flush

Author: oreHGA

.gitignore

@@ -3,4 +3,6 @@
 *.DS_Store
 
 # npm packages
-logger/node_modules/*
+logger/node_modules/*
+
+analysis

explorer_analysis/README.md

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+Fusion Explorer Analysis
+
+A set of scripts and resources for analyzing data recorded on [Fusion](https://usefusion.app)
+
+eeg.py is a file that helps one analyze the data they have collected. Below is a description of what each of the functions in it do.
+
+rnOccur: finds the nth occurrence of v in arr
+
+extractBundledEEG: init: creates files to separte useful information by tags such as event or description addMeta: helps make data more understandable by adding categorical information to the csv file prune: filters out all events that do not have any eeg data to support them extractByID: finds the location of all the json files that have a specific event extractByTags: finds the location of all the json fiels that have a specific tag mergeTagsWithRegex: consolidates data by combining data that have the same tag mergeCategories: creates a new category with all the categories passed in
+
+load_data: loads the eeg data to be used
+
+get_signal_quality_summary: counts how many signals from each eeg channel is good and then returns the percentage of those that are good
+
+load_session_epochs: I was a little confused about this one- i don't know what an epoch is
+
+load_session_summery: computes a quantitive summary of eeg data including average power by band, average power by channel, etc
+
+analysisEngine: init: Generates basic analytics for recording groups distributionVetting: generates graphs for each epoch wave basicComparisons: generates graphs that compare the accummulated power bands for each wave trendAnalysis: generates a graph with how a specific variable progressed with time
+
+get_rolling_powerByBand: checks whether there is a difference in data depending on the time interval in which the data is collected
+
+unix_to_period: converts the timestamps collected to one more readable to us
+
+unix_to_localdate: converts the date collected to one more readable to us
+
+load_sessions: loads the sessions
+
+load_fileset: loads data

explorer_analysis/eeg.py

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+# run fooof implementation

happy.ipynb explorer_notebooks/happy.ipynb

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+import argparse
+import time
+
+from brainflow.board_shim import BoardShim, BrainFlowInputParams
+
+
+def main():
+    BoardShim.enable_dev_board_logger()
+
+    parser = argparse.ArgumentParser()
+    # use docs to check which parameters are required for specific board, e.g. for Cyton - set serial port
+    parser.add_argument('--timeout', type=int, help='timeout for device discovery or connection', required=False,
+                        default=0)
+    parser.add_argument('--ip-port', type=int, help='ip port', required=False, default=0)
+    parser.add_argument('--ip-protocol', type=int, help='ip protocol, check      enum', required=False,
+                        default=0)
+    parser.add_argument('--ip-address', type=str, help='ip address', required=False, default='')
+    parser.add_argument('--serial-port', type=str, help='serial port', required=False, default='')
+    parser.add_argument('--mac-address', type=str, help='mac address', required=False, default='')
+    parser.add_argument('--other-info', type=str, help='other info', required=False, default='')
+    parser.add_argument('--streamer-params', type=str, help='streamer params', required=False, default='')
+    parser.add_argument('--serial-number', type=str, help='serial number', required=False, default='')
+    parser.add_argument('--board-id', type=int, help='board id, check docs to get a list of supported boards',
+                        required=True)
+    parser.add_argument('--file', type=str, help='file', required=False, default='')
+    args = parser.parse_args()
+
+    params = BrainFlowInputParams()
+    params.ip_port = args.ip_port
+    params.serial_port = args.serial_port
+    params.mac_address = args.mac_address
+    params.other_info = args.other_info
+    params.serial_number = args.serial_number
+    params.ip_address = args.ip_address
+    params.ip_protocol = args.ip_protocol
+    params.timeout = args.timeout
+    params.file = args.file
+
+    board = BoardShim(args.board_id, params)
+    board.prepare_session()
+    # board.start_stream () # use this for default options
+    board.start_stream(45000, args.streamer_params)
+    # time.sleep(10)
+    data = board.get_current_board_data (256) # get latest 256 packages or less, doesnt remove them from internal buffer
+    data = board.get_board_data()  # get all data and remove it from internal buffer
+    board.stop_stream()
+    board.release_session()
+
+    print(data)
+
+
+if __name__ == "__main__":
+    main()

music_eeg.ipynb explorer_notebooks/music_eeg.ipynb

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+import time
+
+from brainflow.board_shim import BoardShim, BrainFlowInputParams, LogLevels, BoardIds
+from brainflow.data_filter import DataFilter, WindowOperations, DetrendOperations
+
+
+def main():
+    BoardShim.enable_dev_board_logger()
+
+    # use synthetic board for demo
+    params = BrainFlowInputParams()
+    board_id = BoardIds.SYNTHETIC_BOARD.value
+    board_descr = BoardShim.get_board_descr(board_id)
+    sampling_rate = int(board_descr['sampling_rate'])
+    board = BoardShim(board_id, params)
+    board.prepare_session()
+    board.start_stream()
+    BoardShim.log_message(LogLevels.LEVEL_INFO.value, 'start sleeping in the main thread')
+    time.sleep(10)
+    nfft = DataFilter.get_nearest_power_of_two(sampling_rate)
+    data = board.get_board_data()
+    board.stop_stream()
+    board.release_session()
+
+    eeg_channels = board_descr['eeg_channels']
+    # second eeg channel of synthetic board is a sine wave at 10Hz, should see huge alpha
+    eeg_channel = eeg_channels[1]
+    # optional detrend
+    DataFilter.detrend(data[eeg_channel], DetrendOperations.LINEAR.value)
+    psd = DataFilter.get_psd_welch(data[eeg_channel], nfft, nfft // 2, sampling_rate,
+                                   WindowOperations.BLACKMAN_HARRIS.value)
+
+    band_power_alpha = DataFilter.get_band_power(psd, 7.0, 13.0)
+    band_power_beta = DataFilter.get_band_power(psd, 14.0, 30.0)
+    print("alpha/beta:%f", band_power_alpha / band_power_beta)
+
+
+if __name__ == "__main__":
+    main()

explorer_recordings/read_brainflow.py

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+import argparse
+import logging
+
+import pyqtgraph as pg
+from brainflow.board_shim import BoardShim, BrainFlowInputParams, BoardIds
+from brainflow.data_filter import DataFilter, FilterTypes, DetrendOperations
+from pyqtgraph.Qt import QtGui, QtCore
+
+
+class Graph:
+    def __init__(self, board_shim):
+        self.board_id = board_shim.get_board_id()
+        self.board_shim = board_shim
+        self.exg_channels = BoardShim.get_exg_channels(self.board_id)
+        self.sampling_rate = BoardShim.get_sampling_rate(self.board_id)
+        self.update_speed_ms = 50
+        self.window_size = 4
+        self.num_points = self.window_size * self.sampling_rate
+
+        self.app = QtGui.QApplication([])
+        self.win = pg.GraphicsWindow(title='BrainFlow Plot', size=(800, 600))
+
+        self._init_timeseries()
+
+        timer = QtCore.QTimer()
+        timer.timeout.connect(self.update)
+        timer.start(self.update_speed_ms)
+        QtGui.QApplication.instance().exec_()
+
+    def _init_timeseries(self):
+        self.plots = list()
+        self.curves = list()
+        for i in range(len(self.exg_channels)):
+            p = self.win.addPlot(row=i, col=0)
+            p.showAxis('left', False)
+            p.setMenuEnabled('left', False)
+            p.showAxis('bottom', False)
+            p.setMenuEnabled('bottom', False)
+            if i == 0:
+                p.setTitle('TimeSeries Plot')
+            self.plots.append(p)
+            curve = p.plot()
+            self.curves.append(curve)
+
+    def update(self):
+        data = self.board_shim.get_current_board_data(self.num_points)
+        for count, channel in enumerate(self.exg_channels):
+            # plot timeseries
+            DataFilter.detrend(data[channel], DetrendOperations.CONSTANT.value)
+            DataFilter.perform_bandpass(data[channel], self.sampling_rate, 3.0, 45.0, 2,
+                                        FilterTypes.BUTTERWORTH.value, 0)
+            DataFilter.perform_bandstop(data[channel], self.sampling_rate, 48.0, 52.0, 2,
+                                        FilterTypes.BUTTERWORTH.value, 0)
+            DataFilter.perform_bandstop(data[channel], self.sampling_rate, 58.0, 62.0, 2,
+                                        FilterTypes.BUTTERWORTH.value, 0)
+            self.curves[count].setData(data[channel].tolist())
+
+        self.app.processEvents()
+
+
+def main():
+    BoardShim.enable_dev_board_logger()
+    logging.basicConfig(level=logging.DEBUG)
+
+    parser = argparse.ArgumentParser()
+    # use docs to check which parameters are required for specific board, e.g. for Cyton - set serial port
+    parser.add_argument('--timeout', type=int, help='timeout for device discovery or connection', required=False,
+                        default=0)
+    parser.add_argument('--ip-port', type=int, help='ip port', required=False, default=0)
+    parser.add_argument('--ip-protocol', type=int, help='ip protocol, check IpProtocolType enum', required=False,
+                        default=0)
+    parser.add_argument('--ip-address', type=str, help='ip address', required=False, default='')
+    parser.add_argument('--serial-port', type=str, help='serial port', required=False, default='')
+    parser.add_argument('--mac-address', type=str, help='mac address', required=False, default='')
+    parser.add_argument('--other-info', type=str, help='other info', required=False, default='')
+    parser.add_argument('--streamer-params', type=str, help='streamer params', required=False, default='')
+    parser.add_argument('--serial-number', type=str, help='serial number', required=False, default='')
+    parser.add_argument('--board-id', type=int, help='board id, check docs to get a list of supported boards',
+                        required=False, default=BoardIds.SYNTHETIC_BOARD)
+    parser.add_argument('--file', type=str, help='file', required=False, default='')
+    args = parser.parse_args()
+
+    params = BrainFlowInputParams()
+    params.ip_port = args.ip_port
+    params.serial_port = args.serial_port
+    params.mac_address = args.mac_address
+    params.other_info = args.other_info
+    params.serial_number = args.serial_number
+    params.ip_address = args.ip_address
+    params.ip_protocol = args.ip_protocol
+    params.timeout = args.timeout
+    params.file = args.file
+
+    try:
+        board_shim = BoardShim(args.board_id, params)
+        board_shim.prepare_session()
+        board_shim.start_stream(450000, args.streamer_params)
+        Graph(board_shim)
+    except BaseException:
+        logging.warning('Exception', exc_info=True)
+    finally:
+        logging.info('End')
+        if board_shim.is_prepared():
+            logging.info('Releasing session')
+            board_shim.release_session()
+
+
+if __name__ == '__main__':
+    main()