def make_bads(self, minimal_duration=None):
'''Combine bads (epochs and channels into the format used for artifact clean files.
Clean sections should at least be minimal duration long.
'''
if minimal_duration == None:
minimal_duration = self.minimal_clean_duration
self.temp_bads = []
artifact_channels = [
ch for ch in self.bc.bad_channels
if ch.channel not in self.remove_ch
]
self.bad_channels = artifact_channels[:]
self.temp = artifact_channels + self.be.bad_epochs
self.incorrect_auto_annotations = []
self.ignorably_short = []
for b in self.temp:
if b.annotation == 'clean': continue
if b.correct == 'incorrect' and self.corrected:
self.incorrect_auto_annotations.append(b)
continue
if b.duration <= 30:
self.ignorably_short.append(b)
continue
if b.annotation != 'artifact':
print(
b, 'annotation: ' + b.annotation, 'dur:', b.duration,
'this annotation could be unwanted, (clean annotations are ignored)'
)
start = bad_epoch.Boundary(b.st_sample,
boundary_type='start',
visible=False)
end = bad_epoch.Boundary(b.et_sample,
boundary_type='end',
visible=False)
be = bad_epoch.Bad_epoch(start, end, 'artifact', b.coder, 'blue',
b.pp_id, b.exp_type, b.block_st_sample,
b.bid, self.epoch_id, False, 'correct',
-9, '',
b.block_st_sample + self.block_duration)
self.temp_bads.append(be)
self.epoch_id += 1
self.temp_bads.sort()
if len(self.temp_bads) == 0:
self.bads = []
return
temp_bads = copy.deepcopy(self.temp_bads)
temp_bads = cal.combine_overlaps(temp_bads)
self.stiches = cal.stitch_artifacts(temp_bads, minimal_duration)
self.stiched_stiches = cal.stitch_stiches(self.stiches)
temp_bads = cal.combine_artifacts(temp_bads, self.stiched_stiches)
cal.check_artifacts(artifacts=temp_bads,
fo=self.fo,
default='clean',
minimal_duration=minimal_duration)
self.bads = temp_bads
def toggle_complete_channel(self): if self.channel_mode == 'off': return False channel = self.ch_names[self.channel_mode_index] if channel in self.complete_bad_channel: self.complete_bad_channel.pop(self.complete_bad_channel.index(channel)) for bc in self.bad_channels: if bc.channel == channel and bc.annotation == 'all': self.delete_bad_epoch(bc.epoch_id) break else: sboundary = bad_epoch.Boundary(0,'start') eboundary = bad_epoch.Boundary(self.data.shape[1],'end') self.bad_channels.append(bad_channel.Bad_channel(channel,start_boundary = sboundary,end_boundary = eboundary, pp_id = self.pp_id, coder = self.coder,exp_type = self.exp_type, bid = self.bid, block_st_sample = self.block_st_sample, epoch_id = self.make_bad_epoch_id(),offset = self.channel_mode_index *self.offset_value,annotation = 'all')) self.complete_bad_channel.append(channel) self.handle_plot(force_redraw=True)
def xml2bad_epochs(self, load_data=True, multiplier=1, remove_clean=False):
'''Create a list of bad epochs from xml file.'''
self.bad_epochs = []
if load_data: self.load_xml()
for be_xml in self.artifacts.iter('bad_epoch'):
# fetch subelements
element_names = 'st_sample,et_sample,block_st_sample,block_et_sample,pp_id,bid,annotation,color,exp_type,coder,epoch_ids,coder,correct'.split(
',')
element_values = []
for e in element_names:
if not be_xml.find(e) == None:
element_values.append(be_xml.find(e).text)
else:
element_values.append('NA')
st_sample, et_sample, block_st_sample, block_et_sample, pp_id, bid, annotation, color, exp_type, coder, epoch_ids, coder, correct = element_values
if remove_clean and annotation == 'clean': continue
if st_sample == 'NA' or et_sample == 'NA':
continue
epoch_id = be_xml.attrib['id']
#create start and end boundary
# print(st_sample,et_sample)
start = bad_epoch.Boundary(x=int(int(st_sample) * multiplier),
boundary_type='start',
visible=False)
end = bad_epoch.Boundary(x=int(int(et_sample) * multiplier),
boundary_type='end',
visible=False)
# create bad epoch
be = bad_epoch.Bad_epoch(start_boundary=start,
end_boundary=end,
annotation=annotation,
color=color,
pp_id=pp_id,
exp_type=exp_type,
bid=bid,
block_st_sample=block_st_sample,
epoch_id=epoch_id,
visible=False,
epoch_ids=epoch_ids,
block_et_sample=block_et_sample,
coder=coder,
correct=correct)
self.bad_epochs.append(be)
# print('N bad epoch:',len(self.bad_epochs))
return self.bad_epochs
def xml2bad_epochs(self):
'''Create a list of bad epochs from xml file.'''
self.artifacts = []
# print('Starting with list of',len(self.artifacts),' bad epochs')
for be_xml in self.cnn_result.iter('bad_epoch'):
# fetch subelements
element_names = 'st_sample,et_sample,block_st_sample,pp_id,bid,annotation,color,exp_type,coder,note,correct,corrector,perc_clean'.split(
',')
element_values = []
for e in element_names:
if be_xml.find(e) != None:
element_values.append(be_xml.find(e).text)
else:
element_values.append('NA')
st_sample, et_sample, block_st_sample, pp_id, bid, annotation, color, exp_type, coder, note, correct, corrector, perc_clean = element_values
epoch_id = be_xml.attrib['id']
#create start and end boundary
start = bad_epoch.Boundary(x=int(st_sample),
boundary_type='start',
visible=False)
end = bad_epoch.Boundary(x=int(et_sample),
boundary_type='end',
visible=False)
# create bad epoch
be = bad_epoch.Bad_epoch(start_boundary=start,
end_boundary=end,
annotation=annotation,
color=color,
pp_id=pp_id,
exp_type=exp_type,
bid=bid,
block_st_sample=block_st_sample,
epoch_id=epoch_id,
visible=False,
correct=correct,
perc_clean=perc_clean,
coder=self.cnn_model_name)
self.artifacts.append(be)
# print('N bad epoch:',len(self.artifacts),'artifacts')
return self.artifacts
def handle_end(self):
'''Create a end boundary, and either add this to closest start boundary or create new epoch.'''
if self.event.xdata < self.data.shape[1]: x = self.event.xdata
else: x = self.data.shape[1] - 1
boundary = bad_epoch.Boundary(x,'end')
if self.channel_mode == 'on': self.channel_boundaries.append(boundary)
else: self.boundaries.append(boundary)
be = self.find_completion_bad_epoch(boundary_type = 'start')
if be:
print('combining boundaries')
be.set_end(boundary)
if self.channel_mode == 'on':
i = self.ch_names.index(be.channel)
be.plot(channel_data = self.data[i],offset = i * self.offset_value)
else:
if self.channel_mode == 'on':
channel = self.ch_names[self.channel_mode_index]
self.bad_channels.append(bad_channel.Bad_channel(channel,end_boundary = boundary, pp_id = self.pp_id, exp_type = self.exp_type, bid = self.bid, block_st_sample = self.block_st_sample, epoch_id = self.make_bad_epoch_id(),offset = self.channel_mode_index * self.offset_value,annotation = self.default_annotation_channel))
else:
self.bad_epochs.append(bad_epoch.Bad_epoch(end_boundary = boundary, pp_id = self.pp_id, exp_type = self.exp_type, bid = self.bid, block_st_sample = self.block_st_sample, epoch_id = self.make_bad_epoch_id(),annotation = self.default_annotation))
def make_bad_epochs(self, minimal_duration=2000):
'''Create a list of bad epochs from xml file.'''
self.bad_epochs = []
ws = self.w.windows['sf1000']
previous_annotation = ''
perc_clean = []
for index in range(self.pred_class.shape[0]):
annotation = 'clean' if self.pred_class_adj[
index] == 0 else 'artifact'
perc_clean.append(self.pred_perc[index][0])
if previous_annotation == '':
# first index
st_sample = ws.start_snippets[index]
previous_annotation = annotation
elif previous_annotation != annotation or index == self.pred_class.shape[
0] - 1:
# start of a new bad epoch, handle creation previous bad epoch
b = self.b
if index == self.pred_class.shape[0] - 1:
if b.start_marker_missing or b.end_marker_missing:
et_sample = self.pred_class.shape[0] * 10
else:
et_sample = b.duration_sample
else:
et_sample = (ws.start_snippets[index - 1] +
ws.end_snippets[index - 1]) / 2
start = bad_epoch.Boundary(x=int(st_sample),
boundary_type='start',
visible=False)
end = bad_epoch.Boundary(x=int(et_sample),
boundary_type='end',
visible=False)
epoch_id = get_cnn_epoch_id(increment=True)
perc_clean_last = perc_clean.pop(-1)
perc_clean = ' '.join([
str(np.mean(np.array(perc_clean))),
str(np.std(np.array(perc_clean)))
])
# create bad epoch
be = bad_epoch.Bad_epoch(start_boundary=start,
end_boundary=end,
annotation=previous_annotation,
pp_id=b.pp_id,
exp_type=b.exp_type,
bid=b.bid,
block_st_sample=b.st_sample,
epoch_id=epoch_id,
coder=self.cnn_model_name,
correct='unk',
visible=False,
perc_clean=perc_clean)
self.bad_epochs.append(be)
st_sample = et_sample + 1
previous_annotation = annotation
perc_clean = [perc_clean_last]
if len(self.bad_epochs) > 1: self.combine_bad_epochs(minimal_duration)
else: self.artifacts = copy.deepcopy(self.bad_epochs)
self.calc_clean_artifact_samples()
self.artifacts2indices()