def __init__(self, fs, bands, ch_names, states_labels, indexes):
self.states_labels = states_labels
self.bands = bands
self.prefilter = FilterSequence([ButterFilter((0.5, 45), fs, len(ch_names))])
self.csp_pools = [SpatialDecompositionPool(ch_names, fs, bands, 'csp', indexes) for _label in states_labels]
self.csp_transformer = None
self.var_detector = InstantaneousVarianceFilter(len(bands)*len(indexes)*len(states_labels), n_taps=fs//2)
self.classifier = MLPClassifier(hidden_layer_sizes=(), early_stopping=True, verbose=True)
def __init__(self,
inlet,
include=None,
exclude=None,
start_from_1=True,
subtractive_channel=None,
dc=False,
events_inlet=None,
aux_inlets=None,
aux_interpolate=False,
prefilter_band=(None, None)):
self.last_y = 0
self.inlet = inlet
self.events_inlet = events_inlet
self.aux_inlets = aux_inlets
self.aux_previous_chunks = []
self.aux_interpolate = aux_interpolate
# get names in uppercase format
names = [n.upper() for n in self.inlet.get_channels_labels()]
# cut after first non alphabetic numerical (e.g. 'Fp1-A1' -> 'Fp1')
names = [
''.join([ch if ch.isalnum() else ' ' for ch in name]).split()[0]
for name in names
]
# append aux inlets
if self.aux_inlets is not None:
for aux_inlet in self.aux_inlets:
names += aux_inlet.get_channels_labels()
self.aux_previous_chunks.append(
np.zeros_like((1, aux_inlet.n_channels)))
# append events inlet
if self.events_inlet is not None:
names += [EVENTS_CHANNEL_NAME]
self.channels_names = names
print('Channels:', names)
# get channels indices to select
if include:
include = self.parse_channels_string(include)
if isinstance(include, list):
if isinstance(include[0], int):
include_indices = [j - int(start_from_1) for j in include]
elif isinstance(include[0], str):
include_indices = [names.index(r.upper()) for r in include]
else:
raise TypeError(
'Reference list must contain int or str instances')
else:
raise TypeError('Reference list must be list or None')
else:
include_indices = list(range(len(names)))
# channel to subtract
if (subtractive_channel is not None) and (subtractive_channel != ''):
if isinstance(subtractive_channel, int):
self.sub_channel_index = subtractive_channel - int(
start_from_1)
elif isinstance(subtractive_channel, str):
self.sub_channel_index = names.index(
subtractive_channel.upper())
else:
self.sub_channel_index = None
# exclude channels
if exclude:
exclude = self.parse_channels_string(exclude)
if isinstance(exclude, list):
if isinstance(exclude[0], int):
exclude_indices = [j - int(start_from_1) for j in exclude]
elif isinstance(exclude[0], str):
print('Channels labels:', names)
print('Exclude:', [r.upper() for r in exclude])
exclude_indices = [
names.index(r.upper()) for r in exclude
if r.upper() in names
]
else:
raise TypeError(
'Exclude must contain int or str instances')
else:
raise TypeError('Exclude list must be list or None')
else:
exclude_indices = []
# exclude not valid channels
# exclude_indices += [j for j, isvalid in enumerate(names_isvalid) if not isvalid]
# exclude subtractive channel
if self.sub_channel_index is not None:
if self.sub_channel_index not in exclude_indices:
exclude_indices.append(self.sub_channel_index)
# all indices
exclude_indices = set(exclude_indices)
self.indices = [j for j in include_indices if j not in exclude_indices]
self.other_indices = [
j for j in range(len(names)) if j in exclude_indices
]
self.dc = dc
# pre-filtering settings
if isinstance(prefilter_band, str):
prefilter_band = [(float(s) if s != 'None' else None)
for s in prefilter_band.split(' ')]
if (prefilter_band[0] is None) and (prefilter_band[1] is None):
self.prefilter = IdentityFilter()
else:
self.prefilter = ButterFilter(
prefilter_band, self.inlet.get_frequency(),
len(self.inlet.get_channels_labels()))
class ChannelsSelector:
def __init__(self,
inlet,
include=None,
exclude=None,
start_from_1=True,
subtractive_channel=None,
dc=False,
events_inlet=None,
aux_inlets=None,
aux_interpolate=False,
prefilter_band=(None, None)):
self.last_y = 0
self.inlet = inlet
self.events_inlet = events_inlet
self.aux_inlets = aux_inlets
self.aux_previous_chunks = []
self.aux_interpolate = aux_interpolate
# get names in uppercase format
names = [n.upper() for n in self.inlet.get_channels_labels()]
# cut after first non alphabetic numerical (e.g. 'Fp1-A1' -> 'Fp1')
names = [
''.join([ch if ch.isalnum() else ' ' for ch in name]).split()[0]
for name in names
]
# append aux inlets
if self.aux_inlets is not None:
for aux_inlet in self.aux_inlets:
names += aux_inlet.get_channels_labels()
self.aux_previous_chunks.append(
np.zeros_like((1, aux_inlet.n_channels)))
# append events inlet
if self.events_inlet is not None:
names += [EVENTS_CHANNEL_NAME]
self.channels_names = names
print('Channels:', names)
# get channels indices to select
if include:
include = self.parse_channels_string(include)
if isinstance(include, list):
if isinstance(include[0], int):
include_indices = [j - int(start_from_1) for j in include]
elif isinstance(include[0], str):
include_indices = [names.index(r.upper()) for r in include]
else:
raise TypeError(
'Reference list must contain int or str instances')
else:
raise TypeError('Reference list must be list or None')
else:
include_indices = list(range(len(names)))
# channel to subtract
if (subtractive_channel is not None) and (subtractive_channel != ''):
if isinstance(subtractive_channel, int):
self.sub_channel_index = subtractive_channel - int(
start_from_1)
elif isinstance(subtractive_channel, str):
self.sub_channel_index = names.index(
subtractive_channel.upper())
else:
self.sub_channel_index = None
# exclude channels
if exclude:
exclude = self.parse_channels_string(exclude)
if isinstance(exclude, list):
if isinstance(exclude[0], int):
exclude_indices = [j - int(start_from_1) for j in exclude]
elif isinstance(exclude[0], str):
print('Channels labels:', names)
print('Exclude:', [r.upper() for r in exclude])
exclude_indices = [
names.index(r.upper()) for r in exclude
if r.upper() in names
]
else:
raise TypeError(
'Exclude must contain int or str instances')
else:
raise TypeError('Exclude list must be list or None')
else:
exclude_indices = []
# exclude not valid channels
# exclude_indices += [j for j, isvalid in enumerate(names_isvalid) if not isvalid]
# exclude subtractive channel
if self.sub_channel_index is not None:
if self.sub_channel_index not in exclude_indices:
exclude_indices.append(self.sub_channel_index)
# all indices
exclude_indices = set(exclude_indices)
self.indices = [j for j in include_indices if j not in exclude_indices]
self.other_indices = [
j for j in range(len(names)) if j in exclude_indices
]
self.dc = dc
# pre-filtering settings
if isinstance(prefilter_band, str):
prefilter_band = [(float(s) if s != 'None' else None)
for s in prefilter_band.split(' ')]
if (prefilter_band[0] is None) and (prefilter_band[1] is None):
self.prefilter = IdentityFilter()
else:
self.prefilter = ButterFilter(
prefilter_band, self.inlet.get_frequency(),
len(self.inlet.get_channels_labels()))
def get_next_chunk(self):
chunk, timestamp = self.inlet.get_next_chunk()
if chunk is not None:
if self.dc:
chunk = self.dc_blocker(chunk)
chunk = self.prefilter.apply(chunk)
if self.events_inlet is not None:
events, events_timestamp = self.events_inlet.get_next_chunk()
aug_chunk = np.zeros((chunk.shape[0], 1))
if events is not None:
aug_chunk[np.searchsorted(timestamp[:-1],
events_timestamp)] = events
chunk = np.hstack([chunk, aug_chunk])
if self.aux_inlets is not None:
for j_aux_inlet, aux_inlet in enumerate(self.aux_inlets):
aux_chunk_short, aux_timestamp = aux_inlet.get_next_chunk()
aux_chunk = np.zeros(
(chunk.shape[0], aux_inlet.n_channels)) * np.nan
if aux_chunk_short is not None:
for k in range(aux_inlet.n_channels):
aux_chunk[
np.searchsorted(timestamp[:-1], aux_timestamp),
k] = aux_chunk_short[:, k]
if self.aux_interpolate:
aux_chunk[:, k] = interp_nans(aux_chunk[:, k])
self.aux_previous_chunks[j_aux_inlet] = aux_chunk
else:
if self.aux_interpolate:
aux_chunk = np.ones((chunk.shape[0], aux_inlet.n_channels)) * \
self.aux_previous_chunks[j_aux_inlet][-1]
chunk = np.hstack([chunk, aux_chunk])
if self.sub_channel_index is None:
return chunk[:, self.indices], chunk[:, self.
other_indices], timestamp
else:
return chunk[:, self.indices] - chunk[:, [
self.sub_channel_index
]], chunk[:, self.other_indices], timestamp
else:
return None, None, None
def dc_blocker(self, x, r=0.99):
# DC Blocker https://ccrma.stanford.edu/~jos/fp/DC_Blocker.html
y = np.zeros_like(x)
y[0] = self.last_y
for n in range(1, x.shape[0]):
y[n] = x[n] - x[n - 1] + r * y[n - 1]
self.last_y = y[-1]
return y
def update_action(self):
pass
def save_info(self, file):
try:
return self.inlet.save_info(file)
except UnicodeDecodeError:
print(
"Warning: stream info wasn't saved, because user name id nonlatin"
)
pass
def info_as_xml(self):
try:
return self.inlet.info_as_xml()
except UnicodeDecodeError:
print(
"Warning: stream info wasn't saved, because user name id nonlatin"
)
pass
def get_frequency(self):
return self.inlet.get_frequency()
def get_n_channels(self):
return len(self.indices)
def get_n_channels_other(self):
return len(self.other_indices)
def get_channels_labels(self):
return [self.channels_names[ind] for ind in self.indices]
def disconnect(self):
self.inlet.disconnect()
@staticmethod
def parse_channels_string(string):
import re
_list = [] if string == '' else re.split('; |, |\*|\n| |', string)
if len(_list) > 0:
try:
_list = [int(e) for e in string]
except (ValueError, TypeError):
pass
return _list
def __init__(self, inlet, include=None, exclude=None, start_from_1=True, subtractive_channel=None, dc=False,
events_inlet=None, aux_inlets=None, aux_interpolate=False, prefilter_band=(None, None)):
self.last_y = 0
self.inlet = inlet
self.events_inlet = events_inlet
self.aux_inlets = aux_inlets
self.aux_previous_chunks = []
self.aux_interpolate = aux_interpolate
# get names in uppercase format
names = [n.upper() for n in self.inlet.get_channels_labels()]
# cut after first non alphabetic numerical (e.g. 'Fp1-A1' -> 'Fp1')
names = [''.join([ch if ch.isalnum() else ' ' for ch in name]).split()[0] for name in names]
# append aux inlets
if self.aux_inlets is not None:
for aux_inlet in self.aux_inlets:
names += aux_inlet.get_channels_labels()
self.aux_previous_chunks.append(np.zeros_like((1, aux_inlet.n_channels)))
# append events inlet
if self.events_inlet is not None:
names += [EVENTS_CHANNEL_NAME]
self.channels_names = names
print('Channels:', names)
# get channels indices to select
if include:
include = self.parse_channels_string(include)
if isinstance(include, list):
if isinstance(include[0], int):
include_indices = [j - int(start_from_1) for j in include]
elif isinstance(include[0], str):
include_indices = [names.index(r.upper()) for r in include]
else:
raise TypeError('Reference list must contain int or str instances')
else:
raise TypeError('Reference list must be list or None')
else:
include_indices = list(range(len(names)))
# channel to subtract
if (subtractive_channel is not None) and (subtractive_channel != ''):
if isinstance(subtractive_channel, int):
self.sub_channel_index = subtractive_channel - int(start_from_1)
elif isinstance(subtractive_channel, str):
self.sub_channel_index = names.index(subtractive_channel.upper())
else:
self.sub_channel_index = None
# exclude channels
if exclude:
exclude = self.parse_channels_string(exclude)
if isinstance(exclude, list):
if isinstance(exclude[0], int):
exclude_indices = [j - int(start_from_1) for j in exclude]
elif isinstance(exclude[0], str):
print('Channels labels:', names)
print('Exclude:', [r.upper() for r in exclude])
exclude_indices = [names.index(r.upper()) for r in exclude if r.upper() in names]
else:
raise TypeError('Exclude must contain int or str instances')
else:
raise TypeError('Exclude list must be list or None')
else:
exclude_indices = []
# exclude not valid channels
# exclude_indices += [j for j, isvalid in enumerate(names_isvalid) if not isvalid]
# exclude subtractive channel
if self.sub_channel_index is not None:
if self.sub_channel_index not in exclude_indices:
exclude_indices.append(self.sub_channel_index)
# all indices
exclude_indices = set(exclude_indices)
self.indices = [j for j in include_indices if j not in exclude_indices]
self.other_indices = [j for j in range(len(names)) if j in exclude_indices]
self.dc = dc
# pre-filtering settings
if isinstance(prefilter_band, str):
prefilter_band = [(float(s) if s != 'None' else None) for s in prefilter_band.split(' ')]
if (prefilter_band[0] is None) and (prefilter_band[1] is None):
self.prefilter = IdentityFilter()
else:
self.prefilter = ButterFilter(prefilter_band, self.inlet.get_frequency(),
len(self.inlet.get_channels_labels()))
class ChannelsSelector:
def __init__(self, inlet, include=None, exclude=None, start_from_1=True, subtractive_channel=None, dc=False,
events_inlet=None, aux_inlets=None, aux_interpolate=False, prefilter_band=(None, None)):
self.last_y = 0
self.inlet = inlet
self.events_inlet = events_inlet
self.aux_inlets = aux_inlets
self.aux_previous_chunks = []
self.aux_interpolate = aux_interpolate
# get names in uppercase format
names = [n.upper() for n in self.inlet.get_channels_labels()]
# cut after first non alphabetic numerical (e.g. 'Fp1-A1' -> 'Fp1')
names = [''.join([ch if ch.isalnum() else ' ' for ch in name]).split()[0] for name in names]
# append aux inlets
if self.aux_inlets is not None:
for aux_inlet in self.aux_inlets:
names += aux_inlet.get_channels_labels()
self.aux_previous_chunks.append(np.zeros_like((1, aux_inlet.n_channels)))
# append events inlet
if self.events_inlet is not None:
names += [EVENTS_CHANNEL_NAME]
self.channels_names = names
print('Channels:', names)
# get channels indices to select
if include:
include = self.parse_channels_string(include)
if isinstance(include, list):
if isinstance(include[0], int):
include_indices = [j - int(start_from_1) for j in include]
elif isinstance(include[0], str):
include_indices = [names.index(r.upper()) for r in include]
else:
raise TypeError('Reference list must contain int or str instances')
else:
raise TypeError('Reference list must be list or None')
else:
include_indices = list(range(len(names)))
# channel to subtract
if (subtractive_channel is not None) and (subtractive_channel != ''):
if isinstance(subtractive_channel, int):
self.sub_channel_index = subtractive_channel - int(start_from_1)
elif isinstance(subtractive_channel, str):
self.sub_channel_index = names.index(subtractive_channel.upper())
else:
self.sub_channel_index = None
# exclude channels
if exclude:
exclude = self.parse_channels_string(exclude)
if isinstance(exclude, list):
if isinstance(exclude[0], int):
exclude_indices = [j - int(start_from_1) for j in exclude]
elif isinstance(exclude[0], str):
print('Channels labels:', names)
print('Exclude:', [r.upper() for r in exclude])
exclude_indices = [names.index(r.upper()) for r in exclude if r.upper() in names]
else:
raise TypeError('Exclude must contain int or str instances')
else:
raise TypeError('Exclude list must be list or None')
else:
exclude_indices = []
# exclude not valid channels
# exclude_indices += [j for j, isvalid in enumerate(names_isvalid) if not isvalid]
# exclude subtractive channel
if self.sub_channel_index is not None:
if self.sub_channel_index not in exclude_indices:
exclude_indices.append(self.sub_channel_index)
# all indices
exclude_indices = set(exclude_indices)
self.indices = [j for j in include_indices if j not in exclude_indices]
self.other_indices = [j for j in range(len(names)) if j in exclude_indices]
self.dc = dc
# pre-filtering settings
if isinstance(prefilter_band, str):
prefilter_band = [(float(s) if s != 'None' else None) for s in prefilter_band.split(' ')]
if (prefilter_band[0] is None) and (prefilter_band[1] is None):
self.prefilter = IdentityFilter()
else:
self.prefilter = ButterFilter(prefilter_band, self.inlet.get_frequency(),
len(self.inlet.get_channels_labels()))
def get_next_chunk(self):
chunk, timestamp = self.inlet.get_next_chunk()
if chunk is not None:
if self.dc:
chunk = self.dc_blocker(chunk)
chunk = self.prefilter.apply(chunk)
if self.events_inlet is not None:
events, events_timestamp = self.events_inlet.get_next_chunk()
aug_chunk = np.zeros((chunk.shape[0], 1))
if events is not None:
aug_chunk[np.searchsorted(timestamp[:-1], events_timestamp)] = events
chunk = np.hstack([chunk, aug_chunk])
if self.aux_inlets is not None:
for j_aux_inlet, aux_inlet in enumerate(self.aux_inlets):
aux_chunk_short, aux_timestamp = aux_inlet.get_next_chunk()
aux_chunk = np.zeros((chunk.shape[0], aux_inlet.n_channels)) * np.nan
if aux_chunk_short is not None:
for k in range(aux_inlet.n_channels):
aux_chunk[np.searchsorted(timestamp[:-1], aux_timestamp), k] = aux_chunk_short[:, k]
if self.aux_interpolate:
aux_chunk[:, k] = interp_nans(aux_chunk[:, k])
self.aux_previous_chunks[j_aux_inlet] = aux_chunk
else:
if self.aux_interpolate:
aux_chunk = np.ones((chunk.shape[0], aux_inlet.n_channels)) * \
self.aux_previous_chunks[j_aux_inlet][-1]
chunk = np.hstack([chunk, aux_chunk])
if self.sub_channel_index is None:
return chunk[:, self.indices], chunk[:, self.other_indices], timestamp
else:
return chunk[:, self.indices] - chunk[:, [self.sub_channel_index]], chunk[:, self.other_indices], timestamp
else:
return None, None, None
def dc_blocker(self, x, r=0.99):
# DC Blocker https://ccrma.stanford.edu/~jos/fp/DC_Blocker.html
y = np.zeros_like(x)
y[0] = self.last_y
for n in range(1, x.shape[0]):
y[n] = x[n] - x[n - 1] + r * y[n - 1]
self.last_y = y[-1]
return y
def update_action(self):
pass
def save_info(self, file):
try:
return self.inlet.save_info(file)
except UnicodeDecodeError:
print("Warning: stream info wasn't saved, because user name id nonlatin")
pass
def info_as_xml(self):
try:
return self.inlet.info_as_xml()
except UnicodeDecodeError:
print("Warning: stream info wasn't saved, because user name id nonlatin")
pass
def get_frequency(self):
return self.inlet.get_frequency()
def get_n_channels(self):
return len(self.indices)
def get_n_channels_other(self):
return len(self.other_indices)
def get_channels_labels(self):
return [self.channels_names[ind] for ind in self.indices]
def disconnect(self):
self.inlet.disconnect()
@staticmethod
def parse_channels_string(string):
import re
_list = [] if string == '' else re.split('; |, |\*|\n| |', string)
if len(_list) > 0:
try:
_list = [int(e) for e in string]
except (ValueError, TypeError):
pass
return _list
band = (15, 30)
method = 'ica'
np.random.seed(401)
# load data
df, fs, channels, p_names = load_data(h5_file)
fs = int(fs)
eeg_channels = channels[:30]
n_channels = len(eeg_channels)
montage = Montage(eeg_channels)
print(
'Fs: {}Hz\nAll channels: {}\nEEG channels: {}\nBlock sequence: {}'.format(
fs, ', '.join(channels), ', '.join(eeg_channels), '-'.join(p_names)))
# pre filter
pre_filter = ButterFilter(band, fs, n_channels)
df[eeg_channels] = pre_filter.apply(df[eeg_channels])
df = df.iloc[fs * 5:]
# spatial decomposition
if method == 'ica':
decomposition = ICADecomposition(eeg_channels, fs)
elif method == 'csp':
decomposition = CSPDecomposition(eeg_channels, fs)
else:
raise ValueError('Bad method name. Use "ica" or "csp".')
# select data between first and second "pause" block
first_b_number = p_names.index('Pause') + 1
second_b_number = 10000 # p_names.index('Pause', 1) + 1
X = df.loc[(df.block_number > first_b_number)