How to solve numpy import error when calling Anaconda env from Matlab - matlab

Question

I want to execute a Python script from Matlab (on a Windows 7 machine). The libraries necessary are installed in an Anaconda virtual environment. When running the script from command line, it runs flawlessly.
When calling the script from Matlab as follows:
[status, commandOut] = system('C:/Users/user/AppData/Local/Continuum/anaconda3/envs/tf/python.exe test.py');
or with shell commands, I get an Import Error:
commandOut =
'Traceback (most recent call last):
File "C:\Users\user\AppData\Local\Continuum\anaconda3\envs\tf\lib\site-packages\numpy\core\__init__.py", line 16, in <module>
from . import multiarray
ImportError: DLL load failed: The specified path is invalid.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "test.py", line 2, in <module>
import numpy as np
File "C:\Users\user\AppData\Local\Continuum\anaconda3\envs\tf\lib\site-packages\numpy\__init__.py", line 142, in <module>
from . import add_newdocs
File "C:\Users\user\AppData\Local\Continuum\anaconda3\envs\tf\lib\site-packages\numpy\add_newdocs.py", line 13, in <module>
from numpy.lib import add_newdoc
File "C:\Users\user\AppData\Local\Continuum\anaconda3\envs\tf\lib\site-packages\numpy\lib\__init__.py", line 8, in <module>
from .type_check import *
File "C:\Users\user\AppData\Local\Continuum\anaconda3\envs\tf\lib\site-packages\numpy\lib\type_check.py", line 11, in <module>
import numpy.core.numeric as _nx
File "C:\Users\user\AppData\Local\Continuum\anaconda3\envs\tf\lib\site-packages\numpy\core\__init__.py", line 26, in <module>
raise ImportError(msg)
ImportError:
Importing the multiarray numpy extension module failed. Most
likely you are trying to import a failed build of numpy.
If you're working with a numpy git repo, try `git clean -xdf` (removes all
files not under version control). Otherwise reinstall numpy.
Original error was: DLL load failed: The specified path is invalid.
I already changed the default Matlab Python version to the Anaconda env, but no change:
version: '3.5'
executable: 'C:\Users\user\AppData\Local\Continuum\anaconda3\envs\tf\python.exe'
library: 'C:\Users\user\AppData\Local\Continuum\anaconda3\envs\tf\python35.dll'
home: 'C:\Users\user\AppData\Local\Continuum\anaconda3\envs\tf'
isloaded: 1
Just running my test script without importing numpy works. Reloading numpy (py.importlib.import_module('numpy');) didn't work but threw the same error as before.
Does anyone have an idea how to fix this?

Answer 1

So after corresponding with Matlab support I found out that Matlab depends on the path environment (paths which are deliberately not set when using a virtual environment) and therefore numpy fails to find the necessary paths when called from within Matlab (even if the call contains the path to the virtual environment).
The solution is either to call Matlab from within the virtual environment (via command line) or add the missing paths manually in the path environment.
Maybe this information can help someone else.

Answer 2

First Method
You can change the python interpreter with:
pyversion("/home/nibalysc/Programs/anaconda3/bin/python");
And check it with:
pyversion();
You could also do this in a
startup.m
file in your project folder and every time you start MATLAB from this folder the python interpreter will be changed automatically.
Now you can try to use:
py.importlib.import_module('numpy');
Read up the documentation on how to use the integrated python in MATLAB:
Call user defined custom module
Call modified python module
Alternative Method
Alternative method would be to create a
matlab_shell.sh
file with following content, this is basically the appended code from .bashrc when anaconda is installed and asks you if the installer should modify the .bashrc file:
#!/bin/bash
__conda_setup="$(CONDA_REPORT_ERRORS=false '$HOME/path/to/anaconda3/bin/conda' shell.bash hook 2> /dev/null)"
if [ $? -eq 0 ]; then
\eval "$__conda_setup"
else
if [ -f "$HOME/path/to/anaconda3/etc/profile.d/conda.sh" ]; then
CONDA_CHANGEPS1=false conda activate base
else
\export PATH="$HOME/path/to/anaconda3/bin:$PATH"
fi
fi
unset __conda_setup
# <<< conda init <<<
# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('$HOME/path/to/anaconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
if [ -f "$HOME/path/to/anaconda3/etc/profile.d/conda.sh" ]; then
. "$HOME/path/to/anaconda3/etc/profile.d/conda.sh"
else
export PATH="$HOME/path/to/anaconda3/bin:$PATH"
fi
fi
unset __conda_setup
# <<< conda initialize <<<
conda activate base
eval $2
Then you need to set the MATLAB_SHELL environment variable either before running MATLAB or in MATLAB itself. The best thing in my opinion would be to do it also in the startup.m file like that:
setenv("MATLAB_SHELL", "/path/to/matlab_shell.sh");
Afterwards you can use the system(...) function to run conda python with all your modules installed like that...
String notation:
system("python -c ""python code goes here"");
Char notation:
system('python -c "python code goes here"');
Hope this helps!

Answer 3

Firstly, if you execute your Python script like a regular system command ([status, commandOut] = system('...python.exe test.py'))
the pyversion (and pyenv, since R2019b) got no effect at all. It only matters if you utilize the py. integration, as in the code below (and, in most cases, this is a way better approach).
Currently (I use R2019b update 5) there's a number of pitfalls, that might cause issues similar to yours. I'd recommend to start from the following:
Create a new clean conda environment:
conda create -n test_py36 python=3.6 numpy
Create the following dummy demo1.py:
def dummy_py_method(x):
return x+1
Create the following run_py_code.m:
function run_py_code()
% explicit module import sometimes show more detailed error messages
py.importlib.import_module('numpy');
% to reloads if there would be any changes:
pymodule = py.importlib.import_module('demo1');
py.importlib.reload(pymodule);
% passing data back and forth
x = rand([3 3]);
x_np = py.numpy.array(x);
y_np=pymodule.dummy_py_method(x_np);
y = double(y_np);
disp(y-x);
Create the following before_first_run.m:
setenv('PYTHONUNBUFFERED','1');
setenv('path',['C:\Users\username\Anaconda3\envs\test_py36\Library\bin;'...
getenv('path')]);
pe=pyenv('Version','C:\users\username\Anaconda3\envs\test_py36\pythonw.exe',...
'ExecutionMode','InProcess'...
);
% add "demo1.py" to path
py_file_path = 'W:\tests\Matlab\python_demos\call_pycode\pycode';
if count(py.sys.path,py_file_path) == 0
insert(py.sys.path,int32(0),py_file_path);
end
Run the before_first_run.m first and run the run_py_code.m next.
Notes:
As already mentioned in this answer, one key point is to add the folder, containing the necessary dll files to the %PATH%, before starting python. This could be achieved with setenv from withing Matlab. Usually, the Library\bin is what should be added.
It might be a good idea to try clean officially-supported CPython distribution (e.g. CPython 3.6.8 ). Only install numpy (python -m pip install numpy). To my experience, the setenv is not necessary in this case.
For me, OutOfProcess mode proved to be buggy. Thus, I'd recommend to explicitly setting InProcess mode (for versions before R2019b, the OutOfProcess option is not present, as well as pyenv).
Do not concatenate the two .m files above into one - the py.importlib statements seem to be pre-executed and thus conflict with pyenv.