Resolving the numpy.dtype size changed Error in Matlab-Python Integration

If you’re integrating Python and Matlab, especially for NLP tasks using libraries like spacy, encountering binary incompatibility errors such as numpy.dtype size changed can be a major roadblock. This error typically arises due to a mismatch in the compiled versions of the libraries in use, often between NumPy and its dependent libraries.

Understanding the Error

The error message:

ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject.

indicates a version conflict, where the expected size of a data type in NumPy does not match the actual size in the current environment. This mismatch often occurs after updating or changing versions of libraries without ensuring compatibility.

Typical Scenario

Consider a scenario where you are calling a Python function from Matlab to perform text recognition using a pre-trained spacy model. Below are the Python and Matlab scripts involved:

Python Script: final_output.py

import spacy

def text_recognizer(model_path, text):
    try:
        # Load the trained model
        nlp = spacy.load(model_path)
        print("Model loaded successfully.")
        
        # Process the given text
        doc = nlp(text)
        ent_labels = [(ent.text, ent.label_) for ent in doc.ents]
        return ent_labels
    except Exception as e:
        print(f"Error: {e}")
        return []

Matlab Script

% Set up the Python environment
pe = pyenv;
py.importlib.import_module('final_output');

% Add the directory containing the Python script to the Python path
path_add = fileparts(which('final_output.py'));
if count(py.sys.path, path_add) == 0
    insert(py.sys.path, int64(0), path_add);
end

% Define model path and text to process
model_path = 'D:\trained_model\output\model-best';
text = 'Roses are red';

% Call the Python function
pyOut = py.final_output.text_recognizer(model_path, text);

% Convert the output to a MATLAB cell array
entity_labels = cell(pyOut);
disp(entity_labels);

Diagnosing the Issue

This error frequently occurs after updating NumPy to a version that is incompatible with other installed libraries. For instance, NumPy 2.0.0 may not be compatible with certain versions of pandas or other libraries.

Solution: Downgrading NumPy

The simplest and most effective solution is to downgrade NumPy to a version that is known to be compatible with your setup.

1. Identify Compatible Version:
   Determine a compatible version of NumPy, for example, 1.26.4.

2. Update Dependencies:
   Update your requirements.txt or use pip to install specific versions of the dependencies.

Updating requirements.txt:

numpy==1.26.4
spacy==3.7.5

Using pip:

pip install numpy==1.26.4

Reinstalling Dependencies

If issues persist, a clean installation of the dependencies may help. Here’s a script to remove and reinstall NumPy:

site_packages=$(python -c "from distutils.sysconfig import get_python_lib; print(get_python_lib())")
rm -rf "$site_packages"/numpy*
pip install numpy==1.26.4

Verifying the Environment

Ensure that your Python environment is correctly set up and that Matlab is using the correct version of Python. You can verify this by checking the Python environment from Matlab:

pe = pyenv;
disp(pe.Version);

Resolving the numpy.dtype size changed error often involves aligning the versions of your libraries. By pinning the NumPy version to a compatible release and ensuring a clean installation of dependencies, you can mitigate these issues and achieve seamless integration between Matlab and Python.