def __init__(self, framer, *args, **kwargs):
''' Setup the client and start listening on the serial port
:param factory: The factory to build clients with
'''
self.decoder = ClientDecoder()
proto_cls = kwargs.pop("proto_cls", None)
proto = SerialClientFactory(framer, proto_cls).buildProtocol()
SerialPort.__init__(self, proto, *args, **kwargs)
def __init__(self, framer, *args, **kwargs):
''' Setup the client and start listening on the serial port
:param factory: The factory to build clients with
'''
self.decoder = ClientDecoder()
proto_cls = kwargs.pop("proto_cls", None)
proto = SerialClientFactory(framer, proto_cls).buildProtocol()
SerialPort.__init__(self, proto, *args, **kwargs)
class BioharnessProtocol(LineReceiver):
message_ids = {
"ecg": 0x16,
"breathing": 0x15,
"acceleration": 0x1E,
"rr": 0x19,
"summary": 0xBD,
"life_sign": 0xA4,
}
stream_states = {"ON": 1, "OFF": 0}
columns_of_streams = {
"summary": SummaryMessage._fields,
"breathing": SignalSample._fields,
"ecg": SignalSample._fields,
"rr": SignalSample._fields,
"acceleration": AccelerationSignalSample._fields,
}
def __init__(self, processing_proxy, port, reactor):
self.rr_buffer = deque(maxlen=180)
self.processing_proxy = processing_proxy
self.port = port
self.reactor = reactor
self.serial = None
self.realtimeVisWave = RealtimeVis()
# very slow, discarded
# self.realtimeVisRate = RealtimeVis()
self.count = 0
def send_device_command(self, message_id, payload):
message_frame = create_message_frame(message_id, payload)
logging.info(
"Bioharness - sending a command to the device: msg_id : %s, Payload : %s"
% (message_id, payload))
self.transport.write(message_frame)
def set_stream_state(self, stream_id, state):
self.send_device_command(self.message_ids[stream_id],
[self.stream_states[state]])
def disable_lifesign_timeout(self):
self.send_device_command(self.message_ids["life_sign"], [0, 0, 0, 0])
def set_summary_packet_transmit_interval_to_one_second(self):
self.send_device_command(self.message_ids["summary"], [1, 0])
def send_initialization_commands(self):
self.set_stream_state("ecg", "ON")
self.set_stream_state("breathing", "ON")
self.set_stream_state("acceleration", "OFF")
self.set_stream_state("rr", "ON")
self.disable_lifesign_timeout()
self.set_summary_packet_transmit_interval_to_one_second()
def default_signal_waveform_handler(self, signal_packet, start_new_stream):
samples_iterator = SignalPacketIterator(
signal_packet).iterate_timed_samples()
bb_buffer = []
for signal_sample in samples_iterator:
print signal_sample.type
self.logger_of_stream[signal_sample.type].write_tuple_to_log_file(
signal_sample)
# send data for processing
if signal_sample.type == "breathing":
# pass
# self.count += 1
bb_buffer.append(float(signal_sample.sample))
if signal_sample.type == 'rr':
self.rr_buffer.append(signal_sample.sample)
if len(self.rr_buffer) == self.rr_buffer.maxlen:
self.send_data_for_processing("rr_buffer",
list(self.rr_buffer),
signal_sample.timestamp)
for _i in range(0, 18):
self.rr_buffer.popleft()
self.realtimeVisWave.animate(bb_buffer)
def signal_waveform_handler(self, signal_packet, start_new_stream):
samples_iterator = SignalPacketIterator(
signal_packet).iterate_timed_samples()
bb_buffer = []
ecg_buffer = []
this_SDNN = 0
for signal_sample in samples_iterator:
self.logger_of_stream[signal_sample.type].write_tuple_to_log_file(
signal_sample)
# send data for processing
if signal_sample.type == "breathing":
# pass
# self.count += 1
bb_buffer.append(float(signal_sample.sample))
# elif signal_sample.type == 'rr':
# self.rr_buffer.append(signal_sample.sample)
# if len(self.rr_buffer) == self.rr_buffer.maxlen:
# self.send_data_for_processing("rr_buffer", list(self.rr_buffer), signal_sample.timestamp)
# rr_df = pd.Series(np.array(self.rr_buffer))
# rr_df[rr_df.diff().abs() == 0] = np.nan
# std = rr_df.dropna().std() # drop outliers
# rr_df[rr_df > 5 * std] = np.nan
# rr_df = rr_df.dropna()
# try:
# rr_df = rr_df.abs().interpolate(method='cubic')
# except ValueError:
# logging.warn("Processing - Could not interpolate rr data.")
# return None
# this_SDNN = rr_df.std()
# for _i in range(0,18):
# self.rr_buffer.popleft()
# elif signal_sample.type == "ecg":
# ecg_buffer.append(signal_sample.sample)
self.realtimeVisWave.animate(bb_buffer, True)
def display_status_flags(self, summary_packet):
if (summary_packet.heart_rate_unreliable
or summary_packet.respiration_rate_unreliable) or (
summary_packet.hrv_unreliable
or summary_packet.button_pressed):
logging.warn(
"Bioharness - Heart Rate:%s ; Breathing Rate:%s ; HRV:%s" %
((not summary_packet.heart_rate_unreliable),
(not summary_packet.respiration_rate_unreliable),
(not summary_packet.hrv_unreliable)))
def default_event_callback(self, summary_packet):
self.display_status_flags(summary_packet)
self.logger_of_stream["summary"].write_tuple_to_log_file(
summary_packet)
# send data for processing
self.send_data_for_processing("respiration_rate",
[summary_packet.respiration_rate],
summary_packet.timestamp)
def event_callback(self, summary_packet):
self.default_event_callback(summary_packet)
summary_str = ",".join([str(value) for value in summary_packet])
# Visualize the respiration rate
# print float(str(summary_packet[3]))
# self.realtimeVisRate.animate(float(str(summary_packet[3])))
def send_data_for_processing(self, type, value, timestamp):
data = {"type": type}
data["timestamp"] = timestamp
data["value"] = value
self.processing_proxy.notifyAll(data)
def set_event_callbacks(self, callbacks=None):
if callbacks is None: callbacks = [self.event_callback]
self.event_callbacks = callbacks
def set_waveform_callbacks(self, callbacks=None):
if callbacks is None: callbacks = [self.signal_waveform_handler]
self.waveform_callbacks = callbacks
def set_data_loggers(self, logger_of_stream):
self.logger_of_stream = logger_of_stream
def connectionMade(self):
# Setting the protocol to handle raw data rather than just lines
self.setRawMode()
# Sending commands to enable relevant streams and summary messages
self.send_initialization_commands()
self.signal_packet_handler_bh = BioHarnessPacketHandler(
self.waveform_callbacks, self.event_callbacks)
self.payload_parser = MessagePayloadParser(
[self.signal_packet_handler_bh.handle_packet])
self.message_parser = MessageFrameParser(
self.payload_parser.handle_message)
def rawDataReceived(self, data):
if not data: return
for byte in data:
self.message_parser.parse_data(byte)
def set_serial(self, serial):
self.serial = serial
def connectionLost(self, reason):
logging.error("Bioharness - Lost connection (%s)" % reason)
logging.info("Bioharness - Reconnecting in 5 seconds...")
self.serial._serial.close()
self.retry = self.reactor.callLater(5, self.reconnect)
def reconnect(self):
try:
if self.serial is None:
self.serial = SerialPort(self,
self.port,
self.reactor,
baudrate=115200)
else:
self.serial.__init__(self,
self.port,
self.reactor,
baudrate=115200)
logging.info("Bioharness - Reconnected")
except:
logging.error("Bioharness - Error opening serial port %s (%s)" %
(self.port, sys.exc_info()[1]))
logging.info("Bioharness - Reconnecting in 5 seconds...")
self.retry = self.reactor.callLater(5, self.reconnect)
class BioharnessProtocol(LineReceiver):
message_ids = {
"ecg": 0x16,
"breathing": 0x15,
"acceleration": 0x1E,
"rr": 0x19,
"summary": 0xBD,
"life_sign": 0xA4,
}
stream_states = {"ON": 1, "OFF": 0}
columns_of_streams = {
"summary": SummaryMessage._fields,
"breathing": SignalSample._fields,
"ecg": SignalSample._fields,
"rr": SignalSample._fields,
"acceleration": AccelerationSignalSample._fields,
}
def __init__(self, processing_proxy, port, reactor):
self.rr_buffer = deque(maxlen=1024)
self.processing_proxy = processing_proxy
self.port = port
self.reactor = reactor
self.serial = None
def send_device_command(self, message_id, payload):
message_frame = create_message_frame(message_id, payload)
logging.info(
"Bioharness - sending a command to the device: msg_id : %s, Payload : %s"
% (message_id, payload))
self.transport.write(message_frame)
def set_stream_state(self, stream_id, state):
self.send_device_command(self.message_ids[stream_id],
[self.stream_states[state]])
def disable_lifesign_timeout(self):
self.send_device_command(self.message_ids["life_sign"], [0, 0, 0, 0])
def set_summary_packet_transmit_interval_to_one_second(self):
self.send_device_command(self.message_ids["summary"], [1, 0])
def send_initialization_commands(self):
self.set_stream_state("ecg", "ON")
self.set_stream_state("breathing", "ON")
self.set_stream_state("acceleration", "OFF")
self.set_stream_state("rr", "ON")
self.disable_lifesign_timeout()
self.set_summary_packet_transmit_interval_to_one_second()
def default_signal_waveform_handler(self, signal_packet, start_new_stream):
samples_iterator = SignalPacketIterator(
signal_packet).iterate_timed_samples()
for signal_sample in samples_iterator:
self.logger_of_stream[signal_sample.type].write_tuple_to_log_file(
signal_sample)
# send data for processing
if signal_sample.type == 'rr':
self.rr_buffer.append(signal_sample.sample)
if len(self.rr_buffer) == self.rr_buffer.maxlen:
self.send_data_for_processing("rr_buffer",
list(self.rr_buffer),
signal_sample.timestamp)
#empty buffer partially
for _i in range(0, 18): #self.rr_buffer.maxlen/12):
self.rr_buffer.popleft()
def display_status_flags(self, summary_packet):
if (summary_packet.heart_rate_unreliable
or summary_packet.respiration_rate_unreliable) or (
summary_packet.hrv_unreliable
or summary_packet.button_pressed):
logging.warn(
"Bioharness - Heart Rate:%s ; Breathing Rate:%s ; HRV:%s" %
((not summary_packet.heart_rate_unreliable),
(not summary_packet.respiration_rate_unreliable),
(not summary_packet.hrv_unreliable)))
def default_event_callback(self, summary_packet):
self.display_status_flags(summary_packet)
self.logger_of_stream["summary"].write_tuple_to_log_file(
summary_packet)
# send data for processing
self.send_data_for_processing("respiration_rate",
[summary_packet.respiration_rate],
summary_packet.timestamp)
def send_data_for_processing(self, type, value, timestamp):
data = {"type": type}
data["timestamp"] = timestamp
data["value"] = value
self.processing_proxy.notifyAll(data)
def set_event_callbacks(self, callbacks=None):
if callbacks is None: callbacks = [self.default_event_callback]
self.event_callbacks = callbacks
def set_waveform_callbacks(self, callbacks=None):
if callbacks is None:
callbacks = [self.default_signal_waveform_handler]
self.waveform_callbacks = callbacks
def set_data_loggers(self, logger_of_stream):
self.logger_of_stream = logger_of_stream
def connectionMade(self):
# Setting the protocol to handle raw data rather than just lines
self.setRawMode()
# Sending commands to enable relevant streams and summary messages
self.send_initialization_commands()
self.signal_packet_handler_bh = BioHarnessPacketHandler(
self.waveform_callbacks, self.event_callbacks)
self.payload_parser = MessagePayloadParser(
[self.signal_packet_handler_bh.handle_packet])
self.message_parser = MessageFrameParser(
self.payload_parser.handle_message)
def rawDataReceived(self, data):
if not data: return
for byte in data:
self.message_parser.parse_data(byte)
def set_serial(self, serial):
self.serial = serial
def connectionLost(self, reason):
logging.error("Bioharness - Lost connection (%s)" % reason)
logging.info("Bioharness - Reconnecting in 5 seconds...")
self.serial._serial.close()
self.retry = self.reactor.callLater(5, self.reconnect)
def reconnect(self):
try:
if self.serial is None:
self.serial = SerialPort(self,
self.port,
self.reactor,
baudrate=115200)
else:
self.serial.__init__(self,
self.port,
self.reactor,
baudrate=115200)
logging.info("Bioharness - Reconnected")
except:
logging.error("Bioharness - Error opening serial port %s (%s)" %
(self.port, sys.exc_info()[1]))
logging.info("Bioharness - Reconnecting in 5 seconds...")
self.retry = self.reactor.callLater(5, self.reconnect)
