# Authors: The MNE-Python contributors. # License: BSD-3-Clause # Copyright the MNE-Python contributors. import datetime import os import os.path as op import shutil import numpy as np from .._fiff.pick import pick_channels, pick_types from ..io.egi.egimff import _import_mffpy from ..utils import _check_fname, verbose, warn @verbose def export_evokeds_mff(fname, evoked, history=None, *, overwrite=False, verbose=None): """Export evoked dataset to MFF. %(export_warning)s Parameters ---------- %(fname_export_params)s evoked : list of Evoked instances List of evoked datasets to export to one file. Note that the measurement info from the first evoked instance is used, so be sure that information matches. history : None (default) | list of dict Optional list of history entries (dictionaries) to be written to history.xml. This must adhere to the format described in mffpy.xml_files.History.content. If None, no history.xml will be written. %(overwrite)s .. versionadded:: 0.24.1 %(verbose)s Notes ----- .. versionadded:: 0.24 %(export_warning_note_evoked)s Only EEG channels are written to the output file. ``info['device_info']['type']`` must be a valid MFF recording device (e.g. 'HydroCel GSN 256 1.0'). This field is automatically populated when using MFF read functions. """ mffpy = _import_mffpy("Export evokeds to MFF.") info = evoked[0].info if np.round(info["sfreq"]) != info["sfreq"]: raise ValueError( f'Sampling frequency must be a whole number. sfreq: {info["sfreq"]}' ) sampling_rate = int(info["sfreq"]) # check for unapplied projectors if any(not proj["active"] for proj in evoked[0].info["projs"]): warn( "Evoked instance has unapplied projectors. Consider applying " "them before exporting with evoked.apply_proj()." ) # Initialize writer # Future changes: conditions based on version or mffpy requirement if # https://github.com/BEL-Public/mffpy/pull/92 is merged and released. fname = str(_check_fname(fname, overwrite=overwrite)) if op.exists(fname): os.remove(fname) if op.isfile(fname) else shutil.rmtree(fname) writer = mffpy.Writer(fname) current_time = datetime.datetime.now(datetime.timezone.utc) writer.addxml("fileInfo", recordTime=current_time) try: device = info["device_info"]["type"] except (TypeError, KeyError): raise ValueError("No device type. Cannot determine sensor layout.") writer.add_coordinates_and_sensor_layout(device) # Add EEG data eeg_channels = pick_types(info, eeg=True, exclude=[]) eeg_bin = mffpy.bin_writer.BinWriter(sampling_rate) for ave in evoked: # Signals are converted to µV block = (ave.data[eeg_channels] * 1e6).astype(np.float32) eeg_bin.add_block(block, offset_us=0) writer.addbin(eeg_bin) # Add categories categories_content = _categories_content_from_evokeds(evoked) writer.addxml("categories", categories=categories_content) # Add history if history: writer.addxml("historyEntries", entries=history) writer.write() def _categories_content_from_evokeds(evoked): """Return categories.xml content for evoked dataset.""" content = dict() begin_time = 0 for ave in evoked: # Times are converted to microseconds sfreq = ave.info["sfreq"] duration = np.round(len(ave.times) / sfreq * 1e6).astype(int) end_time = begin_time + duration event_time = begin_time - np.round(ave.tmin * 1e6).astype(int) eeg_bads = _get_bad_eeg_channels(ave.info) content[ave.comment] = [ _build_segment_content( begin_time, end_time, event_time, eeg_bads, name="Average", nsegs=ave.nave, ) ] begin_time += duration return content def _get_bad_eeg_channels(info): """Return a list of bad EEG channels formatted for categories.xml. Given a list of only the EEG channels in file, return the indices of this list (starting at 1) that correspond to bad channels. """ if len(info["bads"]) == 0: return [] eeg_channels = pick_types(info, eeg=True, exclude=[]) bad_channels = pick_channels(info["ch_names"], info["bads"]) bads_elementwise = np.isin(eeg_channels, bad_channels) return list(np.flatnonzero(bads_elementwise) + 1) def _build_segment_content( begin_time, end_time, event_time, eeg_bads, status="unedited", name=None, pns_bads=None, nsegs=None, ): """Build content for a single segment in categories.xml. Segments are sorted into categories in categories.xml. In a segmented MFF each category can contain multiple segments, but in an averaged MFF each category only contains one segment (the average). """ channel_status = [ {"signalBin": 1, "exclusion": "badChannels", "channels": eeg_bads} ] if pns_bads: channel_status.append( {"signalBin": 2, "exclusion": "badChannels", "channels": pns_bads} ) content = { "status": status, "beginTime": begin_time, "endTime": end_time, "evtBegin": event_time, "evtEnd": event_time, "channelStatus": channel_status, } if name: content["name"] = name if nsegs: content["keys"] = {"#seg": {"type": "long", "data": nsegs}} return content