export matlab variable to text for python usage

Question

So let's start off by saying I'm a total beginner in matlab. I'm working with python and now I've recieved some data in a matlab file that I need to export to a format I could use with python.

I've googled around and found I can export a matlab variable to a text file using:

dlmwrite('my_text', MyVariable, 'delimiter' , ',');

Now the variable I need to export is a 16000 x 4000 matrix of doubles of the form 0.006747668446927. Now here is where the problem starts. I need to export the full values for each double. Trying with that function lead me to export the numbers in a format of 0.0067477. This won't do since I need a whole lot more of precision for what I'm doing. So how can I export the full values of each of these variables? Or if you have a more elegant way of using that huge matlab matrix in python please feel free.

Regards, Bogdan

Answer 1

To exchange big chunks of numerical data between Python and Matlab I recommend HDF5

• http://en.wikipedia.org/wiki/Hierarchical_Data_Format

The Python binding is called h5py

• http://code.google.com/p/h5py

Here are two examples for both directions. First from Matlab to Python

% matlab
points = [1 2 3 ; 4 5 6 ; 7 8 9 ; 10 11 12 ];
hdf5write('test.h5', '/Points', points);

# python
import h5py
with h5py.File('test.h5', 'r') as f:
    points = f['/Points'].value    

And now from Python to Matlab

# python
import h5py
import numpy
points = numpy.array([ [1., 2, 3], [4, 5, 6], [7, 8, 9], [10, 11, 12] ])
with h5py.File('test.h5', 'w') as f:
    f['/Points'] = points

% matlab
points = hdf5read('test.h5', '/Points');

NOTE A column in Matlab will come out as a row in Python and vice versa. This isn't a bug but the difference between the way C and Fortran interpret a continuous piece of data in memory.