streamline outputs generation

Author: chrisgorgo

nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py

@@ -77,7 +77,9 @@ def test_DiffusionTensorStreamlineTrack_inputs():
     no_mask_interpolation=dict(argstr='-nomaskinterp',
     ),
     out_file=dict(argstr='%s',
-    genfile=True,
+    name_source=['in_file'],
+    name_template='%s_tracked.tck',
+    output_name='tracked.tck',
     position=-1,
     ),
     seed_file=dict(argstr='-seed %s',

nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py

@@ -75,7 +75,9 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs():
     no_mask_interpolation=dict(argstr='-nomaskinterp',
     ),
     out_file=dict(argstr='%s',
-    genfile=True,
+    name_source=['in_file'],
+    name_template='%s_tracked.tck',
+    output_name='tracked.tck',
     position=-1,
     ),
     seed_file=dict(argstr='-seed %s',

nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py

@@ -73,7 +73,9 @@ def test_SphericallyDeconvolutedStreamlineTrack_inputs():
     no_mask_interpolation=dict(argstr='-nomaskinterp',
     ),
     out_file=dict(argstr='%s',
-    genfile=True,
+    name_source=['in_file'],
+    name_template='%s_tracked.tck',
+    output_name='tracked.tck',
     position=-1,
     ),
     seed_file=dict(argstr='-seed %s',

nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py

@@ -73,7 +73,9 @@ def test_StreamlineTrack_inputs():
     no_mask_interpolation=dict(argstr='-nomaskinterp',
     ),
     out_file=dict(argstr='%s',
-    genfile=True,
+    name_source=['in_file'],
+    name_template='%s_tracked.tck',
+    output_name='tracked.tck',
     position=-1,
     ),
     seed_file=dict(argstr='-seed %s',

nipype/interfaces/mrtrix/tracking.py

@@ -127,7 +127,8 @@ class StreamlineTrackInputSpec(CommandLineInputSpec):
 
     initial_direction = traits.List(traits.Int, desc='Specify the initial tracking direction as a vector',
         argstr='-initdirection %s', minlen=2, maxlen=2, units='voxels')
-    out_file = File(argstr='%s', position= -1, genfile=True, desc='output data file')
+    out_file = File(argstr='%s', position= -1, name_source = ['in_file'], name_template='%s_tracked.tck', 
+                    output_name='tracked.tck', desc='output data file')
 
 class StreamlineTrackOutputSpec(TraitedSpec):
     tracked = File(exists=True, desc='output file containing reconstructed tracts')
@@ -156,20 +157,6 @@ class StreamlineTrack(CommandLine):
     input_spec = StreamlineTrackInputSpec
     output_spec = StreamlineTrackOutputSpec
 
-    def _list_outputs(self):
-        outputs = self.output_spec().get()
-        outputs['tracked'] = op.abspath(self._gen_outfilename())
-        return outputs
-
-    def _gen_filename(self, name):
-        if name is 'out_file':
-            return self._gen_outfilename()
-        else:
-            return None
-
-    def _gen_outfilename(self):
-        _, name , _ = split_filename(self.inputs.in_file)
-        return name + '_tracked.tck'
 
 class DiffusionTensorStreamlineTrackInputSpec(StreamlineTrackInputSpec):
     gradient_encoding_file = File(exists=True, argstr='-grad %s', mandatory=True, position=-2,