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talmolab / dreem

DREEM Relates Every Entities' Motion (DREEM). Global Tracking Transformers for biological multi-object tracking.
https://dreem.sleap.ai
BSD 3-Clause "New" or "Revised" License
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Refactor inference script #51

Closed aaprasad closed 4 months ago

aaprasad commented 4 months ago

Its been a while since I updated the inference script so here I've updated it to work with our API

Summary by CodeRabbit

coderabbitai[bot] commented 4 months ago

Walkthrough

The recent updates in the biogtr project involve significant changes to dataset handling, inference configurations, and tracking logic. Key modifications include parameter reordering in dataset constructors, new configuration settings for tracking, and enhanced methods for handling file paths and video processing. Additionally, the inference function has been renamed and updated to improve tracking accuracy and result handling. These changes collectively enhance the flexibility and functionality of the dataset processing and tracking workflow.

Changes

Files/Modules Change Summary
biogtr/datasets/base_dataset.py Updated BaseDataset constructor to use label_files and vid_files instead of files.
biogtr/datasets/cell_tracking_dataset.py Swapped the order of gt_images and raw_images parameters in the constructor.
biogtr/datasets/microscopy_dataset.py Changed the order of tracks and videos parameters in the constructor.
biogtr/datasets/sleap_dataset.py Split slp_files and video_files into separate arguments in the constructor.
biogtr/inference/configs/inference.yaml Added persistent_tracking and anchor settings in the configuration file.
biogtr/inference/track.py Renamed inference to track, added trainer parameter, and updated logic for tracking and result saving.
biogtr/inference/tracker.py Adjusted track initialization and ID handling during inference.
biogtr/io/config.py Added params_cfg parameter, new methods for loading config from YAML, and retrieving file paths.
biogtr/io/frame.py Updated to_slp method to handle track_lookup and video loading.
biogtr/io/instance.py Modified to_slp method to convert self.pose to a numpy array and updated exception messages.
biogtr/models/gtr_runner.py Removed setting persistent_tracking to True in predict_step function.
tests/configs/inference.yaml Introduced new configurations for tracking and dataset settings for testing.
tests/fixtures/configs.py Added inference_config pytest fixture to retrieve inference params config file path.
tests/test_datasets.py Updated DummyDataset initialization to include label_files and vid_files.
tests/test_inference.py Added new test function test_track and imports for Config and run.
tests/test_training.py Added directory creation with tmp_path and updated hparams dictionary in test configuration.

Poem

In fields of code where changes bloom,
The datasets dance, no longer fume.
With labels clear and videos bright,
They track the paths both day and night.
Configs set and tests in place,
The code now runs a smoother race.
A rabbit's joy, in bytes and lines,
For data's flow in perfect signs.

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