy.
     """
+    from dipy.align.aniso2iso import resample
 
     if out_file is None:
         fname, fext = op.splitext(op.basename(in_file))

nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py

@@ -16,6 +16,7 @@ def test_Surface2VolTransform_inputs():
     usedefault=True,
     ),
     mkmask=dict(argstr='--mkmask',
+    xor=['source_file'],
     ),
     projfrac=dict(argstr='--projfrac %s',
     ),
@@ -26,6 +27,7 @@ def test_Surface2VolTransform_inputs():
     source_file=dict(argstr='--surfval %s',
     copyfile=False,
     mandatory=True,
+    xor=['mkmask'],
     ),
     subject_id=dict(argstr='--identity %s',
     xor=['reg_file'],

nipype/interfaces/freesurfer/utils.py

@@ -390,7 +390,7 @@ def _gen_filename(self, name):
 
 class Surface2VolTransformInputSpec(FSTraitedSpec):
     source_file = File(exists=True, argstr='--surfval %s',
-                       copyfile=False, mandatory=True,
+                       copyfile=False, mandatory=True, xor=['mkmask'],
                        desc='This is the source of the surface values')
     hemi = traits.Str(argstr='--hemi %s', mandatory=True,
                       desc='hemisphere of data')
@@ -404,7 +404,7 @@ class Surface2VolTransformInputSpec(FSTraitedSpec):
     template_file = File(exists=True, argstr='--template %s',
                          desc='Output template volume')
     mkmask = traits.Bool(desc='make a mask instead of loading surface values',
-                         argstr='--mkmask')
+                         argstr='--mkmask', xor=['source_file'])
     vertexvol_file = File(name_template="%s_asVol_vertex.nii",
                           desc=('Path name of the vertex output volume, which '
                                 'is the same as output volume except that the '