File size: 2,726 Bytes
e4fd72a | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 | from __future__ import annotations
import argparse
import sys
from pathlib import Path
from typing import Any
import h5py
import numpy as np
def build_parser() -> argparse.ArgumentParser:
parser = argparse.ArgumentParser(
description=(
"Check every HDF5 file in the script directory and verify that all "
"numeric datasets and numeric attributes are real-valued and finite."
)
)
parser.add_argument(
"--pattern",
default="*.h5",
help="Glob pattern used inside the script directory. Default: %(default)s.",
)
return parser
def iter_datasets(group: h5py.Group, prefix: str = ""):
for name, item in group.items():
path = f"{prefix}/{name}" if prefix else name
if isinstance(item, h5py.Dataset):
yield path, item
elif isinstance(item, h5py.Group):
yield from iter_datasets(item, path)
def validate_numeric_array(values: np.ndarray[Any, Any], *, label: str) -> None:
if np.iscomplexobj(values):
raise ValueError(f"{label} contains complex values.")
if np.issubdtype(values.dtype, np.number) and not np.isfinite(values).all():
raise ValueError(f"{label} contains non-finite values.")
def validate_attr_value(value: Any, *, label: str) -> None:
array = np.asarray(value)
if array.dtype.kind not in {"b", "i", "u", "f", "c"}:
return
validate_numeric_array(array, label=label)
def validate_h5_file(h5_path: Path) -> None:
print(f"Checking {h5_path}", flush=True)
with h5py.File(h5_path, "r") as handle:
for attr_name, attr_value in handle.attrs.items():
validate_attr_value(attr_value, label=f"{h5_path} attr {attr_name!r}")
for dataset_path, dataset in iter_datasets(handle):
values = np.asarray(dataset)
validate_numeric_array(values, label=f"{h5_path}:{dataset_path}")
for attr_name, attr_value in dataset.attrs.items():
validate_attr_value(
attr_value,
label=f"{h5_path}:{dataset_path} attr {attr_name!r}",
)
def main() -> int:
args = build_parser().parse_args()
script_dir = Path(__file__).resolve().parent
h5_paths = sorted(path for path in script_dir.glob(args.pattern) if path.is_file())
if not h5_paths:
print(
f"No HDF5 files found in {script_dir} matching {args.pattern!r}.",
file=sys.stderr,
)
return 1
for h5_path in h5_paths:
validate_h5_file(h5_path)
print(f"Validated {len(h5_paths)} file(s) in {script_dir}.", flush=True)
return 0
if __name__ == "__main__":
raise SystemExit(main())
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