Update a variable in an HDF5 file

General Usage
1

Simple problem, but it’s driving me mad. How do I update a dataset in an HDF5 file?

Thanks

julia> tp2[“callParams”][“width”]
:1234: HDF5.Dataset: /callParams/width (file: testproj2.h5 xfer_mode: 0)

julia> read(tp2[“callParams/width”])
128

julia> tp2[“callParams”][“width”] = 256
ERROR: cannot create dataset: object “width” already exists at /callParams

julia> write(tp2,“callParams/width”,256)
ERROR: cannot create dataset: object “callParams/width” already exists at /

julia> HDF5.h5open(“testproj.h5”,“r+”) do fid
cp=fid[“callParams”]
cp[“width”] = 256
end
ERROR: cannot create dataset: object “width” already exists at /callParams

2

Maybe you can check the key:

julia> file = tempname() * ".h5";

julia> h5write(file, "A/B", 1.1);

julia> h5read(file, "A/B")
1.1

julia> h5open(file, "r+") do f
           if haskey(f, "A/B")
               delete_object(f, "A/B")
           end
           f["A/B"] = 2.2
       end
2.2
2 Likes
3

Yes. That works. Thank you.

Surprised there is not an inbuilt way.

4 
HDF5.h5open(“testproj.h5”,“w”) do fid

Would the above work?
Edit: Sorry, I think you meant to preserve (other) contents of the file, just replace one variable. This will overwrite the file.

5

Yes, and it also refuses to overwrite because the file exists.

6

Be aware that for older versions of HDF5 this didn’t actually free any space (see for example Reclaim storage space when deleting a large dataset in hdf5 file - HDF5 - HDF Forum). One had to explicitly h5repack the file afterwards. From the top of my head, I think they changed this in version 1.10.

1 Like
7

FWIW you can do this in h5py, I don’t know if it is deleting the object under the hood. If you made it a length 1 dataset you could change the content of the dataset like you can with larger ones.

8

Oh, I don’t see a repack function in HDF5.jl. Can you recommend a way to do this?