Merge pull request #760 from dmordom/enh/newvistainterfaces

Enh/newvistainterfaces

Author: chrisgorgo

CHANGES

@@ -3,6 +3,7 @@ Future Release
 
 * 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)
 ============

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
+