refractoring w/ black...

Author: GalKepler

nipype/interfaces/mrtrix/convert.py

@@ -121,7 +121,9 @@ def track_gen(track_points):
                         "Expecting %s points, found only %s" % (stream_count, n_streams)
                     )
                     iflogger.error(
-                        "Expecting %s points, found only %s", stream_count, n_streams
+                        "Expecting %s points, found only %s",
+                        stream_count,
+                        n_streams,
                     )
                 break
             pts = np.ndarray(shape=(n_pts, pt_cols), dtype=f4dt, buffer=pts_str)
@@ -193,7 +195,10 @@ class MRTrix2TrackVis(DipyBaseInterface):
     output_spec = MRTrix2TrackVisOutputSpec
 
     def _run_interface(self, runtime):
-        from dipy.tracking.utils import move_streamlines, affine_from_fsl_mat_file
+        from dipy.tracking.utils import (
+            move_streamlines,
+            affine_from_fsl_mat_file,
+        )
 
         dx, dy, dz = get_data_dims(self.inputs.image_file)
         vx, vy, vz = get_vox_dims(self.inputs.image_file)
@@ -215,7 +220,8 @@ def _run_interface(self, runtime):
             self.inputs.registration_image_file
         ):
             iflogger.info(
-                "Applying transformation from matrix file %s", self.inputs.matrix_file
+                "Applying transformation from matrix file %s",
+                self.inputs.matrix_file,
             )
             xfm = np.genfromtxt(self.inputs.matrix_file)
             iflogger.info(xfm)

nipype/interfaces/mrtrix3/utils.py

@@ -144,9 +144,7 @@ class Generate5ttInputSpec(MRTrix3BaseInputSpec):
         position=-2,
         desc="input image",
     )
-    out_file = File(
-        argstr="%s", mandatory=True, position=-1, desc="output image"
-    )
+    out_file = File(argstr="%s", mandatory=True, position=-1, desc="output image")
 
 
 class Generate5ttOutputSpec(TraitedSpec):
@@ -192,12 +190,8 @@ class TensorMetricsInputSpec(CommandLineInputSpec):
 
     out_fa = File(argstr="-fa %s", desc="output FA file")
     out_adc = File(argstr="-adc %s", desc="output ADC file")
-    out_evec = File(
-        argstr="-vector %s", desc="output selected eigenvector(s) file"
-    )
-    out_eval = File(
-        argstr="-value %s", desc="output selected eigenvalue(s) file"
-    )
+    out_evec = File(argstr="-vector %s", desc="output selected eigenvector(s) file")
+    out_eval = File(argstr="-value %s", desc="output selected eigenvalue(s) file")
     component = traits.List(
         [1],
         usedefault=True,
@@ -212,8 +206,7 @@ class TensorMetricsInputSpec(CommandLineInputSpec):
         exists=True,
         argstr="-mask %s",
         desc=(
-            "only perform computation within the specified binary"
-            " brain mask image"
+            "only perform computation within the specified binary" " brain mask image"
         ),
     )
     modulate = traits.Enum(
@@ -301,8 +294,7 @@ class ComputeTDIInputSpec(CommandLineInputSpec):
     )
     max_tod = traits.Int(
         argstr="-tod %d",
-        desc="generate a Track Orientation "
-        "Distribution (TOD) in each voxel.",
+        desc="generate a Track Orientation " "Distribution (TOD) in each voxel.",
     )
 
     contrast = traits.Enum(
@@ -392,8 +384,7 @@ class ComputeTDIInputSpec(CommandLineInputSpec):
     )
     nthreads = traits.Int(
         argstr="-nthreads %d",
-        desc="number of threads. if zero, the number"
-        " of available cpus will be used",
+        desc="number of threads. if zero, the number" " of available cpus will be used",
         nohash=True,
     )
 
@@ -498,8 +489,7 @@ class TCK2VTKInputSpec(CommandLineInputSpec):
 
     nthreads = traits.Int(
         argstr="-nthreads %d",
-        desc="number of threads. if zero, the number"
-        " of available cpus will be used",
+        desc="number of threads. if zero, the number" " of available cpus will be used",
         nohash=True,
     )
 
@@ -543,9 +533,7 @@ class DWIExtractInputSpec(MRTrix3BaseInputSpec):
         position=-2,
         desc="input image",
     )
-    out_file = File(
-        argstr="%s", mandatory=True, position=-1, desc="output image"
-    )
+    out_file = File(argstr="%s", mandatory=True, position=-1, desc="output image")
     bzero = traits.Bool(argstr="-bzero", desc="extract b=0 volumes")
     nobzero = traits.Bool(argstr="-no_bzero", desc="extract non b=0 volumes")
     singleshell = traits.Bool(
@@ -690,9 +678,7 @@ class MRMathInputSpec(MRTrix3BaseInputSpec):
         position=-3,
         desc="input image",
     )
-    out_file = File(
-        argstr="%s", mandatory=True, position=-1, desc="output image"
-    )
+    out_file = File(argstr="%s", mandatory=True, position=-1, desc="output image")
     operation = traits.Enum(
         "mean",
         "median",
@@ -875,9 +861,7 @@ class SHConvInputSpec(CommandLineInputSpec):
 
 
 class SHConvOutputSpec(TraitedSpec):
-    out_file = File(
-        exists=True, desc="the output convoluted spherical harmonics file"
-    )
+    out_file = File(exists=True, desc="the output convoluted spherical harmonics file")
 
 
 class SHConv(CommandLine):
@@ -941,9 +925,7 @@ class SH2AmpInputSpec(CommandLineInputSpec):
 
 
 class SH2AmpOutputSpec(TraitedSpec):
-    out_file = File(
-        exists=True, desc="the output convoluted spherical harmonics file"
-    )
+    out_file = File(exists=True, desc="the output convoluted spherical harmonics file")
 
 
 class SH2Amp(CommandLine):