Add dwi2mask, fix auto tests

Author: oesteban

nipype/interfaces/mrtrix3/__init__.py

@@ -2,7 +2,7 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 # -*- coding: utf-8 -*-
 
-from utils import Mesh2PVE, Generate5tt
+from utils import Mesh2PVE, Generate5tt, BrainMask
 from preprocess import ResponseSD, ACTPrepareFSL
 from tracking import Tractography
 from reconst import FitTensor, EstimateFOD

nipype/interfaces/mrtrix3/reconst.py

@@ -201,10 +201,12 @@ class EstimateFOD(CommandLine):
     >>> import nipype.interfaces.mrtrix3 as mrt
     >>> fod = mrt.EstimateFOD()
     >>> fod.inputs.in_file = 'dwi.mif'
+    >>> fod.inputs.response = 'response.txt'
     >>> fod.inputs.in_mask = 'mask.nii.gz'
     >>> fod.inputs.grad_fsl = ('bvecs', 'bvals')
     >>> fod.cmdline                               # doctest: +ELLIPSIS
-    'dwi2fod -fslgrad bvecs bvals -mask mask.nii.gz dwi.mif fods.mif'
+    'dwi2fod -fslgrad bvecs bvals -mask mask.nii.gz dwi.mif response.txt\
+ fods.mif'
     >>> fod.run()                                 # doctest: +SKIP
     """
 

nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py

@@ -0,0 +1,46 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.mrtrix3.utils import BrainMask
+
+def test_BrainMask_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    bval_scale=dict(argstr='-bvalue_scaling %s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    grad_file=dict(argstr='-grad %s',
+    ),
+    grad_fsl=dict(argstr='-fslgrad %s %s',
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(argstr='%s',
+    mandatory=True,
+    position=-2,
+    ),
+    out_file=dict(argstr='%s',
+    mandatory=True,
+    position=-1,
+    usedefault=True,
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    )
+    inputs = BrainMask.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_BrainMask_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = BrainMask.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/mrtrix3/utils.py

@@ -22,11 +22,64 @@
 from nipype.interfaces.traits_extension import isdefined
 
 
+class BrainMaskInputSpec(CommandLineInputSpec):
+    in_file = File(exists=True, argstr='%s', mandatory=True, position=-2,
+                   desc='input diffusion weighted images')
+    out_file = File(
+        'brainmask.mif', argstr='%s', mandatory=True, position=-1,
+        usedefault=True, desc='output brain mask')
+    # DW gradient table import options
+    grad_file = File(exists=True, argstr='-grad %s',
+                     desc='dw gradient scheme (MRTrix format')
+    grad_fsl = traits.Tuple(
+        File(exists=True), File(exists=True), argstr='-fslgrad %s %s',
+        desc='(bvecs, bvals) dw gradient scheme (FSL format')
+    bval_scale = traits.Enum(
+        'yes', 'no', argstr='-bvalue_scaling %s',
+        desc=('specifies whether the b - values should be scaled by the square'
+              ' of the corresponding DW gradient norm, as often required for '
+              'multishell or DSI DW acquisition schemes. The default action '
+              'can also be set in the MRtrix config file, under the '
+              'BValueScaling entry. Valid choices are yes / no, true / '
+              'false, 0 / 1 (default: true).'))
+
+class BrainMaskOutputSpec(TraitedSpec):
+    out_file = File(exists=True, desc='the output response file')
+
+
+class BrainMask(CommandLine):
+
+    """
+    Convert a mesh surface to a partial volume estimation image
+
+
+    Example
+    -------
+
+    >>> import nipype.interfaces.mrtrix3 as mrt
+    >>> bmsk = mrt.BrainMask()
+    >>> bmsk.inputs.in_file = 'dwi.mif'
+    >>> bmsk.cmdline                               # doctest: +ELLIPSIS
+    'dwi2mask dwi.mif brainmask.mif'
+    >>> bmsk.run()                                 # doctest: +SKIP
+    """
+
+    _cmd = 'dwi2mask'
+    input_spec = BrainMaskInputSpec
+    output_spec = BrainMaskOutputSpec
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        outputs['out_file'] = op.abspath(self.inputs.out_file)
+        return outputs
+
+
+
 class Mesh2PVEInputSpec(CommandLineInputSpec):
     in_file = File(exists=True, argstr='%s', mandatory=True, position=-3,
-                   desc='input diffusion weighted images')
+                   desc='input mesh')
     reference = File(exists=True, argstr='%s', mandatory=True, position=-2,
-                     desc='input diffusion weighted images')
+                     desc='input reference image')
     in_first = File(
         exists=True, argstr='-first %s',
         desc='indicates that the mesh file is provided by FSL FIRST')