def downsample(mgr, factor):
assert (factor >= 1)
ch_num = len(mgr.get_samples())
ch_len = len(mgr.get_samples()[0])
# To be determined ...
ret_ch_len = 0
i = 0
left_inds = []
# Determine ret_ch_len - a size of returned channel
while i < ch_len:
left_inds.append(i)
ret_ch_len += 1
i += factor
new_samples = array([zeros(ret_ch_len) for i in range(ch_num)])
for i in range(ch_num):
for j, ind in enumerate(left_inds):
new_samples[i, j] = mgr.get_samples()[i, ind]
info_source = copy.deepcopy(mgr.info_source)
info_source.get_params()['number_of_samples'] = str(ret_ch_len * ch_num)
info_source.get_params()['sampling_frequency'] = str(
float(mgr.get_param('sampling_frequency')) / factor)
tags_source = copy.deepcopy(mgr.tags_source)
samples_source = read_data_source.MemoryDataSource(new_samples)
return read_manager.ReadManager(info_source, samples_source, tags_source)
def montage_csa(mgr):
new_samples = get_montage(
mgr.get_samples(),
get_montage_matrix_csa(int(mgr.get_param('number_of_channels'))))
info_source = copy.deepcopy(mgr.info_source)
tags_source = copy.deepcopy(mgr.tags_source)
samples_source = read_data_source.MemoryDataSource(new_samples)
return read_manager.ReadManager(info_source, samples_source, tags_source)
def mgr_filter(mgr,
wp,
ws,
gpass,
gstop,
analog=0,
ftype='ellip',
output='ba',
unit='hz',
use_filtfilt=False,
meancorr=1.0):
if unit == 'radians':
b, a = signal.iirdesign(wp, ws, gpass, gstop, analog, ftype, output)
elif unit == 'hz':
nyquist = float(mgr.get_param('sampling_frequency')) / 2.0
try:
wp = wp / nyquist
ws = ws / nyquist
except TypeError:
wp = [i / nyquist for i in wp]
ws = [i / nyquist for i in ws]
b, a = signal.iirdesign(wp, ws, gpass, gstop, analog, ftype, output)
if use_filtfilt:
from scipy.signal import filtfilt
#samples_source = read_data_source.MemoryDataSource(mgr.get_samples(), False)
for i in range(int(mgr.get_param('number_of_channels'))):
print("FILT FILT CHANNEL " + str(i))
mgr.get_samples()[i, :] = signal.filtfilt(
b, a,
mgr.get_samples()[i] -
np.mean(mgr.get_samples()[i]) * meancorr)
samples_source = read_data_source.MemoryDataSource(
mgr.get_samples(), False)
else:
print("FILTER CHANNELs")
filtered = signal.lfilter(b, a, mgr.get_samples())
print("FILTER CHANNELs finished")
samples_source = read_data_source.MemoryDataSource(filtered, True)
info_source = copy.deepcopy(mgr.info_source)
tags_source = copy.deepcopy(mgr.tags_source)
new_mgr = read_manager.ReadManager(info_source, samples_source,
tags_source)
return new_mgr
def exclude_channels(mgr, channels):
'''exclude all channels in channels list'''
new_params = copy.deepcopy(mgr.get_params())
samples = mgr.get_samples()
new_tags = copy.deepcopy(mgr.get_tags())
ex_channels_inds = [
new_params['channels_names'].index(ch) for ch in channels
]
assert (-1 not in ex_channels_inds)
new_samples = zeros((int(new_params['number_of_channels']) - len(channels),
len(samples[0])))
# Define new samples and params list values
keys = [
'channels_names', 'channels_numbers', 'channels_gains',
'channels_offsets'
]
keys_to_remove = []
for k in keys:
try:
#Exclude from keys those keys that are missing in mgr
mgr.get_params()[k]
except KeyError:
keys_to_remove.append(k)
continue
new_params[k] = []
for k in keys_to_remove:
keys.remove(k)
new_ind = 0
for ch_ind, ch in enumerate(samples):
if ch_ind in ex_channels_inds:
continue
else:
new_samples[new_ind, :] = ch
for k in keys:
new_params[k].append(mgr.get_params()[k][ch_ind])
new_ind += 1
# Define other new new_params
new_params['number_of_channels'] = str(
int(new_params['number_of_channels']) - len(channels))
new_params['number_of_samples'] = str(int(new_params['number_of_samples']) - \
len(channels)*len(samples[0]))
info_source = read_info_source.MemoryInfoSource(new_params)
tags_source = read_tags_source.MemoryTagsSource(new_tags)
samples_source = read_data_source.MemoryDataSource(new_samples)
return read_manager.ReadManager(info_source, samples_source, tags_source)
def montage_ears(mgr, l_ear_channel, r_ear_channel):
left_index = mgr.get_param('channels_names').index(l_ear_channel)
right_index = mgr.get_param('channels_names').index(r_ear_channel)
if left_index < 0 or right_index < 0:
raise Exception("Montage - couldn`t find ears channels: " +
str(l_ear_channel) + ", " + str(r_ear_channel))
new_samples = get_montage(
mgr.get_samples(),
get_montage_matrix_ears(int(mgr.get_param('number_of_channels')),
left_index, right_index))
info_source = copy.deepcopy(mgr.info_source)
tags_source = copy.deepcopy(mgr.tags_source)
samples_source = read_data_source.MemoryDataSource(new_samples)
return read_manager.ReadManager(info_source, samples_source, tags_source)
def montage_custom(mgr, chnls):
'''apply custom montage to manager, by chnls'''
indexes = []
for chnl in chnls:
index = mgr.get_param('channels_names').index(chnl)
if index < 0:
raise Exception("Montage - couldn`t channel: " + str(chnl))
else:
indexes.append(index)
new_samples = get_montage(
mgr.get_samples(),
get_montage_matrix_custom(int(mgr.get_param('number_of_channels')),
indexes))
info_source = copy.deepcopy(mgr.info_source)
tags_source = copy.deepcopy(mgr.tags_source)
samples_source = read_data_source.MemoryDataSource(new_samples)
return read_manager.ReadManager(info_source, samples_source, tags_source)
def montage_custom_matrix(mgr, montage_matrix):
new_samples = get_montage(mgr.get_samples(), montage_matrix)
info_source = copy.deepcopy(mgr.info_source)
tags_source = copy.deepcopy(mgr.tags_source)
samples_source = read_data_source.MemoryDataSource(new_samples)
return read_manager.ReadManager(info_source, samples_source, tags_source)