Reading raw ZStandard (Zstd) chunks from a HDF5 file via numcodecs

h5py_zstd_numcodecs.py

import h5py
import hdf5plugin
import numcodecs
import numpy as np

# Create data
A = np.random.randint(1024, size=(1024, 1024, 128))

print("Data as created:")
print(A[1, 1, :10])
print()

# Write a HDF5 file
f = h5py.File("zstd_chunks.h5", "w")
f.create_dataset(
        "zstd_ds",
        data=A,
        chunks=(128, 128, 128),
        **hdf5plugin.Zstd()
)
f.close()

# Read the HDF5 file
f = h5py.File("zstd_chunks.h5", "r")
dsetid = f["zstd_ds"].id
compressed_bytes = dsetid.read_direct_chunk((0,0,0))[1]

print("Data as read by h5py/HDF5 via plugin:")
print(f["zstd_ds"][1, 1, :10])
print()

# Use numcodecs to decompress
raw_bytes = numcodecs.zstd.decompress(compressed_bytes)
B = np.frombuffer(raw_bytes, dtype=dsetid.dtype).reshape(128, 128, 128)

print("Data decompressed via numcodecs:")
print(B[1, 1, :10])
print()