Suggestions to improve workflow usability

flatironinstitute / Cryo-EM-Heterogeneity-Challenge-1

The Inaugural Flatiron Institute Cryo-EM Heterogeneity Community Challenge

https://osf.io/8h6fz/

MIT License

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Suggestions to improve workflow usability #11

Closed DavidHerreros closed 2 months ago

DavidHerreros commented 3 months ago

[x] Adding a label indicating the execution order to the tutorial notebooks (for example, 1_tutorial_preprocessing, 2_distribution_to_distribution...)
[x] Instead of hardcoding paths in the jupyter notebooks, we could provided a simple "folder/file browser" window so that the user can inspect and easiliy select the desired location on his machine. Most likely, the implementation of this windows will lead to at least one extra dependency (PyQt, TK)
[ ] Implementing a virtualized "Plotting" class to unified the plots across the notebooks and improve mantainability of the code. See issue https://github.com/flatironinstitute/Cryo-EM-Heterogeneity-Challenge-1/issues/18

geoffwoollard commented 3 months ago

I would definitely do #1, with the suggested numbering of 1_tutorial_preprocessing.ipynb, 2_tutorial_svd.ipynb, 3_tutorial_map2map.ipynb, 4_tutorial_distribution2distribution.ipynb

geoffwoollard commented 3 months ago

I don't know how to do #2, but @DavidHerreros , could you implement that for one of the notebooks and we can see how it works?

geoffwoollard commented 3 months ago

I will keep #3 in mind when I make the plotting functionality for the distribution to distribution results. I think it makes sense for there to be plotting functionality synced up with the results (e.g. certain plots for svd, other plots for the map2map results, and still other plots for the dist2dist results).

geoffwoollard commented 2 months ago

Issue https://github.com/flatironinstitute/Cryo-EM-Heterogeneity-Challenge-1/issues/18 subsumes plotting scope of this issue. Closing.