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Add written documentation for errors and metrics #116

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merged 7 commits into from
Sep 18, 2024

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msschwartz21
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@msschwartz21 msschwartz21 commented Nov 10, 2023

I'm opening this as a draft so that we can take a look at the RTD preview while we are working on it.

Pages to write:

  • Track errors / divisions
  • Track errors / edges
  • Track errors / nodes
  • Metrics / divisions
  • Metrics / ctc
  • Metrics / track overlap

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msschwartz21 commented Nov 10, 2023

@cmalinmayor I took a stab at the division errors page. I just used super simple text based diagrams like we use in the docstrings for tests. We may want to upgrade to something fancier in the future, but I don't want the plotting to become a blocker to writing.

https://traccuracy--116.org.readthedocs.build/en/116/track_errors/divisions.html

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codecov-commenter commented Nov 10, 2023

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (27da5a7) 83.01% compared to head (b1f4e49) 83.64%.
Report is 50 commits behind head on main.

❗ Your organization needs to install the Codecov GitHub app to enable full functionality.

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #116      +/-   ##
==========================================
+ Coverage   83.01%   83.64%   +0.62%     
==========================================
  Files          18       19       +1     
  Lines         848      899      +51     
==========================================
+ Hits          704      752      +48     
- Misses        144      147       +3     

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True Positive
-------------

A true positive division is a division event in which the parent and both daughters match between the ground truth and predicted graphs. True positive divisions are annotated on both the ground truth and predicted graphs.
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Can you say that they are annotated on the parent node specifically? That's what we do, right?

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Ooh I like it a lot!! I think if we should implement this for all metrics and then we can make it fancier later if we have time and inclination, but this is so much better than nothing.

@msschwartz21 msschwartz21 added the documentation Improvements or additions to documentation label Nov 13, 2023
@msschwartz21 msschwartz21 linked an issue Nov 29, 2023 that may be closed by this pull request
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@msschwartz21
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@DragaDoncila Caroline and I started this branch to work towards closing #77 by adding pages in the sidebar for each error annotation type and downstream metrics. Can you take a stab at the ctc related pages which I think would be docs/track_errors/nodes.rst, docs/track_errors/edges.rst, and docs/metrics/ctc.rst when you have some time?

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@msschwartz21 would you like me to PR into this branch for these docs, or review this PR independently and make another for the CTC docs

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@msschwartz21 would you like me to PR into this branch for these docs, or review this PR independently and make another for the CTC docs

I'd prefer to get all of the docs changes in place before we merge into main so let's do a PR or direct push to this branch.

* Add some docs

* Hopefully get rid of warning

* Split different error weights into list

* Add TRA def

* Fix space

* Add a bit about AOGM

---------

Co-authored-by: Draga Doncila <[email protected]>
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@msschwartz21 I merged some additions to the CTC docs!

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Since we are starting to get a few more eyes on traccuracy, I'm leaning towards a mindset of some incomplete documentation is better than no documentation at all. To that end, I added a note block to the pages we haven't written yet saying "Coming soon!"

@DragaDoncila @cmalinmayor Does this sound ok to you? I'll open up an issue to keep track of the remaining pages that we need to write.

@msschwartz21 msschwartz21 marked this pull request as ready for review September 17, 2024 22:48
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I very much agree. Some docs better than no docs!

@msschwartz21 msschwartz21 merged commit ab3cccf into main Sep 18, 2024
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@msschwartz21 msschwartz21 deleted the docs-metrics-pages branch September 18, 2024 17:20
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Documentation Update: Give each metric a page on the sidebar
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