generic improvements in muse device support

Signed-off-by: Andrey Parfenov <a1994ndrey@gmail.com>

Author: Andrey1994

docs/SupportedBoards.rst

@@ -0,0 +1,41 @@
+import argparse
+import time
+
+from brainflow.board_shim import BoardShim, BrainFlowInputParams, BoardIds, BrainFlowPresets
+
+
+def main():
+    BoardShim.enable_dev_board_logger()
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--duration', type=int, required=False, default=10)
+    parser.add_argument('--mac-address', type=str, required=False, default='')
+    parser.add_argument('--serial-number', type=str, required=False, default='')
+    parser.add_argument('--timeout', type=int, required=False, default=0)
+    args = parser.parse_args()
+
+    params = BrainFlowInputParams()
+    params.mac_address = args.mac_address
+    params.serial_number = args.serial_number
+    params.timeout = args.timeout
+    params.other_info = 'preset=p21;low_latency=true'
+
+    board_id = BoardIds.MUSE_S_ANTHENA_BOARD.value
+    board = BoardShim(board_id, params)
+
+    try:
+        board.prepare_session()
+        board.start_stream()
+        try:
+            time.sleep(args.duration)
+            eeg_data = board.get_board_data(preset=BrainFlowPresets.DEFAULT_PRESET)
+            print(eeg_data)
+        finally:
+            board.stop_stream()
+    finally:
+        if board.is_prepared():
+            board.release_session()
+
+
+if __name__ == '__main__':
+    main()

python_package/examples/tests/muse_anthena_eeg_p21.py

@@ -0,0 +1,118 @@
+import argparse
+import math
+import time
+
+import matplotlib
+
+matplotlib.use('Agg')
+import matplotlib.pyplot as plt
+import numpy as np
+
+from brainflow.board_shim import BoardShim, BrainFlowInputParams, BoardIds, BrainFlowPresets
+
+
+def print_summary(optics_data, timestamps, sampling_rate, channel_labels):
+    print(f'optics samples: {optics_data.shape[1]}')
+
+    if timestamps.size > 1 and np.all(np.isfinite(timestamps)):
+        timestamp_diffs = np.diff(timestamps)
+        timestamp_diffs = timestamp_diffs[timestamp_diffs > 0]
+        if timestamp_diffs.size > 0:
+            actual_rate = 1.0 / np.median(timestamp_diffs)
+            duration = timestamps[-1] - timestamps[0]
+            print(f'timestamp duration: {duration:.3f} sec')
+            print(f'timestamp sampling rate: {actual_rate:.2f} Hz, expected: {sampling_rate} Hz')
+
+    nan_count = int(np.isnan(optics_data).sum())
+    print(f'nan values: {nan_count}')
+
+    for label, row in zip(channel_labels, optics_data):
+        finite = row[np.isfinite(row)]
+        if finite.size == 0:
+            print(f'{label}: no finite values')
+            continue
+        stddev = float(np.std(finite))
+        print(
+            f'{label}: min={np.min(finite):.3f}, max={np.max(finite):.3f}, '
+            f'mean={np.mean(finite):.3f}, std={stddev:.3f}'
+        )
+        if stddev < 1e-9:
+            print(f'{label}: flat signal')
+
+
+def plot_optics(optics_data, timestamps, sampling_rate, output_file, channel_labels):
+    if timestamps.size == optics_data.shape[1] and timestamps.size > 0 and np.all(np.isfinite(timestamps)):
+        x_axis = timestamps - timestamps[0]
+        x_label = 'Time, sec'
+    else:
+        x_axis = np.arange(optics_data.shape[1]) / sampling_rate
+        x_label = 'Samples'
+
+    num_channels = optics_data.shape[0]
+    cols = min(4, num_channels)
+    rows = math.ceil(num_channels / cols)
+    fig, axes = plt.subplots(rows, cols, figsize=(4 * cols, 2.4 * rows), sharex=True)
+    axes = np.atleast_1d(axes).reshape(-1)
+
+    for index, axis in enumerate(axes):
+        if index < num_channels:
+            axis.plot(x_axis, optics_data[index])
+            axis.set_title(channel_labels[index])
+            axis.grid(True)
+        else:
+            axis.axis('off')
+
+    for axis in axes[-cols:]:
+        axis.set_xlabel(x_label)
+
+    fig.tight_layout()
+    fig.savefig(output_file, dpi=150)
+    print(f'wrote plot: {output_file}')
+
+
+def main():
+    BoardShim.enable_board_logger()
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--duration', type=int, required=False, default=20)
+    parser.add_argument('--mac-address', type=str, required=False, default='')
+    parser.add_argument('--serial-number', type=str, required=False, default='')
+    parser.add_argument('--timeout', type=int, required=False, default=0)
+    parser.add_argument('--other-info', type=str, required=False, default='preset=p1035;low_latency=true')
+    parser.add_argument('--output-file', type=str, required=False, default='muse_anthena_optics_p1035.png')
+    args = parser.parse_args()
+
+    params = BrainFlowInputParams()
+    params.mac_address = args.mac_address
+    params.serial_number = args.serial_number
+    params.timeout = args.timeout
+    params.other_info = args.other_info
+
+    board_id = BoardIds.MUSE_S_ANTHENA_BOARD.value
+    preset = BrainFlowPresets.ANCILLARY_PRESET
+    optical_channels = BoardShim.get_optical_channels(board_id, preset)
+    timestamp_channel = BoardShim.get_timestamp_channel(board_id, preset)
+    sampling_rate = BoardShim.get_sampling_rate(board_id, preset)
+
+    board = BoardShim(board_id, params)
+    try:
+        board.prepare_session()
+        board.start_stream()
+        try:
+            time.sleep(args.duration)
+            data = board.get_board_data(preset=preset)
+        finally:
+            board.stop_stream()
+    finally:
+        if board.is_prepared():
+            board.release_session()
+
+    optics_data = data[optical_channels, :]
+    timestamps = data[timestamp_channel, :]
+    channel_labels = [f'Optics {channel}' for channel in optical_channels]
+    print_summary(optics_data, timestamps, sampling_rate, channel_labels)
+    plot_optics(optics_data, timestamps, sampling_rate, args.output_file, channel_labels)
+
+
+if __name__ == '__main__':
+    main()

python_package/examples/tests/muse_anthena_optics_plot.py

@@ -0,0 +1,48 @@
+import argparse
+import time
+
+from brainflow.board_shim import BoardShim, BrainFlowInputParams, BoardIds, BrainFlowPresets
+from brainflow.data_filter import DataFilter
+
+
+def main():
+    BoardShim.enable_dev_board_logger()
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--duration', type=int, required=False, default=10)
+    parser.add_argument('--mac-address', type=str, required=False, default='')
+    parser.add_argument('--serial-number', type=str, required=False, default='')
+    parser.add_argument('--timeout', type=int, required=False, default=0)
+    parser.add_argument('--output-prefix', type=str, required=False, default='muse_anthena')
+    args = parser.parse_args()
+
+    params = BrainFlowInputParams()
+    params.mac_address = args.mac_address
+    params.serial_number = args.serial_number
+    params.timeout = args.timeout
+    params.other_info = 'preset=p1041;low_latency=true'
+
+    board_id = BoardIds.MUSE_S_ANTHENA_BOARD.value
+    board = BoardShim(board_id, params)
+
+    try:
+        board.prepare_session()
+        board.start_stream()
+        try:
+            time.sleep(args.duration)
+            eeg_data = board.get_board_data(preset=BrainFlowPresets.DEFAULT_PRESET)
+            accel_data = board.get_board_data(preset=BrainFlowPresets.AUXILIARY_PRESET)
+            optics_data = board.get_board_data(preset=BrainFlowPresets.ANCILLARY_PRESET)
+        finally:
+            board.stop_stream()
+    finally:
+        if board.is_prepared():
+            board.release_session()
+
+    DataFilter.write_file(eeg_data, f'{args.output_prefix}_eeg.csv', 'w')
+    DataFilter.write_file(accel_data, f'{args.output_prefix}_accel_gyro.csv', 'w')
+    DataFilter.write_file(optics_data, f'{args.output_prefix}_optics_battery.csv', 'w')
+
+
+if __name__ == '__main__':
+    main()

python_package/examples/tests/muse_anthena_save_all.py

@@ -420,7 +420,8 @@ BrainFlowBoards::BrainFlowBoards()
         {"marker_channel", 5},
         {"package_num_channel", 0},
         {"num_rows", 6},
-        {"ppg_channels", {1, 2, 3}}
+        {"ppg_channels", {1, 2, 3}},
+        {"optical_channels", {1, 2, 3}}
     };
     brainflow_boards_json["boards"]["22"]["default"] =
     {
@@ -453,7 +454,8 @@ BrainFlowBoards::BrainFlowBoards()
         {"marker_channel", 5},
         {"package_num_channel", 0},
         {"num_rows", 6},
-        {"ppg_channels", {1, 2, 3}}
+        {"ppg_channels", {1, 2, 3}},
+        {"optical_channels", {1, 2, 3}}
     };
     brainflow_boards_json["boards"]["23"]["default"] =
     {
@@ -681,7 +683,8 @@ BrainFlowBoards::BrainFlowBoards()
         {"marker_channel", 5},
         {"package_num_channel", 0},
         {"num_rows", 6},
-        {"ppg_channels", {1, 2, 3}}
+        {"ppg_channels", {1, 2, 3}},
+        {"optical_channels", {1, 2, 3}}
     };
     brainflow_boards_json["boards"]["39"]["default"] =
     {
@@ -714,7 +717,8 @@ BrainFlowBoards::BrainFlowBoards()
         {"marker_channel", 5},
         {"package_num_channel", 0},
         {"num_rows", 6},
-        {"ppg_channels", {1, 2, 3}}
+        {"ppg_channels", {1, 2, 3}},
+        {"optical_channels", {1, 2, 3}}
     };
     brainflow_boards_json["boards"]["40"]["default"] =
     {

src/board_controller/brainflow_boards.cpp

@@ -3,6 +3,7 @@
 #include "ble_lib_board.h"
 #include <condition_variable>
 #include <mutex>
+#include <string>
 #include <utility>
 #include <vector>
 
@@ -29,6 +30,7 @@ class Muse : public BLELibBoard
     double last_ppg_timestamp;        // used for timestamp correction
     double last_eeg_timestamp;        // used for timestamp correction
     double last_aux_timestamp;        // used for timestamp correction
+    std::string muse_preset;
 
 public:
     Muse (int board_id, struct BrainFlowInputParams params);

src/board_controller/muse/inc/muse.h

@@ -57,7 +57,7 @@ class MuseAnthena : public BLELibBoard
     std::string bytes_to_string (const uint8_t *data, size_t size);
     void handle_data_notification (const uint8_t *data, size_t size);
     void parse_sensor_payload (
-        uint8_t tag, uint8_t sequence_num, double host_timestamp, const uint8_t *data, size_t size);
+        uint8_t tag, uint32_t package_num, double host_timestamp, const uint8_t *data, size_t size);
     bool get_sensor_config (uint8_t tag, SensorConfig &config);
     int get_optics_canonical_index (uint8_t tag, int channel);
     void reset_timestamps ();

src/board_controller/muse/inc/muse_anthena.h

@@ -9,7 +9,8 @@
 #define MUSE_ANTHENA_GATT_DATA_2 "273e0014-4c4d-454d-96be-f03bac821358"
 
 // info for equations
-#define MUSE_ANTHENA_ACCELEROMETER_SCALE_FACTOR 0.0000610352
-#define MUSE_ANTHENA_GYRO_SCALE_FACTOR -0.0074768
-#define MUSE_ANTHENA_EEG_SCALE_FACTOR (1450.0 / 16383.0)
+#define MUSE_ANTHENA_ACCELEROMETER_SCALE_FACTOR 0.00006103515625
+#define MUSE_ANTHENA_GYRO_SCALE_FACTOR -0.007476806640625
+#define MUSE_ANTHENA_EEG_SCALE_FACTOR 0.40293040293040294
 #define MUSE_ANTHENA_OPTICS_SCALE_FACTOR 1.0
+#define MUSE_ANTHENA_BATTERY_PERCENT_SCALE_FACTOR (1.0 / 512.0)