Merge pull request #18 from PayalLakra/bio_amptool

Timestamp in CSV & Raw EMG and EMG Envelope in different plots.

Author: lorforlinux

README.md

@@ -17,7 +17,7 @@ Chords Python script is designed to interface with an Arduino-based bioamplifier
 
 ## Requirements
 
--  Python 3.x
+-  Python 3.10
 - `pyserial` library (for serial communication)
 - `pylsl` library (for LSL streaming)
 - `argparse`, `time`, `csv`, `datetime` (standard libraries)
@@ -27,12 +27,12 @@ Chords Python script is designed to interface with an Arduino-based bioamplifier
 
 ## Installation
 
-1. Ensure you have Python 3.x installed.
+1. Ensure you have Python 3.10 installed.
 2. Create Virtual Environment
    ```bash
    python -m venv venv    
    ```
-   
+
    ```bash
    .\venv\Scripts\activate  
    ```

applications/emgenvelope.py

@@ -13,13 +13,25 @@ def __init__(self):
         self.setWindowTitle("Real-Time EMG Monitor with EMG Envelope")
         self.setGeometry(100, 100, 800, 600)
 
-        self.plot_widget = PlotWidget(self)
-        self.plot_widget.setBackground('w')
-        self.plot_widget.showGrid(x=True, y=True)
-
+        # Create layout
         layout = QVBoxLayout()
-        layout.addWidget(self.plot_widget)
 
+        # Create plot widgets for raw EMG and EMG envelope
+        self.raw_emg_plot = PlotWidget(self)
+        self.raw_emg_plot.setBackground('w')
+        self.raw_emg_plot.showGrid(x=True, y=True)
+        self.raw_emg_plot.setTitle("Raw EMG Signal")
+
+        self.envelope_plot = PlotWidget(self)
+        self.envelope_plot.setBackground('w')
+        self.envelope_plot.showGrid(x=True, y=True)
+        self.envelope_plot.setTitle("EMG Envelope")
+
+        # Add plots to layout
+        layout.addWidget(self.raw_emg_plot)
+        layout.addWidget(self.envelope_plot)
+
+        # Central widget
         central_widget = QWidget()
         central_widget.setLayout(layout)
         self.setCentralWidget(central_widget)
@@ -47,17 +59,20 @@ def __init__(self):
         self.rms_window_size = int(0.1 * self.sampling_rate)
 
         # Set fixed axis ranges
-        self.plot_widget.setXRange(0, 10, padding=0)
+        self.raw_emg_plot.setXRange(0, 10, padding=0)
+        self.envelope_plot.setXRange(0, 10, padding=0)
 
-        # Set y-axis limits based on sampling rate
+        # Set y-axis limits based on sampling rate for raw EMG
         if self.sampling_rate == 250:  
-            self.plot_widget.setYRange(400,600 ,padding=0)  # for R3 & ensuring no extra spaces at end
+            self.raw_emg_plot.setYRange(-((2**10)/2), ((2**10)/2), padding=0)  # for R3
+            self.envelope_plot.setYRange(0, ((2**10)/2), padding=0)  # for R3
         elif self.sampling_rate == 500:  
-            self.plot_widget.setYRange(400, 10000,padding=0)  # for R4 & ensuring no extra spaces at end
+            self.raw_emg_plot.setYRange(-((2**14)/2), ((2**14)/2), padding=0)  # for R4
+            self.envelope_plot.setYRange(0, ((2**14)/2), padding=0)  # for R4
 
         # Plot curves for EMG data and envelope
-        self.emg_curve = self.plot_widget.plot(self.time_data, self.emg_data, pen=pg.mkPen('b', width=1))
-        self.envelope_curve = self.plot_widget.plot(self.time_data, self.emg_data, pen=pg.mkPen('r', width=2))
+        self.emg_curve = self.raw_emg_plot.plot(self.time_data, self.emg_data, pen=pg.mkPen('b', width=1))
+        self.envelope_curve = self.envelope_plot.plot(self.time_data, self.emg_data, pen=pg.mkPen('r', width=2))
 
         # Timer for plot update
         self.timer = pg.QtCore.QTimer()
@@ -79,11 +94,9 @@ def update_plot(self):
 
             # Filter the EMG data
             filtered_emg = filtfilt(self.b, self.a, self.emg_data)
-            # print(filtered_emg)
 
             # Take absolute value before calculating RMS envelope
             abs_filtered_emg = np.abs(filtered_emg)
-            # print(abs_filtered_emg)
 
             # Calculate the RMS envelope
             rms_envelope = self.calculate_moving_rms(abs_filtered_emg, self.rms_window_size)

chords.py

@@ -166,7 +166,8 @@ def read_arduino_data(ser, csv_writer=None, inverted=False):
                         channel_data.append(float(value))  # Convert to float and add to channel data
 
                 if csv_writer:  # If CSV logging is enabled, write the data to the CSV file
-                    csv_writer.writerow([counter] + channel_data)
+                    current_timestamp = datetime.now().strftime('%H:%M:%S:%f')  # Get the current timestamp
+                    csv_writer.writerow([current_timestamp, counter] + channel_data)
                 if lsl_outlet:  # If LSL streaming is enabled, send the data to the LSL stream
                     lsl_outlet.push_sample(channel_data)
 
@@ -229,7 +230,7 @@ def parse_data(ser, lsl_flag=False, csv_flag=False, verbose=False, run_time=None
         csv_file = open(csv_filename, mode='w', newline='') if csv_flag else None  # Open CSV file if logging is
         if csv_file:
             csv_writer = csv.writer(csv_file)  # Create CSV writer
-            csv_writer.writerow(['Counter', 'Channel1', 'Channel2', 'Channel3', 'Channel4', 'Channel5', 'Channel6'])  # Write header
+            csv_writer.writerow(['Timestamp', 'Counter', 'Channel1', 'Channel2', 'Channel3', 'Channel4', 'Channel5', 'Channel6'])  # Write header
 
         end_time = time.time() + run_time if run_time else None
         send_command(ser, 'START')