Merge remote-tracking branch 'upstream/master' into enh/dcm2nii

* upstream/master:
  updated changelog
  0.9.2 release
  cleanup
  Added VtoMat vista interface and updated CHANGES and autogenerated tests accordingly
  added test for Vnifti2Image interface
  updated CHANGES log
  Created interface for vimage2nifti command from lipvia vista package
  fixed mcflirt mean image output

Author: satra

CHANGES

@@ -1,8 +1,9 @@
-Future Release
-==============
+Release 0.9.2 (January 31, 2014)
+===========
 
 * FIX: DataFinder was broken due to a typo
 * FIX: Order of DataFinder outputs was not guaranteed, it's human sorted now
+* ENH: New interfaces: Vnifti2Image, VtoMat
 
 Release 0.9.1 (December 25, 2013)
 ============

doc/_templates/sidebar_versions.html

@@ -17,7 +17,7 @@ <h3>{{ _('Versions') }}</h3>
                 <td align="left">Release</td><td align="right">Devel</td>
             </tr>
             <tr>
-                <td align="left">0.9.1</td><td align="right">1.0-dev</td>
+                <td align="left">0.9.2</td><td align="right">1.0-dev</td>
             </tr>
             <tr>
                 <td align="left"><a href="{{pathto('users/install')}}">Download</a></td>

doc/users/install.rst

@@ -9,7 +9,7 @@ This page covers the necessary steps to install Nipype.
 Download
 --------
 
-Release 0.9.1: [`zip <https://github.com/nipy/nipype/archive/0.9.1.zip>`__ `tar.gz
+Release 0.9.2: [`zip <https://github.com/nipy/nipype/archive/0.9.2.zip>`__ `tar.gz
 <https://github.com/nipy/nipype/archive/0.9.1.tar.gz>`__]
 
 Development: [`zip <http://github.com/nipy/nipype/zipball/master>`__ `tar.gz

nipype/info.py

@@ -9,8 +9,8 @@
 # version
 _version_major = 0
 _version_minor = 9
-_version_micro = 1
-_version_extra = '.dev'
+_version_micro = 2
+_version_extra = ''
 
 def get_nipype_gitversion():
     """Nipype version as reported by the last commit in git

nipype/interfaces/fsl/preprocess.py

@@ -678,8 +678,17 @@ def _list_outputs(self):
                                                       '_variance.ext', cwd=cwd)
             outputs['std_img'] = self._gen_fname(outputs['out_file'] +
                                                  '_sigma.ext', cwd=cwd)
+                                                  
+        # The mean image created if -stats option is specified ('meanvol')
+        # is missing the top and bottom slices. Therefore we only expose the 
+        # mean image created by -meanvol option ('mean_reg') which isn't 
+        # corrupted.
+        # Note that the same problem holds for the std and variance image.
+                                                  
+        if isdefined(self.inputs.mean_vol) and self.inputs.mean_vol:
             outputs['mean_img'] = self._gen_fname(outputs['out_file'] +
-                                                  '_meanvol.ext', cwd=cwd)
+                                                  '_mean_reg.ext', cwd=cwd)
+                                                  
         if isdefined(self.inputs.save_mats) and self.inputs.save_mats:
             _, filename = os.path.split(outputs['out_file'])
             matpathname = os.path.join(cwd, filename + '.mat')

nipype/interfaces/vista/__init__.py

@@ -0,0 +1,3 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+from .vista import (Vnifti2Image, VtoMat)

nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py

@@ -0,0 +1,44 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.vista.vista import Vnifti2Image
+def test_Vnifti2Image_inputs():
+    input_map = dict(ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    out_file=dict(hash_files=False,
+    name_template='%s.v',
+    name_source=['in_file'],
+    keep_extension=False,
+    position=-1,
+    argstr='-out %s',
+    ),
+    args=dict(argstr='%s',
+    ),
+    terminal_output=dict(nohash=True,
+    mandatory=True,
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(position=1,
+    mandatory=True,
+    argstr='-in %s',
+    ),
+    attributes=dict(position=2,
+    mandatory=False,
+    argstr='-attr %s',
+    ),
+    )
+    inputs = Vnifti2Image.input_spec()
+
+    for key, metadata in input_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+def test_Vnifti2Image_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = Vnifti2Image.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value

nipype/interfaces/vista/tests/test_auto_VtoMat.py

@@ -0,0 +1,40 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.vista.vista import VtoMat
+def test_VtoMat_inputs():
+    input_map = dict(ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    out_file=dict(hash_files=False,
+    name_template='%s.mat',
+    name_source=['in_file'],
+    keep_extension=False,
+    position=-1,
+    argstr='-out %s',
+    ),
+    args=dict(argstr='%s',
+    ),
+    terminal_output=dict(nohash=True,
+    mandatory=True,
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(position=1,
+    mandatory=True,
+    argstr='-in %s',
+    ),
+    )
+    inputs = VtoMat.input_spec()
+
+    for key, metadata in input_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+def test_VtoMat_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = VtoMat.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value

nipype/interfaces/vista/vista.py

@@ -0,0 +1,70 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+"""
+    Change directory to provide relative paths for doctests
+    >>> import os
+    >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
+    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
+    >>> os.chdir(datadir)
+
+"""
+
+from nipype.interfaces.base import CommandLineInputSpec, CommandLine, traits, TraitedSpec, File
+from nipype.utils.filemanip import split_filename
+import os, os.path as op
+from nipype.interfaces.traits_extension import isdefined
+
+class Vnifti2ImageInputSpec(CommandLineInputSpec):
+    in_file = File(exists=True, argstr='-in %s', mandatory=True, position=1, desc='in file')
+    attributes = File(exists=True, argstr='-attr %s', mandatory=False, position=2, desc='attribute file')
+    out_file = File(name_template="%s.v", keep_extension=False, argstr='-out %s', hash_files=False,
+                    position= -1, desc='output data file', name_source=["in_file"])
+
+class Vnifti2ImageOutputSpec(TraitedSpec):
+    out_file = File(exists=True, desc='Output vista file')
+
+class Vnifti2Image(CommandLine):
+    """
+    Convert a nifti file into a vista file.
+
+    Example
+    -------
+
+    >>> vimage = Vnifti2Image()
+    >>> vimage.inputs.in_file = 'image.nii'
+    >>> vimage.cmdline
+    'vnifti2image -in image.nii -out image.v'
+    >>> vimage.run()                                       # doctest: +SKIP
+    """
+
+    _cmd = 'vnifti2image'
+    input_spec=Vnifti2ImageInputSpec
+    output_spec=Vnifti2ImageOutputSpec
+    
+    
+class VtoMatInputSpec(CommandLineInputSpec):
+    in_file = File(exists=True, argstr='-in %s', mandatory=True, position=1, desc='in file')
+    out_file = File(name_template="%s.mat", keep_extension=False, argstr='-out %s', hash_files=False,
+                    position= -1, desc='output mat file', name_source=["in_file"])
+
+class VtoMatOutputSpec(TraitedSpec):
+    out_file = File(exists=True, desc='Output mat file')
+
+class VtoMat(CommandLine):
+    """
+    Convert a nifti file into a vista file.
+
+    Example
+    -------
+
+    >>> vimage = VtoMat()
+    >>> vimage.inputs.in_file = 'image.v'
+    >>> vimage.cmdline
+    'vtomat -in image.v -out image.mat'
+    >>> vimage.run()                                       # doctest: +SKIP
+    """
+
+    _cmd = 'vtomat'
+    input_spec=VtoMatInputSpec
+    output_spec=VtoMatOutputSpec
+