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preprocess_sleep_data

Usage example

First, make sure you "import" the preprocess_sleep_data folder and its helper, the EEGtoolbox folder, if the preprocess_sleep_data folder is not in your current directory. You could use absolute path in addpath. For example,

addpath('C:\Users\yzhao\matlab_projects\preprocess_sleep_data')
addpath('C:\Users\yzhao\matlab_projects\preprocess_sleep_data\EEGtoolbox')

After you have taken care of the "import", you can call the function like this

preprocess_sleep_data( ...
    'C:\Users\yzhao\matlab_projects\sleep_data_extraction\opto_NOR\408_yfp\408_YFP_NOR\408_YFP_NOR_2021-03-08_10-29-08-223.exp', ...
    'ne_dir', 'C:\Users\yzhao\matlab_projects\sleep_data_extraction\opto_NOR\408_yfp', ...
    'chan_465', 'BuBo', ...
    'chan_405', 'V_Bo', ...
    'chan_ttl_pulse', 'Pu2_', ...
    'interval', (100:7000), ...
    'time_correction', 2, ...
    'sleep_score_file', 'C:\Users\yzhao\matlab_projects\sleep_data_extraction\opto_NOR\408_yfp\408_YFP_NOR\408_NOR_sleepscore.xlsx', ...
    'save_path', '408_yfp.mat', ...
    'show_figure', true ...
);

The first parameter is the path to your EEG/EMG data. If your EEG/EMG data was recorded with Viewpoint, then this should be the path to the .exp file. If your EEG/EMG data was recorded using the TDT system, then this should be the directory of the TDT files here.

The rest of the parameters are optional name-value pairs. 'interval' and 'time_correction' are always optional. The last parameter, 'show_figure' is for visualizing the preprocessed data. If you want to see it, set it to 'true'. If you don't need it, just skip it. You may or may not need to provide the other optional parameters depending on your data source. The order in which you write them does not matter. See the flowchart below for the parameters you need. Also check Section More Examples for example usage.

Output

The following fields are saved in the .mat file

  1. eeg
  2. emg
  3. ne
  4. sleep_scores
  5. num_class (fixed to be 3 for now)
  6. eeg_frequency
  7. ne_frequency

Note

  1. ne is downsampled by a factor of 100 before being saved.
  2. eeg, emg, and ne are 1D arrays.
  3. Make sure that your ne_dir only contains one set of TDT files.
  4. Long recordings. When you have EEG/EMG data from Viewpoint and you have multiple bin files, the data in each bin file will be written to a .mat file named after the bin file. When you have EEG/EMG from TDT and the recording is longer than 12 hours, your recording will be segmented into 12-hour bins and the resulting .mat files will be named with a suffix accordingly.

More Examples

  1. EEG/EMG from .exp file, no NE data
preprocess_sleep_data( ...
    'C:\Users\yzhao\matlab_projects\sleep_data_extraction\opto_NOR\408_yfp\408_YFP_NOR\408_YFP_NOR_2021-03-08_10-29-08-223.exp', ...
);
  1. EEG/EMG from .exp file + NE from TDT files.
preprocess_sleep_data( ...
    'C:\Users\yzhao\matlab_projects\sleep_data_extraction\opto_NOR\408_yfp\408_YFP_NOR\408_YFP_NOR_2021-03-08_10-29-08-223.exp', ...
    'ne_dir', 'C:\Users\yzhao\matlab_projects\sleep_data_extraction\opto_NOR\408_yfp', ...
    'chan_465', 'BuBo', ...
    'chan_405', 'V_Bo', ...
    'chan_ttl_pulse', 'Pu2_', ...
    'save_path', '408_yfp.mat', ...
    'show_figure', true ...
);
  1. EEG/EMG + NE from TDT files.
preprocess_sleep_data( ...
    'C:\Users\yzhao\matlab_projects\sleep_data_extraction\830', ...
    'ne_dir', 'C:\Users\yzhao\matlab_projects\sleep_data_extraction\830', ...
    'EEG_stream', 'EEGw', ...
    'EEG_chan', 1, ...
    'EMG_stream', 'EMG1', ...
    'chan_465', 'x465C', ...
    'chan_405', 'x405C', ...
    'save_path', 'C:\Users\yzhao\matlab_projects\sleep_data_extraction\830.mat', ...
    'show_figure', true ...
);
  1. EEG/EMG from TDT files, no NE.
preprocess_sleep_data( ...
    'C:\Users\yzhao\matlab_projects\sleep_data_extraction\20241113_1_263_2_259_24h_test', ...
    'EEG_stream', 'EEG1', ...
    'EEG_chan', 1, ...
    'EMG_stream', 'EMG1', ...
    'save_path', 'C:\Users\yzhao\matlab_projects\sleep_data_extraction\20241113_1_263_2_259_24h_test.mat', ...
    'show_figure', true ...
);
  1. if you already have the sleep scores (this happens if you want to contribute training data for improving the sleep scoring models).
preprocess_sleep_data( ...
    'C:\Users\yzhao\matlab_projects\sleep_data_extraction\20221221_adra_1_238_2_242', ...
    'ne_dir', 'C:\Users\yzhao\matlab_projects\sleep_data_extraction\20221221_adra_1_238_2_242', ...
    'EEG_stream', 'EEGw', ...
    'EEG_chan', 1, ...
    'EMG_stream', 'EMG1', ...
    'chan_465', 'x465A', ...
    'chan_405', 'x405A', ...
    'interval', (1:8000), ...
    'time_correction', 0, ...
    'sleep_score_file', 'C:\Users\yzhao\matlab_projects\sleep_data_extraction\20221221_adra_1_238_2_242\211222_238_adjusted_score.xlsx', ...
    'save_path', 'C:\Users\yzhao\matlab_projects\sleep_data_extraction\20221221_adra_1_238_2_242.mat', ...
    'show_figure', true ...
);