scripts/readh5.py

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

"""
Inspect any HDF5 file as a readable tree, including attributes.

Examples:
    python scripts/readh5.py data/example.h5
    python scripts/readh5.py data/example.h5 --max-depth 3 --max-items 20
    python scripts/readh5.py data/example.h5 --all --preview 5
"""

import argparse
import math

import h5py
import numpy as np


DEFAULT_H5_FILE = "data/hdf5/continuous_waveform_usa_20190701.h5"


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


def format_scalar(value):
    value = safe_decode(value)

    if isinstance(value, np.generic):
        value = value.item()
        value = safe_decode(value)

    return repr(value) if isinstance(value, str) else str(value)


def format_array(value, max_values=8):
    array = np.asarray(value)

    if array.ndim == 0:
        return format_scalar(array[()])

    flat_values = [format_scalar(x) for x in array.flat[:max_values]]
    suffix = ", ..." if array.size > max_values else ""
    preview = ", ".join(flat_values) + suffix

    return (
        f"array(shape={array.shape}, dtype={array.dtype}, "
        f"values=[{preview}])"
    )


def format_attr_value(value, max_values=8):
    if isinstance(value, np.ndarray):
        return format_array(value, max_values=max_values)

    if isinstance(value, (list, tuple)):
        values = [format_attr_value(x, max_values=max_values) for x in value[:max_values]]
        suffix = ", ..." if len(value) > max_values else ""
        return f"{type(value).__name__}([{', '.join(values)}{suffix}])"

    return format_scalar(value)


def format_nbytes(nbytes):
    if nbytes is None:
        return "unknown"

    units = ("B", "KiB", "MiB", "GiB", "TiB")
    value = float(nbytes)
    unit_index = 0

    while value >= 1024 and unit_index < len(units) - 1:
        value /= 1024
        unit_index += 1

    if unit_index == 0:
        return f"{int(value)} {units[unit_index]}"
    return f"{value:.2f} {units[unit_index]}"


def dataset_nbytes(dataset):
    if dataset.shape is None:
        return None

    if any(dim is None for dim in dataset.shape):
        return None

    return math.prod(dataset.shape) * dataset.dtype.itemsize


def print_attrs(obj, indent, max_attr_values):
    prefix = " " * indent

    if not obj.attrs:
        return

    print(f"{prefix}@attrs")
    for key, value in obj.attrs.items():
        formatted = format_attr_value(value, max_values=max_attr_values)
        print(f"{prefix}  - {key}: {formatted}")


def print_dataset(dataset, name, indent, max_attr_values, preview):
    prefix = " " * indent
    details = [
        f"shape={dataset.shape}",
        f"dtype={dataset.dtype}",
        f"size={format_nbytes(dataset_nbytes(dataset))}",
    ]

    if dataset.chunks is not None:
        details.append(f"chunks={dataset.chunks}")

    if dataset.compression is not None:
        compression = dataset.compression
        if dataset.compression_opts is not None:
            compression = f"{compression}:{dataset.compression_opts}"
        details.append(f"compression={compression}")

    if dataset.maxshape is not None and dataset.maxshape != dataset.shape:
        details.append(f"maxshape={dataset.maxshape}")

    print(f"{prefix}{name}  [Dataset] " + ", ".join(details))
    print_attrs(dataset, indent + 2, max_attr_values=max_attr_values)

    if preview > 0:
        print_dataset_preview(dataset, indent + 2, preview)


def print_dataset_preview(dataset, indent, preview):
    prefix = " " * indent

    try:
        if dataset.shape == ():
            values = dataset[()]
        elif dataset.size == 0:
            values = []
        elif dataset.ndim == 1:
            values = dataset[:preview]
        else:
            slices = tuple(slice(0, min(preview, dim)) for dim in dataset.shape)
            values = dataset[slices]

        print(f"{prefix}preview: {format_array(values, max_values=preview)}")
    except Exception as exc:
        print(f"{prefix}preview: <unavailable: {exc}>")


def print_link(group, key, indent):
    prefix = " " * indent
    link = group.get(key, getlink=True)

    if isinstance(link, h5py.SoftLink):
        print(f"{prefix}{key}  [SoftLink] -> {link.path}")
        return True

    if isinstance(link, h5py.ExternalLink):
        print(f"{prefix}{key}  [ExternalLink] -> {link.filename}:{link.path}")
        return True

    return False


def sorted_or_native(keys, sort_keys):
    return sorted(keys) if sort_keys else list(keys)


def iter_limited(values, max_items):
    if max_items is None:
        yield from values
        return

    for value in values[:max_items]:
        yield value


def inspect_group(
    group,
    name,
    indent,
    max_items,
    max_depth,
    max_attr_values,
    preview,
    sort_keys,
    seen,
):
    prefix = " " * indent
    node_type = "File" if isinstance(group, h5py.File) else "Group"
    display_name = "/" if isinstance(group, h5py.File) else f"{name}/"
    print(f"{prefix}{display_name}  [{node_type}]")
    print_attrs(group, indent + 2, max_attr_values=max_attr_values)

    if max_depth is not None and indent // 2 >= max_depth:
        print(f"{prefix}  ... max depth reached")
        return

    keys = sorted_or_native(group.keys(), sort_keys=sort_keys)

    for key in iter_limited(keys, max_items=max_items):
        if print_link(group, key, indent + 2):
            continue

        try:
            item = group[key]
        except Exception as exc:
            print(f"{' ' * (indent + 2)}{key}  [Unreadable] {exc}")
            continue

        object_id = item.id.__hash__()
        if object_id in seen:
            print(f"{' ' * (indent + 2)}{key}  [Already visited]")
            continue

        if isinstance(item, h5py.Group):
            seen.add(object_id)
            inspect_group(
                item,
                name=key,
                indent=indent + 2,
                max_items=max_items,
                max_depth=max_depth,
                max_attr_values=max_attr_values,
                preview=preview,
                sort_keys=sort_keys,
                seen=seen,
            )
        elif isinstance(item, h5py.Dataset):
            print_dataset(
                item,
                name=key,
                indent=indent + 2,
                max_attr_values=max_attr_values,
                preview=preview,
            )
        else:
            print(f"{' ' * (indent + 2)}{key}  [{type(item).__name__}]")

    if max_items is not None:
        remaining = len(keys) - max_items
        if remaining > 0:
            print(f"{prefix}  ... {remaining} more item(s), use --all to show all")


def inspect_hdf5(
    h5_file,
    max_items=50,
    max_depth=None,
    max_attr_values=8,
    preview=0,
    sort_keys=False,
):
    with h5py.File(h5_file, "r") as h5:
        inspect_group(
            h5,
            name="/",
            indent=0,
            max_items=max_items,
            max_depth=max_depth,
            max_attr_values=max_attr_values,
            preview=preview,
            sort_keys=sort_keys,
            seen={h5.id.__hash__()},
        )


def positive_int(value):
    value = int(value)
    if value < 0:
        raise argparse.ArgumentTypeError("value must be >= 0")
    return value


def parse_args():
    parser = argparse.ArgumentParser(
        description="Read any HDF5 file and print its tree structure with attributes."
    )
    parser.add_argument(
        "h5_file",
        nargs="?",
        default=DEFAULT_H5_FILE,
        help=f"Input HDF5 file. Default: {DEFAULT_H5_FILE}",
    )
    parser.add_argument(
        "--h5_file",
        dest="h5_file_option",
        help="Input HDF5 file, kept for compatibility with older commands.",
    )
    parser.add_argument(
        "--max-items",
        "--max_items",
        type=positive_int,
        default=50,
        help="Maximum child items shown under each group. Default: 50.",
    )
    parser.add_argument(
        "--all",
        action="store_true",
        help="Show all child items under each group.",
    )
    parser.add_argument(
        "--max-depth",
        "--max_depth",
        type=positive_int,
        default=None,
        help="Maximum display depth. File root is depth 0. Default: unlimited.",
    )
    parser.add_argument(
        "--max-attr-values",
        type=positive_int,
        default=8,
        help="Maximum values shown for each array-like attribute. Default: 8.",
    )
    parser.add_argument(
        "--preview",
        type=positive_int,
        default=0,
        help="Preview up to N values from each dataset. Default: 0.",
    )
    parser.add_argument(
        "--sort",
        action="store_true",
        help="Sort group keys alphabetically instead of using file order.",
    )

    args = parser.parse_args()

    if args.h5_file_option:
        args.h5_file = args.h5_file_option

    if args.all:
        args.max_items = None

    return args


def main():
    args = parse_args()

    inspect_hdf5(
        h5_file=args.h5_file,
        max_items=args.max_items,
        max_depth=args.max_depth,
        max_attr_values=args.max_attr_values,
        preview=args.preview,
        sort_keys=args.sort,
    )


if __name__ == "__main__":
    main()