scripts/readh5.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-

import argparse
import h5py
import numpy as np


def format_attr_value(value):
    if isinstance(value, bytes):
        return value.decode("utf-8", errors="ignore")

    if isinstance(value, np.ndarray):
        if value.size <= 6:
            return value.tolist()
        return f"array(shape={value.shape}, dtype={value.dtype})"

    return value


def print_attrs(obj, indent):
    if len(obj.attrs) == 0:
        print(" " * indent + "attrs: {}")
        return

    print(" " * indent + "attrs:")
    for key, value in obj.attrs.items():
        value = format_attr_value(value)
        print(" " * (indent + 2) + f"- {key}: {value}")


def inspect_group(group, name="/", indent=0, max_items=3, max_depth=None):
    prefix = " " * indent

    if isinstance(group, h5py.File):
        print(f"{prefix}/  [File]")
    else:
        print(f"{prefix}{name}/  [Group]")

    print_attrs(group, indent + 2)

    if max_depth is not None and indent // 2 >= max_depth:
        print(" " * (indent + 2) + "... max depth reached")
        return

    keys = list(group.keys())
    shown_keys = keys[:max_items]

    for key in shown_keys:
        item = group[key]

        if isinstance(item, h5py.Group):
            inspect_group(
                item,
                name=key,
                indent=indent + 2,
                max_items=max_items,
                max_depth=max_depth,
            )

        elif isinstance(item, h5py.Dataset):
            print_dataset(
                item,
                name=key,
                indent=indent + 2,
            )

    remaining = len(keys) - len(shown_keys)
    if remaining > 0:
        print(" " * (indent + 2) + f"... {remaining} more items not shown")


def print_dataset(dataset, name, indent):
    prefix = " " * indent

    print(
        f"{prefix}{name}  [Dataset] "
        f"shape={dataset.shape}, dtype={dataset.dtype}"
    )

    print_attrs(dataset, indent + 2)


def inspect_hdf5(h5_file, max_items=3, max_depth=None):
    with h5py.File(h5_file, "r") as h5:
        inspect_group(
            h5,
            name="/",
            indent=0,
            max_items=max_items,
            max_depth=max_depth,
        )


def main():
    parser = argparse.ArgumentParser(
        description="Inspect HDF5 hierarchy and attributes."
    )

    parser.add_argument(
        "--h5_file",
        default="data/hdf5/continuous_waveform_usa_20190701.h5",
        help="Input HDF5 file.",
    )

    parser.add_argument(
        "--max_items",
        type=int,
        default=1,
        help="Maximum number of child items shown under each group.",
    )

    parser.add_argument(
        "--max_depth",
        type=int,
        default=None,
        help="Maximum display depth. Default is unlimited.",
    )

    args = parser.parse_args()

    inspect_hdf5(
        h5_file=args.h5_file,
        max_items=args.max_items,
        max_depth=args.max_depth,
    )


if __name__ == "__main__":
    main()