How to read Mat v7.3 files in python?

Question

I am trying to read the mat file listed on the following website ufldl.stanford.edu/housenumbers, in the train.tar.gz file, there is a mat file called digitStruct.mat.

when I used scipy.io to read the mat file, it warns me about the message “please use hdf reader for Matlab v7.3 files”.

matlab source file is below

load digitStruct.mat
for i = 1:length(digitStruct)
    im = imread([digitStruct(i).name]);
    for j = 1:length(digitStruct(i).bbox)
        [height, width] = size(im);
        aa = max(digitStruct(i).bbox(j).top+1,1);
        bb = min(digitStruct(i).bbox(j).top+digitStruct(i).bbox(j).height, height);
        cc = max(digitStruct(i).bbox(j).left+1,1);
        dd = min(digitStruct(i).bbox(j).left+digitStruct(i).bbox(j).width, width);

        imshow(im(aa:bb, cc:dd, :));
        fprintf('%d\n',digitStruct(i).bbox(j).label );
        pause;
    end
end

as shown above, the mat file has the key "digitStruct", and inside the "digitStruct", "name" and "bbox" can be found, I used the h5py API to read the file.

import h5py
f = h5py.File('train.mat')
print len( f['digitStruct']['name'] ), len(f['digitStruct']['bbox']   )

I can read the array, however, when I loop through the array, how can I read each element?

for i in f['digitStruct']['name']:
    print i # only print out the HDF5 ref

Answer 1

Matlab:

test = {'Hello', 'world!'; 'Good', 'morning'; 'See', 'you!'};
save('data.mat', 'test', '-v7.3') % v7.3 so that it is readable by h5py

Python ( , , ):

import h5py
import numpy as np

data = []
with h5py.File("data.mat") as f:
    for column in f['test']:
        row_data = []
        for row_number in range(len(column)):            
            row_data.append(''.join(map(unichr, f[column[row_number]][:])))   
        data.append(row_data)

print data
print np.transpose(data)

:

[[u'Hello', u'Good', u'See'], [u'world!', u'morning', u'you!']]

[[u'Hello' u'world!']
 [u'Good' u'morning']
 [u'See' u'you!']]

Answer 2

import numpy as np
import cPickle as pickle
import h5py

f = h5py.File('train/digitStruct.mat')

metadata= {}
metadata['height'] = []
metadata['label'] = []
metadata['left'] = []
metadata['top'] = []
metadata['width'] = []

def print_attrs(name, obj):
    vals = []
        if obj.shape[0] == 1:
            vals.append(int(obj[0][0]))
        else:
            for k in range(obj.shape[0]):
                vals.append(int(f[obj[k][0]][0][0]))
        metadata[name].append(vals)

for item in f['/digitStruct/bbox']:
    f[item[0]].visititems(print_attrs)

with open('train_metadata.pickle','wb') as pf:
  pickle.dump(metadata, pf, pickle.HIGHEST_PROTOCOL)    

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