Accept expert options as a dictionary

Author: effigies

nipype/interfaces/freesurfer/preprocess.py

@@ -28,6 +28,7 @@
                     Directory, InputMultiPath,
                     OutputMultiPath, CommandLine,
                     CommandLineInputSpec, isdefined)
+from ..traits_extension import DictStrStr
 from .base import (FSCommand, FSTraitedSpec,
                    FSTraitedSpecOpenMP,
                    FSCommandOpenMP, Info)
@@ -634,7 +635,7 @@ class ReconAllInputSpec(CommandLineInputSpec):
                            desc="Enable parallel execution")
     hires = traits.Bool(argstr="-hires", min_ver='6.0.0',
                         desc="Conform to minimum voxel size (for voxels < 1mm)")
-    expert = File(exists=True, argstr='-expert %s',
+    expert = traits.Either(File(exists=True), DictStrStr, argstr='-expert %s',
                   desc="Set parameters using expert file")
     subjects_dir = Directory(exists=True, argstr='-sd %s', hash_files=False,
                              desc='path to subjects directory', genfile=True)
@@ -899,6 +900,12 @@ def _format_arg(self, name, trait_spec, value):
         if name == 'T1_files':
             if self._is_resuming():
                 return ''
+        if name == 'expert' and isinstance(value, dict):
+            expert_fname = os.path.abspath('expert.opts')
+            expert = ['{} {}\n'.format(key, val) for key, val in value.items()]
+            with open(expert_fname, 'w') as fobj:
+                fobj.write(''.join(expert))
+            value = expert_fname
         return super(ReconAll, self)._format_arg(name, trait_spec, value)
 
     @property

nipype/interfaces/freesurfer/tests/test_auto_ExpertOptions.py

@@ -18,8 +18,8 @@
 import shutil
 
 from ...utils.filemanip import fname_presuffix, split_filename
-from ..base import (TraitedSpec, BaseInterface, File, traits, OutputMultiPath,
-                    isdefined, CommandLine, CommandLineInputSpec)
+from ..base import (TraitedSpec, File, traits, OutputMultiPath, isdefined,
+                    CommandLine, CommandLineInputSpec)
 from .base import (FSCommand, FSTraitedSpec,
                    FSScriptCommand, FSScriptOutputSpec,
                    FSTraitedSpecOpenMP, FSCommandOpenMP)
@@ -2879,64 +2879,3 @@ def _list_outputs(self):
         outputs = self._outputs().get()
         outputs["out_file"] = os.path.abspath(self.inputs.out_file)
         return outputs
-
-
-class ExpertOptionsInputSpec(TraitedSpec):
-    talairach = traits.String(desc="Flags to pass to talairach commands")
-    mri_normalize = traits.String(desc="Flags to pass to mri_normalize commands")
-    mri_watershed = traits.String(desc="Flags to pass to mri_watershed commands")
-    mri_em_register = traits.String(desc="Flags to pass to mri_em_register commands")
-    mri_ca_normalize = traits.String(desc="Flags to pass to mri_ca_normalize commands")
-    mri_ca_register = traits.String(desc="Flags to pass to mri_ca_register commands")
-    mri_remove_neck = traits.String(desc="Flags to pass to mri_remove_neck commands")
-    mri_ca_label = traits.String(desc="Flags to pass to mri_ca_label commands")
-    mri_segstats = traits.String(desc="Flags to pass to mri_segstats commands")
-    mri_mask = traits.String(desc="Flags to pass to mri_mask commands")
-    mri_segment = traits.String(desc="Flags to pass to mri_segment commands")
-    mri_edit_wm_with_aseg = traits.String(desc="Flags to pass to mri_edit_wm_with_aseg commands")
-    mri_pretess = traits.String(desc="Flags to pass to mri_pretess commands")
-    mri_fill = traits.String(desc="Flags to pass to mri_fill commands")
-    mri_tessellate = traits.String(desc="Flags to pass to mri_tessellate commands")
-    mris_smooth = traits.String(desc="Flags to pass to mri_smooth commands")
-    mris_inflate = traits.String(desc="Flags to pass to mri_inflate commands")
-    mris_sphere = traits.String(desc="Flags to pass to mris_sphere commands")
-    mris_fix_topology = traits.String(desc="Flags to pass to mris_fix_topology commands")
-    mris_make_surfaces = traits.String(desc="Flags to pass to mris_make_surfaces commands")
-    mris_surf2vol = traits.String(desc="Flags to pass to mris_surf2vol commands")
-    mris_register = traits.String(desc="Flags to pass to mris_register commands")
-    mrisp_paint = traits.String(desc="Flags to pass to mrisp_paint commands")
-    mris_ca_label = traits.String(desc="Flags to pass to mris_ca_label commands")
-    mris_anatomical_stats = traits.String(desc="Flags to pass to mris_anatomical_stats commands")
-    mri_aparc2aseg = traits.String(desc="Flags to pass to mri_aparc2aseg commands")
-    out_file = File("expert.opts", usedefault=True, desc="Output expert options file")
-
-
-class ExpertOptionsOutputSpec(TraitedSpec):
-    out_file = File(exists=False, desc="Output expert options file")
-
-
-class ExpertOptions(BaseInterface):
-    """
-    Creates expert options file
-    https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertOptionsFile
-    """
-    input_spec = ExpertOptionsInputSpec
-    output_spec = ExpertOptionsOutputSpec
-
-    def _list_outputs(self):
-        outputs = self._outputs().get()
-        outputs["out_file"] = os.path.abspath(self.inputs.out_file)
-        return outputs
-
-    def _run_interface(self, runtime):
-        out_file = self.inputs.out_file
-
-        lines = []
-        for binary, args in self.inputs.get().items():
-            if binary == 'out_file' or not isdefined(args):
-                continue
-            lines.append('{} {}\n'.format(binary, args))
-
-        with open(out_file, 'w') as fobj:
-            fobj.write(''.join(lines))
-        return runtime