How do I keep an h5py group in memory after closing the file?

Question

How do I keep an h5py group in memory after closing the file?

After the following code:

import h5py

feature_file = h5py.File(worm_file_path, 'r')
worm_features = feature_file["worm"]

I can access worm_features as it is an h5py group ( <HDF5 group "/worm" (4 members)> )

But after I run the line:

feature_file.close()

I can no longer access worm_features . It now appears as <Closed HDF5 group> .

Since I need to load the worm_features h5py group for about 20 files, I'd like to close those files before doing processing on the data I've loaded into memory. Is this not possible?

Answer 1

Use .value to pull the variable you want from the dataset.

Example:

import h5py

feature_file = h5py.File(worm_file_path, 'r')
worm_features = feature_file["worm"].value
feature_file.close()
print worm_features

Answer 2

Use [:] to copy the value of dataset to a variable to have access the dataset after closing the hdf5 file.

import h5py

feature_file = h5py.File(worm_file_path, 'r')
worm_features = feature_file["worm"] [:]
feature_file.close()
print (worm_features)

.value does not work for me and raised following error:

AttributeError: 'Dataset' object has no attribute 'value'