h5tools.py

import h5py
import numpy as np

def set_h5_attrs(grp, data):
    """Sets attributes of h5py group or File `grp` according to dict `data`.
    
    Args:
        grp (h5py group or File): Group or file you would like to update.
        data (dict): Dict of data with which to update `grp`.
    """
    for name, value in data.items():
        name = str(name)
        if isinstance(value, dict):
            subgrp = grp.require_group(name)
            set_h5_attrs(subgrp, value)
        else:
            if isinstance(value, (list, tuple, np.ndarray)) and len(value):
                if isinstance(value[0], str):
                    grp.attrs[name] = [str(val) for val in value]
                else:
                    # create or overwrite dataset
                    # this only works if value has the same shape as original dataset
                    array = np.array(value)
                    ds = grp.require_dataset(name, shape=array.shape, dtype=array.dtype, exact=True)
                    ds[...] = array
                    # we could instead do the following to overwrite with data of a different shape:
                    # ds = grp.require_dataset(name, shape=array.shape, dtype=array.dtype, exact=True)
                    # del ds
                    # grp.create_dataset(name, data=array)
            else:
                grp.attrs[name] = value

def group_to_dict(group):
    """Recursively load the contents of an h5py group into a dict.
    
    Args:
        group (h5py group): Group from which you want to load all data.
        
    Returns:
        target (dict): Dict with contents of group loaded into it.
    """
    target = {}
    for key, value in group.items():
        target[key] = {}
        if hasattr(value, 'attrs') and len(value.attrs):
            target[key].update(group_to_dict(value.attrs))
        if hasattr(value, 'keys'):
            target[key].update(group_to_dict(value))
        elif isinstance(value, h5py.Dataset):
            target[key] = np.array(value)
        else:
            target[key] = value
    return target