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 init_loop(self):
'''
Initializes the BCI loop parameters
'''
self.updating = False
# Create a stream
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)
self.nb_channels = len(self.sr.get_eeg_channels())
trg_ch = self.sr.get_trigger_channel()
logger.info('Trigger channel is %d' % trg_ch)
data = ['EEG', srate, ['L', 'R'], None, self.nb_channels, 0, trg_ch, \
None, None, None, None, None]
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
}
# For now not a fixed number of samples per chunk
# self.tri = np.zeros(self.config['samples'])
# 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.last_tri = 0
self.ts_list = []
self.ts_list_tri = []
def connect_lsl_stream(cfg, amp_name, amp_serial):
"""
Connect to the lsl stream corresponding to the provided amplifier
name and serial number
cfg = config file
amp_name = amplifier's name to connect to
amp_serial = amplifier's serial number
"""
sr = StreamReceiver(window_size=cfg.WINDOWSIZE, buffer_size=cfg.STREAMBUFFER, amp_serial=amp_serial, eeg_only=False, amp_name=amp_name)
return sr
def connect_lsl_stream(amp_name, amp_serial, window_size, buffer_size):
"""
Connect to the lsl stream corresponding to the provided amplifier
name and serial number
amp_name = amplifier's name to connect to
amp_serial = amplifier's serial number
"""
# Open the stream
return StreamReceiver(window_size=window_size,
buffer_size=buffer_size,
amp_serial=amp_serial,
eeg_only=False,
amp_name=amp_name)
class Scope(QMainWindow):
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()
#
# Main init function
#
def init_scope(self):
# pg.setConfigOption('background', 'w')
# pg.setConfigOption('foreground', 'k')
self.init_config_file()
self.init_loop()
self.init_panel_GUI()
self.init_scope_GUI()
self.init_timer()
#
# Initializes config file
#
def init_config_file(self):
self.scope_settings = RawConfigParser(allow_no_value=True,
inline_comment_prefixes=('#',
';'))
if (len(sys.argv) == 1):
self.show_channel_names = 0
self.device_name = ""
else:
if (sys.argv[1].find("gtec") > -1):
self.device_name = "gtec"
self.show_channel_names = 1
elif (sys.argv[1].find("biosemi") > -1):
self.device_name = "biosemi"
self.show_channel_names = 1
elif (sys.argv[1].find("hiamp") > -1):
self.device_name = "hiamp"
self.show_channel_names = 1
else:
self.device_name = ""
self.show_channel_names = 0
# self.scope_settings.read(os.getenv("HOME") + "/.scope_settings.ini")
self.scope_settings.read(
str(path2_viewerFolder / '.scope_settings.ini'))
#
# Initialize control panel parameter
#
def init_panel_GUI(self):
self.show_TID_events = False
self.show_LPT_events = False
self.show_Key_events = False
# Event handler
self.ui.comboBox_scale.activated.connect(
self.onActivated_combobox_scale)
self.ui.spinBox_time.valueChanged.connect(
self.onValueChanged_spinbox_time)
self.ui.checkBox_car.stateChanged.connect(
self.onActivated_checkbox_car)
self.ui.checkBox_bandpass.stateChanged.connect(
self.onActivated_checkbox_bandpass)
self.ui.checkBox_showTID.stateChanged.connect(
self.onActivated_checkbox_TID)
self.ui.checkBox_showLPT.stateChanged.connect(
self.onActivated_checkbox_LPT)
self.ui.checkBox_showKey.stateChanged.connect(
self.onActivated_checkbox_Key)
self.ui.pushButton_bp.clicked.connect(self.onClicked_button_bp)
self.ui.pushButton_rec.clicked.connect(self.onClicked_button_rec)
self.ui.pushButton_stoprec.clicked.connect(
self.onClicked_button_stoprec)
self.ui.pushButton_stoprec.setEnabled(False)
self.ui.comboBox_scale.setCurrentIndex(4)
self.ui.checkBox_car.setChecked(
int(self.scope_settings.get("filtering", "apply_car_filter")))
self.ui.checkBox_bandpass.setChecked(
int(self.scope_settings.get("filtering", "apply_bandpass_filter")))
self.ui.checkBox_showTID.setChecked(
int(self.scope_settings.get("plot", "show_TID_events")))
self.ui.checkBox_showLPT.setChecked(
int(self.scope_settings.get("plot", "show_LPT_events")))
self.ui.checkBox_showKey.setChecked(
int(self.scope_settings.get("plot", "show_KEY_events")))
self.ui.statusBar.showMessage("[Not recording]")
self.channels_to_show_idx = []
idx = 0
for y in range(0, 4):
for x in range(0, NUM_X_CHANNELS):
if (idx < self.config['eeg_channels']):
# self.table_channels.item(x,y).setTextAlignment(QtCore.Qt.AlignCenter)
self.ui.table_channels.item(x, y).setSelected(True) # Qt5
#self.table_channels.setItemSelected(self.table_channels.item(x, y), True) # Qt4 only
self.channels_to_show_idx.append(idx)
else:
self.ui.table_channels.setItem(x, y,
QTableWidgetItem("N/A"))
self.ui.table_channels.item(x, y).setFlags(
QtCore.Qt.NoItemFlags)
self.ui.table_channels.item(x, y).setTextAlignment(
QtCore.Qt.AlignCenter)
idx += 1
self.ui.table_channels.verticalHeader().setStretchLastSection(True)
self.ui.table_channels.horizontalHeader().setStretchLastSection(True)
self.ui.table_channels.itemSelectionChanged.connect(
self.onSelectionChanged_table)
self.screen_width = 522
self.screen_height = 160
# self.setGeometry(100,100, self.screen_width, self.screen_height)
# self.setFixedSize(self.screen_width, self.screen_height)
self.setWindowTitle('EEG Scope Panel')
self.setFocusPolicy(QtCore.Qt.ClickFocus)
self.setFocus()
self.show()
#
# Initialize scope parameters
#
def init_scope_GUI(self):
self.bool_parser = {True: '1', False: '0'}
# PyQTGraph plot initialization
self.win = pg.GraphicsWindow()
self.win.setWindowTitle('EEG Scope')
self.win.setWindowFlags(QtCore.Qt.WindowMinimizeButtonHint)
self.win.keyPressEvent = self.keyPressEvent
self.win.show()
self.main_plot_handler = self.win.addPlot()
self.win.resize(1280, 800)
# Scales available in the GUI. If you change the options in the GUI
# you should change them here as well
self.scales_range = [1, 10, 25, 50, 100, 250, 500, 1000, 2500, 100000]
# Scale in uV
self.scale = int(self.scope_settings.get("plot", "scale_plot"))
# Time window to show in seconds
self.seconds_to_show = int(self.scope_settings.get(
"plot", "time_plot"))
# Y Tick labels. Use values from the config file.
self.channel_labels = []
values = []
''' For non-LSL systems having no channel names
for x in range(0, self.config['eeg_channels']):
if (self.show_channel_names):
self.channel_labels.append("(" + str(x + 1) + ") " +
self.scope_settings.get("internal",
"channel_names_" + self.device_name + str(
self.config['eeg_channels'])).split(', ')[x])
else:
self.channel_labels.append('CH ' + str(x + 1))
'''
ch_names = np.array(self.sr.get_channel_names())
self.channel_labels = ch_names[self.sr.get_eeg_channels()]
for x in range(0, len(self.channels_to_show_idx)):
values.append((-x * self.scale,
self.channel_labels[self.channels_to_show_idx[x]]))
values_axis = []
values_axis.append(values)
values_axis.append([])
# Update table labels with current names
idx = 0
for y in range(0, 4):
for x in range(0, NUM_X_CHANNELS):
if (idx < self.config['eeg_channels']):
self.ui.table_channels.item(x, y).setText(
self.channel_labels[idx])
idx += 1
# Plot initialization
self.main_plot_handler.getAxis('left').setTicks(values_axis)
self.main_plot_handler.setRange(
xRange=[0, self.seconds_to_show],
yRange=[
+1.5 * self.scale,
-0.5 * self.scale - self.scale * self.config['eeg_channels']
])
self.main_plot_handler.disableAutoRange()
self.main_plot_handler.showGrid(y=True)
self.main_plot_handler.setLabel(axis='left',
text='Scale (uV): ' + str(self.scale))
self.main_plot_handler.setLabel(axis='bottom', text='Time (s)')
# X axis
self.x_ticks = np.zeros(self.config['sf'] * self.seconds_to_show)
for x in range(0, self.config['sf'] * self.seconds_to_show):
self.x_ticks[x] = (x * 1) / float(self.config['sf'])
# Plotting colors. If channels > 16, colors will roll back to the beginning
self.colors = np.array([[255, 0, 0], [0, 255, 0], [0, 0, 255],
[255, 255, 0], [0, 255, 255], [255, 0, 255],
[128, 100, 100], [0, 128, 0], [0, 128, 128],
[128, 128, 0], [255, 128, 128], [128, 0, 128],
[128, 255, 0], [255, 128, 0], [0, 255, 128],
[128, 0, 255]])
# We want a lightweight scope, so we downsample the plotting to 64 Hz
self.subsampling_value = self.config['sf'] / 64
# EEG data for plotting
self.data_plot = np.zeros((self.config['sf'] * self.seconds_to_show,
self.config['eeg_channels']))
self.curve_eeg = []
for x in range(0, len(self.channels_to_show_idx)):
self.curve_eeg.append(
self.main_plot_handler.plot(
x=self.x_ticks,
y=self.data_plot[:, self.channels_to_show_idx[x]],
pen=pg.mkColor(self.colors[self.channels_to_show_idx[x] %
16, :])))
# self.curve_eeg[-1].setDownsampling(ds=self.subsampling_value, auto=False, method="mean")
# Events data
self.events_detected = []
self.events_curves = []
self.events_text = []
# CAR initialization
self.apply_car = int(
self.scope_settings.get("filtering", "apply_car_filter"))
self.matrix_car = np.zeros(
(self.config['eeg_channels'], self.config['eeg_channels']),
dtype=float)
self.matrix_car[:, :] = -1 / float(self.config['eeg_channels'])
np.fill_diagonal(self.matrix_car,
1 - (1 / float(self.config['eeg_channels'])))
# Laplacian initalization. TO BE DONE
self.matrix_lap = np.zeros(
(self.config['eeg_channels'], self.config['eeg_channels']),
dtype=float)
np.fill_diagonal(self.matrix_lap, 1)
self.matrix_lap[2, 0] = -1
self.matrix_lap[0, 2] = -0.25
self.matrix_lap[0, 2] = -0.25
# BP initialization
self.apply_bandpass = int(
self.scope_settings.get("filtering", "apply_bandpass_filter"))
if (self.apply_bandpass):
self.ui.doubleSpinBox_hp.setValue(
float(
self.scope_settings.get(
"filtering",
"bandpass_cutoff_frequency").split(' ')[0]))
self.ui.doubleSpinBox_lp.setValue(
float(
self.scope_settings.get(
"filtering",
"bandpass_cutoff_frequency").split(' ')[1]))
self.ui.pushButton_bp.click()
self.ui.checkBox_bandpass.setChecked(self.apply_car)
self.ui.checkBox_bandpass.setChecked(self.apply_bandpass)
self.update_title_scope()
# Help variables
self.show_help = 0
self.help = pg.TextItem(
"CNBI EEG Scope v0.3 \n" +
"----------------------------------------------------------------------------------\n"
+ "C: De/activate CAR Filter\n" +
"B: De/activate Bandpass Filter (with current settings)\n" +
"T: Show/hide TiD events\n" + "L: Show/hide LPT events\n" +
"K: Show/hide Key events. If not shown, they are NOT recorded!\n" +
"0-9: Add a user-specific Key event. Do not forget to write down why you marked it.\n"
+
"Up, down arrow keys: Increase/decrease the scale, steps of 10 uV\n"
+
"Left, right arrow keys: Increase/decrease the time to show, steps of 1 s\n"
+
"Spacebar: Stop the scope plotting, whereas data acquisition keeps running (EXPERIMENTAL)\n"
+ "Esc: Exits the scope",
anchor=(0, 0),
border=(70, 70, 70),
fill=pg.mkColor(20, 20, 20, 200),
color=(255, 255, 255))
# Stop plot functionality
self.stop_plot = 0
# Force repaint even when we shouldn't repaint.
self.force_repaint = 0
# For some strange reason when the width is > 1 px the scope runs slow.
# self.pen_plot = []
# for x in range(0, self.config['eeg_channels']):
# self.pen_plot.append(pg.mkPen(self.colors[x%16,:], width=3))
#
# Initializes the BCI loop parameters
#
def init_loop_cnbiloop(self):
self.fin = open(self.scope_settings.get("internal", "path_pipe"), 'r')
# 12 unsigned ints (4 bytes)
data = struct.unpack("<12I", self.fin.read(4 * 12))
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.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)
# TID initialization
self.bci = BCI.BciInterface()
#
# Initializes the BCI loop parameters
#
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 = []
#
# Initializes the QT timer, which will call the update function every 20 ms
#
def init_timer(self):
self.tm = qc.Timer() # leeq
QtCore.QCoreApplication.processEvents()
QtCore.QCoreApplication.flush()
self.timer = QtCore.QTimer(self)
self.timer.timeout.connect(self.update_loop)
self.timer.start(20)
# QtCore.QTimer.singleShot( 20, self.update_loop )
#
# Main update function (connected to the timer)
#
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
#
# Read EEG
#
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()
#
# Read EEG
#
def read_eeg_cnbiloop(self):
# Reading in python is blocking, so it will wait until having the amount of data needed
# Read timestamp. 1 value, type double
timestamp = struct.unpack("<d", self.fin.read(8 * 1))
# Read index. 1 value, type uint64
index = struct.unpack("<Q", self.fin.read(8 * 1))
# Read labels. self.config.labels, type double
labels = struct.unpack("<" + str(self.config['labels']) + "I",
self.fin.read(4 * self.config['labels']))
# Read eeg. self.config.samples*self.config.eeg_ch, type float
beeg = struct.unpack(
"<" + str(self.config['samples'] * self.config['eeg_channels']) +
"f",
self.fin.read(4 * self.config['samples'] *
self.config['eeg_channels']))
self.eeg = np.reshape(
list(beeg), (self.config['samples'], self.config['eeg_channels']))
# Read exg. self.config.samples*self.config.exg_ch, type float
bexg = struct.unpack(
"<" + str(self.config['samples'] * self.config['exg_channels']) +
"f",
self.fin.read(4 * self.config['samples'] *
self.config['exg_channels']))
self.exg = np.reshape(
list(bexg), (self.config['samples'], self.config['exg_channels']))
# Read tri. self.config.samples*self.config.tri_ch, type float
self.tri = struct.unpack(
"<" + str(self.config['samples'] * self.config['tri_channels']) +
"i",
self.fin.read(4 * self.config['samples'] *
self.config['tri_channels']))
#
# Bandpas + CAR filtering
#
def filter_signal(self):
if (self.apply_bandpass):
for x in range(0, self.eeg.shape[1]):
self.eeg[:, x], self.zi[:,
x] = lfilter(self.b, self.a,
self.eeg[:, x], -1,
self.zi[:, x])
# We only apply CAR if selected AND there are at least 2 channels. Otherwise it makes no sense
if (self.apply_car) and (len(self.channels_to_show_idx) > 1):
self.eeg = np.dot(self.matrix_car, np.transpose(self.eeg))
self.eeg = np.transpose(self.eeg)
#
# Update ringbuffers and events for plotting
#
def update_ringbuffers(self):
# leeq
self.data_plot = np.roll(self.data_plot, -len(self.ts_list), 0)
self.data_plot[-len(self.ts_list):, :] = self.eeg
# We have to remove those indexes that reached time = 0
delete_indices_e = []
delete_indices_c = []
for x in range(0, len(self.events_detected), 2):
xh = int(x / 2)
self.events_detected[x] -= len(self.ts_list) # leeq
if (self.events_detected[x] < 0) and (not self.stop_plot):
delete_indices_e.append(x)
delete_indices_e.append(x + 1)
delete_indices_c.append(xh)
self.events_curves[xh].clear()
self.main_plot_handler.removeItem(self.events_text[xh])
self.events_detected = [
i for j, i in enumerate(self.events_detected)
if j not in delete_indices_e
]
self.events_curves = [
i for j, i in enumerate(self.events_curves)
if j not in delete_indices_c
]
self.events_text = [
i for j, i in enumerate(self.events_text)
if j not in delete_indices_c
]
# Find LPT events and add them
if (self.show_LPT_events) and (not self.stop_plot):
for x in range(len(self.tri)):
tri = int(self.tri[x])
if tri != 0 and (tri > self.last_tri):
self.addEventPlot("LPT", tri)
logger.info('Trigger %d received' % tri)
self.last_tri = tri
#
# Called by repaint()
#
def paintEvent(self, e):
# Distinguish between paint events from timer and event QT widget resizing, clicking etc (sender is None)
# We should only paint when the timer triggered the event.
# Just in case, there's a flag to force a repaint even when we shouldn't repaint
sender = self.sender()
if 'force_repaint' not in self.__dict__.keys():
logger.warning('force_repaint is not set! Is it a Qt bug?')
self.force_repaint = 0
if (sender is None) and (not self.force_repaint):
pass
else:
self.force_repaint = 0
qp = QPainter()
qp.begin(self)
# Update the interface
self.paintInterface(qp)
qp.end()
#
# Update stuff on the interface. Only graphical updates should be added here
#
def paintInterface(self, qp):
# Update EEG channels
for x in range(0, len(self.channels_to_show_idx)):
self.curve_eeg[x].setData(
x=self.x_ticks,
y=self.data_plot[:, self.channels_to_show_idx[x]] -
x * self.scale)
# Update events
for x in range(0, len(self.events_detected), 2):
xh = int(x / 2)
self.events_curves[xh].setData(
x=np.array([
self.x_ticks[self.events_detected[x]],
self.x_ticks[self.events_detected[x]]
]),
y=np.array([
+1.5 * self.scale, -0.5 * self.scale -
self.scale * self.config['eeg_channels']
]))
self.events_text[xh].setPos(self.x_ticks[self.events_detected[x]],
self.scale)
#
# Do necessary stuff when scale has changed
#
def update_plot_scale(self, new_scale):
if (new_scale < 1):
new_scale = 1
# commented out by dbdq.
# else:
# new_scale = new_scale - new_scale%10
self.scale = new_scale
# Y Tick labels
values = []
for x in range(0, len(self.channels_to_show_idx)):
values.append((-x * self.scale,
self.channel_labels[self.channels_to_show_idx[x]]))
values_axis = []
values_axis.append(values)
values_axis.append([])
self.main_plot_handler.getAxis('left').setTicks(values_axis)
self.main_plot_handler.setRange(
yRange=[+self.scale, -self.scale * len(self.channels_to_show_idx)])
self.main_plot_handler.setLabel(axis='left',
text='Scale (uV): ' + str(self.scale))
self.trigger_help()
# We force an immediate repaint to avoid "shakiness".
if (not self.stop_plot):
self.force_repaint = 1
self.repaint()
#
# Do necessary stuff when seconds to show have changed
#
def update_plot_seconds(self, new_seconds):
# Do nothing unless...
if (new_seconds != self.seconds_to_show) and (new_seconds > 0) and (
new_seconds < 100):
self.ui.spinBox_time.setValue(new_seconds)
self.main_plot_handler.setRange(xRange=[0, new_seconds])
self.x_ticks = np.zeros(self.config['sf'] * new_seconds)
for x in range(0, self.config['sf'] * new_seconds):
self.x_ticks[x] = (x * 1) / float(self.config['sf'])
if (new_seconds > self.seconds_to_show):
padded_signal = np.zeros((self.config['sf'] * new_seconds,
self.config['eeg_channels']))
padded_signal[padded_signal.shape[0] -
self.data_plot.shape[0]:, :] = self.data_plot
for x in range(0, len(self.events_detected), 2):
self.events_detected[x] += padded_signal.shape[0] - \
self.data_plot.shape[0]
self.data_plot = padded_signal
else:
for x in range(0, len(self.events_detected), 2):
self.events_detected[x] -= self.data_plot.shape[0] - \
self.config['sf'] * new_seconds
self.data_plot = self.data_plot[self.data_plot.shape[0] -
self.config['sf'] *
new_seconds:, :]
self.seconds_to_show = new_seconds
self.trigger_help()
# We force an immediate repaint to avoid "shakiness".
if (not self.stop_plot):
self.force_repaint = 1
self.repaint()
#
# Handle TOBI iD events
#
def handle_tobiid_input(self):
data = None
try:
data = self.bci.iDsock_bus.recv(512)
self.bci.idStreamer_bus.Append(data)
except:
self.nS = False
self.dec = 0
pass
# deserialize ID message
if data:
if self.bci.idStreamer_bus.Has("<tobiid", "/>"):
msg = self.bci.idStreamer_bus.Extract("<tobiid", "/>")
self.bci.id_serializer_bus.Deserialize(msg)
self.bci.idStreamer_bus.Clear()
tmpmsg = int(self.bci.id_msg_bus.GetEvent())
if (self.show_TID_events) and (not self.stop_plot):
self.addEventPlot("TID", tmpmsg)
elif self.bci.idStreamer_bus.Has("<tcstatus", "/>"):
MsgNum = self.bci.idStreamer_bus.Count("<tcstatus")
for i in range(1, MsgNum - 1):
# Extract most of these messages and trash them
msg_useless = self.bci.idStreamer_bus.Extract(
"<tcstatus", "/>")
#
# Add an event to the scope
#
def addEventPlot(self, event_name, event_id):
if (event_name == "TID"):
color = pg.mkColor(0, 0, 255)
elif (event_name == "KEY"):
color = pg.mkColor(255, 0, 0)
elif (event_name == "LPT"):
color = pg.mkColor(0, 255, 0)
else:
color = pg.mkColor(255, 255, 255)
self.events_detected.append(self.data_plot.shape[0] - 1)
self.events_detected.append(event_id)
self.events_curves.append(
self.main_plot_handler.plot(
pen=color,
x=np.array([self.x_ticks[-1], self.x_ticks[-1]]),
y=np.array([
+1.5 * self.scale,
-1.5 * self.scale * self.config['eeg_channels']
])))
# text = pg.TextItem(event_name + "(" + str(self.events_detected[-1]) + ")", anchor=(1.1,0), fill=(0,0,0), color=color)
text = pg.TextItem(str(self.events_detected[-1]),
anchor=(1.1, 0),
fill=(0, 0, 0),
color=color)
text.setPos(self.x_ticks[-1], self.scale)
self.events_text.append(text)
self.main_plot_handler.addItem(self.events_text[-1])
#
# Calculation of bandpass coefficients.
# Order is computed automatically.
# Note that if filter is unstable this function crashes (TODO handle problems)
#
def butter_bandpass(self, highcut, lowcut, fs, num_ch):
low = lowcut / (0.5 * fs)
high = highcut / (0.5 * fs)
# get the order. TO BE DONE: Sometimes it fails
#ord = buttord(high, low, 2, 40)
#b, a = butter(ord[0], [high, low], btype='band')
b, a = butter(2, [high, low], btype='band')
zi = np.zeros([a.shape[0] - 1, num_ch])
return b, a, zi
#
# Updates the title shown in the scope
#
def update_title_scope(self):
if (hasattr(self, 'main_plot_handler')):
self.main_plot_handler.setTitle(
title='TLK: ' + self.bool_parser[self.show_TID_events] +
self.bool_parser[self.show_LPT_events] +
self.bool_parser[self.show_Key_events] + ', CAR: ' +
self.bool_parser[self.apply_car] + ', BP: ' +
self.bool_parser[self.apply_bandpass] + ' [' +
str(self.ui.doubleSpinBox_hp.value()) + '-' +
str(self.ui.doubleSpinBox_lp.value()) + '] Hz')
# ', BP: ' + self.bool_parser[self.apply_bandpass] + (' [' + str(self.doubleSpinBox_hp.value()) + '-' + str(self.doubleSpinBox_lp.value()) + '] Hz' if self.apply_bandpass else ''))
#
# Shows / hide help in the scope window
#
def trigger_help(self):
if self.show_help:
self.help.setPos(0, self.scale)
self.main_plot_handler.addItem(self.help)
self.help.setZValue(1)
else:
self.main_plot_handler.removeItem(self.help)
# ----------------------------------------------------------------------------------------------------
# EVENT HANDLERS
# ----------------------------------------------------------------------------------------------------
def onClicked_button_rec(self):
# Simply call cl_rpc for this.
if (len(self.lineEdit_recFilename.text()) > 0):
if ".gdf" in self.lineEdit_recFilename.text():
self.ui.pushButton_stoprec.setEnabled(True)
self.ui.pushButton_rec.setEnabled(False)
# Popen is more efficient than os.open, since it is non-blocking
subprocess.Popen([
"cl_rpc", "openxdf",
str(self.ui.lineEdit_recFilename.text()), "dummy_log",
"dummy_log"
],
close_fds=True)
self.statusBar.showMessage(
"Recording file " +
str(self.ui.lineEdit_recFilename.text()))
elif ".bdf" in self.ui.lineEdit_recFilename.text():
self.ui.pushButton_stoprec.setEnabled(True)
self.ui.pushButton_rec.setEnabled(False)
subprocess.Popen([
"cl_rpc", "openxdf",
str(self.ui.lineEdit_recFilename.text()), "dummy_log",
"dummy_log"
],
close_fds=True)
self.statusBar.showMessage(
"Recording file " +
str(self.ui.lineEdit_recFilename.text()))
else:
pass
def onClicked_button_stoprec(self):
subprocess.Popen(["cl_rpc", "closexdf"], close_fds=True)
self.ui.pushButton_rec.setEnabled(True)
self.ui.pushButton_stoprec.setEnabled(False)
self.ui.statusBar.showMessage("Not recording")
def onActivated_checkbox_bandpass(self):
self.apply_bandpass = False
self.ui.pushButton_bp.setEnabled(self.ui.checkBox_bandpass.isChecked())
self.ui.doubleSpinBox_hp.setEnabled(
self.ui.checkBox_bandpass.isChecked())
self.ui.doubleSpinBox_lp.setEnabled(
self.ui.checkBox_bandpass.isChecked())
self.update_title_scope()
def onActivated_checkbox_car(self):
self.apply_car = self.ui.checkBox_car.isChecked()
self.update_title_scope()
def onActivated_checkbox_TID(self):
self.show_TID_events = self.ui.checkBox_showTID.isChecked()
self.update_title_scope()
def onActivated_checkbox_LPT(self):
self.show_LPT_events = self.ui.checkBox_showLPT.isChecked()
self.update_title_scope()
def onActivated_checkbox_Key(self):
self.show_Key_events = self.ui.checkBox_showKey.isChecked()
self.update_title_scope()
def onValueChanged_spinbox_time(self):
self.update_plot_seconds(self.ui.spinBox_time.value())
def onActivated_combobox_scale(self):
self.update_plot_scale(
self.scales_range[self.ui.comboBox_scale.currentIndex()])
def onClicked_button_bp(self):
if (self.ui.doubleSpinBox_lp.value() >
self.ui.doubleSpinBox_hp.value()):
self.apply_bandpass = True
self.b, self.a, self.zi = self.butter_bandpass(
self.ui.doubleSpinBox_hp.value(),
self.ui.doubleSpinBox_lp.value(), self.config['sf'],
self.config['eeg_channels'])
self.update_title_scope()
def onSelectionChanged_table(self):
# Remove current plot
for x in range(0, len(self.channels_to_show_idx)):
self.main_plot_handler.removeItem(self.curve_eeg[x])
# Which channels should I plot?
self.channels_to_show_idx = []
self.channels_to_hide_idx = []
idx = 0
for y in range(0, 4):
for x in range(0, NUM_X_CHANNELS):
if (idx < self.config['eeg_channels']):
#if (self.table_channels.isItemSelected( # Qt4 only
if (QTableWidgetItem.isSelected( # Qt5
self.ui.table_channels.item(x, y))):
self.channels_to_show_idx.append(idx)
else:
self.channels_to_hide_idx.append(idx)
idx += 1
# Add new plots
self.curve_eeg = []
for x in range(0, len(self.channels_to_show_idx)):
self.curve_eeg.append(
self.main_plot_handler.plot(
x=self.x_ticks,
y=self.data_plot[:, self.channels_to_show_idx[x]],
pen=self.colors[self.channels_to_show_idx[x] %
NUM_X_CHANNELS, :]))
self.curve_eeg[-1].setDownsampling(ds=self.subsampling_value,
auto=False,
method="mean")
# Update CAR so it's computed based only on the shown channels
if (len(self.channels_to_show_idx) > 1):
self.matrix_car = np.zeros(
(self.config['eeg_channels'], self.config['eeg_channels']),
dtype=float)
self.matrix_car[:, :] = -1 / float(len(self.channels_to_show_idx))
np.fill_diagonal(self.matrix_car,
1 - (1 / float(len(self.channels_to_show_idx))))
for x in range(0, len(self.channels_to_hide_idx)):
self.matrix_car[self.channels_to_hide_idx[x], :] = 0
self.matrix_car[:, self.channels_to_hide_idx[x]] = 0
# Refresh the plot
self.update_plot_scale(self.scale)
def keyPressEvent(self, event):
key = event.key()
if (key == QtCore.Qt.Key_Escape):
self.closeEvent(None)
if (key == QtCore.Qt.Key_H):
self.show_help = not self.show_help
self.trigger_help()
if (key == QtCore.Qt.Key_Up):
# Python's log(x, 10) has a rounding bug. Use log10(x) instead.
new_scale = self.scale + max(1, 10**int(math.log10(self.scale)))
self.update_plot_scale(new_scale)
if (key == QtCore.Qt.Key_Space):
self.stop_plot = not self.stop_plot
if (key == QtCore.Qt.Key_Down):
if self.scale >= 2:
# Python's log(x, 10) has a rounding bug. Use log10(x) instead.
new_scale = self.scale - max(
1, 10**int(math.log10(self.scale - 1)))
self.update_plot_scale(new_scale)
if (key == QtCore.Qt.Key_Left):
self.update_plot_seconds(self.seconds_to_show - 1)
if (key == QtCore.Qt.Key_Right):
self.update_plot_seconds(self.seconds_to_show + 1)
if (key == QtCore.Qt.Key_L):
self.ui.checkBox_showLPT.setChecked(
not self.ui.checkBox_showLPT.isChecked())
if (key == QtCore.Qt.Key_T):
self.ui.checkBox_showTID.setChecked(
not self.ui.checkBox_showTID.isChecked())
if (key == QtCore.Qt.Key_K):
self.ui.checkBox_showKey.setChecked(
not self.ui.checkBox_showKey.isChecked())
if (key == QtCore.Qt.Key_C):
self.ui.checkBox_car.setChecked(
not self.ui.checkBox_car.isChecked())
if (key == QtCore.Qt.Key_B):
self.ui.checkBox_bandpass.setChecked(
not self.ui.checkBox_bandpass.isChecked())
if self.ui.checkBox_bandpass.isChecked():
self.ui.pushButton_bp.click()
if ((key >= QtCore.Qt.Key_0) and (key <= QtCore.Qt.Key_9)):
if (self.show_Key_events) and (not self.stop_plot):
self.addEventPlot("KEY", 990 + key - QtCore.Qt.Key_0)
# self.bci.id_msg_bus.SetEvent(990 + key - QtCore.Qt.Key_0)
# self.bci.iDsock_bus.sendall(self.bci.id_serializer_bus.Serialize());
# 666
#
# Function called when a closing event was triggered.
#
def closeEvent(self, event):
'''
reply = QtGui.QMessageBox.question(self, "Quit", "Are you sure you want to quit?", QtGui.QMessageBox.Yes | QtGui.QMessageBox.No, QtGui.QMessageBox.Yes)
if (reply == QtGui.QMessageBox.Yes):
if (self.pushButton_stoprec.isEnabled()):
subprocess.Popen(["cl_rpc", "closexdf"], close_fds=True)
self.fin.close()
exit()
'''
# leeq
if (self.ui.pushButton_stoprec.isEnabled()):
subprocess.Popen(["cl_rpc", "closexdf"], close_fds=True)
with self.state.get_lock():
self.state.value = 0
def record(recordState,
amp_name,
amp_serial,
record_dir,
eeg_only,
recordLogger=logger,
queue=None):
redirect_stdout_to_queue(recordLogger, queue, 'INFO')
# set data file name
timestamp = time.strftime('%Y%m%d-%H%M%S', time.localtime())
pcl_file = "%s/%s-raw.pcl" % (record_dir, timestamp)
eve_file = '%s/%s-eve.txt' % (record_dir, timestamp)
recordLogger.info('>> Output file: %s' % (pcl_file))
# test writability
try:
qc.make_dirs(record_dir)
open(
pcl_file,
'w').write('The data will written when the recording is finished.')
except:
raise RuntimeError('Problem writing to %s. Check permission.' %
pcl_file)
# start a server for sending out data pcl_file when software trigger is used
outlet = start_server('StreamRecorderInfo', channel_format='string',\
source_id=eve_file, stype='Markers')
# connect to EEG stream server
sr = StreamReceiver(buffer_size=0,
amp_name=amp_name,
amp_serial=amp_serial,
eeg_only=eeg_only)
# start recording
recordLogger.info('\n>> Recording started (PID %d).' % os.getpid())
with recordState.get_lock():
recordState.value = 1
tm = qc.Timer(autoreset=True)
next_sec = 1
while recordState.value == 1:
sr.acquire()
if sr.get_buflen() > next_sec:
duration = str(datetime.timedelta(seconds=int(sr.get_buflen())))
recordLogger.info('RECORDING %s' % duration)
next_sec += 1
tm.sleep_atleast(0.001)
# record stop
recordLogger.info('>> Stop requested. Copying buffer')
buffers, times = sr.get_buffer()
signals = buffers
events = None
# channels = total channels from amp, including trigger channel
data = {
'signals': signals,
'timestamps': times,
'events': events,
'sample_rate': sr.get_sample_rate(),
'channels': sr.get_num_channels(),
'ch_names': sr.get_channel_names(),
'lsl_time_offset': sr.lsl_time_offset
}
recordLogger.info('Saving raw data ...')
qc.save_obj(pcl_file, data)
recordLogger.info('Saved to %s\n' % pcl_file)
# automatically convert to fif and use event file if it exists (software trigger)
if os.path.exists(eve_file):
recordLogger.info('Found matching event file, adding events.')
else:
eve_file = None
recordLogger.info('Converting raw file into fif.')
pcl2fif(pcl_file, external_event=eve_file)
# select the same channels used for training
w = w[picks]
# debug: show max - min
# c=1; print( '### %d: %.1f - %.1f = %.1f'% ( picks[c], max(w[c]), min(w[c]), max(w[c])-min(w[c]) ) )
# psde.transform = [channels x freqs]
psd = psde.transform(w)
return psd
if __name__ == '__main__':
sr = StreamReceiver(window_size=w_seconds,
amp_name=amp_name,
amp_serial=amp_serial)
sfreq = sr.sample_rate
psde = PSDEstimator(sfreq=sfreq,
fmin=fmin,
fmax=fmax,
bandwidth=None,
adaptive=False,
low_bias=True,
n_jobs=1,
normalization='length',
verbose=None)
ch_names = sr.get_channel_names()
fq_res = 1 / w_seconds
hz_list = []
f = fmin
def __init__(self,
state=mp.Value('i', 1),
lpttype='USB2LPT',
portaddr=None,
verbose=True,
check_lsl_offset=False):
self.evefile = None
self.lpttype = lpttype
self.verbose = verbose
if self.lpttype in ['USB2LPT', 'DESKTOP']:
if self.lpttype == 'USB2LPT':
if ctypes.sizeof(ctypes.c_voidp) == 4:
dllname = 'LptControl_USB2LPT32.dll' # 32 bit
else:
dllname = 'LptControl_USB2LPT64.dll' # 64 bit
if portaddr not in [0x278, 0x378]:
logger.warning('LPT port address %d is unusual.' %
portaddr)
elif self.lpttype == 'DESKTOP':
if ctypes.sizeof(ctypes.c_voidp) == 4:
dllname = 'LptControl_Desktop32.dll' # 32 bit
else:
dllname = 'LptControl_Desktop64.dll' # 64 bit
if portaddr not in [0x278, 0x378]:
logger.warning('LPT port address %d is unusual.' %
portaddr)
self.portaddr = portaddr
search = []
search.append(os.path.dirname(__file__) + '/' + dllname)
search.append(os.path.dirname(__file__) + '/libs/' + dllname)
search.append(os.getcwd() + '/' + dllname)
search.append(os.getcwd() + '/libs/' + dllname)
for f in search:
if os.path.exists(f):
dllpath = f
break
else:
logger.error('Cannot find the required library %s' % dllname)
raise RuntimeError
logger.info('Loading %s' % dllpath)
self.lpt = ctypes.cdll.LoadLibrary(dllpath)
elif self.lpttype == 'ARDUINO':
import serial, serial.tools.list_ports
BAUD_RATE = 115200
# portaddr should be None or in the form of 'COM1', 'COM2', etc.
if portaddr is None:
arduinos = [x for x in serial.tools.list_ports.grep('Arduino')]
if len(arduinos) == 0:
logger.error('No Arduino found. Stop.')
sys.exit()
for i, a in enumerate(arduinos):
logger.info('Found %s' % a[0])
try:
com_port = arduinos[0].device
except AttributeError: # depends on Python distribution
com_port = arduinos[0][0]
else:
com_port = portaddr
self.ser = serial.Serial(com_port, BAUD_RATE)
time.sleep(1) # doesn't work without this delay. why?
logger.info('Connected to %s.' % com_port)
elif self.lpttype == 'SOFTWARE':
from neurodecode.stream_receiver.stream_receiver import StreamReceiver
logger.info('Using software trigger')
# get data file location
LSL_SERVER = 'StreamRecorderInfo'
inlet = cnbi_lsl.start_client(LSL_SERVER, state)
evefile = inlet.info().source_id()
eveoffset_file = evefile[:-4] + '-offset.txt'
logger.info('Event file is: %s' % evefile)
self.evefile = open(evefile, 'a')
if check_lsl_offset:
# check server LSL time server integrity
logger.info(
"Checking LSL server's timestamp integrity for logging software triggers."
)
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)
local_time = pylsl.local_clock()
server_time = sr.get_window_list()[1][-1]
lsl_time_offset = local_time - server_time
with open(eveoffset_file, 'a') as f:
f.write(
'Local time: %.6f, Server time: %.6f, Offset: %.6f\n' %
(local_time, server_time, lsl_time_offset))
logger.info('LSL timestamp offset (%.3f) saved to %s' %
(lsl_time_offset, eveoffset_file))
elif self.lpttype == 'FAKE' or self.lpttype is None or self.lpttype is False:
logger.warning('Using a fake trigger.')
self.lpttype = 'FAKE'
self.lpt = None
else:
logger.error('Unrecognized lpttype device name %s' % lpttype)
sys.exit(-1)