update mrdegibbs and dwibiascorrect

Author: josephmje

nipype/interfaces/mrtrix3/preprocess.py

@@ -30,19 +30,19 @@ class DWIDenoiseInputSpec(MRTrix3BaseInputSpec):
         name_source='in_file',
         keep_extension=True,
         argstr='-noise %s',
-        desc="the output noise map",
+        desc='the output noise map',
         genfile=True)
     out_file = File(name_template='%s_denoised',
         name_source='in_file',
         keep_extension=True,
-        argstr="%s",
+        argstr='%s',
         position=-1,
-        desc="the output denoised DWI image",
+        desc='the output denoised DWI image',
         genfile=True)
 
 class DWIDenoiseOutputSpec(TraitedSpec):
-    out_noisemap = File(desc="the output noise map", exists=True)
-    out_file = File(desc="the output denoised DWI image", exists=True)
+    out_noisemap = File(desc='the output noise map', exists=True)
+    out_file = File(desc='the output denoised DWI image', exists=True)
 
 class DWIDenoise(MRTrix3Base):
     """
@@ -89,17 +89,18 @@ class MRDeGibbsInputSpec(MRTrix3BaseInputSpec):
         desc='input DWI image')
     axes = traits.ListInt(
         default_value=[0,1],
-        sep=',',
-        minlen=1,
-        maxlen=4,
         usedefault=True,
+        sep=',',
+        minlen=2,
+        maxlen=2,
         argstr='-axes %s',
-        desc='select the slice axes (default = 0,1)')
+        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,
         argstr='-nshifts %d',
-        desc='discretizaiton of subpixel spacing (default = 20)')
+        desc='discretization of subpixel spacing (default = 20)')
     minW = traits.Int(
         default_value=1,
         usedefault=True,
@@ -112,16 +113,16 @@ class MRDeGibbsInputSpec(MRTrix3BaseInputSpec):
         argstr='-maxW %d',
         desc='right border of window used for total variation (TV) computation '
              '(default = 3)')
-    out_file = File(name_template='%s_unring',
+    out_file = File(name_template='%s_unr',
         name_source='in_file',
         keep_extension=True,
-        argstr="%s",
+        argstr='%s',
         position=-1,
-        desc="the output unringed DWI image",
+        desc='the output unringed DWI image',
         genfile=True)
 
 class MRDeGibbsOutputSpec(TraitedSpec):
-    out_file = File(desc="the output unringed DWI image", exists=True)
+    out_file = File(desc='the output unringed DWI image', exists=True)
 
 class MRDeGibbs(MRTrix3Base):
     """
@@ -155,7 +156,7 @@ class MRDeGibbs(MRTrix3Base):
     >>> unring = mrt.MRDeGibbs()
     >>> unring.inputs.in_file = 'dwi.mif'
     >>> unring.cmdline                               # doctest: +ELLIPSIS
-    'mrdegibbs dwi.mif dwi_unring.mif'
+    'mrdegibbs dwi.mif dwi_unr.mif'
     >>> unring.run()                                 # doctest: +SKIP
     """
 
@@ -174,23 +175,27 @@ class DWIBiasCorrectInputSpec(MRTrix3BaseInputSpec):
     in_mask = File(
         argstr='-mask %s',
         desc='input mask image for bias field estimation')
-    _xor_inputs = ('use_ants', 'use_fsl')
+    _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_inputs)
+        xor=_xor_methods)
     use_fsl = traits.Bool(
         argstr='-fsl',
         desc='use FSL FAST to estimate the inhomogeneity field',
-        xor=_xor_inputs,
+        xor=_xor_methods,
         min_ver='5.0.10')
-    # only one of either grad or fslgrad should be supplied
-    grad = File(
+    _xor_grads = ('mrtrix_grad', 'fsl_grad')
+    mrtrix_grad = File(
         argstr='-grad %s',
-        desc='diffusion gradient table in MRtrix format')
-    fslgrad = File(
+        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')
+        desc='diffusion gradient table in FSL bvecs/bvals format',
+        xor=_xor_grads)
     out_bias = File(name_template='%s_biasfield',
         name_source='in_file',
         keep_extension=True,
@@ -200,14 +205,14 @@ class DWIBiasCorrectInputSpec(MRTrix3BaseInputSpec):
     out_file = File(name_template='%s_biascorr',
         name_source='in_file',
         keep_extension=True,
-        argstr="%s",
+        argstr='%s',
         position=-1,
-        desc="the output bias corrected DWI image",
+        desc='the output bias corrected DWI image',
         genfile=True)
 
 class DWIBiasCorrectOutputSpec(TraitedSpec):
-    out_bias = File(desc="the output estimated bias field")
-    out_file = File(desc="the output bias corrected DWI image", exists=True)
+    out_bias = File(desc='the output estimated bias field')
+    out_file = File(desc='the output bias corrected DWI image', exists=True)
 
 class DWIBiasCorrect(MRTrix3Base):
     """
@@ -223,7 +228,7 @@ class DWIBiasCorrect(MRTrix3Base):
     >>> bias_correct = mrt.DWIBiasCorrect()
     >>> bias_correct.inputs.in_file = 'dwi.mif'
     >>> bias_correct.cmdline                           # doctest: +ELLIPSIS
-    'dwibiascorrect dwi.mif dwi_biascorr.mif'
+    'dwibiascorrect -ants dwi.mif dwi_biascorr.mif'
     >>> bias_correct.run()                             # doctest: +SKIP
     """