/
resonance_frequency_gui.py
504 lines (362 loc) · 17.3 KB
/
resonance_frequency_gui.py
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import sys
import numpy as np
import pyqtgraph as pg
from PyQt5.QtChart import QChartView, QChart, QBarSet, QBarSeries, QBarCategoryAxis, QValueAxis
from PyQt5.QtCore import QTimer
from PyQt5.QtCore import Qt
from PyQt5.QtGui import QPainter
from PyQt5.QtWidgets import QWidget, QApplication, QGridLayout, QMainWindow, QLabel, QPushButton, QFileDialog, QSlider, \
QProgressDialog, QErrorMessage
from brainflow.board_shim import BoardShim, BrainFlowInputParams
from brainflow.data_filter import DataFilter
from matplotlib import pyplot as plt
import global_config
import utils
class ResonanceFrequencyFinder(QMainWindow):
# AVAILABLE_WINDOW_SIZES = ["5 Sec", "8 Sec", "10 Sec", "15 Sec", "20 Sec"]
DEFAULT_GRAPH_PADDING = 2
DEFAULT_FFT_WINDOW_SIZE = 5
DEFAULT_SAMPLE_PADDING = 2
DEFAULT_RECORDING_DURATION = 30 + DEFAULT_SAMPLE_PADDING
DEFAULT_MIN_FREQUENCY = 17
DEFAULT_MAX_FREQUENCY = 35
DEFAULT_FREQUENCY_STEP = 2
# Used to create a band for which the average frequency amplitude is computed
DEFAULT_FREQUENCY_PADDING = 0.2
DEFAULT_BANDPASS_MIN = 8
DEFAULT_BANDPASS_MAX = 40
DEFAULT_C3_CHANNEL_INDEX = 4
DEFAULT_CZ_CHANNEL_INDEX = 2
DEFAULT_C4_CHANNEL_INDEX = 0
def __init__(self, board: BoardShim):
super().__init__()
self.setGeometry(0, 0, 1800, 900)
self.setWindowTitle("Resonance-Like Frequency")
self.board = board
self.recording_progress_dialog = None
self.eeg_data_buffer = utils.EegData()
self.reading_timer = QTimer()
self.recording = False
self.recording_reference = False
self.reference_eeg_data = utils.EegData()
self.index_generator = utils.FrequencyIndexGenerator(global_config.SAMPLING_RATE)
self.eeg_sample_count = 0
self.root_widget = QWidget()
self.root_layout = QGridLayout()
self.root_widget.setLayout(self.root_layout)
self.setCentralWidget(self.root_widget)
title = QLabel("<h1>Resonance Frequency Finder</h1>")
title.setAlignment(Qt.AlignCenter)
self.root_layout.addWidget(title, 0, 0, 1, 3)
# window_size_label = QLabel("window size: ")
# window_size_label.setAlignment(Qt.AlignRight)
# self.window_size_combo_box = QComboBox()
# self.window_size_combo_box.addItems(self.AVAILABLE_WINDOW_SIZES)
self.root_directory_label = QLabel()
self.select_root_directory = QPushButton("Select/Change")
self.select_root_directory.clicked.connect(self.pick_root_directory)
self.record_btn = QPushButton("Record")
self.record_btn.setEnabled(False)
self.record_btn.clicked.connect(self.record_clicked)
self.record_reference_btn = QPushButton("Record Reference")
self.record_reference_btn.clicked.connect(self.record_reference_clicked)
# self.root_layout.addWidget(utils.construct_horizontal_box([
# window_size_label, self.window_size_combo_box, self.record_btn
# ]), 1, 0, 1, 3)
self.load_results_btn = QPushButton("Load Existing Data")
self.load_results_btn.clicked.connect(self.load_existing_data)
self.root_layout.addWidget(utils.construct_horizontal_box([
self.record_btn, self.record_reference_btn, self.root_directory_label,
self.select_root_directory, self.load_results_btn
]), 1, 0, 1, 3)
self.current_freq_label = QLabel()
self.root_layout.addWidget(utils.construct_horizontal_box([self.current_freq_label]), 2, 0, 1, 3)
self.frequency_slider = QSlider()
self.frequency_slider.setRange(self.DEFAULT_MIN_FREQUENCY, self.DEFAULT_MAX_FREQUENCY)
self.frequency_slider.setSingleStep(self.DEFAULT_FREQUENCY_STEP)
self.frequency_slider.setTickInterval(self.DEFAULT_FREQUENCY_STEP)
self.frequency_slider.valueChanged.connect(self.update_freq_label)
self.frequency_slider.setTickPosition(QSlider.TicksBelow)
self.frequency_slider.setOrientation(Qt.Horizontal)
min_freq_label = QLabel(f"<b>{self.DEFAULT_MIN_FREQUENCY} Hz</b>")
max_freq_label = QLabel(f"<b>{self.DEFAULT_MAX_FREQUENCY} Hz</b>")
self.root_layout.addWidget(utils.construct_horizontal_box([
min_freq_label, self.frequency_slider, max_freq_label
]), 3, 0, 1, 3)
self.c3_amplitude_bar_set = QBarSet("Electrode C3")
self.cz_amplitude_bar_set = QBarSet("Electrode Cz")
self.c4_amplitude_bar_set = QBarSet("Electrode C4")
self.frequencies = []
for freq in range(self.DEFAULT_MIN_FREQUENCY, self.DEFAULT_MAX_FREQUENCY + 1, self.DEFAULT_FREQUENCY_STEP):
self.frequencies.append(f"{freq} Hz")
self.c3_amplitude_bar_set.append(1)
self.cz_amplitude_bar_set.append(1)
self.c4_amplitude_bar_set.append(1)
self.freq_axis = QBarCategoryAxis()
self.freq_axis.append(self.frequencies)
self.amplitude_axis = QValueAxis()
self.amplitude_axis.setRange(0, 4)
self.freq_chart = QChart()
self.freq_chart.setAnimationOptions(QChart.SeriesAnimations)
self.electrodes_data_series = QBarSeries()
self.electrodes_data_series.append(self.c3_amplitude_bar_set)
self.electrodes_data_series.append(self.cz_amplitude_bar_set)
self.electrodes_data_series.append(self.c4_amplitude_bar_set)
self.freq_chart.addSeries(self.electrodes_data_series)
self.freq_chart.setTitle("<h1>Frequency Amplitude Increase</h1>")
self.freq_chart.addAxis(self.freq_axis, Qt.AlignBottom)
self.freq_chart.addAxis(self.amplitude_axis, Qt.AlignLeft)
self.electrodes_data_series.attachAxis(self.amplitude_axis)
self.electrodes_data_series.attachAxis(self.freq_axis)
self.frequency_amplitude_graph = QChartView(self.freq_chart)
self.frequency_amplitude_graph.setRenderHint(QPainter.Antialiasing)
self.root_layout.addWidget(self.frequency_amplitude_graph, 4, 0, 15, 3)
self.auto_adjust_axis()
def update_freq_label(self):
self.current_freq_label.setText("Selected Frequency: {} Hz".format(self.frequency_slider.value()))
def pick_root_directory(self):
path = QFileDialog.getExistingDirectory(self, "Root Directory...")
self.root_directory_label.setText(path)
def record_clicked(self, reference: bool = False):
# selected_window_text = self.window_size_combo_box.currentText()
# window_size_text = selected_window_text.replace(" Sec", "")
# window_size = -1
#
# if utils.is_integer(window_size_text):
# window_size = int(window_size_text)
# else:
# print("Invalid window size...")
# return
# window_size_in_samples = window_size * SAMPLING_RATE
recording_duration_in_samples = self.DEFAULT_RECORDING_DURATION * global_config.SAMPLING_RATE
if not reference and (self.frequency_slider.value() - self.DEFAULT_MIN_FREQUENCY) % self.DEFAULT_FREQUENCY_STEP != 0:
err = QErrorMessage(self)
err.showMessage("Invalid Frequency Selected")
err.exec()
return
self.recording_progress_dialog = \
QProgressDialog("Reading EEG data from board...", "Stop Recording", 0, int(recording_duration_in_samples), self)
self.recording_progress_dialog.setWindowTitle("Reading Data, Please Wait...")
self.recording_progress_dialog.setWindowModality(Qt.WindowModal)
self.recording_progress_dialog.show()
if reference:
self.recording_reference = True
else:
self.recording = True
self.eeg_data_buffer.clear()
self.board.start_stream()
self.reading_timer = QTimer()
self.reading_timer.timeout.connect(self.read_data)
self.reading_timer.start(100)
def record_reference_clicked(self):
print("Record reference clicked")
if self.reference_eeg_data.get_channel_data(0).shape[0] > 0:
self.reference_eeg_data.clear()
self.record_clicked(reference=True)
def read_data(self):
if not self.recording and not self.recording_reference:
return
recording_duration_in_samples = self.recording_progress_dialog.maximum()
if self.recording_reference:
if self.reference_eeg_data.get_channel_data(0).shape[0] > recording_duration_in_samples or\
self.recording_progress_dialog.wasCanceled():
self.stop_recording(True)
return
if self.recording:
if self.recording_progress_dialog.wasCanceled() or\
self.eeg_data_buffer.get_channel_data(0).shape[0] > recording_duration_in_samples:
self.stop_recording(self.recording_reference)
return
if self.board.get_board_data_count() > 0:
raw_data = self.board.get_board_data()
raw_eeg_data = utils.extract_eeg_data(raw_data, global_config.BOARD_ID)
self.eeg_sample_count += raw_eeg_data.shape[1]
path = self.root_directory_label.text()
if path != "":
full_path = path + "/" + global_config.RESONANCE_DATA_FILE_NAME
DataFilter.write_file(raw_eeg_data, full_path, "a")
# c3 = raw_eeg_data[self.DEFAULT_C3_CHANNEL_INDEX, :]
# cz = raw_eeg_data[self.DEFAULT_CZ_CHANNEL_INDEX, :]
# c4 = raw_eeg_data[self.DEFAULT_C4_CHANNEL_INDEX, :]
if self.recording_reference:
self.reference_eeg_data.append_data(raw_eeg_data)
print(f"reference size: {self.reference_eeg_data.sample_count()}")
self.recording_progress_dialog.setValue(self.reference_eeg_data.get_channel_data(0).shape[0])
else:
self.eeg_data_buffer.append_data(raw_eeg_data)
print(f"data size: {self.eeg_data_buffer.sample_count()}")
self.recording_progress_dialog.setValue(self.eeg_data_buffer.get_channel_data(0).shape[0])
def load_existing_data(self):
path = QFileDialog.getExistingDirectory(self, "Root Directory...")
if path == "":
return
filter_settings = utils.FilterSettings(global_config.SAMPLING_RATE, self.DEFAULT_BANDPASS_MIN, self.DEFAULT_BANDPASS_MAX)
frequencies, eeg_data, reference_data = utils.load_slice_and_filter_resonance_data(path, filter_settings)
print(frequencies)
size = len(frequencies)
x = np.arange(size)
x_ticks = []
plot_data = np.zeros((3, size))
for i in range(size):
current_eeg_data = eeg_data[i]
freq = frequencies[i]
x_ticks.append(f"{freq} Hz")
freq_band = utils.FrequencyBand(
freq - self.DEFAULT_FREQUENCY_PADDING,
freq + self.DEFAULT_FREQUENCY_PADDING)
reference_c3_extractor = reference_data.feature_extractor(
self.DEFAULT_C3_CHANNEL_INDEX, global_config.SAMPLING_RATE
)
reference_cz_extractor = reference_data.feature_extractor(
self.DEFAULT_CZ_CHANNEL_INDEX, global_config.SAMPLING_RATE
)
reference_c4_extractor = reference_data.feature_extractor(
self.DEFAULT_C4_CHANNEL_INDEX, global_config.SAMPLING_RATE
)
data_c3_extractor = current_eeg_data.feature_extractor(
self.DEFAULT_C3_CHANNEL_INDEX, global_config.SAMPLING_RATE
)
data_cz_extractor = current_eeg_data.feature_extractor(
self.DEFAULT_CZ_CHANNEL_INDEX, global_config.SAMPLING_RATE
)
data_c4_extractor = current_eeg_data.feature_extractor(
self.DEFAULT_C4_CHANNEL_INDEX, global_config.SAMPLING_RATE
)
c3_diff, cz_diff, c4_diff = self.amplitude_diff(freq_band, reference_c3_extractor, reference_cz_extractor,
reference_c4_extractor, data_c3_extractor,
data_cz_extractor, data_c4_extractor)
plot_data[0, i] = c3_diff
plot_data[1, i] = cz_diff
plot_data[2, i] = c4_diff
plt.figure()
plt.title("Amplitude Increase")
plt.bar(x, plot_data[0], width=0.25, label="C3 amplitude increase")
plt.bar(x + 0.25, plot_data[1], width=0.25, label="Cz amplitude increase")
plt.bar(x + 0.50, plot_data[2], width=0.25, label="C4 amplitude increase")
plt.xticks(x + 0.25, x_ticks)
plt.ylabel("Average Band Amplitude")
plt.legend(loc="best")
plt.show()
def amplitude_diff(self, freq_band, ref_c3_extractor, ref_cz_extractor, ref_c4_extractor, data_c3_extractor, data_cz_extractor, data_c4_extractor):
ref_c3_amplitude = ref_c3_extractor.average_band_amplitude(freq_band, self.DEFAULT_FFT_WINDOW_SIZE)
ref_cz_amplitude = ref_cz_extractor.average_band_amplitude(freq_band, self.DEFAULT_FFT_WINDOW_SIZE)
ref_c4_amplitude = ref_c4_extractor.average_band_amplitude(freq_band, self.DEFAULT_FFT_WINDOW_SIZE)
data_c3_amplitude = data_c3_extractor.average_band_amplitude(freq_band, self.DEFAULT_FFT_WINDOW_SIZE)
data_cz_amplitude = data_cz_extractor.average_band_amplitude(freq_band, self.DEFAULT_FFT_WINDOW_SIZE)
data_c4_amplitude = data_c4_extractor.average_band_amplitude(freq_band, self.DEFAULT_FFT_WINDOW_SIZE)
c3_diff = data_c3_amplitude - ref_c3_amplitude
cz_diff = data_cz_amplitude - ref_cz_amplitude
c4_diff = data_c4_amplitude - ref_c4_amplitude
return c3_diff, cz_diff, c4_diff
# return data_c3_amplitude, data_cz_amplitude, data_c4_amplitude
def stop_recording(self, reference: bool = False):
if self.reading_timer is not None:
self.reading_timer.deleteLater()
self.board.stop_stream()
self.recording = False
self.recording_reference = False
self.recording_progress_dialog.setValue(self.recording_progress_dialog.maximum())
recording_duration_in_samples = self.recording_progress_dialog.maximum()
selected_freq = self.frequency_slider.value()
if reference:
sample_count = min(self.reference_eeg_data.get_channel_data(0).shape[0], recording_duration_in_samples)
sample_count -= global_config.SAMPLING_RATE * self.DEFAULT_SAMPLE_PADDING
self.index_generator.add_slice(0, self.eeg_sample_count - sample_count, self.eeg_sample_count)
else:
sample_count = min(self.eeg_data_buffer.get_channel_data(0).shape[0], recording_duration_in_samples)
sample_count -= global_config.SAMPLING_RATE * self.DEFAULT_SAMPLE_PADDING
self.index_generator.add_slice(selected_freq, self.eeg_sample_count - sample_count, self.eeg_sample_count)
if self.root_directory_label.text() != "":
self.index_generator.write_to_file(self.root_directory_label.text())
QApplication.beep()
start = self.DEFAULT_SAMPLE_PADDING * global_config.SAMPLING_RATE
if reference:
print(f"reference size: {self.reference_eeg_data.sample_count()}")
self.record_btn.setEnabled(True)
# self.record_reference_btn.setEnabled(False)
self.reference_eeg_data.filter_all_channels(
global_config.SAMPLING_RATE, self.DEFAULT_BANDPASS_MIN, self.DEFAULT_BANDPASS_MAX, True
)
self.reference_eeg_data = utils.EegData(self.reference_eeg_data.to_row_array()[:, start:])
print("Reference data saved...")
else:
print("Stopping the recording...")
print("Filtering data...")
self.eeg_data_buffer.filter_all_channels(
global_config.SAMPLING_RATE, self.DEFAULT_BANDPASS_MIN, self.DEFAULT_BANDPASS_MAX, subtract_average=True
)
self.eeg_data_buffer = utils.EegData(self.eeg_data_buffer.to_row_array()[:, start:])
print(f"data size: {self.eeg_data_buffer.sample_count()}")
reference_c3_extractor = self.reference_eeg_data.feature_extractor(
self.DEFAULT_C3_CHANNEL_INDEX, global_config.SAMPLING_RATE
)
reference_cz_extractor = self.reference_eeg_data.feature_extractor(
self.DEFAULT_CZ_CHANNEL_INDEX, global_config.SAMPLING_RATE
)
reference_c4_extractor = self.reference_eeg_data.feature_extractor(
self.DEFAULT_C4_CHANNEL_INDEX, global_config.SAMPLING_RATE
)
data_c3_extractor = self.eeg_data_buffer.feature_extractor(
self.DEFAULT_C3_CHANNEL_INDEX, global_config.SAMPLING_RATE
)
data_cz_extractor = self.eeg_data_buffer.feature_extractor(
self.DEFAULT_CZ_CHANNEL_INDEX, global_config.SAMPLING_RATE
)
data_c4_extractor = self.eeg_data_buffer.feature_extractor(
self.DEFAULT_C4_CHANNEL_INDEX, global_config.SAMPLING_RATE
)
for i in range(self.c3_amplitude_bar_set.count()):
current_freq = int(self.frequencies[i].replace(" Hz", ""))
if current_freq == selected_freq:
freq_band = utils.FrequencyBand(
current_freq - self.DEFAULT_FREQUENCY_PADDING,
current_freq + self.DEFAULT_FREQUENCY_PADDING)
c3_diff, cz_diff, c4_diff = self.amplitude_diff(freq_band, reference_c3_extractor,reference_cz_extractor, reference_c4_extractor,
data_c3_extractor, data_cz_extractor, data_c4_extractor)
print(f"C3 diff = {c3_diff}")
print(f"Cz diff = {cz_diff}")
print(f"C4 diff = {c4_diff}")
self.c3_amplitude_bar_set.replace(i, c3_diff)
self.cz_amplitude_bar_set.replace(i, cz_diff)
self.c4_amplitude_bar_set.replace(i, c4_diff)
utils.auto_adjust_axis(self.amplitude_axis,
[self.c3_amplitude_bar_set, self.cz_amplitude_bar_set, self.c4_amplitude_bar_set], self.DEFAULT_GRAPH_PADDING)
def auto_adjust_axis(self):
# Adjust the range so that everything is visible and add some gaps
c3_min = sys.maxsize
cz_min = sys.maxsize
c4_min = sys.maxsize
c3_max = -sys.maxsize
cz_max = -sys.maxsize
c4_max = -sys.maxsize
for i in range(self.c3_amplitude_bar_set.count()):
c3_min = min(c3_min, self.c3_amplitude_bar_set.at(i))
cz_min = min(cz_min, self.cz_amplitude_bar_set.at(i))
c4_min = min(c4_min, self.c4_amplitude_bar_set.at(i))
c3_max = max(c3_max, self.c3_amplitude_bar_set.at(i))
cz_max = max(cz_max, self.cz_amplitude_bar_set.at(i))
c4_max = max(c4_max, self.c4_amplitude_bar_set.at(i))
print("c3 min = {}, cz min = {}, c4 min = {}".format(c3_min, cz_min, c4_min))
print("c3 max = {}, cz max = {}, c4 max = {}".format(c3_max, cz_max, c4_max))
axis_min = min(0, c3_min, cz_min, c4_min) - self.DEFAULT_GRAPH_PADDING
axis_max = max(0, c3_max, cz_max, c4_max) + self.DEFAULT_GRAPH_PADDING
print("axis min = {}, axis max = {}".format(axis_min, axis_max))
self.amplitude_axis.setMin(axis_min)
self.amplitude_axis.setMax(axis_max)
def main():
app = QApplication([])
app.setStyle(global_config.APP_STYLE)
BoardShim.enable_board_logger()
params = BrainFlowInputParams()
params.serial_port = utils.cyton_port()
board = BoardShim(global_config.BOARD_ID, params)
# Switch to using white background and black foreground
pg.setConfigOption('background', 'w')
pg.setConfigOption('foreground', 'k')
window = ResonanceFrequencyFinder(board)
window.show()
board.prepare_session()
app.exec()
board.release_session()
if __name__ == "__main__":
main()