Implement fixed temp embedding #30

aaprasad · 2024-04-29T20:57:28Z

Implement fixed sinusoidal temporal embeddings

Summary by CodeRabbit

New Features
- Added sine temporal embedding functionality for more precise model computations.
Bug Fixes
- Corrected data handling in get_instances method to improve accuracy and performance.
Documentation
- Updated method descriptions and docstrings for clarity and detailed understanding of functionalities.
Refactor
- Adjusted default parameter values and internal method functionalities to enhance system robustness and maintainability.
Tests
- Revised test cases for embeddings to ensure reliability and correctness of new features.

…`model_utils.get_boxes_time` to be more clear about the output

coderabbitai · 2024-04-29T20:57:37Z

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Commits

Files that changed from the base of the PR and between bf3ff18 and e3f577b.

Walkthrough

The recent updates encompass a series of refinements and enhancements across various modules, aimed at improving data handling, embedding computations, code clarity, and test case robustness. These changes seek to streamline default settings, method functionalities, and testing procedures for a more efficient and effective codebase.

Changes

File Path	Change Summary
`.../data_structures.py`	Updated default `pose` parameter in a class constructor to `None`.
`.../datasets/sleap_dataset.py`	Simplified `get_instances` method by passing `poses[j]` directly as `pose`.
`.../models/embedding.py`	Added sine temporal embedding functions, updated method documentation, and error handling.
`.../models/model_utils.py`	Enhanced return value descriptions in `get_boxes_times` to include normalization details.
`tests/test_models.py`	Adjusted embedding test cases, improved initialization, and added debugging print statements.

🐰✨
In the code meadow, 'neath the branches of logic's tree,
Changes bloom like daisies, wild and free.
Arrays to dicts, lists find their flight,
Bugs scurry in the moon's soft light.
Oh, how the data dances, a ballet of glee! 🌟📊

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coderabbitai

Actionable comments posted: 1

tests/test_models.py

coderabbitai

Actionable comments posted: 1

tests/test_models.py

talmo · 2024-04-30T04:48:38Z

biogtr/data_structures.py

@@ -21,7 +21,7 @@ def __init__(
        point_scores: ArrayLike = None,
        instance_score: float = -1.0,
        skeleton: sio.Skeleton = None,
-        pose: dict[str, ArrayLike] = np.array([]),
+        pose: dict[str, ArrayLike] = {},


This is still a mutable! Set it to None and initialize in the constructor.

talmo · 2024-04-30T04:49:50Z

biogtr/models/embedding.py

@@ -108,8 +108,8 @@ def _check_init_args(self, emb_type: str, mode: str):
                f"Embedding `mode` must be one of {self.EMB_MODES} not {mode}"
            )

-        if mode == "fixed" and emb_type == "temp":
-            raise NotImplementedError("TODO: Implement Fixed Sinusoidal Temp Embedding")
+        # if mode == "fixed" and emb_type == "temp":


Remove unused comments

talmo · 2024-04-30T04:51:22Z

tests/test_models.py

-    times = torch.rand(size=(N,))
+    boxes = torch.rand(N, 2) * (1024 - 128)
+    boxes = torch.concat([boxes, boxes + 128], axis=-1)
+    print(boxes)


talmo · 2024-04-30T04:51:32Z

tests/test_models.py


+    print(sine_with_args)


talmo · 2024-04-30T04:52:51Z

biogtr/models/embedding.py

+             torch.Tensor, the sine positional embeddings
+             (embedding[:, 4i] = sin(x)
+              embedding[:, 4i+1] = cos(x)
+              embedding[4i+2] = sin(y)


Missing some colons here?

* remove unnecessary comments/print statements * use `None` instead of empty mutables.

* remove unnecessary comment

coderabbitai

Actionable comments posted: 1

tests/test_models.py

aaprasad added 2 commits April 29, 2024 13:50

implement fixed sinusoidal temporal embedding. update docstrings for …

f7f06ff

…`model_utils.get_boxes_time` to be more clear about the output

store poses as node, array dictionaries instead of as arrays

2d4b1ed

coderabbitai bot reviewed Apr 29, 2024

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tests/test_models.py Outdated Show resolved Hide resolved

use kwargs variable instead of hardcoded override

3f21a6e

coderabbitai bot reviewed Apr 29, 2024

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tests/test_models.py Outdated Show resolved Hide resolved

aaprasad requested a review from talmo April 29, 2024 21:15

talmo requested changes Apr 30, 2024

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aaprasad added 2 commits April 30, 2024 10:57

add changes requested by @talmo's code review

ec3639f

* remove unnecessary comments/print statements * use `None` instead of empty mutables.

add changes requested by @talmo's code review

bf3ff18

* remove unnecessary comment

coderabbitai bot reviewed Apr 30, 2024

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tests/test_models.py Show resolved Hide resolved

fix documentation typo

e3f577b

talmo approved these changes Apr 30, 2024

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talmo merged commit a47c48b into main Apr 30, 2024
3 checks passed

talmo deleted the aadi/implement-fixed-temp-embedding branch April 30, 2024 21:23

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Implement fixed temp embedding #30

Implement fixed temp embedding #30

aaprasad commented Apr 29, 2024 •

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Implement fixed temp embedding #30

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aaprasad commented Apr 29, 2024 •

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