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#
# Authors: The MNE-Python contributors.
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.
from datetime import datetime
from glob import glob
from os.path import basename, join, splitext
import numpy as np
from ...utils import _soft_import, _validate_type, logger, warn
def _read_events(input_fname, info):
"""Read events for the record.
Parameters
----------
input_fname : path-like
The file path.
info : dict
Header info array.
"""
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"] = 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]:
if (i < 0) or (i >= events.shape[1]):
continue
events[n][i] = n + 1
return events, info, mff_events
def _read_mff_events(filename, sfreq):
"""Extract the events.
Parameters
----------
filename : path-like
File path.
sfreq : float
The sampling frequency
"""
orig = {}
for xml_file in glob(join(filename, "*.xml")):
xml_type = splitext(basename(xml_file))[0]
orig[xml_type] = _parse_xml(xml_file)
xml_files = orig.keys()
xml_events = [x for x in xml_files if x[:7] == "Events_"]
for item in orig["info"]:
if "recordTime" in item:
start_time = _ns2py_time(item["recordTime"])
break
markers = []
code = []
for xml in xml_events:
for event in orig[xml][2:]:
event_start = _ns2py_time(event["beginTime"])
start = (event_start - start_time).total_seconds()
if event["code"] not in code:
code.append(event["code"])
marker = {
"name": event["code"],
"start": start,
"start_sample": int(np.fix(start * sfreq)),
"end": start + float(event["duration"]) / 1e9,
"chan": None,
}
markers.append(marker)
events_tims = dict()
for ev in code:
trig_samp = list(
c["start_sample"] for n, c in enumerate(markers) if c["name"] == ev
)
events_tims.update({ev: trig_samp})
return events_tims, code
def _parse_xml(xml_file):
"""Parse XML file."""
defusedxml = _soft_import("defusedxml", "reading EGI MFF data")
xml = defusedxml.ElementTree.parse(xml_file)
root = xml.getroot()
return _xml2list(root)
def _xml2list(root):
"""Parse XML item."""
output = []
for element in root:
if len(element) > 0:
if element[0].tag != element[-1].tag:
output.append(_xml2dict(element))
else:
output.append(_xml2list(element))
elif element.text:
text = element.text.strip()
if text:
tag = _ns(element.tag)
output.append({tag: text})
return output
def _ns(s):
"""Remove namespace, but only if there is a namespace to begin with."""
if "}" in s:
return "}".join(s.split("}")[1:])
else:
return s
def _xml2dict(root):
"""Use functions instead of Class.
remove namespace based on
http://stackoverflow.com/questions/2148119
"""
output = {}
if root.items():
output.update(dict(root.items()))
for element in root:
if len(element) > 0:
if len(element) == 1 or element[0].tag != element[1].tag:
one_dict = _xml2dict(element)
else:
one_dict = {_ns(element[0].tag): _xml2list(element)}
if element.items():
one_dict.update(dict(element.items()))
output.update({_ns(element.tag): one_dict})
elif element.items():
output.update({_ns(element.tag): dict(element.items())})
else:
output.update({_ns(element.tag): element.text})
return output
def _ns2py_time(nstime):
"""Parse times."""
nsdate = nstime[0:10]
nstime0 = nstime[11:26]
nstime00 = nsdate + " " + nstime0
pytime = datetime.strptime(nstime00, "%Y-%m-%d %H:%M:%S.%f")
return pytime
def _combine_triggers(data, remapping=None):
"""Combine binary triggers."""
new_trigger = np.zeros(data.shape[1])
if data.astype(bool).sum(axis=0).max() > 1: # ensure no overlaps
logger.info(
" Found multiple events at the same time "
"sample. Cannot create trigger channel."
)
return
if remapping is None:
remapping = np.arange(data) + 1
for d, event_id in zip(data, remapping):
idx = d.nonzero()
if np.any(idx):
new_trigger[idx] += event_id
return new_trigger
def _triage_include_exclude(include, exclude, egi_events, egi_info):
"""Triage include and exclude."""
_validate_type(exclude, (list, None), "exclude")
_validate_type(include, (list, None), "include")
event_codes = list(egi_info["event_codes"])
for name, lst in dict(exclude=exclude, include=include).items():
for ii, item in enumerate(lst or []):
what = f"{name}[{ii}]"
_validate_type(item, str, what)
if item not in event_codes:
raise ValueError(
f"Could not find event channel named {what}={repr(item)}"
)
if include is None:
if exclude is None:
default_exclude = ["sync", "TREV"]
exclude = [code for code in default_exclude if code in event_codes]
for code, event in zip(event_codes, egi_events):
if event.sum() < 1 and code:
exclude.append(code)
if (
len(exclude) == len(event_codes)
and egi_info["n_events"]
and set(exclude) - set(default_exclude)
):
warn(
"Did not find any event code with at least one event.",
RuntimeWarning,
)
include = [k for k in event_codes if k not in exclude]
del exclude
excl_events = ", ".join(k for k in event_codes if k not in include)
logger.info(f" Excluding events {{{excl_events}}} ...")
return include
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