Refactor transformer decoder #36

aaprasad · 2024-05-01T18:49:41Z

Refactor transformer implementation as requested by #34.

emphasis on better variable names
remove confused code paths
store embeddings as a dictionary and always return that dictionary instead of conditionally returning None

Summary by CodeRabbit

Refactor
- Improved type annotations in methods across transformer models for better code clarity and error checking.
Tests
- Enhanced clarity and consistency in variable naming within transformer model test cases.

* use better variable names * remove complicated code pathways * save embeddings in a dictionary and always return that dictionary instead of sometimes returning None

coderabbitai · 2024-05-01T18:49:50Z

Walkthrough

The changes involve refining type annotations in the transformer model classes, improving variable naming in test functions for clarity, and enhancing anomaly detection for debugging in the training tests.

Changes

Files	Change Summary
`biogtr/models/.../transformer.py`	Added type annotations and refined return types in transformer classes.
`tests/test_models.py`	Improved variable naming for clarity in transformer test cases.

Poem

🐇💻 CodeRabbit nibbles on code with glee,
🌟 Typing annotations with a dance and a spree.
Variables renamed, clarity in sight,
Bugs beware, we'll win this fight.
Hopping through tests, errors we smudge,
Joyful coding, a carrot-filled fudge! 🥕🎉

Recent Review Details

Configuration used: CodeRabbit UI
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Commits

Files that changed from the base of the PR and between 74f5bf4 and 67315e7.

Files selected for processing (2)

biogtr/models/transformer.py (10 hunks)
tests/test_models.py (4 hunks)

Files skipped from review as they are similar to previous changes (1)

biogtr/models/transformer.py

Additional Context Used

Ruff (2)

tests/test_models.py (2)

314-314: Local variable img_shape is assigned to but never used

386-386: Local variable cfg is assigned to but never used

Additional comments not posted (6)

tests/test_models.py (6)

235-239: Refactor variable names for clarity.

The renaming of variables from src to queries and out to encoder_features in test_transformer_encoder improves readability and aligns with the PR objectives of improved variable naming.

242-246: Ensure consistent use of positional embeddings.

The addition of positional embeddings (pos_emb) in the test for the transformer encoder layer is a good practice for testing the handling of additional inputs.

265-269: Refactor variable names for clarity.

The renaming of variables from tgt and memory to decoder_queries and encoder_features in test_transformer_decoder enhances clarity and consistency with the encoder tests.

272-278: Ensure consistent use of positional embeddings.

The handling of positional embeddings (pos_emb and query_pos_emb) in the test for the transformer decoder layer is consistent and thorough, testing the decoder's ability to handle complex inputs.

344-352: Validate embedding handling in transformer tests.

The test test_transformer_embedding checks the embeddings dictionary returned by the transformer, ensuring that each type of embedding is correctly sized and labeled, which aligns with the PR's objective of consistent embedding handling.

398-406: Validate embedding handling in tracking transformer tests.

The test test_tracking_transformer effectively checks the embeddings dictionary for correct sizing and labeling, similar to test_transformer_embedding, ensuring consistency across different transformer configurations.

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coderabbitai

Actionable comments posted: 0

Out of diff range and nitpick comments (6)

tests/test_training.py (3)
Line range hint 9-9: Remove unused import GlobalTrackingTransformer.
- from biogtr.models.global_tracking_transformer import GlobalTrackingTransformer
Line range hint 10-10: Remove unused import DictConfig.
- from omegaconf import DictConfig
Line range hint 46-46: The variable feats is declared but never used in test_basic_gtr_runner.

Consider removing or using the variable if it was intended for future use.
tests/test_models.py (2)

Line range hint 314-314: The variable img_shape is declared but never used in test_transformer_basic.

Consider removing or using the variable if it was intended for future use.

Line range hint 386-386: The variable cfg is declared but never used in test_tracking_transformer.

Consider removing or using the variable if it was intended for future use.

biogtr/models/transformer.py (1)

45-45: Ensure the constructor's documentation is updated to reflect all parameters.

Consider updating the documentation to include all new parameters and their descriptions to maintain clarity and developer understanding.

talmo

Looks amazing as-is, but would make some small changes

talmo · 2024-05-02T03:37:32Z

biogtr/models/transformer.py

+
+        reid_features = reid_features.permute(
+            1, 0, 2
+        )  # (total_instances x batch_size x embed_dim)


Use standard shape tuple syntax for documenting shapes:

Suggested change

) # (total_instances x batch_size x embed_dim)

) # (total_instances, batch_size, embed_dim)

talmo · 2024-05-02T03:37:39Z

biogtr/models/transformer.py

        # print(f'T: {window_length}; N: {total_instances}; N_t: {instances_per_frame} n_reid: {reid_features.shape}')
        pred_box, pred_time = get_boxes_times(frames)  # total_instances x 4

        temp_emb = self.temp_emb(pred_time / window_length)
+        if self.return_embedding:
+            embeddings_dict["temp"] = temp_emb  # .detach().cpu()


unused comment

talmo · 2024-05-02T03:37:44Z

biogtr/models/transformer.py


        pos_emb = self.pos_emb(pred_box)
+        if self.return_embedding:
+            embeddings_dict["pos"] = pos_emb  # .detach().cpu()


unused comment

talmo · 2024-05-02T03:40:15Z

biogtr/models/transformer.py

+
+        encoder_queries = reid_features
+
+        encoder_logits = self.encoder(


Are you sure these are logits? That term is usually reserved for the pre-softmax/sigmoid activations in a classification head.

Maybe encoder_features?

talmo · 2024-05-02T03:42:28Z

biogtr/models/transformer.py

-            q,
-            k,
-            value=src,
+        attn_logits = self.self_attn(


attn_features?

talmo · 2024-05-02T03:43:14Z

biogtr/models/transformer.py

+        encoder_logits = self.norm2(queries)

-        return src
+        return encoder_logits


encoder_features?

* replace use of `logits` with more appropriate `features` * remove unnecessary comments * standardize shape hinting format

coderabbitai

Actionable comments posted: 0

Out of diff range and nitpick comments (2)

tests/test_models.py (2)
Line range hint 314-314: Unused variable img_shape.
-    img_shape = (1, 100, 100)
The variable img_shape is defined but never used within the test_transformer_basic function. Consider removing it if it's not needed.

Line range hint 386-386: Unused variable cfg.
-    cfg = {"resnet18", "ResNet18_Weights.DEFAULT"}
The variable cfg is defined but not used in the test_tracking_transformer function. It appears to be a mistake since a dictionary is expected but a set is provided. If cfg is intended for use, correct the syntax and ensure it's utilized.

aaprasad added 2 commits May 1, 2024 11:46

refactor transformer

09d8479

* use better variable names * remove complicated code pathways * save embeddings in a dictionary and always return that dictionary instead of sometimes returning None

update model tests

affa1d6

coderabbitai bot reviewed May 1, 2024

View reviewed changes

replace None norms with nn.Identity

74f5bf4

aaprasad requested a review from talmo May 1, 2024 19:05

talmo approved these changes May 2, 2024

View reviewed changes

talmo changed the title ~~Aadi/refactor transformer decoder~~ Refactor transformer decoder May 2, 2024

add suggestions from @talmo's code review

67315e7

* replace use of `logits` with more appropriate `features` * remove unnecessary comments * standardize shape hinting format

coderabbitai bot reviewed May 3, 2024

View reviewed changes

aaprasad merged commit 9027ca8 into main May 3, 2024
3 checks passed

aaprasad mentioned this pull request May 3, 2024

Refactor the heaviest of lifters #34

Closed

talmo deleted the aadi/refactor-transformer-decoder branch May 14, 2024 21:58

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Refactor transformer decoder #36

Refactor transformer decoder #36

aaprasad commented May 1, 2024 •

edited by coderabbitai bot

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	) # (total_instances x batch_size x embed_dim)
	) # (total_instances, batch_size, embed_dim)


		encoder_queries = reid_features

		encoder_logits = self.encoder(

Refactor transformer decoder #36

Refactor transformer decoder #36

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aaprasad commented May 1, 2024 • edited by coderabbitai bot Loading

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aaprasad commented May 1, 2024 •

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