Added initial foil analysis

[cdunn314]

Added code using libra-toolbox to process foil measurements. This is a work in progress, and I'd like feedback on how to improve the notebook and better integrate it into the rest of the data processing. Then we can apply a similar approach to the other runs.

[RemDelaporteMathurin]

I think the overall workflow is sound. Maybe a few improvements would be to add some text to guide readers or headings (eg. Efficiency curve calculation, etc)

Let's also avoid dead code (ie. large code blocks commented out)

[cdunn314]

I am trying to get the reading from spectra from a saved h5 file to work, but some necessary functions like compute_detection_efficiency on a CheckSourceMeasurement class require there to be events, so looks like if we want to implement this with the h5 spectra reader, we'll need to change libra-toolbox

[cdunn314]

I am trying to get the reading from spectra from a saved h5 file to work, but some necessary functions like compute_detection_efficiency on a CheckSourceMeasurement class require there to be events, so looks like if we want to implement this with the h5 spectra reader, we'll need to change libra-toolbox

This was not the case, I was mistaken

[cdunn314]

@RemDelaporteMathurin do we want to add tests in this PR or a separate one?

[cdunn314]

@RemDelaporteMathurin do we want to add tests in this PR or a separate one?

I realized that the run repos don't have pytests, just continuous integration, so I added running the foils_analysis.ipynb notebook to the CI.

[RemDelaporteMathurin]

Just a bunch of final comments and then we can merge this!

@veliki-filozof feel free to have a look too!

[veliki-filozof]

Just a bunch of final comments and then we can merge this!

@veliki-filozof feel free to have a look too!

Looks great to me, thanks @cdunn314 for working this out! I didn't review the detailed mechanics of how you process the data but the broad logic looks sound to me.

Only thing I'd like to check for easier integration in the following runs: What files should be copied verbatim, and in which files is there run-specific data that needs to be manually tweaked? Perhaps this could be added to the readme checklist too

[cdunn314]

I added papermills to the environment.yml file so that no matter what we set the download_from_raw variable to in the notebook when commits are pushed, it will be overwritten to False during the CI and processing: 0722526

[RemDelaporteMathurin]

I added papermills to the environment.yml file so that no matter what we set the download_from_raw variable to in the notebook when commits are pushed, it will be overwritten to False during the CI and processing: 0722526

Nice find!

[cdunn314]

I'm finished with this batch of changes. @RemDelaporteMathurin @veliki-filozof if everything looks good, I think we can merge this.

[RemDelaporteMathurin]

Thanks @cdunn314 happy to merge this! I like the attenuation factor interpolation function, I think this could go in libra-toolbox also!