Merge branch 'main' into enh/save_movie

Author: GuillaumeFavelier

doc/_static/style.css

@@ -45,6 +45,11 @@ iframe.sg_report {
     display: block;
     border-style: solid;
 }
+/* gallery thumbnail size */
+.sphx-glr-thumbcontainer {
+    min-width: 160px;
+    height: 250px;
+}
 
 /* ******************************** make HTML'd pandas dataframes scrollable */
 output_html {

doc/changes/latest.inc

@@ -19,6 +19,8 @@ Current (0.23.dev0)
 
 .. |New Contributor| replace:: **New Contributor**
 
+.. |Sumalyo Datta| replace:: **Sumalyo Datta**
+
 .. |Anna Padee| replace:: **Anna Padee**
 
 .. |Richard Koehler| replace:: **Richard Koehler**
@@ -55,6 +57,8 @@ Current (0.23.dev0)
 
 Enhancements
 ~~~~~~~~~~~~
+- Add HTML representation for `~mne.Epochs` in Jupyter Notebooks (:gh:`9174` by |Valerii Chirkov|_)
+
 - Speed up :func:`mne.viz.plot_ica_properties` by refactoring (:gh:`9174` **by new contributor** |Valerii Chirkov|_)
 
 - Add ``apply_function`` method to epochs and evoked objects (:gh:`9088` **by new contributor** |Erica Peterson|_ and `Victoria Peterson`_)
@@ -153,8 +157,14 @@ Enhancements
 
 - Add parameter ``theme`` to :class:`mne.viz.Brain` for optional Dark-Mode (:gh:`9149` by `Martin Schulz`_, `Guillaume Favelier`_)
 
+- Add first_samp support for raw simulations with `mne.simulation.simulate_raw` and `mne.simulation.SourceSimulator` (:gh:`9166` by `Steven Bierer`_)
+
 Bugs
 ~~~~
+- Fix bug with :func:`mne.io.read_raw_edf` where µV was not correctly recognized (:gh:`9187` **by new contributor** |Sumalyo Datta|_)
+
+- Fix bug with :func:`mne.viz.plot_compare_evokeds` did not check type of combine. (:gh:`9151` **by new contributor** |Matteo Anelli|_)
+                                        
 - Fix bug with :func:`mne.viz.plot_evoked_topo` where ``ylim`` was only being applied to the first channel in the dataset (:gh:`9162` **by new contributor** |Ram Pari|_ )
 
 - Fix bug with :func:`mne.Epochs.plot_image` allowing interactive zoom to work properly (:gh:`9152` by **by new contributor** |Maggie Clarke|_ and `Daniel McCloy`_)

doc/changes/names.inc

@@ -383,3 +383,5 @@
 .. _Ram Pari: https://github.com/ramkpari
 
 .. _Erica Peterson: https://github.com/nordme
+
+.. _Sumalyo Datta: https://github.com/Sumalyo

examples/preprocessing/plot_run_ica.py

@@ -60,7 +60,7 @@ class to generate source estimates and raw data. It is meant to be a brief
 # of the event, the second is not used, and the third is the event id. Here the
 # events occur every 200 samples.
 n_events = 50
-events = np.zeros((n_events, 3))
+events = np.zeros((n_events, 3), int)
 events[:, 0] = 100 + 200 * np.arange(n_events)  # Events sample.
 events[:, 2] = 1  # All events have the sample id.
 

examples/simulation/plot_source_simulator.py

@@ -75,3 +75,28 @@
     </tr>
 </table>
 """)
+
+epochs_template = Template("""
+<table class="table table-hover">
+    <tr>
+        <th>Number of events</th>
+        <td>{{len(epochs.events)}}</td>
+    </tr>
+    <tr>
+        <th>Events</th>
+        {{if events is not None}}
+        <td>{{events}}</td>
+        {{else}}
+        <td>Not available</td>
+        {{endif}}
+    </tr>
+    <tr>
+        <th>Time range</th>
+        <td>{{f'{epochs.tmin:.3f} – {epochs.tmax:.3f} sec'}}</td>
+    </tr>
+    <tr>
+        <th>Baseline</th>
+        <td>{{baseline}}</td>
+    </tr>
+</table>
+""")

mne/data/html_templates.py

@@ -16,7 +16,6 @@
 import json
 import operator
 import os.path as op
-import warnings
 
 import numpy as np
 
@@ -57,8 +56,9 @@
                     _check_combine, ShiftTimeMixin, _build_data_frame,
                     _check_pandas_index_arguments, _convert_times,
                     _scale_dataframe_data, _check_time_format, object_size,
-                    _on_missing, _validate_type)
+                    _on_missing, _validate_type, _ensure_events)
 from .utils.docs import fill_doc
+from .data.html_templates import epochs_template
 
 
 def _pack_reject_params(epochs):
@@ -397,16 +397,7 @@ def __init__(self, info, data, events, event_id=None, tmin=-0.2, tmax=0.5,
         self.verbose = verbose
 
         if events is not None:  # RtEpochs can have events=None
-            events_type = type(events)
-            with warnings.catch_warnings(record=True):
-                warnings.simplefilter('ignore')  # deprecation for object array
-                events = np.asarray(events)
-            if not np.issubdtype(events.dtype, np.integer):
-                raise TypeError('events should be a NumPy array of integers, '
-                                f'got {events_type}')
-            if events.ndim != 2 or events.shape[1] != 3:
-                raise ValueError(
-                    f'events must be of shape (N, 3), got {events.shape}')
+            events = _ensure_events(events)
             events_max = events.max()
             if events_max > INT32_MAX:
                 raise ValueError(
@@ -1599,6 +1590,31 @@ def __repr__(self):
         class_name = 'Epochs' if class_name == 'BaseEpochs' else class_name
         return '<%s | %s>' % (class_name, s)
 
+    def _repr_html_(self):
+        if self.baseline is None:
+            baseline = 'off'
+        else:
+            baseline = tuple([f'{b:.3f}' for b in self.baseline])
+            baseline = f'{baseline[0]} – {baseline[1]} sec'
+
+        if isinstance(self.event_id, dict):
+            events = ''
+            for k, v in sorted(self.event_id.items()):
+                n_events = sum(self.events[:, 2] == v)
+                events += f'{k}: {n_events}<br>'
+        elif isinstance(self.event_id, list):
+            events = ''
+            for k in self.event_id:
+                n_events = sum(self.events[:, 2] == k)
+                events += f'{k}: {n_events}<br>'
+        elif isinstance(self.event_id, int):
+            n_events = len(self.events[:, 2])
+            events = f'{self.event_id}: {n_events}<br>'
+        else:
+            events = None
+        return epochs_template.substitute(epochs=self, baseline=baseline,
+                                          events=events)
+
     @verbose
     def crop(self, tmin=None, tmax=None, include_tmax=True, verbose=None):
         """Crop a time interval from the epochs.

mne/epochs.py

@@ -613,7 +613,8 @@ def _read_edf_header(fname, exclude):
         for i, unit in enumerate(units):
             if i in exclude:
                 continue
-            if unit == 'uV':
+            # allow both μ (greek mu) and µ (micro symbol) codepoints
+            if unit in ('\u03BCV', '\u00B5V', 'uV'):
                 edf_info['units'].append(1e-6)
             elif unit == 'mV':
                 edf_info['units'].append(1e-3)

mne/io/edf/edf.py

@@ -2072,6 +2072,7 @@ def _render_epochs(self, epo_fname, image_format, data_path):
         html = image_template.substitute(
             img=img, id=global_id, div_klass='epochs', img_klass='epochs',
             caption=caption, show=show, image_format=image_format)
+        html += epochs._repr_html_()
         return html
 
     def _render_cov(self, cov_fname, info_fname, image_format, data_path,

mne/report.py

@@ -33,6 +33,7 @@
 from ..utils import (logger, verbose, check_random_state, _pl, _validate_type,
                      _check_preload)
 from ..parallel import check_n_jobs
+from .source import SourceSimulator
 
 
 def _check_cov(info, cov):
@@ -110,8 +111,11 @@ def _check_head_pos(head_pos, info, first_samp, times=None):
             raise RuntimeError('All position times must be <= t_end (%0.1f '
                                'sec), found %s/%s bad values (is this a split '
                                'file?)' % (times[-1], bad.sum(), len(bad)))
+    # If it starts close to zero, make it zero (else unique(offset) fails)
+    if len(ts) > 0 and ts[0] < (0.5 / info['sfreq']):
+        ts[0] = 0.
     # If it doesn't start at zero, insert one at t=0
-    if len(ts) == 0 or ts[0] > 0:
+    elif len(ts) == 0 or ts[0] > 0:
         ts = np.r_[[0.], ts]
         dev_head_ts.insert(0, info['dev_head_t']['trans'])
     dev_head_ts = [{'trans': d, 'to': info['dev_head_t']['to'],
@@ -140,7 +144,7 @@ def simulate_raw(info, stc=None, trans=None, src=None, bem=None, head_pos=None,
 
         .. versionchanged:: 0.18
            Support for :class:`mne.Info`.
-    stc : iterable | SourceEstimate
+    stc : iterable | SourceEstimate | SourceSimulator
         The source estimates to use to simulate data. Each must have the same
         sample rate as the raw data, and the vertices of all stcs in the
         iterable must match. Each entry in the iterable can also be a tuple of
@@ -149,7 +153,8 @@ def simulate_raw(info, stc=None, trans=None, src=None, bem=None, head_pos=None,
         See Notes for details.
 
         .. versionchanged:: 0.18
-           Support for tuple, and iterable of tuple or SourceEstimate.
+           Support for tuple, iterable of tuple or `~mne.SourceEstimate`,
+           or `~mne.simulation.SourceSimulator`.
     trans : dict | str | None
         Either a transformation filename (usually made using mne_analyze)
         or an info dict (usually opened using read_trans()).
@@ -271,8 +276,10 @@ def simulate_raw(info, stc=None, trans=None, src=None, bem=None, head_pos=None,
     logger.info('Setting up raw simulation: %s position%s, "%s" interpolation'
                 % (len(dev_head_ts), _pl(dev_head_ts), interp))
 
+    if isinstance(stc, SourceSimulator) and stc.first_samp != first_samp:
+        logger.info('SourceSimulator first_samp does not match argument.')
+
     stc_enum, stc_counted, verts = _check_stc_iterable(stc, info)
-    # del stc
     if forward is not None:
         forward = restrict_forward_to_stc(forward, verts)
         src = forward['src']