added kwarg json_import to mrconvert interface

Author: GalKepler

nipype/interfaces/mrtrix3/utils.py

@@ -66,7 +66,11 @@ def _list_outputs(self):
 
 class Mesh2PVEInputSpec(CommandLineInputSpec):
     in_file = File(
-        exists=True, argstr="%s", mandatory=True, position=-3, desc="input mesh"
+        exists=True,
+        argstr="%s",
+        mandatory=True,
+        position=-3,
+        desc="input mesh",
     )
     reference = File(
         exists=True,
@@ -134,9 +138,15 @@ class Generate5ttInputSpec(MRTrix3BaseInputSpec):
         desc="tissue segmentation algorithm",
     )
     in_file = File(
-        exists=True, argstr="%s", mandatory=True, position=-2, desc="input image"
+        exists=True,
+        argstr="%s",
+        mandatory=True,
+        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):
@@ -173,13 +183,21 @@ def _list_outputs(self):
 
 class TensorMetricsInputSpec(CommandLineInputSpec):
     in_file = File(
-        exists=True, argstr="%s", mandatory=True, position=-1, desc="input DTI image"
+        exists=True,
+        argstr="%s",
+        mandatory=True,
+        position=-1,
+        desc="input DTI image",
     )
 
     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,
@@ -194,7 +212,8 @@ 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(
@@ -246,10 +265,18 @@ def _list_outputs(self):
 
 class ComputeTDIInputSpec(CommandLineInputSpec):
     in_file = File(
-        exists=True, argstr="%s", mandatory=True, position=-2, desc="input tractography"
+        exists=True,
+        argstr="%s",
+        mandatory=True,
+        position=-2,
+        desc="input tractography",
     )
     out_file = File(
-        "tdi.mif", argstr="%s", usedefault=True, position=-1, desc="output TDI file"
+        "tdi.mif",
+        argstr="%s",
+        usedefault=True,
+        position=-1,
+        desc="output TDI file",
     )
     reference = File(
         exists=True,
@@ -274,7 +301,8 @@ 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(
@@ -353,7 +381,8 @@ class ComputeTDIInputSpec(CommandLineInputSpec):
         "(these lengths are then taken into account during TWI calculation)",
     )
     ends_only = traits.Bool(
-        argstr="-ends_only", desc="only map the streamline" " endpoints to the image"
+        argstr="-ends_only",
+        desc="only map the streamline" " endpoints to the image",
     )
 
     tck_weights = File(
@@ -363,7 +392,8 @@ 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,
     )
 
@@ -438,10 +468,18 @@ def _list_outputs(self):
 
 class TCK2VTKInputSpec(CommandLineInputSpec):
     in_file = File(
-        exists=True, argstr="%s", mandatory=True, position=-2, desc="input tractography"
+        exists=True,
+        argstr="%s",
+        mandatory=True,
+        position=-2,
+        desc="input tractography",
     )
     out_file = File(
-        "tracks.vtk", argstr="%s", usedefault=True, position=-1, desc="output VTK file"
+        "tracks.vtk",
+        argstr="%s",
+        usedefault=True,
+        position=-1,
+        desc="output VTK file",
     )
     reference = File(
         exists=True,
@@ -460,7 +498,8 @@ 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,
     )
 
@@ -498,9 +537,15 @@ def _list_outputs(self):
 
 class DWIExtractInputSpec(MRTrix3BaseInputSpec):
     in_file = File(
-        exists=True, argstr="%s", mandatory=True, position=-2, desc="input image"
+        exists=True,
+        argstr="%s",
+        mandatory=True,
+        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(
@@ -549,7 +594,11 @@ def _list_outputs(self):
 
 class MRConvertInputSpec(MRTrix3BaseInputSpec):
     in_file = File(
-        exists=True, argstr="%s", mandatory=True, position=-2, desc="input image"
+        exists=True,
+        argstr="%s",
+        mandatory=True,
+        position=-2,
+        desc="input image",
     )
     out_file = File(
         "dwi.mif",
@@ -566,7 +615,10 @@ class MRConvertInputSpec(MRTrix3BaseInputSpec):
         desc="extract data at the specified coordinates",
     )
     vox = traits.List(
-        traits.Float, sep=",", argstr="-vox %s", desc="change the voxel dimensions"
+        traits.Float,
+        sep=",",
+        argstr="-vox %s",
+        desc="change the voxel dimensions",
     )
     axes = traits.List(
         traits.Int,
@@ -580,6 +632,12 @@ class MRConvertInputSpec(MRTrix3BaseInputSpec):
         argstr="-scaling %s",
         desc="specify the data scaling parameter",
     )
+    json_import = File(
+        exists=True,
+        argstr="-json_import %s",
+        mandatory=False,
+        desc="import data from a JSON file into header key-value pairs",
+    )
 
 
 class MRConvertOutputSpec(TraitedSpec):
@@ -615,9 +673,15 @@ def _list_outputs(self):
 
 class MRMathInputSpec(MRTrix3BaseInputSpec):
     in_file = File(
-        exists=True, argstr="%s", mandatory=True, position=-3, desc="input image"
+        exists=True,
+        argstr="%s",
+        mandatory=True,
+        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",
@@ -637,7 +701,9 @@ class MRMathInputSpec(MRTrix3BaseInputSpec):
         desc="operation to computer along a specified axis",
     )
     axis = traits.Int(
-        0, argstr="-axis %d", desc="specfied axis to perform the operation along"
+        0,
+        argstr="-axis %d",
+        desc="specfied axis to perform the operation along",
     )
 
 
@@ -677,7 +743,11 @@ def _list_outputs(self):
 
 class MRResizeInputSpec(MRTrix3BaseInputSpec):
     in_file = File(
-        exists=True, argstr="%s", position=-2, mandatory=True, desc="input DWI image"
+        exists=True,
+        argstr="%s",
+        position=-2,
+        mandatory=True,
+        desc="input DWI image",
     )
     image_size = traits.Tuple(
         (traits.Int, traits.Int, traits.Int),
@@ -794,7 +864,9 @@ 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):
@@ -858,7 +930,9 @@ 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):