How to read a .mat (Matplotlib) file in Python

# How to read a .mat (Matplotlib) file in Python

To read a .mat (Matplotlib) file in Python:

Install the scipy module and import scipy.io.
Pass the path to the file to the scipy.io.loadmat() method.
The loadmat() method will load the file into your Python script.

First, make sure that you've installed scipy.

Open your terminal in your project's root directory and issue the following command.

shell

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pip install scipy

# or with pip3
pip3 install scipy

make sure scipy is installed

Now, import and use the scipy.io module to read the .mat file.

main.py

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import scipy.io

mat_contents = scipy.io.loadmat('example.mat')

print(mat_contents)

Make sure to replace the example.mat placeholder with the path to your .mat file.

Running the code sample produces the following output.

shell

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{'__header__': b'MATLAB 5.0 MAT-file Platform: posix, Created on: Wed Aug 23 13:36:49 2023',
'__version__': '1.0',
'__globals__': [],
'exon': array([[array([[1, 2],
               [3, 4],
               [5, 6]]), array([[ 7,  8],
                                [ 9, 10]])]], dtype=object)}

read mat file in python

And here is the code that I used to create the example.mat file.

main.py

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import scipy
import numpy as np

exon = [
    np.array([[1, 2], [3, 4], [5, 6]]),
    np.array([[7, 8], [9, 10]])
]

obj_arr = np.zeros(
    (2,),
    dtype=object
)
obj_arr[0] = exon[0]
obj_arr[1] = exon[1]

scipy.io.savemat('example.mat', mdict={'exon': obj_arr})

creating the mat file

We used the scipy.io.loadmat method to load the Matlab file into a Python script.

main.py

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import scipy.io

mat_contents = scipy.io.loadmat('example.mat')

print(mat_contents)

print('-' * 50)

# 👇️ <class 'dict'>
print(type(mat_contents))

The only parameter we passed to the method is the filename.

The method returns a dictionary with variable names as keys and loaded matrices as values.

You can use the dict.keys() method if you only want to print the keys of the dictionary.

main.py

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import scipy.io

mat_contents = scipy.io.loadmat('example.mat')

# ['__globals__', '__header__', '__version__', 'exon']
print(sorted(mat_contents.keys()))

# [[array([[1, 2],
#  [3, 4],
#  [5, 6]]) array([[ 7,  8],
#                  [ 9, 10]])]]
print(mat_contents['exon'])

printing only the keys of the dictionary

As shown in the code sample, use bracket notation to access a specific dictionary key.

If you need to convert the data from the .mat file to a DataFrame, use the pandas.DataFrame() constructor.

main.py

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import pandas as pd
import scipy.io

mat_contents = scipy.io.loadmat('example.mat')

print(mat_contents.keys())

print('-' * 50)

print(mat_contents['exon'])

print('-' * 50)

df = pd.DataFrame(mat_contents['exon'], columns=['A', 'B'])

print(df)

Running the code sample produces the following output.

shell

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dict_keys(['__header__', '__version__', '__globals__', 'exon'])
--------------------------------------------------
[[array([[1, 2],
         [3, 4],
         [5, 6]]) array([[ 7,  8],
                         [ 9, 10]])]]
--------------------------------------------------
                          A                  B
0  [[1, 2], [3, 4], [5, 6]]  [[7, 8], [9, 10]]

convert contents of mat file to dataframe

Make sure to adjust the column names and/or massage the data depending on your needs.

# How to read a .mat (Matplotlib) file in Python using `pymatreader`

You can also use the pymatreader package to read a .mat file in Python.

First install the module by opening your terminal in your project's root directory and running the following command.

shell

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pip install pymatreader

# or with pip3
pip3 install pymatreader

install pymatreader module

Now, import and use the module as follows.

main.py

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from pymatreader import read_mat

mat_contents = read_mat('example.mat')

# dict_keys(['__header__', '__version__', '__globals__', 'exon'])
print(mat_contents.keys())

# [array([[1, 2],
#  [3, 4],
#  [5, 6]]), array([[ 7,  8],
#  [ 9, 10]])]
print(mat_contents['exon'])

read mat file in python using pymatreader

The pymatreader module enables us to read Matlab files.

The read_mat() method returns a Python dictionary that contains all variables of the .mat file.

As shown in the example, you can use the .keys() method to find where the data is actually stored.

The only key that is not surrounded by double underscores is xon, so we used bracket notation to access it.

Depending on the stored data, you will have to access a key with a different name.

# Additional Resources

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How to read a .mat (Matplotlib) file in Python

# How to read a .mat (Matplotlib) file in Python

# How to read a .mat (Matplotlib) file in Python using pymatreader

# Additional Resources

Borislav Hadzhiev

# How to read a .mat (Matplotlib) file in Python using `pymatreader`