FIX: Improve output handling in DWIDenoise and DWIBiasCorrect

nipype/interfaces/mrtrix3/base.py

@@ -47,12 +47,14 @@ class MRTrix3BaseInputSpec(CommandLineInputSpec):
     grad_file = File(
         exists=True,
         argstr='-grad %s',
-        desc='dw gradient scheme (MRTrix format')
+        desc='dw gradient scheme (MRTrix format)',
+        xor=['grad_fsl'])
     grad_fsl = traits.Tuple(
         File(exists=True),
         File(exists=True),
         argstr='-fslgrad %s %s',
-        desc='(bvecs, bvals) dw gradient scheme (FSL format')
+        desc='(bvecs, bvals) dw gradient scheme (FSL format)',
+        xor=['grad_file'])
     bval_scale = traits.Enum(
         'yes',
         'no',

nipype/interfaces/mrtrix3/preprocess.py

@@ -23,20 +23,27 @@ class DWIDenoiseInputSpec(MRTrix3BaseInputSpec):
         argstr='-mask %s',
         position=1,
         desc='mask image')
-    extent = traits.Tuple((traits.Int, traits.Int, traits.Int),
+    extent = traits.Tuple(
+        (traits.Int, traits.Int, traits.Int),
         argstr='-extent %d,%d,%d',
         desc='set the window size of the denoising filter. (default = 5,5,5)')
     noise = File(
         argstr='-noise %s',
-        desc='the output noise map')
-    out_file = File(name_template='%s_denoised',
+        name_template='%s_noise',
         name_source='in_file',
         keep_extension=True,
+        desc='the output noise map',
+        genfile=True)
+    out_file = File(
         argstr='%s',
         position=-1,
+        name_template='%s_denoised',
+        name_source='in_file',
+        keep_extension=True,
         desc='the output denoised DWI image',
         genfile=True)
 
+
 class DWIDenoiseOutputSpec(TraitedSpec):
     noise = File(desc='the output noise map', exists=True)
     out_file = File(desc='the output denoised DWI image', exists=True)
@@ -67,22 +74,16 @@ class DWIDenoise(MRTrix3Base):
     >>> denoise = mrt.DWIDenoise()
     >>> denoise.inputs.in_file = 'dwi.mif'
     >>> denoise.inputs.mask = 'mask.mif'
+    >>> denoise.inputs.noise = 'noise.mif'
     >>> denoise.cmdline                               # doctest: +ELLIPSIS
-    'dwidenoise -mask mask.mif dwi.mif dwi_denoised.mif'
+    'dwidenoise -mask mask.mif -noise noise.mif dwi.mif dwi_denoised.mif'
     >>> denoise.run()                                 # doctest: +SKIP
     """
 
     _cmd = 'dwidenoise'
     input_spec = DWIDenoiseInputSpec
     output_spec = DWIDenoiseOutputSpec
 
-    def _list_outputs(self):
-        outputs = self.output_spec().get()
-        outputs['out_file'] = op.abspath(self.inputs.out_file)
-        if self.inputs.noise != Undefined:
-            outputs['noise'] = op.abspath(self.inputs.noise)
-        return outputs
-
 
 class MRDeGibbsInputSpec(MRTrix3BaseInputSpec):
     in_file = File(
@@ -92,32 +93,29 @@ class MRDeGibbsInputSpec(MRTrix3BaseInputSpec):
         mandatory=True,
         desc='input DWI image')
     axes = traits.ListInt(
-        default_value=[0,1],
-        usedefault=True,
+        [0,1],
         sep=',',
         minlen=2,
         maxlen=2,
         argstr='-axes %s',
         desc='indicate the plane in which the data was acquired (axial = 0,1; '
              'coronal = 0,2; sagittal = 1,2')
     nshifts = traits.Int(
-        default_value=20,
-        usedefault=True,
+        20,
         argstr='-nshifts %d',
         desc='discretization of subpixel spacing (default = 20)')
     minW = traits.Int(
-        default_value=1,
-        usedefault=True,
+        1,
         argstr='-minW %d',
         desc='left border of window used for total variation (TV) computation '
              '(default = 1)')
     maxW = traits.Int(
-        default_value=3,
-        usedefault=True,
+        3,
         argstr='-maxW %d',
         desc='right border of window used for total variation (TV) computation '
              '(default = 3)')
-    out_file = File(name_template='%s_unr',
+    out_file = File(
+        name_template='%s_unr',
         name_source='in_file',
         keep_extension=True,
         argstr='%s',
@@ -160,7 +158,7 @@ class MRDeGibbs(MRTrix3Base):
     >>> unring = mrt.MRDeGibbs()
     >>> unring.inputs.in_file = 'dwi.mif'
     >>> unring.cmdline
-    'mrdegibbs -axes 0,1 -maxW 3 -minW 1 -nshifts 20 dwi.mif dwi_unr.mif'
+    'mrdegibbs dwi.mif dwi_unr.mif'
     >>> unring.run()                                 # doctest: +SKIP
     """
 
@@ -179,31 +177,19 @@ class DWIBiasCorrectInputSpec(MRTrix3BaseInputSpec):
     in_mask = File(
         argstr='-mask %s',
         desc='input mask image for bias field estimation')
-    _xor_methods = ('use_ants', 'use_fsl')
     use_ants = traits.Bool(
-        default_value=True,
-        usedefault=True,
         argstr='-ants',
         desc='use ANTS N4 to estimate the inhomogeneity field',
-        xor=_xor_methods)
+        xor=['use_fsl'])
     use_fsl = traits.Bool(
         argstr='-fsl',
         desc='use FSL FAST to estimate the inhomogeneity field',
-        xor=_xor_methods,
-        min_ver='5.0.10')
-    _xor_grads = ('mrtrix_grad', 'fsl_grad')
-    mrtrix_grad = File(
-        argstr='-grad %s',
-        desc='diffusion gradient table in MRtrix format',
-        xor=_xor_grads)
-    fsl_grad = File(
-        argstr='-fslgrad %s %s',
-        desc='diffusion gradient table in FSL bvecs/bvals format',
-        xor=_xor_grads)
+        xor=['use_ants'])
     bias = File(
         argstr='-bias %s',
         desc='bias field')
-    out_file = File(name_template='%s_biascorr',
+    out_file = File(
+        name_template='%s_biascorr',
         name_source='in_file',
         keep_extension=True,
         argstr='%s',
@@ -228,6 +214,7 @@ class DWIBiasCorrect(MRTrix3Base):
     >>> import nipype.interfaces.mrtrix3 as mrt
     >>> bias_correct = mrt.DWIBiasCorrect()
     >>> bias_correct.inputs.in_file = 'dwi.mif'
+    >>> bias_correct.inputs.use_ants = True
     >>> bias_correct.cmdline
     'dwibiascorrect -ants dwi.mif dwi_biascorr.mif'
     >>> bias_correct.run()                             # doctest: +SKIP
@@ -237,13 +224,6 @@ class DWIBiasCorrect(MRTrix3Base):
     input_spec = DWIBiasCorrectInputSpec
     output_spec = DWIBiasCorrectOutputSpec
 
-    def _list_outputs(self):
-        outputs = self.output_spec().get()
-        outputs['out_file'] = op.abspath(self.inputs.out_file)
-        if self.inputs.bias != Undefined:
-            outputs['bias'] = op.abspath(self.inputs.bias)
-        return outputs
-
 
 class ResponseSDInputSpec(MRTrix3BaseInputSpec):
     algorithm = traits.Enum(

nipype/interfaces/mrtrix3/tests/test_auto_DWIBiasCorrect.py

@@ -15,16 +15,15 @@ def test_DWIBiasCorrect_inputs():
             nohash=True,
             usedefault=True,
         ),
-        fsl_grad=dict(
-            argstr='-fslgrad %s %s',
-            extensions=None,
-            xor=('mrtrix_grad', 'fsl_grad'),
-        ),
         grad_file=dict(
             argstr='-grad %s',
             extensions=None,
+            xor=['grad_fsl'],
+        ),
+        grad_fsl=dict(
+            argstr='-fslgrad %s %s',
+            xor=['grad_file'],
         ),
-        grad_fsl=dict(argstr='-fslgrad %s %s', ),
         in_bval=dict(extensions=None, ),
         in_bvec=dict(
             argstr='-fslgrad %s %s',
@@ -40,11 +39,6 @@ def test_DWIBiasCorrect_inputs():
             argstr='-mask %s',
             extensions=None,
         ),
-        mrtrix_grad=dict(
-            argstr='-grad %s',
-            extensions=None,
-            xor=('mrtrix_grad', 'fsl_grad'),
-        ),
         nthreads=dict(
             argstr='-nthreads %d',
             nohash=True,
@@ -60,13 +54,11 @@ def test_DWIBiasCorrect_inputs():
         ),
         use_ants=dict(
             argstr='-ants',
-            usedefault=True,
-            xor=('use_ants', 'use_fsl'),
+            xor=['use_fsl'],
         ),
         use_fsl=dict(
             argstr='-fsl',
-            min_ver='5.0.10',
-            xor=('use_ants', 'use_fsl'),
+            xor=['use_ants'],
         ),
     )
     inputs = DWIBiasCorrect.input_spec()

nipype/interfaces/mrtrix3/tests/test_auto_DWIDenoise.py

@@ -15,8 +15,12 @@ def test_DWIDenoise_inputs():
         grad_file=dict(
             argstr='-grad %s',
             extensions=None,
+            xor=['grad_fsl'],
+        ),
+        grad_fsl=dict(
+            argstr='-fslgrad %s %s',
+            xor=['grad_file'],
         ),
-        grad_fsl=dict(argstr='-fslgrad %s %s', ),
         in_bval=dict(extensions=None, ),
         in_bvec=dict(
             argstr='-fslgrad %s %s',
@@ -36,6 +40,10 @@ def test_DWIDenoise_inputs():
         noise=dict(
             argstr='-noise %s',
             extensions=None,
+            genfile=True,
+            keep_extension=True,
+            name_source='in_file',
+            name_template='%s_noise',
         ),
         nthreads=dict(
             argstr='-nthreads %d',

nipype/interfaces/mrtrix3/tests/test_auto_MRDeGibbs.py

@@ -11,7 +11,6 @@ def test_MRDeGibbs_inputs():
             maxlen=2,
             minlen=2,
             sep=',',
-            usedefault=True,
         ),
         bval_scale=dict(argstr='-bvalue_scaling %s', ),
         environ=dict(
@@ -21,8 +20,12 @@ def test_MRDeGibbs_inputs():
         grad_file=dict(
             argstr='-grad %s',
             extensions=None,
+            xor=['grad_fsl'],
+        ),
+        grad_fsl=dict(
+            argstr='-fslgrad %s %s',
+            xor=['grad_file'],
         ),
-        grad_fsl=dict(argstr='-fslgrad %s %s', ),
         in_bval=dict(extensions=None, ),
         in_bvec=dict(
             argstr='-fslgrad %s %s',
@@ -34,18 +37,9 @@ def test_MRDeGibbs_inputs():
             mandatory=True,
             position=-2,
         ),
-        maxW=dict(
-            argstr='-maxW %d',
-            usedefault=True,
-        ),
-        minW=dict(
-            argstr='-minW %d',
-            usedefault=True,
-        ),
-        nshifts=dict(
-            argstr='-nshifts %d',
-            usedefault=True,
-        ),
+        maxW=dict(argstr='-maxW %d', ),
+        minW=dict(argstr='-minW %d', ),
+        nshifts=dict(argstr='-nshifts %d', ),
         nthreads=dict(
             argstr='-nthreads %d',
             nohash=True,