Python-created HDF5 dataset transposed in Matlab

Question

I have some data that I share between Python and Matlab. I used to do it by saving NumPy arrays in MATLAB-style .mat files but would like to switch to HDF5 datasets. However, I've noticed a funny feature: when I save a NumPy array in an HDF5 file (using h5py) and then read it in Matlab (using h5read), it ends up being transposed. Is there something I'm missing?

Python code:

import numpy as np
import h5py

mystuff = np.random.rand(10,30)

f = h5py.File('/home/user/test.h5', 'w')
f['mydataset'] = mystuff
f.close()

Matlab code:

mystuff = h5read('/home/user/test.h5', '/mydataset');
size(mystuff) % 30 by 10

Answer 1

When reading data from MatLab, dimensions of the data read need to be permuted to retrieve data layout. To do so, permute function is used. The code below gives the general case with any number of dimensions

rawdata = h5read(h5Filename,h5Dataset);
ndim = numel(size(rawdata));
data = permute(rawdata,[ndim:-1:1]);

When one works with 2D data, one can only transpose result from h5read

data = h5read(h5Filename,h5Dataset)';