Add FSSurfaceCommand and change MRIsCombine setup.

Author: tsalo

nipype/interfaces/freesurfer/base.py

@@ -162,8 +162,45 @@ def version(self):
                 return ver.rstrip().split('-v')[-1]
 
 
+class FSSurfaceCommand(FSCommand):
+    """Support for FreeSurfer surface-related functions.
+    For some functions, if the output file is not specified starting with
+    'lh.' or 'rh.', FreeSurfer prepends the prefix from the input file to the
+    output filename. Output out_file must be adjusted to accommodate this.
+    By including the full path in the filename, we can also avoid this behavior.
+    """
+    def __init__(self, **inputs):
+        super(FSSurfaceCommand, self).__init__(**inputs)
+
+    def _get_filecopy_info(self):
+        """Filename normalization routine to perform only when run in Node
+        context
+        """
+        self._normalize_filenames()
+        return super(FSSurfaceCommand, self)._get_filecopy_info()
+
+    def _normalize_filenames(self):
+        pass
+
+    @staticmethod
+    def _associated_file(in_file, out_name):
+        """Based on MRIsBuildFileName in freesurfer/utils/mrisurf.c
+
+        Use in_file prefix to indicate hemisphere for out_name, rather than
+        inspecting the surface data structure.
+        """
+        path, base = os.path.split(out_name)
+        if path == '':
+            _, in_file = os.path.split(in_file)
+            hemis = ('lh.', 'rh.')
+            if in_file[:3] in hemis and base[:3] not in hemis:
+                base = in_file[:3] + base
+        return os.path.abspath(os.path.join(path, base))
+
+
 class FSScriptCommand(FSCommand):
-    """ Support for Freesurfer script commands with log inputs.terminal_output """
+    """ Support for Freesurfer script commands with log inputs.terminal_output
+    """
     _terminal_output = 'file'
     _always_run = False
 

nipype/interfaces/freesurfer/tests/test_auto_FSSurfaceCommand.py

@@ -0,0 +1,24 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..base import FSSurfaceCommand
+
+
+def test_FSSurfaceCommand_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    subjects_dir=dict(),
+    terminal_output=dict(nohash=True,
+    ),
+    )
+    inputs = FSSurfaceCommand.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+

nipype/interfaces/freesurfer/utils.py

@@ -21,7 +21,7 @@
 from ...utils.filemanip import fname_presuffix, split_filename
 from ..base import (TraitedSpec, File, traits, OutputMultiPath, isdefined,
                     CommandLine, CommandLineInputSpec)
-from .base import (FSCommand, FSTraitedSpec,
+from .base import (FSCommand, FSTraitedSpec, FSSurfaceCommand,
                    FSScriptCommand, FSScriptOutputSpec,
                    FSTraitedSpecOpenMP, FSCommandOpenMP)
 __docformat__ = 'restructuredtext'
@@ -974,7 +974,7 @@ class MRIsCombineOutputSpec(TraitedSpec):
                                       'in_files.')
 
 
-class MRIsCombine(FSCommand):
+class MRIsCombine(FSSurfaceCommand):
     """
     Uses Freesurfer's mris_convert to combine two surface files into one.
 
@@ -997,19 +997,28 @@ class MRIsCombine(FSCommand):
     output_spec = MRIsCombineOutputSpec
 
     def _list_outputs(self):
+        outputs = self._outputs().get()
+        outputs['out_file'] = self._associated_file(self.inputs.in_files[0],
+                                                    self.inputs.out_file)
+        return outputs
+
+    @staticmethod
+    def _associated_file(in_file, out_name):
+        """Unlike the standard _associated_file, which uses the prefix from
+        in_file, in MRIsCombine, it uses 'lh.' as the prefix for the output
+        file no matter what the inputs are.
         """
-        If the output file is not specified starting with 'lh.' or 'rh.',
-        FreeSurfer prepends 'lh.' to the filename. It never adds 'rh.', even if
-        both input files are from the right hemisphere. Output out_file must be
-        adjusted to accommodate this.
-        """
-        outputs = self.output_spec().get()
-        if any(self.inputs.out_file.startswith(pre) for pre in ['lh.', 'rh.']):
-            outputs['out_file'] = self.inputs.out_file
-        else:
-            outputs['out_file'] = 'lh.' + self.inputs.out_file
+        path, base = os.path.split(out_name)
+        if path == '':
+            _, in_file = os.path.split(in_file)
+            hemis = ('lh.', 'rh.')
+            if base[:3] not in hemis:
+                base = 'lh.' + base
+        return os.path.abspath(os.path.join(path, base))
 
-        return outputs
+    def _normalize_filenames(self):
+        if isdefined(self.inputs.out_file):
+            self.inputs.out_file = os.path.abspath(self.inputs.out_file)
 
 
 class MRITessellateInputSpec(FSTraitedSpec):