fix: replace all traits.File -> File

Author: oesteban

nipype/algorithms/misc.py

@@ -727,7 +727,7 @@ def _list_outputs(self):
 
 
 class AddCSVRowInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
-    in_file = traits.File(
+    in_file = File(
         mandatory=True, desc='Input comma-separated value (CSV) files')
     _outputs = traits.Dict(traits.Any, value={}, usedefault=True)
 

nipype/interfaces/afni/model.py

@@ -383,7 +383,7 @@ class RemlfitInputSpec(AFNICommandInputSpec):
         'produces a matrix with a single column of all ones',
         argstr='-polort %d',
         xor=['matrix'])
-    matim = traits.File(
+    matim = File(
         desc='read a standard file as the matrix. You can use only Col as '
         'a name in GLTs with these nonstandard matrix input methods, '
         'since the other names come from the \'matrix\' file. '

nipype/interfaces/afni/preprocess.py

@@ -369,7 +369,7 @@ class AllineateInputSpec(AFNICommandInputSpec):
         'larger weights mean that voxel count more in the cost function. '
         'If an image file is given, the volume must be defined on the '
         'same grid as the base dataset')
-    out_weight_file = traits.File(
+    out_weight_file = File(
         argstr='-wtprefix %s',
         desc='Write the weight volume to disk as a dataset',
         xor=['allcostx'])
@@ -966,7 +966,7 @@ class ClipLevelInputSpec(CommandLineInputSpec):
         argstr='-doall',
         position=3,
         xor=('grad'))
-    grad = traits.File(
+    grad = File(
         desc='Also compute a \'gradual\' clip level as a function of voxel '
         'position, and output that to a dataset.',
         argstr='-grad %s',
@@ -1831,7 +1831,7 @@ class ROIStatsInputSpec(CommandLineInputSpec):
              'a \'0\' in the output file. Only active if `num_roi` is '
              'enabled.',
         argstr='-zerofill %s')
-    roisel = traits.File(
+    roisel = File(
         exists=True,
         desc='Only considers ROIs denoted by values found in the specified '
              'file. Note that the order of the ROIs as specified in the file '
@@ -2260,7 +2260,7 @@ class TCorrMapInputSpec(AFNICommandInputSpec):
     polort = traits.Int(argstr='-polort %d')
     bandpass = traits.Tuple(
         (traits.Float(), traits.Float()), argstr='-bpass %f %f')
-    regress_out_timeseries = traits.File(exists=True, argstr='-ort %s')
+    regress_out_timeseries = File(exists=True, argstr='-ort %s')
     blur_fwhm = traits.Float(argstr='-Gblur %f')
     seeds_width = traits.Float(argstr='-Mseed %f', xor=('seeds'))
 
@@ -3249,7 +3249,7 @@ class QwarpInputSpec(AFNICommandInputSpec):
         '* As with \'-wball\', the factor \'f\' should be between 1 and 100.'
         '* You cannot use \'-wball\' and \'-wmask\' together!',
         argstr='-wpass %s %f')
-    out_weight_file = traits.File(
+    out_weight_file = File(
         argstr='-wtprefix %s',
         desc='Write the weight volume to disk as a dataset')
     blur = traits.List(

nipype/interfaces/afni/utils.py

@@ -1397,7 +1397,7 @@ class LocalBistatInputSpec(AFNICommandInputSpec):
              '  * ALL      = all of the above, in that order'
              'More than one option can be used.',
         argstr='-stat %s...')
-    mask_file = traits.File(
+    mask_file = File(
         exists=True,
         desc='mask image file name. Voxels NOT in the mask will not be used '
              'in the neighborhood of any voxel. Also, a voxel NOT in the mask '
@@ -1407,13 +1407,13 @@ class LocalBistatInputSpec(AFNICommandInputSpec):
         desc='Compute the mask as in program 3dAutomask.',
         argstr='-automask',
         xor=['weight_file'])
-    weight_file = traits.File(
+    weight_file = File(
         exists=True,
         desc='File name of an image to use as a weight.  Only applies to '
              '\'pearson\' statistics.',
         argstr='-weight %s',
         xor=['automask'])
-    out_file = traits.File(
+    out_file = File(
         desc='Output dataset.',
         argstr='-prefix %s',
         name_source='in_file1',
@@ -1527,7 +1527,7 @@ class LocalstatInputSpec(AFNICommandInputSpec):
              '            mean, median, MAD, P2skew\n'
              'More than one option can be used.',
         argstr='-stat %s...')
-    mask_file = traits.File(
+    mask_file = File(
         exists=True,
         desc='Mask image file name. Voxels NOT in the mask will not be used '
              'in the neighborhood of any voxel. Also, a voxel NOT in the '
@@ -1589,7 +1589,7 @@ class LocalstatInputSpec(AFNICommandInputSpec):
     overwrite = traits.Bool(
         desc='overwrite output file if it already exists',
         argstr='-overwrite')
-    out_file = traits.File(
+    out_file = File(
         desc='Output dataset.',
         argstr='-prefix %s',
         name_source='in_file',
@@ -1905,7 +1905,7 @@ class NwarpApplyInputSpec(CommandLineInputSpec):
     inv_warp = traits.Bool(
         desc='After the warp specified in \'-nwarp\' is computed, invert it',
         argstr='-iwarp')
-    master = traits.File(
+    master = File(
         exists=True,
         desc='the name of the master dataset, which defines the output grid',
         argstr='-master %s')
@@ -1980,10 +1980,10 @@ class NwarpApply(AFNICommandBase):
 
 class NwarpCatInputSpec(AFNICommandInputSpec):
     in_files = traits.List(
-        traits.Either(traits.File(),
+        traits.Either(File(),
                       traits.Tuple(
                           traits.Enum('IDENT', 'INV', 'SQRT', 'SQRTINV'),
-                          traits.File())),
+                          File())),
         desc="list of tuples of 3D warps and associated functions",
         mandatory=True,
         argstr="%s",
@@ -2137,7 +2137,7 @@ class OneDToolPyInputSpec(AFNIPythonCommandInputSpec):
         desc=
         'display a list of TRs which were not censored in the specified style',
         argstr='-show_trs_uncensored %s')
-    show_cormat_warnings = traits.File(
+    show_cormat_warnings = File(
         desc='Write cormat warnings to a file',
         argstr="-show_cormat_warnings |& tee %s",
         position=-1,
@@ -2226,7 +2226,7 @@ class RefitInputSpec(CommandLineInputSpec):
         desc='Associates the dataset with a specific template type, e.g. '
         'TLRC, MNI, ORIG')
     atrcopy = traits.Tuple(
-        traits.File(exists=True),
+        File(exists=True),
         traits.Str(),
         argstr='-atrcopy %s %s',
         desc='Copy AFNI header attribute from the given file into the header '
@@ -2310,7 +2310,7 @@ class ReHoInputSpec(CommandLineInputSpec):
         position=1,
         mandatory=True,
         exists=True)
-    out_file = traits.File(
+    out_file = File(
         desc='Output dataset.',
         argstr='-prefix %s',
         name_source='in_file',
@@ -2323,7 +2323,7 @@ class ReHoInputSpec(CommandLineInputSpec):
              'Kendall\'s W. This option is currently compatible only with '
              'the AFNI (BRIK/HEAD) output type; the chi-squared value will '
              'be the second sub-brick of the output dataset.')
-    mask_file = traits.File(
+    mask_file = File(
         desc='Mask within which ReHo should be calculated voxelwise',
         argstr='-mask %s')
     neighborhood = traits.Enum(
@@ -2451,7 +2451,7 @@ class ResampleInputSpec(AFNICommandInputSpec):
         *[traits.Float()] * 3,
         argstr='-dxyz %f %f %f',
         desc='resample to new dx, dy and dz')
-    master = traits.File(
+    master = File(
         argstr='-master %s', desc='align dataset grid to a reference file')
 
 
@@ -3247,7 +3247,7 @@ class ZeropadInputSpec(AFNICommandInputSpec):
         'and slice thickness = 2.5 mm ==> 2 slices added',
         argstr='-mm',
         xor=['master'])
-    master = traits.File(
+    master = File(
         desc='match the volume described in dataset '
         '\'mset\', where mset must have the same '
         'orientation and grid spacing as dataset to be '

nipype/interfaces/base/specs.py

@@ -25,6 +25,8 @@
     md5, hash_infile, hash_timestamp, to_str, USING_PATHLIB2)
 from .traits_extension import (
     traits,
+    File,
+    Str,
     Undefined,
     isdefined,
     has_metadata,
@@ -373,13 +375,13 @@ class DynamicTraitedSpec(BaseTraitedSpec):
 
 
 class CommandLineInputSpec(BaseInterfaceInputSpec):
-    args = traits.Str(argstr='%s', desc='Additional parameters to the command')
+    args = Str(argstr='%s', desc='Additional parameters to the command')
     environ = traits.DictStrStr(
         desc='Environment variables', usedefault=True, nohash=True)
 
 
 class StdOutCommandLineInputSpec(CommandLineInputSpec):
-    out_file = traits.File(argstr="> %s", position=-1, genfile=True)
+    out_file = File(argstr="> %s", position=-1, genfile=True)
 
 
 class MpiCommandLineInputSpec(CommandLineInputSpec):

nipype/interfaces/dipy/base.py

@@ -100,7 +100,7 @@ def convert_to_traits_type(dipy_type, is_file=False):
     elif "string" in dipy_type and not is_file:
         return traits.Str, is_mandatory
     elif "string" in dipy_type and is_file:
-        return traits.File, is_mandatory
+        return File, is_mandatory
     elif "int" in dipy_type:
         return traits.Int, is_mandatory
     elif "float" in dipy_type:

nipype/interfaces/dipy/tests/test_base.py

@@ -1,6 +1,6 @@
 import pytest
 from collections import namedtuple
-from ...base import traits, TraitedSpec, BaseInterfaceInputSpec
+from ...base import traits, File, TraitedSpec, BaseInterfaceInputSpec
 from ..base import (convert_to_traits_type, create_interface_specs,
                     dipy_to_nipype_interface, DipyBaseInterface, no_dipy,
                     get_dipy_workflows)
@@ -35,10 +35,10 @@ def test_convert_to_traits_type():
                   Res(traits.ListStr, False), Res(traits.ListFloat, False),
                   Res(traits.ListBool, False), Res(traits.ListComplex, False),
                   Res(traits.Str, True), Res(traits.Int, True),
-                  Res(traits.File, True), Res(traits.Float, True),
+                  Res(File, True), Res(traits.Float, True),
                   Res(traits.Bool, True), Res(traits.Complex, True),
                   Res(traits.Str, False), Res(traits.Int, False),
-                  Res(traits.File, False), Res(traits.Float, False),
+                  Res(File, False), Res(traits.Float, False),
                   Res(traits.Bool, False), Res(traits.Complex, False),
                   ]
 

nipype/interfaces/freesurfer/model.py

@@ -988,7 +988,7 @@ class SegStatsReconAllInputSpec(SegStatsInputSpec):
         mandatory=True,
         desc="Subject id being processed")
     # implicit
-    ribbon = traits.File(
+    ribbon = File(
         mandatory=True, exists=True, desc="Input file mri/ribbon.mgz")
     presurf_seg = File(exists=True, desc="Input segmentation volume")
     transform = File(mandatory=True, exists=True, desc="Input transform file")
@@ -1216,19 +1216,19 @@ class MS_LDAInputSpec(FSTraitedSpec):
         maxlen=2,
         sep=' ',
         desc='pair of class labels to optimize')
-    weight_file = traits.File(
+    weight_file = File(
         argstr='-weight %s',
         mandatory=True,
         desc='filename for the LDA weights (input or output)')
-    vol_synth_file = traits.File(
+    vol_synth_file = File(
         exists=False,
         argstr='-synth %s',
         mandatory=True,
         desc=('filename for the synthesized output '
               'volume'))
-    label_file = traits.File(
+    label_file = File(
         exists=True, argstr='-label %s', desc='filename of the label volume')
-    mask_file = traits.File(
+    mask_file = File(
         exists=True,
         argstr='-mask %s',
         desc='filename of the brain mask volume')
@@ -1532,7 +1532,7 @@ class SphericalAverageInputSpec(FSTraitedSpec):
         exists=False,
         position=-1,
         desc="Output filename")
-    in_average = traits.Directory(
+    in_average = Directory(
         argstr="%s",
         exists=True,
         genfile=True,

nipype/interfaces/freesurfer/preprocess.py

@@ -2313,7 +2313,7 @@ class NormalizeInputSpec(FSTraitedSpec):
 
 
 class NormalizeOutputSpec(TraitedSpec):
-    out_file = traits.File(exists=False, desc="The output file for Normalize")
+    out_file = File(exists=False, desc="The output file for Normalize")
 
 
 class Normalize(FSCommand):
@@ -2379,7 +2379,7 @@ class CANormalizeInputSpec(FSTraitedSpec):
 
 
 class CANormalizeOutputSpec(TraitedSpec):
-    out_file = traits.File(exists=False, desc="The output file for Normalize")
+    out_file = File(exists=False, desc="The output file for Normalize")
     control_points = File(
         exists=False, desc="The output control points for Normalize")
 
@@ -2460,7 +2460,7 @@ class CARegisterInputSpec(FSTraitedSpecOpenMP):
 
 
 class CARegisterOutputSpec(TraitedSpec):
-    out_file = traits.File(exists=False, desc="The output file for CARegister")
+    out_file = File(exists=False, desc="The output file for CARegister")
 
 
 class CARegister(FSCommandOpenMP):
@@ -2540,13 +2540,13 @@ class CALabelInputSpec(FSTraitedSpecOpenMP):
         desc=("Reclassify voxels at least some std"
               " devs from the mean using some size"
               " Gaussian window"))
-    label = traits.File(
+    label = File(
         argstr="-l %s",
         exists=True,
         desc=
         "Undocumented flag. Autorecon3 uses ../label/{hemisphere}.cortex.label as input file"
     )
-    aseg = traits.File(
+    aseg = File(
         argstr="-aseg %s",
         exists=True,
         desc=
@@ -2630,13 +2630,13 @@ class MRIsCALabelInputSpec(FSTraitedSpecOpenMP):
         name_template="%s.aparc.annot",
         desc="Annotated surface output file")
     # optional
-    label = traits.File(
+    label = File(
         argstr="-l %s",
         exists=True,
         desc=
         "Undocumented flag. Autorecon3 uses ../label/{hemisphere}.cortex.label as input file"
     )
-    aseg = traits.File(
+    aseg = File(
         argstr="-aseg %s",
         exists=True,
         desc=
@@ -2985,13 +2985,13 @@ class ConcatenateLTAInputSpec(FSTraitedSpec):
         'VOX2VOX', 'RAS2RAS', argstr='-out_type %d', desc='set final LTA type')
 
     # Talairach options
-    tal_source_file = traits.File(
+    tal_source_file = File(
         exists=True,
         argstr='-tal %s',
         position=-5,
         requires=['tal_template_file'],
         desc='if in_lta2 is talairach.xfm, specify source for talairach')
-    tal_template_file = traits.File(
+    tal_template_file = File(
         exists=True,
         argstr='%s',
         position=-4,

nipype/interfaces/freesurfer/registration.py

@@ -134,7 +134,7 @@ class RegisterAVItoTalairachInputSpec(FSTraitedSpec):
 
 
 class RegisterAVItoTalairachOutputSpec(FSScriptOutputSpec):
-    out_file = traits.File(
+    out_file = File(
         exists=False, desc="The output file for RegisterAVItoTalairach")