[med-svn] [python-mne] 95/353: ENH : new mne_surf2bem.py that mimics mne_surf2bem without crashing when surface is not clean

[Yaroslav Halchenko]

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yoh pushed a commit to tag 0.4
in repository python-mne.

commit 5f33313ef77c781eae08cb93e6a91c2b3986eb5d
Author: Alexandre Gramfort <alexandre.gramfort at inria.fr>
Date:   Fri Mar 2 11:16:15 2012 +0100

    ENH : new mne_surf2bem.py that mimics mne_surf2bem without crashing when surface is not clean
---
 bin/mne_surf2bem.py | 34 ++++++++++++++++++++++++++++++++++
 mne/surface.py      |  5 +++--
 setup.py            |  3 ++-
 3 files changed, 39 insertions(+), 3 deletions(-)

diff --git a/bin/mne_surf2bem.py b/bin/mne_surf2bem.py
new file mode 100755
index 0000000..368b9f4
--- /dev/null
+++ b/bin/mne_surf2bem.py
@@ -0,0 +1,34 @@
+#!/usr/bin/env python
+"""Example usage
+
+mne_surf2bem.py --surf ${SUBJECTS_DIR}/${SUBJECT}/surf/lh.seghead --fif \
+    ${SUBJECTS_DIR}/${SUBJECT}/bem/${SUBJECT}-head.fif --id=4
+
+"""
+# Authors: Alexandre Gramfort <gramfort at nmr.mgh.harvard.edu>
+#
+# License: BSD (3-clause)
+
+import mne
+
+if __name__ == '__main__':
+
+    from optparse import OptionParser
+
+    parser = OptionParser()
+    parser.add_option("-s", "--surf", dest="surf",
+                    help="Surface in Freesurfer format", metavar="FILE")
+    parser.add_option("-f", "--fif", dest="fif",
+                    help="FIF file produced", metavar="FILE")
+    parser.add_option("-i", "--id", dest="id", default=4,
+                    help=("Surface Id (e.g. 4 sur head surface)"))
+
+    (options, args) = parser.parse_args()
+
+    print "Converting %s to BEM FIF file." % options.surf
+
+    points, tris = mne.read_surface(options.surf)
+    points *= 1e-3
+    surf = dict(coord_frame=5, id=int(options.id), nn=None, np=len(points),
+                ntri=len(tris), rr=points, sigma=1, tris=tris)
+    mne.write_bem_surface(options.fif, surf)
diff --git a/mne/surface.py b/mne/surface.py
index b99b6c7..9ea7b8a 100644
--- a/mne/surface.py
+++ b/mne/surface.py
@@ -245,7 +245,7 @@ def read_surface(filepath):
     """Load in a Freesurfer surface mesh in triangular format."""
     with open(filepath, "rb") as fobj:
         magic = _fread3(fobj)
-        if magic == 16777215:  # Quad file
+        if (magic == 16777215) or (magic == 16777213):  # Quad file or new quad
             nvert = _fread3(fobj)
             nquad = _fread3(fobj)
             coords = np.fromfile(fobj, ">i2", nvert * 3).astype(np.float)
@@ -277,7 +277,8 @@ def read_surface(filepath):
             coords = np.fromfile(fobj, ">f4", vnum * 3).reshape(vnum, 3)
             faces = np.fromfile(fobj, ">i4", fnum * 3).reshape(fnum, 3)
         else:
-            raise ValueError("File does not appear to be a Freesurfer surface")
+            raise ValueError("%s does not appear to be a Freesurfer surface"
+                             % filepath)
 
     coords = coords.astype(np.float)  # XXX: due to mayavi bug on mac 32bits
     return coords, faces
diff --git a/setup.py b/setup.py
index 398d104..e1f513b 100755
--- a/setup.py
+++ b/setup.py
@@ -59,4 +59,5 @@ if __name__ == "__main__":
                    'mne.minimum_norm', 'mne.minimum_norm.tests',
                    'mne.layouts',
                    'mne.time_frequency', 'mne.time_frequency.tests'],
-         scripts=['bin/mne_clean_eog_ecg.py', 'bin/mne_flash_bem_model.py'])
+         scripts=['bin/mne_clean_eog_ecg.py', 'bin/mne_flash_bem_model.py',
+                  'bin/mne_surf2bem.py'])

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