FIX: Fixes for TRIUX and MEG ordering

mne/chpi.py

@@ -127,6 +127,9 @@ def read_head_pos(fname):
     _check_fname(fname, must_exist=True, overwrite=True)
     data = np.loadtxt(fname, skiprows=1)  # first line is header, skip it
     data.shape = (-1, 10)  # ensure it's the right size even if empty
+    if np.isnan(data).any():  # make sure we didn't do something dumb
+        raise RuntimeError('positions could not be read properly from %s'
+                           % fname)
     return data
 
 

mne/datasets/utils.py

@@ -167,7 +167,7 @@ def _data_path(path=None, force_update=False, update_path=True, download=True,
     path = _get_path(path, key, name)
     # To update the testing or misc dataset, push commits, then make a new
     # release on GitHub. Then update the "releases" variable:
-    releases = dict(testing='0.19', misc='0.1')
+    releases = dict(testing='0.20', misc='0.1')
     # And also update the "hashes['testing']" variable below.
 
     # To update any other dataset, update the data archive itself (upload
@@ -211,7 +211,7 @@ def _data_path(path=None, force_update=False, update_path=True, download=True,
         sample='1d5da3a809fded1ef5734444ab5bf857',
         somato='f3e3a8441477bb5bacae1d0c6e0964fb',
         spm='f61041e3f3f2ba0def8a2ca71592cc41',
-        testing='77b2a435d80adb23cbe7e19144e7bc47'
+        testing='625cb9c1c62de03bd2bc6a3ca9a6f2d8'
     )
     folder_origs = dict(  # not listed means None
         misc='mne-misc-data-%s' % releases['misc'],

mne/preprocessing/_fine_cal.py

@@ -0,0 +1,84 @@
+# -*- coding: utf-8 -*-
+# Authors: Eric Larson <larson.eric.d@gmail.com>
+
+# License: BSD (3-clause)
+
+import numpy as np
+
+from ..utils import check_fname, _check_fname
+
+
+def read_fine_calibration(fname):
+    """Read fine calibration information from a .dat file
+
+    The fine calibration typically includes improved sensor locations,
+    calibration coefficients, and gradiometer imbalance information.
+
+    Parameters
+    ----------
+    fname : str
+        The filename.
+
+    Returns
+    -------
+    calibration : dict
+        Fine calibration information.
+    """
+    # Read new sensor locations
+    _check_fname(fname, overwrite=True, must_exist=True)
+    check_fname(fname, 'cal', ('.dat',))
+    ch_names = list()
+    locs = list()
+    imb_cals = list()
+    with open(fname, 'r') as fid:
+        for line in fid:
+            if line[0] in '#\n':
+                continue
+            vals = line.strip().split()
+            if len(vals) not in [14, 16]:
+                raise RuntimeError('Error parsing fine calibration file, '
+                                   'should have 14 or 16 entries per line '
+                                   'but found %s on line:\n%s'
+                                   % (len(vals), line))
+            # `vals` contains channel number
+            ch_name = vals[0]
+            if len(ch_name) in (3, 4):  # heuristic for Neuromag fix
+                try:
+                    ch_name = int(ch_name)
+                except ValueError:  # something other than e.g. 113 or 2642
+                    pass
+                else:
+                    ch_name = 'MEG' + '%04d' % ch_name
+            ch_names.append(ch_name)
+            # (x, y, z), x-norm 3-vec, y-norm 3-vec, z-norm 3-vec
+            locs.append(np.array([float(x) for x in vals[1:13]]))
+            # and 1 or 3 imbalance terms
+            imb_cals.append([float(x) for x in vals[13:]])
+    locs = np.array(locs)
+    return dict(ch_names=ch_names, locs=locs, imb_cals=imb_cals)
+
+
+def write_fine_calibration(fname, calibration):
+    """Write fine calibration information to a .dat file
+
+    Parameters
+    ----------
+    fname : str
+        The filename to write out.
+    calibration : dict
+        Fine calibration information.
+    """
+    _check_fname(fname, overwrite=True)
+    check_fname(fname, 'cal', ('.dat',))
+
+    with open(fname, 'wb') as cal_file:
+        for ci, chan in enumerate(calibration['ch_names']):
+            # Write string containing 1) channel, 2) loc info, 3) calib info
+            # with field widths (e.g., %.6f) chosen to match how Elekta writes
+            # them out
+            cal_line = np.concatenate([calibration['locs'][ci],
+                                       calibration['imb_cals'][ci]]).round(6)
+            cal_str = str(chan) + ' ' + ' '.join(map(lambda x: "%.6f" % x,
+                                                     cal_line))
+
+            cal_file.write((cal_str + '\n').encode('ASCII'))