hd5f to access to nested structures in *.mat files

General information

• Operating System (e.g. Windows 10, MacOS 10.11, Ubuntu 16.04.2 LTS, CentOS 7): Windows 10
• Python version (e.g. 2.7, 3.5): 3.7.3
• Where Python was acquired (e.g. system Python on MacOS or Linux, Anaconda on Windows): Anaconda
• h5py version (e.g. 2.6): 2.9
• HDF5 version (e.g. 1.8.17) 1.10.4
• The full traceback/stack trace shown (if it appears)

I getting access to the following structure of matlab file (*.mat):

which contains the following set of structures:

I try to access to the fields inside each structure using hd5f python lib

using the following code:

mat_dict = h5py.File(file_path, 'r')
result = mat_dict['JKPRR']['results']['ChangingKnob'][0]['result']

But apparently I can’t go deep from:

result = mat_dict['JKPRR']['results']['ChangingKnob'][0]

Do you know how I can go to the deeper fields?

[takluyver]

First, the easy bit: it looks like the ChangingKnob dataset is 2D, so to get one item out, you need two indices:

mat_dict['JKPRR']['results']['ChangingKnob'][0, 0]

# This is equivalent but a bit easier to read:
mat_dict['JKPRR/results/ChangingKnob'][0, 0]

It looks like Matlab is storing HDF5 references (a kind of link) in the dataset, so then you need to follow the reference:

ref = mat_dict['JKPRR/results/ChangingKnob'][0, 0]
dataset = mat_dict[ref]

Hopefully after that you can do dataset['result'] to access one field, unless Matlab has made more obstacles.

[takluyver]

Closing this as it looks (from the 👍) like it’s resolved. We can continue the discussion or reopen it if needed.

To summarise for other people looking at this: Matlab’s .mat files do appear to be HDF5, but they might be oddly structured and require some fiddling to work out how to get the data you want. You may want to use a HDF viewer tool like HDFview or h5glance to inspect it.