correcting traits to remove warnings

Author: djarecka

nipype/algorithms/confounds.py

@@ -391,6 +391,7 @@ class CompCorInputSpec(BaseInterfaceInputSpec):
         'extraction')
     use_regress_poly = traits.Bool(
         True,
+        usedefault=True,
         deprecated='0.15.0',
         new_name='pre_filter',
         desc=('use polynomial regression '

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_ACompCor.py

@@ -32,6 +32,7 @@ def test_ACompCor_inputs():
         use_regress_poly=dict(
             deprecated='0.15.0',
             new_name='pre_filter',
+            usedefault=True,
         ),
     )
     inputs = ACompCor.input_spec()

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_TCompCor.py

@@ -33,6 +33,7 @@ def test_TCompCor_inputs():
         use_regress_poly=dict(
             deprecated='0.15.0',
             new_name='pre_filter',
+            usedefault=True,
         ),
     )
     inputs = TCompCor.input_spec()

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_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/ants/registration.py

@@ -338,7 +338,7 @@ 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(
@@ -349,7 +349,7 @@ 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(
@@ -1521,10 +1521,10 @@ 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',
@@ -1554,7 +1554,7 @@ 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
@@ -1565,7 +1565,7 @@ 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/segmentation.py

@@ -1511,12 +1511,12 @@ class KellyKapowskiInputSpec(ANTSCommandInputSpec):
         desc="Gradient step size for the optimization.")
 
     smoothing_variance = traits.Float(
-        1.0,
+        1.0, usedefault=True,
         argstr="--smoothing-variance %f",
         desc="Defines the Gaussian smoothing of the hit and total images.")
 
     smoothing_velocity_field = traits.Float(
-        1.5,
+        1.5, usedefault=True,
         argstr="--smoothing-velocity-field-parameter %f",
         desc=
         "Defines the Gaussian smoothing of the velocity field (default = 1.5).\n"
@@ -1528,12 +1528,12 @@ class KellyKapowskiInputSpec(ANTSCommandInputSpec):
         desc="Sets the option for B-spline smoothing of the velocity field.")
 
     number_integration_points = traits.Int(
-        10,
+        10, usedefault=True,
         argstr="--number-of-integration-points %d",
         desc="Number of compositions of the diffeomorphism per iteration.")
 
     max_invert_displacement_field_iters = traits.Int(
-        20,
+        20, usedefault=True,
         argstr="--maximum-number-of-invert-displacement-field-iterations %d",
         desc="Maximum number of iterations for estimating the invert \n"
         "displacement field.")
@@ -1574,16 +1574,12 @@ class KellyKapowski(ANTSCommand):
     >>> kk.inputs.dimension = 3
     >>> kk.inputs.segmentation_image = "segmentation0.nii.gz"
     >>> kk.inputs.convergence = "[45,0.0,10]"
-    >>> kk.inputs.gradient_step = 0.025
-    >>> kk.inputs.smoothing_variance = 1.0
-    >>> kk.inputs.smoothing_velocity_field = 1.5
-    >>> #kk.inputs.use_bspline_smoothing = False
-    >>> kk.inputs.number_integration_points = 10
     >>> kk.inputs.thickness_prior_estimate = 10
     >>> kk.cmdline
     'KellyKapowski --convergence "[45,0.0,10]" \
 --output "[segmentation0_cortical_thickness.nii.gz,segmentation0_warped_white_matter.nii.gz]" \
---image-dimensionality 3 --gradient-step 0.025000 --number-of-integration-points 10 \
+--image-dimensionality 3 --gradient-step 0.025000 \
+--maximum-number-of-invert-displacement-field-iterations 20 --number-of-integration-points 10 \
 --segmentation-image "[segmentation0.nii.gz,2,3]" --smoothing-variance 1.000000 \
 --smoothing-velocity-field-parameter 1.500000 --thickness-prior-estimate 10.000000'
 

nipype/interfaces/ants/tests/test_auto_KellyKapowski.py

@@ -39,20 +39,29 @@ def test_KellyKapowski_inputs():
         ),
         max_invert_displacement_field_iters=dict(
             argstr=
-            '--maximum-number-of-invert-displacement-field-iterations %d', ),
+            '--maximum-number-of-invert-displacement-field-iterations %d',
+            usedefault=True,
+        ),
         num_threads=dict(
             nohash=True,
             usedefault=True,
         ),
         number_integration_points=dict(
-            argstr='--number-of-integration-points %d', ),
+            argstr='--number-of-integration-points %d',
+            usedefault=True,
+        ),
         segmentation_image=dict(
             argstr='--segmentation-image "%s"',
             mandatory=True,
         ),
-        smoothing_variance=dict(argstr='--smoothing-variance %f', ),
+        smoothing_variance=dict(
+            argstr='--smoothing-variance %f',
+            usedefault=True,
+        ),
         smoothing_velocity_field=dict(
-            argstr='--smoothing-velocity-field-parameter %f', ),
+            argstr='--smoothing-velocity-field-parameter %f',
+            usedefault=True,
+        ),
         terminal_output=dict(
             deprecated='1.0.0',
             nohash=True,

nipype/interfaces/ants/tests/test_auto_Registration.py

@@ -71,7 +71,7 @@ def test_Registration_inputs():
             requires=['metric'],
             usedefault=True,
         ),
-        metric_weight_item_trait=dict(),
+        metric_weight_item_trait=dict(usedefault=True, ),
         metric_weight_stage_trait=dict(),
         moving_image=dict(mandatory=True, ),
         moving_image_mask=dict(
@@ -97,7 +97,7 @@ def test_Registration_inputs():
             usedefault=True,
         ),
         output_warped_image=dict(hash_files=False, ),
-        radius_bins_item_trait=dict(),
+        radius_bins_item_trait=dict(usedefault=True, ),
         radius_bins_stage_trait=dict(),
         radius_or_number_of_bins=dict(
             requires=['metric_weight'],

nipype/interfaces/ants/tests/test_auto_RegistrationSynQuick.py

@@ -18,7 +18,10 @@ def test_RegistrationSynQuick_inputs():
             argstr='-f %s...',
             mandatory=True,
         ),
-        histogram_bins=dict(argstr='-r %d', ),
+        histogram_bins=dict(
+            argstr='-r %d',
+            usedefault=True,
+        ),
         ignore_exception=dict(
             deprecated='1.0.0',
             nohash=True,
@@ -40,7 +43,10 @@ def test_RegistrationSynQuick_inputs():
             argstr='-p %s',
             usedefault=True,
         ),
-        spline_distance=dict(argstr='-s %d', ),
+        spline_distance=dict(
+            argstr='-s %d',
+            usedefault=True,
+        ),
         terminal_output=dict(
             deprecated='1.0.0',
             nohash=True,

nipype/interfaces/dipy/preprocess.py

@@ -106,8 +106,8 @@ class DenoiseInputSpec(TraitedSpec):
         desc=('mask in which the standard deviation of noise '
               'will be computed'),
         exists=True)
-    patch_radius = traits.Int(1, desc='patch radius')
-    block_radius = traits.Int(5, desc='block_radius')
+    patch_radius = traits.Int(1, usedefault=True, desc='patch radius')
+    block_radius = traits.Int(5, usedefault=True, desc='block_radius')
     snr = traits.Float(desc='manually set an SNR')
 
 

nipype/interfaces/dipy/tests/test_auto_Denoise.py

@@ -5,15 +5,15 @@
 
 def test_Denoise_inputs():
     input_map = dict(
-        block_radius=dict(),
+        block_radius=dict(usedefault=True, ),
         in_file=dict(mandatory=True, ),
         in_mask=dict(),
         noise_mask=dict(),
         noise_model=dict(
             mandatory=True,
             usedefault=True,
         ),
-        patch_radius=dict(),
+        patch_radius=dict(usedefault=True, ),
         signal_mask=dict(),
         snr=dict(),
     )

nipype/interfaces/dtitk/tests/test_auto_BinThresh.py

@@ -30,6 +30,7 @@ def test_BinThresh_inputs():
             argstr='%g',
             mandatory=True,
             position=2,
+            usedefault=True,
         ),
         out_file=dict(
             argstr='%s',
@@ -52,6 +53,7 @@ def test_BinThresh_inputs():
             argstr='%g',
             mandatory=True,
             position=3,
+            usedefault=True,
         ),
     )
     inputs = BinThresh.input_spec()

nipype/interfaces/dtitk/tests/test_auto_BinThreshTASK.py

@@ -30,6 +30,7 @@ def test_BinThreshTask_inputs():
             argstr='%g',
             mandatory=True,
             position=2,
+            usedefault=True,
         ),
         out_file=dict(
             argstr='%s',
@@ -52,6 +53,7 @@ def test_BinThreshTask_inputs():
             argstr='%g',
             mandatory=True,
             position=3,
+            usedefault=True,
         ),
     )
     inputs = BinThreshTask.input_spec()

nipype/interfaces/dtitk/utils.py

@@ -265,9 +265,11 @@ class BinThreshInputSpec(CommandLineInputSpec):
     out_file = File(desc='output path',  position=1, argstr="%s",
                     keep_extension=True, name_source='in_file',
                     name_template='%s_thrbin')
-    lower_bound = traits.Float(0.01, position=2, argstr="%g", mandatory=True,
+    lower_bound = traits.Float(0.01, usedefault=True,
+                               position=2, argstr="%g", mandatory=True,
                                desc='lower bound of binarization range')
-    upper_bound = traits.Float(100, position=3, argstr="%g", mandatory=True,
+    upper_bound = traits.Float(100, usedefault=True,
+                               position=3, argstr="%g", mandatory=True,
                                desc='upper bound of binarization range')
     inside_value = traits.Float(1, position=4, argstr="%g", usedefault=True,
                                 mandatory=True, desc='value for voxels in '

nipype/interfaces/elastix/base.py

@@ -26,7 +26,7 @@ class ElastixBaseInputSpec(CommandLineInputSpec):
         argstr='-out %s',
         desc='output directory')
     num_threads = traits.Int(
-        1,
+        1, usedefault=True,
         argstr='-threads %01d',
         nohash=True,
         desc='set the maximum number of threads of elastix')

nipype/interfaces/elastix/registration.py

@@ -65,7 +65,7 @@ class Registration(CommandLine):
     >>> reg.inputs.moving_image = 'moving1.nii'
     >>> reg.inputs.parameters = ['elastix.txt']
     >>> reg.cmdline
-    'elastix -f fixed1.nii -m moving1.nii -out ./ -p elastix.txt'
+    'elastix -f fixed1.nii -m moving1.nii -threads 1 -out ./ -p elastix.txt'
 
 
     """
@@ -162,7 +162,7 @@ class ApplyWarp(CommandLine):
     >>> reg.inputs.moving_image = 'moving1.nii'
     >>> reg.inputs.transform_file = 'TransformParameters.0.txt'
     >>> reg.cmdline
-    'transformix -in moving1.nii -out ./ -tp TransformParameters.0.txt'
+    'transformix -in moving1.nii -threads 1 -out ./ -tp TransformParameters.0.txt'
 
 
     """
@@ -205,7 +205,7 @@ class AnalyzeWarp(CommandLine):
     >>> reg = AnalyzeWarp()
     >>> reg.inputs.transform_file = 'TransformParameters.0.txt'
     >>> reg.cmdline
-    'transformix -def all -jac all -jacmat all -out ./ -tp TransformParameters.0.txt'
+    'transformix -def all -jac all -jacmat all -threads 1 -out ./ -tp TransformParameters.0.txt'
 
 
     """
@@ -252,7 +252,7 @@ class PointsWarp(CommandLine):
     >>> reg.inputs.points_file = 'surf1.vtk'
     >>> reg.inputs.transform_file = 'TransformParameters.0.txt'
     >>> reg.cmdline
-    'transformix -out ./ -def surf1.vtk -tp TransformParameters.0.txt'
+    'transformix -threads 1 -out ./ -def surf1.vtk -tp TransformParameters.0.txt'
 
 
     """

nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py

@@ -18,6 +18,7 @@ def test_AnalyzeWarp_inputs():
         num_threads=dict(
             argstr='-threads %01d',
             nohash=True,
+            usedefault=True,
         ),
         output_path=dict(
             argstr='-out %s',

nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py

@@ -22,6 +22,7 @@ def test_ApplyWarp_inputs():
         num_threads=dict(
             argstr='-threads %01d',
             nohash=True,
+            usedefault=True,
         ),
         output_path=dict(
             argstr='-out %s',

nipype/interfaces/elastix/tests/test_auto_PointsWarp.py

@@ -18,6 +18,7 @@ def test_PointsWarp_inputs():
         num_threads=dict(
             argstr='-threads %01d',
             nohash=True,
+            usedefault=True,
         ),
         output_path=dict(
             argstr='-out %s',

nipype/interfaces/elastix/tests/test_auto_Registration.py

@@ -29,6 +29,7 @@ def test_Registration_inputs():
         num_threads=dict(
             argstr='-threads %01d',
             nohash=True,
+            usedefault=True,
         ),
         output_path=dict(
             argstr='-out %s',