How can I run python scripts that depend on imported libraries using matlab?

Hi, I have a python script that depends on imported packages, as shown:

#script stored as get_command_Voltage.py

import pyabf
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd

#load data
def get_command_V(filepath):
    abfdata = pyabf.ABF(filepath)
    return abfdata


commandv = get_command_V(filepath1)

and I'd like to store the python output, commandv, in the variable commandV in matlab.

I wrote the following code on Matlab (script called vclampanal.m):

pyenv
clear classes
setenv("PYTHONPATH", "/usr/local/bin/python3")
%make this folder searchable by python
if count(py.sys.path,pwd) == 0
    insert(py.sys.path,int32(0),pwd);
end


pyabf = py.importlib.import_module('pyabf');

filepath_this = "..." %full file path

commandV = pyrunfile("get_command_Voltage.py","commandv",filepath1 = filepath_this)

but it gives me the error:

Warning: Unable to load Python object. Saving (serializing) Python objects into a MAT-file
is not supported. 
> In vclampanal (line 35) 
Error using <frozen importlib>_find_and_load_unlocked (line 1140)
Python Error: ModuleNotFoundError: No module named 'pyabf'

Error in <frozen importlib>_find_and_load (line 1176)

Error in <frozen importlib>_gcd_import (line 1204)

Error in __init__>import_module (line 126)
 
>> 

I'm just wondering how I could resolve this issue and run python scripts that depend on imports from python libraries (which were installed using pip).

Any advice would be greatly appreciated!

Thank you

Answer 1

[Nicholas Zhou]

you don't need to import anything before calling pyrunfile.

Once you have the get_command_voltage.py ready, this python file does import everything needed, so you just simply call pyrunfile directly as below (which I tried it on Windows with MATLAB R2024a and Python 3.10.4):

>> filepath_this = "130618-1-12.abf"

filepath_this =

"130618-1-12.abf"

>> commandV = pyrunfile("get_command_Voltage.py","commandv",filepath1 = filepath_this)

commandV =

Python ABF - 属性:

fileGUID: [1×36 py.str]

fileUUID: [1×36 py.str]

headerHTML: [1×16209 py.str]

headerMarkdown: [1×9706 py.str]

headerText: [1×9570 py.str]

md5: [1×32 py.str]

sampleRate: [1×1 py.int]

sweepC: [1×1 py.numpy.ndarray]

sweepDerivative: [1×1 py.numpy.ndarray]

sweepTimesMin: [1×1 py.numpy.ndarray]

sweepTimesSec: [1×1 py.numpy.ndarray]

sweepY: [1×1 py.numpy.ndarray]

channelList: [1×1 py.list]

sweepUnitsY: [1×2 py.str]

sweepPointCount: [1×1 py.int]

dataPointByteSize: [1×1 py.int]

dataLengthSec: 4

holdingCommand: [1×20 py.list]

abfVersion: [1×1 py.dict]

abfID: [1×11 py.str]

data: [1×1 py.numpy.ndarray]

abfDateTimeString: [1×23 py.str]

abfFolderPath: [1×16 py.str]

userListParamToVaryName: [1×0 py.list]

userListParamToVary: [1×0 py.list]

dataSecPerPoint: 2.0000e-05

nOperationMode: [1×1 py.int]

channelCount: [1×1 py.int]

sweepEpochs: [1×1 py.pyabf.waveform.EpochSweepWaveform]

sweepChannel: [1×1 py.int]

sweepX: [1×1 py.numpy.ndarray]

dataByteStart: [1×1 py.int]

tagTimesSec: [1×0 py.list]

tagComments: [1×0 py.list]

dataLengthMin: 0.0667

dacUnits: [1×4 py.list]

stimulusByChannel: [1×1 py.list]

sweepList: [1×3 py.list]

abfDateTime: 1806-01-08 17:34:27

sweepIntervalSec: 1

dataPointsPerMs: [1×1 py.int]

userListRepeat: [1×0 py.list]

tagTimesMin: [1×0 py.list]

userListEnable: [1×0 py.list]

sweepNumber: [1×1 py.int]

protocolPath: [1×4 py.str]

userList: [1×0 py.list]

abfFilePath: [1×32 py.str]

sweepLabelX: [1×14 py.str]

adcNames: [1×1 py.list]

creatorVersion: [1×1 py.dict]

dataPointCount: [1×1 py.int]

adcUnits: [1×1 py.list]

sweepUnitsC: [1×2 py.str]

dacNames: [1×4 py.list]

sweepUnitsX: [1×3 py.str]

dataRate: [1×1 py.int]

creatorVersionString: [1×19 py.str]

creator: [1×36 py.str]

stimulusFileFolder: [1×16 py.str]

protocol: [1×4 py.str]

sweepLengthSec: 1

abfVersionString: [1×7 py.str]

sweepLabelC: [1×23 py.str]

tagSweeps: [1×0 py.list]

sweepCount: [1×1 py.int]

sweepLabelD: [1×18 py.str]

abfFileComment: [1×2 py.str]

sweepLabelY: [1×18 py.str]

ABF (v1.299) with 1 channel (pA), sampled at 50.0 kHz, containing 3 sweeps, having no tags, with a total length of 0.07 minutes, recorded without a protocol file.

>>

[Sayaka Minegishi]

Thank you so much! This solved my problem.