[med-svn] [python-mne] 203/376: ENH : rm some XXX for speed

[Yaroslav Halchenko]

This is an automated email from the git hooks/post-receive script.

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

commit 49c4df618be02f7e0722e9c8e26790a2afac62e2
Author: Alexandre Gramfort <alexandre.gramfort at inria.fr>
Date:   Sun Apr 17 19:59:26 2011 -0400

    ENH : rm some XXX for speed
---
 examples/read_bem_surfaces.py |  2 +-
 mne/bem_surfaces.py           | 20 ++++++--------------
 mne/fiff/raw.py               |  3 +--
 3 files changed, 8 insertions(+), 17 deletions(-)

diff --git a/examples/read_bem_surfaces.py b/examples/read_bem_surfaces.py
index d70d3c1..fc8cb47 100755
--- a/examples/read_bem_surfaces.py
+++ b/examples/read_bem_surfaces.py
@@ -15,7 +15,7 @@ from mne.datasets import sample
 data_path = sample.data_path('.')
 fname = data_path + '/subjects/sample/bem/sample-5120-5120-5120-bem-sol.fif'
 
-surfaces = mne.read_bem_surfaces(fname)
+surfaces = mne.read_bem_surfaces(fname, add_geom=True)
 
 print "Number of surfaces : %d" % len(surfaces)
 
diff --git a/mne/bem_surfaces.py b/mne/bem_surfaces.py
index 90fbb0f..2c62811 100755
--- a/mne/bem_surfaces.py
+++ b/mne/bem_surfaces.py
@@ -4,7 +4,6 @@
 # License: BSD (3-clause)
 
 import numpy as np
-from scipy import linalg
 
 from .fiff.constants import FIFF
 from .fiff.open import fiff_open
@@ -173,8 +172,7 @@ def _read_bem_surface(fid, this, def_coord_frame):
 
 
 def _complete_surface_info(this):
-    """ XXX : should be factorize with complete_source_space_info
-    """
+    """Complete surface info"""
     #
     #   Main triangulation
     #
@@ -189,27 +187,21 @@ def _complete_surface_info(this):
     #
     #   Triangle normals and areas
     #
-    for p in range(this['ntri']):
-        size = linalg.norm(this['tri_nn'][p, :])
-        this['tri_area'][p] = size / 2.0
-    if size > 0.0:
-        this['tri_nn'][p, :] = this['tri_nn'][p, :] / size
+    size = np.sqrt(np.sum(this['tri_nn'] ** 2, axis=1))
+    this['tri_area'] = size / 2.0
+    this['tri_nn'] /= size[:, None]
     #
     #   Accumulate the vertex normals
     #
     print 'vertex normals...',
     this['nn'] = np.zeros((this['np'], 3))
     for p in range(this['ntri']):
-        this['nn'][this['tris'][p, :], :] = this['nn'][this['tris'][p, :], :] \
-                              + np.kron(np.ones((3, 1)), this['tri_nn'][p, :])
+        this['nn'][this['tris'][p, :], :] += this['tri_nn'][p, :]
     #
     #   Compute the lengths of the vertex normals and scale
     #
     print 'normalize...',
-    for p in range(this['np']):
-        size = linalg.norm(this['nn'][p, :])
-        if size > 0:
-            this['nn'][p, :] = this['nn'][p, :] / size
+    this['nn'] /= np.sqrt(np.sum(this['nn'] ** 2, axis=1))[:, None]
 
     print '[done]'
     return this
diff --git a/mne/fiff/raw.py b/mne/fiff/raw.py
index 702da96..5d9d15a 100755
--- a/mne/fiff/raw.py
+++ b/mne/fiff/raw.py
@@ -611,8 +611,7 @@ def write_raw_buffer(fid, buf, cals):
     if buf.shape[0] != len(cals):
         raise ValueError('buffer and calibration sizes do not match')
 
-    write_float(fid, FIFF.FIFF_DATA_BUFFER,  # XXX can do better
-                                    np.dot(np.diag(1.0 / np.ravel(cals)), buf))
+    write_float(fid, FIFF.FIFF_DATA_BUFFER, buf / np.ravel(cals)[:, None])
 
 
 def finish_writing_raw(fid):

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-mne.git