#!/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: ") 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()