[MRG+2] Unify meas_date (to use a tuple) (mne-tools#5500)

Closes mne-tools#5499.

mne/forward/forward.py

@@ -1108,7 +1108,7 @@ def _fill_measurement_info(info, fwd, sfreq):
     sec = np.floor(now)
     usec = 1e6 * (now - sec)
 
-    info['meas_date'] = np.array([sec, usec], dtype=np.int32)
+    info['meas_date'] = (int(sec), int(usec))
     info['highpass'] = 0.0
     info['lowpass'] = sfreq / 2.0
     info['sfreq'] = sfreq

mne/io/artemis123/artemis123.py

@@ -143,7 +143,7 @@ def _get_artemis123_info(fname, pos_fname=None):
     try:
         date = datetime.datetime.strptime(
             op.basename(fname).split('_')[2], '%Y-%m-%d-%Hh-%Mm')
-        meas_date = calendar.timegm(date.utctimetuple())
+        meas_date = (calendar.timegm(date.utctimetuple()), 0)
     except Exception:
         meas_date = None
 

mne/io/brainvision/brainvision.py

@@ -18,7 +18,6 @@
 
 import numpy as np
 
-from ..write import DATE_NONE
 from ...utils import verbose, logger, warn
 from ..constants import FIFF
 from ..meas_info import _empty_info
@@ -542,11 +541,11 @@ def _get_vhdr_info(vhdr_fname, eog, misc, scale, montage):
             unix_time = (meas_date - epoch).total_seconds()
             unix_secs = int(modf(unix_time)[1])
             microsecs = int(modf(unix_time)[0] * 1e6)
-            info['meas_date'] = [unix_secs, microsecs]
+            info['meas_date'] = (unix_secs, microsecs)
             break
 
     else:
-        info['meas_date'] = DATE_NONE
+        info['meas_date'] = None
 
     # load channel labels
     nchan = cfg.getint(cinfostr, 'NumberOfChannels') + 1

mne/io/brainvision/tests/test_brainvision.py

@@ -20,7 +20,6 @@
 from mne.io.constants import FIFF
 from mne.io import read_raw_fif, read_raw_brainvision
 from mne.io.tests.test_raw import _test_raw_reader
-from mne.io.write import DATE_NONE
 from mne.datasets import testing
 
 FILE = inspect.getfile(inspect.currentframe())
@@ -82,7 +81,7 @@ def test_vmrk_meas_date():
     # Test files with no date, we should get DATE_NONE from mne.io.write
     with pytest.warns(RuntimeWarning, match='coordinate information'):
         raw = read_raw_brainvision(vhdr_v2_path)
-    assert_allclose(raw.info['meas_date'], DATE_NONE)
+    assert raw.info['meas_date'] is None
     assert 'unspecified' in repr(raw.info)
 
 
@@ -607,7 +606,7 @@ def test_brainvision_with_montage():
 def test_brainvision_neuroone_export():
     """Test Brainvision file exported with neuroone system."""
     raw = read_raw_brainvision(neuroone_vhdr, verbose='error')
-    assert raw.info['meas_date'] == DATE_NONE
+    assert raw.info['meas_date'] is None
     assert len(raw.info['chs']) == 66
     assert raw.info['sfreq'] == 5000.
 

mne/io/bti/bti.py

@@ -1147,7 +1147,7 @@ def _get_bti_info(pdf_fname, config_fname, head_shape_fname, rotation_x,
     if pdf_fname is not None:
         info = _empty_info(sfreq)
         date = bti_info['processes'][0]['timestamp']
-        info['meas_date'] = [date, 0]
+        info['meas_date'] = (date, 0)
     else:  # these cannot be guessed from config, see docstring
         info = _empty_info(1.0)
         info['sfreq'] = None

mne/io/cnt/cnt.py

@@ -145,7 +145,7 @@ def _get_cnt_info(input_fname, eog, ecg, emg, misc, data_format, date_format):
             date = datetime.datetime(int(date[2]), int(date[0]),
                                      int(date[1]), int(time[0]),
                                      int(time[1]), int(time[2]))
-            meas_date = np.array([calendar.timegm(date.utctimetuple()), 0])
+            meas_date = (calendar.timegm(date.utctimetuple()), 0)
         else:
             warn('  Could not parse meas date from the header. '
                  'Setting to None.')

mne/io/edf/edf.py

@@ -661,7 +661,7 @@ def _read_edf_header(fname, annot, annotmap, exclude):
             ch_names=ch_names, data_offset=header_nbytes,
             digital_max=digital_max, digital_min=digital_min,
             highpass=highpass, sel=sel, lowpass=lowpass,
-            meas_date=calendar.timegm(date.utctimetuple()),
+            meas_date=(calendar.timegm(date.utctimetuple()), 0),
             n_records=n_records, n_samps=n_samps, nchan=nchan,
             subject_info=patient, physical_max=physical_max,
             physical_min=physical_min, record_length=record_length,
@@ -800,7 +800,7 @@ def _read_gdf_header(fname, stim_channel, exclude):
                 dtype_byte=[gdftype_byte[t] for t in dtype],
                 dtype_np=[gdftype_np[t] for t in dtype], exclude=exclude,
                 highpass=highpass, sel=sel, lowpass=lowpass,
-                meas_date=calendar.timegm(date.utctimetuple()),
+                meas_date=(calendar.timegm(date.utctimetuple()), 0),
                 meas_id=meas_id, n_records=n_records, n_samps=n_samps,
                 nchan=nchan, subject_info=patient, physical_max=physical_max,
                 physical_min=physical_min, record_length=record_length,
@@ -1023,7 +1023,7 @@ def _read_gdf_header(fname, stim_channel, exclude):
                 digital_min=digital_min, digital_max=digital_max,
                 exclude=exclude, gnd=gnd, highpass=highpass, sel=sel,
                 impedance=impedance, lowpass=lowpass,
-                meas_date=calendar.timegm(date.utctimetuple()),
+                meas_date=(calendar.timegm(date.utctimetuple()), 0),
                 meas_id=meas_id, n_records=n_records, n_samps=n_samps,
                 nchan=nchan, notch=notch, subject_info=patient,
                 physical_max=physical_max, physical_min=physical_min,

mne/io/egi/egi.py

@@ -245,7 +245,7 @@ def __init__(self, input_fname, montage=None, eog=None, misc=None,
             egi_info['year'], egi_info['month'], egi_info['day'],
             egi_info['hour'], egi_info['minute'], egi_info['second'])
         my_timestamp = time.mktime(my_time.timetuple())
-        info['meas_date'] = np.array([my_timestamp, 0], dtype=np.float32)
+        info['meas_date'] = (my_timestamp, 0)
         ch_names = [channel_naming % (i + 1) for i in
                     range(egi_info['n_channels'])]
         ch_names.extend(list(egi_info['event_codes']))

mne/io/egi/egimff.py

@@ -344,7 +344,7 @@ def __init__(self, input_fname, montage=None, eog=None, misc=None,
             egi_info['year'], egi_info['month'], egi_info['day'],
             egi_info['hour'], egi_info['minute'], egi_info['second'])
         my_timestamp = time.mktime(my_time.timetuple())
-        info['meas_date'] = np.array([my_timestamp, 0], dtype=np.float32)
+        info['meas_date'] = (my_timestamp, 0)
         ch_names = [channel_naming % (i + 1) for i in
                     range(egi_info['n_channels'])]
         ch_names.extend(list(egi_info['event_codes']))

mne/io/fiff/tests/test_raw_fiff.py

@@ -1219,7 +1219,7 @@ def test_save():
 
     # test abspath support and annotations
     annot = Annotations([10], [5], ['test'],
-                        raw.info['meas_date'] +
+                        raw.info['meas_date'][0] +
                         raw.first_samp / raw.info['sfreq'])
     raw.set_annotations(annot)
     new_fname = op.join(op.abspath(op.curdir), 'break_raw.fif')

mne/io/kit/kit.py

@@ -740,7 +740,7 @@ def get_kit_info(rawfile, allow_unknown_format):
 
     # Create raw.info dict for raw fif object with SQD data
     info = _empty_info(float(sqd['sfreq']))
-    info.update(meas_date=create_time, lowpass=sqd['lowpass'],
+    info.update(meas_date=(create_time, 0), lowpass=sqd['lowpass'],
                 highpass=sqd['highpass'], kit_system_id=sysid)
 
     # Creates a list of dicts of meg channels for raw.info

mne/io/meas_info.py

@@ -146,7 +146,7 @@ class Info(dict):
         Tilt angle of the gantry in degrees.
     lowpass : float | None
         Lowpass corner frequency in Hertz.
-    meas_date : list of int
+    meas_date : tuple of int
         The first element of this list is a UNIX timestamp (seconds since
         1970-01-01 00:00:00) denoting the date and time at which the
         measurement was taken. The second element is the additional number of
@@ -409,8 +409,8 @@ def __repr__(self):
                                  {0: 'ff', 1: 'n'}[p['active']] for p in v)
                 if len(entr) >= 56:
                     entr = _summarize_str(entr)
-            elif k == 'meas_date' and np.iterable(v):
-                if np.array_equal(v, DATE_NONE):
+            elif k == 'meas_date':
+                if v is None:
                     entr = 'unspecified'
                 else:
                     # first entry in meas_date is meaningful
@@ -449,6 +449,13 @@ def _check_consistency(self):
         if len(missing) > 0:
             raise RuntimeError('bad channel(s) %s marked do not exist in info'
                                % (missing,))
+        meas_date = self.get('meas_date')
+        if meas_date is not None and (
+                not isinstance(self['meas_date'], tuple) or
+                len(self['meas_date']) != 2):
+            raise RuntimeError('info["meas_date"] must be a tuple of length '
+                               '2 or None, got "%r"'
+                               % (repr(self['meas_date']),))
 
         chs = [ch['ch_name'] for ch in self['chs']]
         if len(self['ch_names']) != len(chs) or any(
@@ -943,7 +950,9 @@ def read_meas_info(fid, tree, clean_bads=False, verbose=None):
                 highpass = float(tag.data)
         elif kind == FIFF.FIFF_MEAS_DATE:
             tag = read_tag(fid, pos)
-            meas_date = tag.data
+            meas_date = tuple(tag.data)
+            if len(meas_date) == 1:  # can happen from old C conversions
+                meas_date = (meas_date[0], 0)
         elif kind == FIFF.FIFF_COORD_TRANS:
             tag = read_tag(fid, pos)
             cand = tag.data
@@ -1236,7 +1245,7 @@ def read_meas_info(fid, tree, clean_bads=False, verbose=None):
     info['proj_id'] = proj_id
     info['proj_name'] = proj_name
     if meas_date is None:
-        meas_date = [info['meas_id']['secs'], info['meas_id']['usecs']]
+        meas_date = (info['meas_id']['secs'], info['meas_id']['usecs'])
     if np.array_equal(meas_date, DATE_NONE):
         meas_date = None
     info['meas_date'] = meas_date
@@ -1528,17 +1537,18 @@ def write_info(fname, info, data_type=None, reset_range=True):
 
 
 @verbose
-def _merge_dict_values(dicts, key, verbose=None):
+def _merge_info_values(infos, key, verbose=None):
     """Merge things together.
 
     Fork for {'dict', 'list', 'array', 'other'}
     and consider cases where one or all are of the same type.
 
     Does special things for "projs", "bads", and "meas_date".
     """
-    values = [d[key] for d in dicts]
+    values = [d[key] for d in infos]
     msg = ("Don't know how to merge '%s'. Make sure values are "
-           "compatible." % key)
+           "compatible, got types:\n    %s"
+           % (key, [type(v) for v in values]))
 
     def _flatten(lists):
         return [item for sublist in lists for item in sublist]
@@ -1552,7 +1562,7 @@ def _where_isinstance(values, kind):
 
     # list
     if _check_isinstance(values, list, all):
-        lists = (d[key] for d in dicts)
+        lists = (d[key] for d in infos)
         if key == 'projs':
             return _uniquify_projs(_flatten(lists))
         elif key == 'bads':
@@ -1564,7 +1574,7 @@ def _where_isinstance(values, kind):
         if len(idx) == 1:
             return values[int(idx)]
         elif len(idx) > 1:
-            lists = (d[key] for d in dicts if isinstance(d[key], list))
+            lists = (d[key] for d in infos if isinstance(d[key], list))
             return _flatten(lists)
     # dict
     elif _check_isinstance(values, dict, all):
@@ -1580,8 +1590,9 @@ def _where_isinstance(values, kind):
         elif len(idx) > 1:
             raise RuntimeError(msg)
     # ndarray
-    elif _check_isinstance(values, np.ndarray, all):
-        is_qual = all(np.all(values[0] == x) for x in values[1:])
+    elif _check_isinstance(values, np.ndarray, all) or \
+            _check_isinstance(values, tuple, all):
+        is_qual = all(np.array_equal(values[0], x) for x in values[1:])
         if is_qual:
             return values[0]
         elif key == 'meas_date':
@@ -1590,7 +1601,7 @@ def _where_isinstance(values, kind):
             return None
         else:
             raise RuntimeError(msg)
-    elif _check_isinstance(values, np.ndarray, any):
+    elif _check_isinstance(values, (np.ndarray, tuple), any):
         idx = _where_isinstance(values, np.ndarray)
         if len(idx) == 1:
             return values[int(idx)]
@@ -1709,7 +1720,7 @@ def _merge_info(infos, force_update_to_first=False, verbose=None):
                     'proj_id', 'proj_name', 'projs', 'sfreq', 'gantry_angle',
                     'subject_info', 'sfreq', 'xplotter_layout', 'proc_history']
     for k in other_fields:
-        info[k] = _merge_dict_values(infos, k)
+        info[k] = _merge_info_values(infos, k)
 
     info._check_consistency()
     return info

mne/io/nicolet/nicolet.py

@@ -104,7 +104,7 @@ def _get_nicolet_info(fname, ch_type, eog, ecg, emg, misc):
     date = datetime.datetime(int(date[0]), int(date[1]), int(date[2]),
                              int(time[0]), int(time[1]), int(sec), int(msec))
     info = _empty_info(header_info['sample_freq'])
-    info['meas_date'] = calendar.timegm(date.utctimetuple())
+    info['meas_date'] = (calendar.timegm(date.utctimetuple()), 0)
 
     if ch_type == 'eeg':
         ch_coil = FIFF.FIFFV_COIL_EEG

mne/io/tests/test_meas_info.py

@@ -429,7 +429,8 @@ def test_anonymize():
         for key in ('file_id', 'meas_id'):
             assert inst.info[key]['secs'] != DATE_NONE[0]
             assert inst.info[key]['usecs'] != DATE_NONE[1]
-        assert tuple(inst.info['meas_date']) != DATE_NONE
+        assert isinstance(inst.info['meas_date'], tuple)
+        assert inst.info['meas_date'] != DATE_NONE
         inst.anonymize()
         assert 'subject_info' not in inst.info.keys()
         for key in ('file_id', 'meas_id'):

mne/tests/test_annotations.py

@@ -65,7 +65,7 @@ def test_basics():
     sfreq = 100.
     info = create_info(ch_names=['MEG1', 'MEG2'], ch_types=['grad'] * 2,
                        sfreq=sfreq)
-    info['meas_date'] = np.pi
+    info['meas_date'] = (np.pi, 0)
     raws = []
     for first_samp in [12300, 100, 12]:
         raw = RawArray(data.copy(), info, first_samp=first_samp)

mne/tests/test_epochs.py

@@ -286,7 +286,7 @@ def test_reject():
         onsets[0] = onsets[0] + tmin - 0.499  # tmin < 0
         onsets[1] = onsets[1] + tmax - 0.001
         first_time = (raw.info['meas_date'][0] + raw.info['meas_date'][1] *
-                      0.000001 + raw.first_samp / sfreq)
+                      1e-6 + raw.first_samp / sfreq)
         for orig_time in [None, first_time]:
             annot = Annotations(onsets, [0.5, 0.5, 0.5], 'BAD', orig_time)
             raw.set_annotations(annot)
@@ -1940,7 +1940,7 @@ def make_epochs(picks, proj):
         assert_allclose(data1, data2, atol=1e-25)
 
     epochs_meg2 = epochs_meg.copy()
-    epochs_meg2.info['meas_date'] += 10
+    epochs_meg2.info['meas_date'] = (0, 0)
     add_channels_epochs([epochs_meg2, epochs_eeg])
 
     epochs_meg2 = epochs_meg.copy()

mne/viz/tests/test_raw.py

@@ -231,8 +231,7 @@ def test_plot_raw():
 
         plt.close('all')
     # test if meas_date has only one element
-    raw.info['meas_date'] = np.array([raw.info['meas_date'][0]],
-                                     dtype=np.int32)
+    raw.info['meas_date'] = (raw.info['meas_date'][0], 0)
     annot = Annotations([1 + raw.first_samp / raw.info['sfreq']],
                         [5], ['bad'])
     with pytest.warns(RuntimeWarning, match='outside data range'):