balintbalazs / b3d Goto Github PK

Currently only HDF5 1.8.x versions are supported, but many software ships already with HDF5 1.10.x. Especially important is h5py, as currently B3D is incompatible with the latest version.

Currently it's not possible to save B3D compressed files from Fiji, only reading. Furthermore, a separate HDF5 installation is necessary, as well as a custom version of jhdf5-14.12.5.jar

• add B3D saving
  • custom plugin
  • modify existing HDF5 plugin
  • add support to BDV saving
• statically compile HDF5 with B3D and include in jhdf jar

Matlab (2019b) internally uses HDF5 1.8.12, which in principle already supports dynamically loaded filter, however to safely deallocate any unneeded buffers H5free_memory should be used: https://portal.hdfgroup.org/display/HDF5/H5_FREE_MEMORY

This feature was introduced in HDF5 1.8.15, and is not supported in Matlab. Using free directly requires to match the plugin compiler version with the one that was used for Matlab to avoid memory corruption.

Still missing:

• cmake for B3D HDF5 plugin