ENH: json-related entities in MRConvert's inputs specification

doc/devel/matlab_example1.py

@@ -1,13 +1,17 @@
 from nipype.interfaces.matlab import MatlabCommand
-from nipype.interfaces.base import TraitedSpec, \
-    BaseInterface, BaseInterfaceInputSpec, File
+from nipype.interfaces.base import (
+    TraitedSpec,
+    BaseInterface,
+    BaseInterfaceInputSpec,
+    File,
+)
 import os
 from string import Template
 
 
 class ConmapTxt2MatInputSpec(BaseInterfaceInputSpec):
     in_file = File(exists=True, mandatory=True)
-    out_file = File('cmatrix.mat', usedefault=True)
+    out_file = File("cmatrix.mat", usedefault=True)
 
 
 class ConmapTxt2MatOutputSpec(TraitedSpec):
@@ -19,14 +23,15 @@ class ConmapTxt2Mat(BaseInterface):
     output_spec = ConmapTxt2MatOutputSpec
 
     def _run_interface(self, runtime):
-        d = dict(in_file=self.inputs.in_file,
-                 out_file=self.inputs.out_file)
+        d = dict(in_file=self.inputs.in_file, out_file=self.inputs.out_file)
         # This is your MATLAB code template
-        script = Template("""in_file = '$in_file';
+        script = Template(
+            """in_file = '$in_file';
                              out_file = '$out_file';
                              ConmapTxt2Mat(in_file, out_file);
                              exit;
-                          """).substitute(d)
+                          """
+        ).substitute(d)
 
         # mfile = True  will create an .m file with your script and executed.
         # Alternatively
@@ -43,5 +48,5 @@ def _run_interface(self, runtime):
 
     def _list_outputs(self):
         outputs = self._outputs().get()
-        outputs['out_file'] = os.path.abspath(self.inputs.out_file)
+        outputs["out_file"] = os.path.abspath(self.inputs.out_file)
         return outputs

doc/devel/matlab_example2.py

@@ -4,8 +4,7 @@
 
 
 class HelloWorldInputSpec(MatlabInputSpec):
-    name = traits.Str(mandatory=True,
-                      desc='Name of person to say hello to')
+    name = traits.Str(mandatory=True, desc="Name of person to say hello to")
 
 
 class HelloWorldOutputSpec(TraitedSpec):
@@ -29,6 +28,7 @@ class HelloWorld(MatlabCommand):
     >>> out = hello.run()
     >>> print out.outputs.matlab_output
     """
+
     input_spec = HelloWorldInputSpec
     output_spec = HelloWorldOutputSpec
 
@@ -37,7 +37,9 @@ def _my_script(self):
         script = """
         disp('Hello %s Python')
         two = 1 + 1
-        """ % (self.inputs.name)
+        """ % (
+            self.inputs.name
+        )
         return script
 
     def run(self, **inputs):

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/tests/test_auto_MRConvert.py

@@ -44,6 +44,16 @@ def test_MRConvert_inputs():
             mandatory=True,
             position=-2,
         ),
+        json_export=dict(
+            argstr="-json_export %s",
+            extensions=None,
+            mandatory=False,
+        ),
+        json_import=dict(
+            argstr="-json_import %s",
+            extensions=None,
+            mandatory=False,
+        ),
         nthreads=dict(
             argstr="-nthreads %d",
             nohash=True,
@@ -73,6 +83,9 @@ def test_MRConvert_inputs():
 
 def test_MRConvert_outputs():
     output_map = dict(
+        json_export=dict(
+            extensions=None,
+        ),
         out_file=dict(
             extensions=None,
         ),

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,
@@ -134,7 +138,11 @@ 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")
 
@@ -173,7 +181,11 @@ 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")
@@ -246,10 +258,18 @@ 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,
@@ -353,7 +373,8 @@ 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(
@@ -438,10 +459,18 @@ 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,
@@ -498,7 +527,11 @@ 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")
     bzero = traits.Bool(argstr="-bzero", desc="extract b=0 volumes")
@@ -549,7 +582,11 @@ 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 +603,10 @@ 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,
@@ -580,10 +620,26 @@ 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",
+    )
+    json_export = File(
+        exists=False,
+        argstr="-json_export %s",
+        mandatory=False,
+        desc="export data from an image header key-value pairs into a JSON file",
+    )
 
 
 class MRConvertOutputSpec(TraitedSpec):
     out_file = File(exists=True, desc="output image")
+    json_export = File(
+        exists=True,
+        desc="exported data from an image header key-value pairs in a JSON file",
+    )
 
 
 class MRConvert(MRTrix3Base):
@@ -610,12 +666,18 @@ class MRConvert(MRTrix3Base):
     def _list_outputs(self):
         outputs = self.output_spec().get()
         outputs["out_file"] = op.abspath(self.inputs.out_file)
+        if self.inputs.json_export:
+            outputs["json_export"] = op.abspath(self.inputs.json_export)
         return outputs
 
 
 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")
     operation = traits.Enum(
@@ -637,7 +699,9 @@ 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 +741,11 @@ 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),

tools/checkspecs.py

@@ -13,8 +13,7 @@
 
 # Functions and classes
 class InterfaceChecker(object):
-    """Class for checking all interface specifications
-    """
+    """Class for checking all interface specifications"""
 
     def __init__(
         self,
@@ -23,7 +22,7 @@ def __init__(
         module_skip_patterns=None,
         class_skip_patterns=None,
     ):
-        r""" Initialize package for parsing
+        r"""Initialize package for parsing
 
         Parameters
         ----------
@@ -113,14 +112,14 @@ def _uri2path(self, uri):
         return path
 
     def _path2uri(self, dirpath):
-        """ Convert directory path to uri """
+        """Convert directory path to uri"""
         relpath = dirpath.replace(self.root_path, self.package_name)
         if relpath.startswith(os.path.sep):
             relpath = relpath[1:]
         return relpath.replace(os.path.sep, ".")
 
     def _parse_module(self, uri):
-        """ Parse module defined in *uri* """
+        """Parse module defined in *uri*"""
         filename = self._uri2path(uri)
         if filename is None:
             # nothing that we could handle here.
@@ -131,7 +130,7 @@ def _parse_module(self, uri):
         return functions, classes
 
     def _parse_lines(self, linesource, module):
-        """ Parse lines of text for functions and classes """
+        """Parse lines of text for functions and classes"""
         functions = []
         classes = []
         for line in linesource:
@@ -387,7 +386,7 @@ def test_specs(self, uri):
         return bad_specs
 
     def _survives_exclude(self, matchstr, match_type):
-        """ Returns True if *matchstr* does not match patterns
+        """Returns True if *matchstr* does not match patterns
 
         ``self.package_name`` removed from front of string if present
 
@@ -429,7 +428,7 @@ def _survives_exclude(self, matchstr, match_type):
         return True
 
     def discover_modules(self):
-        """ Return module sequence discovered from ``self.package_name``
+        """Return module sequence discovered from ``self.package_name``
 
 
         Parameters