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Experiment Class Refactor (update to #183), converting specific experiments to subclasses #184

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merged 24 commits into from
Aug 10, 2022
Merged

Experiment Class Refactor (update to #183), converting specific experiments to subclasses #184

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1634e81
First commit
Parvfect May 30, 2022
d48093a
Second commit
Parvfect May 30, 2022
f05f1c4
Modifications
Parvfect Jun 4, 2022
38993e6
Lol
Parvfect Jun 4, 2022
ba01229
Lol
Parvfect Jun 4, 2022
19ffcdc
Merge branch 'parv' into experimentClassFirstRun
Parvfect Jun 9, 2022
42d3f26
Incorporated N170 and p300, looking good for a PR
Parvfect Jun 9, 2022
76c5036
ssvep update
Parvfect Jun 9, 2022
dd958d2
Implementing subclasses instead of loose functions
Parvfect Jun 15, 2022
f208e08
fix: fixed import (brainflow updated API)
ErikBjare Jun 16, 2022
5db55f3
Playing around still
Parvfect Jun 17, 2022
efb1928
Fixing import errors
Parvfect Jun 17, 2022
251d04e
Merge branch 'master' of https://github.com/NeuroTechX/eeg-notebooks …
Parvfect Jun 17, 2022
7436444
Adding abstractmethod decorators
Parvfect Jun 17, 2022
ee7cca9
Still working on the import error
Parvfect Jun 17, 2022
d73abe0
Guess what's finally working
Parvfect Jun 27, 2022
ee5ab09
Comments and naming ticks
Parvfect Jul 6, 2022
cb7895b
More comments
Parvfect Jul 6, 2022
4815d28
Live coding demonstration
Parvfect Jul 7, 2022
3ec461a
ssvep adapted
Parvfect Jul 8, 2022
b1000bd
Adapting Auditory Oddball
Parvfect Jul 11, 2022
d9f53b2
changing save_fn to self.save_fun
Parvfect Jul 25, 2022
dc97fb5
This maybe the last big change
Parvfect Jul 29, 2022
ef3dba0
utils file changed, changes work through cli
Parvfect Aug 3, 2022
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28 changes: 19 additions & 9 deletions eegnb/cli/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,24 +7,26 @@

from eegnb.devices.eeg import EEG

from eegnb.experiments.visual_n170 import n170
from eegnb.experiments.visual_p300 import p300
from eegnb.experiments.visual_ssvep import ssvep
from eegnb.experiments import VisualN170
from eegnb.experiments import VisualP300
from eegnb.experiments import VisualSSVEP
from eegnb.experiments import AuditoryOddball
from eegnb.experiments.visual_cueing import cueing
from eegnb.experiments.visual_codeprose import codeprose
from eegnb.experiments.auditory_oddball import aob, diaconescu
from eegnb.experiments.auditory_oddball import diaconescu
from eegnb.experiments.auditory_ssaep import ssaep, ssaep_onefreq


# New Experiment Class structure has a different initilization, to be noted
experiments = {
"visual-N170": n170,
"visual-P300": p300,
"visual-SSVEP": ssvep,
"visual-N170": VisualN170(),
"visual-P300": VisualP300(),
"visual-SSVEP": VisualSSVEP(),
"visual-cue": cueing,
"visual-codeprose": codeprose,
"auditory-SSAEP orig": ssaep,
"auditory-SSAEP onefreq": ssaep_onefreq,
"auditory-oddball orig": aob,
"auditory-oddball orig": AuditoryOddball(),
"auditory-oddball diaconescu": diaconescu,
Comment on lines 21 to 30
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@ErikBjare ErikBjare Aug 11, 2022 •
edited
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These should not be instantiated globally, just leave the class in the dict and let the caller handle initialization.

So that, for example:

    "visual-N170": VisualN170(),

Just becomes

    "visual-N170": VisualN170,

}

Expand All @@ -42,7 +44,15 @@ def run_experiment(
):
if experiment in experiments:
module = experiments[experiment]
module.present(duration=record_duration, eeg=eeg_device, save_fn=save_fn) # type: ignore

# Condition added for different run types of old and new experiment class structure
if experiment == "visual-N170" or experiment == "visual-P300" or experiment == "visual-SSVEP" or experiment == "auditory-oddball orig":
module.duration = record_duration
module.eeg = eeg_device
module.save_fn = save_fn
module.run()
Comment on lines +49 to +53
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Should be replaced with:

if isinstance(experiment, BaseExperiment.__class__):
    exp = experiment(eeg=eeg, duration=record_duration, save_fn=save_fn)
    exp.run()

else:
module.present(duration=record_duration, eeg=eeg_device, save_fn=save_fn) # type: ignore
else:
print("\nError: Unknown experiment '{}'".format(experiment))
print("\nExperiment can be one of:")
Expand Down
57 changes: 29 additions & 28 deletions eegnb/devices/eeg.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,11 +14,17 @@
import numpy as np
import pandas as pd

from brainflow import BoardShim, BoardIds, BrainFlowInputParams
from brainflow.board_shim import BoardShim, BoardIds, BrainFlowInputParams
from muselsl import stream, list_muses, record, constants as mlsl_cnsts
from pylsl import StreamInfo, StreamOutlet, StreamInlet, resolve_byprop

from eegnb.devices.utils import get_openbci_usb, create_stim_array,SAMPLE_FREQS,EEG_INDICES,EEG_CHANNELS
from eegnb.devices.utils import (
get_openbci_usb,
create_stim_array,
SAMPLE_FREQS,
EEG_INDICES,
EEG_CHANNELS,
)


logger = logging.getLogger(__name__)
Expand All @@ -39,18 +45,19 @@
"notion2",
"freeeeg32",
"crown",
"museS_bfn", # bfn = brainflow with native bluetooth;
"museS_bfb", # bfb = brainflow with BLED dongle bluetooth
"museS_bfn", # bfn = brainflow with native bluetooth;
"museS_bfb", # bfb = brainflow with BLED dongle bluetooth
"muse2_bfn",
"muse2_bfb",
"muse2016_bfn",
"muse2016_bfb"
"muse2016_bfb",
]


class EEG:
device_name: str
stream_started: bool = False

def __init__(
self,
device=None,
Expand Down Expand Up @@ -85,8 +92,8 @@ def initialize_backend(self):
self.timestamp_channel = BoardShim.get_timestamp_channel(self.brainflow_id)
elif self.backend == "muselsl":
self._init_muselsl()
self._muse_get_recent() # run this at initialization to get some
# stream metadata into the eeg class
self._muse_get_recent() # run this at initialization to get some
# stream metadata into the eeg class

def _get_backend(self, device_name):
if device_name in brainflow_devices:
Expand Down Expand Up @@ -126,7 +133,7 @@ def _start_muse(self, duration):
print("will save to file: %s" % self.save_fn)
self.recording = Process(target=record, args=(duration, self.save_fn))
self.recording.start()

time.sleep(5)
self.stream_started = True
self.push_sample([99], timestamp=time.time())
Expand All @@ -137,7 +144,7 @@ def _stop_muse(self):
def _muse_push_sample(self, marker, timestamp):
self.muse_StreamOutlet.push_sample(marker, timestamp)

def _muse_get_recent(self, n_samples: int=256, restart_inlet: bool=False):
def _muse_get_recent(self, n_samples: int = 256, restart_inlet: bool = False):
if self._muse_recent_inlet and not restart_inlet:
inlet = self._muse_recent_inlet
else:
Expand All @@ -157,9 +164,8 @@ def _muse_get_recent(self, n_samples: int=256, restart_inlet: bool=False):
self.info = info
self.n_chans = n_chans

timeout = (n_samples/sfreq)+0.5
samples, timestamps = inlet.pull_chunk(timeout=timeout,
max_samples=n_samples)
timeout = (n_samples / sfreq) + 0.5
samples, timestamps = inlet.pull_chunk(timeout=timeout, max_samples=n_samples)

samples = np.array(samples)
timestamps = np.array(timestamps)
Expand Down Expand Up @@ -260,13 +266,13 @@ def _init_brainflow(self):

elif self.device_name == "muse2_bfn":
self.brainflow_id = BoardIds.MUSE_2_BOARD.value

elif self.device_name == "muse2_bfb":
self.brainflow_id = BoardIds.MUSE_2_BLED_BOARD.value

elif self.device_name == "muse2016_bfn":
self.brainflow_id = BoardIds.MUSE_2016_BOARD.value

elif self.device_name == "muse2016_bfb":
self.brainflow_id = BoardIds.MUSE_2016_BLED_BOARD.value

Expand All @@ -291,11 +297,13 @@ def _start_brainflow(self):
# only start stream if non exists
if not self.stream_started:
self.board.start_stream()

self.stream_started = True

# wait for signal to settle
if (self.device_name.find("cyton") != -1) or (self.device_name.find("ganglion") != -1):
if (self.device_name.find("cyton") != -1) or (
self.device_name.find("ganglion") != -1
):
# wait longer for openbci cyton / ganglion
sleep(10)
else:
Expand All @@ -314,21 +322,19 @@ def _stop_brainflow(self):

# Create a column for the stimuli to append to the EEG data
stim_array = create_stim_array(timestamps, self.markers)
timestamps = timestamps[ ..., None ]
timestamps = timestamps[..., None]

# Add an additional dimension so that shapes match
total_data = np.append(timestamps, eeg_data, 1)

# Append the stim array to data.
total_data = np.append(total_data, stim_array, 1)
total_data = np.append(total_data, stim_array, 1)

# Subtract five seconds of settling time from beginning
total_data = total_data[5 * self.sfreq :]
data_df = pd.DataFrame(total_data, columns=["timestamps"] + ch_names + ["stim"])
data_df.to_csv(self.save_fn, index=False)



def _brainflow_extract(self, data):
"""
Formats the data returned from brainflow to get
Expand Down Expand Up @@ -357,14 +363,12 @@ def _brainflow_extract(self, data):
eeg_data = data[:, BoardShim.get_eeg_channels(self.brainflow_id)]
timestamps = data[:, BoardShim.get_timestamp_channel(self.brainflow_id)]

return ch_names,eeg_data,timestamps

return ch_names, eeg_data, timestamps

def _brainflow_push_sample(self, marker):
last_timestamp = self.board.get_current_board_data(1)[self.timestamp_channel][0]
self.markers.append([marker, last_timestamp])


def _brainflow_get_recent(self, n_samples=256):

# initialize brainflow if not set
Expand Down Expand Up @@ -405,7 +409,6 @@ def start(self, fn, duration=None):
elif self.backend == "muselsl":
self._start_muse(duration)


def push_sample(self, marker, timestamp):
"""
Universal method for pushing a marker and its timestamp to store alongside the EEG data.
Expand Down Expand Up @@ -445,6 +448,4 @@ def get_recent(self, n_samples: int = 256):
sorted_cols = sorted(df.columns)
df = df[sorted_cols]


return df

14 changes: 7 additions & 7 deletions eegnb/devices/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,14 +3,14 @@
import platform
import serial

from brainflow import BoardShim, BoardIds
from brainflow.board_shim import BoardShim, BoardIds


# Default channel names for the various EEG devices.
EEG_CHANNELS = {
"muse2016": ['TP9', 'AF7', 'AF8', 'TP10', 'Right AUX'],
"muse2": ['TP9', 'AF7', 'AF8', 'TP10', 'Right AUX'],
"museS": ['TP9', 'AF7', 'AF8', 'TP10', 'Right AUX'],
"muse2016": ["TP9", "AF7", "AF8", "TP10", "Right AUX"],
"muse2": ["TP9", "AF7", "AF8", "TP10", "Right AUX"],
"museS": ["TP9", "AF7", "AF8", "TP10", "Right AUX"],
"muse2016_bfn": BoardShim.get_eeg_names(BoardIds.MUSE_2016_BOARD.value),
"muse2016_bfb": BoardShim.get_eeg_names(BoardIds.MUSE_2016_BLED_BOARD.value),
"muse2_bfn": BoardShim.get_eeg_names(BoardIds.MUSE_2_BOARD.value),
Expand All @@ -26,7 +26,7 @@
"notion1": BoardShim.get_eeg_names(BoardIds.NOTION_1_BOARD.value),
"notion2": BoardShim.get_eeg_names(BoardIds.NOTION_2_BOARD.value),
"crown": BoardShim.get_eeg_names(BoardIds.CROWN_BOARD.value),
"freeeeg32": [f'eeg_{i}' for i in range(0,32)],
"freeeeg32": [f"eeg_{i}" for i in range(0, 32)],
}

BRAINFLOW_CHANNELS = {
Expand Down Expand Up @@ -62,9 +62,9 @@
"muse2016": 256,
"muse2": 256,
"museS": 256,
"muse2016_bfn": BoardShim.get_sampling_rate(BoardIds.MUSE_2016_BOARD.value),
"muse2016_bfn": BoardShim.get_sampling_rate(BoardIds.MUSE_2016_BOARD.value),
"muse2016_bfb": BoardShim.get_sampling_rate(BoardIds.MUSE_2016_BLED_BOARD.value),
"muse2_bfn": BoardShim.get_sampling_rate(BoardIds.MUSE_2_BOARD.value),
"muse2_bfn": BoardShim.get_sampling_rate(BoardIds.MUSE_2_BOARD.value),
"muse2_bfb": BoardShim.get_sampling_rate(BoardIds.MUSE_2_BLED_BOARD.value),
"museS_bfn": BoardShim.get_sampling_rate(BoardIds.MUSE_S_BOARD.value),
"museS_bfb": BoardShim.get_sampling_rate(BoardIds.MUSE_S_BLED_BOARD.value),
Expand Down
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