python - How to overwrite array inside h5 file using h5py

Question

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?

question from:https://stackoverflow.com/questions/22922584/how-to-overwrite-array-inside-h5-file-using-h5py

Answer 1

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