Import numpy and scipy (maybe through Anaconda) in Matlab
(1) Introduction.
This is a follow up question of Call a Python function inside a MATLAB loop.
I am trying to run the following Python function (which is saved as anderson_darling.py) on Matlab:
def ADtest(a,b):
rng = np.random.default_rng()
method = stats.PermutationMethod(n_resamples=9999, random_state=rng)
res = stats.anderson_ksamp([a,b], method=method)
print(a)
print(b)
print(res.statistic)
print(res.critical_values)
print(res.pvalue)
if __name__ == "__main__":
import sys
import numpy as np
from scipy import stats
input_list1 = list(map(int, sys.argv[1].strip(‘[]’).split(‘,’)))
input_list2 = list(map(int, sys.argv[2].strip(‘[]’).split(‘,’)))
a = np.array(input_list1)
b = np.array(input_list2)
ADtest(a,b)
To run this file, I open a Terminal (throgh Visual Studio Code, but this is not relevant), and I give the following command:
(base) xyz@xyz myfolder % python3 anderson_darling.py "[1,3,5,6,4,6,7,1,2,7]" "[1,3,5,6,4,6,7,1,2,7]"
The result, that appears on the Terminal is the following:
[1 3 5 6 4 6 7 1 2 7] % <– array a
[1 3 5 6 4 6 7 1 2 7] % <– array b
-1.4363560826434034 % <– res.statistic
[0.325 1.226 1.961 2.718 3.752 4.592 6.546] % <– res.critical_values
1.0 % <– res.pvalue
(2) Problem.
Now, when I go to the editor of Matlab, I try to follow some indications of @Pavan Sahith, from Call a Python function inside a MATLAB loop:
a = [1,3,5,6,4,6,7,1,2,7];
b = [1,3,5,6,4,6,7,1,2,7];
% Convert MATLAB arrays to Python lists
py_a = py.list(a);
py_b = py.list(b);
py.anderson_darling.ADtest(py_a,py_b)
However, I get the following error on the Matlab Command Window:
Error using anderson_darling>ADtest
Python Error: NameError: name ‘np’ is not defined
(3) Potential source/reason of the problem & Question
I guess the problem is related to the way of importing "numpy" and "scipy" to Matlab. I found the following discussions on the Matlab forum, but it looks like they are related to Windows:
How to activate Anaconda environment in Matlab?
MATLAB Crashes when Using Conda Environment Other than Base
import numpy to matlab
problem with python numpy
I instead use Mac and I do not know what to do.
Therefore, how can I successfully import and use "numpy" and "scipy" to Matlab?
(4) Additional information on my system.
If it can help, my Python, Anaconda (the "numpy" and "scipy" packages are contained in (Ana)conda) and Matlab versions are the following ones:
From Terminal:
(base) xyz@xyz ~ % python3 –version
Python 3.12.4
(base) xyz@xyz ~ % conda –version
conda 24.7.1
(base) xyz@xyz ~ % conda info –envs
# conda environments:
#
base * /opt/anaconda3
/usr/local/anaconda3
From the Matlab’s Command Window:
% Python Version for your system (inside Matlab)
% https://ch.mathworks.com/help/matlab/ref/pyenv.html
>> pyenv
ans =
PythonEnvironment with properties:
Version: "3.9"
Executable: "/Library/Developer/CommandLineTools/usr/bin/python3"
Library: "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9/lib/libpython3.9.dylib"
Home: "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
Status: Loaded
ExecutionMode: InProcess
ProcessID: "4128"
ProcessName: "MATLAB"
% Matlab version
>> version
ans =
‘23.2.0.2515942 (R2023b) Update 7′(1) Introduction.
This is a follow up question of Call a Python function inside a MATLAB loop.
I am trying to run the following Python function (which is saved as anderson_darling.py) on Matlab:
def ADtest(a,b):
rng = np.random.default_rng()
method = stats.PermutationMethod(n_resamples=9999, random_state=rng)
res = stats.anderson_ksamp([a,b], method=method)
print(a)
print(b)
print(res.statistic)
print(res.critical_values)
print(res.pvalue)
if __name__ == "__main__":
import sys
import numpy as np
from scipy import stats
input_list1 = list(map(int, sys.argv[1].strip(‘[]’).split(‘,’)))
input_list2 = list(map(int, sys.argv[2].strip(‘[]’).split(‘,’)))
a = np.array(input_list1)
b = np.array(input_list2)
ADtest(a,b)
To run this file, I open a Terminal (throgh Visual Studio Code, but this is not relevant), and I give the following command:
(base) xyz@xyz myfolder % python3 anderson_darling.py "[1,3,5,6,4,6,7,1,2,7]" "[1,3,5,6,4,6,7,1,2,7]"
The result, that appears on the Terminal is the following:
[1 3 5 6 4 6 7 1 2 7] % <– array a
[1 3 5 6 4 6 7 1 2 7] % <– array b
-1.4363560826434034 % <– res.statistic
[0.325 1.226 1.961 2.718 3.752 4.592 6.546] % <– res.critical_values
1.0 % <– res.pvalue
(2) Problem.
Now, when I go to the editor of Matlab, I try to follow some indications of @Pavan Sahith, from Call a Python function inside a MATLAB loop:
a = [1,3,5,6,4,6,7,1,2,7];
b = [1,3,5,6,4,6,7,1,2,7];
% Convert MATLAB arrays to Python lists
py_a = py.list(a);
py_b = py.list(b);
py.anderson_darling.ADtest(py_a,py_b)
However, I get the following error on the Matlab Command Window:
Error using anderson_darling>ADtest
Python Error: NameError: name ‘np’ is not defined
(3) Potential source/reason of the problem & Question
I guess the problem is related to the way of importing "numpy" and "scipy" to Matlab. I found the following discussions on the Matlab forum, but it looks like they are related to Windows:
How to activate Anaconda environment in Matlab?
MATLAB Crashes when Using Conda Environment Other than Base
import numpy to matlab
problem with python numpy
I instead use Mac and I do not know what to do.
Therefore, how can I successfully import and use "numpy" and "scipy" to Matlab?
(4) Additional information on my system.
If it can help, my Python, Anaconda (the "numpy" and "scipy" packages are contained in (Ana)conda) and Matlab versions are the following ones:
From Terminal:
(base) xyz@xyz ~ % python3 –version
Python 3.12.4
(base) xyz@xyz ~ % conda –version
conda 24.7.1
(base) xyz@xyz ~ % conda info –envs
# conda environments:
#
base * /opt/anaconda3
/usr/local/anaconda3
From the Matlab’s Command Window:
% Python Version for your system (inside Matlab)
% https://ch.mathworks.com/help/matlab/ref/pyenv.html
>> pyenv
ans =
PythonEnvironment with properties:
Version: "3.9"
Executable: "/Library/Developer/CommandLineTools/usr/bin/python3"
Library: "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9/lib/libpython3.9.dylib"
Home: "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
Status: Loaded
ExecutionMode: InProcess
ProcessID: "4128"
ProcessName: "MATLAB"
% Matlab version
>> version
ans =
‘23.2.0.2515942 (R2023b) Update 7’ (1) Introduction.
This is a follow up question of Call a Python function inside a MATLAB loop.
I am trying to run the following Python function (which is saved as anderson_darling.py) on Matlab:
def ADtest(a,b):
rng = np.random.default_rng()
method = stats.PermutationMethod(n_resamples=9999, random_state=rng)
res = stats.anderson_ksamp([a,b], method=method)
print(a)
print(b)
print(res.statistic)
print(res.critical_values)
print(res.pvalue)
if __name__ == "__main__":
import sys
import numpy as np
from scipy import stats
input_list1 = list(map(int, sys.argv[1].strip(‘[]’).split(‘,’)))
input_list2 = list(map(int, sys.argv[2].strip(‘[]’).split(‘,’)))
a = np.array(input_list1)
b = np.array(input_list2)
ADtest(a,b)
To run this file, I open a Terminal (throgh Visual Studio Code, but this is not relevant), and I give the following command:
(base) xyz@xyz myfolder % python3 anderson_darling.py "[1,3,5,6,4,6,7,1,2,7]" "[1,3,5,6,4,6,7,1,2,7]"
The result, that appears on the Terminal is the following:
[1 3 5 6 4 6 7 1 2 7] % <– array a
[1 3 5 6 4 6 7 1 2 7] % <– array b
-1.4363560826434034 % <– res.statistic
[0.325 1.226 1.961 2.718 3.752 4.592 6.546] % <– res.critical_values
1.0 % <– res.pvalue
(2) Problem.
Now, when I go to the editor of Matlab, I try to follow some indications of @Pavan Sahith, from Call a Python function inside a MATLAB loop:
a = [1,3,5,6,4,6,7,1,2,7];
b = [1,3,5,6,4,6,7,1,2,7];
% Convert MATLAB arrays to Python lists
py_a = py.list(a);
py_b = py.list(b);
py.anderson_darling.ADtest(py_a,py_b)
However, I get the following error on the Matlab Command Window:
Error using anderson_darling>ADtest
Python Error: NameError: name ‘np’ is not defined
(3) Potential source/reason of the problem & Question
I guess the problem is related to the way of importing "numpy" and "scipy" to Matlab. I found the following discussions on the Matlab forum, but it looks like they are related to Windows:
How to activate Anaconda environment in Matlab?
MATLAB Crashes when Using Conda Environment Other than Base
import numpy to matlab
problem with python numpy
I instead use Mac and I do not know what to do.
Therefore, how can I successfully import and use "numpy" and "scipy" to Matlab?
(4) Additional information on my system.
If it can help, my Python, Anaconda (the "numpy" and "scipy" packages are contained in (Ana)conda) and Matlab versions are the following ones:
From Terminal:
(base) xyz@xyz ~ % python3 –version
Python 3.12.4
(base) xyz@xyz ~ % conda –version
conda 24.7.1
(base) xyz@xyz ~ % conda info –envs
# conda environments:
#
base * /opt/anaconda3
/usr/local/anaconda3
From the Matlab’s Command Window:
% Python Version for your system (inside Matlab)
% https://ch.mathworks.com/help/matlab/ref/pyenv.html
>> pyenv
ans =
PythonEnvironment with properties:
Version: "3.9"
Executable: "/Library/Developer/CommandLineTools/usr/bin/python3"
Library: "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9/lib/libpython3.9.dylib"
Home: "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
Status: Loaded
ExecutionMode: InProcess
ProcessID: "4128"
ProcessName: "MATLAB"
% Matlab version
>> version
ans =
‘23.2.0.2515942 (R2023b) Update 7’ numpy, scipy, module, matlab, python, import, python function, anaconda, conda, python3, py, pyenv MATLAB Answers — New Questions
