Why Matlab do not import full python library?

Question

DavidePiccinini 2024-1-11

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此问题的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/2068841-why-matlab-do-not-import-full-python-library

编辑： Hassaan 2024-1-12

在 MATLAB Online 中打开

Hi to all,

I want to use the obspy python library (installed in a mamba environment).

I setup the pyenv using the correct path:

pyenv
ans = 
  PythonEnvironment with properties:
          Version: "3.11"
       Executable: "/homes/piccinini/bin/mambaforge/envs/seismat/bin/python"
          Library: "/homes/piccinini/bin/mambaforge/envs/seismat/lib/libpython3.11.so"
             Home: "/homes/piccinini/bin/mambaforge/envs/seismat"
           Status: Loaded
    ExecutionMode: OutOfProcess
        ProcessID: "4436"
      ProcessName: "MATLABPyHost"

The problem is when I invoke some obspy functions, I get the "Unable to resolve the name" error, but this happen just for a part of the libraries, not for the whole one.

For example this

py.obspy.UTCDateTime
ans = 
  Python UTCDateTime with properties:
           date: [1×1 py.datetime.date]
       datetime: [1×1 py.datetime.datetime]
            day: [1×1 py.int]
           hour: [1×1 py.int]
         julday: [1×1 py.int]
    microsecond: [1×1 py.int]
         minute: [1×1 py.int]
          month: [1×1 py.int]
             ns: [1×1 py.int]
      precision: [1×1 py.int]
         second: [1×1 py.int]
           time: [1×1 py.datetime.time]
      timestamp: 1.7050e+09
        weekday: [1×1 py.int]
           year: [1×1 py.int]
    2024-01-11T13:45:13.774588Z

work perfectly.

But if I type:

py.obspy.clients.fdsn.Client
Unable to resolve the name 'py.obspy.clients.fdsn.Client'.

I get the error.

It seems a path (or permission) problem but I can't figure how to solve the problem.

MATLAB Version: 23.2.0.2459199 (R2023b) Update 5 on Linux

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Answer 1

Hassaan 2024-1-11

0
链接

此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/2068841-why-matlab-do-not-import-full-python-library#answer_1387906

编辑：Hassaan 2024-1-12

Some steps and considerations to help troubleshoot and potentially resolve the issue:

Check Python Path in MATLAB: Make sure MATLAB is recognizing the correct Python environment where obspy is installed. You can check this using the pyenv command, which you've already done. Ensure that the environment is active and that the paths are correctly set.
Verify Installation of Obspy: Ensure that obspy is correctly installed in the specified environment. You can verify this by running Python within the same environment outside of MATLAB and checking if you can import and access obspy.clients.fdsn.Client without any issues.
MATLAB Python Compatibility: Ensure that your version of MATLAB is compatible with Python 3.11. While MATLAB typically supports the latest versions of Python, there can sometimes be compatibility issues, especially with newer Python versions.
Module Initialization: Some Python modules require initialization steps that might not be automatically handled by MATLAB's Python integration. It's worth checking obspy's documentation to see if there are any such requirements.
Dependencies and Submodules: Sometimes, the issue might be with dependencies of a particular submodule within a Python package. Ensure all dependencies of obspy.clients.fdsn are properly installed and accessible in the environment.
MATLAB's Python Integration Limitations: Be aware that MATLAB's integration with Python has certain limitations. Not all Python libraries and their functionalities are fully compatible or accessible from within MATLAB.
Test with a Simple Python Script: Create a simple Python script that imports and uses obspy.clients.fdsn.Client, and run this script from MATLAB using the system command. This can help you determine if the issue is with MATLAB's Python interface or with the Python setup itself.
MATLAB Support and Documentation: Consult MATLAB's documentation for any known issues or special instructions regarding Python integration, especially with complex libraries like obspy. Additionally, consider reaching out to MathWorks support for assistance.
Permission Issues: While less likely, there could be permission issues, especially if MATLAB is running with different permissions compared to your standard Python environment.
Reinstall Obspy: As a last resort, try reinstalling obspy in your Python environment. Occasionally, reinstallation can resolve path or dependency issues.
Downgrading/Upgrading libraries: Downgrading or updating the libary may help.

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DavidePiccinini 2024-1-11

编辑：DavidePiccinini 2024-1-12

在 MATLAB Online 中打开

Thanks a lot but no one of the proposed solutions work.

I currently use Obspy from Matlab under MacOS, and it works perfectly.

Thinking it might be a Python-Obspy version alignment issue, I also reinstalled a completely new environment with an older but Matlab-compatible Python, but I get the same error.

pyenv
ans = 
  PythonEnvironment with properties:
          Version: "3.8"
       Executable: "/homes/piccinini/.conda/envs/seis/bin/python"
          Library: "/homes/piccinini/.conda/envs/seis/lib/libpython3.8.so"
             Home: "/homes/piccinini/.conda/envs/seis"
           Status: Loaded
    ExecutionMode: OutOfProcess
        ProcessID: "88387"
      ProcessName: "MATLABPyHost"

When I try to import the library on Linux:

      py.importlib.import_module('obspy')
ans = 
  Python module with properties:
                 read: [1×1 py.function]
              imaging: [1×1 py.module]
            geodetics: [1×1 py.module]
                  sys: [1×1 py.module]
          UTCDateTime: [1×1 py.type]
    ObsPyReadingError: [1×1 py.type]
            Inventory: [1×1 py.type]
               Stream: [1×1 py.type]
       read_inventory: [1×1 py.function]
                 core: [1×1 py.module]
              Catalog: [1×1 py.type]
          read_events: [1×1 py.function]
       ObsPyException: [1×1 py.type]
                Trace: [1×1 py.type]
             warnings: [1×1 py.module]
    <module 'obspy' from '/homes/piccinini/.conda/envs/seis/lib/python3.8/site-packages/obspy/__init__.py'>

These are the modules/function loaded.

While this is the result on MacOS

    py.importlib.import_module('obspy')
ans = 
  Python module with properties:
       read_inventory: [1×1 py.function]
                 core: [1×1 py.module]
             warnings: [1×1 py.module]
                   io: [1×1 py.module]
              clients: [1×1 py.module]
                 read: [1×1 py.function]
    ObsPyReadingError: [1×1 py.type]
              imaging: [1×1 py.module]
                  sys: [1×1 py.module]
               Stream: [1×1 py.type]
            Inventory: [1×1 py.type]
       ObsPyException: [1×1 py.type]
          read_events: [1×1 py.function]
              Catalog: [1×1 py.type]
                Trace: [1×1 py.type]
          UTCDateTime: [1×1 py.type]
            geodetics: [1×1 py.module]
    <module 'obspy' from '/Users/davide/opt/anaconda3/envs/py3.8/lib/python3.8/site-packages/obspy/__init__.py'>

As you can see on Linux side Python cannot import some modules (io, clients,...)

The conda environment instead works perfectly and also python can import without any problem the whole obspy library.

DavidePiccinini 2024-1-12

::: SOLVED :::

downgraded Obspy from 1.4.0 to 1.3.1, numpy to 1.22.

Now seems to work fine.

Hassaan 2024-1-12

@DavidePiccinini Thats good news.

-------------------------------------------------------------------------------------------------------------------------------------------------

If you find the solution helpful and it resolves your issue, it would be greatly appreciated if you could accept the answer. Also, leaving an upvote and a comment are also wonderful ways to provide feedback.

Professional Interests