def connect(self, device_name=None, mac_address=None):
r"""
Connects to the nearby device. If there are more than one device, the user is asked to choose one of them.
Args:
device_name (str): Device name("Explore_XXXX"). Either mac address or name should be in the input
mac_address (str): The MAC address in format "XX:XX:XX:XX:XX:XX"
"""
if device_name:
self.device_name = device_name
else:
self.device_name = 'Explore_' + mac_address[-5:-3] + mac_address[
-2:]
logger.info(f"Connecting to {self.device_name} ...")
self.stream_processor = StreamProcessor()
self.stream_processor.start(device_name=device_name,
mac_address=mac_address)
cnt = 0
while "adc_mask" not in self.stream_processor.device_info:
logger.info("Waiting for device info packet...")
time.sleep(1)
if cnt >= 10:
raise ConnectionAbortedError(
"Could not get info packet from the device")
cnt += 1
logger.info(
'Device info packet has been received. Connection has been established. Streaming...'
)
logger.info("Device info: " + str(self.stream_processor.device_info))
self.is_connected = True
self.stream_processor.send_timestamp()
def connect(self, device_name=None, mac_address=None):
r"""
Connects to the nearby device. If there are more than one device, the user is asked to choose one of them.
Args:
device_name (str): Device name("Explore_XXXX"). Either mac address or name should be in the input
mac_address (str): The MAC address in format "XX:XX:XX:XX:XX:XX"
"""
if device_name:
self.device_name = device_name
else:
self.device_name = 'Explore_' + mac_address[-5:-3] + mac_address[
-2:]
self.stream_processor = StreamProcessor()
self.stream_processor.start(device_name=device_name,
mac_address=mac_address)
while "adc_mask" not in self.stream_processor.device_info:
print('Waiting for device info packet...')
time.sleep(.2)
print(
'Device info packet has been received. Connection has been established. Streaming...'
)
self.is_connected = True
self.stream_processor.send_timestamp()
plot.x_range.follow = "end"
plot.x_range.follow_interval = t_length
plot.x_range.range_padding = 0.
plot.x_range.min_interval = t_length
def get_fft(exg, s_rate):
"""Compute FFT"""
n_point = 1024
exg -= exg.mean(axis=1)[:, np.newaxis]
freq = s_rate * np.arange(int(n_point / 2)) / n_point
fft_content = np.fft.fft(exg, n=n_point) / n_point
fft_content = np.abs(fft_content[:, range(int(n_point / 2))])
fft_content = gaussian_filter1d(fft_content, 1)
return fft_content[:, 1:], freq[1:]
if __name__ == '__main__':
from explorepy import Explore
from explorepy.stream_processor import StreamProcessor
explore = Explore()
explore.stream_processor = StreamProcessor()
explore.stream_processor.device_info = {'firmware_version': '0.0.0',
'adc_mask': [1 for i in range(8)],
'sampling_rate': 250}
dashboard = Dashboard(explore=explore)
dashboard.start_server()
dashboard.start_loop()
class Explore:
r"""Mentalab Explore device"""
def __init__(self):
self.is_connected = False
self.stream_processor = None
self.recorders = {}
self.device_name = None
def connect(self, device_name=None, mac_address=None):
r"""
Connects to the nearby device. If there are more than one device, the user is asked to choose one of them.
Args:
device_name (str): Device name("Explore_XXXX"). Either mac address or name should be in the input
mac_address (str): The MAC address in format "XX:XX:XX:XX:XX:XX"
"""
if device_name:
self.device_name = device_name
else:
self.device_name = 'Explore_' + mac_address[-5:-3] + mac_address[
-2:]
logger.info(f"Connecting to {self.device_name} ...")
self.stream_processor = StreamProcessor()
self.stream_processor.start(device_name=device_name,
mac_address=mac_address)
cnt = 0
while "adc_mask" not in self.stream_processor.device_info:
logger.info("Waiting for device info packet...")
time.sleep(1)
if cnt >= 10:
raise ConnectionAbortedError(
"Could not get info packet from the device")
cnt += 1
logger.info(
'Device info packet has been received. Connection has been established. Streaming...'
)
logger.info("Device info: " + str(self.stream_processor.device_info))
self.is_connected = True
self.stream_processor.send_timestamp()
def disconnect(self):
r"""Disconnects from the device
"""
self.stream_processor.stop()
self.is_connected = False
logger.debug("Device has been disconnected.")
def acquire(self, duration=None):
r"""Start getting data from the device
Args:
duration (float): duration of acquiring data (if None it streams data endlessly)
"""
self._check_connection()
duration = self._check_duration(duration)
def callback(packet):
print(packet)
self.stream_processor.subscribe(callback=callback,
topic=TOPICS.raw_ExG)
logger.debug(f"Acquiring and printing data stream for {duration}s ...")
time.sleep(duration)
self.stream_processor.unsubscribe(callback=callback,
topic=TOPICS.raw_ExG)
def record_data(self,
file_name,
do_overwrite=False,
duration=None,
file_type='csv',
block=False):
r"""Records the data in real-time
Args:
file_name (str): Output file name
do_overwrite (bool): Overwrite if files exist already
duration (float): Duration of recording in seconds (if None records endlessly).
file_type (str): File type of the recorded file. Supported file types: 'csv', 'edf'
"""
self._check_connection()
# Check invalid characters
if set(r'<>{}[]~`*%').intersection(file_name):
raise ValueError("Invalid character in file name")
if file_type not in ['edf', 'csv']:
raise ValueError(
'{} is not a supported file extension!'.format(file_type))
duration = self._check_duration(duration)
exg_out_file = file_name + "_ExG"
orn_out_file = file_name + "_ORN"
marker_out_file = file_name + "_Marker"
self.recorders['exg'] = create_exg_recorder(
filename=exg_out_file,
file_type=file_type,
fs=self.stream_processor.device_info['sampling_rate'],
adc_mask=self.stream_processor.device_info['adc_mask'],
do_overwrite=do_overwrite)
self.recorders['orn'] = create_orn_recorder(filename=orn_out_file,
file_type=file_type,
do_overwrite=do_overwrite)
if file_type == 'csv':
self.recorders['marker'] = create_marker_recorder(
filename=marker_out_file, do_overwrite=do_overwrite)
elif file_type == 'edf':
self.recorders['marker'] = self.recorders['exg']
self.stream_processor.subscribe(
callback=self.recorders['exg'].write_data, topic=TOPICS.raw_ExG)
self.stream_processor.subscribe(
callback=self.recorders['orn'].write_data, topic=TOPICS.raw_orn)
self.stream_processor.subscribe(
callback=self.recorders['marker'].set_marker, topic=TOPICS.marker)
logger.info("Recording...")
self.recorders['timer'] = Timer(duration, self.stop_recording)
self.recorders['timer'].start()
if block:
try:
while self.recorders['timer'].is_alive():
time.sleep(.3)
except KeyboardInterrupt:
logger.info(
"Got Keyboard Interrupt while recording in blocked mode!")
self.stop_recording()
def stop_recording(self):
"""Stop recording"""
self.stream_processor.unsubscribe(
callback=self.recorders['exg'].write_data, topic=TOPICS.raw_ExG)
self.stream_processor.unsubscribe(
callback=self.recorders['orn'].write_data, topic=TOPICS.raw_orn)
self.stream_processor.unsubscribe(
callback=self.recorders['marker'].set_marker, topic=TOPICS.marker)
self.recorders['exg'].stop()
self.recorders['orn'].stop()
if self.recorders['exg'].file_type == 'csv':
self.recorders['marker'].stop()
if self.recorders['timer'].is_alive():
self.recorders['timer'].cancel()
logger.info('Recording stopped.')
def convert_bin(self,
bin_file,
out_dir='',
file_type='edf',
do_overwrite=False):
"""Convert a binary file to EDF or CSV file
Args:
bin_file (str): Path to the binary file recorded by Explore device
out_dir (str): Output directory path (must be relative path to the current working directory)
file_type (str): Output file type: 'edf' for EDF format and 'csv' for CSV format
do_overwrite (bool): Whether to overwrite an existing file
"""
if file_type not in ['edf', 'csv']:
raise ValueError('Invalid file type is given!')
self.recorders['file_type'] = file_type
head_path, full_filename = os.path.split(bin_file)
filename, extension = os.path.splitext(full_filename)
assert os.path.isfile(bin_file), "Error: File does not exist!"
assert extension == '.BIN', "File type error! File extension must be BIN."
out_full_path = os.path.join(os.getcwd(), out_dir)
exg_out_file = out_full_path + filename + '_exg'
orn_out_file = out_full_path + filename + '_orn'
marker_out_file = out_full_path + filename + '_marker'
self.stream_processor = StreamProcessor()
self.stream_processor.read_device_info(bin_file=bin_file)
self.recorders['exg'] = create_exg_recorder(
filename=exg_out_file,
file_type=self.recorders['file_type'],
fs=self.stream_processor.device_info['sampling_rate'],
adc_mask=self.stream_processor.device_info['adc_mask'],
do_overwrite=do_overwrite)
self.recorders['orn'] = create_orn_recorder(
filename=orn_out_file,
file_type=self.recorders['file_type'],
do_overwrite=do_overwrite)
if self.recorders['file_type'] == 'csv':
self.recorders['marker'] = create_marker_recorder(
filename=marker_out_file, do_overwrite=do_overwrite)
else:
self.recorders['marker'] = self.recorders['exg']
self.stream_processor.subscribe(
callback=self.recorders['exg'].write_data, topic=TOPICS.raw_ExG)
self.stream_processor.subscribe(
callback=self.recorders['orn'].write_data, topic=TOPICS.raw_orn)
self.stream_processor.subscribe(
callback=self.recorders['marker'].set_marker, topic=TOPICS.marker)
def device_info_callback(packet):
new_device_info = packet.get_info()
if not self.stream_processor.compare_device_info(new_device_info):
new_file_name = exg_out_file + "_" + str(
np.round(packet.timestamp, 0))
logger.warning("Creating a new file: " + new_file_name + '.' +
self.recorders['file_type'])
self.stream_processor.unsubscribe(
callback=self.recorders['exg'].write_data,
topic=TOPICS.raw_ExG)
self.stream_processor.unsubscribe(
callback=self.recorders['marker'].set_marker,
topic=TOPICS.marker)
self.recorders['exg'].stop()
self.recorders['exg'] = create_exg_recorder(
filename=new_file_name,
file_type=self.recorders['file_type'],
fs=self.stream_processor.device_info['sampling_rate'],
adc_mask=self.stream_processor.device_info['adc_mask'],
do_overwrite=do_overwrite)
self.recorders['marker'] = self.recorders['exg']
self.stream_processor.subscribe(
callback=self.recorders['exg'].write_data,
topic=TOPICS.raw_ExG)
self.stream_processor.subscribe(
callback=self.recorders['marker'].set_marker,
topic=TOPICS.marker)
self.stream_processor.subscribe(callback=device_info_callback,
topic=TOPICS.device_info)
self.stream_processor.open_file(bin_file=bin_file)
logger.info("Converting...")
while self.stream_processor.is_connected:
time.sleep(.1)
logger.info('Conversion finished.')
def push2lsl(self, duration=None):
r"""Push samples to two lsl streams (ExG and ORN streams)
Args:
duration (float): duration of data acquiring (if None it streams for one hour).
"""
self._check_connection()
duration = self._check_duration(duration)
lsl_server = LslServer(self.stream_processor.device_info)
self.stream_processor.subscribe(topic=TOPICS.raw_ExG,
callback=lsl_server.push_exg)
self.stream_processor.subscribe(topic=TOPICS.raw_orn,
callback=lsl_server.push_orn)
self.stream_processor.subscribe(topic=TOPICS.marker,
callback=lsl_server.push_marker)
time.sleep(duration)
logger.info("Data acquisition finished after " + duration +
" seconds.")
self.stream_processor.stop()
time.sleep(1)
def visualize(self, bp_freq=(1, 30), notch_freq=50):
r"""Visualization of the signal in the dashboard
Args:
bp_freq (tuple): Bandpass filter cut-off frequencies (low_cutoff_freq, high_cutoff_freq), No bandpass filter
if it is None.
notch_freq (int): Line frequency for notch filter (50 or 60 Hz), No notch filter if it is None
"""
self._check_connection()
if notch_freq:
self.stream_processor.add_filter(cutoff_freq=notch_freq,
filter_type='notch')
if bp_freq:
if bp_freq[0] and bp_freq[1]:
self.stream_processor.add_filter(cutoff_freq=bp_freq,
filter_type='bandpass')
elif bp_freq[0]:
self.stream_processor.add_filter(cutoff_freq=bp_freq[0],
filter_type='highpass')
elif bp_freq[1]:
self.stream_processor.add_filter(cutoff_freq=bp_freq[1],
filter_type='lowpass')
dashboard = explorepy.Dashboard(explore=self)
dashboard.start_server()
dashboard.start_loop()
def measure_imp(self):
"""
Visualization of the electrode impedances
Args:
notch_freq (int): Notch frequency for filtering the line noise (50 or 60 Hz)
"""
self._check_connection()
assert self.stream_processor.device_info['sampling_rate'] == 250, \
"Impedance mode only works in 250 Hz sampling rate!"
self.stream_processor.imp_initialize(notch_freq=50)
try:
dashboard = explorepy.Dashboard(explore=self, mode='impedance')
dashboard.start_server()
dashboard.start_loop()
except KeyboardInterrupt:
self.stream_processor.disable_imp()
def set_marker(self, code):
"""Sets a digital event marker while streaming
Args:
code (int): Marker code. It must be an integer larger than 7
(codes from 0 to 7 are reserved for hardware markers).
"""
self._check_connection()
self.stream_processor.set_marker(code=code)
def format_memory(self):
"""Format memory of the device"""
self._check_connection()
cmd = MemoryFormat()
self.stream_processor.configure_device(cmd)
def set_sampling_rate(self, sampling_rate):
"""Set sampling rate
Args:
sampling_rate (int): Desired sampling rate. Options: 250, 500, 1000
"""
self._check_connection()
if sampling_rate not in [250, 500, 1000]:
raise ValueError("Sampling rate must be 250, 500 or 1000.")
cmd = SetSPS(sampling_rate)
self.stream_processor.configure_device(cmd)
def reset_soft(self):
"""Reset the device to the default settings"""
self._check_connection()
cmd = SoftReset()
self.stream_processor.configure_device(cmd)
def set_channels(self, channel_mask):
"""Set the channel mask of the device
The channels can be disabled/enabled by calling this function and passing an integer which represents the
binary form of the mask. For example in a 4 channel device, if you want to disable channel 4, the adc mask
should be b'0111' (LSB is channel 1). The integer value of 0111 which is 7 must be given to this function
Args:
channel_mask (int): Integer representation of the binary channel mask
Examples:
>>> from explorepy.explore import Explore
>>> explore = Explore()
>>> explore.connect(device_name='Explore_2FA2')
>>> explore.set_channels(channel_mask=7) # disable channel 4 - mask:0111
"""
if not isinstance(channel_mask, int):
raise TypeError("Input must be an integer!")
self._check_connection()
cmd = SetCh(channel_mask)
self.stream_processor.configure_device(cmd)
def disable_module(self, module_name):
"""Disable module
Args:
module_name (str): Module to be disabled (options: 'ENV', 'ORN', 'EXG')
Examples:
>>> from explorepy.explore import Explore
>>> explore = Explore()
>>> explore.connect(device_name='Explore_2FA2')
>>> explore.disable_module('ORN')
"""
if module_name not in ['ORN', 'ENV', 'EXG']:
raise ValueError('Module name must be one of ORN, ENV or EXG.')
self._check_connection()
cmd = ModuleDisable(module_name)
self.stream_processor.configure_device(cmd)
def enable_module(self, module_name):
"""Enable module
Args:
module_name (str): Module to be disabled (options: 'ENV', 'ORN', 'EXG')
Examples:
>>> from explorepy.explore import Explore
>>> explore = Explore()
>>> explore.connect(device_name='Explore_2FA2')
>>> explore.enable_module('ORN')
"""
if module_name not in ['ORN', 'ENV', 'EXG']:
raise ValueError('Module name must be one of ORN, ENV or EXG.')
self._check_connection()
cmd = ModuleEnable(module_name)
self.stream_processor.configure_device(cmd)
def calibrate_orn(self, do_overwrite=False):
"""Calibrate orientation module
This method calibrates orientation sensors in order to get the real physical orientation in addition to raw sensor
data. While running this function you would need to move and rotate the device. This function will store
calibration info in the configuration file which will be used later during streaming to calculate physical
orientation from raw sensor data.
Args:
do_overwrite: to overwrite the calibration data if already exists or not
"""
assert not (PhysicalOrientation.check_calibre_data(device_name=self.device_name) and not(do_overwrite)), \
"Calibration data already exists!"
PhysicalOrientation.init_dir()
logger.info(
"Start recording for 100 seconds, please move the device around during this time, in all directions"
)
file_name = user_cache_dir(
appname="explorepy",
appauthor="Mentalab") + '//temp_' + self.device_name
self.record_data(file_name,
do_overwrite=do_overwrite,
duration=100,
file_type='csv')
time.sleep(105)
PhysicalOrientation.calibrate(cache_dir=file_name,
device_name=self.device_name)
def _check_connection(self):
assert self.is_connected, "Explore device is not connected. Please connect the device first."
@staticmethod
def _check_duration(duration):
if duration:
if duration <= 0:
raise ValueError("Recording time must be a positive number!")
else:
logger.warning(
"Duration has not been set by the user. The duration is 3600 seconds by default."
)
duration = 60 * 60 # one hour
return duration
def convert_bin(self,
bin_file,
out_dir='',
file_type='edf',
do_overwrite=False):
"""Convert a binary file to EDF or CSV file
Args:
bin_file (str): Path to the binary file recorded by Explore device
out_dir (str): Output directory path (must be relative path to the current working directory)
file_type (str): Output file type: 'edf' for EDF format and 'csv' for CSV format
do_overwrite (bool): Whether to overwrite an existing file
"""
if file_type not in ['edf', 'csv']:
raise ValueError('Invalid file type is given!')
self.recorders['file_type'] = file_type
head_path, full_filename = os.path.split(bin_file)
filename, extension = os.path.splitext(full_filename)
assert os.path.isfile(bin_file), "Error: File does not exist!"
assert extension == '.BIN', "File type error! File extension must be BIN."
out_full_path = os.path.join(os.getcwd(), out_dir)
exg_out_file = out_full_path + filename + '_exg'
orn_out_file = out_full_path + filename + '_orn'
marker_out_file = out_full_path + filename + '_marker'
self.stream_processor = StreamProcessor()
self.stream_processor.read_device_info(bin_file=bin_file)
self.recorders['exg'] = create_exg_recorder(
filename=exg_out_file,
file_type=self.recorders['file_type'],
fs=self.stream_processor.device_info['sampling_rate'],
adc_mask=self.stream_processor.device_info['adc_mask'],
do_overwrite=do_overwrite)
self.recorders['orn'] = create_orn_recorder(
filename=orn_out_file,
file_type=self.recorders['file_type'],
do_overwrite=do_overwrite)
if self.recorders['file_type'] == 'csv':
self.recorders['marker'] = create_marker_recorder(
filename=marker_out_file, do_overwrite=do_overwrite)
else:
self.recorders['marker'] = self.recorders['exg']
self.stream_processor.subscribe(
callback=self.recorders['exg'].write_data, topic=TOPICS.raw_ExG)
self.stream_processor.subscribe(
callback=self.recorders['orn'].write_data, topic=TOPICS.raw_orn)
self.stream_processor.subscribe(
callback=self.recorders['marker'].set_marker, topic=TOPICS.marker)
def device_info_callback(packet):
new_device_info = packet.get_info()
if not self.stream_processor.compare_device_info(new_device_info):
new_file_name = exg_out_file + "_" + str(
np.round(packet.timestamp, 0))
logger.warning("Creating a new file: " + new_file_name + '.' +
self.recorders['file_type'])
self.stream_processor.unsubscribe(
callback=self.recorders['exg'].write_data,
topic=TOPICS.raw_ExG)
self.stream_processor.unsubscribe(
callback=self.recorders['marker'].set_marker,
topic=TOPICS.marker)
self.recorders['exg'].stop()
self.recorders['exg'] = create_exg_recorder(
filename=new_file_name,
file_type=self.recorders['file_type'],
fs=self.stream_processor.device_info['sampling_rate'],
adc_mask=self.stream_processor.device_info['adc_mask'],
do_overwrite=do_overwrite)
self.recorders['marker'] = self.recorders['exg']
self.stream_processor.subscribe(
callback=self.recorders['exg'].write_data,
topic=TOPICS.raw_ExG)
self.stream_processor.subscribe(
callback=self.recorders['marker'].set_marker,
topic=TOPICS.marker)
self.stream_processor.subscribe(callback=device_info_callback,
topic=TOPICS.device_info)
self.stream_processor.open_file(bin_file=bin_file)
logger.info("Converting...")
while self.stream_processor.is_connected:
time.sleep(.1)
logger.info('Conversion finished.')