Add swint #41

gitttt-1234 · 2024-03-15T16:56:18Z

Add SwinT backbone

coderabbitai · 2024-03-15T16:56:23Z

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* Add Centroid model pipeline * Auto select max instances * Add test cases * Format files * Fix centroid crop inference * Update CI (#43) * Initial CI update * Update deps * Add Cycler from torchdata to remove torchdata dep * Fix import * Fix ruff and lint * Fix wandb test * Fix attrs * Ignore vendored torchdata module * Add Mac * Update mac conda versions * More conda * Typo: exclude cycleR from coverage * More conda packages * Even more conda packages --------- Co-authored-by: Talmo Pereira <[email protected]>

codecov · 2024-04-23T19:32:29Z

Codecov Report

Attention: Patch coverage is 85.18519% with 48 lines in your changes are missing coverage. Please review.

❗ No coverage uploaded for pull request base (divya/convnext@094fc25). Click here to learn what that means.

Files	Patch %	Lines
sleap_nn/inference/inference.py	77.86%	27 Missing ⚠️
sleap_nn/model_trainer.py	75.00%	14 Missing ⚠️
sleap_nn/data/confidence_maps.py	87.87%	4 Missing ⚠️
sleap_nn/architectures/common.py	0.00%	2 Missing ⚠️
sleap_nn/architectures/swint.py	98.59%	1 Missing ⚠️

Additional details and impacted files

@@                Coverage Diff                @@
##             divya/convnext      #41   +/-   ##
=================================================
  Coverage                  ?   94.82%           
=================================================
  Files                     ?       25           
  Lines                     ?     2182           
  Branches                  ?        0           
=================================================
  Hits                      ?     2069           
  Misses                    ?      113           
  Partials                  ?        0

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

* Add predictor class * Fix to peak finding * Modify docstrings * Minor fix to Predictor * Modify config load * Add ckpt paths * Format file * Add training and inference for single instance * Change ckpt * Add test for single instance model * Fix for symmetries in skeleton * Modify skeleton key * Add max instances * Minor fix to max instances * Changes to file path * Format file * Add max instances * Fix edges in skeletons * Update symmetries * Modify training config * Add convnext backbone * Minor fix in convnext * Add swint (#41) * Add swint * Add param count * Update model_trainer.py * Add swintv1 * Change default width * modify inference class * Update model_trainer.py * Update model_trainer.py * Update xavier init * Update bias init in xavier * Add steps per epoch * Add tests for swint * Format files * Fix instance cropper test * Fix to sigma in confmaps * Add Centroid model pipeline (#42) * Add Centroid model pipeline * Auto select max instances * Add test cases * Format files * Fix centroid crop inference * Update CI (#43) * Initial CI update * Update deps * Add Cycler from torchdata to remove torchdata dep * Fix import * Fix ruff and lint * Fix wandb test * Fix attrs * Ignore vendored torchdata module * Add Mac * Update mac conda versions * More conda * Typo: exclude cycleR from coverage * More conda packages * Even more conda packages --------- Co-authored-by: Talmo Pereira <[email protected]> --------- Co-authored-by: Talmo Pereira <[email protected]> * Add test files * Fix Providers * Update providers.py * Fix multi confmap * Add suggestions * Fix decoder * Format Files * Add SizeMatcher class * Fix Normalizer * Update normalization.py * Format file * Remove max_instances * Format files --------- Co-authored-by: Talmo Pereira <[email protected]>

* Add predictor class * Fix to peak finding * Modify docstrings * Minor fix to Predictor * Modify config load * Add ckpt paths * Format file * Add training and inference for single instance * Change ckpt * Add test for single instance model * Fix for symmetries in skeleton * Modify skeleton key * Add max instances * Minor fix to max instances * Changes to file path * Format file * Add max instances * Fix edges in skeletons * Update symmetries * Modify training config * Add convnext backbone * Minor fix in convnext * Add swint (#41) * Add swint * Add param count * Update model_trainer.py * Add swintv1 * Change default width * modify inference class * Update model_trainer.py * Update model_trainer.py * Update xavier init * Update bias init in xavier * Add steps per epoch * Add tests for swint * Format files * Fix instance cropper test * Fix to sigma in confmaps * Add Centroid model pipeline (#42) * Add Centroid model pipeline * Auto select max instances * Add test cases * Format files * Fix centroid crop inference * Update CI (#43) * Initial CI update * Update deps * Add Cycler from torchdata to remove torchdata dep * Fix import * Fix ruff and lint * Fix wandb test * Fix attrs * Ignore vendored torchdata module * Add Mac * Update mac conda versions * More conda * Typo: exclude cycleR from coverage * More conda packages * Even more conda packages --------- Co-authored-by: Talmo Pereira <[email protected]> --------- Co-authored-by: Talmo Pereira <[email protected]> * Add test files * Fix Providers * Update providers.py * Fix multi confmap * Add suggestions * Fix decoder * Format Files * Add SizeMatcher class * Fix Normalizer * Update normalization.py * Format file * Add VideoReader module * Format Docstrings * Remove max_instances * Add VideoReader to Inference module * Format files * Add test cases * Add config.md * Fix FindPeaksGroundTruth module * Add image resizing modules * Add Resizer after crop * Format docstring --------- Co-authored-by: Talmo Pereira <[email protected]>

Add swint

1c5b353

gitttt-1234 and others added 14 commits March 15, 2024 11:11

Add param count

edf4a44

Update model_trainer.py

748c4f0

Add swintv1

403004e

Change default width

2a16b80

modify inference class

a895cfa

Update model_trainer.py

4f21dd1

Update model_trainer.py

5e91808

Update xavier init

21dc5df

Update bias init in xavier

60727a4

Add steps per epoch

bb0c246

Add tests for swint

28510ca

Merge branch 'divya/convnext' into divya/swint

08fa68b

Format files

2af31f0

Fix instance cropper test

ca3e932

gitttt-1234 requested a review from talmo April 12, 2024 18:39

gitttt-1234 and others added 2 commits April 12, 2024 12:24

Fix to sigma in confmaps

a3e1f4c

gitttt-1234 merged commit 02872c1 into divya/convnext Apr 23, 2024

gitttt-1234 deleted the divya/swint branch April 23, 2024 19:58

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Add swint #41

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gitttt-1234 commented Mar 15, 2024 •

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gitttt-1234 commented Mar 15, 2024 •

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