Merge pull request #1948 from tsalo/mriscombine

[ENH] Add MRIsCombine to FreeSurfer utils.

Author: satra

nipype/interfaces/freesurfer/__init__.py

@@ -21,7 +21,7 @@
                     MRIFill, MRIsInflate, Sphere, FixTopology, EulerNumber,
                     RemoveIntersection, MakeSurfaces, Curvature, CurvatureStats,
                     Jacobian, MRIsCalc, VolumeMask, ParcellationStats, Contrast,
-                    RelabelHypointensities, Aparc2Aseg, Apas2Aseg, MRIsExpand)
+                    RelabelHypointensities, Aparc2Aseg, Apas2Aseg, MRIsExpand, MRIsCombine)
 from .longitudinal import (RobustTemplate, FuseSegmentations)
 from .registration import (MPRtoMNI305, RegisterAVItoTalairach, EMRegister, Register,
                            Paint)

nipype/interfaces/freesurfer/base.py

@@ -162,8 +162,44 @@ 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 _get_filecopy_info(self):
+        self._normalize_filenames()
+        return super(FSSurfaceCommand, self)._get_filecopy_info()
+
+    def _normalize_filenames(self):
+        """Filename normalization routine to perform only when run in Node
+        context
+        """
+        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.
+        Also, output to in_file's directory if path information not provided
+        for out_name.
+        """
+        path, base = os.path.split(out_name)
+        if path == '':
+            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/tests/test_auto_MRIsCombine.py

@@ -0,0 +1,42 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..utils import MRIsCombine
+
+
+def test_MRIsCombine_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_files=dict(argstr='--combinesurfs %s',
+    mandatory=True,
+    position=1,
+    ),
+    out_file=dict(argstr='%s',
+    genfile=True,
+    mandatory=True,
+    position=-1,
+    ),
+    subjects_dir=dict(),
+    terminal_output=dict(nohash=True,
+    ),
+    )
+    inputs = MRIsCombine.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+
+
+def test_MRIsCombine_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = MRIsCombine.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.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'
@@ -954,6 +954,77 @@ def _gen_outfilename(self):
         return name + ext + "_converted." + self.inputs.out_datatype
 
 
+class MRIsCombineInputSpec(FSTraitedSpec):
+    """
+    Uses Freesurfer's mris_convert to combine two surface files into one.
+    """
+    in_files = traits.List(File(Exists=True), maxlen=2, minlen=2,
+                           mandatory=True, position=1, argstr='--combinesurfs %s',
+                           desc='Two surfaces to be combined.')
+    out_file = File(argstr='%s', position=-1, genfile=True,
+                    mandatory=True,
+                    desc='Output filename. Combined surfaces from in_files.')
+
+
+class MRIsCombineOutputSpec(TraitedSpec):
+    """
+    Uses Freesurfer's mris_convert to combine two surface files into one.
+    """
+    out_file = File(exists=True, desc='Output filename. Combined surfaces from '
+                                      'in_files.')
+
+
+class MRIsCombine(FSSurfaceCommand):
+    """
+    Uses Freesurfer's mris_convert to combine two surface files into one.
+
+    For complete details, see the `mris_convert Documentation.
+    <https://surfer.nmr.mgh.harvard.edu/fswiki/mris_convert>`_
+
+    If given an out_file that does not begin with 'lh.' or 'rh.',
+    mris_convert will prepend 'lh.' to the file name.
+    To avoid this behavior, consider setting out_file = './<filename>', or
+    leaving out_file blank.
+
+    Example
+    -------
+
+    >>> import nipype.interfaces.freesurfer as fs
+    >>> mris = fs.MRIsCombine()
+    >>> mris.inputs.in_files = ['lh.pial', 'rh.pial']
+    >>> mris.inputs.out_file = 'bh.pial'
+    >>> mris.cmdline  # doctest: +ALLOW_UNICODE
+    'mris_convert --combinesurfs lh.pial rh.pial bh.pial'
+    >>> mris.run()  # doctest: +SKIP
+    """
+    _cmd = 'mris_convert'
+    input_spec = MRIsCombineInputSpec
+    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.
+        """
+        path, base = os.path.split(out_name)
+        if path == '':
+            hemis = ('lh.', 'rh.')
+            if base[:3] not in hemis:
+                base = 'lh.' + base
+        return os.path.abspath(os.path.join(path, base))
+
+    def _normalize_filenames(self):
+        if isdefined(self.inputs.out_file):
+            self.inputs.out_file = os.path.abspath(self.inputs.out_file)
+
+
 class MRITessellateInputSpec(FSTraitedSpec):
     """
     Uses Freesurfer's mri_tessellate to create surfaces by tessellating a given input volume