Deleting hdf5 dataset using h5py

Question

Is there any way to remove a dataset from an hdf5 file, preferably using h5py? Or alternatively, is it possible to overwrite a dataset while keeping the other datasets intact?

To my understanding, h5py can read/write hdf5 files in 5 modes

f = h5py.File("filename.hdf5",'mode')

where mode can be r for read, r+ for read-write, a for read-write but creates a new file if it doesn't exist, w for write/overwrite, and w- which is same as w but fails if file already exists. I have tried all but none seem to work.

Any suggestions are much appreciated.

Answer 1

Yes, this can be done.

with h5py.File(input,  "a") as f:
    del f[datasetname]

You will need to have the file open in a writeable mode, for example append (as above) or write.

As noted by @seppo-enarvi in the comments the purpose of the previously recommended f.__delitem__(datasetname) function is to implement the del operator, so that one can delete a dataset using del f[datasetname]

Answer 2

I tried this out and the only way I could actually reduce the size of the file is by copying everything to a new file and just leaving out the dataset I was not interested in:

fs = h5py.File('WFA.h5', 'r')
fd = h5py.File('WFA_red.h5', 'w')
for a in fs.attrs:
    fd.attrs[a] = fs.attrs[a]
for d in fs:
    if not 'SFS_TRANSITION' in d: fs.copy(d, fd)

Answer 3

I do not understand what has your question to do with the file open modes. For read/write r+ is the way to go.

To my knowledge, removing is not easy/possible, in particular no matter what you do the file size will not shrink.

But overwriting content is no problem

f['mydataset'][:] = 0

Answer 4

I wanted to make you aware of a development one of my colleagues made and put online in opensource. It's called h5nav . You can download it with pip install ( https://pypi.org/project/h5nav/ ).

pip install h5nav

h5nav toto.h5
ls
rm the_group_you_want_to_delete
exit

Note that you'll still have to use h5repack to lower the size of your file.

Best, Jérôme