Adding PDF calculation function

[cophus]

Both reduced and full PDFs added. Tested against simulated data. Still needs more work but basic functionality is there.

[bsavitzky]

Thanks Colin! Starting a review now.

The first thing you'll want to do is pull from the dev branch (into your local version of this branch, then push to your remote fork you made the PR from) so that there aren't any merge conflicts in the PR. Happy to help if you run into any issues with that.

[bsavitzky]

Also - could you attach some demo code with a (small) dataset that it runs on? It will make reviewing this easier :)

[cophus]

Here are the notebooks I used for testing - an (incomplete) abTEM simulation for amorphous Ta, plus a quick and dirty pair distribution function calculation:

the PDF calculation notebook produces:

Data is here:
https://drive.google.com/file/d/1g2d_uSTyVWr8zITLuVdzMVUkIPnLAvmL/view?usp=sharing

amor_Ta.zip

[bsavitzky]

Hey @cophus - I've made a number of changes, including

• added documentation to all methods
• modified input args to remove unused values, tweaked names
• fixed return and plotting behaviors
• fixed a .scattering_vectors bug - in the future use polardata.qq instead
• fixed a bug where .radial_var_norm was assigned to radial_var rather than copied
• added storage of and independent plotting methods for the outputs of the final calculate_pair_dist_function method
• removed an extraneous call to .scattering_model

In the new doc strings for .calculate_radial_statistics and .calculate_pair_dist_function I've added specific descriptions of what these methods are computing. When you get a chance, please

• review these equations for correctness, and
• add citations to the docstrings for these two methods where noted ([@cophus TODO ADD CITATION])

[bsavitzky]

Attached is an updated version of the .ipynb that runs on the code following my commits!

Once you've had a chance to check out these changes and make that edit, let me know and I can complete the review :)

RDF01.ipynb.zip

[bsavitzky]

I'm merging this before the citations requested above have been added in order to have this module available in release code for a tutorial - the citations can get added in the next cycle...