def run(cfg, state=mp.Value('i', 1), queue=None):
"""
Training protocol for Alpha/Theta neurofeedback.
"""
redirect_stdout_to_queue(logger, queue, 'INFO')
# add tdef object
cfg.tdef = trigger_def(cfg.TRIGGER_FILE)
# Extract features
if not state.value:
sys.exit(-1)
freqs = np.arange(cfg.FEATURES['PSD']['fmin'], cfg.FEATURES['PSD']['fmax']+0.5, 1/cfg.FEATURES['PSD']['wlen'])
featdata = features.compute_features(cfg)
# Average the PSD over the windows
window_avg_psd = np.mean(np.squeeze(featdata['X_data']), 0)
# Alpha ref over the alpha band
alpha_ref = round(np.mean(window_avg_psd[freqs>=8]))
alpha_thr = round(alpha_ref - (0.5 * np.std(window_avg_psd[freqs>=8]) ))
# Theta ref over Theta band
theta_ref = round(np.mean(window_avg_psd[freqs<8]))
theta_thr = round(theta_ref - (0.5 * np.std(window_avg_psd[freqs<8]) ))
logger.info('Theta ref = {}; alpha ref ={}' .format(theta_ref, alpha_ref))
logger.info('Theta thr = {}; alpha thr ={}' .format(theta_thr, alpha_thr))
def main():
fmin = 1
fmax = 40
channels = 64
wlen = 0.5 # window length in seconds
sfreq = 512
num_iterations = 500
signal = np.random.rand(channels, int(np.round(sfreq * wlen)))
psde = mne.decoding.PSDEstimator(sfreq=sfreq, fmin=fmin,\
fmax=fmax, bandwidth=None, adaptive=False, low_bias=True,\
n_jobs=1, normalization='length', verbose=None)
tm = qc.Timer()
times = []
for i in range(num_iterations):
tm.reset()
psd = psde.transform(
signal.reshape((1, signal.shape[0], signal.shape[1])))
times.append(tm.msec())
if i % 100 == 0:
logger.info('%d / %d' % (i, num_iterations))
ms = np.mean(times)
fps = 1000 / ms
logger.info('Average = %.1f ms (%.1f Hz)' % (ms, fps))
def epochs2mat(data_dir,
channel_picks,
event_id,
tmin,
tmax,
merge_epochs=False,
spfilter=None,
spchannels=None):
if merge_epochs:
# load all raw files in the directory and merge epochs
fiflist = []
for data_file in qc.get_file_list(data_dir, fullpath=True):
if data_file[-4:] != '.fif':
continue
fiflist.append(data_file)
raw, events = pu.load_multi(fiflist,
spfilter=spfilter,
spchannels=spchannels)
matfile = data_dir + '/epochs_all.mat'
save_mat(raw, events, channel_picks, event_id, tmin, tmax, matfile)
else:
# process individual raw file separately
for data_file in qc.get_file_list(data_dir, fullpath=True):
if data_file[-4:] != '.fif':
continue
[base, fname, fext] = qc.parse_path_list(data_file)
matfile = '%s/%s-epochs.mat' % (base, fname)
raw, events = pu.load_raw(data_file)
save_mat(raw, events, channel_picks, event_id, tmin, tmax, matfile)
logger.info('Exported to %s' % matfile)
def update_loop(self):
# Sharing variable to stop at the GUI level
if not self.state.value:
logger.info('Viewer stopped')
sys.exit()
try:
# assert self.updating==False, 'thread destroyed?'
# self.updating= True
# self.handle_tobiid_input() # Read TiDs
self.read_eeg() # Read new chunk
if len(self.ts_list) > 0:
self.filter_signal() # Filter acquired data
self.update_ringbuffers() # Update the plotting infor
if (not self.stop_plot):
self.repaint() # Call paint event
except:
logger.exception('Exception. Dropping into a shell.')
pdb.set_trace()
finally:
# self.updating= False
# using singleShot instead
# QtCore.QTimer.singleShot( 20, self.update_loop )
pass
def any2fif(filename, interactive=False, outdir=None, channel_file=None):
"""
Generic file format converter
"""
p = qc.parse_path(filename)
if outdir is not None:
qc.make_dirs(outdir)
if p.ext == 'pcl':
eve_file = '%s/%s.txt' % (p.dir, p.name.replace('raw', 'eve'))
if os.path.exists(eve_file):
logger.info('Adding events from %s' % eve_file)
else:
eve_file = None
pcl2fif(filename,
interactive=interactive,
outdir=outdir,
external_event=eve_file)
elif p.ext == 'eeg':
eeg2fif(filename, interactive=interactive, outdir=outdir)
elif p.ext in ['edf', 'bdf']:
bdf2fif(filename, interactive=interactive, outdir=outdir)
elif p.ext == 'gdf':
gdf2fif(filename,
interactive=interactive,
outdir=outdir,
channel_file=channel_file)
elif p.ext == 'xdf':
xdf2fif(filename, interactive=interactive, outdir=outdir)
else: # unknown format
logger.error(
'Ignored unrecognized file extension %s. It should be [.pcl | .eeg | .gdf | .bdf]'
% p.ext)
def config_run(featfile=None):
if featfile is None or len(featfile.strip()) == 0:
if os.path.exists('good_features.txt'):
featfile = os.path.realpath('good_features.txt').replace('\\', '/')
logger.info('Found %s in the current folder.' % featfile)
else:
featfile = input('Feature file path? ')
feature_info(featfile)
def __init__(self, cfg, viz, tdef, trigger, logfile=None):
self.cfg = cfg
self.tdef = tdef
self.trigger = trigger
self.viz = viz
self.viz.fill()
self.refresh_delay = 1.0 / self.cfg.REFRESH_RATE
self.bar_step_left = self.cfg.BAR_STEP['left']
self.bar_step_right = self.cfg.BAR_STEP['right']
self.bar_step_up = self.cfg.BAR_STEP['up']
self.bar_step_down = self.cfg.BAR_STEP['down']
self.bar_step_both = self.cfg.BAR_STEP['both']
if type(self.cfg.BAR_BIAS) is tuple:
self.bar_bias = list(self.cfg.BAR_BIAS)
else:
self.bar_bias = self.cfg.BAR_BIAS
# New decoder: already smoothed by the decoder so bias after.
#self.alpha_old = self.cfg.PROB_ACC_ALPHA
#self.alpha_new = 1.0 - self.cfg.PROB_ACC_ALPHA
if hasattr(self.cfg,
'BAR_REACH_FINISH') and self.cfg.BAR_REACH_FINISH == True:
self.premature_end = True
else:
self.premature_end = False
self.tm_trigger = qc.Timer()
self.tm_display = qc.Timer()
self.tm_watchdog = qc.Timer()
if logfile is not None:
self.logf = open(logfile, 'w')
else:
self.logf = None
# STIMO only
if self.cfg.WITH_STIMO is True:
if self.cfg.STIMO_COMPORT is None:
atens = [x for x in serial.tools.list_ports.grep('ATEN')]
if len(atens) == 0:
raise RuntimeError('No ATEN device found. Stop.')
try:
self.stimo_port = atens[0].device
except AttributeError: # depends on Python distribution
self.stimo_port = atens[0][0]
else:
self.stimo_port = self.cfg.STIMO_COMPORT
self.ser = serial.Serial(self.stimo_port, self.cfg.STIMO_BAUDRATE)
logger.info('STIMO serial port %s is_open = %s' %
(self.stimo_port, self.ser.is_open))
# FES only
if self.cfg.WITH_FES is True:
self.stim = fes.Motionstim8()
self.stim.OpenSerialPort(self.cfg.FES_COMPORT)
self.stim.InitializeChannelListMode()
logger.info('Opened FES serial port')
def fit_predict_thres(cls,
X_train,
Y_train,
X_test,
Y_test,
cnum,
label_list,
ignore_thres=None,
decision_thres=None):
"""
Any likelihood lower than a threshold is not counted as classification score
Confusion matrix, accuracy and F1 score (macro average) are computed.
Params
======
ignore_thres:
if not None or larger than 0, likelihood values lower than ignore_thres will be ignored
while computing confusion matrix.
"""
timer = qc.Timer()
cls.fit(X_train, Y_train)
assert ignore_thres is None or ignore_thres >= 0
if ignore_thres is None or ignore_thres == 0:
Y_pred = cls.predict(X_test)
score = skmetrics.accuracy_score(Y_test, Y_pred)
cm = skmetrics.confusion_matrix(Y_test, Y_pred, label_list)
f1 = skmetrics.f1_score(Y_test, Y_pred, average='macro')
else:
if decision_thres is not None:
logger.error(
'decision threshold and ignore_thres cannot be set at the same time.'
)
raise ValueError
Y_pred = cls.predict_proba(X_test)
Y_pred_labels = np.argmax(Y_pred, axis=1)
Y_pred_maxes = np.array([x[i] for i, x in zip(Y_pred_labels, Y_pred)])
Y_index_overthres = np.where(Y_pred_maxes >= ignore_thres)[0]
Y_index_underthres = np.where(Y_pred_maxes < ignore_thres)[0]
Y_pred_overthres = np.array(
[cls.classes_[x] for x in Y_pred_labels[Y_index_overthres]])
Y_pred_underthres = np.array(
[cls.classes_[x] for x in Y_pred_labels[Y_index_underthres]])
Y_pred_underthres_count = np.array(
[np.count_nonzero(Y_pred_underthres == c) for c in label_list])
Y_test_overthres = Y_test[Y_index_overthres]
score = skmetrics.accuracy_score(Y_test_overthres, Y_pred_overthres)
cm = skmetrics.confusion_matrix(Y_test_overthres, Y_pred_overthres,
label_list)
cm = np.concatenate((cm, Y_pred_underthres_count[:, np.newaxis]),
axis=1)
f1 = skmetrics.f1_score(Y_test_overthres,
Y_pred_overthres,
average='macro')
logger.info('Cross-validation %d (%.3f) - %.1f sec' %
(cnum, score, timer.sec()))
return score, cm, f1
def balance_samples(X, Y, balance_type, verbose=False):
if balance_type == 'OVER':
"""
Oversample from classes that lack samples
"""
label_set = np.unique(Y)
max_set = []
X_balanced = np.array(X)
Y_balanced = np.array(Y)
# find a class with maximum number of samples
for c in label_set:
yl = np.where(Y == c)[0]
if len(max_set) == 0 or len(yl) > max_set[1]:
max_set = [c, len(yl)]
for c in label_set:
if c == max_set[0]: continue
yl = np.where(Y == c)[0]
extra_samples = max_set[1] - len(yl)
extra_idx = np.random.choice(yl, extra_samples)
X_balanced = np.append(X_balanced, X[extra_idx], axis=0)
Y_balanced = np.append(Y_balanced, Y[extra_idx], axis=0)
elif balance_type == 'UNDER':
"""
Undersample from classes that are excessive
"""
label_set = np.unique(Y)
min_set = []
# find a class with minimum number of samples
for c in label_set:
yl = np.where(Y == c)[0]
if len(min_set) == 0 or len(yl) < min_set[1]:
min_set = [c, len(yl)]
yl = np.where(Y == min_set[0])[0]
X_balanced = np.array(X[yl])
Y_balanced = np.array(Y[yl])
for c in label_set:
if c == min_set[0]: continue
yl = np.where(Y == c)[0]
reduced_idx = np.random.choice(yl, min_set[1])
X_balanced = np.append(X_balanced, X[reduced_idx], axis=0)
Y_balanced = np.append(Y_balanced, Y[reduced_idx], axis=0)
elif balance_type is None or balance_type is False:
return X, Y
else:
logger.error('Unknown balancing type %s' % balance_type)
raise ValueError
logger.info_green('\nNumber of samples after %ssampling' %
balance_type.lower())
for c in label_set:
logger.info(
'%s: %d -> %d' %
(c, len(np.where(Y == c)[0]), len(np.where(Y_balanced == c)[0])))
return X_balanced, Y_balanced
def raw2mat(infile, outfile):
'''
Convert raw data file to MATLAB file
'''
raw, events = load_raw(infile)
header = dict(bads=raw.info['bads'], ch_names=raw.info['ch_names'],\
sfreq=raw.info['sfreq'], events=events)
scipy.io.savemat(outfile, dict(signals=raw._data, header=header))
logger.info('Exported to %s' % outfile)
def set_pin(self, pin):
if self.lpttype == 'SOFTWARE':
logger.error('set_pin() not supported for software trigger.')
return False
elif self.lpttype == 'FAKE':
logger.info('FAKE trigger pin %s' % pin)
return True
else:
self.set_data(2**(pin - 1))
def signal_off(self):
if self.lpttype == 'SOFTWARE':
return self.write_event(0)
elif self.lpttype == 'FAKE':
logger.info('FAKE trigger off')
return True
else:
self.set_data(0)
self.offtimer = threading.Timer(self.delay, self.signal_off)
def __del__(self):
# STIMO only
if self.cfg.WITH_STIMO is True:
self.ser.close()
logger.info('Closed STIMO serial port %s' % self.stimo_port)
# FES only
if self.cfg.WITH_FES is True:
stim_code = [0, 0, 0, 0, 0, 0, 0, 0]
self.stim.UpdateChannelSettings(stim_code)
self.stim.CloseSerialPort()
logger.info('Closed FES serial port')
def get_predict_proba(cls, X_train, Y_train, X_test, Y_test, cnum):
"""
All likelihoods will be collected from every fold of a cross-validaiton. Based on these likelihoods,
a threshold will be computed that will balance the true positive rate of each class.
Available with binary classification scenario only.
"""
timer = qc.Timer()
cls.fit(X_train, Y_train)
Y_pred = cls.predict_proba(X_test)
logger.info('Cross-validation %d (%d tests) - %.1f sec' %
(cnum, Y_pred.shape[0], timer.sec()))
return Y_pred[:, 0]
def config_run(featfile=None, topo_layout_file=None):
if featfile is None or len(featfile.strip()) == 0:
if os.path.exists('good_features.txt'):
featfile = os.path.realpath('good_features.txt').replace('\\', '/')
logger.info('Found %s in the current folder.' % featfile)
else:
featfile = input('Feature file path? ')
if topo_layout_file is None or len(topo_layout_file.strip()) == 0:
topo_layout_file = 'antneuro_64ch.lay'
feature_importances(featfile, topo_layout_file)
def cva_features(datadir):
"""
(DEPRECATED FUNCTION)
"""
for fin in qc.get_file_list(datadir, fullpath=True):
if fin[-4:] != '.gdf': continue
fout = fin + '.cva'
if os.path.exists(fout):
logger.info('Skipping', fout)
continue
logger.info("cva_features('%s')" % fin)
qc.matlab("cva_features('%s')" % fin)
def fif_resample(fif_dir, sfreq_target):
out_dir = fif_dir + '/fif_resample%d' % sfreq_target
qc.make_dirs(out_dir)
for f in qc.get_file_list(fif_dir):
pp = qc.parse_path(f)
if pp.ext != 'fif':
continue
logger.info('Resampling %s' % f)
raw, events = pu.load_raw(f)
raw.resample(sfreq_target)
fif_out = '%s/%s.fif' % (out_dir, pp.name)
raw.save(fif_out)
logger.info('Exported to %s' % fif_out)
def read_eeg(self):
# if self.updating==True: print( '##### ERROR: thread destroyed ? ######' )
# self.updating= True
try:
# data, self.ts_list= self.sr.inlets[0].pull_chunk(max_samples=self.config['sf']) # [frames][channels]
data, self.ts_list = self.sr.acquire(blocking=False)
# TODO: check and change to these two lines
#self.sr.acquire(blocking=False, decim=DECIM)
#data, self.ts_list = self.sr.get_window()
if len(self.ts_list) == 0:
# self.eeg= None
# self.tri= None
return
n = self.config['eeg_channels']
'''
x= np.array( data )
trg_ch= self.config['tri_channels']
if trg_ch is not None:
self.tri= np.reshape( x[:,trg_ch], (-1,1) ) # samples x 1
self.eeg= np.reshape( x[:,self.sr.eeg_channels], (-1,n) ) # samples x channels
'''
trg_ch = self.config['tri_channels']
if trg_ch is not None:
self.tri = np.reshape(data[:, trg_ch], (-1, 1)) # samples x 1
self.eeg = np.reshape(data[:, self.sr.eeg_channels],
(-1, n)) # samples x channels
if DEBUG_TRIGGER:
# show trigger value
try:
trg_value = max(self.tri)
if trg_value > 0:
logger.info('Received trigger %s' % trg_value)
except:
logger.exception('Error! self.tri = %s' % self.tri)
# Read exg. self.config.samples*self.config.exg_ch, type float
# bexg = np.random.rand( 1, self.config['samples'] * self.config['exg_channels'] )
# self.exg = np.reshape(list(bexg), (self.config['samples'],self.config['exg_channels']))
except WindowsError:
# print('**** Access violation in read_eeg():\n%s\n%s'% (sys.exc_info()[0], sys.exc_info()[1]))
pass
except:
logger.exception()
pdb.set_trace()
def main(input_dir, channel_file=None):
count = 0
for f in qc.get_file_list(input_dir, fullpath=True, recursive=True):
p = qc.parse_path(f)
outdir = p.dir + '/fif/'
if p.ext in ['pcl', 'bdf', 'edf', 'gdf', 'eeg', 'xdf']:
logger.info('Converting %s' % f)
any2fif(f,
interactive=True,
outdir=outdir,
channel_file=channel_file)
count += 1
logger.info('%d files converted.' % count)
def convert2mat(filename, matfile):
"""
Convert to mat using MATLAB BioSig sload().
"""
basename = '.'.join(filename.split('.')[:-1])
# extension= filename.split('.')[-1]
matfile = basename + '.mat'
if not os.path.exists(matfile):
logger.info('Converting input to mat file')
run = "[sig,header]=sload('%s'); save('%s.mat','sig','header');" % (
filename, basename)
qc.matlab(run)
if not os.path.exists(matfile):
logger.error('mat file convertion error.')
sys.exit()
def stop(self):
"""
Stop the daemon
"""
if self.is_running() == 0:
logger.warning('Decoder already stopped.')
return
for running in self.running:
running.value = 0
for proc in self.procs:
proc.join(10)
if proc.is_alive():
logger.warning('Process %s did not die properly.' % proc.pid())
self.reset()
logger.info(self.stopmsg)
def set_data(self, value):
if self.lpttype == 'SOFTWARE':
logger.error('set_data() not supported for software trigger.')
return False
elif self.lpttype == 'FAKE':
logger.info('FAKE trigger value %s' % value)
return True
else:
if self.lpttype == 'USB2LPT':
self.lpt.setdata(value)
elif self.lpttype == 'DESKTOP':
self.lpt.setdata(self.portaddr, value)
elif self.lpttype == 'ARDUINO':
self.ser.write(bytes([value]))
else:
raise RuntimeError('Wrong trigger device')
def start(self):
"""
Start the daemon
"""
if self.is_running() > 0:
msg = 'Cannot start. Daemon already running. (PID' + ', '.join(
['%d' % proc.pid for proc in self.procs]) + ')'
logger.error(msg)
return
for proc in self.procs:
proc.start()
if self.wait_init:
for running in self.running:
while running.value == 0:
time.sleep(0.001)
logger.info(self.startmsg)
def init_loop(self):
self.updating = False
self.sr = StreamReceiver(window_size=1,
buffer_size=10,
amp_serial=self.amp_serial,
amp_name=self.amp_name)
srate = int(self.sr.sample_rate)
# n_channels= self.sr.channels
# 12 unsigned ints (4 bytes)
########## TODO: assumkng 32 samples chunk => make it read from LSL header
data = [
'EEG', srate, ['L', 'R'], 32,
len(self.sr.get_eeg_channels()), 0,
self.sr.get_trigger_channel(), None, None, None, None, None
]
logger.info('Trigger channel is %d' % self.sr.get_trigger_channel())
self.config = {
'id': data[0],
'sf': data[1],
'labels': data[2],
'samples': data[3],
'eeg_channels': data[4],
'exg_channels': data[5],
'tri_channels': data[6],
'eeg_type': data[8],
'exg_type': data[9],
'tri_type': data[10],
'lbl_type': data[11],
'tim_size': 1,
'idx_size': 1
}
self.tri = np.zeros(self.config['samples'])
self.last_tri = 0
self.eeg = np.zeros(
(self.config['samples'], self.config['eeg_channels']),
dtype=np.float)
self.exg = np.zeros(
(self.config['samples'], self.config['exg_channels']),
dtype=np.float)
self.ts_list = []
self.ts_list_tri = []
def fif2mat(data_dir):
out_dir = '%s/mat_files' % data_dir
qc.make_dirs(out_dir)
for rawfile in qc.get_file_list(data_dir, fullpath=True):
if rawfile[-4:] != '.fif': continue
raw, events = pu.load_raw(rawfile)
events[:, 0] += 1 # MATLAB uses 1-based indexing
sfreq = raw.info['sfreq']
data = dict(signals=raw._data,
events=events,
sfreq=sfreq,
ch_names=raw.ch_names)
fname = qc.parse_path(rawfile).name
matfile = '%s/%s.mat' % (out_dir, fname)
scipy.io.savemat(matfile, data)
logger.info('Exported to %s' % matfile)
logger.info('Finished exporting.')
def shell():
"""
Enter interactive shell within the caller's scope
"""
logger.info('*** Entering interactive shell. Ctrl+D to return. ***')
stack = inspect.stack()
try: # globals are first loaded, then overwritten by locals
globals_ = {}
globals_.update(
{key: value
for key, value in stack[1][0].f_globals.items()})
globals_.update(
{key: value
for key, value in stack[1][0].f_locals.items()})
finally:
del stack
code.InteractiveConsole(globals_).interact()
def __init__(self,
amp_name,
amp_serial,
state=mp.Value('i', 1),
queue=None):
super(Scope, self).__init__()
self.ui = Ui_MainWindow()
self.ui.setupUi(self)
redirect_stdout_to_queue(logger, queue, 'INFO')
logger.info('Viewer launched')
self.amp_name = amp_name
self.amp_serial = amp_serial
self.state = state
self.init_scope()
def _log_decoding_helper(state, event_queue, amp_name=None, autostop=False):
"""
Helper function to run StreamReceiver object in background
Parameters
----------
state : mp.Value
The multiprocessing sharing variable
event_queue : mp.Queue
The queue used to share new events
amp_name : str
The stream name to connect to
autostop : bool
If True, automatically finish when no more data is received.
"""
logger.info('Event acquisition subprocess started.')
# wait for the start signal
while state.value == 0:
time.sleep(0.01)
# acquire event values and returns event times and event values
sr = StreamReceiver(bufsize=0, stream_name=amp_name)
tm = Timer(autoreset=True)
started = False
while state.value == 1:
chunk, ts_list = sr.acquire()
if autostop:
if started is True:
if len(ts_list) == 0:
state.value = 0
break
elif len(ts_list) > 0:
started = True
tm.sleep_atleast(0.001)
logger.info('Event acquisition subprocess finishing up ...')
buffers, times = sr.get_buffer()
events = buffers[:, 0] # first channel is the trigger channel
event_index = np.where(events != 0)[0]
event_times = times[event_index].reshape(-1).tolist()
event_values = events[event_index].tolist()
assert len(event_times) == len(event_values)
event_queue.put((event_times, event_values))
def run_multi(cmd_list, cores=0, quiet=False):
"""
Input
-----
cmd_list: list of commands just like when you type on bash
cores: number of cores to use (use all cores if 0)
Logging tip: "command args > log.txt 2>&1"
"""
if cores == 0: cores = mp.cpu_count()
pool = mp.Pool(cores)
processes = []
for c in cmd_list:
if not quiet:
logger.info(cmd)
processes.append(pool.apply_async(os.system, [cmd]))
for proc in processes:
proc.get()
pool.close()
pool.join()
def export_topo(data,
pos,
pngfile,
xlabel='',
vmin=None,
vmax=None,
chan_vis=None,
res=64,
contours=0):
mne.viz.plot_topomap(data,
pos,
names=chan_vis,
show_names=True,
res=res,
contours=contours,
show=False)
plt.suptitle(xlabel)
plt.savefig(pngfile)
logger.info('Exported %s' % pngfile)