Simplify DWIDenoiseInputSpec

Author: mvdoc

nipype/interfaces/mrtrix3/preprocess.py

@@ -16,25 +16,21 @@ class DWIDenoiseInputSpec(MRTrix3BaseInputSpec):
         exists=True,
         argstr='%s',
         position=-2,
-        mandatory=True,
         desc='input DWI image')
     mask = File(
         exists=True,
         argstr='-mask %s',
         position=1,
-        mandatory=False,
         desc='mask image')
     extent = traits.Tuple((traits.Int, traits.Int, traits.Int),
         argstr='-extent %d,%d,%d',
-        mandatory=False,
         desc='set the window size of the denoising filter. (default = 5,5,5)')
     noise = File(
         argstr='-noise %s',
-        mandatory=False,
         desc='noise map')
-    out_file = File('dwi_denoised.mif',
-        exists=False,
-        usedefault=True,
+    out_file = File(name_template='%s_denoised',
+        name_source='in_file',
+        keep_extension=True,
         argstr="%s",
         position=-1,
         desc="the output denoised DWI image")
@@ -77,11 +73,6 @@ class DWIDenoise(MRTrix3Base):
     input_spec = DWIDenoiseInputSpec
     output_spec = DWIDenoiseOutputSpec
 
-    def _list_outputs(self):
-        outputs = self.output_spec().get()
-        outputs['out_file'] = op.abspath(self.inputs.out_file)
-        return outputs
-
 
 class ResponseSDInputSpec(MRTrix3BaseInputSpec):
     algorithm = traits.Enum(

nipype/interfaces/mrtrix3/tests/test_auto_DWIDenoise.py

@@ -11,10 +11,7 @@ def test_DWIDenoise_inputs():
             nohash=True,
             usedefault=True,
         ),
-        extent=dict(
-            argstr='-extent %d,%d,%d',
-            mandatory=False,
-        ),
+        extent=dict(argstr='-extent %d,%d,%d', ),
         grad_file=dict(argstr='-grad %s', ),
         grad_fsl=dict(argstr='-fslgrad %s %s', ),
         ignore_exception=dict(
@@ -26,26 +23,23 @@ def test_DWIDenoise_inputs():
         in_bvec=dict(argstr='-fslgrad %s %s', ),
         in_file=dict(
             argstr='%s',
-            mandatory=True,
             position=-2,
         ),
         mask=dict(
             argstr='-mask %s',
-            mandatory=False,
             position=1,
         ),
-        noise=dict(
-            argstr='-noise %s',
-            mandatory=False,
-        ),
+        noise=dict(argstr='-noise %s', ),
         nthreads=dict(
             argstr='-nthreads %d',
             nohash=True,
         ),
         out_file=dict(
             argstr='%s',
+            keep_extension=True,
+            name_source='in_file',
+            name_template='%s_denoised',
             position=-1,
-            usedefault=True,
         ),
         terminal_output=dict(
             deprecated='1.0.0',