RF: Subclass traits.Tuple to accept lists

Author: effigies

nipype/algorithms/confounds.py

@@ -24,6 +24,7 @@
     InputMultiPath,
     OutputMultiPath,
     SimpleInterface,
+    Tuple,
 )
 from ..utils.misc import normalize_mc_params
 
@@ -64,7 +65,7 @@ class ComputeDVARSInputSpec(BaseInterfaceInputSpec):
     series_tr = traits.Float(desc="repetition time in sec.")
     save_plot = traits.Bool(False, usedefault=True, desc="write DVARS plot")
     figdpi = traits.Int(100, usedefault=True, desc="output dpi for the plot")
-    figsize = traits.Tuple(
+    figsize = Tuple(
         traits.Float(11.7),
         traits.Float(2.3),
         usedefault=True,
@@ -286,7 +287,7 @@ class FramewiseDisplacementInputSpec(BaseInterfaceInputSpec):
     save_plot = traits.Bool(False, usedefault=True, desc="write FD plot")
     normalize = traits.Bool(False, usedefault=True, desc="calculate FD in mm/s")
     figdpi = traits.Int(100, usedefault=True, desc="output dpi for the FD plot")
-    figsize = traits.Tuple(
+    figsize = Tuple(
         traits.Float(11.7),
         traits.Float(2.3),
         usedefault=True,

nipype/algorithms/mesh.py

@@ -14,6 +14,7 @@
     TraitedSpec,
     File,
     BaseInterfaceInputSpec,
+    Tuple,
 )
 from ..interfaces.vtkbase import tvtk
 from ..interfaces import vtkbase as VTKInfo
@@ -289,7 +290,7 @@ class MeshWarpMathsInputSpec(BaseInterfaceInputSpec):
     )
     float_trait = traits.Either(
         traits.Float(1.0),
-        traits.Tuple(traits.Float(1.0), traits.Float(1.0), traits.Float(1.0)),
+        Tuple(traits.Float(1.0), traits.Float(1.0), traits.Float(1.0)),
     )
 
     operator = traits.Either(

nipype/algorithms/misc.py

@@ -23,6 +23,7 @@
     isdefined,
     DynamicTraitedSpec,
     Undefined,
+    Tuple,
 )
 from ..utils.filemanip import fname_presuffix, split_filename, ensure_list
 
@@ -1176,7 +1177,7 @@ def _list_outputs(self):
 class SplitROIsInputSpec(TraitedSpec):
     in_file = File(exists=True, mandatory=True, desc="file to be split")
     in_mask = File(exists=True, desc="only process files inside mask")
-    roi_size = traits.Tuple(traits.Int, traits.Int, traits.Int, desc="desired ROI size")
+    roi_size = Tuple(traits.Int, traits.Int, traits.Int, desc="desired ROI size")
 
 
 class SplitROIsOutputSpec(TraitedSpec):

nipype/interfaces/afni/model.py

@@ -22,6 +22,7 @@
     InputMultiPath,
     Undefined,
     Str,
+    Tuple,
 )
 from ...external.due import BibTeX
 
@@ -127,7 +128,7 @@ class DeconvolveInputSpec(AFNICommandInputSpec):
         "that 'gotforit' is needed to ignore.",
         argstr="-allzero_OK",
     )
-    dname = traits.Tuple(
+    dname = Tuple(
         Str, Str, desc="set environmental variable to provided value", argstr="-D%s=%s"
     )
     mask = File(
@@ -162,7 +163,7 @@ class DeconvolveInputSpec(AFNICommandInputSpec):
         "[default: 1]",
         argstr="-polort %d",
     )
-    ortvec = traits.Tuple(
+    ortvec = Tuple(
         File(desc="filename", exists=True),
         Str(desc="label"),
         desc="this option lets you input a rectangular array of 1 or more "
@@ -213,7 +214,7 @@ class DeconvolveInputSpec(AFNICommandInputSpec):
         desc="number of stimulus timing files", argstr="-num_stimts %d", position=-6
     )
     stim_times = traits.List(
-        traits.Tuple(
+        Tuple(
             traits.Int(desc="k-th response model"),
             File(desc="stimulus timing file", exists=True),
             Str(desc="model"),
@@ -223,9 +224,7 @@ class DeconvolveInputSpec(AFNICommandInputSpec):
         position=-5,
     )
     stim_label = traits.List(
-        traits.Tuple(
-            traits.Int(desc="k-th input stimulus"), Str(desc="stimulus label")
-        ),
+        Tuple(traits.Int(desc="k-th input stimulus"), Str(desc="stimulus label")),
         desc="label for kth input stimulus (e.g., Label1)",
         argstr="-stim_label %d %s...",
         requires=["stim_times"],
@@ -251,9 +250,7 @@ class DeconvolveInputSpec(AFNICommandInputSpec):
         position=-2,
     )
     glt_label = traits.List(
-        traits.Tuple(
-            traits.Int(desc="k-th general linear test"), Str(desc="GLT label")
-        ),
+        Tuple(traits.Int(desc="k-th general linear test"), Str(desc="GLT label")),
         desc="general linear test (i.e., contrast) labels",
         argstr="-glt_label %d %s...",
         requires=["gltsym"],
@@ -488,9 +485,7 @@ class RemlfitInputSpec(AFNICommandInputSpec):
         argstr="-nobout",
     )
     gltsym = traits.List(
-        traits.Either(
-            traits.Tuple(File(exists=True), Str()), traits.Tuple(Str(), Str())
-        ),
+        traits.Either(Tuple(File(exists=True), Str()), Tuple(Str(), Str())),
         desc="read a symbolic GLT from input file and associate it with a "
         "label. As in Deconvolve, you can also use the 'SYM:' method "
         "to provide the definition of the GLT directly as a string "

nipype/interfaces/ants/registration.py

@@ -5,7 +5,7 @@
 import os
 
 from ...utils.filemanip import ensure_list
-from ..base import TraitedSpec, File, Str, traits, InputMultiPath, isdefined
+from ..base import TraitedSpec, File, Str, traits, InputMultiPath, isdefined, Tuple
 from .base import ANTSCommand, ANTSCommandInputSpec, LOCAL_DEFAULT_NUMBER_OF_THREADS
 
 
@@ -423,11 +423,9 @@ class RegistrationInputSpec(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 (interpolator)
+        Tuple(traits.Int()),  # BSpline (order)
+        Tuple(traits.Float(), traits.Float()),  # Gaussian/MultiLabel (sigma, alpha)
+        Tuple(traits.Str()),  # GenericLabel (interpolator)
     )
 
     write_composite_transform = traits.Bool(
@@ -491,34 +489,34 @@ class RegistrationInputSpec(ANTSCommandInputSpec):
     # Exponential, and BSplineExponential. EVEN DEFAULTS!
     transform_parameters = traits.List(
         traits.Either(
-            traits.Tuple(traits.Float()),  # Translation, Rigid, Affine,
+            Tuple(traits.Float()),  # Translation, Rigid, Affine,
             # CompositeAffine, Similarity
-            traits.Tuple(
+            Tuple(
                 traits.Float(),  # GaussianDisplacementField, SyN
                 traits.Float(),
                 traits.Float(),
             ),
-            traits.Tuple(
+            Tuple(
                 traits.Float(),  # BSplineSyn,
                 traits.Int(),  # BSplineDisplacementField,
                 traits.Int(),  # TimeVaryingBSplineVelocityField
                 traits.Int(),
             ),
-            traits.Tuple(
+            Tuple(
                 traits.Float(),  # TimeVaryingVelocityField
                 traits.Int(),
                 traits.Float(),
                 traits.Float(),
                 traits.Float(),
                 traits.Float(),
             ),
-            traits.Tuple(
+            Tuple(
                 traits.Float(),  # Exponential
                 traits.Float(),
                 traits.Float(),
                 traits.Int(),
             ),
-            traits.Tuple(
+            Tuple(
                 traits.Float(),  # BSplineExponential
                 traits.Int(),
                 traits.Int(),

nipype/interfaces/base/__init__.py

@@ -45,6 +45,7 @@
     InputMultiObject,
     OutputMultiPath,
     InputMultiPath,
+    Tuple,
 )
 
 from .support import Bunch, InterfaceResult, NipypeInterfaceError

nipype/interfaces/base/traits_extension.py

@@ -370,6 +370,14 @@ def __init__(
         )
 
 
+class Tuple(traits.BaseTuple):
+    def validate(self, objekt, name, value):
+        if isinstance(value, list):
+            value = tuple(value)
+
+        return super().validate(objekt, name, value)
+
+
 def isdefined(objekt):
     return not isinstance(objekt, _Undefined)