add FSL bvec/bval format explicit to all interfaces

Author: oesteban

nipype/interfaces/mrtrix3/base.py

@@ -44,6 +44,10 @@ class MRTrix3BaseInputSpec(CommandLineInputSpec):
         'BValueScaling entry. Valid choices are yes / no, true / '
         'false, 0 / 1 (default: true).')
 
+    in_bvec = File(exists=True, argstr='-fslgrad %s %s',
+                   desc='bvecs file in FSL format')
+    in_bval = File(exists=True, desc='bvals file in FSL format')
+
 
 class MRTrix3Base(CommandLine):
 
@@ -58,4 +62,24 @@ def _format_arg(self, name, trait_spec, value):
                 pass
             return trait_spec.argstr % value
 
+        if name == 'in_bvec':
+            return trait_spec.argstr % (value, self.inputs.in_bval)
+
         return super(MRTrix3Base, self)._format_arg(name, trait_spec, value)
+
+    def _parse_inputs(self, skip=None):
+        if skip is None:
+            skip = []
+        if (isdefined(self.inputs.grad_file) or
+                isdefined(self.inputs.grad_fsl)):
+            skip += ['in_bvec', 'in_bval']
+
+        is_bvec = isdefined(self.inputs.in_bvec)
+        is_bval = isdefined(self.inputs.in_bval)
+        if is_bvec or is_bval:
+            if not is_bvec or not is_bval:
+                raise RuntimeError('If using bvecs and bvals inputs, both'
+                                   'should be defined')
+            skip += ['in_bval']
+
+        return super(MRTrix3Base, self)._parse_inputs(skip=skip)

nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py

@@ -17,6 +17,9 @@ def test_BrainMask_inputs():
     ignore_exception=dict(nohash=True,
     usedefault=True,
     ),
+    in_bval=dict(),
+    in_bvec=dict(argstr='-fslgrad %s %s',
+    ),
     in_file=dict(argstr='%s',
     mandatory=True,
     position=-2,

nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py

@@ -17,6 +17,9 @@ def test_EstimateFOD_inputs():
     ignore_exception=dict(nohash=True,
     usedefault=True,
     ),
+    in_bval=dict(),
+    in_bvec=dict(argstr='-fslgrad %s %s',
+    ),
     in_dirs=dict(argstr='-directions %s',
     ),
     in_file=dict(argstr='%s',

nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py

@@ -17,6 +17,9 @@ def test_FitTensor_inputs():
     ignore_exception=dict(nohash=True,
     usedefault=True,
     ),
+    in_bval=dict(),
+    in_bvec=dict(argstr='-fslgrad %s %s',
+    ),
     in_file=dict(argstr='%s',
     mandatory=True,
     position=-2,

nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py

@@ -19,6 +19,9 @@ def test_ResponseSD_inputs():
     ignore_exception=dict(nohash=True,
     usedefault=True,
     ),
+    in_bval=dict(),
+    in_bvec=dict(argstr='-fslgrad %s %s',
+    ),
     in_file=dict(argstr='%s',
     mandatory=True,
     position=-2,

nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py

@@ -34,6 +34,9 @@ def test_Tractography_inputs():
     ignore_exception=dict(nohash=True,
     usedefault=True,
     ),
+    in_bval=dict(),
+    in_bvec=dict(argstr='-fslgrad %s %s',
+    ),
     in_file=dict(argstr='%s',
     mandatory=True,
     position=-2,