[med-svn] [python-mne] 214/376: renaming bem_surfaces.py to surface.py + merge surfer.py and surface.py

[Yaroslav Halchenko]

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yoh pushed a commit to annotated tag v0.1
in repository python-mne.

commit 00a3aad7bf8df30a6ccea827508ed51b41c6181a
Author: Alexandre Gramfort <alexandre.gramfort at inria.fr>
Date:   Fri Apr 22 13:45:47 2011 -0400

    renaming bem_surfaces.py to surface.py + merge surfer.py and surface.py
---
 mne/__init__.py                                    |  2 +-
 mne/source_estimate.py                             |  3 +-
 mne/{bem_surfaces.py => surface.py}                | 43 +++++++++++++++++++
 mne/surfer.py                                      | 48 ----------------------
 mne/tests/test_source_space.py                     |  2 -
 .../{test_bem_surfaces.py => test_surface.py}      |  0
 6 files changed, 45 insertions(+), 53 deletions(-)

diff --git a/mne/__init__.py b/mne/__init__.py
index 5326d54..e81addc 100755
--- a/mne/__init__.py
+++ b/mne/__init__.py
@@ -5,7 +5,7 @@ from .cov import read_cov, write_cov, write_cov_file, Covariance, \
 from .event import read_events, write_events, find_events
 from .forward import read_forward_solution
 from .source_estimate import read_stc, write_stc, SourceEstimate, morph_data
-from .bem_surfaces import read_bem_surfaces
+from .surface import read_bem_surfaces
 from .source_space import read_source_spaces
 from .epochs import Epochs
 from .label import label_time_courses, read_label
diff --git a/mne/source_estimate.py b/mne/source_estimate.py
index 71a620a..453b318 100755
--- a/mne/source_estimate.py
+++ b/mne/source_estimate.py
@@ -163,8 +163,7 @@ from .fiff.constants import FIFF
 from .fiff.tag import find_tag
 from .fiff.open import fiff_open
 from .fiff.tree import dir_tree_find
-from .bem_surfaces import read_bem_surfaces
-from .surfer import read_surface
+from .surface import read_bem_surfaces, read_surface
 
 
 def read_morph_map(subject_from, subject_to, subjects_dir=None):
diff --git a/mne/bem_surfaces.py b/mne/surface.py
similarity index 79%
rename from mne/bem_surfaces.py
rename to mne/surface.py
index eb2c18a..fed41f5 100755
--- a/mne/bem_surfaces.py
+++ b/mne/surface.py
@@ -205,3 +205,46 @@ def _complete_surface_info(this):
 
     print '[done]'
     return this
+
+
+###############################################################################
+# Handle freesurfer
+
+def fread3(fobj):
+    """Docstring"""
+    b1, b2, b3 = np.fromfile(fobj, ">u1", 3)
+    return (b1 << 16) + (b2 << 8) + b3
+
+
+def read_curvature(filepath):
+    """Load in curavature values from the ?h.curv file."""
+    with open(filepath, "rb") as fobj:
+        magic = fread3(fobj)
+        if magic == 16777215:
+            vnum = np.fromfile(fobj, ">i4", 3)[0]
+            curv = np.fromfile(fobj, ">f4", vnum)
+        else:
+            vnum = magic
+            fread3(fobj)
+            curv = np.fromfile(fobj, ">i2", vnum) / 100
+        bin_curv = 1 - np.array(curv != 0, np.int)
+    return bin_curv
+
+
+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:
+            raise NotImplementedError("Quadrangle surface format reading not "
+                                      "implemented")
+        elif magic != 16777214:
+            raise ValueError("File does not appear to be a Freesurfer surface")
+        create_stamp = fobj.readline()
+        blankline = fobj.readline()
+        del blankline
+        vnum = np.fromfile(fobj, ">i4", 1)[0]
+        fnum = np.fromfile(fobj, ">i4", 1)[0]
+        vertex_coords = np.fromfile(fobj, ">f4", vnum * 3).reshape(vnum, 3)
+        faces = np.fromfile(fobj, ">i4", fnum * 3).reshape(fnum, 3)
+    return vertex_coords, faces
diff --git a/mne/surfer.py b/mne/surfer.py
deleted file mode 100644
index 21f77de..0000000
--- a/mne/surfer.py
+++ /dev/null
@@ -1,48 +0,0 @@
-"""Set of tools to interact with Freesurfer data
-"""
-
-# Authors: Alexandre Gramfort <gramfort at nmr.mgh.harvard.edu>
-#
-# License: BSD (3-clause)
-
-import numpy as np
-
-
-def fread3(fobj):
-    """Docstring"""
-    b1, b2, b3 = np.fromfile(fobj, ">u1", 3)
-    return (b1 << 16) + (b2 << 8) + b3
-
-
-def read_curvature(filepath):
-    """Load in curavature values from the ?h.curv file."""
-    with open(filepath, "rb") as fobj:
-        magic = fread3(fobj)
-        if magic == 16777215:
-            vnum = np.fromfile(fobj, ">i4", 3)[0]
-            curv = np.fromfile(fobj, ">f4", vnum)
-        else:
-            vnum = magic
-            fread3(fobj)
-            curv = np.fromfile(fobj, ">i2", vnum) / 100
-        bin_curv = 1 - np.array(curv != 0, np.int)
-    return bin_curv
-
-
-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:
-            raise NotImplementedError("Quadrangle surface format reading not "
-                                      "implemented")
-        elif magic != 16777214:
-            raise ValueError("File does not appear to be a Freesurfer surface")
-        create_stamp = fobj.readline()
-        blankline = fobj.readline()
-        del blankline
-        vnum = np.fromfile(fobj, ">i4", 1)[0]
-        fnum = np.fromfile(fobj, ">i4", 1)[0]
-        vertex_coords = np.fromfile(fobj, ">f4", vnum * 3).reshape(vnum, 3)
-        faces = np.fromfile(fobj, ">i4", fnum * 3).reshape(fnum, 3)
-    return vertex_coords, faces
diff --git a/mne/tests/test_source_space.py b/mne/tests/test_source_space.py
index dedfdca..693e3b7 100755
--- a/mne/tests/test_source_space.py
+++ b/mne/tests/test_source_space.py
@@ -31,5 +31,3 @@ def test_read_source_spaces():
     assert rh_faces.max() == rh_points.shape[0] - 1
     assert rh_use_faces.min() >= 0
     assert rh_use_faces.max() <= lh_points.shape[0] - 1
-
-def test_morph_data():
\ No newline at end of file
diff --git a/mne/tests/test_bem_surfaces.py b/mne/tests/test_surface.py
similarity index 100%
rename from mne/tests/test_bem_surfaces.py
rename to mne/tests/test_surface.py

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