mergen mergen - 3 months ago 30
Python Question

scipy.io.loadmat nested structures (i.e. dictionaries)

Using the given routines (how to load Matlab .mat files with scipy), I could not access deeper nested structures to recover them into dictionaries

To present the problem I run into in more detail, I give the following toy example:

load scipy.io as spio
a = {'b':{'c':{'d': 3}}}
# my dictionary: a['b']['c']['d'] = 3
spio.savemat('xy.mat',a)


Now I want to read the mat-File back into python. I tried the following:

vig=spio.loadmat('xy.mat',squeeze_me=True)


If I now want to access the fields I get:

>> vig['b']
array(((array(3),),), dtype=[('c', '|O8')])
>> vig['b']['c']
array(array((3,), dtype=[('d', '|O8')]), dtype=object)
>> vig['b']['c']['d']
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)

/<ipython console> in <module>()

ValueError: field named d not found.


However, by using the option
struct_as_record=False
the field could be accessed:

v=spio.loadmat('xy.mat',squeeze_me=True,struct_as_record=False)


Now it was possible to access it by

>> v['b'].c.d
array(3)

Answer

Here are the functions, which reconstructs the dictionaries just use this loadmat instead of scipy.io's loadmat:

import scipy.io as spio

def loadmat(filename):
    '''
    this function should be called instead of direct spio.loadmat
    as it cures the problem of not properly recovering python dictionaries
    from mat files. It calls the function check keys to cure all entries
    which are still mat-objects
    '''
    data = spio.loadmat(filename, struct_as_record=False, squeeze_me=True)
    return _check_keys(data)

def _check_keys(dict):
    '''
    checks if entries in dictionary are mat-objects. If yes
    todict is called to change them to nested dictionaries
    '''
    for key in dict:
        if isinstance(dict[key], spio.matlab.mio5_params.mat_struct):
            dict[key] = _todict(dict[key])
    return dict        

def _todict(matobj):
    '''
    A recursive function which constructs from matobjects nested dictionaries
    '''
    dict = {}
    for strg in matobj._fieldnames:
        elem = matobj.__dict__[strg]
        if isinstance(elem, spio.matlab.mio5_params.mat_struct):
            dict[strg] = _todict(elem)
        else:
            dict[strg] = elem
    return dict
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