Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Use Bitshuffle instead of hdf5plugin #49

Open
noemifrisina opened this issue May 19, 2022 · 0 comments
Open

Use Bitshuffle instead of hdf5plugin #49

noemifrisina opened this issue May 19, 2022 · 0 comments
Labels
bug Something isn't working

Comments

@noemifrisina
Copy link
Collaborator

Bitshuffle is generally faster than hdf5plugin for data compression.

When trying to copy and compress mask and flatfield for Tristan, there was an issue with Bishuffle that caused an Illegal instruction (core dumped) error when running code blocks like the following:

flatfield=h5py.File(flatfieldfile, "r")["image"]
bitshuffle.h5.create_bitshuffle_compressed_dataset(nxdetector, b"flatfield", shape=flatfield.shape, dtype=flatfield.dtype, chunks=(100, flatfield.shape[1]))
nxdetector["flatfield"][:] = flatfield[()] 
block_size=0
flatfield=h5py.File(flatfieldfile, "r")["image"]
nxdetector.create_dataset("flatfield", data=flatfield[()], chunks=(100, flatfield.shape[1]), compression=bitshuffle.h5.H5FILTER, compression_opts=(block_size, bitshuffle.h5.H5_COMPRESS_LZ4))

For now nexgen is using hdf5plugin.

@noemifrisina noemifrisina added the bug Something isn't working label May 19, 2022
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug Something isn't working
Projects
None yet
Development

No branches or pull requests

1 participant