Open mat files in python

How to load Matlab .mat files in Python

Matlab is a really popular platform for scientific computing in the academia. I’ve used it my throughout my engineering degree and chances are, you will come across .mat files for datasets released by the universities.

This is a brief post which explains how to load these files using python, the most popular language for machine learning today.

The data

I wanted to build a classifier for detecting cars of different models and makes and so the Stanford Cars Dataset appeared to be a great starting point. Coming from the academia, the annotations for the dataset was in the .mat format. You can get the file used in this post here.

Loading .mat files

Scipy is a really popular python library used for scientific computing and quite naturally, they have a method which lets you read in .mat files. Reading them in is definitely the easy part. You can get it done in one line of code:

from scipy.io import loadmat
annots = loadmat('cars_train_annos.mat')

Well, it’s really that simple. But let’s go on and actually try to get the data we need out of this dictionary.

Formatting the data

The loadmat method returns a more familiar data structure, a python dictionary. If we peek into the keys, we’ll see how at home we feel now compared to dealing with a .mat file:

annots.keys()
> dict_keys(['__header__', '__version__', '__globals__', 'annotations'])

Looking at the documentation for this dataset, we’ll get to learn what this is really made of. The README.txt gives us the following information:

This file gives documentation for the cars 196 dataset.
(http://ai.stanford.edu/~jkrause/cars/car_dataset.html) — — — — — — — — — — — — — — — — — — — — 
Metadata/Annotations 
— — — — — — — — — — — — — — — — — — — — 
Descriptions of the files are as follows:-cars_meta.mat: 
Contains a cell array of class names, one for each class.-cars_train_annos.mat: 
Contains the variable ‘annotations’, which is a struct array of length 
num_images and where each element has the fields: 
bbox_x1: Min x-value of the…

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How to Open and Read .mat Files in Python: Tips and Best Practices

Learn how to open and read .mat files in Python using loadmat function, scipy module, PyTables, h5py packages and NumPy. Follow best practices and tricks to work with .mat files in Python.

• Using the loadmat function
• Installing and using the scipy module
• How to load .mat file in python [reading MATLAB files in
• PyTables and h5py packages
• Using NumPy with scipy to read .mat files
• Other considerations when working with .mat files in Python
• Other code samples for opening .mat files in Python
• Conclusion
• How do I open a .MAT file in Python?
• How do I open a .MAT file?
• Can I open mat file without MATLAB?
• How do I run a MATLAB file in Python?

If you have ever worked with MATLAB, you are probably familiar with .mat files. These files are commonly used to store variables and data in MATLAB. However, opening and reading .mat files in Python can be a challenge. Fortunately, there are several ways to do this, including using the loadmat function, installing the scipy module, and using PyTables or h5py packages. In this blog post, we will explore these methods in detail and provide some tips and best practices for working with .mat files in Python.

Using the loadmat function

One of the easiest ways to open and read .mat files in Python is to use the loadmat function. This function is a built-in function in Python’s scipy module and can be used to load all variables stored in a .mat file into a simple Python data structure. Here is the syntax for using the loadmat function:

import scipy.io as siodata = sio.loadmat('example.mat') 

In the above example, we import the scipy.io module and use the loadmat function to load the data from the ‘example.mat’ file. Once the data is loaded, it can be accessed like any other Python object. The loadmat function can also be customized to suit your needs. For example, you can specify which variables to load from the .mat file by passing a list of variable names to the function.

Installing and using the scipy module

Another way to open and read .mat files in Python is to install and use the scipy module. The scipy module is a collection of mathematical algorithms and functions built on top of the NumPy library. It provides several functions for reading and writing files, including the loadmat function.

To install the scipy module, you can use pip:

Once the module is installed, you can import it in Python and use the loadmat function:

import scipy.io as siodata = sio.loadmat('example.mat') 

Using the scipy module can be a convenient way to work with .mat files in Python, especially for users who are already familiar with the module.

How to load .mat file in python [reading MATLAB files in

Tutorial on how to Load (read) .mat type files (MATLAB files) in python programming language Duration: 2:52

PyTables and h5py packages

PyTables and h5py are two popular packages that can be used to read and manipulate .mat files in Python. These packages provide a range of functions for working with .mat files, including opening, reading, and writing files.

To install the PyTables package, you can use pip:

Once the package is installed, you can use it in Python to open and read .mat files:

import tables as tbh5file = tb.open_file('example.mat', mode='r') data = h5file.root.mydata[:] 

The h5py package can also be used to open and read .mat files:

import h5pywith h5py.File('example.mat', 'r') as f: data = f['mydata'][:] 

Both PyTables and h5py packages offer a lot of flexibility and functionality for working with .mat files in Python.

Using NumPy with scipy to read .mat files

NumPy is a Python library that provides support for large, multi-dimensional arrays. It can be used in conjunction with the scipy module to read .mat files in Python. Here is an example of using NumPy with scipy to open and read a .mat file:

import numpy as np import scipy.io as siodata = sio.loadmat('example.mat') mydata = np.array(data['mydata']) 

Using NumPy with scipy can be a powerful way to work with .mat files in Python, especially for users who are already familiar with NumPy.

Other considerations when working with .mat files in Python

When working with .mat files in Python, there are a few other considerations to keep in mind:

• The HDF5 Python library may be required to read MATLAB 7.3 format .mat files.
• Pandas dataframes can be used to work with .mat files in Python.
• Object References point to other objects in the .mat file and can be printed to see how they work.
• MATLAB files used by the program can be opened in MATLAB from MathWorks.

Other code samples for opening .mat files in Python

In Python case in point, python open mat file

import scipy.io mat = scipy.io.loadmat('file.mat')

In Python case in point, open mat file in python

#!python #!/usr/bin/env python from scipy.io import loadmat x = loadmat('test.mat') lon = x['lon'] lat = x['lat'] # one-liner to read a single variable lon = loadmat('test.mat')['lon'] 

In Python , for instance, open mat python code example

from mat4py import loadmatdata = loadmat('datafile.mat')

In Python case in point, read .mat file in python code example

import h5py with h5py.File('test.mat', 'r') as file: print(list(file.keys())) 

In Python case in point, read .mat file in python

with h5py.File('test.mat', 'r') as file: a = list(file['a']) 

Conclusion

Opening and reading .mat files in Python can be done using several different methods, including using the loadmat function, installing and using the scipy module, and using PyTables or h5py packages. NumPy can also be used in conjunction with scipy to read .mat files in Python. When working with .mat files in Python, it is important to consider the type and size of the data stored in the file, as well as any compatibility issues between different versions of Python or MATLAB. By following best practices and using helpful tips and tricks, users can successfully work with .mat files in Python and create valuable insights from the data.

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Reading mat files¶

Here are examples of how to read two variables lat and lon from a mat file called «test.mat».

= Matlab up to 7.1 = mat files created with Matlab up to version 7.1 can be read using the mio module part of scipy.io . Reading structures (and arrays of structures) is supported, elements are accessed with the same syntax as in Matlab: after reading a structure called e.g. struct , its lat element can be obtained with struct.lat , or struct.__getattribute__(‘lat’) if the element name comes from a string.

#!python #!/usr/bin/env python from scipy.io import loadmat x = loadmat('test.mat') lon = x['lon'] lat = x['lat'] # one-liner to read a single variable lon = loadmat('test.mat')['lon'] 

Matlab 7.3 and greater¶

Beginning at release 7.3 of Matlab, mat files are actually saved using the HDF5 format by default (except if you use the -vX flag at save time, see in Matlab). These files can be read in Python using, for instance, the PyTables or h5py package. Reading Matlab structures in mat files does not seem supported at this point.

#!python #!/usr/bin/env python import tables file = tables.openFile('test.mat') lon = file.root.lon[:] lat = file.root.lat[:] # Alternate syntax if the variable name is in a string varname = 'lon' lon = file.getNode('/' + varname)[:] 

Section author: Unknown[16], DavidPowell, srvanrell

© Copyright 2015, Various authors Revision 5e2833af .

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Read Matlab mat Files in Python

1. Use the scipy.io Module to Read .mat Files in Python
2. Use the NumPy Module to Read mat Files in Python
3. Use the mat4py Module to Read mat Files in Python
4. Use the matlab.engine Module to Read mat Files in Python

MATLAB is a programming platform that is widely used these days for numerical computation, statistical analysis, and generating algorithms. It is a very flexible language and allows us to integrate our work with different programming languages like Python.

The MATLAB workspace saves all its variables and contents in a mat file. In this tutorial, we will learn how to open and read mat files in Python.

Use the scipy.io Module to Read .mat Files in Python

The scipy.io module has the loadmat() function, which can open and read mat files. The following code shows how to use this function.

import scipy.io mat = scipy.io.loadmat('file.mat') 

Note that this method does not work for the MATLAB version below 7.3. We can either save the mat file in lower versions using the below command in MATLAB to avoid this.

Use the NumPy Module to Read mat Files in Python

It is discussed earlier how we cannot open files in MATLAB 7.3 using the scipy.io module in Python. It is worth noting that files in version 7.3 and above are hdf5 datasets, which means we can open them using the NumPy library. For this method to work, the h5py module needs to be installed, which requires HDF5 on your system.

The code below shows how to read mat files using this method.

import numpy as np import h5py f = h5py.File('somefile.mat','r') data = f.get('data/variable1') data = np.array(data) # For converting to a NumPy array 

Use the mat4py Module to Read mat Files in Python

This module has functions that allow us to write and read data to and from MATLAB files.

The loadmat() function reads MATLAB files and stores them in basic Python structures like a list or a dictionary and is similar to the loadmat() from scipy.io .

from mat4py import loadmat  data = loadmat('example.mat') 

Use the matlab.engine Module to Read mat Files in Python

For users who already have MATLAB can use the matlab.engine which is provided by MathWorks itself. It has a lot of functionality, which extends to more than just reading and writing “.mat” files.

The following code shows how to read MATLAB files using this method.

import matlab.engine eng = matlab.engine.start_matlab() content = eng.load("example.mat", nargout=1) 

Manav is a IT Professional who has a lot of experience as a core developer in many live projects. He is an avid learner who enjoys learning new things and sharing his findings whenever possible.

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