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Call MATLAB Functions from Python
Return Output Argument from MATLAB Function
You can call any MATLAB^{®} function directly and return the results to Python^{®}. For example, to determine if a number is prime, use the engine to call the function.
Return Multiple Output Arguments from MATLAB Function
When you call a function with the engine, by default the engine returns a single output argument. If you know that the function can return multiple arguments, use the argument to specify the number of output arguments.
To determine the greatest common denominator of two numbers, use the function. Set to return the three output arguments from .
Return No Output Arguments from MATLAB Function
Some MATLAB functions return no output arguments. If the function returns no arguments, set to 0.
Open the MATLAB Help browser from Python.
The MATLAB function opens the browser, but does not return output arguments. If you do not specify , the engine raises an error.
Stop Execution of Function
To stop execution of a MATLAB function press Ctrl+C. Control returns to Python.
Use Function Names for MATLAB Operators
You can use a MATLAB operator in Python by calling the equivalent function. For a list of operators and associated function names, see MATLAB Operators and Associated Functions. For example, to add two numbers, use the function instead of the operator.
See Also

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How can I import python libraries inside a python script that am calling from Matlab?
This is a question from someone who primary works in python, and has some Matlab experience (but not much in nuances of Matlab environment).
I have a custom python module 'pymodule' on my os (mac) and I need to call it from inside a Matlab routine. I have placed it inside my Matlab working directory. There is a script inside the module that needs to import some standard and pipinstalled libaries, such as 'urllib' and 'boto3'. In my case, urllib came standard with my Anaconda 3.6 install, and I installed boto3 with conda.
In both cases, Matlab can call these modules directly, and they work (I can use them). From the matlab cmd window:
mod = py.importlib.import_module('boto3');
mod = py.importlib.import_module('urllib');
However, when I call my python module test.py (this method is tested) from 'test.m' in Matlab:
path = '/Users/drewthayer/Dropbox/path/to/current/';
script = 'test.py';
cmdstr = sprintf('python %s%s', path, script);
[status, cmdout] = system(cmdstr, 'echo');
if status==0
fprintf('data shape= %s\n',cmdout);
end
I get the following error:
>> run test.m
ans =
Python module with properties:
splitattr: [1×1 py.function]
ParseResult: [1×1 py.type]
<module 'urllib.parse' from '/anaconda3/lib/python3.6/urllib/parse.py'>
Traceback (most recent call last):
File "/Users/drewthayer/Dropbox/path/to/current/test.py", line 10, in <module>
import pymodule.iq_parser
File "/Users/drewthayer/Dropbox/path/to/current/pymodule/iq_parser.py", line 7, in <module>
from . import s3io
File "/Users/drewthayer/Dropbox/path/to/current/pymodule/s3io.py", line 9, in <module>
import boto3
ImportError: No module named boto3
It seems like Matlab, working through python, can recognize and import urllib, but can't recognize and import boto3, even though it CAN import boto3 through the py.importlib.import_module('boto3') routine.
In trying to debug this, I've tried the following steps:
 adding paths to urllib and boto3 to my $PYTHONPATH in my ~/.bash_profile (they are visibile to python via sys.path)
 manually adding boto3 path to sys.path in the test.py script, e.g.
sys.path.insert(1,'/anaconda3/lib/python3.6/sitepackages/boto3')
 manually adding boto3 path inside the matlab script to py.sys.path (python's path known to Matlab)
>> modpath = '/anaconda3/lib/python3.6/sitepackages/boto3';
P = py.sys.path;
if count(P,modpath) == 0
insert(P,int32(0),modpath);
end
Any help would be very much appreciated
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.
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.
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 loadmatannots = 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.
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 xvalue of the bounding box, in pixels
bbox_x2: Max xvalue of the bounding box, in pixels
bbox_y1: Min yvalue of the bounding box, in pixels
bbox_y2: Max yvalue of the bounding box, in pixels
class: Integral id of the class the image belongs to.
fname: Filename of the image within the folder of images.cars_test_annos.mat:
Same format as ‘cars_train_annos.mat’, except the class is not provided. — — — — — — — — — — — — — — — — — — — —
Submission file format
— — — — — — — — — — — — — — — — — — — —
Files for submission should be .txt files with the class prediction for
image M on line M. Note that image M corresponds to the Mth annotation in
the provided annotation file. An example of a file in this format is
train_perfect_preds.txtIncluded in the devkit are a script for evaluating training accuracy,
eval_train.m. Usage is:(in MATLAB)
>> [accuracy, confusion_matrix] = eval_train(‘train_perfect_preds.txt’)If your training predictions work with this function then your testing
predictions should be good to go for the evaluation server, assuming
that they’re in the same format as your training predictions.
Our interest is in the 'annotations' variable, as it contains our class labels and bounding boxes. It’s a struct, a data type very familiar to folks coming from a strongly typed language like a flavour of C or java.
A little digging into the object gives us some interesting things to work with:
type(annots[‘annotations’]),annots[‘annotations’].shape>(numpy.ndarray, (1, 8144))type(annots['annotations'][0][0]),annots['annotations'][0][0].shape
>(numpy.void, ())
The annotations are stored in a numpy.ndarray format, however the data type for the items inside this array is numpy.void and numpy doesn’t really seem to know the shape of them.
The documentation page for the loadmat method tells us how it loads matlab structs into numpy structured arrays.You can access the members of the structs using the keys:
annots[‘annotations’][0][0][‘bbox_x1’], annots[‘annotations’][0][0][‘fname’]> (array([[39]], dtype=uint8), array(['00001.jpg'], dtype='<U9'))So now that we know how to access the members of the struct, we can iterate through all of them and store them in a list:
[item.flat[0] for item in annots[‘annotations’][0][0]]> [39, 116, 569, 375, 14, '00001.jpg']Here, we can use the flat method to squeeze the value out of the array.
Now that we know how to deal with matlab files in python, let’s convert it into a pandas data frame. We can do so easily using a list of lists:
data = [[row.flat[0] for row in line] for line in annots[‘annotations’][0]]columns = [‘bbox_x1’, ‘bbox_y1’, ‘bbox_x2’, ‘bbox_y2’, ‘class’, ‘fname’]df_train = pd.DataFrame(data, columns=columns)
Finally, familiar territory!
The code for this post can be found here.
Easily integrate Custom Functions in MATLAB with Python
MATLAB implementation is usually quite reliable as it is developed by professionals. But the advantages of using Python are immense. In this post, I will show how you can integrate your custom MATLAB function into your Python script.
Let us make a custom function in MATLAB that we can use in Python. For demonstration, I will use an elementary function, but the same idea applies to any function.
Eigenvalues and eigenvectors in MATLAB
function [V,D] = eigFunc(A)%returns diagonal matrix D of eigenvalues and matrix V
% whose columns are the corresponding right eigenvectors,
% so that A*V = V*D.
[V, D] = eig(A);
end
I saved the above function as . This function takes in a square matrix as input and outputs diagonal matrix of eigenvalues and matrix whose columns are the corresponding right eigenvectors [ see eig function in MATLAB].
Let’s first use this function in MATLAB for test purpose.
clear; close all; clcA = gallery('lehmer',4);
[V,D] = eigFunc(A)
This returns:
V =0.0693 0.4422 0.8105 0.3778
0.3618 0.7420 0.1877 0.5322
0.7694 0.0486 0.3010 0.5614
0.5219 0.5014 0.4662 0.5088
D =
0.2078 0 0 0
0 0.4078 0 0
0 0 0.8482 0
0 0 0 2.5362
This function works excellent in MATLAB as expected (because the function is an exact copy of the function in MATLAB. But how can we use this function in Python?
Using MATLAB Engine API for Python
The easiest way to use the matlab function in Python is by using the . You can install library by following these two ways.
Install from inside MATLAB:
cd (fullfile(matlabroot,'extern','engines','python'))system('python setup.py install')
Install directly from the terminal:
Navigate to the MATLAB source location and compile the python
python setup.py installPlease note that this MATLAB engine API will be installed for the specific version of . If you are using anaconda, you can inspect the version of Python you are installing the MATLAB engine API for. It is essentially the same way you install other Python libraries. For details, visit here.
import matlabimport matlab.engine
eng = matlab.engine.start_matlab()
A = [[1.0000, 0.5000, 0.3333, 0.2500],
[0.5000, 1.0000, 0.6667, 0.5000],
[0.3333, 0.6667, 1.0000, 0.7500],
[0.2500, 0.5000, 0.7500, 1.0000]]
A = matlab.double(A)
V, D = eng.eigFunc(A, nargout=2)
print("V: ", V)
print("D: ", D)
eng.quit()
Here is the output:
V: [[0.06939950784450351,0.4421928183150595,0.8104910184495989,0.37782737957175255], [0.3619020163563876,0.7419860358173743,0.18770341448628555,0.5322133795757004],[0.7693553355549393,0.04873539080548356,0.30097912769034274,0.5613633351323756],[0.5218266058004974,0.5015447096377744,0.4661365700065611,0.5087893432606572]]D: [[0.20775336892808516,0.0,0.0,0.0],[0.0,0.40783672775946245,0.0,0.0],[0.0,0.0,0.8482416513967358,0.0],[0.0,0.0,0.0,2.536168251915717]]
The results are the same as before. The argument tells the matlab based function to output results here.
This is all well and good if you have MATLAB installed in your system. But what if you want to give your Python script to someone who does not have MATLAB installed on their system. In that case, you can build a Python library using the app in MATLAB. For details, visit Generate a Python Package and Build a Python Application.
MATLAB Runtime installation
Please note that the user needs to install MATLAB runtime to successfully using this library. MATLAB runtime helps in running compiled MATLAB applications or components without installing MATLAB. The runtime can be downloaded from here for Windows, Mac, and Linux OS, and it is free to download.
Import MATLAB based library for Python
import eigFunceigFuncAnalyzer = eigFunc.initialize() #calls the matlab runtime
A = [[1.0000, 0.5000, 0.3333, 0.2500],
[0.5000, 1.0000, 0.6667, 0.5000],
[0.3333, 0.6667, 1.0000, 0.7500],
[0.2500, 0.5000, 0.7500, 1.0000]]
A = array.array(A) %not tested
V, D = eigFuncAnalyzer.eigFunc(A, nargout=2)
print("V: ", V)
print("D: ", D)
eigFuncAnalyzer.terminate()
Please note that you can design your in a way that you can simply load the mat data and you can use function to save the python data to mat format. For details, see the scipy documentation.
 How to Call MATLAB from Python
 Call MATLAB Functions from Python
 Generate a Python Package and Build a Python Application
Matlab python import
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Start and Stop MATLAB Engine for Python
Start MATLAB Engine for Python
Start Python^{®} at the operating system prompt.
Import the package into your Python session.
Start a new MATLAB^{®} process by calling . The function returns a Python object, , which enables you to pass data and call functions executed by MATLAB.
Run Multiple Engines
Start each engine separately. Each engine starts and communicates with its own MATLAB process.
Stop Engine
Call either the or the function.
If you exit Python with an engine still running, then Python automatically stops the engine and its MATLAB process.
Start Engine with Startup Options
Start the engine and pass the options as an input argument string to . For example, start MATLAB with the desktop.
You can define multiple startup options with a single string. For example, start the desktop and set the numeric display format to .
You also can start the desktop after you start the engine.
Start Engine Asynchronously
Start the engine asynchronously. While MATLAB starts, you can enter commands at the Python command line.
Create the MATLAB instance so you can perform computations in MATLAB.
See Also
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Install MATLAB Engine API for Python
To start the MATLAB^{®} engine within a Python^{®} session, you first must install the engine API as a Python package. MATLAB provides a standard Python file for building and installing the engine using the module. You can use the same commands to build and install the engine on Windows^{®}, Mac, or Linux^{®} systems.
Each MATLAB release has a Python package. When you use the package, it runs the specified MATLAB version. To switch between MATLAB versions, you need to switch between the Python packages. For more information, see Install Supported Python Implementation.
Verify Your Configuration
Before you install, verify your Python and MATLAB configurations.
Check that your system has a supported version of Python and MATLAB R2014b or later. For more information, see Versions of Python Compatible with MATLAB Products by Release .
To check that Python is installed on your system, run Python at the operating system prompt.
Add the folder that contains the Python interpreter to your path, if it is not already there.
Find the path to the MATLAB folder. Start MATLAB and type in the command window. Copy the path returned by .
Install the Engine API
To install the engine API, choose one of the following. You must call this install command in the specified folder.
At a Windows operating system prompt (you might need administrator privileges to execute these commands) —
cd "matlabroot\extern\engines\python" python setup.py installAt a macOS or Linux operating system prompt (you might need administrator privileges to execute these commands) —
cd "matlabroot/extern/engines/python" python setup.py installAt the MATLAB command prompt —
cd (fullfile(matlabroot,'extern','engines','python')) system('python setup.py install')Use one of the nondefault options described in Install MATLAB Engine API for Python in Nondefault Locations.
Start MATLAB Engine
Start Python, import the module, and start the MATLAB engine:
Install Python Engine for Multiple MATLAB Versions
You can specify a MATLAB version to run from a Python script by installing the MATLAB Python packages to versionspecific locations. For example, suppose that you want to call either MATLAB R2019a or R2019b from a Python version 3.6 script.
From the Windows system prompt, install the R2019a package in a subfolder named :
Install the R2019b package in a subfolder:
From a Linux system prompt:
From a Mac Terminal:
Start Specific MATLAB Engine Version
To start a specific version of the MATLAB engine, set the environment variable to the location of the package. This code assumes you used the setup shown in the previous section. To set on Windows to call MATLAB R2019b, type:
On Linux or Mac:
To check which version of MATLAB was imported, in Python type:
Python might use different folder names for installation. For example, Python might create a subfolder before installing the MATLAB engine. Verify the folder on your system to use with the command.
Troubleshooting MATLAB Engine API for Python Installation
Make sure that your MATLAB release supports your Python version. See Versions of Python Compatible with MATLAB Products by Release .
You must run the Python install command from the specified MATLAB folder. See Install the Engine API.
Make sure that you have administrator privileges to execute the install command from the operating system prompt. On Windows, open the command prompt with the Run as administrator option.
The installer installs the engine in the default Python folder. To use nondefault location, see Install MATLAB Engine API for Python in Nondefault Locations.
If you installed the package in a nondefault folder, make sure to set the environment variable. For example, suppose that you used this installation command:
python setup.py install prefix="matlab19bPy36"In Python, update with this command:
sys.path.append("matlab19bPy36")
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How does one get MATLAB to load Python libraries and scripts?
I'm working on MATLAB 2018a, so cannot use pyenv, so I've been using pyversion.
OS: Windows 10 Pro, version 1809, 64 bit.
I can get MATLAB to call simple Python code, as long as it has no library calls:
If the Python code is called tryRunInMATLAB.py, and it is:
# * coding: utf8 *
def printThis():
Lisa = list([9,18,27])
print("Lisa is " + str(Lisa) )
return
Then trying to call it in MATLAB 2018a:
folder = "ThisHereFolder"
file = "tryRunInMATLAB.py"
addpath(folder)
P = py.sys.path;
if count(P,folder) == 0
insert(P,int32(0),folder);
end
py.tryRunInMATLAB.printThis()
Undefined variable "py" or class "py.tryRunInMATLAB.printThis".
Oh, maybe it does't even work for that now.
Maybe this'll help?
py.importlib.import_module("Drive:\\path\\PythonTest\tryRunInMATLAB.py")
Nope:
Error using <frozen importlib>_find_and_load_unlocked (line 965)
Python Error: ModuleNotFoundError: No module named 'Drive:\\path\\PythonTest\\tryRunInMATLAB'
Error in <frozen importlib>_find_and_load (line 983)
Error in <frozen importlib>_gcd_import (line 1006)
Error in <frozen importlib>_call_with_frames_removed (line 219)
Error in <frozen importlib>_find_and_load_unlocked (line 953)
Error in <frozen importlib>_find_and_load (line 983)
Error in <frozen importlib>_gcd_import (line 1006)
Error in __init__>import_module (line 127)
return _bootstrap._gcd_import(name[level:], package, level)
Also tried these:
py.importlib.import_module(file)
Error using <frozen importlib>_find_and_load_unlocked (line 962)
Python Error: ModuleNotFoundError: No module named 'tryRunInMATLAB.py'; 'tryRunInMATLAB' is not a package
Error in <frozen importlib>_find_and_load (line 983)
Error in <frozen importlib>_gcd_import (line 1006)
Error in __init__>import_module (line 127)
return _bootstrap._gcd_import(name[level:], package, level)
py.importlib.reload(file)
Error using __init__>reload (line 140)
Python Error: TypeError: reload() argument must be a module
Same answer
Anyway, I've also tried to add libraries by:
anacond = "Drive:\path\Continuum\anaconda3\"
if count(P,anacond) == 0
insert(P,int32(0),anacond)
end
if count(P,"Drive:\path\Continuum\anaconda3\Lib\sitepackages\")==0
insert(P,int32(0),"Drive:\path\Continuum\anaconda3\Lib\sitepackages\")
end
plt = py.matplotlib.plot([9,8,7,6,4])
Undefined variable "py" or class "py.matplotlib.plot".
Obviously, I'm not giving my true paths here.
What about just importing a library?
>> py.importlib.import_module('matplotlib')
Error using _distributor_init><module> (line 34)
Python Error: ImportError: DLL load failed: The specified module could not be found.
Error in __init__><module> (line 140)
from . import _distributor_init
Error in __init__><module> (line 33)
import numpy as np
Error in __init__><module> (line 141)
from . import cbook, rcsetup
Error in <frozen importlib>_call_with_frames_removed (line 219)
Error in <frozen importlib>exec_module (line 728)
Error in <frozen importlib>_load_unlocked (line 677)
Error in <frozen importlib>_find_and_load_unlocked (line 967)
Error in <frozen importlib>_find_and_load (line 983)
Error in <frozen importlib>_gcd_import (line 1006)
Error in __init__>import_module (line 127)
return _bootstrap._gcd_import(name[level:], package, level)
What about?
py.importlib.import_module('matplotlib\pyplot.py')
No luck anywhere.
Am I doing something stupid or obviously missing something?
Thanks.