Create feature to be able to export current visualisation setup to a python script for calibration

[FinbarArgus]

Once setting up a visualisation with sliders and bringing in experimental data it would be great to be able to click a button which creates a python script that sets up a calibration problem for the parameters in the sliders (with the set ranges), the cellml model, and the imported experimental data. Then the user could adapt the calibration script as needed.

I am planning on creating a feature in circulatory autogen to create such a script from an omex file as an exemplar for this (and a temporary way to do it through the omex archive export).

[agarny]

@FinbarArgus, could you provide an OMEX file that includes the UI settings and the kind of corresponding Python script you would like to see generated?

[FinbarArgus]

I was going to ask if you have an example OMEX file with experimental data included? I don't know how to include experimental data into plots on WebOpenCOR yet? Any example model is fine.

I'm happy to get physiomelinks/circulatory_autogen#187 running first to demonstrate what I am thinking.

[agarny]

Here is an OMEX file with some made-up experimental data. That's something that I used for my testing, so clearly not meaningful but it might still be useful. Go the settings dialog and select the Interactive tab and then the External data and Plots tabs. These are where you will see the external data being reference and used, respectively.

[agarny]

I'm happy to get physiomelinks/circulatory_autogen#187 running first to demonstrate what I am thinking.

Yes, definitely! :)

[FinbarArgus]

omex_analysis_pipeline.py

Implemented for this issue in circulatory autogen, physiomelinks/circulatory_autogen#187 , which generates the above python script. A similar thing could be done in webopencor to create a script and open it in google collab or something similar, once circulatory autogen has a pip install.

Configs for param id parameters and observable data should be cross-compatible with param id standardisation in the future.