RF: Adopt traits_extension.Tuple throughout

Author: effigies

nipype/interfaces/afni/preprocess.py

@@ -11,6 +11,7 @@
     CommandLine,
     TraitedSpec,
     traits,
+    Tuple,
     isdefined,
     File,
     InputMultiPath,
@@ -2439,7 +2440,7 @@ class TCorrMapInputSpec(AFNICommandInputSpec):
     mask = File(exists=True, argstr="-mask %s")
     automask = traits.Bool(argstr="-automask")
     polort = traits.Int(argstr="-polort %d")
-    bandpass = traits.Tuple((traits.Float(), traits.Float()), argstr="-bpass %f %f")
+    bandpass = Tuple((traits.Float(), traits.Float()), argstr="-bpass %f %f")
     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"))
@@ -3011,13 +3012,13 @@ class TProjectInputSpec(AFNICommandInputSpec):
 
 """,
     )
-    bandpass = traits.Tuple(
+    bandpass = Tuple(
         traits.Float,
         traits.Float,
         desc="""Remove all frequencies EXCEPT those in the range""",
         argstr="-bandpass %g %g",
     )
-    stopband = traits.Tuple(
+    stopband = Tuple(
         traits.Float,
         traits.Float,
         desc="""Remove all frequencies in the range""",
@@ -3394,7 +3395,7 @@ class VolregInputSpec(AFNICommandInputSpec):
         copyfile=False,
     )
     in_weight_volume = traits.Either(
-        traits.Tuple(File(exists=True), traits.Int),
+        Tuple(File(exists=True), traits.Int),
         File(exists=True),
         desc="weights for each voxel specified by a file with an "
         "optional volume number (defaults to 0)",
@@ -3821,8 +3822,8 @@ class QwarpInputSpec(AFNICommandInputSpec):
         maxlen=5,
         xor=["wmask"],
     )
-    traits.Tuple((traits.Float(), traits.Float()), argstr="-bpass %f %f")
-    wmask = traits.Tuple(
+    bandpass = Tuple((traits.Float(), traits.Float()), argstr="-bpass %f %f")
+    wmask = Tuple(
         (File(exists=True), traits.Float()),
         desc="""\
 Similar to '-wball', but here, you provide a dataset 'ws'

nipype/interfaces/afni/utils.py

@@ -13,6 +13,7 @@
     Directory,
     TraitedSpec,
     traits,
+    Tuple,
     isdefined,
     File,
     InputMultiObject,
@@ -261,7 +262,7 @@ class BrickStatInputSpec(CommandLineInputSpec):
     mean = traits.Bool(desc="print the mean value in the dataset", argstr="-mean")
     sum = traits.Bool(desc="print the sum of values in the dataset", argstr="-sum")
     var = traits.Bool(desc="print the variance in the dataset", argstr="-var")
-    percentile = traits.Tuple(
+    percentile = Tuple(
         traits.Float,
         traits.Float,
         traits.Float,
@@ -330,7 +331,7 @@ def aggregate_outputs(self, runtime=None, needed_outputs=None):
 
 class BucketInputSpec(AFNICommandInputSpec):
     in_file = traits.List(
-        traits.Tuple(
+        Tuple(
             (File(exists=True, copyfile=False), traits.Str(argstr="'%s'")),
             artstr="%s%s",
         ),
@@ -590,7 +591,7 @@ class Cat(AFNICommand):
 
 class CatMatvecInputSpec(AFNICommandInputSpec):
     in_file = traits.List(
-        traits.Tuple(traits.Str(), traits.Str()),
+        Tuple(traits.Str(), traits.Str()),
         desc="list of tuples of mfiles and associated opkeys",
         mandatory=True,
         argstr="%s",
@@ -683,7 +684,7 @@ class CenterMassInputSpec(CommandLineInputSpec):
         exists=True,
     )
     automask = traits.Bool(desc="Generate the mask automatically", argstr="-automask")
-    set_cm = traits.Tuple(
+    set_cm = Tuple(
         (traits.Float(), traits.Float(), traits.Float()),
         desc="After computing the center of mass, set the origin fields in "
         "the header so that the center of mass will be at (x,y,z) in "
@@ -711,7 +712,7 @@ class CenterMassOutputSpec(TraitedSpec):
     out_file = File(exists=True, desc="output file")
     cm_file = File(desc="file with the center of mass coordinates")
     cm = traits.List(
-        traits.Tuple(traits.Float(), traits.Float(), traits.Float()),
+        Tuple(traits.Float(), traits.Float(), traits.Float()),
         desc="center of mass",
     )
 
@@ -889,7 +890,7 @@ class DotInputSpec(AFNICommandInputSpec):
     )
     out_file = File(desc="collect output to a file", argstr=" |& tee %s", position=-1)
     mask = File(desc="Use this dataset as a mask", argstr="-mask %s")
-    mrange = traits.Tuple(
+    mrange = Tuple(
         (traits.Float(), traits.Float()),
         desc="Means to further restrict the voxels from 'mset' so that"
         "only those mask values within this range (inclusive) willbe used.",
@@ -1214,7 +1215,7 @@ class FWHMxInputSpec(CommandLineInputSpec):
     acf = traits.Either(
         traits.Bool(),
         File(),
-        traits.Tuple(File(exists=True), traits.Float()),
+        Tuple(File(exists=True), traits.Float()),
         default=False,
         usedefault=True,
         argstr="-acf",
@@ -1227,13 +1228,13 @@ class FWHMxOutputSpec(TraitedSpec):
     out_subbricks = File(exists=True, desc="output file (subbricks)")
     out_detrend = File(desc="output file, detrended")
     fwhm = traits.Either(
-        traits.Tuple(traits.Float(), traits.Float(), traits.Float()),
-        traits.Tuple(traits.Float(), traits.Float(), traits.Float(), traits.Float()),
+        Tuple(traits.Float(), traits.Float(), traits.Float()),
+        Tuple(traits.Float(), traits.Float(), traits.Float(), traits.Float()),
         desc="FWHM along each axis",
     )
     acf_param = traits.Either(
-        traits.Tuple(traits.Float(), traits.Float(), traits.Float()),
-        traits.Tuple(traits.Float(), traits.Float(), traits.Float(), traits.Float()),
+        Tuple(traits.Float(), traits.Float(), traits.Float()),
+        Tuple(traits.Float(), traits.Float(), traits.Float(), traits.Float()),
         desc="fitted ACF model parameters",
     )
     out_acf = File(exists=True, desc="output acf file")
@@ -1429,10 +1430,10 @@ class LocalBistatInputSpec(AFNICommandInputSpec):
         desc="Filename of the second image",
     )
     neighborhood = traits.Either(
-        traits.Tuple(traits.Enum("SPHERE", "RHDD", "TOHD"), traits.Float()),
-        traits.Tuple(
+        Tuple(traits.Enum("SPHERE", "RHDD", "TOHD"), traits.Float()),
+        Tuple(
             traits.Enum("RECT"),
-            traits.Tuple(traits.Float(), traits.Float(), traits.Float()),
+            Tuple(traits.Float(), traits.Float(), traits.Float()),
         ),
         mandatory=True,
         desc="The region around each voxel that will be extracted for "
@@ -1557,10 +1558,10 @@ class LocalstatInputSpec(AFNICommandInputSpec):
         exists=True, mandatory=True, argstr="%s", position=-1, desc="input dataset"
     )
     neighborhood = traits.Either(
-        traits.Tuple(traits.Enum("SPHERE", "RHDD", "TOHD"), traits.Float()),
-        traits.Tuple(
+        Tuple(traits.Enum("SPHERE", "RHDD", "TOHD"), traits.Float()),
+        Tuple(
             traits.Enum("RECT"),
-            traits.Tuple(traits.Float(), traits.Float(), traits.Float()),
+            Tuple(traits.Float(), traits.Float(), traits.Float()),
         ),
         mandatory=True,
         desc="The region around each voxel that will be extracted for "
@@ -1594,9 +1595,9 @@ class LocalstatInputSpec(AFNICommandInputSpec):
     stat = InputMultiObject(
         traits.Either(
             traits.Enum(_stat_names),
-            traits.Tuple(
+            Tuple(
                 traits.Enum("perc"),
-                traits.Tuple(traits.Float, traits.Float, traits.Float),
+                Tuple(traits.Float, traits.Float, traits.Float),
             ),
         ),
         mandatory=True,
@@ -1669,7 +1670,7 @@ class LocalstatInputSpec(AFNICommandInputSpec):
     )
     reduce_grid = traits.Either(
         traits.Float,
-        traits.Tuple(traits.Float, traits.Float, traits.Float),
+        Tuple(traits.Float, traits.Float, traits.Float),
         argstr="-reduce_grid %s",
         xor=["reduce_restore_grid", "reduce_max_vox"],
         desc="Compute output on a grid that is reduced by the specified "
@@ -1683,7 +1684,7 @@ class LocalstatInputSpec(AFNICommandInputSpec):
     )
     reduce_restore_grid = traits.Either(
         traits.Float,
-        traits.Tuple(traits.Float, traits.Float, traits.Float),
+        Tuple(traits.Float, traits.Float, traits.Float),
         argstr="-reduce_restore_grid %s",
         xor=["reduce_max_vox", "reduce_grid"],
         desc="Like reduce_grid, but also resample output back to input grid.",
@@ -2127,7 +2128,7 @@ class NwarpApply(AFNICommandBase):
 class NwarpCatInputSpec(AFNICommandInputSpec):
     in_files = traits.List(
         traits.Either(
-            File(), traits.Tuple(traits.Enum("IDENT", "INV", "SQRT", "SQRTINV"), File())
+            File(), Tuple(traits.Enum("IDENT", "INV", "SQRT", "SQRTINV"), File())
         ),
         desc="list of tuples of 3D warps and associated functions",
         mandatory=True,
@@ -2273,7 +2274,7 @@ class OneDToolPyInputSpec(AFNIPythonCommandInputSpec):
         "file, and zeros are simply counted.",
         argstr="-show_censor_count",
     )
-    censor_motion = traits.Tuple(
+    censor_motion = Tuple(
         (traits.Float(), File()),
         desc="Tuple of motion limit and outfile prefix. need to also set set_nruns -r set_run_lengths",
         argstr="-censor_motion %f %s",
@@ -2381,7 +2382,7 @@ class RefitInputSpec(CommandLineInputSpec):
         desc="Associates the dataset with a specific template type, e.g. "
         "TLRC, MNI, ORIG",
     )
-    atrcopy = traits.Tuple(
+    atrcopy = Tuple(
         File(exists=True),
         traits.Str(),
         argstr="-atrcopy %s %s",
@@ -2392,15 +2393,15 @@ class RefitInputSpec(CommandLineInputSpec):
         "advanced users only. Do NOT use -atrcopy or -atrstring with "
         "other modification options. See also -copyaux.",
     )
-    atrstring = traits.Tuple(
+    atrstring = Tuple(
         traits.Str(),
         traits.Str(),
         argstr="-atrstring %s %s",
         desc="Copy the last given string into the dataset(s) being modified, "
         "giving it the attribute name given by the last string."
         "To be safe, the last string should be in quotes.",
     )
-    atrfloat = traits.Tuple(
+    atrfloat = Tuple(
         traits.Str(),
         traits.Str(),
         argstr="-atrfloat %s %s",
@@ -2410,7 +2411,7 @@ class RefitInputSpec(CommandLineInputSpec):
         "'1 0.2 0 0 -0.2 1 0 0 0 0 1 0' or "
         "flipZ.1D or '1D:1,0.2,2@0,-0.2,1,2@0,2@0,1,0'",
     )
-    atrint = traits.Tuple(
+    atrint = Tuple(
         traits.Str(),
         traits.Str(),
         argstr="-atrint %s %s",
@@ -2524,7 +2525,7 @@ class ReHoInputSpec(CommandLineInputSpec):
 
 but you can choose most any value.""",
     )
-    ellipsoid = traits.Tuple(
+    ellipsoid = Tuple(
         traits.Float,
         traits.Float,
         traits.Float,
@@ -2618,7 +2619,7 @@ class ResampleInputSpec(AFNICommandInputSpec):
         'for "Nearest Neighbor", "Linear", "Cubic" and "Blocky"'
         "interpolation, respectively. Default is NN.",
     )
-    voxel_size = traits.Tuple(
+    voxel_size = Tuple(
         *[traits.Float()] * 3,
         argstr="-dxyz %f %f %f",
         desc="resample to new dx, dy and dz",
@@ -2711,7 +2712,7 @@ class TCat(AFNICommand):
 
 class TCatSBInputSpec(AFNICommandInputSpec):
     in_files = traits.List(
-        traits.Tuple(File(exists=True), Str()),
+        Tuple(File(exists=True), Str()),
         desc="List of tuples of file names and subbrick selectors as strings."
         "Don't forget to protect the single quotes in the subbrick selector"
         "so the contents are protected from the command line interpreter.",
@@ -2933,7 +2934,7 @@ class UndumpInputSpec(AFNICommandInputSpec):
         "then each input data line sets the value in only one voxel.",
         argstr="-srad %f",
     )
-    orient = traits.Tuple(
+    orient = Tuple(
         traits.Enum("R", "L"),
         traits.Enum("A", "P"),
         traits.Enum("I", "S"),
@@ -3057,7 +3058,7 @@ class UnifizeInputSpec(AFNICommandInputSpec):
         requires=["no_duplo", "t2"],
         xor=["gm"],
     )
-    rbt = traits.Tuple(
+    rbt = Tuple(
         traits.Float(),
         traits.Float(),
         traits.Float(),

nipype/interfaces/ants/resampling.py

@@ -4,7 +4,7 @@
 import os
 
 from .base import ANTSCommand, ANTSCommandInputSpec
-from ..base import TraitedSpec, File, traits, isdefined, InputMultiObject
+from ..base import TraitedSpec, File, traits, Tuple, isdefined, InputMultiObject
 from ...utils.filemanip import split_filename
 
 
@@ -355,11 +355,9 @@ class ApplyTransformsInputSpec(ANTSCommandInputSpec):
         usedefault=True,
     )
     interpolation_parameters = traits.Either(
-        traits.Tuple(traits.Int()),  # BSpline (order)
-        traits.Tuple(
-            traits.Float(), traits.Float()  # Gaussian/MultiLabel (sigma, alpha)
-        ),
-        traits.Tuple(traits.Str()),  # GenericLabel
+        Tuple(traits.Int()),  # BSpline (order)
+        Tuple(traits.Float(), traits.Float()),  # Gaussian/MultiLabel (sigma, alpha)
+        Tuple(traits.Str()),  # GenericLabel
     )
     transforms = InputMultiObject(
         traits.Either(File(exists=True), "identity"),

nipype/interfaces/ants/segmentation.py

@@ -4,7 +4,15 @@
 from glob import glob
 from ...external.due import BibTeX
 from ...utils.filemanip import split_filename, copyfile, which, fname_presuffix
-from ..base import TraitedSpec, File, traits, InputMultiPath, OutputMultiPath, isdefined
+from ..base import (
+    TraitedSpec,
+    File,
+    traits,
+    Tuple,
+    InputMultiPath,
+    OutputMultiPath,
+    isdefined,
+)
 from ..mixins import CopyHeaderInterface
 from .base import ANTSCommand, ANTSCommandInputSpec
 
@@ -401,7 +409,7 @@ class N4BiasFieldCorrectionInputSpec(ANTSCommandInputSpec):
 This option rescales to the [min,max] range of the original image intensities
 within the user-specified mask.""",
     )
-    histogram_sharpening = traits.Tuple(
+    histogram_sharpening = Tuple(
         (0.15, 0.01, 200),
         traits.Float,
         traits.Float,