Accessing Matlab Structure Data in Python

[pblelloch]

I used the scipy.io.loadmat function to read a Matlab save file that
includes some structures. In particular my Matlab code looks
something like:

a=randn(10,10);
e=eig(a);
c.mat=a;
c.eig=e;
save

When I read this in I have not trouble getting the a and e matrices,
but when I look at the structure c I get something that looks like:

array([[ ([[-1.918381876114684, 0.35909312220124379,
0.071481108399536447, 0.19413316926540342, -0.16044557980861471,
-1.2431101120071242, 1.1728553895658809, 0.48682974787947486,
-2.6862862203427951, 1.6479268546008081], [-0.13106782428104052,
-0.79434474702678692, 0.15562063581539223, 0.29769161930929805,
0.37883517610546497, 0.13185918869913515, -2.1155833182251094,
-0.4459044413697299, 1.5483561910050594, -0.30667757004699159],
[-0.76863166681707873, -0.22731164066134216, -0.18219139268446782,
-0.71012508212938263, -0.10716072249907738, -0.99947508351036363,
0.46216113959481137, 0.32567307426214315, -0.92437868406001578,
-0.77404140889205997], [2.3899518363067971, 1.5938213548880649,
0.73101584111958162, -0.68767410135748297, 0.21283509315953025,
-0.35421345818508981, -2.4599031616561144, -0.02009780648140742,
-0.72040490902555765, -1.3542395842984021], [0.077245679591339572,
0.15520563382674926, -0.34756806580692184, 0.57283812483950614,
0.46806391670861758, 0.10558871537972472, -0.30485718475158774,
-1.8884755753587876, 0.83350531035866249, -0.32592678918795287],
[0.37560745023340852, 0.17859562900297904, 0.23442400798144603,
0.44521760367790375, -1.6160743410467069, 0.95542626643090245,
0.39823325391367814, 0.33836146832009201, -0.56649185628868159,
1.5532163153526557], [0.39556416936787731, -0.33773084599208325,
-0.86772936409388435, -1.3259592591460707, 0.014738006197359526,
0.46479897799135333, -1.7057865505375613, 0.33780540287940392,
-0.99915099624077919, 0.62813120976932557], [-0.11249908896048552,
-1.5249918897593304, -0.98253858503060265, -1.4998754094582201,
-0.037764347672058281, 0.26670638822706283, 0.75940981180842837,
0.42433121858231648, 0.64126705212804702, -1.0275461814124498],
[-1.8290367022161331, -0.70940664667282161, -0.29357242375327913,
1.0159682271872925, 0.40380900009311393, -1.4232233423222125,
0.20323761868334428, 0.11287078734861246, -0.25395009085808468,
-0.20194229402517888], [2.0914521934834784, -0.86661663365224473,
0.82446963631241454, -0.027515788346229055, 0.30525439285092776,
0.11105730902622701, 0.95868278992227296, -0.11827036575813449,
-1.1216999904267995, 0.86106602555594924]],
[[(-4.5696334670036887+0j)], [(3.7785600753832629+0j)],
[(-2.5789412296806438+0j)],
[(0.30103481909678725+1.8315300529614498j)],
[(0.30103481909678725-1.8315300529614498j)],
[(1.4965987808471322+0j)], [(-0.6068802651298042+1.19212639770675j)],
[(-0.6068802651298042-1.19212639770675j)],
[(-0.54808825947184969+0j)], [(0.19975366069054107+0j)]])]],
dtype=[('mat', '|O4'), ('eig', '|O4')])

Looking through the numpy documentation I can't figure out how to
interpret that. How do I pull the fields out of the structure?

THANKS, Paul

[Matthew Brett]

Hi,

I think you want the scipy mailing list for this one.

What you got here was a structured array. You can get what you want
with something like:

>>> import scipy.io as sio
>>> ws = sio.loadmat('matlab.mat')
>>> c = ws['c']

You got this far already of course.

Notice that 'c' is a 2D array with a composite 'dtype':

>>> c.shape
(1, 1)
>>> c.dtype
dtype([('mat', '|O8'), ('eig', '|O8')]

To get the underlying fields you need:

>>> eig = c[0,0]['eig']
>>> mat = c[0,0]['mat']

To learn more it might be worth reading a little about structured
arrays in numpy.

Best,

Matthew