I'm trying to overwrite a numpy array that's a small part of a pretty complicated h5 file.
I'm extracting an array, changing some values, then want to re-insert the array into the h5 file.
I have no problem extracting the array that's nested.
f1 = h5py.File(file_name,'r')
X1 = f1['meas/frame1/data'].value
f1.close()
My attempted code looks something like this with no success:
f1 = h5py.File(file_name,'r+')
dset = f1.create_dataset('meas/frame1/data', data=X1)
f1.close()
As a sanity check, I executed this in Matlab using the following code, and it worked with no problems.
h5write(file1, '/meas/frame1/data', X1);
Does anyone have any suggestions on how to do this successfully?
You want to assign values, not create a dataset:
f1 = h5py.File(file_name, 'r+') # open the file
data = f1['meas/frame1/data'] # load the data
data[...] = X1 # assign new values to data
f1.close() # close the file
To confirm the changes were properly made and saved:
f1 = h5py.File(file_name, 'r')
np.allclose(f1['meas/frame1/data'].value, X1)
#True