Test the package with example data

[bobleesj]

Problem

The current package does not provide example data while the main app below requires input_directory

def main():
    args = create_parser()
    if args.input_directory is None:
        args.input_directory = Path.cwd()
    grid, input_data = load_input_signals(args.input_directory)

Proposed solution

We can attempt to use test data nmf_mapping from https://github.com/diffpy/diffpy.nmf_mapping/blob/main/diffpy/nmf_mapping/tests/data and see whether the code works.

[bobleesj]

Noticed that data are provided under examples/mix___ZnSe-w_0.4___BaTiO3_c-w_0.6 Have you tried running the package with these data? @Fil158

[sbillinge]

if the data are small, we can add it to the repo to make it easy for users.

[Fil158]

This error occurs when I try with those data

[bobleesj]

Yes, I had reproduced the error before. It is because the code wasn't tested using real files/data.

As of now, our current priority is to implement/interpret the snmf algo

[sbillinge]

Also, I suggest when we work on this issue, let's change the filename of the example data to something more readable and easy to type......

[Andrea-gm]

Hello. I see that there is example data but no script to run them? It would be nice to have one in order to get acquainted with the code.

[sbillinge]

thanks @Andrea-gm we will work on this. @john-halloran has finals but I hope can move this towards its release over the winter break. Its great to know there is interest from the community! Very motivating.

[Andrea-gm]

That would be great thank you! I would like to start using this package asap on my in-situ XRD data

[Andrea-gm]

Hello! I was wondering if there is any work ongoing for the tutorial? I would really like to use this package but I struggle to understand how to use it. Thanks!

[john-halloran]

Hi @Andrea-gm. Thanks for your patience and continued interest in sNMF. There is not a tutorial yet, but hopefully I can guide you a little. The version of the package in active development (and ready to use) is located on the john-development branch for now. All the critical code used in the optimization is located in the snmf_class.py file. You can see a very basic example of how to execute the program in main.py. Your data will need to be in the form of a NumPy array, where each column is a complete 1D signal, such as an XRD pattern. You also need a guess for the number of components, n_components. Let me know if you run into any issues.

[Andrea-gm]

Hi John, thanks a lot! This is already very useful. Do you mind providing also example data to be run with main.py?

[john-halloran]

Hi John, thanks a lot! This is already very useful. Do you mind providing also example data to be run with main.py?

Sure. If you want to try with the data from the original paper, that's here. Just load the CSVs and discard the first column. More examples coming soon hopefully.

[sbillinge]

@john-halloran please could you make a PR to put these data into docs/examples/data. We can then add an example in the docs if that is useful to folks.