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?

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 

Answer 2

askewchan's answer describes the way to do it (you cannot create a dataset under a name that already exists, but you can of course modify the dataset's data). Note, however, that the dataset must have the same shape as the data (X1) you are writing to it. If you want to replace the dataset with some other dataset of different shape, you first have to delete it:

del f1['meas/frame1/data'] dset = f1.create_dataset('meas/frame1/data', data=X1)