Reading HDF5-format MATLAB File In Python With H5py

I am trying to read a HDF5-format MATLAB file in python, using the h5py library. This file is called 'Q_visSDF_accurate.mat' and has two keys: 'filename' and 'sdf'. 'filename conta

Solution 1:

In Octave I created a file with cell and matrix

>> xmat = [1,2,3;4,5,6;7,8,9];
>> xcell = {1,2,3;4,5,6;7,8,9};
>> save -hdf5 testmat.h5 xmat xcell

In ipython with h5py, I find that this file contains 2 groups

In [283]: F = h5py.File('../testmat.h5','r')
In [284]: list(F.keys())
Out[284]: ['xcell', 'xmat']

The matrix group has a type and value dataset:

In [285]: F['xmat']
Out[285]: <HDF5 group "/xmat" (2 members)>
In [286]: list(F['xmat'].keys())
Out[286]: ['type', 'value']
In [287]: F['xmat']['type']
Out[287]: <HDF5 dataset "type": shape (), type "|S7">
In [288]: F['xmat']['value']
Out[288]: <HDF5 dataset "value": shape (3, 3), type "<f8">
In [289]: F['xmat']['value'][:]
Out[289]: 
array([[ 1.,  4.,  7.],
       [ 2.,  5.,  8.],
       [ 3.,  6.,  9.]])

The cell has the same type and value, but value is another group:

In [291]: F['xcell']['type']
Out[291]: <HDF5 dataset "type": shape (), type "|S5">
In [292]: F['xcell']['value']
Out[292]: <HDF5 group "/xcell/value" (10 members)>

In [294]: list(F['xcell']['value'].keys())
Out[294]: ['_0', '_1', '_2', '_3', '_4', '_5', '_6', '_7', '_8', 'dims']
...
In [296]: F['xcell']['value']['dims'][:]
Out[296]: array([3, 3])

I had to use the [...] to fetch the value of a cell, since it is a 0d array:

In [301]: F['xcell']['value']['_0']['value'][...]
Out[301]: array(1.0)

To really replicate the question I should have created string cells values, but I think this illustrates well enough how a cells are stored - as named datasets within a data group.

I'm assuming the Octave h5 storage is compatible with MATLAB's.