Comments (8)
Array types are definitely supported (see the examples in test/
), and JLD supports saving a loading Julia types (which are compound objects). However, our support for HDF5 compound objects is still poor, largely because C structure support is still unfinished in Julia itself JuliaLang/julia#2818.
Am I correct in guessing that you have an HDF5 file written by other software that you want to read into Julia? If you can email me a small test file, I'd be happy to play with this a bit.
from hdf5.jl.
I sent you a small dataset
from hdf5.jl.
Thanks, got it. Indeed we don't yet support the fixed-size H5T_ARRAY
type. I've looked into it a bit, and it's not entirely trivial, because Julia doesn't support fixed-size arrays. The hdf5_to_julia
infrastructure might need a little reworking.
Because my ability to work on this over the next couple of weeks will be limited, I've started a branch called h5array
that contains my initial efforts. If you or anyone else wants to take a stab at this, be my guest. Otherwise I'll plug away as time allows, but my guess is that not much will happen until near the end of this month. If you're up to it, it would be a great contribution.
from hdf5.jl.
The h5ex_t_array.h5
example on http://www.hdfgroup.org/ftp/HDF5/examples/examples-by-api/api18-c.html is relevant, and slightly simpler than the file you sent me (since it doesn't involve nesting array types inside a compound object).
from hdf5.jl.
Thanks a lot Tim. I'm not sure sure if I have the ability to proceed on this. I tried a workaround with PyCall
and the python module h5py
but it was unbelievable slow and couldn't handle integer conversion.
from hdf5.jl.
I fully understand. I will get to this as soon as I can. In the meantime, is there an option to convert the files to a different saving style? For example, instead of a compound type can you use 3 different variables, and instead of a fixed-size array can you use the (more common) variable-length arrays?
from hdf5.jl.
We're halfway there, see 5679103.
from hdf5.jl.
closed by #592.
from hdf5.jl.
Related Issues (20)
- Test failures in h5a_iterate HOT 1
- Changed requirements in HDF5_jll's `libhdf5.so` for `libcurl.so`? HOT 8
- Can't get HDF5.jl work with Julia running in docker (julia:1.8-alpine3.17) - can't find libmpi.so.12 HOT 6
- Add mid/high level interface for HDF5 Dimension Scale HOT 1
- Writing scalar datasets of compound types HOT 3
- freeze when `hdf5_type_id` on self-referential datatype HOT 17
- Get rid of HISTORY.md? HOT 1
- Segfault when writing variable length string as attribute HOT 8
- Feature request - add support for SparseMatrixCSC HOT 1
- Support szip (freely) HOT 5
- Installing HDF5.jl on ARM M1 HOT 5
- HDF5.jl triggers segfault in ccall with openmp+clang(m1) with julia 1.10 HOT 20
- Inconsistent writing of complex data inside compound type HOT 1
- `set_libraries!()` fails on fresh install HOT 7
- h5_is_library_threadsafe() gives unreliable results due to unspecified initial value HOT 1
- The HDF Group CI
- Examine error handling per thread
- The H5T_BITFIELD class should not be directly mapped to Bool HOT 1
- Would it be possible to be able to save @enum values?
- View to a subset of a dataset HOT 1
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