Aadi/sample-efficiency #24

aaprasad · 2023-11-10T03:52:46Z

Add functionality to randomly sample chunks from dataset to be used for training to enable sample-efficiency experiments

Summary by CodeRabbit

New Features
- Introduced data classes Instance and Frame for enhanced data handling in tracking applications.
- Added new EvalDataset class for merging datasets during evaluation.
- Implemented TrackQueue class for managing tracking queues.
- New persistent tracking settings in model configurations to improve tracking consistency.
- Enhanced visualization options in video annotation.
Enhancements
- Improved model loading and checkpoint handling in configuration settings.
- Refined data handling in various datasets to work with new data structures.
- Updated inference functions to handle frames and instances more effectively.
Bug Fixes
- Fixed device compatibility issues in model embedding operations.
- Corrected bounding box calculations in data utilities.
Documentation
- Updated function docstrings for clarity and consistency across modules.
Refactor
- Optimized memory usage by altering data handling in post-processing.
- Streamlined metrics evaluation in the model runner.
Tests
- Expanded test coverage for new data structures and tracking functionalities.
Chores
- Updated dependencies in environment configurations to support new functionalities.

codecov · 2023-11-10T03:55:01Z

Codecov Report

Attention: Patch coverage is 93.54839% with 2 lines in your changes are missing coverage. Please review.

Project coverage is 75.65%. Comparing base (3f21a02) to head (e7ca49f).

❗ Current head e7ca49f differs from pull request most recent head dd51119. Consider uploading reports for the commit dd51119 to get more accurate results

Files	Patch %	Lines
biogtr/datasets/cell_tracking_dataset.py	80.00%	1 Missing ⚠️
biogtr/datasets/microscopy_dataset.py	80.00%	1 Missing ⚠️

Additional details and impacted files

@@                 Coverage Diff                 @@
##           aadi-device-fix      #24      +/-   ##
===================================================
+ Coverage            75.39%   75.65%   +0.25%     
===================================================
  Files                   24       24              
  Lines                 1508     1532      +24     
===================================================
+ Hits                  1137     1159      +22     
- Misses                 371      373       +2

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

Co-authored-by: aaprasad <aaprasad.ucsd.edu> Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

coderabbitai · 2024-04-22T22:32:31Z

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Walkthrough

The recent updates focus on enhancing the BioGTR framework by refining data structures, improving dataset handling, and optimizing inference and tracking functionalities. Major enhancements include the integration of new data classes for better data representation and management, adjustments in dataset modules for efficient data processing, and significant refinements in inference methods to support robust tracking and evaluation.

Changes

Files	Change Summary
`biogtr/data_structures.py`, `.../datasets/...`	Introduced new data classes `Instance` and `Frame`, updated dataset handling with new parameters and methods.
`biogtr/config.py`, `.../models/...`	Enhanced configuration and model handling including imports, parameter updates, and method refinements.
`biogtr/inference/...`	Improved inference functionalities, added new tracking and evaluation methods, and updated existing functions.
`biogtr/training/...`, `environment.yml`, `.../environment_cpu.yml`	Updated training configurations, added new dependencies, and refined loss computation methods.
`biogtr/visualize.py`, `tests/...`	Modified visualization tools and expanded testing coverage to include new functionalities and data structures.

Poem

🐇✨
In the land of code, where the data hops,
A rabbit tweaked the locks and props.
Frames and tracks now neatly align,
With models that learn and beautifully define.
Oh, how the bytes dance and twirl,
In this ever-updating digital world! 🌍💻
🐇✨

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aaprasad · 2024-04-22T22:33:14Z

@coderabbitai review

coderabbitai

Actionable comments posted: 3

Actionable comments outside the diff hunks (1)

biogtr/models/attention_head.py (1)

Line range hint 9-9: Consider addressing the TODO about adding named tensors.

Would you like me to help implement this feature or should I open a GitHub issue to track this task?

biogtr/inference/tracker.py

tests/fixtures/torch.py

coderabbitai · 2024-04-22T22:42:35Z

biogtr/training/train.py

@@ -80,7 +81,7 @@ def main(cfg: DictConfig):
        if cfg.view_batch.no_train:
            return

-    model = train_cfg.get_gtr_runner()
+    model = train_cfg.get_gtr_runner()  # TODO see if we can use torch.compile()


Consider addressing the TODO about using torch.compile().

Would you like me to help implement this feature or should I open a GitHub issue to track this task?

open an issue

@aaprasad, I've successfully opened a GitHub issue to track the task of investigating and potentially implementing torch.compile() in train.py. You can view and manage the issue here. If there's anything else you need, feel free to let me know!

Analysis chain

Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash # Create a GitHub issue regarding the implementation of `torch.compile()` in `train.py` gh issue create --title "Investigate and potentially implement \`torch.compile()\` in \`train.py\`" --body "There is a TODO comment in the \`train.py\` script suggesting the potential use of \`torch.compile()\`. This issue is to investigate whether \`torch.compile()\` can be beneficial for the project and, if so, to plan its implementation. Related PR: https://github.com/talmolab/biogtr/pull/24 Comment URL: https://github.com/talmolab/biogtr/pull/24#discussion_r1575428228" --repo talmolab/biogtr

Length of output: 538

add subsampling to datasets

e7ca49f

aaprasad changed the base branch from main to aadi-device-fix November 10, 2023 06:30

Aadi/refactor-tracker (#23)

dd51119

Co-authored-by: aaprasad <aaprasad.ucsd.edu> Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

coderabbitai bot reviewed Apr 22, 2024

View reviewed changes

coderabbitai bot mentioned this pull request Apr 22, 2024

Investigate and potentially implement torch.compile() in train.py #28

Open

aaprasad marked this pull request as ready for review April 22, 2024 22:47

aaprasad merged commit e4dd76a into aadi-device-fix Apr 22, 2024
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Aadi/sample-efficiency #24

Aadi/sample-efficiency #24

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Aadi/sample-efficiency #24

Aadi/sample-efficiency #24

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