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# -*- coding: utf-8 -*-
#
# License: BSD (3-clause)
from datetime import datetime
from glob import glob
from os.path import basename, join, splitext
from xml.etree.ElementTree import parse
import numpy as np
from ...utils import logger
def _read_events(input_fname, info):
"""Read events for the record.
Parameters
----------
input_fname : str
The file path.
info : dict
Header info array.
"""
mff_events, event_codes = _read_mff_events(input_fname, info['sfreq'],
info['n_samples'])
info['n_events'] = len(event_codes)
info['event_codes'] = np.asarray(event_codes).astype('<U4')
events = np.zeros([info['n_events'],
info['n_segments'] * info['n_samples']])
for n, event in enumerate(event_codes):
for i in mff_events[event]:
events[n][i] = n + 1
return events, info
def _read_mff_events(filename, sfreq, nsamples):
"""Extract the events.
Parameters
----------
filename : str
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 and
c['start_sample'] < nsamples))
events_tims.update({ev: trig_samp})
return events_tims, code
def _parse_xml(xml_file):
"""Parse XML file."""
xml = 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
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