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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
7 stars 1 forks source link

Remove kwargs and mutable defaults #48

Closed aaprasad closed 5 months ago

aaprasad commented 6 months ago

As per #40 and #43, mutable defaults are very dangerous and kwargs are opaque. Thus we should never use mutable defaults and only use kwargs when absolutely necessary (i.e. for downstream function params). Thus here we remove any usage of mutable defaults and remove the use of kwargs from `GlobalTrackingTransformer

Summary by CodeRabbit

coderabbitai[bot] commented 6 months ago

[!WARNING]

Review failed

The pull request is closed.

Walkthrough

The changes primarily involve updating import paths for Frame and Instance classes across multiple files in the biogtr project. These classes have been moved from biogtr.data_structures to biogtr.io.frame and biogtr.io.instance, respectively. Additionally, new functionalities and methods have been introduced in the biogtr/io module to enhance data handling and manipulation capabilities.

Changes

File(s) Change Summary
biogtr/datasets/base_dataset.py Updated import for Frame from biogtr.data_structures to biogtr.io.frame.
biogtr/datasets/cell_tracking_dataset.py Updated imports for Frame and Instance from biogtr.data_structures to biogtr.io.frame and biogtr.io.instance.
biogtr/datasets/eval_dataset.py Updated imports for Frame and Instance to reference biogtr/io.
biogtr/datasets/microscopy_dataset.py Changed imports and documentation references from biogtr.data_structures to biogtr.io.
biogtr/datasets/sleap_dataset.py Restructured imports for Frame and Instance to new module paths.
biogtr/inference/metrics.py Updated import for Frame and docstring references to biogtr.io.
biogtr/inference/track.py Adjusted imports for Config and Frame to new locations within biogtr/io.
biogtr/inference/track_queue.py Updated import for Frame from biogtr.data_structures to biogtr.io.frame.
biogtr/inference/tracker.py Updated imports and method signatures to reference Frame from biogtr/io. Modified tracking logic and method calls.
biogtr/io/__init__.py Introduced new classes and methods for handling Frame, Instance, AssociationMatrix, and Track.
biogtr/io/association_matrix.py Added AssociationMatrix class with methods for matrix manipulation and conversion.
biogtr/io/config.py Modified get_model and get_gtr_runner methods to handle ckpt_path parameter.
biogtr/io/frame.py Introduced Frame class with methods for metadata handling and conversion.
biogtr/io/instance.py Introduced Instance class with methods for data conversion and manipulation.
biogtr/io/track.py Introduced Track class for storing and managing track instances.
biogtr/models/global_tracking_transformer.py Updated GlobalTrackingTransformer class to use torch.nn.Module and modified forward method to handle Instance objects.

Poem

In the code, a shift so grand,
Imports moved across the land.
Frames and Instances now reside,
In biogtr/io, they proudly abide.
New methods, classes, all in line,
To make our tracking algorithms shine.
🎉✨ Let's toast to progress, swift and bright,
As we code through day and night! 🚀🐇

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