Merge pull request #1886 from effigies/freesurfer_outtypes

[RTM] Support GIFTI outputs in SampleToSurface

Author: chrisgorgo

nipype/interfaces/freesurfer/utils.py

@@ -17,6 +17,7 @@
 import re
 import shutil
 
+from ... import logging
 from ...utils.filemanip import fname_presuffix, split_filename
 from ..base import (TraitedSpec, File, traits, OutputMultiPath, isdefined,
                     CommandLine, CommandLineInputSpec)
@@ -29,13 +30,15 @@
                afni='brik', brik='brik', bshort='bshort',
                spm='img', analyze='img', analyze4d='img',
                bfloat='bfloat', nifti1='img', nii='nii',
-               niigz='nii.gz')
+               niigz='nii.gz', gii='gii')
 
 filetypes = ['cor', 'mgh', 'mgz', 'minc', 'analyze',
              'analyze4d', 'spm', 'afni', 'brik', 'bshort',
              'bfloat', 'sdt', 'outline', 'otl', 'gdf',
              'nifti1', 'nii', 'niigz']
+implicit_filetypes = ['gii']
 
+logger = logging.getLogger('interface')
 
 def copy2subjdir(cls, in_file, folder=None, basename=None, subject_id=None):
     """Method to copy an input to the subjects directory"""
@@ -151,7 +154,8 @@ class SampleToSurfaceInputSpec(FSTraitedSpec):
     frame = traits.Int(argstr="--frame %d", desc="save only one frame (0-based)")
 
     out_file = File(argstr="--o %s", genfile=True, desc="surface file to write")
-    out_type = traits.Enum(filetypes, argstr="--out_type %s", desc="output file type")
+    out_type = traits.Enum(filetypes + implicit_filetypes,
+                           argstr="--out_type %s", desc="output file type")
     hits_file = traits.Either(traits.Bool, File(exists=True), argstr="--srchit %s",
                               desc="save image with number of hits at each voxel")
     hits_type = traits.Enum(filetypes, argstr="--srchit_type", desc="hits file type")
@@ -201,12 +205,6 @@ class SampleToSurface(FSCommand):
     input_spec = SampleToSurfaceInputSpec
     output_spec = SampleToSurfaceOutputSpec
 
-    filemap = dict(cor='cor', mgh='mgh', mgz='mgz', minc='mnc',
-                   afni='brik', brik='brik', bshort='bshort',
-                   spm='img', analyze='img', analyze4d='img',
-                   bfloat='bfloat', nifti1='img', nii='nii',
-                   niigz='nii.gz')
-
     def _format_arg(self, name, spec, value):
         if name == "sampling_method":
             range = self.inputs.sampling_range
@@ -226,16 +224,29 @@ def _format_arg(self, name, spec, value):
             return spec.argstr % self.inputs.subject_id
         if name in ["hits_file", "vox_file"]:
             return spec.argstr % self._get_outfilename(name)
+        if name == "out_type":
+            if isdefined(self.inputs.out_file):
+                _, base, ext = split_filename(self._get_outfilename())
+                if ext != filemap[value]:
+                    if ext in filemap.values():
+                        raise ValueError(
+                            "Cannot create {} file with extension "
+                            "{}".format(value, ext))
+                    else:
+                        logger.warn("Creating {} file with extension {}: "
+                                    "{}{}".format(value, ext, base, ext))
+            if value in implicit_filetypes:
+                return ""
         return super(SampleToSurface, self)._format_arg(name, spec, value)
 
     def _get_outfilename(self, opt="out_file"):
         outfile = getattr(self.inputs, opt)
         if not isdefined(outfile) or isinstance(outfile, bool):
             if isdefined(self.inputs.out_type):
                 if opt == "hits_file":
-                    suffix = '_hits.' + self.filemap[self.inputs.out_type]
+                    suffix = '_hits.' + filemap[self.inputs.out_type]
                 else:
-                    suffix = '.' + self.filemap[self.inputs.out_type]
+                    suffix = '.' + filemap[self.inputs.out_type]
             elif opt == "hits_file":
                 suffix = "_hits.mgz"
             else:
@@ -365,7 +376,7 @@ class SurfaceTransformInputSpec(FSTraitedSpec):
     source_type = traits.Enum(filetypes, argstr='--sfmt %s',
                               requires=['source_file'],
                               desc="source file format")
-    target_type = traits.Enum(filetypes, argstr='--tfmt %s',
+    target_type = traits.Enum(filetypes + implicit_filetypes, argstr='--tfmt %s',
                               desc="output format")
     reshape = traits.Bool(argstr="--reshape",
                           desc="reshape output surface to conform with Nifti")
@@ -402,6 +413,22 @@ class SurfaceTransform(FSCommand):
     input_spec = SurfaceTransformInputSpec
     output_spec = SurfaceTransformOutputSpec
 
+    def _format_arg(self, name, spec, value):
+        if name == "target_type":
+            if isdefined(self.inputs.out_file):
+                _, base, ext = split_filename(self._list_outputs()['out_file'])
+                if ext != filemap[value]:
+                    if ext in filemap.values():
+                        raise ValueError(
+                            "Cannot create {} file with extension "
+                            "{}".format(value, ext))
+                    else:
+                        logger.warn("Creating {} file with extension {}: "
+                                    "{}{}".format(value, ext, base, ext))
+            if value in implicit_filetypes:
+                return ""
+        return super(SurfaceTransform, self)._format_arg(name, spec, value)
+
     def _list_outputs(self):
         outputs = self._outputs().get()
         outputs["out_file"] = self.inputs.out_file