[med-svn] [python-mne] 18/353: ENH: support loading of .w files for SourceEstimate

[Yaroslav Halchenko]

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

commit 7befeb085eb9140c3f8624e2ece4c1979ccd1e07
Author: Martin Luessi <mluessi at nmr.mgh.harvard.edu>
Date:   Fri Dec 2 10:38:51 2011 -0500

    ENH: support loading of .w files for SourceEstimate
---
 mne/source_estimate.py | 76 +++++++++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 72 insertions(+), 4 deletions(-)

diff --git a/mne/source_estimate.py b/mne/source_estimate.py
index 1f6a315..089df7e 100644
--- a/mne/source_estimate.py
+++ b/mne/source_estimate.py
@@ -103,10 +103,64 @@ def write_stc(filename, tmin, tstep, vertices, data):
     fid.close()
 
 
+def _read_3(fid):
+    """ Read 3 byte integer from file
+    """
+    data = np.fromfile(fid, dtype=np.uint8, count=3).astype(np.int32)
+
+    out = np.left_shift(data[0], 16) + np.left_shift(data[1], 8) + data[2]
+
+    return out
+
+
+def read_w(filename):
+    """Read a w file
+
+    w files contain activations or source reconstructions for a single time
+    point
+
+    Parameters
+    ----------
+    filename: string
+        The name of the w file
+
+    Returns
+    -------
+    data: dict
+        The w structure. It has the following keys:
+           vertices       vertex indices (0 based)
+           data           The data matrix (nvert)
+    """
+    fid = open(filename, 'rb')
+
+    # skip first 2 bytes
+    fid.read(2)
+
+    # read number of vertices/sources (3 byte integer)
+    vertices_n = int(_read_3(fid))
+
+    vertices = np.zeros((vertices_n), dtype=np.int32)
+    data = np.zeros((vertices_n), dtype=np.float32)
+
+    # read the data
+    for i in range(vertices_n):
+        vertices[i] = _read_3(fid)
+        data[i] = np.fromfile(fid, dtype=">f4", count=1)
+
+    w = dict()
+    w['vertices'] = vertices
+    w['data'] = data
+
+    # close the file
+    fid.close()
+    return w
+
+
 class SourceEstimate(object):
     """SourceEstimate container
 
-    Can be saved and loaded from .stc files
+    Can be saved and loaded from .stc files. Loading of .w files is supported
+    as well.
 
     Attributes
     ----------
@@ -127,9 +181,9 @@ class SourceEstimate(object):
                 self.times = self.tmin + (self.tstep *
                                           np.arange(self.data.shape[1]))
                 self.vertno = [vl['vertices']]
-            else:  # surface source spaces
-                if fname.endswith('-lh.stc') or fname.endswith('-rh.stc'):
-                    fname = fname[:-7]
+            elif fname.endswith('-lh.stc') or fname.endswith('-rh.stc'):
+                # stc file with surface source spaces
+                fname = fname[:-7]
                 lh = read_stc(fname + '-lh.stc')
                 rh = read_stc(fname + '-rh.stc')
                 self.data = np.r_[lh['data'], rh['data']]
@@ -140,6 +194,20 @@ class SourceEstimate(object):
                 self.times = self.tmin + (self.tstep *
                                           np.arange(self.data.shape[1]))
                 self.vertno = [lh['vertices'], rh['vertices']]
+            elif fname.endswith('-lh.w') or fname.endswith('-rh.w'):
+                # w file with surface source spaces
+                fname = fname[:-5]
+                lh = read_w(fname + '-lh.w')
+                rh = read_w(fname + '-rh.w')
+                self.data = np.atleast_2d(np.r_[lh['data'], rh['data']]).T
+
+                # w files only have a single time point
+                self.tmin = 0.0
+                self.tstep = 1.0
+                self.times = np.array([0.0])
+                self.vertno = [lh['vertices'], rh['vertices']]
+            else:
+                raise ValueError('file type not supported')
 
     def _init_times(self):
         """create self.times"""

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