openephys-fileIO

Allow one to write data into open-ephys continuous and binary format. Useful for offline development and debugging of online algorithms.

Features

• Fast reading of open-ephys continuous file (9x speed up compared to original Python 3 version)
• Writing of open-ephys flat binary file (including the oebin and timestamp file)
• Writing of open-ephys continuous file in Python
• Writing any numpy array into openephys binary format
• Basically allow one to convert any neuron data readable in python to open-ephys format

Installation

• clone the repository git clone https://github.com/teristam/openephys-fileIO.git
• go to the openephys-fileIO folder, then pip install .

Usage

Fast load a continuous file:

from openephys_fileIO import fileIO
file = fileIO.loadContinuousFast('test/data/100_CH1.continuous')

Writing of continuous file

file = fileIO.loadContinuousFast('test/data/100_CH1.continuous')
fileIO.writeContinuousFile('test/data/test.continuous',file['header'],file['timestamps'],file['data'],file['recordingNumber'])
   

Convert a continuous file into flat binary format

dataFolder = 'test/data'

data,headers = load_OpenEphysRecording4BinaryFile(dataFolder,
    num_data_channel=1,num_aux_channel=1, num_adc_channel=1)

writeBinaryData(dataFolder+'/experiment1/recording1/',data)
writeStructFile(dataFolder+'/experiment1/recording1/structure.oebin',headers)

Convert a numpy array into openEphys binary data (useful for generating simulated recording)

Fs = 30000
x = np.random.randn(3*Fs,4)
bitVolts = 0.195
dataFolder = 'test/data2'
channel_names = [f'CH{i}' for i in range(x.shape[1])]
writeBinaryData(dataFolder+'/experiment1/recording1/', x, bitVolts)
writeStructFile(dataFolder+'/experiment1/recording1/structure.oebin',samplerate=30000,
    num_channels= x.shape[1], bit_volts=bitVolts,channel_names=channel_names)

Further example can be seen in the example_*.py python scripts.

For ease of use, this repo contains some Python module from the original analysis-tool repo

TODO

• Event data are not yet supported in writing of binary file