Set up logging #63
Set up logging #63
Conversation
WalkthroughThe updates to the Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant CLI
participant DreemTrain
participant DreemTrack
User->>CLI: Execute `dreem-train` command
CLI->>DreemTrain: Start training process
DreemTrain-->>CLI: Training status
User->>CLI: Execute `dreem-track` command
CLI->>DreemTrack: Start inference process
DreemTrack-->>CLI: Inference status
Poem
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Actionable comments posted: 39
Outside diff range and nitpick comments (55)
dreem/__init__.py (1)
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6-15: Remove unused imports to clean up the code.- from dreem.models.global_tracking_transformer import GlobalTrackingTransformer - from dreem.models.gtr_runner import GTRRunner - from dreem.models.transformer import Transformer - from dreem.models.visual_encoder import VisualEncoder - from dreem.io.frame import Frame - from dreem.io.instance import Instance - from dreem.io.association_matrix import AssociationMatrix - from dreem.io.config import Config - from dreem.io.visualize.annotate_videoTools
Ruff
3-3:
logging.configimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
4-4:
dreem.version.__version__imported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
6-6:
dreem.models.global_tracking_transformer.GlobalTrackingTransformerimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)docs/index.md (5)
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20-20: Ensure headings are surrounded by blank lines to comply with Markdown best practices.+ <!-- Add a blank line above and below each heading -->Also applies to: 21-21, 25-25, 26-26, 27-27, 31-31, 35-35, 39-39
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21-21: Remove trailing punctuation from headings to comply with Markdown best practices.- #### Clone the repository: + #### Clone the repositoryAlso applies to: 25-25, 26-26, 31-31
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22-22: Ensure fenced code blocks are surrounded by blank lines.+ <!-- Add a blank line above and below each code block -->Also applies to: 24-24, 28-28, 30-30, 32-32, 34-34, 36-36, 38-38, 40-40
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40-40: Specify the language for the fenced code block to enable syntax highlighting.- ``` + ```bash
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42-42: Ensure the file ends with a single newline character.+ <!-- Ensure there's a newline at the end of the file -->dreem/training/train.py (2)
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37-37: Optimize dictionary key check.- if "batch_config" in cfg.keys(): + if "batch_config" in cfg:
[!TIP]
Codebase VerificationThe context around the
tryblock shows that it handles a potentialKeyErrorwhen accessing an environment variable. However, there are no additionaltry-exceptblocks orwithstatements for broader resource management and error handling in the training setup.
- Ensure proper resource management and error handling in the training setup, especially around resource-intensive operations like model training and data loading.
Analysis chain
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78-90: Ensure proper resource management and error handling in the training setup.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify proper error handling and resource management in training setup. # Test: Search for error handling patterns. Expect: Proper try-except blocks around resource-intensive operations. rg --type python $'try { $$$ } catch { $$$ }' ./dreem/training/train.pyLength of output: 186
Script:
#!/bin/bash # Description: Verify proper error handling and resource management in training setup. # Test: Search for try-except blocks. Expect: Proper try-except blocks around resource-intensive operations. rg --type py 'try:' ./dreem/training/train.py # Test: Search for with statements. Expect: Proper use of context managers for resource management. rg --type py 'with ' ./dreem/training/train.pyLength of output: 277
Script:
#!/bin/bash # Description: Extract context around the try block and check for resource management practices. # Extract 10 lines before and after the try block to understand the context. rg --type py -A 10 -B 10 'try:' ./dreem/training/train.pyLength of output: 728
dreem/inference/track.py (2)
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37-37: Optimize loop variable usage.- for i, instance in enumerate(frame.instances): + for _i, instance in enumerate(frame.instances):Tools
Ruff
20-20: Undefined name
dreem(F821)
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101-101: Optimize dictionary key check.- if "checkpoints" in cfg.keys(): + if "checkpoints" in cfg:Tools
Ruff
20-20: Undefined name
dreem(F821)dreem/models/global_tracking_transformer.py (2)
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81-82: Undefined names in type hints.- ref_instances: list["Instance"], query_instances: list["Instance"] = None + ref_instances: list[Instance], query_instances: list[Instance] = None - instances: list["Instance"], force_recompute: bool = False + instances: list[Instance], force_recompute: bool = FalseAlso applies to: 103-103
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82-82: Undefined name 'AssociationMatrix' in return type.- ) -> list["AssociationMatrix"]: + ) -> list[AssociationMatrix]:dreem/datasets/base_dataset.py (1)
124-124: Clarify the purpose ofno_batching_fnin the docstring.Consider enhancing the docstring of
no_batching_fnto explain why this method is necessary and how it differs from standard batching functions.dreem/datasets/microscopy_dataset.py (2)
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85-85: Replace lambda with a function definition for better readability and maintainability.- parser = lambda x: data_utils.parse_synthetic(x, source=source) + def parser(x): + return data_utils.parse_synthetic(x, source=source)Using a function definition instead of a lambda expression enhances readability and maintainability, especially for more complex logic.
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171-172: Combine nestedifstatements into a single statement.- if len(img.shape) == 2: - img = img.unsqueeze(0) - elif len(img.shape) == 3: - if img.shape[2] == 3: - img = img.T + if len(img.shape) == 2: + img = img.unsqueeze(0) + elif len(img.shape) == 3 and img.shape[2] == 3: + img = img.TCombining these conditions into a single statement simplifies the code and reduces nesting.
dreem/models/model_utils.py (1)
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19-19: Loop control variableiis not used within the loop body.- for i, instance in enumerate(instances): + for _i, instance in enumerate(instances):Tools
Ruff
8-8: Undefined name
dreem(F821)dreem/inference/boxes.py (1)
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129-129: Use f-string for better readability and performance.- "Indexing on Boxes with {} failed to return a matrix!".format(item) + f"Indexing on Boxes with {item} failed to return a matrix!"dreem/datasets/cell_tracking_dataset.py (1)
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132-135: Simplify the assignment using a ternary operator.- if self.gt_list is not None: - gt_list = self.gt_list[label_idx] - else: - gt_list = None + gt_list = self.gt_list[label_idx] if self.gt_list is not None else Nonedreem/models/gtr_runner.py (1)
5-5: Add a module-level docstring for theloggingimport to explain its usage.dreem/inference/metrics.py (2)
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142-142: Rename the unused loop variablefidxto_fidxto indicate it is intentionally unused.- for fidx, frame in enumerate(frames): + for _fidx, frame in enumerate(frames):
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230-230: Rename the unused loop variablemetric_nameto_metric_nameto indicate it is intentionally unused.- for metric_name, metric in metrics.items(): + for _metric_name, metric in metrics.items():dreem/inference/track_queue.py (2)
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199-202: Replace theif-elseblock with a ternary operator for cleaner code.- if isinstance(frame.video, str): - vid_name = frame.video - else: - vid_name = frame.video.filename + vid_name = frame.video if isinstance(frame.video, str) else frame.video.filename
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211-211: Usekey not in dictinstead ofkey not in dict.keys()for better performance.- if pred_track_id not in self._queues.keys(): + if pred_track_id not in self._queues:dreem/io/visualize.py (1)
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286-286: Rename the unused loop variableidxto_idxto indicate it is intentionally unused.- for idx, (ds_name, data) in enumerate([(save_path, annotated_frames)]): + for _idx, (ds_name, data) in enumerate([(save_path, annotated_frames)]):dreem/io/association_matrix.py (5)
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41-44: Remove extraneous parentheses to improve readability.- raise ValueError( - ( - "Ref instances must equal number of columns in Association matrix" - f"Found {len(value)} ref instances but {self.matrix.shape[-1]} columns." - ) - ) + raise ValueError( + "Ref instances must equal number of columns in Association matrix" + f"Found {len(value)} ref instances but {self.matrix.shape[-1]} columns." + )
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60-63: Remove extraneous parentheses to improve readability.- raise ValueError( - ( - "Query instances must equal number of rows in Association matrix" - f"Found {len(value)} query instances but {self.matrix.shape[0]} rows." - ) - ) + raise ValueError( + "Query instances must equal number of rows in Association matrix" + f"Found {len(value)} query instances but {self.matrix.shape[0]} rows." + )
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117-117: Remove extraneousfprefix from the string as there are no placeholders.- f"Mismatched # of rows and labels!", + "Mismatched # of rows and labels!",
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143-143: Remove extraneousfprefix from the string as there are no placeholders.- f"Mismatched # of columns and labels!", + "Mismatched # of columns and labels!",
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208-209: Rename unused loop control variables to indicate they are not used.- for row_track, row_instances in row_tracks.items(): - for col_track, col_instances in col_tracks.items(): + for _row_track, row_instances in row_tracks.items(): + for _col_track, col_instances in col_tracks.items():tests/test_datasets.py (1)
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11-11: Remove unused import to clean up the code.- from dreem.models.model_utils get_devicedreem/datasets/sleap_dataset.py (1)
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150-150: Rename unused loop control variable to indicate it is not used.- for i, frame_ind in enumerate(frame_idx): + for _i, frame_ind in enumerate(frame_idx):dreem/models/embedding.py (1)
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154-157: Remove extraneous parentheses to improve readability.- raise RuntimeError( - ( - f"Output embedding dimension is {emb.shape[-1]} but requested {self.features} dimensions! \n" - f"hint: Try turning the MLP on by passing `mlp_cfg` to the constructor to project to the correct embedding dimensions." - ) - ) + raise RuntimeError( + f"Output embedding dimension is {emb.shape[-1]} but requested {self.features} dimensions! \n" + f"hint: Try turning the MLP on by passing `mlp_cfg` to the constructor to project to the correct embedding dimensions." + )dreem/io/config.py (3)
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86-86: Undefined nameGlobalTrackingTransformer. Ensure that the necessary imports are included or correct the type annotations.- def get_model(self) -> "GlobalTrackingTransformer": + from dreem.models import GlobalTrackingTransformer + def get_model(self) -> GlobalTrackingTransformer:
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98-98: Undefined nameGTRRunner. Ensure that the necessary imports are included or correct the type annotations.- def get_gtr_runner(self) -> "GTRRunner": + from dreem.models import GTRRunner + def get_gtr_runner(self) -> GTRRunner:
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405-409: Use a ternary operator for cleaner code when settingtrainer_params.- if "trainer" in self.cfg: - trainer_params = self.cfg.trainer - else: - trainer_params = {} + trainer_params = self.cfg.trainer if "trainer" in self.cfg else {}docs/usage.md (10)
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3-3: Consider replacing "thru" with "through" for a more formal tone.- thru training and running inference. + through training and running inference.Tools
LanguageTool
[uncategorized] ~119-~119: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...nside my/home/aaprasad/dreem_configsdirectory I can call ```bash dreem-train --config...
[uncategorized] ~124-~124: A comma might be missing here. (AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)
Context: ... > Note: you can use relative paths as well but may be a bit riskier so we recommen...
[uncategorized] ~124-~124: A comma might be missing here. (AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)
Context: ...relative paths as well but may be a bit riskier so we recommend absolute paths whenever...Markdownlint
116-116: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
120-120: null (MD031, blanks-around-fences)
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36-36: Clarify "In order to train a model you need 2 things." to be more concise.- In order to train a model you need 2 things. + To train a model, you need two things:Tools
LanguageTool
[uncategorized] ~119-~119: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...nside my/home/aaprasad/dreem_configsdirectory I can call ```bash dreem-train --config...
[uncategorized] ~124-~124: A comma might be missing here. (AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)
Context: ... > Note: you can use relative paths as well but may be a bit riskier so we recommen...
[uncategorized] ~124-~124: A comma might be missing here. (AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)
Context: ...relative paths as well but may be a bit riskier so we recommend absolute paths whenever...Markdownlint
116-116: null (MD031, blanks-around-fences)
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120-120: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
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41-41: Add a comma after "microscopy data" for better readability.- For microscopy data we currently support `.tif` files. + For microscopy data, we currently support `.tif` files.Tools
LanguageTool
[uncategorized] ~119-~119: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...nside my/home/aaprasad/dreem_configsdirectory I can call ```bash dreem-train --config...
[uncategorized] ~124-~124: A comma might be missing here. (AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)
Context: ... > Note: you can use relative paths as well but may be a bit riskier so we recommen...
[uncategorized] ~124-~124: A comma might be missing here. (AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)
Context: ...relative paths as well but may be a bit riskier so we recommend absolute paths whenever...Markdownlint
116-116: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
120-120: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
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47-47: Replace "a couple methods" with "a couple of methods" for grammatical correctness.- we recommend a couple methods. + we recommend a couple of methods.Tools
LanguageTool
[uncategorized] ~119-~119: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...nside my/home/aaprasad/dreem_configsdirectory I can call ```bash dreem-train --config...
[uncategorized] ~124-~124: A comma might be missing here. (AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)
Context: ... > Note: you can use relative paths as well but may be a bit riskier so we recommen...
[uncategorized] ~124-~124: A comma might be missing here. (AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)
Context: ...relative paths as well but may be a bit riskier so we recommend absolute paths whenever...Markdownlint
116-116: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
120-120: null (MD031, blanks-around-fences)
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49-49: Correct "work flow" to "workflow" for consistency.- through their work flow. + through their workflow.Tools
LanguageTool
[uncategorized] ~119-~119: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...nside my/home/aaprasad/dreem_configsdirectory I can call ```bash dreem-train --config...
[uncategorized] ~124-~124: A comma might be missing here. (AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)
Context: ... > Note: you can use relative paths as well but may be a bit riskier so we recommen...
[uncategorized] ~124-~124: A comma might be missing here. (AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)
Context: ...relative paths as well but may be a bit riskier so we recommend absolute paths whenever...Markdownlint
116-116: null (MD031, blanks-around-fences)
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120-120: null (MD031, blanks-around-fences)
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52-52: Add periods to "e.g" and "etc," and insert a comma before "but."- (e.g DeepLabCut or ilastik etc), the easiest + (e.g., DeepLabCut or ilastik, etc.), the easiestTools
LanguageTool
[uncategorized] ~119-~119: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...nside my/home/aaprasad/dreem_configsdirectory I can call ```bash dreem-train --config...
[uncategorized] ~124-~124: A comma might be missing here. (AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)
Context: ... > Note: you can use relative paths as well but may be a bit riskier so we recommen...
[uncategorized] ~124-~124: A comma might be missing here. (AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)
Context: ...relative paths as well but may be a bit riskier so we recommend absolute paths whenever...Markdownlint
116-116: null (MD031, blanks-around-fences)
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120-120: null (MD031, blanks-around-fences)
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54-54: Add a hyphen to "high quality" when used as a compound adjective.- to have high quality data. + to have high-quality data.Tools
LanguageTool
[uncategorized] ~119-~119: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...nside my/home/aaprasad/dreem_configsdirectory I can call ```bash dreem-train --config...
[uncategorized] ~124-~124: A comma might be missing here. (AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)
Context: ... > Note: you can use relative paths as well but may be a bit riskier so we recommen...
[uncategorized] ~124-~124: A comma might be missing here. (AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)
Context: ...relative paths as well but may be a bit riskier so we recommend absolute paths whenever...Markdownlint
116-116: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
120-120: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
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58-58: Insert a comma before "however."- unavoidable however, in cases of occlusion and overlap. + unavoidable, however, in cases of occlusion and overlap.Tools
LanguageTool
[uncategorized] ~119-~119: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...nside my/home/aaprasad/dreem_configsdirectory I can call ```bash dreem-train --config...
[uncategorized] ~124-~124: A comma might be missing here. (AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)
Context: ... > Note: you can use relative paths as well but may be a bit riskier so we recommen...
[uncategorized] ~124-~124: A comma might be missing here. (AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)
Context: ...relative paths as well but may be a bit riskier so we recommend absolute paths whenever...Markdownlint
116-116: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
120-120: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
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63-63: Simplify "In order to use the SLEAP gui" to a more concise form.- In order to use the SLEAP gui + To use the SLEAP guiTools
LanguageTool
[uncategorized] ~119-~119: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...nside my/home/aaprasad/dreem_configsdirectory I can call ```bash dreem-train --config...
[uncategorized] ~124-~124: A comma might be missing here. (AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)
Context: ... > Note: you can use relative paths as well but may be a bit riskier so we recommen...
[uncategorized] ~124-~124: A comma might be missing here. (AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)
Context: ...relative paths as well but may be a bit riskier so we recommend absolute paths whenever...Markdownlint
116-116: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
120-120: null (MD031, blanks-around-fences)
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70-70: Correct "its" to "it's" in two places for grammatical accuracy.- easy its best to save your labels and vid files + easy it's best to save your labels and video files - Its also just best practice + It's also just best practiceTools
LanguageTool
[uncategorized] ~119-~119: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...nside my/home/aaprasad/dreem_configsdirectory I can call ```bash dreem-train --config...
[uncategorized] ~124-~124: A comma might be missing here. (AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)
Context: ... > Note: you can use relative paths as well but may be a bit riskier so we recommen...
[uncategorized] ~124-~124: A comma might be missing here. (AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)
Context: ...relative paths as well but may be a bit riskier so we recommend absolute paths whenever...Markdownlint
116-116: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
120-120: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank linesdreem/io/frame.py (2)
3-3: Consider adding a module-level docstring to explain the purpose of the__future__ import annotationsfor clarity.
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556-556: Usekey in dictinstead ofkey in dict.keys()for checking key existence in dictionaries. This is more Pythonic and efficient.- if key in dict.keys(): + if key in dict:README.md (5)
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43-43: Replace informal language for professionalism.- Here we describe a basic workflow from setting up data thru training and running inference. + Here we describe a basic workflow from setting up data through training and running inference.
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43-43: Consider adding a comma for better readability.- Regardless if you're only interested in running inference, we recommend at least skimming thru the entire tutorial as there may be useful information that applies to both training and inference! + Regardless, if you're only interested in running inference, we recommend at least skimming through the entire tutorial as there may be useful information that applies to both training and inference!
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75-75: Clarify the necessity of the steps listed.- In order to train a model you need 2 things. + To train a model, you need 2 things:
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85-85: Use "a couple of" instead of "a couple" for formal writing.- To generate your initial labels we recommend a couple methods. + To generate your initial labels, we recommend a couple of methods.
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89-89: Correct the abbreviation and punctuation.- If you'd like to use a different method, (e.g DeepLabCut or ilastik etc), the easiest way to make your data compatible with `dreem` is to convert your labels to a `.slp` file and your video to an [`imageio`-supported]((https://imageio.readthedocs.io/en/v2.4.1/formats.html)) video format. + If you'd like to use a different method (e.g., DeepLabCut or ilastik, etc.), the easiest way to make your data compatible with `dreem` is to convert your labels to a `.slp` file and your video to an [`imageio`-supported](https://imageio.readthedocs.io/en/v2.4.1/formats.html) video format.dreem/inference/tracker.py (1)
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179-179: The variablecurr_trackis used before it is defined, which will lead to a runtime error. Initializecurr_trackbefore its use.+ curr_track = 0 for i, instance in enumerate(frames[batch_idx].instances): if instance.pred_track_id == -1: curr_track += 1 instance.pred_track_id = curr_track_iddreem/io/instance.py (2)
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215-215: Avoid using mutable default arguments for function parameters to prevent unintended side effects.- def to_slp(self, track_lookup: dict[int, sio.Track] = {}): + def to_slp(self, track_lookup: dict[int, sio.Track] = None): + if track_lookup is None: + track_lookup = {}
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293-293: Simplify the return statements by returning the condition directly.- if self._gt_track_id.shape[0] == 0: - return False - else: - return True + return self._gt_track_id.shape[0] != 0Also applies to: 325-325, 365-365, 435-435, 473-473
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (40)
- README.md (6 hunks)
- docs/cli.md (1 hunks)
- docs/index.md (1 hunks)
- docs/usage.md (5 hunks)
- dreem/init.py (2 hunks)
- dreem/datasets/base_dataset.py (5 hunks)
- dreem/datasets/cell_tracking_dataset.py (3 hunks)
- dreem/datasets/data_utils.py (6 hunks)
- dreem/datasets/eval_dataset.py (2 hunks)
- dreem/datasets/microscopy_dataset.py (3 hunks)
- dreem/datasets/sleap_dataset.py (4 hunks)
- dreem/datasets/tracking_dataset.py (2 hunks)
- dreem/inference/boxes.py (6 hunks)
- dreem/inference/metrics.py (4 hunks)
- dreem/inference/post_processing.py (3 hunks)
- dreem/inference/track.py (5 hunks)
- dreem/inference/track_queue.py (7 hunks)
- dreem/inference/tracker.py (11 hunks)
- dreem/io/association_matrix.py (5 hunks)
- dreem/io/config.py (8 hunks)
- dreem/io/frame.py (10 hunks)
- dreem/io/instance.py (9 hunks)
- dreem/io/track.py (2 hunks)
- dreem/io/visualize.py (8 hunks)
- dreem/models/embedding.py (4 hunks)
- dreem/models/global_tracking_transformer.py (2 hunks)
- dreem/models/gtr_runner.py (4 hunks)
- dreem/models/model_utils.py (4 hunks)
- dreem/models/transformer.py (6 hunks)
- dreem/models/visual_encoder.py (3 hunks)
- dreem/training/init.py (1 hunks)
- dreem/training/losses.py (4 hunks)
- dreem/training/train.py (5 hunks)
- environment.yml (1 hunks)
- environment_cpu.yml (1 hunks)
- environment_osx-arm64.yml (1 hunks)
- logging.yaml (1 hunks)
- mkdocs.yml (1 hunks)
- pyproject.toml (2 hunks)
- tests/test_datasets.py (1 hunks)
Files not reviewed due to errors (1)
- dreem/datasets/data_utils.py (no review received)
Files skipped from review due to trivial changes (4)
- dreem/datasets/tracking_dataset.py
- dreem/training/init.py
- environment.yml
- mkdocs.yml
Additional context used
Ruff
dreem/__init__.py
3-3:
logging.configimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
4-4:
dreem.version.__version__imported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
6-6:
dreem.models.global_tracking_transformer.GlobalTrackingTransformerimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
7-7:
dreem.models.gtr_runner.GTRRunnerimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
8-8:
dreem.models.transformer.Transformerimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
9-9:
dreem.models.visual_encoder.VisualEncoderimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
11-11:
dreem.io.frame.Frameimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
12-12:
dreem.io.instance.Instanceimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
13-13:
dreem.io.association_matrix.AssociationMatriximported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
14-14:
dreem.io.config.Configimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
15-15:
dreem.io.visualize.annotate_videoimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
19-19:
dreem.inference.tracker.Trackerimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
30-30: Unnecessary open mode parameters (UP015)
Remove open mode parameters
34-34: Local variable
loggeris assigned to but never used (F841)Remove assignment to unused variable
loggerdreem/io/track.py
17-17: Remove quotes from type annotation (UP037)
Remove quotes
17-17: Undefined name
Instance(F821)
46-46: Remove quotes from type annotation (UP037)
Remove quotes
46-46: Undefined name
Instances(F821)
64-64: Remove quotes from type annotation (UP037)
Remove quotes
64-64: Undefined name
Frame(F821)
80-80: Remove quotes from type annotation (UP037)
Remove quotes
80-80: Undefined name
Instance(F821)
80-80: Remove quotes from type annotation (UP037)
Remove quotes
80-80: Undefined name
Instance(F821)dreem/training/train.py
37-37: Use
key in dictinstead ofkey in dict.keys()(SIM118)Remove
.keys()dreem/inference/track.py
20-20: Undefined name
dreem(F821)
37-37: Loop control variable
inot used within loop body (B007)Rename unused
ito_i
101-101: Use
key in dictinstead ofkey in dict.keys()(SIM118)Remove
.keys()
119-119: f-string without any placeholders (F541)
Remove extraneous
fprefixdreem/models/global_tracking_transformer.py
81-81: Undefined name
Instance(F821)
81-81: Undefined name
Instance(F821)
82-82: Undefined name
AssociationMatrix(F821)
103-103: Undefined name
Instance(F821)dreem/datasets/microscopy_dataset.py
85-85: Do not assign a
lambdaexpression, use adef(E731)Rewrite
parseras adef
171-172: Use a single
ifstatement instead of nestedifstatements (SIM102)Combine
ifstatements usinganddreem/models/model_utils.py
8-8: Undefined name
dreem(F821)
19-19: Loop control variable
inot used within loop body (B007)Rename unused
ito_i
32-32: Undefined name
dreem(F821)
33-33: Undefined name
dreem(F821)dreem/inference/boxes.py
129-129: Use f-string instead of
formatcall (UP032)Convert to f-string
dreem/datasets/cell_tracking_dataset.py
132-135: Use ternary operator
gt_list = self.gt_list[label_idx] if self.gt_list is not None else Noneinstead ofif-else-block (SIM108)Replace
if-else-block withgt_list = self.gt_list[label_idx] if self.gt_list is not None else Nonedreem/training/losses.py
36-36: Undefined name
Frame(F821)dreem/models/gtr_runner.py
80-80: Undefined name
dreem(F821)
81-81: Undefined name
dreem(F821)
96-96: Undefined name
dreem(F821)
114-114: Undefined name
dreem(F821)
132-132: Undefined name
dreem(F821)
150-150: Undefined name
dreem(F821)
151-151: Undefined name
dreem(F821)
168-168: Undefined name
dreem(F821)dreem/inference/metrics.py
16-16: Undefined name
dreem(F821)
107-107: Undefined name
dreem(F821)
142-142: Loop control variable
fidxnot used within loop body (B007)Rename unused
fidxto_fidx
230-230: Loop control variable
metric_namenot used within loop body (B007)Rename unused
metric_nameto_metric_namedreem/inference/track_queue.py
199-202: Use ternary operator
vid_name = frame.video if isinstance(frame.video, str) else frame.video.filenameinstead ofif-else-block (SIM108)Replace
if-else-block withvid_name = frame.video if isinstance(frame.video, str) else frame.video.filename
211-211: Use
key not in dictinstead ofkey not in dict.keys()(SIM118)Remove
.keys()
254-254: Loop control variable
tracknot used within loop body (B007)Rename unused
trackto_track
256-256: Use
key not in dictinstead ofkey not in dict.keys()(SIM118)Remove
.keys()dreem/io/visualize.py
286-286: Loop control variable
idxnot used within loop body (B007)Rename unused
idxto_idxdreem/io/association_matrix.py
41-44: Avoid extraneous parentheses (UP034)
Remove extraneous parentheses
60-63: Avoid extraneous parentheses (UP034)
Remove extraneous parentheses
117-117: f-string without any placeholders (F541)
Remove extraneous
fprefix
143-143: f-string without any placeholders (F541)
Remove extraneous
fprefix
208-208: Loop control variable
row_tracknot used within loop body (B007)Rename unused
row_trackto_row_track
209-209: Loop control variable
col_tracknot used within loop body (B007)Rename unused
col_trackto_col_tracktests/test_datasets.py
11-11:
dreem.models.model_utils.get_deviceimported but unused (F401)Remove unused import:
dreem.models.model_utils.get_devicedreem/datasets/sleap_dataset.py
150-150: Loop control variable
inot used within loop body (B007)Rename unused
ito_idreem/models/embedding.py
154-157: Avoid extraneous parentheses (UP034)
Remove extraneous parentheses
dreem/io/config.py
60-60: Undefined name
params_cfg(F821)
86-86: Remove quotes from type annotation (UP037)
Remove quotes
86-86: Undefined name
GlobalTrackingTransformer(F821)
98-98: Undefined name
GTRRunner(F821)
114-114: Remove quotes from type annotation (UP037)
Remove quotes
114-114: Undefined name
GTRRunner(F821)
175-175: Remove quotes from type annotation (UP037)
Remove quotes
175-175: Undefined name
SleapDataset(F821)
175-175: Remove quotes from type annotation (UP037)
Remove quotes
175-175: Undefined name
MicroscopyDataset(F821)
175-175: Remove quotes from type annotation (UP037)
Remove quotes
175-175: Undefined name
CellTrackingDataset(F821)
239-239: Remove quotes from type annotation (UP037)
Remove quotes
239-239: Undefined name
SleapDataset(F821)
239-239: Remove quotes from type annotation (UP037)
Remove quotes
239-239: Undefined name
MicroscopyDataset(F821)
239-239: Remove quotes from type annotation (UP037)
Remove quotes
239-239: Undefined name
CellTrackingDataset(F821)
310-310: Remove quotes from type annotation (UP037)
Remove quotes
310-310: Undefined name
dreem(F821)
405-409: Use ternary operator
trainer_params = self.cfg.trainer if "trainer" in self.cfg else {}instead ofif-else-block (SIM108)Replace
if-else-block withtrainer_params = self.cfg.trainer if "trainer" in self.cfg else {}dreem/datasets/data_utils.py
6-6:
cElementTreeis deprecated, useElementTree(UP023)Replace with
ElementTree
264-264: Use context handler for opening files (SIM115)
385-388: Use
contextlib.suppress(Exception)instead oftry-except-pass(SIM105)Replace with
contextlib.suppress(Exception)
387-387: Do not use bare
except(E722)dreem/io/frame.py
61-61: Remove quotes from type annotation (UP037)
Remove quotes
61-61: Undefined name
Instance(F821)
62-62: Remove quotes from type annotation (UP037)
Remove quotes
62-62: Undefined name
AssociationMatrix(F821)
305-305: Remove quotes from type annotation (UP037)
Remove quotes
305-305: Undefined name
Instance(F821)
314-314: Remove quotes from type annotation (UP037)
Remove quotes
314-314: Undefined name
Instance(F821)
344-344: Remove quotes from type annotation (UP037)
Remove quotes
344-344: Undefined name
AssociationMatrix(F821)
363-363: Remove quotes from type annotation (UP037)
Remove quotes
363-363: Undefined name
AssociationMatrix(F821)
556-556: Use
key in dictinstead ofkey in dict.keys()(SIM118)Remove
.keys()dreem/inference/tracker.py
126-126: f-string without any placeholders (F541)
Remove extraneous
fprefix
173-173: Loop control variable
inot used within loop body (B007)Rename unused
ito_i
177-177: Loop control variable
inot used within loop body (B007)Rename unused
ito_i
179-179: Undefined name
curr_track(F821)
179-179: Local variable
curr_trackis assigned to but never used (F841)
434-434: Avoid extraneous parentheses (UP034)
Remove extraneous parentheses
dreem/models/transformer.py
144-144: Undefined name
dreem(F821)
145-145: Undefined name
dreem(F821)dreem/io/instance.py
96-96: Undefined name
Frame(F821)
215-215: Do not use mutable data structures for argument defaults (B006)
Replace with
None; initialize within function
246-246: Within an
exceptclause, raise exceptions withraise ... from errorraise ... from Noneto distinguish them from errors in exception handling (B904)
293-296: Return the condition
not self._gt_track_id.shape[0] == 0directly (SIM103)Replace with
return not self._gt_track_id.shape[0] == 0
325-328: Return the negated condition directly (SIM103)
Inline condition
365-368: Return the condition
not self._bbox.shape[1] == 0directly (SIM103)Replace with
return not self._bbox.shape[1] == 0
435-438: Return the condition
not self._crop.shape[-1] == 0directly (SIM103)Replace with
return not self._crop.shape[-1] == 0
473-476: Return the condition
not self._features.shape[-1] == 0directly (SIM103)Replace with
return not self._features.shape[-1] == 0
523-523: Undefined name
Frame(F821)
532-532: Undefined name
Frame(F821)
Markdownlint
docs/index.md
20-20: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
21-21: Expected: 1; Actual: 0; Above (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
21-21: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
25-25: Expected: 1; Actual: 0; Above (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
25-25: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
26-26: Expected: 1; Actual: 0; Above (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
26-26: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
27-27: Expected: 1; Actual: 0; Above (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
27-27: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
31-31: Expected: 1; Actual: 0; Above (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
31-31: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
35-35: Expected: 1; Actual: 0; Above (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
35-35: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
39-39: Expected: 1; Actual: 0; Above (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
39-39: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
21-21: Punctuation: ':' (MD026, no-trailing-punctuation)
Trailing punctuation in heading
25-25: Punctuation: ':' (MD026, no-trailing-punctuation)
Trailing punctuation in heading
26-26: Punctuation: ':' (MD026, no-trailing-punctuation)
Trailing punctuation in heading
31-31: Punctuation: ':' (MD026, no-trailing-punctuation)
Trailing punctuation in heading
22-22: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
24-24: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
28-28: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
30-30: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
32-32: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
34-34: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
36-36: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
38-38: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
40-40: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
40-40: null (MD040, fenced-code-language)
Fenced code blocks should have a language specified
42-42: null (MD047, single-trailing-newline)
Files should end with a single newline characterdocs/cli.md
47-47: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
13-13: null (MD040, fenced-code-language)
Fenced code blocks should have a language specified
35-35: null (MD040, fenced-code-language)
Fenced code blocks should have a language specified
56-56: null (MD040, fenced-code-language)
Fenced code blocks should have a language specified
104-104: null (MD047, single-trailing-newline)
Files should end with a single newline characterdocs/usage.md
49-49: Expected: 0; Actual: 1 (MD007, ul-indent)
Unordered list indentation
50-50: Expected: 0; Actual: 1 (MD007, ul-indent)
Unordered list indentation
10-10: Expected: 0 or 2; Actual: 1 (MD009, no-trailing-spaces)
Trailing spaces
49-49: Expected: 0 or 2; Actual: 1 (MD009, no-trailing-spaces)
Trailing spaces
61-61: Expected: 0 or 2; Actual: 1 (MD009, no-trailing-spaces)
Trailing spaces
71-71: Expected: 0 or 2; Actual: 1 (MD009, no-trailing-spaces)
Trailing spaces
152-152: Expected: 0 or 2; Actual: 1 (MD009, no-trailing-spaces)
Trailing spaces
159-159: Expected: 0 or 2; Actual: 1 (MD009, no-trailing-spaces)
Trailing spaces
160-160: Expected: 0 or 2; Actual: 1 (MD009, no-trailing-spaces)
Trailing spaces
165-165: Expected: 0 or 2; Actual: 1 (MD009, no-trailing-spaces)
Trailing spaces
173-173: Expected: 0 or 2; Actual: 1 (MD009, no-trailing-spaces)
Trailing spaces
175-175: Expected: 0 or 2; Actual: 1 (MD009, no-trailing-spaces)
Trailing spaces
200-200: Expected: 0 or 2; Actual: 1 (MD009, no-trailing-spaces)
Trailing spaces
218-218: Expected: 0 or 2; Actual: 1 (MD009, no-trailing-spaces)
Trailing spaces
234-234: Expected: 0 or 2; Actual: 1 (MD009, no-trailing-spaces)
Trailing spaces
255-255: Expected: 1; Actual: 2 (MD012, no-multiple-blanks)
Multiple consecutive blank lines
4-4: Expected: 1; Actual: 0; Above (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
14-14: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
15-15: Expected: 1; Actual: 0; Above (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
15-15: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
21-21: Expected: 1; Actual: 0; Above (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
21-21: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
27-27: Expected: 1; Actual: 0; Above (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
27-27: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
36-36: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
46-46: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
53-53: Expected: 1; Actual: 0; Above (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
53-53: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
63-63: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
126-126: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
132-132: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
145-145: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
179-179: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
184-184: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
185-185: Expected: 1; Actual: 0; Above (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
185-185: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
195-195: Expected: 1; Actual: 0; Above (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
240-240: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
252-252: Expected: 1; Actual: 0; Above (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
252-252: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
15-15: Punctuation: ':' (MD026, no-trailing-punctuation)
Trailing punctuation in heading
21-21: Punctuation: ':' (MD026, no-trailing-punctuation)
Trailing punctuation in heading
63-63: Punctuation: '.' (MD026, no-trailing-punctuation)
Trailing punctuation in heading
66-66: Punctuation: '.' (MD026, no-trailing-punctuation)
Trailing punctuation in heading
106-106: Punctuation: ':' (MD026, no-trailing-punctuation)
Trailing punctuation in heading
240-240: Punctuation: '.' (MD026, no-trailing-punctuation)
Trailing punctuation in heading
17-17: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
19-19: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
23-23: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
25-25: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
29-29: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
31-31: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
74-74: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
116-116: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
120-120: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
156-156: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
166-166: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
168-168: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
170-170: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
172-172: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
203-203: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
247-247: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
249-249: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
251-251: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
74-74: null (MD040, fenced-code-language)
Fenced code blocks should have a language specified
203-203: null (MD040, fenced-code-language)
Fenced code blocks should have a language specifiedREADME.md
86-86: Expected: 0; Actual: 1 (MD007, ul-indent)
Unordered list indentation
87-87: Expected: 0; Actual: 1 (MD007, ul-indent)
Unordered list indentation
49-49: Expected: 0 or 2; Actual: 1 (MD009, no-trailing-spaces)
Trailing spaces
86-86: Expected: 0 or 2; Actual: 1 (MD009, no-trailing-spaces)
Trailing spaces
98-98: Expected: 0 or 2; Actual: 1 (MD009, no-trailing-spaces)
Trailing spaces
108-108: Expected: 0 or 2; Actual: 1 (MD009, no-trailing-spaces)
Trailing spaces
164-164: Expected: 0 or 2; Actual: 1 (MD009, no-trailing-spaces)
Trailing spaces
188-188: Expected: 0 or 2; Actual: 1 (MD009, no-trailing-spaces)
Trailing spaces
195-195: Expected: 0 or 2; Actual: 1 (MD009, no-trailing-spaces)
Trailing spaces
196-196: Expected: 0 or 2; Actual: 1 (MD009, no-trailing-spaces)
Trailing spaces
201-201: Expected: 0 or 2; Actual: 1 (MD009, no-trailing-spaces)
Trailing spaces
209-209: Expected: 0 or 2; Actual: 1 (MD009, no-trailing-spaces)
Trailing spaces
211-211: Expected: 0 or 2; Actual: 1 (MD009, no-trailing-spaces)
Trailing spaces
234-234: Expected: 0 or 2; Actual: 1 (MD009, no-trailing-spaces)
Trailing spaces
251-251: Expected: 0 or 2; Actual: 1 (MD009, no-trailing-spaces)
Trailing spaces
267-267: Expected: 0 or 2; Actual: 1 (MD009, no-trailing-spaces)
Trailing spaces
17-17: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
18-18: Expected: 1; Actual: 0; Above (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
18-18: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
22-22: Expected: 1; Actual: 0; Above (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
22-22: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
23-23: Expected: 1; Actual: 0; Above (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
23-23: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
24-24: Expected: 1; Actual: 0; Above (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
24-24: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
28-28: Expected: 1; Actual: 0; Above (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
28-28: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
32-32: Expected: 1; Actual: 0; Above (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
32-32: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
36-36: Expected: 1; Actual: 0; Above (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
36-36: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
44-44: Expected: 1; Actual: 0; Above (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
53-53: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
54-54: Expected: 1; Actual: 0; Above (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
54-54: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
60-60: Expected: 1; Actual: 0; Above (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
60-60: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
66-66: Expected: 1; Actual: 0; Above (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
66-66: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
75-75: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
84-84: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
90-90: Expected: 1; Actual: 0; Above (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
90-90: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
100-100: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
163-163: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
168-168: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
181-181: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
215-215: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
220-220: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
221-221: Expected: 1; Actual: 0; Above (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
221-221: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
230-230: Expected: 1; Actual: 0; Above (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
273-273: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
285-285: Expected: 1; Actual: 0; Above (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
285-285: Expected: 1; Actual: 0; Below (MD022, blanks-around-headings)
Headings should be surrounded by blank lines
18-18: Punctuation: ':' (MD026, no-trailing-punctuation)
Trailing punctuation in heading
22-22: Punctuation: ':' (MD026, no-trailing-punctuation)
Trailing punctuation in heading
23-23: Punctuation: ':' (MD026, no-trailing-punctuation)
Trailing punctuation in heading
28-28: Punctuation: ':' (MD026, no-trailing-punctuation)
Trailing punctuation in heading
54-54: Punctuation: ':' (MD026, no-trailing-punctuation)
Trailing punctuation in heading
60-60: Punctuation: ':' (MD026, no-trailing-punctuation)
Trailing punctuation in heading
100-100: Punctuation: '.' (MD026, no-trailing-punctuation)
Trailing punctuation in heading
103-103: Punctuation: '.' (MD026, no-trailing-punctuation)
Trailing punctuation in heading
143-143: Punctuation: ':' (MD026, no-trailing-punctuation)
Trailing punctuation in heading
273-273: Punctuation: '.' (MD026, no-trailing-punctuation)
Trailing punctuation in heading
19-19: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
21-21: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
25-25: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
27-27: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
29-29: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
31-31: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
33-33: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
35-35: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
37-37: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
56-56: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
58-58: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
62-62: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
64-64: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
68-68: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
70-70: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
111-111: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
153-153: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
157-157: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
192-192: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
202-202: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
204-204: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
206-206: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
208-208: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
237-237: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
280-280: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
282-282: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
284-284: null (MD031, blanks-around-fences)
Fenced code blocks should be surrounded by blank lines
47-47: null (MD032, blanks-around-lists)
Lists should be surrounded by blank lines
77-77: null (MD032, blanks-around-lists)
Lists should be surrounded by blank lines
86-86: null (MD032, blanks-around-lists)
Lists should be surrounded by blank lines
165-165: null (MD032, blanks-around-lists)
Lists should be surrounded by blank lines
223-223: null (MD032, blanks-around-lists)
Lists should be surrounded by blank lines
233-233: null (MD032, blanks-around-lists)
Lists should be surrounded by blank lines
252-252: null (MD032, blanks-around-lists)
Lists should be surrounded by blank lines
37-37: null (MD040, fenced-code-language)
Fenced code blocks should have a language specified
111-111: null (MD040, fenced-code-language)
Fenced code blocks should have a language specified
237-237: null (MD040, fenced-code-language)
Fenced code blocks should have a language specified
LanguageTool
docs/cli.md
[uncategorized] ~86-~86: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...pecifying each individual+annotate.*param we recommend setting up a visualize con...docs/usage.md
[uncategorized] ~3-~3: The preposition “through” seems more likely in this position. (AI_EN_LECTOR_REPLACEMENT_PREPOSITION)
Context: ...e a basic workflow from setting up data thru training and running inference. Regardl...
[style] ~3-~3: The word ‘thru’ is informal. Consider replacing it with “through”. (THRU)
Context: ...ference, we recommend at least skimming thru the entire tutorial as there may be use...
[style] ~36-~36: Consider a shorter alternative to avoid wordiness. (IN_ORDER_TO_PREMIUM)
Context: ... ### Step 1: Generate Ground Truth Data In order to train a model you need 2 things. 1. A ...
[uncategorized] ~37-~37: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...e Ground Truth Data In order to train a model you need 2 things. 1. A video. - F...
[uncategorized] ~41-~41: A comma might be missing here. (AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)
Context: ...ported file types. - For microscopy data we currently support.tiffiles. Vide...
[uncategorized] ~47-~47: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...Initial labels To generate your initial labels we recommend a couple methods. - For ...
[grammar] ~47-~47: Using ‘couple’ without ‘of’ is considered to be informal. (PLENTY_OF_NOUNS)
Context: ...rate your initial labels we recommend a couple methods. - For animal pose-estimation, we hig...
[uncategorized] ~49-~49: Write this as one word if you mean the noun “workflow”. (WORK_COMPOUNDS)
Context: ...s://sleap.ai) and running through their work flow. - For microscopy tracking, check out...
[uncategorized] ~52-~52: The abbreviation “e.g.” (= for example) requires two periods. (E_G)
Context: ... you'd like to use a different method, (e.g DeepLabCut or ilastik etc), the easiest...
[style] ~52-~52: In American English, abbreviations like “etc.” require a period. (ETC_PERIOD)
Context: ...rent method, (e.g DeepLabCut or ilastik etc), the easiest way to make your data com...
[uncategorized] ~52-~52: Use a comma before ‘but’ if it connects two independent clauses (unless they are closely connected and short). (COMMA_COMPOUND_SENTENCE_2)
Context: ...ively, you can write a custom dataloader but that will take significantly more overh...
[uncategorized] ~54-~54: If this is a compound adjective that modifies the following noun, use a hyphen. (EN_COMPOUND_ADJECTIVE_INTERNAL)
Context: ... thing to train a good model is to have high quality data. In our case good quality means tw...
[typographical] ~54-~54: At the start of a sentence, a comma is usually required for the expression ‘In “our case,”’. (COMMA_OF_IN_PRPS_CASE)
Context: ... model is to have high quality data. In our case good quality means two things: 1. No i...
[style] ~58-~58: To elevate your writing, try using a synonym here. (HARD_TO)
Context: ...o avoid having detection coordinates be hard to distinguish. For instance, with anim...
[uncategorized] ~58-~58: The preposition “in” seems more likely in this position than the preposition “on”. (AI_EN_LECTOR_REPLACEMENT_PREPOSITION_ON_IN)
Context: ... we want to avoid having the key points on two instances. For segmentation, the bo...
[formatting] ~58-~58: Consider inserting a comma before ‘however’. (HOWEVER_MISSING_COMMA)
Context: ...ld be as tight as possible. This may be unavoidable however, in cases of occlusion and overlap. See ...
[uncategorized] ~59-~59: Possible missing preposition found. (AI_EN_LECTOR_MISSING_PREPOSITION)
Context: ... and bad detections. //TODO add example good vs bad detection. We recommend using t...
[style] ~63-~63: Consider a shorter alternative to avoid wordiness. (IN_ORDER_TO_PREMIUM)
Context: ...ting data to a SLEAP compatible format. In order to use the SLEAP gui you'll need to have y...
[uncategorized] ~64-~64: A comma may be missing after the conjunctive/linking adverb ‘Otherwise’. (SENT_START_CONJUNCTIVE_LINKING_ADVERB_COMMA)
Context: ... you can start proofreading right away. Otherwise if you used a different system (e.g Dee...
[uncategorized] ~64-~64: The abbreviation “e.g.” (= for example) requires two periods. (E_G)
Context: ...herwise if you used a different system (e.g DeepLabCut) check out [`sleap.io.conver...
[uncategorized] ~64-~64: A comma might be missing here. (AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)
Context: ... used a different system (e.g DeepLabCut) check out [sleap.io.convert](https://...
[uncategorized] ~64-~64: A punctuation mark might be missing here. (AI_EN_LECTOR_MISSING_PUNCTUATION)
Context: ... converter from trackmate's output to a.slp](https://gist.github.com/aaprasad/...
[uncategorized] ~64-~64: The grammatical number of this noun doesn’t look right. Consider replacing it. (AI_EN_LECTOR_REPLACEMENT_NOUN_NUMBER)
Context: ...freading. Once you've ensured that your labels files have no identity switches and you...
[grammar] ~68-~68: Using ‘couple’ without ‘of’ is considered to be informal. (PLENTY_OF_NOUNS)
Context: ...e recommend organizing your data with a couple things in mind. 1. Match video and labels fil...
[uncategorized] ~70-~70: The grammatical number of this noun doesn’t look right. Consider replacing it. (AI_EN_LECTOR_REPLACEMENT_NOUN_NUMBER)
Context: ...ple things in mind. 1. Match video and labels file stems. Because our dataloaders jus...
[style] ~70-~70: Consider a shorter alternative to avoid wordiness. (IN_ORDER_TO_PREMIUM)
Context: ...lp, file2.slp], [vid1.mp4, vid2.mp4]`). In order to make programmatic file searching easy i...
[uncategorized] ~70-~70: A comma might be missing here. (AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)
Context: ...der to make programmatic file searching easy its best to save your labels and vid fi...
[uncategorized] ~70-~70: “its” (belonging to it) seems less likely than “it’s” (it is) (AI_HYDRA_LEO_CPT_ITS_ITIS)
Context: ...o make programmatic file searching easy its best to save your labels and vid files ...
[style] ~70-~70: ‘vid’ is informal. Consider replacing it. (VID)
Context: ...g easy its best to save your labels and vid files with the same stem so that you ca...
[uncategorized] ~70-~70: “its” (belonging to it) seems less likely than “it’s” (it is) (AI_HYDRA_LEO_CPT_ITS_ITIS)
Context: ...ensure the ordering will be consistent. Its also just best practice so you know whi...
[uncategorized] ~70-~70: It seems likely that a singular genitive (’s) apostrophe is missing. (AI_HYDRA_LEO_APOSTROPHE_S_XS)
Context: ...best practice so you know which video a labels file corresponds to. 2. Store correspon...
[style] ~104-~104: Consider replacing this word to strengthen your wording. (AND_THAT)
Context: ...train script if you're an advanced user and would like to have some additional flex...
[uncategorized] ~108-~108: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...set of parameters when training (for an example see [here](configs/training.md#override...
[uncategorized] ~119-~119: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...nside my/home/aaprasad/dreem_configsdirectory I can call ```bash dreem-train --config...
[uncategorized] ~124-~124: A comma might be missing here. (AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)
Context: ... > Note: you can use relative paths as well but may be a bit riskier so we recommen...
[uncategorized] ~124-~124: A comma might be missing here. (AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)
Context: ...relative paths as well but may be a bit riskier so we recommend absolute paths whenever...
[grammar] ~139-~139: It seems like one article is redundant in this context. (A_RB_A_JJ_NN)
Context: .../dreem_configs` directory that contains a only a small selection of parameters that I'd like t...
[uncategorized] ~146-~146: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...g a specific param via the command line directly you can use thesection.param=keysyn...
[uncategorized] ~151-~151: The abbreviation “e.g.” (= for example) requires two periods. (E_G)
Context: ...E_CONFIG_STEM] section.param=value ``` e.g If now I want to override a couple para...
[grammar] ~152-~152: Using ‘couple’ without ‘of’ is considered to be informal. (PLENTY_OF_NOUNS)
Context: ...ue ``` e.g If now I want to override a couple parameters again, say change the number of attenti...
[grammar] ~158-~158: The verb “add” needs to be in the to-infinitive form. (MISSING_TO_BEFORE_A_VERB)
Context: ...wise an error will be thrown > if you'd like add a new parameter you can add++to the...
[uncategorized] ~159-~159: A comma might be missing here. (AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)
Context: ...arameter exists, otherwise create a new one you can add a single+to the front o...
[typographical] ~160-~160: The word “otherwise” is an adverb that can’t be used like a conjunction, and therefore needs to be separated from the sentence. (THUS_SENTENCE)
Context: ...t to make sure you've matched the param exactly, otherwise it will simply add a new parameter with...
[uncategorized] ~161-~161: The abbreviation “e.g.” (= for example) requires two periods. (E_G)
Context: ...and the original value won't change. > e.g doingmodel.n_head=3will cause the o...
[uncategorized] ~165-~165: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...d the direct override or the file-based override however you can technically do both via...
[uncategorized] ~175-~175: The abbreviation “e.g.” (= for example) requires two periods. (E_G)
Context: ...g CLI and file-based override syntax > (e.g make suresection.paramdoesn't appea...
[style] ~186-~186: Consider a shorter alternative to avoid wordiness. (IN_ORDER_TO_PREMIUM)
Context: ...estimators/segementors. This means that in order to run inference(tracking) with our model ...
[uncategorized] ~186-~186: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...der to run inference(tracking) with our model you need 3 things. 1. A pretrained mod...
[uncategorized] ~191-~191: A comma might be missing here. (AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)
Context: ...ported file types. - For microscopy data we currently support.tiffiles. Vide...
[style] ~192-~192: Did you mean ‘different from’? ‘Different than’ is often considered colloquial style. (DIFFERENT_THAN)
Context: ... This labels file is slightly different than in training because we only need detect...
[uncategorized] ~192-~192: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...ing because we only need detections for tracking since the tracks will of course come fr...
[typographical] ~192-~192: Consider adding two commas here. (OF_COURSE_COMMA)
Context: ...tions for tracking since the tracks will of course come from our model predictions. We st...
[uncategorized] ~194-~194: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...g SLEAP and TrackMate to generate these labels however this time you would only need t...
[uncategorized] ~194-~194: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...d your detections if you'd like to. For TrackMate we recommend using the "spots table" la...
[uncategorized] ~199-~199: The grammatical number of this noun doesn’t look right. Consider replacing it. (AI_EN_LECTOR_REPLACEMENT_NOUN_NUMBER)
Context: ... used for training. 1. Match video and labels file stems. Because our dataloaders jus...
[style] ~199-~199: Consider a shorter alternative to avoid wordiness. (IN_ORDER_TO_PREMIUM)
Context: ...lp, file2.slp], [vid1.mp4, vid2.mp4]`). In order to make programmatic file searching easy i...
[uncategorized] ~199-~199: A comma might be missing here. (AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)
Context: ...der to make programmatic file searching easy its best to save your labels and vid fi...
[uncategorized] ~199-~199: “its” (belonging to it) seems less likely than “it’s” (it is) (AI_HYDRA_LEO_CPT_ITS_ITIS)
Context: ...o make programmatic file searching easy its best to save your labels and vid files ...
[style] ~199-~199: ‘vid’ is informal. Consider replacing it. (VID)
Context: ...g easy its best to save your labels and vid files with the same stem so that you ca...
[uncategorized] ~199-~199: “its” (belonging to it) seems less likely than “it’s” (it is) (AI_HYDRA_LEO_CPT_ITS_ITIS)
Context: ...ensure the ordering will be consistent. Its also just best practice so you know whi...
[uncategorized] ~199-~199: It seems likely that a singular genitive (’s) apostrophe is missing. (AI_HYDRA_LEO_APOSTROPHE_S_XS)
Context: ...best practice so you know which video a labels file corresponds to. 2. Store correspon...
[misspelling] ~219-~219: Use “an” instead of ‘a’ if the following word starts with a vowel sound, e.g. ‘an article’, ‘an hour’. (EN_A_VS_AN)
Context: ...et up a config file that specifies 1. ackpt_path2. aout_dir3. a `Tracke...
[misspelling] ~220-~220: Use “an” instead of ‘a’ if the following word starts with a vowel sound, e.g. ‘an article’, ‘an hour’. (EN_A_VS_AN)
Context: ...le that specifies 1. ackpt_path2. aout_dir3. aTrackerconfig 4. a `d...
[uncategorized] ~228-~228: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...e. ### Step 3 Run Inference Just like training we can use the hydra syntax for specify...
[uncategorized] ~228-~228: A comma may be missing after the conjunctive/linking adverb ‘Thus’. (SENT_START_CONJUNCTIVE_LINKING_ADVERB_COMMA)
Context: ...x for specifying arguments via the cli. Thus you can run inference via: ```bash dre...
[uncategorized] ~241-~241: Use a comma before ‘but’ if it connects two independent clauses (unless they are closely connected and short). (COMMA_COMPOUND_SENTENCE)
Context: ...ased override rather than the file based but you're more than welcome to do so. In ...
[style] ~242-~242: Consider a shorter alternative to avoid wordiness. (IN_ORDER_TO_PREMIUM)
Context: ...but you're more than welcome to do so. In order to override params via the CLI, we can use...
[uncategorized] ~247-~247: The abbreviation “e.g.” (= for example) requires two periods. (E_G)
Context: ...[CONFIG_STEM] section.param=[VALUE] ``` e.g if I want to set the window size of the...
[typographical] ~253-~253: The word “otherwise” is an adverb that can’t be used like a conjunction, and therefore needs to be separated from the sentence. (THUS_SENTENCE)
Context: ...pecified in the config it will save to./[OUTDIR]/[VID_NAME].dreem_inference.slp, otherwise it will just save to `./results/[VID_NA...README.md
[style] ~43-~43: The word ‘thru’ is informal. Consider replacing it with “through”. (THRU)
Context: ...e a basic workflow from setting up data thru training and running inference. Regardl...
[uncategorized] ~43-~43: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...ta thru training and running inference. Regardless if you're only interested in running in...
[style] ~43-~43: The word ‘thru’ is informal. Consider replacing it with “through”. (THRU)
Context: ...ference, we recommend at least skimming thru the entire tutorial as there may be use...
[uncategorized] ~51-~51: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ... respective docs to get some familiarity but is not necessary. ### Setup #### Step ...
[style] ~75-~75: Consider a shorter alternative to avoid wordiness. (IN_ORDER_TO_PREMIUM)
Context: ...#### Step 1: Generate Ground Truth Data In order to train a model you need 2 things. 1. A v...
[uncategorized] ~76-~76: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...e Ground Truth Data In order to train a model you need 2 things. 1. A video. - Fo...
[uncategorized] ~78-~78: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ... 2 things. 1. A video. - For animal data see the [imageio](https://imageio.rea...
[uncategorized] ~79-~79: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...ported file types. - For microscopy data we currently support.tiffiles. Vide...
[uncategorized] ~85-~85: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...Initial labels To generate your initial labels we recommend a couple methods. - For a...
[grammar] ~85-~85: Using ‘couple’ without ‘of’ is considered to be informal. (PLENTY_OF_NOUNS)
Context: ...rate your initial labels we recommend a couple methods. - For animal pose-estimation, we high...
[uncategorized] ~86-~86: Write this as one word if you mean the noun “workflow”. (WORK_COMPOUNDS)
Context: ...s://sleap.ai) and running through their work flow. - For microscopy tracking, check out...
[uncategorized] ~89-~89: The abbreviation “e.g.” (= for example) requires two periods. (E_G)
Context: ... you'd like to use a different method, (e.g DeepLabCut or ilastik etc), the easiest...
[style] ~89-~89: In American English, abbreviations like “etc.” require a period. (ETC_PERIOD)
Context: ...rent method, (e.g DeepLabCut or ilastik etc), the easiest way to make your data com...
[uncategorized] ~89-~89: Use a comma before ‘but’ if it connects two independent clauses (unless they are closely connected and short). (COMMA_COMPOUND_SENTENCE_2)
Context: ...ively, you can write a custom dataloader but that will take significantly more overh...
[uncategorized] ~91-~91: If this is a compound adjective that modifies the following noun, use a hyphen. (EN_COMPOUND_ADJECTIVE_INTERNAL)
Context: ... thing to train a good model is to have high quality data. In our case good quality means tw...
[typographical] ~91-~91: At the start of a sentence, a comma is usually required for the expression ‘In “our case,”’. (COMMA_OF_IN_PRPS_CASE)
Context: ... model is to have high quality data. In our case good quality means two things: 1. No i...
[style] ~95-~95: To elevate your writing, try using a synonym here. (HARD_TO)
Context: ...o avoid having detection coordinates be hard to distinguish. For instance, with anim...
[formatting] ~95-~95: Consider inserting a comma before ‘however’. (HOWEVER_MISSING_COMMA)
Context: ...ld be as tight as possible. This may be unavoidable however, in cases of occlusion and overlap. See ...
[style] ~100-~100: Consider a shorter alternative to avoid wordiness. (IN_ORDER_TO_PREMIUM)
Context: ...ting data to a SLEAP compatible format. In order to use the SLEAP gui you'll need to have y...
[uncategorized] ~101-~101: A comma may be missing after the conjunctive/linking adverb ‘Otherwise’. (SENT_START_CONJUNCTIVE_LINKING_ADVERB_COMMA)
Context: ... you can start proofreading right away. Otherwise if you used a different system (e.g Dee...
[uncategorized] ~101-~101: The abbreviation “e.g.” (= for example) requires two periods. (E_G)
Context: ...herwise if you used a different system (e.g DeepLabCut) check out [`sleap.io.conver...
[grammar] ~105-~105: Using ‘couple’ without ‘of’ is considered to be informal. (PLENTY_OF_NOUNS)
Context: ...e recommend organizing your data with a couple things in mind. 1. Match video and labels fil...
[style] ~107-~107: Consider a shorter alternative to avoid wordiness. (IN_ORDER_TO_PREMIUM)
Context: ...lp, file2.slp], [vid1.mp4, vid2.mp4]`). In order to make programmatic file searching easy i...
[uncategorized] ~107-~107: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...der to make programmatic file searching easy its best to save your labels and vid fi...
[uncategorized] ~107-~107: “its” (belonging to it) seems less likely than “it’s” (it is) (AI_HYDRA_LEO_CPT_ITS_ITIS)
Context: ...o make programmatic file searching easy its best to save your labels and vid files ...
[style] ~107-~107: ‘vid’ is informal. Consider replacing it. (VID)
Context: ...g easy its best to save your labels and vid files with the same stem so that you ca...
[uncategorized] ~107-~107: “its” (belonging to it) seems less likely than “it’s” (it is) (AI_HYDRA_LEO_CPT_ITS_ITIS)
Context: ...ensure the ordering will be consistent. Its also just best practice so you know whi...
[uncategorized] ~107-~107: It seems likely that a singular genitive (’s) apostrophe is missing. (AI_HYDRA_LEO_APOSTROPHE_S_XS)
Context: ...best practice so you know which video a labels file corresponds to. 2. Store correspon...
[style] ~141-~141: Consider replacing this word to strengthen your wording. (AND_THAT)
Context: ...train script if you're an advanced user and would like to have some additional flex...
[grammar] ~145-~145: The word “checkout” is a noun. The verb is spelled with a space. (NOUN_VERB_CONFUSION)
Context: ... parameters needed for training. Please checkout the [README](dreem/training/configs/R...
[uncategorized] ~156-~156: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...nside my/home/aaprasad/dreem_configsdirectory I can call ```bash dreem-train --config...
[uncategorized] ~161-~161: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...relative paths as well but may be a bit riskier so we recommend absolute paths whenever...
[grammar] ~175-~175: It seems like one article is redundant in this context. (A_RB_A_JJ_NN)
Context: .../dreem_configs` directory that contains a only a small selection of parameters that I'd like t...
[uncategorized] ~187-~187: The abbreviation “e.g.” (= for example) requires two periods. (E_G)
Context: ...E_CONFIG_STEM] section.param=value ``` e.g If now I want to override a couple para...
[grammar] ~188-~188: Using ‘couple’ without ‘of’ is considered to be informal. (PLENTY_OF_NOUNS)
Context: ...ue ``` e.g If now I want to override a couple parameters again, say change the number of attenti...
[grammar] ~194-~194: The verb “add” needs to be in the to-infinitive form. (MISSING_TO_BEFORE_A_VERB)
Context: ...wise an error will be thrown > if you'd like add a new parameter you can add++to the...
[typographical] ~196-~196: The word “otherwise” is an adverb that can’t be used like a conjunction, and therefore needs to be separated from the sentence. (THUS_SENTENCE)
Context: ...t to make sure you've matched the param exactly, otherwise it will simply add a new parameter with...
[uncategorized] ~197-~197: The abbreviation “e.g.” (= for example) requires two periods. (E_G)
Context: ...and the original value won't change. > e.g doingmodel.n_head=3will cause the o...
[uncategorized] ~211-~211: The abbreviation “e.g.” (= for example) requires two periods. (E_G)
Context: ...g CLI and file-based override syntax > (e.g make suresection.paramdoesn't appea...
[uncategorized] ~222-~222: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...tem is that we decouple detection and tracking so you can use off-the-shelf high perfo...
[style] ~222-~222: Consider a shorter alternative to avoid wordiness. (IN_ORDER_TO_PREMIUM)
Context: ...estimators/segementors. This means that in order to run inference(tracking) with our model ...
[uncategorized] ~225-~225: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...kptfile. 2. A video. - For animal data see the [imageio`](https://imageio.rea...
[uncategorized] ~226-~226: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...ported file types. - For microscopy data we currently support.tiffiles. Vide...
[style] ~227-~227: Did you mean ‘different from’? ‘Different than’ is often considered colloquial style. (DIFFERENT_THAN)
Context: ... This labels file is slightly different than in training because we only need detect...
[typographical] ~227-~227: Consider adding two commas here. (OF_COURSE_COMMA)
Context: ...tions for tracking since the tracks will of course come from our model predictions. We st...
[style] ~233-~233: Consider a shorter alternative to avoid wordiness. (IN_ORDER_TO_PREMIUM)
Context: ...lp, file2.slp], [vid1.mp4, vid2.mp4]`). In order to make programmatic file searching easy i...
[uncategorized] ~233-~233: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: ...der to make programmatic file searching easy its best to save your labels and vid fi...
[uncategorized] ~233-~233: “its” (belonging to it) seems less likely than “it’s” (it is) (AI_HYDRA_LEO_CPT_ITS_ITIS)
Context: ...o make programmatic file searching easy its best to save your labels and vid files ...
[style] ~233-~233: ‘vid’ is informal. Consider replacing it. (VID)
Context: ...g easy its best to save your labels and vid files with the same stem so that you ca...
[uncategorized] ~233-~233: “its” (belonging to it) seems less likely than “it’s” (it is) (AI_HYDRA_LEO_CPT_ITS_ITIS)
Context: ...ensure the ordering will be consistent. Its also just best practice so you know whi...
[uncategorized] ~233-~233: It seems likely that a singular genitive (’s) apostrophe is missing. (AI_HYDRA_LEO_APOSTROPHE_S_XS)
Context: ...best practice so you know which video a labels file corresponds to. 2. Store correspon...
[misspelling] ~252-~252: Use “an” instead of ‘a’ if the following word starts with a vowel sound, e.g. ‘an article’, ‘an hour’. (EN_A_VS_AN)
Context: ...set up a config file that specifies 1. ackpt_path2. aout_dir3. a `Tracke...
[misspelling] ~253-~253: Use “an” instead of ‘a’ if the following word starts with a vowel sound, e.g. ‘an article’, ‘an hour’. (EN_A_VS_AN)
Context: ...ile that specifies 1. ackpt_path2. aout_dir3. aTrackerconfig 4. a `d...
[uncategorized] ~261-~261: Possible missing comma found. (AI_HYDRA_LEO_MISSING_COMMA)
Context: .... #### Step 3 Run Inference Just like training we can use the hydra syntax for specify...
[uncategorized] ~261-~261: A comma may be missing after the conjunctive/linking adverb ‘Thus’. (SENT_START_CONJUNCTIVE_LINKING_ADVERB_COMMA)
Context: ...x for specifying arguments via the cli. Thus you can run inference via: ```bash dre...
[uncategorized] ~274-~274: Use a comma before ‘but’ if it connects two independent clauses (unless they are closely connected and short). (COMMA_COMPOUND_SENTENCE)
Context: ...ased override rather than the file based but you're more than welcome to do so. In ...
[style] ~275-~275: Consider a shorter alternative to avoid wordiness. (IN_ORDER_TO_PREMIUM)
Context: ...but you're more than welcome to do so. In order to override params via the CLI, we can use...
[uncategorized] ~280-~280: The abbreviation “e.g.” (= for example) requires two periods. (E_G)
Context: ...[CONFIG_STEM] section.param=[VALUE] ``` e.g if I want to set the window size of the...
[typographical] ~286-~286: The word “otherwise” is an adverb that can’t be used like a conjunction, and therefore needs to be separated from the sentence. (THUS_SENTENCE)
Context: ...pecified in the config it will save to./[OUTDIR]/[VID_NAME].dreem_inference.slp, otherwise it will just save to `./results/[VID_NA...
Additional comments not posted (52)
environment_osx-arm64.yml (1)
9-9: Ensure compatibility with Python 3.11 for all dependencies.environment_cpu.yml (1)
10-10: Ensure compatibility with Python 3.11 for all dependencies, especiallyconda-forge::opencv <4.9.0.docs/index.md (1)
5-5: Added GitHub stars badge to enhance the visibility and credibility of the project.pyproject.toml (1)
21-22: Updated Python version classifiers to include Python 3.10 and 3.11.dreem/datasets/eval_dataset.py (1)
28-28: Updated the__getitem__method to handle merging of ground truth and predicted datasets. Ensure that the error handling for index mismatches is robust.dreem/io/track.py (2)
3-3: Addedfrom __future__ import annotationsto use postponed evaluation of annotations.
80-80: Updated the__getitem__method to handle both single and list indices. Ensure that the type checking is robust and consider adding more specific error messages.Tools
Ruff
80-80: Remove quotes from type annotation (UP037)
Remove quotes
80-80: Undefined name
Instance(F821)
80-80: Remove quotes from type annotation (UP037)
Remove quotes
80-80: Undefined name
Instance(F821)dreem/training/train.py (2)
18-20: Logging setup looks good and follows best practices.
49-50: Good use of logging for debugging.dreem/inference/track.py (2)
14-16: Logging setup looks good and follows best practices.
81-81: Ensure proper logging of video information.dreem/models/visual_encoder.py (3)
3-3: Import statements are organized and clear.
27-27: Proper use of type hints and default arguments in constructor.
60-60: Ensure that the feature extractor selection handles different backends correctly.dreem/models/global_tracking_transformer.py (1)
Line range hint
15-26: Proper use of type hints and default arguments in constructor.dreem/models/gtr_runner.py (3)
14-14: Logger setup is appropriate for the module scope.
204-207: Excellent use of logging for exception handling. This will aid in debugging by providing context about the failure.
36-42: Ensure that the type annotations are consistent across the project, especially for dictionary types.dreem/inference/metrics.py (2)
7-7: Logger setup is appropriate for the module scope.
45-46: Good use of logging to handle cases where no instances are detected.dreem/inference/track_queue.py (2)
7-7: Logger setup is appropriate for the module scope.
181-181: Proper use of logging to handle exceptions when a track ID is not found in the queue.dreem/io/visualize.py (2)
14-14: Logger setup is appropriate for the module scope.
328-330: Effective logging for success and error scenarios in video annotation.dreem/io/association_matrix.py (3)
7-7: Logging module imported for better logging practices.
24-24: Updated type annotations using modern Python syntax for union types.
Line range hint
226-251: Improved error handling by logging exceptions before re-raising them.dreem/datasets/sleap_dataset.py (2)
9-9: Logging module imported for better logging practices.
26-33: Updated type annotations using modern Python syntax for union types and added more descriptive comments for parameters.dreem/models/embedding.py (1)
5-5: Logging module imported for better logging practices.dreem/io/config.py (4)
52-52: This method correctly implements configuration loading from YAML files.
76-76: Proper handling of empty orNonehyperparameters with appropriate logging.
162-168: Proper use of globbing to retrieve data paths and appropriate logging of the process.
19-19: Consider initializingparams_cfgin the method signature to ensure it's defined before use.- def __init__(self, cfg: DictConfig, params_cfg: DictConfig | None = None): + def __init__(self, cfg: DictConfig, params_cfg: DictConfig | None = None):Likely invalid or redundant comment.
docs/usage.md (2)
115-115: Ensure consistency in command examples and clarify the use of hydra override syntax.Also applies to: 121-121, 136-136, 142-142, 149-149, 155-155, 167-167, 171-171
231-231: Review the command syntax fordreem-trackto ensure it aligns with the project's standards.Also applies to: 237-237, 246-246, 250-250
Verification successful
The command syntax for
dreem-trackin thedocs/usage.mdfile appears consistent across multiple instances. Each instance follows the patterndreem-track --config-base=[CONFIG_DIR] --config-name=[CONFIG_STEM]with additional parameters as needed.
- Line 231:
dreem-track --config-base=[CONFIG_DIR] --config-name=[CONFIG_STEM]- Line 237:
dreem-track --config-base=/home/aaprasad/dreem_configs --config-name=track- Line 246:
dreem-track --config-base=[CONFIG_DIR] --config-name=[CONFIG_STEM] section.param=[VALUE]- Line 250:
dreem-track --config-base=/home/aaprasad/dreem_configs --config-name=track ckpt_path="/home/aaprasad/models/new_best.ckpt" tracker.window_size=32The syntax is consistent and aligns with the project's standards.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Check for consistency in the command syntax for `dreem-track`. grep 'dreem-track --config-base=' docs/usage.mdLength of output: 427
dreem/io/frame.py (4)
12-12: Logger setup looks good and follows best practices.
15-15: The function_to_tensoris well-documented and correctly handles different data types. Good use of type annotations.
100-100: The methodtois well-implemented with comprehensive handling of different types and properties. Good use of type annotations and device handling.
135-137: The methodfrom_slpis well-documented and correctly convertssio.LabeledFrametodreem.io.Frame. The use of unpacking inimg_shapeis a nice touch for handling different dimensions.dreem/inference/tracker.py (4)
5-5: Import ofloggingmodule is appropriate for the logging improvements described in the PR.
15-16: Initialization ofloggeris correctly done at the module level, which is a good practice for centralized logging.
27-29: The use of union types with|for optional parameters is a modern Python feature that enhances readability and type clarity.
153-153: The addition of debug logging statements is a good practice for tracing and diagnosing issues during development and maintenance phases.Also applies to: 159-159, 168-170, 243-243, 251-251, 293-295, 334-335, 448-450, 453-453, 456-456
dreem/models/transformer.py (2)
42-42: The addition ofembedding_metaand related logic for handling positional embeddings is a significant enhancement, allowing for more flexible configuration of the model.
145-145: The type hint forquery_instancesnow correctly allows forNoneas a valid type, aligning with the function's capability to handle cases where no query instances are provided.Tools
Ruff
145-145: Undefined name
dreem(F821)dreem/io/instance.py (6)
7-7: Ensure that theloggingmodule is used consistently throughout the file for debugging and error messages.
9-9: The use ofSelffromtypingis appropriate for methods that return an instance of the class they are defined in.
11-11: Proper initialization of the logger for this module. Good practice for consistent logging.
14-14: The_to_tensorfunction is well-documented and handles different types of input correctly.
92-92: The use of union types for optional fields is a good practice for clarity and type safety.Also applies to: 93-93, 95-95
137-137: Thetomethod is well-implemented, ensuring the instance can be moved to a different device or dtype efficiently.
| print(asso_output) | ||
| print(traj_score) | ||
| raise (e) | ||
| match_i, match_j = linear_sum_assignment((-traj_score)) |
There was a problem hiding this comment.
Remove extraneous parentheses to improve readability.
- match_i, match_j = linear_sum_assignment((-traj_score))
+ match_i, match_j = linear_sum_assignment(-traj_score)Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| match_i, match_j = linear_sum_assignment((-traj_score)) | |
| match_i, match_j = linear_sum_assignment(-traj_score) |
Tools
Ruff
434-434: Avoid extraneous parentheses (UP034)
Remove extraneous parentheses
| @@ -120,8 +123,7 @@ def track( | |||
| instances_pred = self.sliding_inference(model, frames) | |||
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| if not self.persistent_tracking: | |||
| if self.verbose: | |||
| warnings.warn(f"Clearing Queue after tracking") | |||
| logger.debug(f"Clearing Queue after tracking") | |||
There was a problem hiding this comment.
Remove the unnecessary f prefix from the debug log statement as it does not contain any placeholders.
- logger.debug(f"Clearing Queue after tracking")
+ logger.debug("Clearing Queue after tracking")Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| logger.debug(f"Clearing Queue after tracking") | |
| logger.debug("Clearing Queue after tracking") |
Tools
Ruff
126-126: f-string without any placeholders (F541)
Remove extraneous
fprefix
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|
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| logger.debug( | ||
| f"Initializing track on clip ind {batch_idx} frame {frame_to_track.frame_id.item()}" | ||
| ) | ||
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| curr_track_id = 0 | ||
| for i, instance in enumerate(frames[batch_idx].instances): |
There was a problem hiding this comment.
Loop control variables i are not used within the loop body. Consider renaming them to _i to indicate that they are intentionally unused.
- for i, instance in enumerate(frames[batch_idx].instances):
+ for _i, instance in enumerate(frames[batch_idx].instances):Also applies to: 177-177
Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| for i, instance in enumerate(frames[batch_idx].instances): | |
| for _i, instance in enumerate(frames[batch_idx].instances): |
Tools
Ruff
173-173: Loop control variable
inot used within loop body (B007)Rename unused
ito_i
| @@ -237,7 +240,7 @@ def to_slp( | |||
| track_lookup, | |||
| ) | |||
| except Exception as e: | |||
| print( | |||
| logger.exception( | |||
There was a problem hiding this comment.
Use raise ... from e to provide more context about the exception chain.
- raise RuntimeError(f"Failed to convert to sio.PredictedInstance: {e}")
+ raise RuntimeError(f"Failed to convert to sio.PredictedInstance: {e}") from eCommittable suggestion
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Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| logger.exception( | |
| raise RuntimeError(f"Failed to convert to sio.PredictedInstance: {e}") from e |
| @@ -16,3 +17,18 @@ | |||
| # from .training import run | |||
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| from dreem.inference.tracker import Tracker | |||
There was a problem hiding this comment.
Remove unused import dreem.inference.tracker.Tracker.
- from dreem.inference.tracker import TrackerCommittable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| from dreem.inference.tracker import Tracker |
Tools
Ruff
19-19:
dreem.inference.tracker.Trackerimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
| @@ -1,5 +1,6 @@ | |||
| """Top-level package for dreem.""" | |||
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|||
| import logging.config | |||
| from dreem.version import __version__ | |||
There was a problem hiding this comment.
Remove unused import dreem.version.__version__.
- from dreem.version import __version__Committable suggestion
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Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| from dreem.version import __version__ |
Tools
Ruff
4-4:
dreem.version.__version__imported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
| logging_cfg = yaml.load(stream, Loader=yaml.FullLoader) | ||
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| logging.config.dictConfig(logging_cfg) | ||
| logger = logging.getLogger("dreem") |
There was a problem hiding this comment.
Remove assignment to unused variable logger.
- logger = logging.getLogger("dreem")Committable suggestion
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Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| logger = logging.getLogger("dreem") |
Tools
Ruff
34-34: Local variable
loggeris assigned to but never used (F841)Remove assignment to unused variable
logger
| @@ -1,5 +1,6 @@ | |||
| """Top-level package for dreem.""" | |||
|
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|||
| import logging.config | |||
There was a problem hiding this comment.
Remove unused import logging.config.
- import logging.configCommittable suggestion
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| import logging.config |
Tools
Ruff
3-3:
logging.configimported but unused; consider removing, adding to__all__, or using a redundant alias (F401)
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| package_directory = os.path.dirname(os.path.abspath(__file__)) | ||
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| with open(os.path.join(package_directory, "..", "logging.yaml"), "r") as stream: |
There was a problem hiding this comment.
Remove unnecessary open mode parameters from the file open function.
- with open(os.path.join(package_directory, "..", "logging.yaml"), "r") as stream:
+ with open(os.path.join(package_directory, "..", "logging.yaml")) as stream:Committable suggestion
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Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| with open(os.path.join(package_directory, "..", "logging.yaml"), "r") as stream: | |
| with open(os.path.join(package_directory, "..", "logging.yaml")) as stream: |
Tools
Ruff
30-30: Unnecessary open mode parameters (UP015)
Remove open mode parameters
| logger.info(f"Using the following params for tracker:") | ||
| logger.info(model.tracker_cfg) |
There was a problem hiding this comment.
Remove extraneous f prefix from logging statement.
- logger.info(f"Using the following params for tracker:")
+ logger.info("Using the following params for tracker:")Committable suggestion
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Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| logger.info(f"Using the following params for tracker:") | |
| logger.info(model.tracker_cfg) | |
| logger.info("Using the following params for tracker:") | |
| logger.info(model.tracker_cfg) |
Tools
Ruff
119-119: f-string without any placeholders (F541)
Remove extraneous
fprefix
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… of `typing.Union` and referring to standard collections directly rather than `typing.Collection`
* replace print statements and warnings with logger emissions * get rid of unnecessary/commented out exceptions/print statements
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Actionable comments posted: 5
Outside diff range, codebase verification and nitpick comments (1)
dreem/inference/track.py (1)
117-120: Remove extraneousfprefix from logging statement.The
fprefix is unnecessary in the logging statement.- logger.info(f"Using the following params for tracker:") + logger.info("Using the following params for tracker:")Tools
Ruff
119-119: f-string without any placeholders
Remove extraneous
fprefix(F541)
Review details
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Files selected for processing (21)
- dreem/init.py (2 hunks)
- dreem/datasets/data_utils.py (2 hunks)
- dreem/datasets/microscopy_dataset.py (1 hunks)
- dreem/datasets/sleap_dataset.py (2 hunks)
- dreem/inference/metrics.py (3 hunks)
- dreem/inference/track.py (5 hunks)
- dreem/inference/track_queue.py (5 hunks)
- dreem/inference/tracker.py (10 hunks)
- dreem/io/association_matrix.py (2 hunks)
- dreem/io/config.py (5 hunks)
- dreem/io/frame.py (3 hunks)
- dreem/io/instance.py (3 hunks)
- dreem/io/visualize.py (5 hunks)
- dreem/models/embedding.py (2 hunks)
- dreem/models/gtr_runner.py (2 hunks)
- dreem/models/model_utils.py (1 hunks)
- dreem/training/init.py (1 hunks)
- dreem/training/losses.py (1 hunks)
- dreem/training/train.py (4 hunks)
- logging.yaml (1 hunks)
- tests/test_datasets.py (1 hunks)
Files skipped from review due to trivial changes (3)
- dreem/datasets/data_utils.py
- dreem/datasets/microscopy_dataset.py
- tests/test_datasets.py
Additional context used
yamllint
logging.yaml
[error] 36-36: trailing spaces
(trailing-spaces)
Ruff
dreem/__init__.py
3-3:
logging.configimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
34-34: Local variable
loggeris assigned to but never usedRemove assignment to unused variable
logger(F841)
dreem/inference/track.py
119-119: f-string without any placeholders
Remove extraneous
fprefix(F541)
dreem/inference/tracker.py
126-126: f-string without any placeholders
Remove extraneous
fprefix(F541)
Additional comments not posted (61)
dreem/training/__init__.py (1)
1-1: Verify the impact of removing thetrainimport.The
trainfunction import has been removed. Ensure that this change does not break any existing functionality and that users are informed of how to access thetrainfunctionality if it has been moved.dreem/__init__.py (6)
3-3: Remove unused importlogging.config.The
logging.configimport is unused and should be removed.Tools
Ruff
3-3:
logging.configimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
4-4: Remove unused importdreem.version.__version__.The
__version__import is unused and should be removed.Tools
Ruff
4-4:
dreem.version.__version__imported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
19-19: Remove unused importdreem.inference.tracker.Tracker.The
Trackerimport is unused and should be removed.Tools
Ruff
19-19:
dreem.inference.tracker.Trackerimported but unused; consider removing, adding to__all__, or using a redundant alias(F401)
30-30: Remove unnecessary open mode parameters from the file open function.The open mode parameters are unnecessary and should be removed.
34-34: Remove assignment to unused variablelogger.The
loggervariable is assigned but never used.Tools
Ruff
34-34: Local variable
loggeris assigned to but never usedRemove assignment to unused variable
logger(F841)
22-34: LGTM! Thesetup_loggingfunction is a good addition.The new
setup_loggingfunction is well-implemented and enhances the logging capabilities.Tools
Ruff
34-34: Local variable
loggeris assigned to but never usedRemove assignment to unused variable
logger(F841)
dreem/training/train.py (3)
49-53: LGTM!The changes improve the logging mechanism by replacing
logger.debugandlogger.infocalls.
Line range hint
78-90:
LGTM!The change in the logger variable name from
loggertorun_loggerhelps avoid potential conflicts and provides clearer context.
18-20: Verify logger configuration.Ensure that the logger is properly configured with appropriate handlers and formatters.
dreem/inference/track.py (4)
81-81: LGTM!The changes improve the logging mechanism by replacing
logger.infocalls.
108-108: LGTM!The changes improve the logging mechanism by replacing
logger.infocalls.
141-141: LGTM!The changes improve the logging mechanism by replacing
logger.infocalls.
14-16: Verify logger configuration.Ensure that the logger is properly configured with appropriate handlers and formatters.
dreem/models/gtr_runner.py (3)
5-5: LGTM!The import statement for the
loggingmodule is necessary for adding logging functionality.
14-14: LGTM!The logger instance is correctly initialized for logging messages.
204-207: LGTM! But verify logger configuration.The added logging for exceptions improves traceability and debugging. Ensure that the logger is properly configured to capture and store these logs.
dreem/inference/metrics.py (3)
7-7: LGTM!The import statement for the
loggingmodule is necessary for adding logging functionality.
10-10: LGTM!The logger instance is correctly initialized for logging messages.
45-46: LGTM!The added debug log statement improves observability without altering the core logic.
dreem/inference/track_queue.py (5)
7-10: LGTM! Logger initialization is correct.The logger is correctly initialized for the
dreem.inferencenamespace.
181-181: LGTM! Exception handling with logger is appropriate.The use of
logger.exception()provides a detailed stack trace, which is useful for debugging.
217-219: LGTM! Debug logging is appropriate.The use of
logger.debug()for logging the creation of a new track is appropriate for debug-level information.
293-295: LGTM! Debug logging is appropriate.The use of
logger.debug()for logging the gap increment information is appropriate for debug-level information.
305-307: LGTM! Debug logging is appropriate.The use of
logger.debug()for logging the termination of a track is appropriate for debug-level information.dreem/io/visualize.py (3)
14-16: LGTM! Logger initialization is correct.The logger is correctly initialized for the
dreem.ionamespace.
267-267: LGTM! Exception handling with logger is appropriate.The use of
logger.exception()provides a detailed stack trace, which is useful for debugging.
328-330: LGTM! Info and error logging are appropriate.The use of
logger.info()for logging success andlogger.error()for logging failure is appropriate for information and error-level messages.dreem/io/association_matrix.py (2)
7-12: LGTM! Logger initialization is correct.The logger is correctly initialized for the
dreem.ionamespace.
247-251: LGTM! Exception handling with logger is appropriate.The use of
logger.exception()provides a detailed stack trace, which is useful for debugging.dreem/datasets/sleap_dataset.py (3)
9-9: LGTM! Import statement changes are correct.The
loggingmodule is correctly imported, and the unusedwarningsmodule is removed.
14-14: LGTM! Logger instance creation is correct.The logger instance for the
dreem.datasetsnamespace is correctly created.
170-172: LGTM! Logging warning is correctly implemented.The
dreem/models/embedding.py (3)
5-5: LGTM! Import statement changes are correct.The
loggingmodule is correctly imported.
8-8: LGTM! Logger instance creation is correct.The logger instance for the
dreem.modelsnamespace is correctly created.
287-290: LGTM! Logging exception is correctly implemented.The
logger.exception, enhancing error handling.dreem/io/config.py (10)
8-8: LGTM! Import statement changes are correct.The
loggingmodule is correctly imported.
13-13: LGTM! Logger instance creation is correct.The logger instance for the
dreem.ionamespace is correctly created.
31-31: LGTM! Logging info is correctly implemented.The
logger.info, enhancing logging practices.
37-37: LGTM! Logging info is correctly implemented.The
logger.info, enhancing logging practices.
76-76: LGTM! Logging warning is correctly implemented.The
logger.warning, enhancing logging practices.
82-82: LGTM! Logging exception is correctly implemented.The
logger.exception, enhancing error handling.
164-164: LGTM! Logging debug is correctly implemented.The
logger.debug, enhancing logging practices.
166-166: LGTM! Logging debug is correctly implemented.The
logger.debug, enhancing logging practices.
168-168: LGTM! Logging debug is correctly implemented.The
logger.debug, enhancing logging practices.
366-366: LGTM! Logging exception is correctly implemented.The
logger.exception, enhancing error handling.dreem/io/frame.py (2)
417-419: Enhanced error logging withlogger.exception.The use of
logger.exceptionimproves error handling by logging the exception details, which is a best practice for maintainability and debuggability.
517-518: Simplifiedget_cropsmethod.The removal of the try-except block and directly returning the concatenated tensor simplifies the method, assuming the presence of instances is already verified by
has_instances.dreem/inference/tracker.py (11)
126-127: Improved logging intrackmethod.The use of
logger.debugto log the message about clearing the queue after tracking improves logging practices.Tools
Ruff
126-126: f-string without any placeholders
Remove extraneous
fprefix(F541)
153-159: Improved logging insliding_inferencemethod.The use of
logger.debugto log messages about the current number of tracks and the resetting of the track queue improves logging practices.
167-170: Improved logging insliding_inferencemethod.The use of
logger.debugto log messages about initializing tracks improves logging practices.
243-243: Improved logging in_run_global_trackermethod.The use of
logger.debugto log the frame ID improves logging practices.
251-251: Improved logging in_run_global_trackermethod.The use of
logger.debugto log the total number of instances improves logging practices.
293-295: Improved logging in_run_global_trackermethod.The use of
logger.debugto log the number of non-query and query instances improves logging practices.
334-335: Improved logging in_run_global_trackermethod.The use of
logger.debugto log instance IDs and unique IDs improves logging practices.
448-450: Improved logging in_run_global_trackermethod.The use of
logger.debugto log the assignment of instances to tracks improves logging practices.
453-456: Improved logging in_run_global_trackermethod.The use of
logger.debugto log the creation of new tracks improves logging practices.
434-434: Remove extraneous parentheses to improve readability.Remove the extraneous parentheses around
-traj_scoreto improve readability.- match_i, match_j = linear_sum_assignment((-traj_score)) + match_i, match_j = linear_sum_assignment(-traj_score)
15-16: Set up logger forTrackerclass.The initialization of the logger instance named
loggersets up logging for theTrackerclass, which is a best practice for maintainability and debuggability.dreem/io/instance.py (2)
243-245: Enhanced error logging withlogger.exception.The use of
logger.exceptionimproves error handling by logging the exception details, which is a best practice for maintainability and debuggability.
507-509: Enhanced error logging withlogger.exception.The use of
logger.exceptionimproves error handling by logging the exception details, which is a best practice for maintainability and debuggability.
| target_inst_id = torch.cat( | ||
| [frame.get_gt_track_ids().to(asso_preds[-1].device) for frame in frames] | ||
| ) |
There was a problem hiding this comment.
Reconsider removing error handling.
The removal of the try-except block for handling RuntimeError during the concatenation of track IDs can lead to unhandled exceptions and potential crashes. Ensure that the inputs are always valid or re-add the error handling to manage possible exceptions gracefully.
- target_inst_id = torch.cat(
- [frame.get_gt_track_ids().to(asso_preds[-1].device) for frame in frames]
- )
+ try:
+ target_inst_id = torch.cat(
+ [frame.get_gt_track_ids().to(asso_preds[-1].device) for frame in frames]
+ )
+ except RuntimeError as e:
+ print(f"RuntimeError: {e}")
+ raiseCommittable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| target_inst_id = torch.cat( | |
| [frame.get_gt_track_ids().to(asso_preds[-1].device) for frame in frames] | |
| ) | |
| try: | |
| target_inst_id = torch.cat( | |
| [frame.get_gt_track_ids().to(asso_preds[-1].device) for frame in frames] | |
| ) | |
| except RuntimeError as e: | |
| print(f"RuntimeError: {e}") | |
| raise |
| level: [INFO] | ||
| handlers: [empty] | ||
|
|
||
|
|
There was a problem hiding this comment.
Remove trailing spaces.
Trailing spaces should be removed to adhere to YAML formatting standards.
-
+Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
Tools
yamllint
[error] 36-36: trailing spaces
(trailing-spaces)
| propagate: yes | ||
| parent: [loggers.dreem] | ||
| root: | ||
| level: [INFO] |
There was a problem hiding this comment.
Fix the root logger's level configuration.
The root logger's level should be set as a string, not a list.
- level: [INFO]
+ level: INFOCommittable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| level: [INFO] | |
| level: INFO |
| except Exception as e: | ||
| print(gt_ids) | ||
| raise (e) | ||
| data["gt_ids"] = gt_ids |
There was a problem hiding this comment.
Reconsider removing error handling.
The removal of the try-except block for handling errors during the assignment of gt_ids to the data dictionary can lead to unhandled exceptions and potential crashes. Ensure that the inputs are always valid or re-add the error handling to manage possible exceptions gracefully.
- data["gt_ids"] = gt_ids
+ try:
+ data["gt_ids"] = gt_ids
+ except Exception as e:
+ logger.error(f"Error assigning gt_ids: {e}")
+ raiseCommittable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| data["gt_ids"] = gt_ids | |
| try: | |
| data["gt_ids"] = gt_ids | |
| except Exception as e: | |
| logger.error(f"Error assigning gt_ids: {e}") | |
| raise |
| ref_inds = torch.concat([instance.frame.frame_id for instance in ref_instances]) | ||
|
|
There was a problem hiding this comment.
Reintroduce error handling for robustness.
The removal of the try-except block reduces the robustness against runtime errors. Consider reintroducing error handling to prevent potential crashes.
- ref_inds = torch.concat([instance.frame.frame_id for instance in ref_instances])
+ try:
+ ref_inds = torch.concat([instance.frame.frame_id for instance in ref_instances])
+ except RuntimeError as e:
+ print(f"Error concatenating frame IDs: {e}")
+ raiseCommittable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| ref_inds = torch.concat([instance.frame.frame_id for instance in ref_instances]) | |
| try: | |
| ref_inds = torch.concat([instance.frame.frame_id for instance in ref_instances]) | |
| except RuntimeError as e: | |
| print(f"Error concatenating frame IDs: {e}") | |
| raise |
Here we address #57 by setting up the
loggingmodule indreemSummary by CodeRabbit
Documentation
New Features
dreem-trainanddreem-trackcommands for training and inference.Refactor
printstatements withloggingacross various files for improved logging practices.|syntax for union types.Chores
setup_logging()for logging configuration.