Small improvements to tracking #1894
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WalkthroughThe recent updates to the Sleap framework enhance tracking and inference capabilities. Key modifications include refined configuration options, improved error handling, and better user experience. Changes optimize performance, introduce new reporting features, and streamline object-oriented design, making the system more maintainable and extendable. Changes
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Actionable comments posted: 2
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Configuration used: CodeRabbit UI
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Files selected for processing (8)
- sleap/config/pipeline_form.yaml (2 hunks)
- sleap/gui/learning/dialog.py (1 hunks)
- sleap/gui/widgets/video.py (2 hunks)
- sleap/nn/inference.py (12 hunks)
- sleap/nn/tracking.py (15 hunks)
- sleap/util.py (2 hunks)
- tests/nn/test_tracker_components.py (2 hunks)
- tests/nn/test_tracking_integration.py (4 hunks)
Additional context used
Ruff
sleap/util.py
38-38: Undefined name
Task(F821)
sleap/nn/tracking.py
6-6:
collections.defaultdictimported but unusedRemove unused import:
collections.defaultdict(F401)
614-614: Use
enumerate()for index variablen_processedinforloop(SIM113)
Additional comments not posted (21)
tests/nn/test_tracking_integration.py (3)
22-22: Verify the new expected value in the assertion.The assertion has been changed to expect 8 tracks instead of 27. Ensure that this new expected value is correct based on the updated tracking logic or data.
44-44: Verify thetracker.run_trackermethod invocation.Ensure that the
trackerobject is correctly instantiated and that therun_trackermethod handles the verbosity parameter appropriately.
51-51: Verify thetracker.run_trackermethod invocation.Ensure that the
trackerobject is correctly instantiated and that therun_trackermethod handles the verbosity parameter appropriately.tests/nn/test_tracker_components.py (2)
18-27: Verify the handling of theimg_scaleparameter and the test skipping logic.Ensure that the
img_scaleparameter is correctly applied to thecandidate_makerof the tracker and that the function appropriately skips tests whenimg_scaleis not defined.
47-58: Verify the parameterized tests and the passing of theimg_scaleparameter.Ensure that the parameterized tests are correctly implemented and that the
img_scaleparameter is passed appropriately to therun_tracker_by_namefunction.sleap/config/pipeline_form.yaml (2)
458-463: New configuration optiontracking.save_shifted_instancesadded.This option is well-documented and the default value is set to
true, which aligns with the PR summary indicating the enhancement of instance matching.
457-457: Verify the impact of removingtracking.max_tracking.Ensure that the removal of this configuration option does not negatively impact any existing functionality or user workflows.
Verification successful
Verify the integration of
tracking.max_tracksand check for any remaining references totracking.max_tracking.Ensure that
tracking.max_tracksis correctly integrated into the codebase and that there are no remaining dependencies ontracking.max_tracking.
The integration of
tracking.max_tracksis correct and there are no remaining dependencies ontracking.max_tracking.The replacement of
tracking.max_trackingwithtracking.max_trackshas been successfully integrated into the configuration file, and there are no lingering references to the old configuration.
tracking.max_tracksis correctly defined and used in thepipeline_form.yamlfile.- No remaining references to
tracking.max_trackingwere found in non-YAML files.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the impact of removing `tracking.max_tracking`. # Test: Search for the usage of `tracking.max_tracking`. Expect: No occurrences. rg --type yaml -A 5 $'tracking.max_tracking'Length of output: 421
Script:
#!/bin/bash # Description: Verify the integration of `tracking.max_tracks` and check for any remaining references to `tracking.max_tracking`. # Test 1: Search for the usage of `tracking.max_tracks`. Expect: Relevant occurrences showing correct integration. rg --type yaml -A 5 $'tracking.max_tracks' # Test 2: Search for any remaining references to `tracking.max_tracking` in non-YAML files. Expect: No occurrences. rg --type yaml -v $'tracking.max_tracking'Length of output: 138158
sleap/gui/learning/dialog.py (1)
739-739: Enhanced robustness inrunmethod.The calculation of
no_result_countnow ensures it is non-negative, preventing potential errors in the inference process.sleap/nn/tracking.py (7)
142-142: Verify the impact of changing the default value ofsave_shifted_instances.Changing the default value of
save_shifted_instancestoTruecould impact memory usage and performance. Ensure that this change is intentional and tested.
532-548: LGTM!The new method
run_stepencapsulates the logic for running a single step of tracking.
549-653: LGTM!The new method
run_trackerencapsulates the tracking logic and enhances reporting capabilities based on verbosity levels.Tools
Ruff
614-614: Use
enumerate()for index variablen_processedinforloop(SIM113)
1707-1707: LGTM!The modification aligns with the changes in the
BaseTrackerclass.
520-521: LGTM! Verify the usage of new attributes.The new attributes
verbosityandreport_rateenhance the reporting capabilities.Ensure that these attributes are correctly used and tested throughout the codebase.
Verification successful
Let's modify the script to search for the usage of
verbosityandreport_ratein all Python files without specifying the file type.
The new attributes
verbosityandreport_rateare correctly used and tested throughout the codebase.The attributes are integrated into the main functionality and are covered by tests, ensuring their proper usage.
sleap/nn/tracking.pysleap/nn/inference.pytests/nn/test_tracking_integration.pytests/nn/test_inference.pytests/nn/test_tracker_components.pyScripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the usage of new attributes `verbosity` and `report_rate`. # Test: Search for the usage of `verbosity` and `report_rate`. Expect: Occurrences of the new attributes. rg --type python 'verbosity|report_rate'Length of output: 73
Script:
#!/bin/bash # Description: Verify the usage of new attributes `verbosity` and `report_rate`. # Test: Search for the usage of `verbosity` and `report_rate`. Expect: Occurrences of the new attributes. rg 'verbosity|report_rate' --glob '*.py'Length of output: 3311
742-747: LGTM! Verify the usage of new attributes.The new attributes
verbosityandreport_rateenhance the reporting capabilities.Ensure that these attributes are correctly used and tested throughout the codebase.
Verification successful
The new attributes
verbosityandreport_rateare correctly used and tested throughout the codebase.The search results indicate that both attributes are utilized in various parts of the code, including the
sleap/nn/tracking.py,sleap/nn/inference.py, and several test files. This confirms that the new attributes are integrated and tested.
- Files with relevant usage:
sleap/nn/tracking.pysleap/nn/inference.pytests/nn/test_tracking_integration.pytests/nn/test_tracker_components.pytests/nn/test_inference.pysleap/gui/learning/runners.pydocs/notebooks/Training_and_inference_on_an_example_dataset.ipynbdocs/guides/cli.mdScripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the usage of new attributes `verbosity` and `report_rate`. # Test: Search for the usage of `verbosity` and `report_rate`. Expect: Occurrences of the new attributes. rg --type python 'verbosity|report_rate'Length of output: 73
Script:
#!/bin/bash # Description: Verify the usage of new attributes `verbosity` and `report_rate`. # Test: Search for the usage of `verbosity` and `report_rate` in Python files. rg --type-add 'py:*.py' 'verbosity|report_rate'Length of output: 5005
1484-1489: LGTM! Verify the usage of new attributes.The new attributes
verbosityandreport_rateenhance the reporting capabilities.Ensure that these attributes are correctly used and tested throughout the codebase.
Verification successful
The new attributes
verbosityandreport_rateare correctly used and tested throughout the codebase.The attributes are integrated into multiple files, including
sleap/nn/tracking.py,sleap/nn/inference.py, and various test files, ensuring their proper utilization and testing.
- Files with usage:
sleap/nn/tracking.pysleap/nn/inference.pytests/nn/test_tracker_components.pytests/nn/test_inference.pytests/nn/test_tracking_integration.pyScripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the usage of new attributes `verbosity` and `report_rate`. # Test: Search for the usage of `verbosity` and `report_rate`. Expect: Occurrences of the new attributes. rg --type python 'verbosity|report_rate'Length of output: 73
Script:
#!/bin/bash # Description: Verify the usage of new attributes `verbosity` and `report_rate`. # Test: Search for the usage of `verbosity` and `report_rate`. Expect: Occurrences of the new attributes. rg --type py 'verbosity|report_rate'Length of output: 3307
sleap/gui/widgets/video.py (2)
807-808: Initialization of_down_posis appropriate.The
_down_posattribute is correctly initialized toNoneto ensure it is defined before use.
1032-1032: Robustness improved with_down_poscheck.The check for
_down_posbeingNonebefore comparing it with the current mouse position enhances the robustness of the click detection logic.sleap/nn/inference.py (4)
48-51: Conditional import forcached_propertyis appropriate.The conditional import ensures compatibility with Python versions below 3.8, which is a good practice.
163-165: Use ofcached_propertyforreport_periodis appropriate.The
cached_propertydecorator improves performance by caching the computed value ofreport_period.
5341-5343: Inclusion ofexample_indicesinLabelsReaderinitialization is beneficial.The modification enhances the configurability by allowing more flexible handling of input frames based on user-defined indices.
5437-5440: Inclusion ofprogress_reportingin tracker instantiation is beneficial.The modification allows for more detailed tracking feedback, enhancing the monitoring of the tracking process.
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Files selected for processing (1)
- sleap/nn/tracking.py (15 hunks)
Additional context used
Ruff
sleap/nn/tracking.py
614-614: Use
enumerate()for index variablen_processedinforloop(SIM113)
Additional comments not posted (12)
sleap/nn/tracking.py (12)
4-5: Imports approved.The additions of
json,sys, andrich.progressare appropriate for the new reporting functionality.
520-521: New attributesverbosityandreport_rateapproved.These attributes enhance user control over the output of the tracking process.
532-547: Newrun_stepmethod approved.This method clears tracks and processes instances for tracking.
742-746: New attributesverbosityandreport_rateapproved.These attributes enhance user control over the output of the tracking process.
1484-1488: New attributesverbosityandreport_rateapproved.These attributes enhance user control over the output of the tracking process.
1014-1015: New parametersprogress_reportingandreport_rateapproved.These parameters enhance user control over the output of the tracking process.
Line range hint
1226-1248:
Updatedadd_cli_parser_argsmethod approved.The method updates the CLI parser to include the new
progress_reportingandreport_rateparameters.
1280-1283: Updatedget_by_name_factory_optionsmethod approved.The method updates the factory options to include the new
progress_reportingandreport_rateparameters.
1484-1489: Updatedtrackmethod approved.The method enhances the tracking process by incorporating Kalman filters for better accuracy.
1707-1707: Modifiedretrackfunction approved.The modification aligns with the removal of the standalone
run_trackerfunction.However, ensure that all function calls to
retrackmatch the new implementation.Verification successful
Modified
retrackfunction approved.The modification aligns with the removal of the standalone
run_trackerfunction. The function calls toretrackmatch the new implementation.
tests/nn/test_inference.py: Verified test case involvingretrack.sleap/nn/tracking.py: Verified function definition and call.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify all function calls to `retrack` match the new implementation. # Test: Search for the function usage. Expect: Only occurrences of the new implementation. rg --type python -A 5 $'retrack'Length of output: 62
Script:
#!/bin/bash # Description: Verify all function calls to `retrack` match the new implementation. # Test: Search for the function usage. Expect: Only occurrences of the new implementation. rg --type py -A 5 $'retrack'Length of output: 1193
142-142: Verify the impact of changing the default value ofsave_shifted_instancestoTrue.This change could affect memory usage and performance.
Verification successful
Verify the impact of changing the default value of
save_shifted_instancestoTrue.This change could affect memory usage and performance.
Verify the impact of changing the default value of
save_shifted_instancestoTrue.The change in the default value of
save_shifted_instancestoTruewill increase memory usage due to the saving of shifted instances between frames. However, it is expected to improve instance matching. This behavior is documented and tested in the codebase.
sleap/nn/tracking.py: Multiple references tosave_shifted_instancesshow its impact on saving shifted instances.sleap/gui/learning/runners.py: Configuration references.tests/nn/test_inference.py: Test cases covering the new default behavior.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the impact of changing the default value of `save_shifted_instances` to `True`. # Test: Search for the usage of `save_shifted_instances` in the codebase. Expect: Analyze its impact on memory and performance. rg --type python -A 5 $'save_shifted_instances'Length of output: 77
Script:
#!/bin/bash # Description: Verify the impact of changing the default value of `save_shifted_instances` to `True`. # Test: Search for the usage of `save_shifted_instances` in the codebase. Expect: Analyze its impact on memory and performance. rg --type py -A 5 $'save_shifted_instances'Length of output: 5528
549-653: Newrun_trackermethod approved.This method includes logic for different verbosity modes, providing visual feedback via a progress bar or JSON-formatted progress updates.
However, ensure that all function calls to
run_trackermatch the new signature.Tools
Ruff
614-614: Use
enumerate()for index variablen_processedinforloop(SIM113)
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Files selected for processing (8)
- sleap/config/pipeline_form.yaml (2 hunks)
- sleap/gui/learning/dialog.py (1 hunks)
- sleap/gui/widgets/video.py (2 hunks)
- sleap/nn/inference.py (12 hunks)
- sleap/nn/tracking.py (24 hunks)
- sleap/util.py (2 hunks)
- tests/nn/test_tracker_components.py (2 hunks)
- tests/nn/test_tracking_integration.py (4 hunks)
Files skipped from review as they are similar to previous changes (5)
- sleap/config/pipeline_form.yaml
- sleap/gui/learning/dialog.py
- sleap/gui/widgets/video.py
- sleap/nn/inference.py
- sleap/util.py
Additional context used
Ruff
sleap/nn/tracking.py
614-614: Use
enumerate()for index variablen_processedinforloop(SIM113)
Additional comments not posted (10)
tests/nn/test_tracking_integration.py (3)
22-22: Verify the updated assertion.The expected number of tracks has been reduced from 27 to 8. Ensure this change is correct and consistent with the updated tracking logic.
44-44: LGTM! Ensure correct initialization oftrackerobject.The change to use
tracker.run_trackerwith verbosity improves encapsulation and maintainability.
51-51: LGTM! Ensure correct initialization oftrackerobject.The change to use
tracker.run_trackerwith verbosity improves encapsulation and maintainability.tests/nn/test_tracker_components.py (2)
18-28: LGTM! Improved flexibility and error handling.The addition of the
img_scaleparameter and the use ofpytest.skip()enhance the function's flexibility and robustness.
40-58: LGTM! Enhanced testing coverage.The inclusion of
img_scaleas a parameter broadens the scope of the tests to include variations in image scaling.sleap/nn/tracking.py (5)
520-531: LGTM! Improved user control and reporting.The addition of
verbosityandreport_rateattributes, along with the enhancedrun_trackermethod, improve user control and reporting capabilities.
532-548: LGTM! New methodrun_stepimproves modularity.The
run_stepmethod enhances modularity by encapsulating the logic for processing a single frame.
549-654: LGTM! Enhancedrun_trackermethod.The
run_trackermethod now includes logic for different verbosity modes, providing better user feedback during the tracking process.Tools
Ruff
614-614: Use
enumerate()for index variablen_processedinforloop(SIM113)
704-709: LGTM! Improved user control and reporting.The addition of
verbosityandreport_rateattributes improves user control and reporting capabilities.
1009-1010: LGTM! Updatedmake_tracker_by_namemethod.The
make_tracker_by_namemethod now includesprogress_reportingandreport_rateparameters, enhancing user control over the tracking process.
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Files selected for processing (3)
- sleap/nn/tracking.py (23 hunks)
- tests/nn/test_tracker_components.py (2 hunks)
- tests/nn/test_tracking_integration.py (5 hunks)
Additional context used
Ruff
sleap/nn/tracking.py
614-614: Use
enumerate()for index variablen_processedinforloop(SIM113)
Additional comments not posted (10)
tests/nn/test_tracking_integration.py (3)
22-22: Verify the change in the expected number of tracks.The assertion change from 27 to 8 indicates a significant reduction in the number of tracks. Verify if this change aligns with the intended behavior and updated tracking logic.
45-45: LGTM! Verify the handling of the verbosity parameter.The change to use
tracker.run_trackerwith an additional verbosity parameter is approved. Ensure that the verbosity parameter is handled correctly within thetrackerclass.
52-52: LGTM! Verify the handling of the verbosity parameter.The change to use
tracker.run_trackerwith an additional verbosity parameter is approved. Ensure that the verbosity parameter is handled correctly within thetrackerclass.tests/nn/test_tracker_components.py (2)
18-27: LGTM! Verify the handling of the newimg_scaleparameter.The changes to rename the function and include the
img_scaleparameter enhance flexibility. Ensure that the new parameter and logic are correctly implemented.
40-40: LGTM! Verify the integration of the newimg_scaleparameter.The changes to include the
img_scaleparameter in the tests enhance coverage. Ensure that the new parameter is correctly integrated into the tests.sleap/nn/tracking.py (5)
141-141: Verify the change in the default value ofsave_shifted_instances.The default value of
save_shifted_instancesis changed fromFalsetoTrue. Verify if this change aligns with the intended functionality and does not adversely impact memory usage and performance.
520-521: LGTM! Verify the implementation of new attributes and methods.The new attributes (
verbosity,report_rate) and methods (run_step,run_tracker) enhance the tracking process. Ensure that they are correctly implemented and integrated.Also applies to: 527-531, 532-548, 549-654
704-709: LGTM! Verify the implementation of new attributes and modifications.The new attributes (
verbosity,report_rate) and modifications enhance the tracking process. Ensure that they are correctly implemented and integrated.Also applies to: 742-747
1477-1482: LGTM! Verify the implementation of new attributes.The new attributes (
verbosity,report_rate) enhance the tracking process. Ensure that they are correctly implemented and integrated.
1699-1699: LGTM! Verify the modification to calltracker.run_tracker.The change to call
tracker.run_trackeraligns with the refactor. Ensure that the modification is correctly implemented.
|
Also fixes a bug introduced by #1875, where the |
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- sleap/nn/inference.py (13 hunks)
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- sleap/nn/inference.py
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## develop #1894 +/- ##
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+ Coverage 73.30% 74.95% +1.64%
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Files 134 133 -1
Lines 24087 24344 +257
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+ Hits 17658 18247 +589
+ Misses 6429 6097 -332 ☔ View full report in Codecov by Sentry. |
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Actionable comments posted: 3
Outside diff range, codebase verification and nitpick comments (14)
tests/nn/test_tracking_integration.py (2)
131-134: Approve use ofos.path.joinfor file path handling.The replacement of string concatenation with
os.path.joinfor file path handling is a good improvement. It enhances the robustness of the code across different operating systems.Consider using an f-string for the filename part to improve readability:
return os.path.join( dir, f"{tracker_name}_{int(scale * 100)}_{matcher_name}_{sim_name}.h5" )
40-40: Incomplete refactoring ofrun_trackerfunction.The
run_trackerfunction is still being used directly in the following test files, indicating that the refactoring might not be complete:
tests/nn/test_tracking_integration.pytests/nn/test_tracker_components.pyPlease review these instances to ensure consistency and alignment with the PR objectives.
Analysis chain
Approve removal of
run_trackerfunction.The removal of the
run_trackerfunction and its replacement with direct calls totracker.run_tracker(frames, verbosity="none")in bothmake_ground_truthandcompare_ground_truthfunctions simplifies the code and aligns with the PR objectives.To ensure this change doesn't affect test coverage or introduce regressions, consider running the full test suite and comparing the results with the previous version.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Search for other usages of run_tracker to ensure complete refactoring rg --type python "run_tracker\(" tests/Length of output: 72
Script:
#!/bin/bash # Correcting the file type to search for other usages of run_tracker to ensure complete refactoring rg --type py "run_tracker\(" tests/Length of output: 320
tests/nn/test_tracker_components.py (1)
18-32: Improved function with better naming and image scaling support.The changes to this function are well-implemented:
- The new name
run_tracker_by_namebetter reflects its functionality.- The addition of the
img_scaleparameter increases flexibility.- The error handling for unsupported
img_scaleis good.Consider using a custom exception instead of
pytest.skipfor better error handling outside of test scenarios. For example:class UnsupportedImageScaleError(Exception): pass # ... if img_scale: if hasattr(t, "candidate_maker") and hasattr(t.candidate_maker, "img_scale"): t.candidate_maker.img_scale = img_scale else: raise UnsupportedImageScaleError("img_scale is not defined for this tracker")This would allow for more flexible error handling in non-test environments.
sleap/config/pipeline_form.yaml (2)
458-463: Consider adding a performance note to the documentationThe help text for
save_shifted_instancesmentions improved instance matching at the cost of more memory usage. It might be beneficial to add a note in the user documentation about the performance implications of this option.Consider adding a brief performance note in the user documentation for this new option. This will help users make informed decisions about whether to enable this feature based on their hardware capabilities and project requirements.
458-463: Potential Impact of Removingtracking.max_tracksThe
tracking.max_tracksparameter has been removed from the configuration file, but it is still referenced in several parts of the codebase. This could lead to issues if these parts of the code expect this parameter to be present. Please review the following files and references to ensure consistency and functionality:
sleap/nn/tracking.py: Multiple references tomax_tracksas a parameter and in tracking logic.sleap/nn/inference.py: Reference tomax_tracksin a function call.sleap/gui/learning/runners.py: References totracking.max_tracksin inference parameter logic.Analysis chain
Removal of
tracking.max_tracksparameterThe
tracking.max_tracksparameter has been removed from the configuration. This change might affect users who were relying on this option to limit the number of tracks.Let's check if there are any references to
max_tracksin the codebase that might need to be updated:Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Search for references to max_tracks in Python files rg --type python '\bmax_tracks\b' -g '!tests/'Length of output: 79
Script:
#!/bin/bash # Corrected command to search for references to max_tracks in Python files rg -t py '\bmax_tracks\b' -g '!tests/'Length of output: 1659
sleap/nn/tracking.py (5)
35-38: Conditional import for cached_property added.The addition of the conditional import for
cached_propertyimproves compatibility across different Python versions. This is a good practice for maintaining backwards compatibility while leveraging newer features when available.Consider adding a comment explaining why
cached_propertyis preferred over regularpropertywhen available, to provide context for future maintainers.
520-522: New attributes added for progress reporting.The addition of
verbosityandreport_rateattributes to theBaseTrackerclass supports the enhanced progress reporting feature mentioned in the PR objectives. This will allow for more flexible and customizable tracking progress updates.Consider adding docstring comments for these new attributes to explain their purpose and expected values, improving the class's documentation.
532-547: New run_step method added to BaseTracker class.The
run_stepmethod encapsulates the logic for processing a single frame in the tracking process. This improves modularity and reusability of the tracking code. The method handles both image-based and non-image-based tracking scenarios, making it versatile.Consider adding a docstring to the
run_stepmethod to explain its purpose, parameters, and return value. This would improve the method's documentation and make it easier for other developers to understand and use.
742-747: Tracker class updated with new progress reporting attributes.The addition of
verbosityandreport_rateattributes to theTrackerclass ensures consistency with theBaseTrackerclass. The use of a validator for theverbosityattribute is a good practice to ensure only valid values are used.Consider adding a validator for the
report_rateattribute to ensure it's a positive number, preventing potential issues with invalid reporting rates:report_rate: float = attr.ib( default=2.0, validator=attr.validators.instance_of(float) and attr.validators.gt(0) )This addition would improve the robustness of the class by preventing invalid input for the reporting rate.
1477-1482: KalmanTracker class updated with progress reporting attributes.The addition of
verbosityandreport_rateattributes to theKalmanTrackerclass ensures consistency with theBaseTrackerandTrackerclasses. This change maintains a uniform interface for progress reporting across different tracker implementations.For consistency with the
Trackerclass, consider usingattr.ib()for thereport_rateattribute and adding a validator:report_rate: float = attr.ib( default=2.0, validator=attr.validators.instance_of(float) and attr.validators.gt(0) )This change would align the attribute definition style with the
verbosityattribute and add an extra layer of input validation.sleap/nn/inference.py (4)
433-434: Consider using enumerate for better readability.Instead of iterating directly over
examples, consider usingenumerate(examples)to get both the index and the example in each iteration. This can make the code more readable and provide the iteration count if needed.for i, ex in enumerate(examples): ex = process_batch(ex) progress.update(task, advance=len(ex["frame_ind"]))
453-454: Consider using enumerate for better readability.Similar to the previous comment, using
enumerate(examples)here could improve readability and provide the iteration count if needed.for i, ex in enumerate(examples): # Process batch of examples. ex = process_batch(ex)
490-491: Consider using enumerate for consistency.For consistency with the previous loops, consider using
enumerate(examples)here as well, even if the index is not used.for i, ex in enumerate(examples): yield process_batch(ex)
5663-5663: Consider adding error handling for tracker.run_tracker.While the change itself is good, it might be beneficial to add some error handling around the
tracker.run_tracker(frames=frames)call. This could help catch and report any issues that might occur during the tracking process.try: frames = tracker.run_tracker(frames=frames) except Exception as e: print(f"Error occurred during tracking: {e}") # Handle the error appropriately
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Files selected for processing (8)
- sleap/config/pipeline_form.yaml (2 hunks)
- sleap/gui/learning/dialog.py (1 hunks)
- sleap/gui/widgets/video.py (2 hunks)
- sleap/nn/inference.py (13 hunks)
- sleap/nn/tracking.py (23 hunks)
- sleap/util.py (2 hunks)
- tests/nn/test_tracker_components.py (2 hunks)
- tests/nn/test_tracking_integration.py (5 hunks)
Additional context used
Ruff
sleap/nn/tracking.py
614-614: Use
enumerate()for index variablen_processedinforloop(SIM113)
Additional comments not posted (30)
tests/nn/test_tracking_integration.py (2)
45-45: Approve direct call totracker.run_tracker.The replacement of the
run_trackerfunction call with a direct call totracker.run_tracker(frames, verbosity="none")is consistent with the earlier changes and simplifies the code.
22-22: Verify the change in expected number of tracks.The assertion for the number of tracks has been significantly reduced from 27 to 8. This change might be related to the improvements in tracking functionality mentioned in the PR objectives.
Could you provide more context on why the expected number of tracks has changed so drastically? This change might have implications for other parts of the system that depend on the number of tracks.
sleap/util.py (7)
6-6: LGTM: Good use of postponed annotation evaluation.The addition of
from __future__ import annotationsis a good practice. It enables postponed evaluation of annotations, which can improve performance and reduce circular import issues.
16-16: LGTM: Improved import for type checking.The addition of
TYPE_CHECKINGto the import statement is a good practice. It allows for conditional imports that are only evaluated during type checking, which can optimize runtime performance.
20-24: LGTM: Improved import handling and new feature support.The try-except block for importing
filesensures compatibility with different Python versions. The addition ofrich.progressimport supports the newRateColumnclass functionality.Also applies to: 30-30
36-38: LGTM: Fixed undefined name issue.The conditional import of
Taskfromrich.progressaddresses the issue mentioned in the previous comment about the undefined nameTask. It's now properly imported only during type checking.
40-48: LGTM: New feature for improved progress visualization.The new
RateColumnclass is a great addition that aligns with the PR objective of improving progress visualization. It provides a custom rendering of the progress rate, displaying the speed in FPS.
Line range hint
315-315: LGTM: Improved path handling.The modification to use
files("sleap").joinpath(filename)is a more modern and flexible approach for creating the package file path.
Line range hint
320-321: LGTM: Enhanced config file handling.The additions to the
get_config_filefunction provide more flexibility in config file handling. The new parametersignore_file_not_foundandget_defaults, along with the associated logic, allow for ignoring file not found errors and retrieving default configs. This aligns well with the PR objective of improving default options handling.Also applies to: 332-333, 340-341, 349-350
sleap/config/pipeline_form.yaml (3)
458-463: New option to save shifted instances during trackingThe addition of the
tracking.save_shifted_instancesparameter aligns with the PR objectives of improving tracking functionality. This new option allows users to save flow-shifted instances between frames, which can enhance instance matching at the cost of increased memory usage.This change improves the flexibility of the tracking process and gives users more control over the trade-off between accuracy and memory usage.
458-463: Summary of changes to tracking configurationThe modifications to the tracking configuration in this file align with the PR objectives of improving tracking functionality. The addition of the
save_shifted_instancesoption provides users with more control over the tracking process, allowing for a trade-off between improved instance matching and memory usage.However, the removal of the
max_tracksparameter might affect existing users who relied on this option. It's important to ensure that this change doesn't break any existing functionality and that appropriate alternatives are provided if necessary.These changes enhance the flexibility of the tracking process. However, please consider the following actions:
- Update the user documentation to reflect these changes, especially regarding the new
save_shifted_instancesoption and its performance implications.- Verify that the removal of
max_tracksdoesn't negatively impact existing users or workflows.- If
max_tracksfunctionality is still needed, consider implementing it in a different way or providing clear migration instructions for users.
458-463: Verify the impact of saving shifted instances on memory usageWhile the new
save_shifted_instancesoption can improve instance matching, it's important to ensure that the increased memory usage doesn't cause issues in resource-constrained environments.Let's check if there are any memory-related comments or considerations in the codebase:
sleap/gui/learning/dialog.py (2)
736-736: Approve: Prevent negative count with max functionThe modification to use
max(0, total_count - new_counts)is a good improvement. It ensures thatno_result_countis never negative, which could happen ifnew_countssomehow exceededtotal_count. This change adds robustness to the code and prevents potential issues or confusing output related to negative frame counts.
736-736: Verify similar calculations in the codebaseWhile this change is good, it might be worth checking if there are similar calculations elsewhere in the codebase that could benefit from the same robustness check.
Let's search for similar patterns in the codebase:
sleap/nn/tracking.py (7)
4-9: Imports updated to support new functionality.The new imports (json, sys, time) are added to support the enhanced tracking and reporting features. The removal of the unused
defaultdictimport aligns with the previous review comment and improves code cleanliness.
33-34: New import for progress reporting.The addition of
RateColumnfromsleap.utilsupports the enhanced progress reporting feature in the tracking system.
141-141: Default value for save_shifted_instances changed to True.This change aligns with the PR objectives, which mentioned changing the default value for the
save_shifted_instancesoption to True. This modification will likely improve the default behavior of instance tracking.
527-531: New cached_property for report_period added.The addition of the
report_periodcached_property provides a clean and efficient way to calculate the time interval between progress reports. This improves code readability and potentially performance by caching the calculated value.
1085-1086: Progress reporting parameters added to make_tracker_by_name method.The addition of
progress_reportingandreport_rateparameters to themake_tracker_by_namemethod allows for customization of the progress reporting features when creating a tracker instance. This change provides flexibility in how tracking progress is reported, aligning with the enhanced progress reporting capabilities introduced in this update.
Line range hint
1-1699: Summary of changes and overall assessment.The modifications in this file significantly enhance the progress reporting capabilities of the tracking system, aligning well with the PR objectives. Key improvements include:
- Addition of verbosity modes for flexible progress reporting.
- Implementation of a rich progress bar and JSON output options.
- Consistent updates across different tracker implementations (BaseTracker, Tracker, KalmanTracker).
- New methods for step-by-step tracking with progress updates.
These changes will greatly improve the user experience by providing better feedback during the tracking process. The code is generally well-structured and consistent, with only minor suggestions for improvements in documentation and input validation.
The overall changes are well-implemented and will positively impact the SLEAP application's tracking functionality.
Tools
Ruff
614-614: Use
enumerate()for index variablen_processedinforloop(SIM113)
614-614: False positive from static analysis tool.The static analysis tool (Ruff) suggests using
enumerate()for the index variablen_processedin the for loop. However, this suggestion is not applicable in this context. The variablen_processedis not used as an index for the loop, but rather as a counter of processed frames. The current implementation is correct and more efficient for its purpose.The current implementation is appropriate for the intended functionality.
Tools
Ruff
614-614: Use
enumerate()for index variablen_processedinforloop(SIM113)
sleap/gui/widgets/video.py (3)
819-820: LGTM: Good addition for mouse event handling.The new instance variable
_down_posis a good practice for tracking the initial position of the mouse when a button is pressed. This will allow for more precise control over mouse events, such as distinguishing between clicks and drags.
1044-1045: LGTM: Improved mouse movement detection.The updated logic for detecting mouse movement during a click is more robust. By checking if
_down_posis not None before comparing it with the current position, we prevent potential errors that could occur if_down_poshasn't been set (e.g., if mouseReleaseEvent is somehow triggered without a corresponding mousePressEvent).
Line range hint
1-1185: Overall: Good improvements to mouse event handling.The changes in this file are focused on improving the mouse event handling, particularly in the
mouseReleaseEventmethod. The addition of the_down_posinstance variable and its use in detecting mouse movement during clicks enhance the robustness of the user interaction logic.These modifications should lead to more reliable distinction between clicks and drags, improving the overall user experience without introducing unnecessary complexity.
sleap/nn/inference.py (6)
49-53: LGTM: Conditional import of cached_property.This change adds compatibility for Python versions below 3.8 by conditionally importing
cached_property. This is a good practice for maintaining backwards compatibility.
415-417: Improved ETA calculation.Compiling the loop examples before starting the timer is a good optimization for improving the accuracy of the ETA calculation. This change addresses the PR objective of enhancing the ETA calculation in the GUI progress bar.
5388-5390: Updated LabelsReader initialization.The change in the LabelsReader initialization adds the
example_indicesparameter, which is derived fromframe_list(args.frames). This modification allows for more flexible frame selection during inference, addressing the PR objective of adding functionality to run tracking only on defined frames.
5484-5487: Added progress_reporting to tracker initialization.The addition of the
progress_reportingparameter to the tracker initialization is a good improvement. It allows for consistent progress reporting between the predictor and the tracker.
5655-5660: Improved frame filtering for tracking.This change improves the efficiency of frame filtering when running tracking on an existing prediction file. By converting the
example_indicesto a set, the search operation becomes O(1) instead of O(n), which can significantly speed up the process for large datasets.
5684-5684: Use of os.fspath for consistent path handling.The use of
os.fspath(data_path)is a good practice for ensuring consistent path handling across different operating systems. This change improves the robustness of the code.
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Files selected for processing (2)
- sleap/nn/inference.py (11 hunks)
- sleap/nn/tracking.py (23 hunks)
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Learnings (1)
sleap/nn/inference.py (1)
Learnt from: getzze PR: talmolab/sleap#1894 File: sleap/nn/inference.py:164-167 Timestamp: 2024-09-03T14:11:31.284Z Learning: When deciding between `@cached_property` and `@lru_cache`, prefer `@cached_property` when the goal is to ensure that the cached value is automatically deleted when the instance is deleted, avoiding potential memory leaks.
Ruff
sleap/nn/tracking.py
568-568: Use
enumerate()for index variablen_processedinforloop(SIM113)
Additional comments not posted (13)
sleap/nn/tracking.py (9)
141-141: Approved: Default value forsave_shifted_instanceschanged toTrue.The default value has been appropriately changed from
FalsetoTrue. As mentioned in the PR objectives, this restores access to thesave_shifted_instancessetting in the GUI, which was removed in a previous commit.Saving the shifted instances between elapsed frames uses a bit more memory but leads to better instance matches.
520-521: Approved: Newverbosityandreport_rateattributes added toBaseTracker.The addition of the
verbosityandreport_rateattributes to theBaseTrackerclass aligns with the PR objective of introducing different verbosity modes for progress reporting during tracking.
verbositylikely controls the mode of progress reporting (e.g., "rich", "json", "none").report_ratelikely controls the frequency of progress updates.These attributes will enable more flexible and informative progress reporting during the tracking process.
527-530: Approved: Newreport_periodproperty added toBaseTracker.The addition of the
report_periodproperty to theBaseTrackerclass is a useful enhancement. It provides a convenient way to access the time interval between progress reports, calculated based on thereport_rateattribute.Using the
@cached_propertydecorator ensures that the value is calculated only once and cached for subsequent accesses, which can improve performance by avoiding redundant calculations.
549-597: Approved: New_run_tracker_jsonmethod added toBaseTracker.The addition of the
_run_tracker_jsonmethod to theBaseTrackerclass is a significant enhancement that implements the "json" verbosity mode for progress reporting during tracking. This aligns with the PR objective of introducing different verbosity modes for progress reporting.Key features of the
_run_tracker_jsonmethod:
- Iterates over the frames, calls
run_stepon each frame, and yields the new labeled frame.- Tracks the progress and timing information, including the number of processed frames, total frames, elapsed time, processing rate, and estimated time remaining (ETA).
- Reports the progress in JSON format, which can be easily captured and parsed for programmatic monitoring.
- Uses the
max_lengthargument to limit the length of the deques used for calculating the recent processing rate.This method will greatly enhance the ability to monitor the progress of the tracking process programmatically, especially in scenarios like headless servers or notebooks.
Tools
Ruff
568-568: Use
enumerate()for index variablen_processedinforloop(SIM113)
599-623: Approved: New_run_tracker_richmethod added toBaseTracker.The addition of the
_run_tracker_richmethod to theBaseTrackerclass is another significant enhancement that implements the "rich" verbosity mode for progress reporting during tracking. This aligns with the PR objective of introducing different verbosity modes for progress reporting.Key features of the
_run_tracker_richmethod:
- Uses the
richlibrary to display a visually appealing and informative progress bar during tracking.- Iterates over the frames, calls
run_stepon each frame, and yields the new labeled frame.- Updates the progress bar with the current progress percentage, estimated time remaining (ETA), and processing rate.
- Manually refreshes the progress bar based on the
report_periodto support notebooks.This method will greatly improve the user experience by providing a clear and informative visual representation of the tracking progress, especially when running in interactive environments like notebooks.
625-661: Approved: Updatedrun_trackermethod inBaseTracker.The updates to the
run_trackermethod in theBaseTrackerclass are a significant improvement that incorporates the new verbosity modes for progress reporting during tracking. This aligns with the PR objective of introducing different verbosity modes for progress reporting.Key changes in the updated
run_trackermethod:
- Accepts
frames,verbosity, andfinal_passas arguments.- Checks the
is_validproperty to determine if tracking should be performed.- Uses the
verbosityargument or theverbosityattribute to determine the progress reporting mode.- Delegates the actual tracking and progress reporting to the appropriate
_run_tracker_*method based on the verbosity mode.- Supports running a final pass after tracking if
final_passisTrue.These updates provide flexibility and modularity in the tracking process, allowing users to choose the desired verbosity mode and enabling the integration of different progress reporting mechanisms.
750-754: Approved: Updatedverbosityand addedreport_rateattributes inTracker.The changes to the
verbosityandreport_rateattributes in theTrackerclass are in line with the PR objective of introducing different verbosity modes for progress reporting during tracking.
- The
verbosityattribute now has a default value of"none", meaning that by default, no progress reporting will be displayed during tracking.- The validator for the
verbosityattribute ensures that only valid verbosity modes ("none","rich","json") can be assigned.- The addition of the
report_rateattribute with a default value of2.0allows controlling the frequency of progress updates during tracking.These changes provide flexibility in configuring the progress reporting behavior of the
Trackerclass, enabling users to choose the desired verbosity mode and update frequency.
1228-1233: Verify the data type consistency for thesave_shifted_instancesoption.The default value for the
save_shifted_instancesoption in theTracker.get_by_name_factory_optionsmethod has been changed fromFalseto1. This change aligns with the modification made to thesave_shifted_instancesattribute in theFlowCandidateMakerclass, as mentioned in the PR objectives.However, there seems to be an inconsistency in the data type used for the default value. The option's data type is specified as
int, but using1instead ofTruemight cause confusion.Please ensure that the data type for the
save_shifted_instancesoption is consistently used throughout the codebase. If the intended data type isbool, consider updating the default value toTruefor clarity.
1247-1250: Approved: Updated help text for thekf_init_frame_countoption.The changes to the help text for the
kf_init_frame_countoption in theTracker.get_by_name_factory_optionsmethod provide clearer guidance on the behavior of this option.By explicitly mentioning that setting
kf_init_frame_countto0means no Kalman filters will be used, the updated help text improves the understanding of this option's functionality and makes it easier for users to configure the tracking behavior correctly.sleap/nn/inference.py (4)
49-53: LGTM!The code changes are approved. Conditionally defining
cached_propertybased on the Python version is a good way to maintain compatibility.
164-167: The existing discussion in the comments is still relevant. No need to duplicate the reasoning for using@cached_propertyhere.
371-407: LGTM!The new
_process_batchmethod looks good. It nicely encapsulates the batch processing logic and correctly handles updating the input dictionary with model predictions and adjusting for potential scaling.
Line range hint
408-523: Looks good!The new
_run_batch_jsonand_run_batch_richmethods are a nice addition to provide different progress reporting modes. The implementation looks solid, correctly tracking progress, timing and reporting.Updating
_predict_generatorto use these methods based on theverbositysetting is the right approach.
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Outside diff range, codebase verification and nitpick comments (1)
sleap/nn/tracking.py (1)
549-597: Useenumerate()for index variablen_processed.The static analysis tool suggests using
enumerate()for the index variablen_processedin theforloop.Consider applying this change to improve code readability:
for n_processed, lf in enumerate(frames, start=1): new_lf = self.run_step(lf) # Track timing and progress elapsed_all = time() - t0_all n_batch += 1 # Report if time() > last_report + self.report_period: # ... (rest of the code remains the same)Tools
Ruff
568-568: Use
enumerate()for index variablen_processedinforloop(SIM113)
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Files selected for processing (2)
- sleap/nn/inference.py (11 hunks)
- sleap/nn/tracking.py (23 hunks)
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Learnings (1)
sleap/nn/inference.py (1)
Learnt from: getzze PR: talmolab/sleap#1894 File: sleap/nn/inference.py:164-167 Timestamp: 2024-09-03T14:11:31.284Z Learning: When deciding between `@cached_property` and `@lru_cache`, prefer `@cached_property` when the goal is to ensure that the cached value is automatically deleted when the instance is deleted, avoiding potential memory leaks.
Ruff
sleap/nn/tracking.py
568-568: Use
enumerate()for index variablen_processedinforloop(SIM113)
Additional comments not posted (14)
sleap/nn/tracking.py (10)
532-661: New run_tracker method added with enhanced progress reporting.The
run_trackermethod is a significant addition that implements comprehensive progress reporting for the tracking process. It supports different verbosity modes ("rich", "json", and default) as mentioned in the PR objectives. This enhancement will greatly improve user experience by providing better feedback during the tracking process.Key improvements:
- Support for rich progress bar display
- JSON output option for programmatic monitoring
- Flexible reporting rate
Consider the following improvements:
- Extract the progress reporting logic for each verbosity mode into separate methods to improve readability and maintainability.
- Add error handling for potential exceptions during the tracking process.
- Consider using a context manager for the "json" verbosity mode to ensure proper resource management, similar to the "rich" mode.
Tools
Ruff
568-568: Use
enumerate()for index variablen_processedinforloop(SIM113)
599-623: LGTM!The
_run_tracker_richmethod effectively utilizes therichlibrary to display an informative and visually appealing progress bar for the "rich" verbosity mode. The code is well-structured and follows best practices.
750-754: LGTM!The addition of the
verbosityandreport_rateattributes to theTrackerclass aligns with the enhanced progress reporting feature. The validation of theverbosityattribute ensures that only valid verbosity modes are accepted, and the default value ofreport_rateis reasonable.
1305-1319: LGTM!The changes to the
add_cli_parser_argsmethod are necessary to support the new "tracker" option without a default value, allowing for the detection of malformed command-line arguments. The addition of the other command-line arguments with their default values is consistent with the existing code.
Line range hint
1017-1094: LGTM!The changes to the
make_tracker_by_namemethod are consistent with the enhanced progress reporting feature. The newprogress_reportingargument allows for specifying the desired verbosity mode when creating aTrackerinstance, and theverbosityandreport_rateattributes are set accordingly. The changes are well-integrated with the existing code.
1228-1233: LGTM!The change in the default value of the
save_shifted_instancesoption fromFalsetoTruealigns with the PR objective of restoring access to this setting in the GUI. The updated help text accurately reflects the change in default value and provides clarity on the behavior of the option. The change is consistent with the overall goals of the PR.
1247-1250: LGTM!The updated help text for the
kf_init_frame_countoption provides clearer guidance on the behavior of the option. It explicitly states that a value of 0 indicates that no Kalman filters will be used. This clarification improves the usability and understanding of the option. The change is minor but beneficial.
1271-1274: LGTM!The updated help text for the
oks_score_weightingoption provides a clearer explanation of the behavior when the value is set to 0 or 1. It specifies that a value of 0 (default) means only the distance between the reference and query keypoint is used to compute the similarity, while a value of 1 means each distance is weighted by the prediction scores of the reference and query keypoint. This clarification enhances the understanding and usability of the option. The change is minor but valuable.
1282-1285: LGTM!The updated help text for the
oks_normalizationoption provides a detailed explanation of the behavior for different values. It clarifies that a value of "all" means the similarity score is normalized by the number of reference points, "ref" means the score is normalized by the number of visible reference points, and "union" means the score is normalized by the number of points both visible in query and reference instance. This detailed explanation improves the understanding and usability of the option. The change is valuable for users to make informed decisions when configuring the tracker.
1485-1489: LGTM!The addition of the
verbosityand `report_sleap/nn/inference.py (4)
49-53: LGTM!The code adds compatibility for Python versions below 3.8 by conditionally defining
cached_property. This is a good practice to ensure backward compatibility.
164-167: Good optimization based on learnings!The change from
@propertyto@cached_propertyforreport_periodis a good optimization. As mentioned in the learnings:When deciding between
@cached_propertyand@lru_cache, prefer@cached_propertywhen the goal is to ensure that the cached value is automatically deleted when the instance is deleted, avoiding potential memory leaks.This ensures that the cached value is automatically deleted when the instance is deleted, avoiding potential memory leaks.
371-407: Improved modularity and clarity!The new
_process_batchmethod encapsulates the logic for running inference on a batch and updating the input dictionary with predictions. This improves modularity and clarity by extracting the inline processing logic into a dedicated method. The method handles important postprocessing steps such as:
- Skipping inference if the model is not loaded
- Running inference on the current batch
- Adding model outputs to the input data example
- Converting
video_indandframe_indto numpy arrays if they are TensorFlow tensors- Adjusting
instance_peaksbased on potentialSizeMatcherscalingThe code is well-structured and follows good practices.
508-523: Improved ETA calculation and flexible progress reporting!The changes introduce several improvements to the inference loop:
Compiling loop examples before starting the timer improves the ETA calculation by providing a more accurate estimate of the total number of examples. This enhances the user experience by providing a more reliable progress estimate.
The optional progress reporting based on the
verbosityattribute allows for flexibility in how progress is displayed:
- The
"rich"option displays an informative and visually appealing progress bar using the_run_batch_richmethod.- The
"json"option outputs progress information as JSON using the_run_batch_jsonmethod, which can be useful for programmatic monitoring or logging.- The
"none"option allows for silent execution without any progress reporting, suitable for scenarios where progress updates are not needed.The code is well-organized and uses appropriate methods for different verbosity levels, making it easy to understand and maintain.
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Files selected for processing (8)
- sleap/config/pipeline_form.yaml (2 hunks)
- sleap/gui/learning/dialog.py (1 hunks)
- sleap/gui/widgets/video.py (2 hunks)
- sleap/nn/inference.py (11 hunks)
- sleap/nn/tracking.py (23 hunks)
- sleap/util.py (2 hunks)
- tests/nn/test_tracker_components.py (2 hunks)
- tests/nn/test_tracking_integration.py (5 hunks)
Files skipped from review as they are similar to previous changes (4)
- sleap/config/pipeline_form.yaml
- sleap/gui/learning/dialog.py
- sleap/gui/widgets/video.py
- sleap/util.py
Additional context used
Learnings (1)
sleap/nn/inference.py (1)
Learnt from: getzze PR: talmolab/sleap#1894 File: sleap/nn/inference.py:164-167 Timestamp: 2024-09-03T14:11:31.284Z Learning: When deciding between `@cached_property` and `@lru_cache`, prefer `@cached_property` when the goal is to ensure that the cached value is automatically deleted when the instance is deleted, avoiding potential memory leaks.
Ruff
sleap/nn/tracking.py
568-568: Use
enumerate()for index variablen_processedinforloop(SIM113)
Additional comments not posted (22)
tests/nn/test_tracking_integration.py (4)
22-22: Verify the change in the expected number of tracks.The assertion in the
test_simple_trackerfunction has been updated to expect 8 tracks instead of 27. This change suggests a potential adjustment in the underlying tracking logic or the data being processed.Please confirm that this change aligns with the intended behavior and provide a brief explanation for the adjustment in the expected number of tracks.
45-45: Verify the impact of removing therun_trackerfunction.The
run_trackerfunction has been removed, and its functionality has been replaced by a direct call totracker.run_tracker(frames, verbosity="none")in themake_ground_truthfunction. While this change simplifies the code, it's important to ensure that it doesn't introduce any unintended side effects or break existing functionality.Please confirm that the removal of the
run_trackerfunction and the direct utilization of the tracker's method have been thoroughly tested and do not negatively impact the overall behavior of the code.
52-52: Verify the impact of removing therun_trackerfunction in thecompare_ground_truthfunction.Similar to the change in the
make_ground_truthfunction, therun_trackerfunction has been removed, and its functionality has been replaced by a direct call totracker.run_tracker(frames, verbosity="none")in thecompare_ground_truthfunction. While this change simplifies the code, it's important to ensure that it doesn't introduce any unintended side effects or break existing functionality.Please confirm that the removal of the
run_trackerfunction and the direct utilization of the tracker's method in thecompare_ground_truthfunction have been thoroughly tested and do not negatively impact the overall behavior of the code.
131-133: LGTM!The modification in the
make_filenamefunction, where the string concatenation for the file path has been replaced withos.path.join, improves the robustness of file path handling across different operating systems. This change enhances the portability and maintainability of the code.tests/nn/test_tracker_components.py (3)
18-32: LGTM!The new
run_tracker_by_namefunction is well-structured and handles theimg_scaleparameter appropriately. Skipping the tracking process whenimg_scaleis not supported is a good practice to prevent unnecessary execution. The assertion at the end ensures that the tracking process produces the expected number of frames.
40-40: Also applies to: 47-47, 53-58
Line range hint
77-84:sleap/nn/tracking.py (11)
625-661: New run_tracker method added with enhanced progress reporting.The
run_trackermethod is a significant addition that implements comprehensive progress reporting for the tracking process. It supports different verbosity modes ("rich", "json", and default) as mentioned in the PR objectives. This enhancement will greatly improve user experience by providing better feedback during the tracking process.
599-623: LGTM!The
_run_tracker_richmethod is well-implemented and provides a rich progress bar for tracking progress. It uses a context manager to ensure proper resource management.
532-547: LGTM!The
run_stepmethod is correctly implemented and clears the tracks before running the tracking step.
527-530: LGTM!The
report_periodcached property is correctly implemented and uses thereport_rateattribute to calculate the report period.
750-754: LGTM!The new
verbosityandreport_rateattributes are correctly added to theTrackerclass and will be used for progress reporting during tracking.
1017-1018: LGTM!The
make_tracker_by_nameclass method correctly handles the newprogress_reportingandreport_ratearguments and passes them to theTrackerconstructor.
1228-1233: LGTM!The
get_by_name_factory_optionsclass method correctly updates the default value ofsave_shifted_instancesto 1. This change aligns with the PR objective of restoring access to this setting in the GUI.
1305-1312: LGTM!The
add_cli_parser_argsclass method correctly handles the case when the default value is defined for "tracking.tracker" by not passing the default value to the argument parser. This change prevents the detection of malformed command line arguments.
1485-1489: LGTM!The new
verbosityandreport_rateattributes are correctly added to theKalmanTrackerclass and will be used for progress reporting during tracking.
1707-1707: LGTM!The
run_trackermethod of theKalmanTrackerclass correctly passes theframesargument to theinit_tracker.run_trackermethod.
568-568: Skip the Ruff suggestion.The suggestion to use
enumerate()for index variablen_processedis not applicable in this case becausen_processedis not used as an index variable in theforloop. It is a counter variable that is incremented in each iteration of the loop. Usingenumerate()would not provide any benefit here.Tools
Ruff
568-568: Use
enumerate()for index variablen_processedinforloop(SIM113)
sleap/nn/inference.py (4)
164-167: LGTM!The code changes are approved. Using
@cached_propertyis the right choice here to avoid potential memory leaks.
371-407: Looks good!The new
_process_batchfunction correctly handles running inference on a batch and postprocessing the results. The logic for skipping inference when the model is not loaded, running inference, updating the input dictionary, and adjusting for SizeMatcher scaling is implemented properly.
408-455: LGTM!The new
_run_batch_jsonfunction correctly processes batches of examples and reports the progress in JSON format. The logic for tracking timing and progress, computing the recent rate and ETA, and printing the JSON progress information at the specified report period is implemented properly.
456-486: Looks good!The new
_run_batch_richfunction correctly processes batches of examples and reports the progress using the rich progress bar. The setup of the rich progress bar with custom configuration, updating the progress for each batch, and manually refreshing the progress bar to support notebooks is implemented properly.
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It's ready for review! |
change default save_shifted_instances
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Thanks for the updates @getzze! Just keep us posted on when it's ready for review again. |
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It's ready to review! |
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Actionable comments posted: 11
🧹 Outside diff range and nitpick comments (3)
sleap/util.py (1)
40-48: LGTM: Well-implementedRateColumnclass for progress tracking.The
RateColumnclass is a good addition for displaying the progress rate in FPS. It handles edge cases well and provides a clear, formatted output.Consider adding a brief comment explaining the meaning of FPS in this context, as it might not be immediately clear to all developers that it refers to "Frames Per Second" in this tracking scenario. For example:
return rich.progress.Text(f"{speed:.1f} FPS", style="progress.data.speed") # FPS: Frames Per Secondsleap/config/pipeline_form.yaml (1)
458-463: LGTM! Consider a minor improvement in the help text.The addition of the
tracking.save_shifted_instancesoption is well-placed and aligns with the PR objectives. The configuration is clear and the default value is set correctly.Consider slightly rewording the help text for clarity:
- help: 'Save the flow-shifted instances between elapsed frames. It improves - instance matching at the cost of using a bit more of memory.' + help: 'Save the flow-shifted instances between elapsed frames. This improves + instance matching at the cost of using more memory.'This minor change improves readability and precision in describing the memory impact.
sleap/nn/inference.py (1)
51-51: Typographical error in commentThere's a typo in the comment on line 51: "define" should be "defined".
Apply this diff to correct the typo:
-else: # cached_property is define only for python >=3.8 +else: # cached_property is defined only for python >=3.8
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📒 Files selected for processing (6)
- sleap/config/pipeline_form.yaml (1 hunks)
- sleap/nn/inference.py (10 hunks)
- sleap/nn/tracking.py (13 hunks)
- sleap/util.py (1 hunks)
- tests/nn/test_tracker_components.py (3 hunks)
- tests/nn/test_tracking_integration.py (4 hunks)
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📓 Learnings (1)
sleap/nn/inference.py (1)
<retrieved_learning>
Learnt from: getzze
PR: #1894
File: sleap/nn/inference.py:164-167
Timestamp: 2024-09-03T14:11:31.284Z
Learning: When deciding between@cached_propertyand@lru_cache, prefer@cached_propertywhen the goal is to ensure that the cached value is automatically deleted when the instance is deleted, avoiding potential memory leaks.
</retrieved_learning>
🪛 Ruff
sleap/nn/tracking.py
571-571: Use
enumerate()for index variablen_processedinforloop(SIM113)
sleap/util.py
8-8:
base64imported but unusedRemove unused import:
base64(F401)
31-31:
PIL.Imageimported but unusedRemove unused import:
PIL.Image(F401)
🔇 Additional comments (14)
tests/nn/test_tracking_integration.py (4)
5-5: LGTM: Import Path from pathlibThe addition of
from pathlib import Pathis a good change. It aligns with the project's move towards usingpathlibfor cross-platform path handling.
46-46: LGTM: Simplified tracker executionThe direct use of
tracker.run_tracker(frames, verbosity="none")in bothmake_ground_truthandcompare_ground_truthfunctions is a good simplification. It removes the unnecessary intermediaterun_trackerfunction, making the code more straightforward.Also applies to: 53-53
134-136: LGTM: Improved path handlingThe use of
Path.joinpathfor constructing the file path is an excellent change. It improves cross-platform compatibility and follows the project's move towards usingpathlibfor path handling.
23-23: Verify the change in expected number of tracksThe assertion for the number of tracks has been significantly reduced from 27 to 8. This change might reflect improvements in the tracking algorithm or changes in its configuration.
Please confirm:
- Is this change intentional?
- What improvements or changes in the tracking algorithm led to this reduction?
- Are there any implications for the overall tracking performance?
sleap/util.py (2)
29-29: LGTM: New imports for progress tracking and type hinting.The addition of
rich.progressimport and the conditional import ofTaskfor type hinting are appropriate for the newRateColumnclass and improve type checking without affecting runtime performance.Also applies to: 36-37
1-49: Summary: Enhancements align well with PR objectives.The changes in this file, particularly the addition of the
RateColumnclass, contribute significantly to the PR's goal of improving tracking functionality and progress display in the SLEAP application. These modifications lay the groundwork for implementing the progress bar during tracking, as outlined in the PR objectives.The new imports and class definition are well-structured and follow best practices. With the suggested minor improvements (removing unused imports and adding a clarifying comment), this file will be in excellent shape to support the enhanced tracking features.
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🪛 Ruff
8-8:
base64imported but unusedRemove unused import:
base64(F401)
31-31:
PIL.Imageimported but unusedRemove unused import:
PIL.Image(F401)
tests/nn/test_tracker_components.py (2)
18-32: Functionrun_tracker_by_nameimplemented correctlyThe new
run_tracker_by_namefunction correctly replacestracker_by_nameand appropriately handles theimg_scaleparameter.
50-61: Parameters added totest_tracker_by_nameappropriatelyThe addition of
img_scaleandcountparameters totest_tracker_by_nameis appropriate and correctly integrated into the test function.sleap/nn/tracking.py (5)
4-8: LGTM on added imports for progress reporting functionalityThe newly added imports are appropriate and necessary for the implementation of progress reporting features.
12-13: Importingrich.progressenhances progress bar capabilitiesThe addition of
import rich.progressis essential for the rich progress bar implementation in the tracking process.
602-627: New method_run_tracker_richadds rich progress bar displayThe
_run_tracker_richmethod introduces a rich progress bar during tracking, significantly improving user experience by providing visual feedback.
552-601: New method_run_tracker_jsonprovides JSON-based progress reportingThe implementation of the
_run_tracker_jsonmethod effectively adds JSON-based progress reporting, enabling programmatic monitoring of the tracking process.🧰 Tools
🪛 Ruff
571-571: Use
enumerate()for index variablen_processedinforloop(SIM113)
628-665: Updates torun_trackermethod to incorporate verbosity optionsThe
run_trackermethod now supports different verbosity levels, allowing for flexible progress reporting tailored to various use cases.sleap/nn/inference.py (1)
508-509: Confirm thatdata_providersupportslen()In the line
n_total = len(data_provider), ensure thatdata_providerimplements the__len__method. If not, this will raise aTypeError. Verify thatdata_providersupports the length operation.
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| Try not to put things in here unless they really have no other place. | ||
| """ | ||
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| from __future__ import annotations | ||
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| import base64 |
There was a problem hiding this comment.
Remove unused imports to improve code cleanliness.
The following imports are not used in this file and should be removed:
base64(line 8)PIL.Image(line 31)
Apply this diff to remove the unused imports:
-import base64
-from PIL import ImageThis will help maintain a clean and efficient codebase by removing unnecessary dependencies.
Also applies to: 31-31
🧰 Tools
🪛 Ruff
8-8:
base64imported but unusedRemove unused import:
base64(F401)
| pytest.skip("img_scale is not defined for this tracker") | ||
| return |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Unnecessary return statement after pytest.skip
The pytest.skip function raises an exception and halts the test execution. The return statement following it is redundant and can be removed.
Apply this diff to remove the unnecessary return statement:
pytest.skip("img_scale is not defined for this tracker")
- return📝 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.
| pytest.skip("img_scale is not defined for this tracker") | |
| return | |
| pytest.skip("img_scale is not defined for this tracker") |
| @cached_property | ||
| def report_period(self) -> float: | ||
| """Time between progress reports in seconds.""" | ||
| return 1.0 / self.report_rate | ||
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There was a problem hiding this comment.
Ensure report_rate is non-zero to prevent division by zero
In the report_period property, dividing by self.report_rate could result in a division by zero if report_rate is zero. Please add validation to ensure report_rate is not zero.
Apply this diff to add validation:
@cached_property
def report_period(self) -> float:
"""Time between progress reports in seconds."""
+ if self.report_rate == 0:
+ raise ValueError("report_rate must be non-zero")
return 1.0 / self.report_rate📝 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.
| @cached_property | |
| def report_period(self) -> float: | |
| """Time between progress reports in seconds.""" | |
| return 1.0 / self.report_rate | |
| @cached_property | |
| def report_period(self) -> float: | |
| """Time between progress reports in seconds.""" | |
| if self.report_rate == 0: | |
| raise ValueError("report_rate must be non-zero") | |
| return 1.0 / self.report_rate |
| progress_reporting: str = "rich", | ||
| report_rate: float = 2.0, |
There was a problem hiding this comment.
Align default verbosity values across classes for consistency
The default value for progress_reporting in make_tracker_by_name is 'rich', whereas the default verbosity in Tracker and KalmanTracker classes is 'none'. This inconsistency might lead to unexpected behavior. Consider setting the default verbosity in Tracker and KalmanTracker to 'rich' for consistency.
Apply this diff to align the default values:
# In the Tracker class
verbosity: str = attr.ib(
validator=attr.validators.in_(["none", "rich", "json"]),
- default="none",
+ default="rich",
)
# In the KalmanTracker class
verbosity: str = attr.ib(
validator=attr.validators.in_(["none", "rich", "json"]),
- default="none",
+ default="rich",
)Committable suggestion was skipped due to low confidence.
| for lf in frames: | ||
| new_lf = self.run_step(lf) | ||
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| # Track timing and progress | ||
| elapsed_all = time() - t0_all | ||
| n_processed += 1 | ||
| n_batch += 1 | ||
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There was a problem hiding this comment.
🛠️ Refactor suggestion
Simplify loop by using enumerate for n_processed
You can simplify the loop by using enumerate to automatically increment n_processed, enhancing code readability.
Apply this diff to refactor the loop:
for n_processed, lf in enumerate(frames, start=1):
new_lf = self.run_step(lf)
# Track timing and progress
elapsed_all = time() - t0_all
- n_processed += 1
n_batch += 1📝 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 lf in frames: | |
| new_lf = self.run_step(lf) | |
| # Track timing and progress | |
| elapsed_all = time() - t0_all | |
| n_processed += 1 | |
| n_batch += 1 | |
| for n_processed, lf in enumerate(frames, start=1): | |
| new_lf = self.run_step(lf) | |
| # Track timing and progress | |
| elapsed_all = time() - t0_all | |
| n_batch += 1 | |
🧰 Tools
🪛 Ruff
571-571: Use
enumerate()for index variablen_processedinforloop(SIM113)
| if sys.version_info >= (3, 8): | ||
| from functools import cached_property | ||
| else: # cached_property is define only for python >=3.8 | ||
| cached_property = property |
There was a problem hiding this comment.
Use a proper fallback for cached_property in Python < 3.8
Replacing cached_property with property in versions below Python 3.8 does not replicate the caching behavior, which may lead to performance issues. Consider using functools.lru_cache as a fallback to maintain similar functionality.
Additionally, there's a typographical error in the comment on line 39: "define" should be "defined".
Apply this diff to fix the issue:
import functools
if sys.version_info >= (3, 8):
from functools import cached_property
else: # cached_property is defined only for python >=3.8
- cached_property = property
+ def cached_property(func):
+ return property(functools.lru_cache()(func))📝 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.
| if sys.version_info >= (3, 8): | |
| from functools import cached_property | |
| else: # cached_property is define only for python >=3.8 | |
| cached_property = property | |
| import functools | |
| if sys.version_info >= (3, 8): | |
| from functools import cached_property | |
| else: # cached_property is defined only for python >=3.8 | |
| def cached_property(func): | |
| return property(functools.lru_cache()(func)) |
| @@ -167,7 +161,7 @@ class Predictor(ABC): | |||
| report_rate: float = attr.ib(default=2.0, kw_only=True) | |||
| model_paths: List[str] = attr.ib(factory=list, kw_only=True) | |||
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| @property | |||
| @cached_property | |||
There was a problem hiding this comment.
Handle potential ZeroDivisionError when computing report_period
Since report_period is calculated as 1.0 / self.report_rate, if self.report_rate is zero, it will raise a ZeroDivisionError. Ensure that self.report_rate is initialized to a non-zero value or add a check to prevent division by zero.
| rate = sum(n_recent) / sum(elapsed_recent) | ||
| eta = (n_total - n_processed) / rate |
There was a problem hiding this comment.
Prevent division by zero in rate calculation
In the calculation of rate = sum(n_recent) / sum(elapsed_recent), there's a possibility of ZeroDivisionError if sum(elapsed_recent) is zero. Ensure that elapsed_recent contains non-zero values or add a condition to handle the zero case.
Apply this diff to handle the zero division case:
-rate = sum(n_recent) / sum(elapsed_recent)
+if sum(elapsed_recent) > 0:
+ rate = sum(n_recent) / sum(elapsed_recent)
+else:
+ rate = 0📝 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.
| rate = sum(n_recent) / sum(elapsed_recent) | |
| eta = (n_total - n_processed) / rate | |
| if sum(elapsed_recent) > 0: | |
| rate = sum(n_recent) / sum(elapsed_recent) | |
| else: | |
| rate = 0 | |
| eta = (n_total - n_processed) / rate |
| if isinstance(ex["video_ind"], tf.Tensor): | ||
| ex["video_ind"] = ex["video_ind"].numpy().flatten() | ||
| if isinstance(ex["frame_ind"], tf.Tensor): | ||
| ex["frame_ind"] = ex["frame_ind"].numpy().flatten() | ||
|
|
There was a problem hiding this comment.
Verify existence of keys before accessing dictionary items
When accessing ex["video_ind"] and ex["frame_ind"], ensure that these keys exist in the ex dictionary to prevent potential KeyError. Consider using ex.get("video_ind") and ex.get("frame_ind") with default values or add checks before accessing.
Apply this diff to safely access the keys:
-if isinstance(ex["video_ind"], tf.Tensor):
+if "video_ind" in ex and isinstance(ex["video_ind"], tf.Tensor):
-if isinstance(ex["frame_ind"], tf.Tensor):
+if "frame_ind" in ex and isinstance(ex["frame_ind"], tf.Tensor):📝 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.
| if isinstance(ex["video_ind"], tf.Tensor): | |
| ex["video_ind"] = ex["video_ind"].numpy().flatten() | |
| if isinstance(ex["frame_ind"], tf.Tensor): | |
| ex["frame_ind"] = ex["frame_ind"].numpy().flatten() | |
| if "video_ind" in ex and isinstance(ex["video_ind"], tf.Tensor): | |
| ex["video_ind"] = ex["video_ind"].numpy().flatten() | |
| if "frame_ind" in ex and isinstance(ex["frame_ind"], tf.Tensor): | |
| ex["frame_ind"] = ex["frame_ind"].numpy().flatten() |
| if sys.version_info >= (3, 8): | ||
| from functools import cached_property | ||
| else: # cached_property is define only for python >=3.8 | ||
| cached_property = property |
There was a problem hiding this comment.
Ensure consistent caching behavior across Python versions
Currently, the fallback for Python versions earlier than 3.8 assigns cached_property = property, which means that caching will not occur and report_period will be recalculated each time it's accessed. To maintain the intended caching behavior across all supported Python versions, consider using the cached_property backport available in the backports.cached_property package.
Apply this diff to fix the issue:
-if sys.version_info >= (3, 8):
- from functools import cached_property
-else: # cached_property is define only for python >=3.8
- cached_property = property
+try:
+ from functools import cached_property
+except ImportError:
+ from backports.cached_property import cached_property📝 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.
| if sys.version_info >= (3, 8): | |
| from functools import cached_property | |
| else: # cached_property is define only for python >=3.8 | |
| cached_property = property | |
| try: | |
| from functools import cached_property | |
| except ImportError: | |
| from backports.cached_property import cached_property |
|
Hi @getzze , I rebased you branch off of our updated Thanks, Divya |
|
Hi @gitttt-1234, Thanks |
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
sleap/nn/tracking.py (1)
37-40: Typographical error in comment on line 39.The comment on line 39 contains a typo: "define" should be "defined".
Apply this diff to correct the typo:
-else: # cached_property is define only for python >=3.8 +else: # cached_property is defined only for python >=3.8
📜 Review details
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Review profile: CHILL
📒 Files selected for processing (3)
- sleap/nn/tracking.py (14 hunks)
- tests/nn/test_tracker_components.py (3 hunks)
- tests/nn/test_tracking_integration.py (4 hunks)
🚧 Files skipped from review as they are similar to previous changes (2)
- tests/nn/test_tracker_components.py
- tests/nn/test_tracking_integration.py
🧰 Additional context used
🪛 Ruff
sleap/nn/tracking.py
572-572: Use
enumerate()for index variablen_processedinforloop(SIM113)
🔇 Additional comments (14)
sleap/nn/tracking.py (14)
4-9: Imports are appropriately added for new functionality.The imports of
json,sys,deque,time, and typing annotations are necessary for the added methods and enhancements.
12-13: Necessary importsnumpyandrich.progressadded.These imports are required for numerical computations and enhanced progress reporting.
35-36: Import ofRateColumnfor progress bar display.The
RateColumnis used in the rich progress bar to display processing rates.
523-525: Duplicate comment: Missing default values and validators forverbosityandreport_rate.
530-534: Duplicate comment: Potential division by zero inreport_perioddue toreport_ratebeing zero.
553-602: The_run_tracker_jsonmethod is correctly implemented for JSON progress reporting.The method effectively handles progress calculations and outputs, providing useful feedback during tracking.
🧰 Tools
🪛 Ruff
572-572: Use
enumerate()for index variablen_processedinforloop(SIM113)
603-628: The_run_tracker_richmethod utilizesrichlibrary effectively for progress display.The implementation is appropriate and follows best practices for progress bar integration.
630-666:run_trackermethod incorporates verbosity options and handles execution flow correctly.The method correctly delegates to the appropriate progress reporting method based on the
verbositysetting.
755-760: Addedverbosityandreport_ratewith validation inTrackerclass.Including validators and default values ensures robust usage of these attributes.
1029-1030: Duplicate comment: Inconsistent defaultverbosityvalues across classes.
1105-1106: Passingverbosityandreport_rateto the tracker instance.This ensures that the configured verbosity and report rate are correctly applied.
1497-1502: Addedverbosityandreport_ratewith validation inKalmanTrackerclass.Consistent implementation with the
Trackerclass.
1566-1566: Thetrackmethod inKalmanTrackercorrectly implements the abstract base class signature.Ensures compatibility with the
BaseTracker.
1720-1720: Updatedretrackfunction to userun_trackermethod.This change aligns the main function with the new tracking workflow.
Description
Several things were buggy when running
tracking-onlyfrom GUI orsleap-trackfrom CLI with only tracking:Nonevalue, which is boolean-False, so it could give the opposite for True-by-default options (there are none so far, fortunately).save_shifted_instancesto True and give back access to setting it from the GUI (removed in Limit max tracks via track-local queues #1447, I don't know why)data_pathvariable was overwritten.Types of changes
Does this address any currently open issues?
None
Outside contributors checklist
Thank you for contributing to SLEAP!
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Summary by CodeRabbit
Summary by CodeRabbit
New Features
Bug Fixes
Refactor
Trackerclass, removing standalone functions for better encapsulation.Tests