8000 Fix multi size video support by arie-matsliah · Pull Request #501 · talmolab/sleap · GitHub
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Fix multi size video support #501

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Merged
merged 11 commits into from
Mar 8, 2021
Merged

Fix multi size video support #501

merged 11 commits into from
Mar 8, 2021

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arie-matsliah
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Description

[describe your changes here]

Types of changes

  • Bugfix
  • 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]

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Codecov Report

Merging #501 (dbbf443) into develop (819387d) will increase coverage by 0.02%.
The diff coverage is 83.33%.

Impacted file tree graph

@@             Coverage Diff             @@
##           develop     #501      +/-   ##
===========================================
+ Coverage    64.94%   64.97%   +0.02%     
===========================================
  Files          124      124              
  Lines        19669    19691      +22     
===========================================
+ Hits         12775    12795      +20     
- Misses        6894     6896       +2     
Impacted Files Coverage Δ
sleap/nn/data/confidence_maps.py 73.58% <ø> (ø)
sleap/nn/data/resizing.py 66.66% <57.14%> (+0.45%) ⬆️
sleap/nn/data/providers.py 62.69% <66.66%> (+0.09%) ⬆️
sleap/nn/inference.py 63.96% <83.33%> (+0.51%) ⬆️
sleap/nn/data/pipelines.py 88.85% <100.00%> (+0.07%) ⬆️

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@arie-matsliah arie-matsliah marked this pull request as ready for review March 8, 2021 19:56
@arie-matsliah arie-matsliah merged commit 3e36eed into develop Mar 8, 2021
@arie-matsliah arie-matsliah changed the title [WIP] Fix multi size video support Fix multi size video support Mar 8, 2021
@arie-matsliah arie-matsliah deleted the arie/fix_multi_size branch March 8, 2021 19:57
arie-matsliah added a commit that referenced this pull request Mar 8, 2021
* Merge main back into develop (#491)

* Prep for master->main (#475)

Co-authored-by: Arie Matsliah <arie.matsliah@gmail.com>

* Release version 1.1.0

* Remove appveyor

Co-authored-by: Talmo Pereira <talmo@princeton.edu>
Co-authored-by: Arie Matsliah <arie.matsliah@gmail.com>

* Merge main to develop post release (#492)

* Prep for master->main (#475)

Co-authored-by: Arie Matsliah <arie.matsliah@gmail.com>

* Release version 1.1.0

* Remove appveyor

* Test docs subfolders

* Test keep_files

Co-authored-by: Talmo Pereira <talmo@princeton.edu>
Co-authored-by: Arie Matsliah <arie.matsliah@gmail.com>

* Pulling finished work from #484 into a separate PR (#493)

* Pulling finished work into a separate PR

* fix test

* fix

* Simplify + tweak background

* Update docs (#495)

* Isolated fix for issue #480 (#498)

* Add support for specifying the minimum score in PAF matching (#502)

Effective at filtering out explicitly spurious matches when no better match is available

* Fix post-training errors (#503)

- Catch filesystem busy error when deleting viz dir
- Don't throw an error after training with no inference target

* Revert "Pulling finished work from #484 into a separate PR" (#504)

* Minor fixes and enhacements (#505)

- Add skeleton.find_neighbors convenience graph op
- Add Instance.fill_missing to initialize new nodes in the skeleton
- Also add numpy() and from_pointsarray() aliases to PredictedInstance
  to prevent crashes from using the inherited versions
- Initialize missing instance nodes when plotting user instances
- Fix serialization after loading MediaVideo from high level API
- Fix single instance visualization during training
- Add --open-in-gui CLI option to sleap-track
- Clearer error message when running sleap-track without args

* [WIP] Fix multi size video support (#501)

* wip

* cleanup

* Add `max_height_and_width` property to `VideoReader`

* Fix SizeMatcher instantiation without specified targets
- Lint/line length

* Provider now recreates the data pipeline with new providers

* Vectorize padding test for SizeMatcher

* Do not require instances key if not available from provider

* Size matching

* Size matching fix

* Fix shapes in output dataset

* lint

Co-authored-by: Talmo Pereira <talmo@princeton.edu>

* Bump version for release (#506)

Co-authored-by: Talmo Pereira <talmo@princeton.edu>
Co-authored-by: Arie Matsliah <arie.matsliah@gmail.com>
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