SPL_single_units_reaching_task/code/python/supportFunctions/get_all_data_from_level_h5_rec.py

import h5py
import numpy as np

def get_all_data_from_level_h5_rec(filename, group_name, markers, all_strings_mk, spikes, all_strings_sp):
    """
    This function recursively reads data from an HDF5 file.

    Parameters:
    filename (str): A string that identifies the HDF5 file from which to extract data.
    group_name (str): The group from which to start extracting data.
    data (list, optional): A list to add and store the extracted data. Defaults to None.
    all_strings (list, optional): A list to add and store the paths of the extracted datasets. Defaults to None.

    Returns:
    data (list): A list containing the extracted data for each dataset.
    all_strings (list): A list containing the paths of the extracted datasets.
    
    authors: Stefano Diomedi and Francesco E. Vaccari
    date: 03/2024
    """
    
    def visitor_func(name, node):
        if isinstance(node, h5py.Group):
            node.visititems(visitor_func)
        if isinstance(node, h5py.Dataset):
            # ...read the data from the dataset and append it to the 'data' list.
            if name == 'event_markers' and node.name not in all_strings_mk:
                markers.append(node[()])
            # ...append the path of the dataset to the 'all_strings' list.
                all_strings_mk.append(node.name)
            if name == 'spike_trains' and node.name not in all_strings_sp:
                spikes.append(node[()])
                all_strings_sp.append(node.name)



    with h5py.File(filename, 'r') as f:
        f[group_name].visititems(visitor_func)

    return markers, all_strings_mk, spikes, all_strings_sp