Deleting hdf5 dataset using h5py
Solution 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]
Solution 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)
hsnee
Updated on September 17, 2020Comments
-
hsnee over 3 years
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, andw-
which is same asw
but fails if file already exists. I have tried all but none seem to work.Any suggestions are much appreciated.