FIX: Ensure H5-writeable

doc/changes/latest.inc

@@ -132,6 +132,8 @@ Bug
 
 - Fix default to be ``foreground=None`` in :func:`mne.viz.plot_source_estimates` to use white or black text based on the background color by `Eric Larson`_
 
+- Fix bug with writing EGI and CTF `mne.Info` to H5 format, e.g., with `mne.time_frequency.AverageTFR.save` by `Eric Larson`_
+
 - Fix bug with :func:`mne.io.Raw.plot` where toggling all projectors did not actually take effect by `Eric Larson`_
 
 - Fix bug with :func:`mne.read_epochs` when loading data in complex format with ``preload=False`` by `Eric Larson`_

mne/io/ctf/info.py

@@ -296,7 +296,7 @@ def _conv_comp(comp, first, last, chs):
     col_names = comp[first]['sensors'][:n_col]
     row_names = [comp[p]['sensor_name'] for p in range(first, last + 1)]
     mask = np.in1d(col_names, ch_names)  # missing channels excluded
-    col_names = np.array(col_names)[mask]
+    col_names = np.array(col_names)[mask].tolist()
     n_col = len(col_names)
     n_row = len(row_names)
     ccomp = dict(ctfkind=np.array([comp[first]['coeff_type']]),

mne/io/egi/egi.py

@@ -63,7 +63,6 @@ def my_fread(*x, **y):
         for event in range(info['n_events']):
             event_codes = ''.join(np.fromfile(fid, 'S1', 4).astype('U1'))
             info['event_codes'].append(event_codes)
-        info['event_codes'] = np.array(info['event_codes'])
     else:
         raise NotImplementedError('Only continuous files are supported')
     info['unsegmented'] = unsegmented

mne/io/egi/events.py

@@ -25,7 +25,7 @@ def _read_events(input_fname, info):
     n_samples = info['last_samps'][-1]
     mff_events, event_codes = _read_mff_events(input_fname, info['sfreq'])
     info['n_events'] = len(event_codes)
-    info['event_codes'] = np.asarray(event_codes).astype('<U4')
+    info['event_codes'] = event_codes
     events = np.zeros([info['n_events'], info['n_segments'] * n_samples])
     for n, event in enumerate(event_codes):
         for i in mff_events[event]:

mne/io/meas_info.py

@@ -21,7 +21,8 @@
 from .open import fiff_open
 from .tree import dir_tree_find
 from .tag import read_tag, find_tag, _coord_dict
-from .proj import _read_proj, _write_proj, _uniquify_projs, _normalize_proj
+from .proj import (_read_proj, _write_proj, _uniquify_projs, _normalize_proj,
+                   Projection)
 from .ctf_comp import read_ctf_comp, write_ctf_comp
 from .write import (start_file, end_file, start_block, end_block,
                     write_string, write_dig_points, write_float, write_int,
@@ -31,7 +32,7 @@
 from ..transforms import invert_transform, Transform, _coord_frame_name
 from ..utils import (logger, verbose, warn, object_diff, _validate_type,
                      _stamp_to_dt, _dt_to_stamp, _pl, _is_numeric)
-from ._digitization import (_format_dig_points, _dig_kind_proper,
+from ._digitization import (_format_dig_points, _dig_kind_proper, DigPoint,
                             _dig_kind_rev, _dig_kind_ints, _read_dig_fif)
 from ._digitization import write_dig as _dig_write_dig
 from .compensator import get_current_comp
@@ -179,6 +180,16 @@ def set_montage(self, montage, match_case=True,
         return self
 
 
+def _format_trans(obj, key):
+    try:
+        t = obj[key]
+    except KeyError:
+        pass
+    else:
+        if t is not None:
+            obj[key] = Transform(t['from'], t['to'], t['trans'])
+
+
 # XXX Eventually this should be de-duplicated with the MNE-MATLAB stuff...
 class Info(dict, MontageMixin):
     """Measurement information.
@@ -523,12 +534,16 @@ class Info(dict, MontageMixin):
     def __init__(self, *args, **kwargs):
         super(Info, self).__init__(*args, **kwargs)
         # Deal with h5io writing things as dict
-        try:
-            t = self['dev_head_t']
-        except KeyError:
-            pass
-        else:
-            self['dev_head_t'] = Transform(t['from'], t['to'], t['trans'])
+        for key in ('dev_head_t', 'ctf_head_t', 'dev_ctf_t'):
+            _format_trans(self, key)
+        for res in self.get('hpi_results', []):
+            _format_trans(res, 'coord_trans')
+        if self.get('dig', None) is not None and len(self['dig']) and \
+                not isinstance(self['dig'][0], DigPoint):
+            self['dig'] = _format_dig_points(self['dig'])
+        for pi, proj in enumerate(self.get('projs', [])):
+            if not isinstance(proj, Projection):
+                self['projs'][pi] = Projection(proj)
         # Old files could have meas_date as tuple instead of datetime
         try:
             meas_date = self['meas_date']

mne/io/tests/test_raw.py

@@ -16,8 +16,10 @@
 
 from mne import concatenate_raws, create_info, Annotations
 from mne.datasets import testing
-from mne.io import read_raw_fif, RawArray, BaseRaw
-from mne.utils import _TempDir, catch_logging, _raw_annot, _stamp_to_dt
+from mne.externals.h5io import read_hdf5, write_hdf5
+from mne.io import read_raw_fif, RawArray, BaseRaw, Info
+from mne.utils import (_TempDir, catch_logging, _raw_annot, _stamp_to_dt,
+                       object_diff)
 from mne.io.meas_info import _get_valid_units
 from mne.io._digitization import DigPoint
 
@@ -201,6 +203,12 @@ def _test_raw_reader(reader, test_preloading=True, test_kwargs=True,
         assert_array_equal(times, times_2,)
         assert_array_equal(data[picks_2], data_2)
 
+    # Make sure that writing info to h5 format
+    # (all fields should be compatible)
+    fname_h5 = op.join(tempdir, 'info.h5')
+    write_hdf5(fname_h5, raw.info)
+    new_info = Info(read_hdf5(fname_h5))
+    assert object_diff(new_info, raw.info) == ''
     return raw