def feature_importances_topo(featfile,
topo_layout_file=None,
channels=None,
channel_name_show=None):
"""
Compute feature importances across frequency bands and channels
@params
topo_laytout_file: if not None, topography map images will be generated and saved.
channel_name_show: list of channel names to show on topography map.
"""
print('Loading %s' % featfile)
if channels is None:
channel_set = set()
with open(featfile) as f:
f.readline()
for l in f:
ch = l.strip().split('\t')[1]
channel_set.add(ch)
channels = list(channel_set)
# channel index lookup table
ch2index = {ch: i for i, ch in enumerate(channels)}
data_delta = np.zeros(len(channels))
data_theta = np.zeros(len(channels))
data_mu = np.zeros(len(channels))
data_beta = np.zeros(len(channels))
data_beta1 = np.zeros(len(channels))
data_beta2 = np.zeros(len(channels))
data_beta3 = np.zeros(len(channels))
data_lgamma = np.zeros(len(channels))
data_hgamma = np.zeros(len(channels))
data_per_ch = np.zeros(len(channels))
f = open(featfile)
f.readline()
for l in f:
token = l.strip().split('\t')
importance = float(token[0])
ch = token[1]
fq = float(token[2])
if fq <= 3:
data_delta[ch2index[ch]] += importance
elif fq <= 7:
data_theta[ch2index[ch]] += importance
elif fq <= 12:
data_mu[ch2index[ch]] += importance
elif fq <= 30:
data_beta[ch2index[ch]] += importance
elif fq <= 70:
data_lgamma[ch2index[ch]] += importance
else:
data_hgamma[ch2index[ch]] += importance
if 12.5 <= fq <= 16:
data_beta1[ch2index[ch]] += importance
elif fq <= 20:
data_beta2[ch2index[ch]] += importance
elif fq <= 28:
data_beta3[ch2index[ch]] += importance
data_per_ch[ch2index[ch]] += importance
hlen = 18 + len(channels) * 7
result = '>> Feature importance distribution\n'
result += 'bands ' + qc.list2string(channels,
'%6s') + ' | ' + 'per band\n'
result += '-' * hlen + '\n'
result += 'delta ' + qc.list2string(
data_delta, '%6.2f') + ' | %6.2f\n' % np.sum(data_delta)
result += 'theta ' + qc.list2string(
data_theta, '%6.2f') + ' | %6.2f\n' % np.sum(data_theta)
result += 'mu ' + qc.list2string(
data_mu, '%6.2f') + ' | %6.2f\n' % np.sum(data_mu)
#result += 'beta ' + qc.list2string(data_beta, '%6.2f') + ' | %6.2f\n' % np.sum(data_beta)
result += 'beta1 ' + qc.list2string(
data_beta1, '%6.2f') + ' | %6.2f\n' % np.sum(data_beta1)
result += 'beta2 ' + qc.list2string(
data_beta2, '%6.2f') + ' | %6.2f\n' % np.sum(data_beta2)
result += 'beta3 ' + qc.list2string(
data_beta3, '%6.2f') + ' | %6.2f\n' % np.sum(data_beta3)
result += 'lgamma ' + qc.list2string(
data_lgamma, '%6.2f') + ' | %6.2f\n' % np.sum(data_lgamma)
result += 'hgamma ' + qc.list2string(
data_hgamma, '%6.2f') + ' | %6.2f\n' % np.sum(data_hgamma)
result += '-' * hlen + '\n'
result += 'per_ch ' + qc.list2string(data_per_ch, '%6.2f') + ' | 100.00\n'
print(result)
p = qc.parse_path(featfile)
open('%s/%s_summary.txt' % (p.dir, p.name), 'w').write(result)
# export topo maps
if topo_layout_file is not None:
# default visualization setting
res = 64
contours = 6
# select channel names to show
if channel_name_show is None:
channel_name_show = channels
chan_vis = [''] * len(channels)
for ch in channel_name_show:
chan_vis[channels.index(ch)] = ch
# set channel locations and reverse lookup table
chanloc = {}
if not os.path.exists(topo_layout_file):
topo_layout_file = PYCNBI_ROOT + '/layout/' + topo_layout_file
if not os.path.exists(topo_layout_file):
raise FileNotFoundError('Layout file %s not found.' %
topo_layout_file)
print('Using layout %s' % topo_layout_file)
for l in open(topo_layout_file):
token = l.strip().split('\t')
ch = token[5]
x = float(token[1])
y = float(token[2])
chanloc[ch] = [x, y]
pos = np.zeros((len(channels), 2))
for i, ch in enumerate(channels):
pos[i] = chanloc[ch]
vmin = min(data_per_ch)
vmax = max(data_per_ch)
total = sum(data_per_ch)
rate_delta = sum(data_delta) * 100.0 / total
rate_theta = sum(data_theta) * 100.0 / total
rate_mu = sum(data_mu) * 100.0 / total
rate_beta = sum(data_beta) * 100.0 / total
rate_beta1 = sum(data_beta1) * 100.0 / total
rate_beta2 = sum(data_beta2) * 100.0 / total
rate_beta3 = sum(data_beta3) * 100.0 / total
rate_lgamma = sum(data_lgamma) * 100.0 / total
rate_hgamma = sum(data_hgamma) * 100.0 / total
export_topo(data_per_ch,
pos,
'features_topo_all.png',
xlabel='all bands 1-40 Hz',
chan_vis=chan_vis)
export_topo(data_delta,
pos,
'features_topo_delta.png',
xlabel='delta 1-3 Hz (%.1f%%)' % rate_delta,
chan_vis=chan_vis)
export_topo(data_theta,
pos,
'features_topo_theta.png',
xlabel='theta 4-7 Hz (%.1f%%)' % rate_theta,
chan_vis=chan_vis)
export_topo(data_mu,
pos,
'features_topo_mu.png',
xlabel='mu 8-12 Hz (%.1f%%)' % rate_mu,
chan_vis=chan_vis)
export_topo(data_beta,
pos,
'features_topo_beta.png',
xlabel='beta 13-30 Hz (%.1f%%)' % rate_beta,
chan_vis=chan_vis)
export_topo(data_beta1,
pos,
'features_topo_beta1.png',
xlabel='beta 12.5-16 Hz (%.1f%%)' % rate_beta1,
chan_vis=chan_vis)
export_topo(data_beta2,
pos,
'features_topo_beta2.png',
xlabel='beta 16-20 Hz (%.1f%%)' % rate_beta2,
chan_vis=chan_vis)
export_topo(data_beta3,
pos,
'features_topo_beta3.png',
xlabel='beta 20-28 Hz (%.1f%%)' % rate_beta3,
chan_vis=chan_vis)
export_topo(data_lgamma,
pos,
'features_topo_lowgamma.png',
xlabel='low gamma 31-40 Hz (%.1f%%)' % rate_lgamma,
chan_vis=chan_vis)
def run(file_flag):
# Shimer MAC addresses
shimm_addr = [
"00:06:66:46:B7:D4"
] # , "00:06:66:46:B6:4A"]#, "00:06:66:46:BD:8D", "00:06:66:46:9A:1A", "00:06:66:46:BD:BF"]
emg_addr = [] # ["00:06:66:46:9A:1A", "00:06:66:46:BD:BF"]
# Configuration parameters
scan_flag = 1
plot_flag = 0
sock_port = 1
nodes = []
plt_axx = 500
plt_ylim = 4000
plt_rate = 20
rng_size = 50
# rng_acc_x=RingBuffer(50)
# Add sample to ringbuffer
# rng_acc_x.append(pack_0)
# buff1= np.zeros((n_nodes,10,rng_size),dtype=np.int)
# buff2= np.zeros((n_nodes,10,rng_size),dtype=np.int)
# buff_flag= 1
# buff= [[[0 for x in range(10)] for y in range(2)] for z in range(rng_size)]
# buff_idx= 0
if plot_flag == 1:
# plot parameters
sample_idx = 0
analogData = AnalogData(plt_axx)
# Get the list of available nodes
if scan_flag == 0:
target_addr = shimm_addr
else:
try:
target_addr = []
print("Scanning bluetooth devices...")
nearby_devices = bluetooth.discover_devices()
for bdaddr in nearby_devices:
print(" " + str(bdaddr) + " - " +
bluetooth.lookup_name(bdaddr))
if bdaddr in shimm_addr:
target_addr.append(bdaddr)
except:
print("[Error] Problem while scanning bluetooth")
sys.exit(1)
n_nodes = len(target_addr)
if n_nodes > 0:
print(("Found %d target Shimmer nodes") % (len(target_addr)))
else:
print("Could not find target bluetooth device nearby. Exiting")
sys.exit(1)
print("Configuring the nodes...")
for node_idx, bdaddr in enumerate(target_addr):
try:
# Connecting to the sensors
sock = bluetooth.BluetoothSocket(bluetooth.RFCOMM)
if bdaddr in emg_addr:
n = shimmer_node(bdaddr, sock, 0x2)
else:
n = shimmer_node(bdaddr, sock, 0x1)
nodes.append(n)
print((bdaddr, sock_port), end=' ')
nodes[-1].sock.connect((bdaddr, sock_port))
print(" Shimmer %d (" % (node_idx) +
bluetooth.lookup_name(bdaddr) + ") [Connected]")
# send the set sensors command
nodes[-1].sock.send(
struct.pack('BBB', 0x08, nodes[-1].senscfg_hi,
nodes[-1].senscfg_lo))
nodes[-1].wait_for_ack()
# send the set sampling rate command
nodes[-1].sock.send(struct.pack('BB', 0x05, 0x14)) # 51.2Hz
nodes[-1].wait_for_ack()
# Inquiry command
print(" Shimmer %d (" % (node_idx) +
bluetooth.lookup_name(bdaddr) + ") [Configured]")
nodes[-1].sock.send(struct.pack('B', 0x01))
nodes[-1].wait_for_ack()
inq = nodes[-1].read_inquiry()
except bluetooth.btcommon.BluetoothError as e:
print(("BluetoothError during read_data: {0}".format(e.strerror)))
print("Unable to connect to the nodes. Exiting")
sys.exit(1)
# Create file and plot
try:
if file_flag == 1:
# Create buffer
now = datetime.datetime.now()
qc.makeDirs('../DATA')
logname = "../DATA/IMU_" + now.strftime("%Y%m%d%H%M") + ".log"
print("[cnbi_shimmer] Creating file: %s" % (logname))
outfile = open(logname, "w")
for node_idx, shim in enumerate(nodes):
outfile.write(str(node_idx) + ": " + str(shim.addr) + "\n")
outfile.close()
fname = "../DATA/IMU_" + now.strftime("%Y%m%d%H%M") + ".dat"
print("[cnbi_shimmer] Creating file: %s" % (fname))
outfile = open(fname, "w")
# Create plot
if plot_flag == 1:
analogPlot = AnalogPlot(analogData)
plt.axis([0, plt_axx, 0, plt_ylim])
plt.ion()
plt.show()
except:
print("[Error]: Error creating file/plot!! Exiting")
# close the socket
print("Closing nodes")
for node_idx, shim in enumerate(nodes):
shim.sock.close()
print(" Shimmer %d [Ok]" % (node_idx))
sys.exit(1)
print(
"[cnbi_shimmer] Recording started. Press Ctrl+C to finish recording.")
# send start streaming command
for shim in nodes:
shim.sock.send(struct.pack('B', 0x07))
for node_idx, shim in enumerate(nodes):
shim.wait_for_ack()
shim.up = 1
print(" Shimmer %d [Ok]" % (node_idx))
# Main acquisition loop
while True:
try:
sample = []
sample_lslclock = []
for shim in nodes:
if shim.up == 1:
sample.append(shim.read_data())
else:
sample.append([0] * (shim.n_fields))
for samp in sample:
sample_lslclock.append([pylsl.local_clock()] + list(samp[1:]))
if file_flag == 1:
simplejson.dump(sample_lslclock,
outfile,
separators=(',', ';'))
outfile.write('\n')
# print sample
# plt.title(str(sample[0][0]))
# leeq
if plot_flag == 1:
analogData.add([sample[0][1], sample[0][2]])
sample_idx = sample_idx + 1
if sample_idx % plt_rate == 0:
analogPlot.update(analogData)
if file_flag == 0:
print(qc.list2string(sample_lslclock[0], '%9.1f', ' '))
# Exit if key is pressed
except KeyboardInterrupt:
print("\n[cnbi_shimmer] Stopping acquisition....")
break
except bluetooth.btcommon.BluetoothError as e:
print(("[Error] BluetoothError during read_data: {0}".format(
e.strerror)))
# send stop streaming command
print("[cnbi_shimmer] Stopping streaming")
try:
for shim in nodes:
shim.sock.send(struct.pack('B', 0x20))
for node_idx, shim in enumerate(nodes):
shim.wait_for_ack()
print(" Shimmer %d [Ok]" % (node_idx))
except bluetooth.btcommon.BluetoothError as e:
print(("[Error] BluetoothError during read_data: {0}".format(
e.strerror)))
'''
n_nodes = len(target_addr)
while n_nodes>0:
sample= []
for node_idx,shim in enumerate(nodes):
pckt= shim.wait_stop_streaming()
print " Shimmer %d [waiting]" % (node_idx)
if len(pckt) != 1:
sample.append(pckt)
else:
sample.append(str("0"*(shim.samplesize)))
nodes.remove(shim)
n_nodes= n_nodes-1
print " Shimmer %d [Ok]" % (node_idx)
simplejson.dump(sample, outfile, separators=(',',';'))
analogData.add([sample[0][1],sample[1][1]])
analogPlot.update(analogData)
'''
# Closing file
if file_flag == 1:
print("[cnbi_shimmer] Closing file: %s" % (fname))
try:
outfile.close()
except:
print(" [Error] Problem closing file!")
# close the socket
print("[cnbi_shimmer] Closing nodes")
for node_idx, shim in enumerate(nodes):
shim.sock.close()
print(" Shimmer %d [Ok]" % (node_idx))
print("[cnbi_shimmer] Recording Finished. Please close this window.")
getch()
def classify(self,
decoder,
true_label,
title_text,
bar_dirs,
state='start',
prob_history=None):
"""
Run a single trial
"""
true_label_index = bar_dirs.index(true_label)
self.tm_trigger.reset()
if self.bar_bias is not None:
bias_idx = bar_dirs.index(self.bar_bias[0])
if self.logf is not None:
self.logf.write('True label: %s\n' % true_label)
tm_classify = qc.Timer(autoreset=True)
self.stimo_timer = qc.Timer()
while True:
self.tm_display.sleep_atleast(self.refresh_delay)
self.tm_display.reset()
if state == 'start' and self.tm_trigger.sec(
) > self.cfg.TIMINGS['INIT']:
state = 'gap_s'
if self.cfg.TRIALS_PAUSE:
self.viz.put_text('Press any key')
self.viz.update()
key = cv2.waitKeyEx()
if key == KEYS['esc'] or not self.protocol_state.value:
return
self.viz.fill()
self.tm_trigger.reset()
self.trigger.signal(self.tdef.INIT)
elif state == 'gap_s':
if self.cfg.TIMINGS['GAP'] > 0:
self.viz.put_text(title_text)
state = 'gap'
self.tm_trigger.reset()
elif state == 'gap' and self.tm_trigger.sec(
) > self.cfg.TIMINGS['GAP']:
state = 'cue'
self.viz.fill()
self.viz.draw_cue()
self.viz.glass_draw_cue()
self.trigger.signal(self.tdef.CUE)
self.tm_trigger.reset()
elif state == 'cue' and self.tm_trigger.sec(
) > self.cfg.TIMINGS['READY']:
state = 'dir_r'
if self.cfg.SHOW_CUE is True:
if self.cfg.FEEDBACK_TYPE == 'BAR':
self.viz.move(true_label,
100,
overlay=False,
barcolor='G')
elif self.cfg.FEEDBACK_TYPE == 'BODY':
self.viz.put_text(DIRS[true_label], 'R')
if true_label == 'L': # left
self.trigger.signal(self.tdef.LEFT_READY)
elif true_label == 'R': # right
self.trigger.signal(self.tdef.RIGHT_READY)
elif true_label == 'U': # up
self.trigger.signal(self.tdef.UP_READY)
elif true_label == 'D': # down
self.trigger.signal(self.tdef.DOWN_READY)
elif true_label == 'B': # both hands
self.trigger.signal(self.tdef.BOTH_READY)
else:
raise RuntimeError('Unknown direction %s' % true_label)
self.tm_trigger.reset()
'''
if self.cfg.FEEDBACK_TYPE == 'BODY':
self.viz.set_pc_feedback(False)
self.viz.move(true_label, 100, overlay=False, barcolor='G')
if self.cfg.FEEDBACK_TYPE == 'BODY':
self.viz.set_pc_feedback(True)
if self.cfg.SHOW_CUE is True:
self.viz.put_text(dirs[true_label], 'R')
if true_label == 'L': # left
self.trigger.signal(self.tdef.LEFREADY)
elif true_label == 'R': # right
self.trigger.signal(self.tdef.RIGHT_READY)
elif true_label == 'U': # up
self.trigger.signal(self.tdef.UP_READY)
elif true_label == 'D': # down
self.trigger.signal(self.tdef.DOWN_READY)
elif true_label == 'B': # both hands
self.trigger.signal(self.tdef.BOTH_READY)
else:
raise RuntimeError('Unknown direction %s' % true_label)
self.tm_trigger.reset()
'''
elif state == 'dir_r' and self.tm_trigger.sec(
) > self.cfg.TIMINGS['DIR_CUE']:
self.viz.fill()
self.viz.draw_cue()
self.viz.glass_draw_cue()
state = 'dir'
# initialize bar scores
bar_label = bar_dirs[0]
bar_score = 0
probs = [1.0 / len(bar_dirs)] * len(bar_dirs)
self.viz.move(bar_label, bar_score, overlay=False)
probs_acc = np.zeros(len(probs))
if true_label == 'L': # left
self.trigger.signal(self.tdef.LEFT_GO)
elif true_label == 'R': # right
self.trigger.signal(self.tdef.RIGHT_GO)
elif true_label == 'U': # up
self.trigger.signal(self.tdef.UP_GO)
elif true_label == 'D': # down
self.trigger.signal(self.tdef.DOWN_GO)
elif true_label == 'B': # both
self.trigger.signal(self.tdef.BOTH_GO)
else:
raise RuntimeError('Unknown truedirection %s' % true_label)
self.tm_watchdog.reset()
self.tm_trigger.reset()
elif state == 'dir':
if self.tm_trigger.sec() > self.cfg.TIMINGS['CLASSIFY'] or (
self.premature_end and bar_score >= 100):
if not hasattr(
self.cfg,
'SHOW_RESULT') or self.cfg.SHOW_RESULT is True:
# show classfication result
if self.cfg.WITH_STIMO is True:
if self.cfg.STIMO_FULLGAIT_CYCLE is not None and bar_label == 'U':
res_color = 'G'
elif self.cfg.TRIALS_RETRY is False or bar_label == true_label:
res_color = 'G'
else:
res_color = 'Y'
else:
res_color = 'Y'
if self.cfg.FEEDBACK_TYPE == 'BODY':
self.viz.move(bar_label,
bar_score,
overlay=False,
barcolor=res_color,
caption=DIRS[bar_label],
caption_color=res_color)
else:
self.viz.move(bar_label,
100,
overlay=False,
barcolor=res_color)
else:
res_color = 'Y'
if self.cfg.FEEDBACK_TYPE == 'BODY':
self.viz.move(bar_label,
bar_score,
overlay=False,
barcolor=res_color,
caption='TRIAL END',
caption_color=res_color)
else:
self.viz.move(bar_label,
0,
overlay=False,
barcolor=res_color)
self.trigger.signal(self.tdef.FEEDBACK)
# STIMO
if self.cfg.WITH_STIMO is True and self.cfg.STIMO_CONTINUOUS is False:
if self.cfg.STIMO_FULLGAIT_CYCLE is not None:
if bar_label == 'U':
self.ser.write(
self.cfg.STIMO_FULLGAIT_PATTERN[0])
logger.info('STIMO: Sent 1')
time.sleep(self.cfg.STIMO_FULLGAIT_CYCLE)
self.ser.write(
self.cfg.STIMO_FULLGAIT_PATTERN[1])
logger.info('STIMO: Sent 2')
time.sleep(self.cfg.STIMO_FULLGAIT_CYCLE)
elif self.cfg.TRIALS_RETRY is False or bar_label == true_label:
if bar_label == 'L':
self.ser.write(b'1')
logger.info('STIMO: Sent 1')
elif bar_label == 'R':
self.ser.write(b'2')
logger.info('STIMO: Sent 2')
if self.cfg.DEBUG_PROBS:
msg = 'DEBUG: Accumulated probabilities = %s' % qc.list2string(
probs_acc, '%.3f')
logger.info(msg)
if self.logf is not None:
self.logf.write(msg + '\n')
if self.logf is not None:
self.logf.write('%s detected as %s (%d)\n\n' %
(true_label, bar_label, bar_score))
self.logf.flush()
# end of trial
state = 'feedback'
self.tm_trigger.reset()
else:
# classify
probs_new = decoder.get_prob_smooth_unread()
if probs_new is None:
if self.tm_watchdog.sec() > 3:
logger.warning(
'No classification being done. Are you receiving data streams?'
)
self.tm_watchdog.reset()
else:
self.tm_watchdog.reset()
if prob_history is not None:
prob_history[true_label].append(
probs_new[true_label_index])
probs_acc += np.array(probs_new)
'''
New decoder: already smoothed by the decoder so bias after.
'''
probs = list(probs_new)
if self.bar_bias is not None:
probs[bias_idx] += self.bar_bias[1]
newsum = sum(probs)
probs = [p / newsum for p in probs]
'''
# Method 2: bias and smoothen
if self.bar_bias is not None:
# print('BEFORE: %.3f %.3f'% (probs_new[0], probs_new[1]) )
probs_new[bias_idx] += self.bar_bias[1]
newsum = sum(probs_new)
probs_new = [p / newsum for p in probs_new]
# print('AFTER: %.3f %.3f'% (probs_new[0], probs_new[1]) )
for i in range(len(probs_new)):
probs[i] = probs[i] * self.alpha_old + probs_new[i] * self.alpha_new
'''
''' Original method
# Method 1: smoothen and bias
for i in range( len(probs_new) ):
probs[i] = probs[i] * self.alpha_old + probs_new[i] * self.alpha_new
# bias bar
if self.bar_bias is not None:
probs[bias_idx] += self.bar_bias[1]
newsum = sum(probs)
probs = [p/newsum for p in probs]
'''
# determine the direction
# TODO: np.argmax(probs)
max_pidx = qc.get_index_max(probs)
max_label = bar_dirs[max_pidx]
if self.cfg.POSITIVE_FEEDBACK is False or \
(self.cfg.POSITIVE_FEEDBACK and true_label == max_label):
dx = probs[max_pidx]
if max_label == 'R':
dx *= self.bar_step_right
elif max_label == 'L':
dx *= self.bar_step_left
elif max_label == 'U':
dx *= self.bar_step_up
elif max_label == 'D':
dx *= self.bar_step_down
elif max_label == 'B':
dx *= self.bar_step_both
else:
logger.debug('Direction %s using bar step %d' %
(max_label, self.bar_step_left))
dx *= self.bar_step_left
# slow start
selected = self.cfg.BAR_SLOW_START['selected']
if self.cfg.BAR_SLOW_START[
selected] and self.tm_trigger.sec(
) < self.cfg.BAR_SLOW_START[selected]:
dx *= self.tm_trigger.sec(
) / self.cfg.BAR_SLOW_START[selected][0]
# add likelihoods
if max_label == bar_label:
bar_score += dx
else:
bar_score -= dx
# change of direction
if bar_score < 0:
bar_score = -bar_score
bar_label = max_label
bar_score = int(bar_score)
if bar_score > 100:
bar_score = 100
if self.cfg.FEEDBACK_TYPE == 'BODY':
if self.cfg.SHOW_CUE:
self.viz.move(bar_label,
bar_score,
overlay=False,
caption=DIRS[true_label],
caption_color='G')
else:
self.viz.move(bar_label,
bar_score,
overlay=False)
else:
self.viz.move(bar_label,
bar_score,
overlay=False)
# send the confidence value continuously
if self.cfg.WITH_STIMO and self.cfg.STIMO_CONTINUOUS:
if self.stimo_timer.sec(
) >= self.cfg.STIMO_COOLOFF:
if bar_label == 'U':
stimo_code = bar_score
else:
stimo_code = 0
self.ser.write(bytes([stimo_code]))
logger.info('Sent STIMO code %d' %
stimo_code)
self.stimo_timer.reset()
if self.cfg.DEBUG_PROBS:
if self.bar_bias is not None:
biastxt = '[Bias=%s%.3f] ' % (
self.bar_bias[0], self.bar_bias[1])
else:
biastxt = ''
msg = '%s%s prob %s acc %s bar %s%d (%.1f ms)' % \
(biastxt, bar_dirs, qc.list2string(probs_new, '%.2f'), qc.list2string(probs, '%.2f'),
bar_label, bar_score, tm_classify.msec())
logger.info(msg)
if self.logf is not None:
self.logf.write(msg + '\n')
elif state == 'feedback' and self.tm_trigger.sec(
) > self.cfg.TIMINGS['FEEDBACK']:
self.trigger.signal(self.tdef.BLANK)
if self.cfg.FEEDBACK_TYPE == 'BODY':
state = 'return'
self.tm_trigger.reset()
else:
state = 'gap_s'
self.viz.fill()
self.viz.update()
return bar_label
elif state == 'return':
self.viz.set_glass_feedback(False)
if self.cfg.WITH_STIMO:
self.viz.move(bar_label,
bar_score,
overlay=False,
barcolor='B')
else:
self.viz.move(bar_label,
bar_score,
overlay=False,
barcolor='Y')
self.viz.set_glass_feedback(True)
bar_score -= 5
if bar_score <= 0:
state = 'gap_s'
self.viz.fill()
self.viz.update()
return bar_label
self.viz.update()
key = cv2.waitKeyEx(1)
if key == KEYS['esc'] or not self.protocol_state.value:
return
elif key == KEYS['space']:
dx = 0
bar_score = 0
probs = [1.0 / len(bar_dirs)] * len(bar_dirs)
self.viz.move(bar_dirs[0], bar_score, overlay=False)
self.viz.update()
logger.info('probs and dx reset.')
self.tm_trigger.reset()
elif key in ARROW_KEYS and ARROW_KEYS[key] in bar_dirs:
# change bias on the fly
if self.bar_bias is None:
self.bar_bias = [ARROW_KEYS[key], BIAS_INCREMENT]
else:
if ARROW_KEYS[key] == self.bar_bias[0]:
self.bar_bias[1] += BIAS_INCREMENT
elif self.bar_bias[1] >= BIAS_INCREMENT:
self.bar_bias[1] -= BIAS_INCREMENT
else:
self.bar_bias = [ARROW_KEYS[key], BIAS_INCREMENT]
if self.bar_bias[1] == 0:
self.bar_bias = None
else:
bias_idx = bar_dirs.index(self.bar_bias[0])
# pick channels
if CHANNEL_PICKS is None:
picks = [
raw.ch_names.index(c) for c in raw.ch_names if c not in EXCLUDES
]
elif type(CHANNEL_PICKS[0]) == str:
picks = [raw.ch_names.index(c) for c in CHANNEL_PICKS]
else:
assert type(CHANNEL_PICKS[0]) is int
picks = CHANNEL_PICKS
# do epoching
for epname, epval in EPOCHS.items():
epochs = mne.Epochs(raw,
events,
dict(epname=epval),
tmin=TMIN,
tmax=TMAX,
proj=False,
picks=picks,
baseline=None,
preload=True)
data = epochs.get_data() # epochs x channels x times
for i, ep_data in enumerate(data):
fout = '%s/%s-%d.txt' % (out_path, epname, i + 1)
with open(fout, 'w') as f:
for t in range(ep_data.shape[1]):
f.write(qc.list2string(ep_data[:, t], '%.6f') + '\n')
print('Exported %s' % fout)
def classify(self,
decoder,
true_label,
title_text,
bar_dirs,
state='start'):
"""
Run a single trial
"""
self.tm_trigger.reset()
if self.bar_bias is not None:
bias_idx = bar_dirs.index(self.bar_bias[0])
if self.logf is not None:
self.logf.write('True label: %s\n' % true_label)
tm_classify = qc.Timer()
while True:
self.tm_display.sleep_atleast(self.refresh_delay)
self.tm_display.reset()
if state == 'start' and self.tm_trigger.sec() > self.cfg.T_INIT:
state = 'gap_s'
self.bar.fill()
self.tm_trigger.reset()
self.trigger.signal(self.tdef.INIT)
elif state == 'gap_s':
self.bar.put_text(title_text)
state = 'gap'
self.tm_trigger.reset()
elif state == 'gap' and self.tm_trigger.sec() > self.cfg.T_GAP:
state = 'cue'
self.bar.fill()
self.bar.draw_cue()
self.bar.glass_draw_cue()
self.trigger.signal(self.tdef.CUE)
self.tm_trigger.reset()
elif state == 'cue' and self.tm_trigger.sec() > self.cfg.T_READY:
state = 'dir_r'
if self.cfg.FEEDBACK_TYPE == 'BODY':
self.bar.set_pc_feedback(False)
self.bar.move(true_label, 100, overlay=False, barcolor='G')
if self.cfg.FEEDBACK_TYPE == 'BODY':
self.bar.set_pc_feedback(True)
if self.cfg.SHOW_CUE is True:
self.bar.put_text(dirs[true_label], 'R')
if true_label == 'L': # left
self.trigger.signal(self.tdef.LEFT_READY)
elif true_label == 'R': # right
self.trigger.signal(self.tdef.RIGHT_READY)
elif true_label == 'U': # up
self.trigger.signal(self.tdef.UP_READY)
elif true_label == 'D': # down
self.trigger.signal(self.tdef.DOWN_READY)
elif true_label == 'B': # both hands
self.trigger.signal(self.tdef.BOTH_READY)
else:
raise RuntimeError('Unknown direction %s' % true_label)
self.tm_trigger.reset()
##################################################################
##################################################################
#qc.print_c('Executing Rex action %s' % 'N', 'W')
#os.system('%s/Rex/RexControlSimple.exe %s %s' % (pycnbi.ROOT, 'COM3', 'N'))
##################################################################
##################################################################
elif state == 'dir_r' and self.tm_trigger.sec(
) > self.cfg.T_DIR_CUE:
self.bar.fill()
self.bar.draw_cue()
self.bar.glass_draw_cue()
state = 'dir'
# initialize bar scores
bar_label = bar_dirs[0]
bar_score = 0
probs = [1.0 / len(bar_dirs)] * len(bar_dirs)
self.bar.move(bar_label, bar_score, overlay=False)
probs_acc = np.zeros(len(probs))
if true_label == 'L': # left
self.trigger.signal(self.tdef.LEFT_GO)
elif true_label == 'R': # right
self.trigger.signal(self.tdef.RIGHT_GO)
elif true_label == 'U': # up
self.trigger.signal(self.tdef.UP_GO)
elif true_label == 'D': # down
self.trigger.signal(self.tdef.DOWN_GO)
elif true_label == 'B': # both
self.trigger.signal(self.tdef.BOTH_GO)
else:
raise RuntimeError('Unknown truedirection %s' % true_label)
self.tm_watchdog.reset()
self.tm_trigger.reset()
elif state == 'dir':
if self.tm_trigger.sec() > self.cfg.T_CLASSIFY or (
self.premature_end and bar_score >= 100):
if not hasattr(
self.cfg,
'SHOW_RESULT') or self.cfg.SHOW_RESULT is True:
# show classfication result
if self.cfg.FEEDBACK_TYPE == 'BODY':
self.bar.move(bar_label,
bar_score,
overlay=False,
barcolor='Y',
caption=dirs[bar_label],
caption_color='Y')
else:
self.bar.move(bar_label,
100,
overlay=False,
barcolor='Y')
else:
self.bar.move(bar_label,
bar_score,
overlay=False,
barcolor='Y',
caption='TRIAL END',
caption_color='Y')
########################## TEST WITH BAR #############################
'''
if self.cfg.FEEDBACK_TYPE == 'BODY':
self.bar.move(bar_label, bar_score, overlay=False, barcolor='Y', caption='TRIAL END', caption_color='Y')
else:
self.bar.move(bar_label, 0, overlay=False, barcolor='Y')
'''
self.trigger.signal(self.tdef.FEEDBACK)
probs_acc /= sum(probs_acc)
if self.cfg.DEBUG_PROBS:
msg = 'DEBUG: Accumulated probabilities = %s' % qc.list2string(
probs_acc, '%.3f')
logger.info(msg)
if self.logf is not None:
self.logf.write(msg + '\n')
if self.logf is not None:
self.logf.write('%s detected as %s (%d)\n\n' %
(true_label, bar_label, bar_score))
self.logf.flush()
# end of trial
state = 'feedback'
self.tm_trigger.reset()
else:
# classify
probs_new = decoder.get_prob_unread()
if probs_new is None:
if self.tm_watchdog.sec() > 3:
logger.warning(
'No classification being done. Are you receiving data streams?'
)
self.tm_watchdog.reset()
else:
self.tm_watchdog.reset()
# bias and accumulate
if self.bar_bias is not None:
probs_new[bias_idx] += self.bar_bias[1]
newsum = sum(probs_new)
probs_new = [p / newsum for p in probs_new]
probs_acc += np.array(probs_new)
for i in range(len(probs_new)):
probs[i] = probs[i] * self.alpha1 + probs_new[
i] * self.alpha2
''' Original: accumulate and bias
# accumulate probs
for i in range( len(probs_new) ):
probs[i]= probs[i] * self.alpha1 + probs_new[i] * self.alpha2
# bias bar
if self.bar_bias is not None:
probs[bias_idx] += self.bar_bias[1]
newsum= sum(probs)
probs= [p/newsum for p in probs]
'''
# determine the direction
max_pidx = qc.get_index_max(probs)
max_label = bar_dirs[max_pidx]
if self.cfg.POSITIVE_FEEDBACK is False or \
(self.cfg.POSITIVE_FEEDBACK and true_label == max_label):
dx = probs[max_pidx]
if max_label == 'R':
dx *= self.bar_step_right
elif max_label == 'L':
dx *= self.bar_step_left
elif max_label == 'U':
dx *= self.bar_step_up
elif max_label == 'D':
dx *= self.bar_step_down
elif max_label == 'B':
dx *= self.bar_step_both
else:
logger.debug('Direction %s using bar step %d' %
(max_label, self.bar_step_left))
dx *= self.bar_step_left
################################################
################################################
# slower in the beginning
#if self.tm_trigger.sec() < 2.0:
# dx *= self.tm_trigger.sec() * 0.5
################################################
################################################
# add likelihoods
if max_label == bar_label:
bar_score += dx
else:
bar_score -= dx
# change of direction
if bar_score < 0:
bar_score = -bar_score
bar_label = max_label
bar_score = int(bar_score)
if bar_score > 100:
bar_score = 100
if self.cfg.FEEDBACK_TYPE == 'BODY':
if self.cfg.SHOW_CUE:
self.bar.move(bar_label,
bar_score,
overlay=False,
caption=dirs[true_label],
caption_color='G')
else:
self.bar.move(bar_label,
bar_score,
overlay=False)
else:
self.bar.move(bar_label,
bar_score,
overlay=False)
if self.cfg.DEBUG_PROBS:
if self.bar_bias is not None:
biastxt = '[Bias=%s%.3f] ' % (
self.bar_bias[0], self.bar_bias[1])
else:
biastxt = ''
msg = '%s%s raw %s acc %s bar %s%d (%.1f ms)' % \
(biastxt, bar_dirs, qc.list2string(probs_new, '%.2f'), qc.list2string(probs, '%.2f'),
bar_label, bar_score, tm_classify.msec())
logger.info(msg)
if self.logf is not None:
self.logf.write(msg + '\n')
tm_classify.reset()
elif state == 'feedback' and self.tm_trigger.sec(
) > self.cfg.T_FEEDBACK:
self.trigger.signal(self.tdef.BLANK)
if self.cfg.FEEDBACK_TYPE == 'BODY':
state = 'return'
self.tm_trigger.reset()
else:
state = 'gap_s'
self.bar.fill()
self.bar.update()
return bar_label
elif state == 'return':
self.bar.set_glass_feedback(False)
self.bar.move(bar_label,
bar_score,
overlay=False,
barcolor='Y')
self.bar.set_glass_feedback(True)
bar_score -= 5
if bar_score <= 0:
state = 'gap_s'
self.bar.fill()
self.bar.update()
return bar_label
self.bar.update()
key = 0xFF & cv2.waitKey(1)
if key == keys['esc']:
return None
if key == keys['space']:
dx = 0
bar_score = 0
probs = [1.0 / len(bar_dirs)] * len(bar_dirs)
self.bar.move(bar_dirs[0], bar_score, overlay=False)
self.bar.update()
logger.info('probs and dx reset.')
# print event values
tsnew = np.where(np.array(tslist) > last_ts)[0][0]
trigger = np.unique(window[trg_ch, tsnew:])
# for Biosemi
# if sr.amp_name=='BioSemi':
# trigger= set( [255 & int(x-1) for x in trigger ] )
if len(trigger) > 0:
qc.print_c('Triggers: %s' % np.array(trigger), 'G')
print('[%.1f] Receiving data...' % watchdog.sec())
if TIME_INDEX is None:
datatxt = qc.list2string(np.mean(window[CH_INDEX, :], axis=1),
'%-15.6f')
print('[%.3f : %.3f]' % (tslist[0], tslist[1]) +
' data: %s' % datatxt)
else:
datatxt = qc.list2string(window[CH_INDEX, TIME_INDEX], '%-15.6f')
print('[%.3f]' % tslist[TIME_INDEX] + ' data: %s' % datatxt)
# show PSD
if SHOW_PSD:
psd = psde.transform(
window.reshape((1, window.shape[0], window.shape[1])))
psd = psd.reshape((psd.shape[1], psd.shape[2]))
psdmean = np.mean(psd, axis=1)
for p in psdmean:
print('%.1f' % p, end=' ')
def test_receiver():
import mne
import os
CH_INDEX = [1] # channel to monitor
TIME_INDEX = None # integer or None. None = average of raw values of the current window
SHOW_PSD = False
mne.set_log_level('ERROR')
os.environ[
'OMP_NUM_THREADS'] = '1' # actually improves performance for multitaper
# connect to LSL server
amp_name, amp_serial = pu.search_lsl()
sr = StreamReceiver(window_size=1,
buffer_size=1,
amp_serial=amp_serial,
eeg_only=False,
amp_name=amp_name)
sfreq = sr.get_sample_rate()
trg_ch = sr.get_trigger_channel()
logger.info('Trigger channel = %d' % trg_ch)
# PSD init
if SHOW_PSD:
psde = mne.decoding.PSDEstimator(sfreq=sfreq, fmin=1, fmax=50, bandwidth=None, \
adaptive=False, low_bias=True, n_jobs=1, normalization='length', verbose=None)
watchdog = qc.Timer()
tm = qc.Timer(autoreset=True)
last_ts = 0
while True:
sr.acquire()
window, tslist = sr.get_window() # window = [samples x channels]
window = window.T # chanel x samples
qc.print_c('LSL Diff = %.3f' % (pylsl.local_clock() - tslist[-1]), 'G')
# print event values
tsnew = np.where(np.array(tslist) > last_ts)[0]
if len(tsnew) == 0:
logger.warning('There seems to be delay in receiving data.')
time.sleep(1)
continue
trigger = np.unique(window[trg_ch, tsnew[0]:])
# for Biosemi
# if sr.amp_name=='BioSemi':
# trigger= set( [255 & int(x-1) for x in trigger ] )
if len(trigger) > 0:
logger.info('Triggers: %s' % np.array(trigger))
logger.info('[%.1f] Receiving data...' % watchdog.sec())
if TIME_INDEX is None:
datatxt = qc.list2string(np.mean(window[CH_INDEX, :], axis=1),
'%-15.6f')
print('[%.3f : %.3f]' % (tslist[0], tslist[-1]) +
' data: %s' % datatxt)
else:
datatxt = qc.list2string(window[CH_INDEX, TIME_INDEX], '%-15.6f')
print('[%.3f]' % tslist[TIME_INDEX] + ' data: %s' % datatxt)
# show PSD
if SHOW_PSD:
psd = psde.transform(
window.reshape((1, window.shape[0], window.shape[1])))
psd = psd.reshape((psd.shape[1], psd.shape[2]))
psdmean = np.mean(psd, axis=1)
for p in psdmean:
print('%.1f' % p, end=' ')
last_ts = tslist[-1]
tm.sleep_atleast(0.05)
