changing arguments names to default values for traits (closes #2532)

nipype/algorithms/confounds.py

@@ -390,13 +390,12 @@ class CompCorInputSpec(BaseInterfaceInputSpec):
         desc='Detrend time series prior to component '
         'extraction')
     use_regress_poly = traits.Bool(
-        True,
         deprecated='0.15.0',
         new_name='pre_filter',
         desc=('use polynomial regression '
               'pre-component extraction'))
     regress_poly_degree = traits.Range(
-        low=1, default=1, usedefault=True, desc='the degree polynomial to use')
+        low=1, value=1, usedefault=True, desc='the degree polynomial to use')
     header_prefix = traits.Str(
         desc=('the desired header for the output tsv '
               'file (one column). If undefined, will '

nipype/algorithms/mesh.py

@@ -289,6 +289,7 @@ class MeshWarpMathsInputSpec(BaseInterfaceInputSpec):
         float_trait,
         File(exists=True),
         default=1.0,
+        usedefault=True,
         mandatory=True,
         desc='image, float or tuple of floats to act as operator')
 

nipype/algorithms/rapidart.py

@@ -234,8 +234,9 @@ class ArtifactDetectInputSpec(BaseInterfaceInputSpec):
         desc=("Mask threshold to be used if mask_type"
               " is 'thresh'."))
     intersect_mask = traits.Bool(
-        True, desc=("Intersect the masks when computed from "
-                    "spm_global."))
+        True, usedefault=True,
+        desc=("Intersect the masks when computed from "
+              "spm_global."))
     save_plot = traits.Bool(
         True, desc="save plots containing outliers", usedefault=True)
     plot_type = traits.Enum(

nipype/algorithms/tests/test_auto_ArtifactDetect.py

@@ -12,7 +12,7 @@ def test_ArtifactDetect_inputs():
             nohash=True,
             usedefault=True,
         ),
-        intersect_mask=dict(),
+        intersect_mask=dict(usedefault=True, ),
         mask_file=dict(),
         mask_threshold=dict(),
         mask_type=dict(mandatory=True, ),

nipype/algorithms/tests/test_auto_MeshWarpMaths.py

@@ -13,7 +13,10 @@ def test_MeshWarpMaths_inputs():
         ),
         in_surf=dict(mandatory=True, ),
         operation=dict(usedefault=True, ),
-        operator=dict(mandatory=True, ),
+        operator=dict(
+            mandatory=True,
+            usedefault=True,
+        ),
         out_file=dict(usedefault=True, ),
         out_warp=dict(usedefault=True, ),
     )

nipype/interfaces/afni/preprocess.py

@@ -1612,6 +1612,7 @@ class OutlierCountInputSpec(CommandLineInputSpec):
         value=1e-3,
         low=0.0,
         high=1.0,
+        usedefault=True,
         argstr='-qthr %.5f',
         desc='indicate a value for q to compute alpha')
     autoclip = traits.Bool(
@@ -1681,7 +1682,7 @@ class OutlierCount(CommandLine):
     >>> toutcount = afni.OutlierCount()
     >>> toutcount.inputs.in_file = 'functional.nii'
     >>> toutcount.cmdline  # doctest: +ELLIPSIS
-    '3dToutcount functional.nii'
+    '3dToutcount -qthr 0.00100 functional.nii'
     >>> res = toutcount.run()  # doctest: +SKIP
 
     """

nipype/interfaces/afni/tests/test_auto_Cat.py

@@ -38,6 +38,7 @@ def test_Cat_inputs():
             argstr='> %s',
             mandatory=True,
             position=-1,
+            usedefault=True,
         ),
         out_fint=dict(
             argstr='-f',

nipype/interfaces/afni/tests/test_auto_NwarpApply.py

@@ -20,7 +20,10 @@ def test_NwarpApply_inputs():
             argstr='-source %s',
             mandatory=True,
         ),
-        interp=dict(argstr='-interp %s', ),
+        interp=dict(
+            argstr='-interp %s',
+            usedefault=True,
+        ),
         inv_warp=dict(argstr='-iwarp', ),
         master=dict(argstr='-master %s', ),
         out_file=dict(

nipype/interfaces/afni/tests/test_auto_NwarpCat.py

@@ -21,7 +21,10 @@ def test_NwarpCat_inputs():
             mandatory=True,
             position=-1,
         ),
-        interp=dict(argstr='-interp %s', ),
+        interp=dict(
+            argstr='-interp %s',
+            usedefault=True,
+        ),
         inv_warp=dict(argstr='-iwarp', ),
         num_threads=dict(
             nohash=True,

nipype/interfaces/afni/tests/test_auto_OneDToolPy.py

@@ -34,7 +34,6 @@ def test_OneDToolPy_inputs():
         show_cormat_warnings=dict(
             argstr='-show_cormat_warnings |& tee %s',
             position=-1,
-            usedefault=False,
             xor=['out_file'],
         ),
         show_indices_interest=dict(argstr='-show_indices_interest', ),

nipype/interfaces/afni/tests/test_auto_OutlierCount.py

@@ -59,7 +59,10 @@ def test_OutlierCount_inputs():
             output_name='out_outliers',
         ),
         polort=dict(argstr='-polort %d', ),
-        qthr=dict(argstr='-qthr %.5f', ),
+        qthr=dict(
+            argstr='-qthr %.5f',
+            usedefault=True,
+        ),
         save_outliers=dict(usedefault=True, ),
         terminal_output=dict(
             deprecated='1.0.0',

nipype/interfaces/afni/utils.py

@@ -479,7 +479,8 @@ class CatInputSpec(AFNICommandInputSpec):
         File(exists=True), argstr="%s", mandatory=True, position=-2)
     out_file = File(
         argstr='> %s',
-        default='catout.1d',
+        value='catout.1d',
+        usedefault=True,
         desc='output (concatenated) file name',
         position=-1,
         mandatory=True)
@@ -1610,6 +1611,7 @@ class NwarpApplyInputSpec(CommandLineInputSpec):
         desc='the name of the master dataset, which defines the output grid',
         argstr='-master %s')
     interp = traits.Enum(
+        'wsinc5',
         'NN',
         'nearestneighbour',
         'nearestneighbor',
@@ -1619,10 +1621,9 @@ class NwarpApplyInputSpec(CommandLineInputSpec):
         'tricubic',
         'quintic',
         'triquintic',
-        'wsinc5',
         desc='defines interpolation method to use during warp',
         argstr='-interp %s',
-        default='wsinc5')
+        usedefault=True)
     ainterp = traits.Enum(
         'NN',
         'nearestneighbour',
@@ -1636,8 +1637,7 @@ class NwarpApplyInputSpec(CommandLineInputSpec):
         'wsinc5',
         desc='specify a different interpolation method than might '
         'be used for the warp',
-        argstr='-ainterp %s',
-        default='wsinc5')
+        argstr='-ainterp %s')
     out_file = File(
         name_template='%s_Nwarp',
         desc='output image file name',
@@ -1670,7 +1670,7 @@ class NwarpApply(AFNICommandBase):
     >>> nwarp.inputs.master = 'NWARP'
     >>> nwarp.inputs.warp = "'Fred_WARP+tlrc Fred.Xaff12.1D'"
     >>> nwarp.cmdline
-    "3dNwarpApply -source Fred+orig -master NWARP -prefix Fred+orig_Nwarp -nwarp \'Fred_WARP+tlrc Fred.Xaff12.1D\'"
+    "3dNwarpApply -source Fred+orig -interp wsinc5 -master NWARP -prefix Fred+orig_Nwarp -nwarp \'Fred_WARP+tlrc Fred.Xaff12.1D\'"
     >>> res = nwarp.run()  # doctest: +SKIP
 
     """
@@ -1696,13 +1696,13 @@ class NwarpCatInputSpec(AFNICommandInputSpec):
     inv_warp = traits.Bool(
         desc='invert the final warp before output', argstr='-iwarp')
     interp = traits.Enum(
+        'wsinc5',
         'linear',
         'quintic',
-        'wsinc5',
         desc='specify a different interpolation method than might '
         'be used for the warp',
         argstr='-interp %s',
-        default='wsinc5')
+        usedefault=True)
     expad = traits.Int(
         desc='Pad the nonlinear warps by the given number of voxels voxels in '
         'all directions. The warp displacements are extended by linear '
@@ -1764,7 +1764,7 @@ class NwarpCat(AFNICommand):
     >>> nwarpcat.inputs.in_files = ['Q25_warp+tlrc.HEAD', ('IDENT', 'structural.nii')]
     >>> nwarpcat.inputs.out_file = 'Fred_total_WARP'
     >>> nwarpcat.cmdline
-    "3dNwarpCat -prefix Fred_total_WARP Q25_warp+tlrc.HEAD 'IDENT(structural.nii)'"
+    "3dNwarpCat -interp wsinc5 -prefix Fred_total_WARP Q25_warp+tlrc.HEAD 'IDENT(structural.nii)'"
     >>> res = nwarpcat.run()  # doctest: +SKIP
 
     """
@@ -1841,8 +1841,6 @@ class OneDToolPyInputSpec(AFNIPythonCommandInputSpec):
     show_cormat_warnings = traits.File(
         desc='Write cormat warnings to a file',
         argstr="-show_cormat_warnings |& tee %s",
-        default="out.cormat_warn.txt",
-        usedefault=False,
         position=-1,
         xor=['out_file'])
     show_indices_interest = traits.Bool(

nipype/interfaces/ants/registration.py

@@ -17,7 +17,6 @@ class ANTSInputSpec(ANTSCommandInputSpec):
         3,
         2,
         argstr='%d',
-        usedefault=False,
         position=1,
         desc='image dimension (2 or 3)')
     fixed_image = InputMultiPath(
@@ -98,7 +97,7 @@ class ANTSInputSpec(ANTSCommandInputSpec):
     symmetry_type = traits.Float(requires=['delta_time'], desc='')
 
     use_histogram_matching = traits.Bool(
-        argstr='%s', default=True, usedefault=True)
+        argstr='%s', default_value=True, usedefault=True)
     number_of_iterations = traits.List(
         traits.Int(), argstr='--number-of-iterations %s', sep='x')
     smoothing_sigmas = traits.List(
@@ -324,7 +323,6 @@ class RegistrationInputSpec(ANTSCommandInputSpec):
         1,
         2,
         argstr='%s',
-        default=0,
         xor=['initial_moving_transform'],
         desc="Align the moving_image nad fixed_image befor registration using"
         "the geometric center of the images (=0), the image intensities (=1),"
@@ -339,7 +337,7 @@ class RegistrationInputSpec(ANTSCommandInputSpec):
         desc='the metric(s) to use for each stage. '
         'Note that multiple metrics per stage are not supported '
         'in ANTS 1.9.1 and earlier.')
-    metric_weight_item_trait = traits.Float(1.0)
+    metric_weight_item_trait = traits.Float(1.0, usedefault=True)
     metric_weight_stage_trait = traits.Either(
         metric_weight_item_trait, traits.List(metric_weight_item_trait))
     metric_weight = traits.List(
@@ -350,7 +348,7 @@ class RegistrationInputSpec(ANTSCommandInputSpec):
         mandatory=True,
         desc='the metric weight(s) for each stage. '
         'The weights must sum to 1 per stage.')
-    radius_bins_item_trait = traits.Int(5)
+    radius_bins_item_trait = traits.Int(5, usedefault=True)
     radius_bins_stage_trait = traits.Either(
         radius_bins_item_trait, traits.List(radius_bins_item_trait))
     radius_or_number_of_bins = traits.List(
@@ -405,20 +403,20 @@ class RegistrationInputSpec(ANTSCommandInputSpec):
 
     write_composite_transform = traits.Bool(
         argstr='--write-composite-transform %d',
-        default=False,
+        default_value=False,
         usedefault=True,
         desc='')
     collapse_output_transforms = traits.Bool(
         argstr='--collapse-output-transforms %d',
-        default=True,
+        default_value=True,
         usedefault=True,  # This should be true for explicit completeness
         desc=('Collapse output transforms. Specifically, enabling this option '
               'combines all adjacent linear transforms and composes all '
               'adjacent displacement field transforms before writing the '
               'results to disk.'))
     initialize_transforms_per_stage = traits.Bool(
         argstr='--initialize-transforms-per-stage %d',
-        default=False,
+        default_value=False,
         usedefault=True,  # This should be true for explicit completeness
         desc=
         ('Initialize linear transforms from the previous stage. By enabling this option, '
@@ -430,7 +428,7 @@ class RegistrationInputSpec(ANTSCommandInputSpec):
     # values instead of booleans
     float = traits.Bool(
         argstr='--float %d',
-        default=False,
+        default_value=False,
         desc='Use float instead of double for computations.')
 
     transforms = traits.List(
@@ -532,7 +530,7 @@ class RegistrationInputSpec(ANTSCommandInputSpec):
         usedefault=True,
         desc="The Lower quantile to clip image ranges")
 
-    verbose = traits.Bool(argstr='-v', default=False)
+    verbose = traits.Bool(argstr='-v', default_value=False, usedefault=True)
 
 
 class RegistrationOutputSpec(TraitedSpec):
@@ -1386,7 +1384,7 @@ class MeasureImageSimilarityInputSpec(ANTSCommandInputSpec):
     )
     metric_weight = traits.Float(
         requires=['metric'],
-        default=1.0,
+        default_value=1.0,
         usedefault=True,
         desc='The "metricWeight" variable is not used.',
     )
@@ -1401,7 +1399,6 @@ class MeasureImageSimilarityInputSpec(ANTSCommandInputSpec):
         "Regular",
         "Random",
         requires=['metric'],
-        default="None",
         usedefault=True,
         desc='Manner of choosing point set over which to optimize the metric. '
         'Defaults to "None" (i.e. a dense sampling of one sample per voxel).')
@@ -1523,10 +1520,10 @@ class RegistrationSynQuickInputSpec(ANTSCommandInputSpec):
 
     use_histogram_matching = traits.Bool(False, argstr='-j %d',
                                          desc='use histogram matching')
-    histogram_bins = traits.Int(default_value=32, argstr='-r %d',
+    histogram_bins = traits.Int(default_value=32, usedefault=True, argstr='-r %d',
                                 desc='histogram bins for mutual information in SyN stage \
                                  (default = 32)')
-    spline_distance = traits.Int(default_value=26, argstr='-s %d',
+    spline_distance = traits.Int(default_value=26, usedefault=True, argstr='-s %d',
                                  desc='spline distance for deformable B-spline SyN transform \
                                  (default = 26)')
     precision_type = traits.Enum('double', 'float', argstr='-p %s',
@@ -1556,7 +1553,7 @@ class RegistrationSynQuick(ANTSCommand):
     >>> reg.inputs.moving_image = 'moving1.nii'
     >>> reg.inputs.num_threads = 2
     >>> reg.cmdline
-    'antsRegistrationSyNQuick.sh -d 3 -f fixed1.nii -m moving1.nii -n 2 -o transform -p d -t s'
+    'antsRegistrationSyNQuick.sh -d 3 -f fixed1.nii -r 32 -m moving1.nii -n 2 -o transform -p d -s 26 -t s'
     >>> reg.run()  # doctest: +SKIP
 
     example for multiple images
@@ -1567,7 +1564,8 @@ class RegistrationSynQuick(ANTSCommand):
     >>> reg.inputs.moving_image = ['moving1.nii', 'moving2.nii']
     >>> reg.inputs.num_threads = 2
     >>> reg.cmdline
-    'antsRegistrationSyNQuick.sh -d 3 -f fixed1.nii -f fixed2.nii -m moving1.nii -m moving2.nii -n 2 -o transform -p d -t s'
+    'antsRegistrationSyNQuick.sh -d 3 -f fixed1.nii -f fixed2.nii -r 32 -m moving1.nii -m moving2.nii \
+-n 2 -o transform -p d -s 26 -t s'
     >>> reg.run()  # doctest: +SKIP
     """
 

nipype/interfaces/ants/resampling.py

@@ -359,7 +359,8 @@ class ApplyTransformsInputSpec(ANTSCommandInputSpec):
         desc='output a composite warp file instead of a transformed image')
     float = traits.Bool(
         argstr='--float %d',
-        default=False,
+        default_value=False,
+        usedefault=True,
         desc='Use float instead of double for computations.')
 
 
@@ -380,7 +381,7 @@ class ApplyTransforms(ANTSCommand):
     >>> at.inputs.reference_image = 'fixed1.nii'
     >>> at.inputs.transforms = 'identity'
     >>> at.cmdline
-    'antsApplyTransforms --default-value 0 --input moving1.nii \
+    'antsApplyTransforms --default-value 0 --float 0 --input moving1.nii \
 --interpolation Linear --output moving1_trans.nii \
 --reference-image fixed1.nii -t identity'
 
@@ -394,9 +395,9 @@ class ApplyTransforms(ANTSCommand):
     >>> at.inputs.transforms = ['ants_Warp.nii.gz', 'trans.mat']
     >>> at.inputs.invert_transform_flags = [False, False]
     >>> at.cmdline
-    'antsApplyTransforms --default-value 0 --dimensionality 3 --input moving1.nii --interpolation Linear \
---output deformed_moving1.nii --reference-image fixed1.nii --transform [ ants_Warp.nii.gz, 0 ] \
---transform [ trans.mat, 0 ]'
+    'antsApplyTransforms --default-value 0 --dimensionality 3 --float 0 --input moving1.nii \
+--interpolation Linear --output deformed_moving1.nii --reference-image fixed1.nii \
+--transform [ ants_Warp.nii.gz, 0 ] --transform [ trans.mat, 0 ]'
 
     >>> at1 = ApplyTransforms()
     >>> at1.inputs.dimension = 3
@@ -409,9 +410,9 @@ class ApplyTransforms(ANTSCommand):
     >>> at1.inputs.transforms = ['ants_Warp.nii.gz', 'trans.mat']
     >>> at1.inputs.invert_transform_flags = [False, False]
     >>> at1.cmdline
-    'antsApplyTransforms --default-value 0 --dimensionality 3 --input moving1.nii --interpolation BSpline[ 5 ] \
---output deformed_moving1.nii --reference-image fixed1.nii --transform [ ants_Warp.nii.gz, 0 ] \
---transform [ trans.mat, 0 ]'
+    'antsApplyTransforms --default-value 0 --dimensionality 3 --float 0 --input moving1.nii \
+--interpolation BSpline[ 5 ] --output deformed_moving1.nii --reference-image fixed1.nii \
+--transform [ ants_Warp.nii.gz, 0 ] --transform [ trans.mat, 0 ]'
     """
     _cmd = 'antsApplyTransforms'
     input_spec = ApplyTransformsInputSpec