Saving multiple gt3x files to hdf5

Most of the times you have multiple GT3X files you want to analyze. In this case it is often easier to process all files first and save them as one hdf5 file. The Hierarchical Data Format (HDF5) is a file format specifically designed to handle large amounts of data. When you process GT3X files, especially if they contain multi-day recordings, it takes a considerable amount of time to read these files due to their binary nature. HDF5 significantly reduces data loading time, but only makes sense if the data is used multiple times. In the case only one analysis is performed it might be quicker to analyze the data directly.

The following example illustrates how to create a HDF5 file from a list of GT3X files. If you don’t know how to get this list have a look at the Read GT3X Files with PAAT tutorial.

import h5py
import paat

hdf5_file_path = 'path/to/hdf5/file'
files = ['path/to/file1.gt3x', 'path/to/file2.gt3x', ...]

# Create new empty h5 file
h5py.File(hdf5_file_path, 'w').close()

for file in files:

  # Load the data
  data, sample_freq = paat.read_gt3x(file)

  # Save data to HDF5 file
  data.to_hdf(hdf5_file, key=file)