How to preserve matlab struct when accessing in python?

Question

I have a mat-file that I accessed using

from scipy import io
mat = io.loadmat('example.mat')

From matlab, example.mat contains the following struct

    >> load example.mat
    >> data1

    data1 =

            LAT: [53x1 double]
            LON: [53x1 double]
            TIME: [53x1 double]
            units: {3x1 cell}


    >> data2

    data2 = 

            LAT: [100x1 double]
            LON: [100x1 double]
            TIME: [100x1 double]
            units: {3x1 cell}

In matlab, I can access data as easy as data2.LON, etc.. It's not as trivial in python. It give me several option though like

mat.clear       mat.get         mat.iteritems   mat.keys        mat.setdefault  mat.viewitems   
mat.copy        mat.has_key     mat.iterkeys    mat.pop         mat.update      mat.viewkeys    
mat.fromkeys    mat.items       mat.itervalues  mat.popitem     mat.values      mat.viewvalues

Is is possible to preserve the same structure in python? If not, how to best access the data? The present python code that I am using is very difficult to work with.

Thanks

Can you explain what it looks like when you load it into python? — Ben A., Aug 14 '12 at 14:58
Also, another thought. If you're using SciPi have you tried using `SciPi.loadmat`? — Ben A., Aug 14 '12 at 15:02
yes, I tried loadmat. The output in python is just difficult to use. I don't even know how to access LON or LAT in either data1 or data2. — mikeP, Aug 14 '12 at 15:06
@mikeP -- My guess is that it's probably just `data1['LAT']` (python) as opposed to `data1.LAT` (matlab). — mgilson, Aug 14 '12 at 16:06
If you're still having issues (and don't mind/can share) feel free to pass along a sample .mat file and I'll play around with it after I get home from work. — Ben A., Aug 14 '12 at 17:07

mikeP · Accepted Answer · 2012-08-14T18:05:40.580

13

Found this tutorial about matlab struct and python

http://docs.scipy.org/doc/scipy/reference/tutorial/io.html

edited Aug 14 '12 at 18:05

answered Aug 14 '12 at 15:22

mikeP

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2
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This might be able to add a layer of additional information for you as well: http://stackoverflow.com/questions/1984714/how-to-access-fields-in-a-struct-imported-from-a-mat-file-using-loadmat-in-pyth?rq=1 – Ben A. Aug 14 '12 at 17:06
1

The tutorial has now moved to: https://docs.scipy.org/doc/scipy/tutorial/io.html#matlab-files – Rodrigo Zepeda May 24 '23 at 19:46

Austin Downey · Answer 2 · 2018-03-04T18:13:48.320

When I need to load data into Python from MATLAB that is stored in an array of structs {strut_1,struct_2} I extract a list of keys and values from the object that I load with scipy.io.loadmat. I can then assemble these into there own variables, or if needed, repackage them into a dictionary. The use of the exec command may not be appropriate in all cases, but if you are just trying to processes data it works well.

# Load the data into Python     
D= sio.loadmat('data.mat')

# build a list of keys and values for each entry in the structure
vals = D['results'][0,0] #<-- set the array you want to access. 
keys = D['results'][0,0].dtype.descr

# Assemble the keys and values into variables with the same name as that used in MATLAB
for i in range(len(keys)):
    key = keys[i][0]
    val = np.squeeze(vals[key][0][0])  # squeeze is used to covert matlat (1,n) arrays into numpy (1,) arrays. 
    exec(key + '=val')

score 4 · Answer 3 · answered Dec 08 '20 at 08:36

this will return the mat structure as a dictionary

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], sio.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, sio.matlab.mio5_params.mat_struct):
            dict[strg] = _todict(elem)
        else:
            dict[strg] = elem
    return dict


def loadmat(filename):
    """
    this function should be called instead of direct scipy.io .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 = sio.loadmat(filename, struct_as_record=False, squeeze_me=True)
    return _check_keys(data)

score 0 · Answer 4 · edited May 23 '17 at 11:46

(!) In case of nested structures saved in *.mat files, is necessary to check if the items in the dictionary that io.loadmat outputs are Matlab structures. For example if in Matlab

>> thisStruct

ans =
      var1: [1x1 struct]
      var2: 3.5

>> thisStruct.var1

ans =
      subvar1: [1x100 double]
      subvar2: [32x233 double]

Then use the code by mergen in scipy.io.loadmat nested structures (i.e. dictionaries)

How to preserve matlab struct when accessing in python?

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