support loading slp files with non-compound types and str in metadata

lambdaloop commented 1 year ago

Description

This makes the loading of slp files more robust. Specifically, it allows storing points, pred_points, frames, and instances as non-compound types in the h5 file, by casting them as needed.

It is backwards compatible with the previous code, so that the default slp files load fine.

Types of changes

[ ] Bugfix
[x] New feature
[ ] Refactor / Code style update (no logical changes)
[ ] Build / CI changes
[ ] Documentation Update
[ ] Other (explain)

Does this address any currently open issues?

[list open issues here]

Outside contributors checklist

[x] Review the guidelines for contributing to this repository
[x] Read and sign the CLA and add yourself to the authors list
[x] Make sure you are making a pull request against the develop branch (not main). Also you should start your branch off develop
[x] Add tests that prove your fix is effective or that your feature works
[x] Add necessary documentation (if appropriate)

Thank you for contributing to SLEAP!

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Summary by CodeRabbit

Bug Fix: Improved the handling of data types in our software. This includes better management of complex data types and ensuring that all data is in the correct format for processing. This will enhance the reliability of our software and reduce the likelihood of errors.
New Feature: Added a function to automatically convert certain data arrays into complex data types if they are not already. This will improve the software's performance and ensure consistency in data processing.

coderabbitai[bot] commented 1 year ago

Walkthrough

The changes primarily focus on enhancing data handling in the HDF5 format. They introduce checks for data types, conversion of JSON attributes, and casting of arrays into complex data types. The modifications ensure robustness and consistency in data processing.

Changes

File	Summary
`.../format/hdf5.py`	Introduced checks for JSON attribute data types and conversion if necessary. Added `cast_as_compound` function to cast arrays into complex data types. Arrays `points_dset`, `pred_points_dset`, `instances_dset`, and `frames_dset` are now cast into complex dtypes. `old_labels` variable is assigned the result of decoding the JSON attribute.

🐇

"In the land of code, where the shadows lie,

A rabbit hopped, with a twinkle in its eye.

Casting arrays, checking types, oh so sly,

Ensuring data flows, under the binary sky. 🌌"

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codecov[bot] commented 1 year ago

Codecov Report

Attention: 10 lines in your changes are missing coverage. Please review.

Comparison is base (2d24296) 73.38% compared to head (4e5ce45) 73.36%. Report is 1 commits behind head on develop.

Files	Patch %	Lines
sleap/io/format/hdf5.py	61.53%	10 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## develop #1566 +/- ## =========================================== - Coverage 73.38% 73.36% -0.02% =========================================== Files 134 134 Lines 24024 24048 +24 =========================================== + Hits 17629 17643 +14 - Misses 6395 6405 +10 ```

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

lambdaloop commented 10 months ago

@roomrys @talmo Any chance you could merge this? This would allow people to export slp datasets from a web annotation system (such as https://lambdaloop.com/anivia/ ) and then load them into SLEAP.

talmolab / sleap