Updating eog.py file: Now blink detection is better and also now the peaks are to marked till new data is overwrite on the old one.

Author: PayalLakra

applications/eog.py

@@ -1,318 +1,3 @@
-# import numpy as np
-# from scipy.signal import butter, filtfilt
-# from PyQt5.QtWidgets import QApplication, QVBoxLayout, QMainWindow, QWidget, QHBoxLayout
-# import pyqtgraph as pg
-# import pylsl
-# import sys
-
-# class EOGMonitor(QMainWindow):
-#     def __init__(self):
-#         super().__init__()
-
-#         self.setWindowTitle("Real-Time EOG Monitor - Eye Blink Detection")
-#         self.setGeometry(100, 100, 800, 400)
-
-#         # Create layout
-#         layout = QVBoxLayout()
-#         central_widget = QWidget()
-#         central_widget.setLayout(layout)
-#         self.setCentralWidget(central_widget)
-
-#         # Create plot widget for EOG
-#         self.eog_plot = pg.PlotWidget(self)
-#         self.eog_plot.setBackground('w')
-#         self.eog_plot.showGrid(x=True, y=True)
-#         self.eog_plot.setTitle("Filtered EOG Signal (Low Pass: 10 Hz)")
-
-#         # Bottom layout for Blink Detection
-#         self.bottom_layout = QHBoxLayout()
-
-#         # Blink detection plot
-#         self.blink_plot = pg.PlotWidget(self)
-#         self.blink_plot.setBackground('w')
-#         self.blink_plot.showGrid(x=True, y=True)
-#         self.blink_plot.setYRange(0, 1, padding=0)
-#         self.blink_plot.setMouseEnabled(x=False, y=False)  # Disable zoom
-#         self.blink_plot.setTitle("Blink Detection")
-
-#         # Add both plots to the layout
-#         layout.addWidget(self.eog_plot)
-#         layout.addWidget(self.blink_plot)
-
-#         # Set up LSL stream inlet
-#         streams = pylsl.resolve_stream('name', 'BioAmpDataStream')
-#         if not streams:
-#             print("No LSL stream found!")
-#             sys.exit(0)
-#         self.inlet = pylsl.StreamInlet(streams[0])
-
-#         self.sampling_rate = int(self.inlet.info().nominal_srate())
-#         print(f"Sampling rate: {self.sampling_rate} Hz")
-
-#         self.buffer_size = self.sampling_rate * 5  # 5 seconds buffer for recent data
-#         self.eog_data = np.zeros(self.buffer_size)
-#         self.time_data = np.linspace(0, 5, self.buffer_size)
-#         self.blink_data = np.zeros(self.buffer_size)  # Blink data array
-#         self.current_index = 0
-
-#         # Low-pass filter for EOG (10 Hz)
-#         self.b, self.a = butter(4, 10.0 / (0.5 * self.sampling_rate), btype='low')
-
-#         self.eog_plot.setXRange(0, 5, padding=0)
-#         if self.sampling_rate == 250:
-#             self.eog_plot.setYRange(-((2**10)/2), ((2**10)/2), padding=0)
-#         elif self.sampling_rate == 500:
-#             self.eog_plot.setYRange(-((2**14)/2), ((2**14)/2), padding=0)
-
-#         # Plot curves
-#         self.eog_curve = self.eog_plot.plot(self.time_data, self.eog_data, pen=pg.mkPen('b', width=1))
-#         self.blink_curve = self.blink_plot.plot(self.time_data, self.blink_data, pen=pg.mkPen('r', width=2))
-
-#         # Timer for plot update
-#         self.timer = pg.QtCore.QTimer()
-#         self.timer.timeout.connect(self.update_plot)
-#         self.timer.start(15)
-
-#     def update_plot(self):
-#         samples, _ = self.inlet.pull_chunk(timeout=0.0, max_samples=30)
-#         if samples:
-#             for sample in samples:
-#                 # Overwrite the oldest data point in the buffer
-#                 self.eog_data[self.current_index] = sample[0]
-#                 self.current_index = (self.current_index + 1) % self.buffer_size
-
-#             filtered_eog = filtfilt(self.b, self.a, self.eog_data)
-
-#             # Update curve with the filtered EOG signal (5-second window)
-#             self.eog_plot.clear()    # Clear the previous peaks from the plot
-#             self.eog_curve = self.eog_plot.plot(self.time_data, filtered_eog, pen=pg.mkPen('b', width=1))
-
-#             # Peak detection (1-second moving window)
-#             self.detect_blinks(filtered_eog)
-
-#     def detect_blinks(self, filtered_eog):
-#         mean_signal = np.mean(filtered_eog)
-#         stdev_signal = np.std(filtered_eog)
- 
-#         threshold = mean_signal + (2 * stdev_signal)
-
-#         # Calculate the start and end indices for the 1-second window
-#         window_size = 1 * self.sampling_rate  # 1 seconds in samples
-#         start_index = self.current_index - window_size
-#         if start_index < 0:
-#             start_index = 0
-#         end_index = self.current_index
-
-#         # Use a 1-second window for peak detection
-#         filtered_window = filtered_eog[start_index:end_index]
-#         peaks = self.detect_peaks(filtered_window, threshold)
-
-#         # Reset blink data to zero
-#         self.blink_data[:] = 0
-
-#         # Mark detected peaks in blink_data
-#         for peak in peaks:
-#             full_peak_index = start_index + peak
-#             self.blink_data[full_peak_index] = 1
-
-#         # Mark peaks with red dots on the EOG plot
-#         self.eog_plot.plot(self.time_data[start_index:end_index][peaks], filtered_window[peaks], pen=None, symbol='o', symbolPen='r', symbolSize=6)
-
-#         # Update the blink plot with the current blink data
-#         self.blink_curve.setData(self.time_data, self.blink_data)
-
-#     def detect_peaks(self, signal, threshold):
-#         # List to store detected peak indices
-#         peaks = []
-#         prev_peak_time = None  # Variable to store the timestamp of the previous peak
-#         min_peak_gap = 0.1  # Minimum time gap between two peaks in seconds
-
-#         for i in range(1, len(signal) - 1):
-#             # Check if the current point is greater than the previous and next point (local maximum)
-#             if signal[i] > signal[i - 1] and signal[i] > signal[i + 1] and signal[i] > threshold:
-#                 current_peak_time = i / self.sampling_rate  # Time in seconds based on the sampling rate
-
-#                 if prev_peak_time is not None:
-#                     time_gap = current_peak_time - prev_peak_time
-#                     if time_gap < min_peak_gap:  # Ignore if the time gap is less than the threshold
-#                         continue
-
-#                 peaks.append(i)
-#                 prev_peak_time = current_peak_time  # Update previous peak time
-
-#         return peaks
-
-# if __name__ == "__main__":
-#     app = QApplication(sys.argv)
-#     window = EOGMonitor()
-#     window.show()
-#     sys.exit(app.exec_())
-
-
-
-
-
-# import numpy as np
-# from scipy.signal import butter, lfilter
-# from PyQt5.QtWidgets import QApplication, QVBoxLayout, QMainWindow, QWidget, QHBoxLayout
-# import pyqtgraph as pg
-# import pylsl
-# import sys
-# import time
-
-# class EOGMonitor(QMainWindow):
-#     def __init__(self):
-#         super().__init__()
-
-#         self.setWindowTitle("Real-Time EOG Monitor - Eye Blink Detection")
-#         self.setGeometry(100, 100, 800, 400)
-
-#         # Create layout
-#         layout = QVBoxLayout()
-#         central_widget = QWidget()
-#         central_widget.setLayout(layout)
-#         self.setCentralWidget(central_widget)
-
-#         # Create plot widget for EOG
-#         self.eog_plot = pg.PlotWidget(self)
-#         self.eog_plot.setBackground('w')
-#         self.eog_plot.showGrid(x=True, y=True)
-#         self.eog_plot.setTitle("Filtered EOG Signal (Low Pass: 10 Hz)")
-
-#         # Bottom layout for Blink Detection
-#         self.bottom_layout = QHBoxLayout()
-
-#         # Blink detection plot
-#         self.blink_plot = pg.PlotWidget(self)
-#         self.blink_plot.setBackground('w')
-#         self.blink_plot.showGrid(x=True, y=True)
-#         self.blink_plot.setYRange(0, 1, padding=0)
-#         self.blink_plot.setMouseEnabled(x=False, y=False)  # Disable zoom
-#         self.blink_plot.setTitle("Blink Detection")
-
-#         # Add both plots to the layout
-#         layout.addWidget(self.eog_plot)
-#         layout.addWidget(self.blink_plot)
-
-#         # Set up LSL stream inlet
-#         streams = pylsl.resolve_stream('name', 'BioAmpDataStream')
-#         if not streams:
-#             print("No LSL stream found!")
-#             sys.exit(0)
-#         self.inlet = pylsl.StreamInlet(streams[0])
-
-#         self.sampling_rate = int(self.inlet.info().nominal_srate())
-#         print(f"Sampling rate: {self.sampling_rate} Hz")
-
-#         self.buffer_size = self.sampling_rate * 5  # 5 seconds buffer for recent data
-#         self.eog_data = np.zeros(self.buffer_size)
-#         self.time_data = np.linspace(0, 5, self.buffer_size)
-#         self.blink_data = np.zeros(self.buffer_size)  # Blink data array
-#         self.current_index = 0
-
-#         # Low-pass filter for EOG (10 Hz)
-#         self.b, self.a = butter(4, 10.0 / (0.5 * self.sampling_rate), btype='low')
-
-#         self.eog_plot.setXRange(0, 5, padding=0)
-#         if self.sampling_rate == 250:
-#             self.eog_plot.setYRange(-((2**10)/2), ((2**10)/2), padding=0)
-#         elif self.sampling_rate == 500:
-#             self.eog_plot.setYRange(-((2**14)/2), ((2**14)/2), padding=0)
-
-#         # Plot curves
-#         self.eog_curve = self.eog_plot.plot(self.time_data, self.eog_data, pen=pg.mkPen('b', width=1))
-#         self.blink_curve = self.blink_plot.plot(self.time_data, self.blink_data, pen=pg.mkPen('r', width=2))
-
-#         # List to store detected peaks with timestamps
-#         self.detected_peaks = []
-
-#         # Timer for plot update
-#         self.timer = pg.QtCore.QTimer()
-#         self.timer.timeout.connect(self.update_plot)
-#         self.timer.start(15)
-
-#     def update_plot(self):
-#         samples, _ = self.inlet.pull_chunk(timeout=0.0, max_samples=30)
-#         if samples:
-#             for sample in samples:
-#                 # Overwrite the oldest data point in the buffer
-#                 self.eog_data[self.current_index] = sample[0]
-#                 self.current_index = (self.current_index + 1) % self.buffer_size
-
-#             filtered_eog = lfilter(self.b, self.a, self.eog_data)
-
-#             # Update curve with the filtered EOG signal (5-second window)
-#             self.eog_plot.clear()    # Clear the previous peaks from the plot
-#             self.eog_curve = self.eog_plot.plot(self.time_data, filtered_eog, pen=pg.mkPen('b', width=1))
-
-#             # Peak detection (1-second moving window)
-#             self.detect_blinks(filtered_eog)
-
-#             # Clear out old peaks from self.detected_peaks after 5 seconds
-#             current_time = time.time()
-#             self.detected_peaks = [(index, t) for index, t in self.detected_peaks if current_time - t < 5]
-
-#             # Update the blink plot based on stored peaks
-#             self.blink_data[:] = 0  # Reset blink data
-#             for index, _ in self.detected_peaks:
-#                 if 0 <= index < self.buffer_size:
-#                     self.blink_data[index] = 1  # Keep blink data high at detected peaks
-
-#             # Mark the stored peaks on the EOG plot
-#             peak_indices = [index for index, t in self.detected_peaks]
-#             peak_values = [filtered_eog[i] for i in peak_indices]
-#             self.eog_plot.plot(self.time_data[peak_indices], peak_values, pen=None, symbol='o', symbolPen='r', symbolSize=6)
-
-#             # Update the blink plot with the current blink data
-#             self.blink_curve.setData(self.time_data, self.blink_data)
-
-#     def detect_blinks(self, filtered_eog):
-#         mean_signal = np.mean(filtered_eog)
-#         stdev_signal = np.std(filtered_eog)
-#         threshold = mean_signal + (2 * stdev_signal)
-
-#         # Calculate the start and end indices for the 1-second window
-#         window_size = 1 * self.sampling_rate
-#         start_index = self.current_index - window_size
-#         if start_index < 0:
-#             start_index = 0
-#         end_index = self.current_index
-
-#         # Use a 1-second window for peak detection
-#         filtered_window = filtered_eog[start_index:end_index]
-#         peaks = self.detect_peaks(filtered_window, threshold)
-
-#         # Mark detected peaks and store them with timestamps
-#         for peak in peaks:
-#             full_peak_index = start_index + peak
-#             self.detected_peaks.append((full_peak_index, time.time()))  # Add detected peak with current timestamp
-
-#     def detect_peaks(self, signal, threshold):
-#         peaks = []
-#         prev_peak_time = None  # Variable to store the timestamp of the previous peak
-#         min_peak_gap = 0.1  # Minimum time gap between two peaks in seconds
-
-#         for i in range(1, len(signal) - 1):
-#             if signal[i] > signal[i - 1] and signal[i] > signal[i + 1] and signal[i] > threshold:
-#                 current_peak_time = i / self.sampling_rate  # Time in seconds based on the sampling rate
-
-#                 if prev_peak_time is not None:
-#                     time_gap = current_peak_time - prev_peak_time
-#                     if time_gap < min_peak_gap:
-#                         continue
-
-#                 peaks.append(i)
-#                 prev_peak_time = current_peak_time
-
-#         return peaks
-
-# if __name__ == "__main__":
-#     app = QApplication(sys.argv)
-#     window = EOGMonitor()
-#     window.show()
-#     sys.exit(app.exec_())
-
-#Use deque that remove the oldest peak after 5 seconds.
 import numpy as np
 from scipy.signal import butter, lfilter
 from PyQt5.QtWidgets import QApplication, QVBoxLayout, QMainWindow, QWidget, QHBoxLayout
@@ -349,7 +34,7 @@ def __init__(self):
         self.blink_plot.setBackground('w')
         self.blink_plot.showGrid(x=True, y=True)
         self.blink_plot.setYRange(0, 1, padding=0)
-        self.blink_plot.setMouseEnabled(x=False, y=False)  # Disable zoom
+        self.blink_plot.setMouseEnabled(x=False, y=False)  # To Disable zoom functionality mark it as true
         self.blink_plot.setTitle("Blink Detection")
 
         # Add both plots to the layout
@@ -410,7 +95,7 @@ def update_plot(self):
             # Peak detection (1-second moving window)
             self.detect_blinks(filtered_eog)
 
-            # Clear out old peaks from the circular buffer after 4 seconds(because we want to clear the peaks just after the data overwrite.)
+            # Clear out old peaks from the circular buffer after 4 seconds(As we want to clear the peaks just after the data overwrite.)
             current_time = time.time()
             while self.detected_peaks and (current_time - self.detected_peaks[0][1] > 4):
                 self.detected_peaks.popleft()  # Remove old peaks from the buffer
@@ -432,7 +117,7 @@ def update_plot(self):
     def detect_blinks(self, filtered_eog):
         mean_signal = np.mean(filtered_eog)
         stdev_signal = np.std(filtered_eog)
-        threshold = mean_signal + (1.5 * stdev_signal)
+        threshold = mean_signal + (1.8 * stdev_signal)
 
         # Calculate the start and end indices for the 1-second window
         window_size = 1 * self.sampling_rate
@@ -453,7 +138,7 @@ def detect_blinks(self, filtered_eog):
     def detect_peaks(self, signal, threshold):
         peaks = []
         prev_peak_time = None  # Variable to store the timestamp of the previous peak
-        min_peak_gap = 0.01 # Minimum time gap between two peaks in seconds
+        min_peak_gap = 0.1 # Minimum time gap between two peaks in seconds
 
         for i in range(1, len(signal) - 1):
             if signal[i] > signal[i - 1] and signal[i] > signal[i + 1] and signal[i] > threshold: