Utility programs, scripts, and resources for use by Stanford Center for Sleep Sciences and Behavioral Research and its collaborators.
Use the channel_label_identifier.py tool by running
python channel_label_identifier.py <path to folder containing EDFs and hypnograms> montage.json C3 C4 A1 A2 EOGL EOGR LChin RChin EMG
This will create a JSON file (montage.json) containing key-value pairs to map the desired electrode labels shown above with the electrode configurations available in the data. This is also a useful way to assess the exact distribution of channel labels found in the .edf files located in a specific folder.
This folder contains a Python script to verify if EDF files will work with pyedflib.EdfReader.
From a command prompt
-
To run interactively with a prompt for the path to check (Enter 'x' to quit):
python3.6 -m edf_verify -
To run once, specify which path to check (e.g. '/path/to/check/'):
python3.6 -m edf_verify ~/path/to/check
This folder contains a Ruby script from the NSRR which may be used to deidentify edf files.
This folder contains MATLAB code that is helpful for curating and normalizing EDF files to include:
- Updating header information
- Removing bad header data, such as unrecognized characters,
- Correcting discrepancies between file size listed in the header and the actual file size found
- Resampling an .EDF to a specified sample rate.
- Referencing channels (e.g. combinging 'C3' and 'M2' to get 'C3-M2').
- Culling unwanted channels to produce smaller files.
This folder contains helper methods for Sherlock.
edf_headers/
This repository is implemented for retreiving header information, duration, and location of the .edf
files we have on Oak to CSV.
To simplify a set of .edf files in place (i.e. rewrite them):
psgPath = 'G:\OAK\narco_validation\edf_path';
normalize_edfs(psgPath);To save a simplified version of .edf files in a different folder (e.g. destPath below):
psgPath = 'G:\OAK\narco_validation\edf_path';
destPath = 'G:\OAK\narco_validation\normalized_edfs';
normalize_edfs(psgPath, destPath);To obtain a list of all unique channel labels found in the .edf files at a particular path
s = 'G:\OAK\narco_validation\edf_path\'
[channelNames, channelNamesAll] = CLASS_converter.getAllChannelNames(s);