Add feature to evaluate network for specfic, named snapshots. - #2508
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MMathisLab merged 30 commits intoJul 5, 2024
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…isting functionality. - Replace snapindex with more explicit snapshot_name. snapshotindex from config is used to identify the snapshot name instead. - Refactor logic for snapshotindex allowed values. Add limit to negative index values.
- Replace snapshots_to_evaluate numpy indexing with list loop - Raise error if no snapshots are found
# Conflicts: # deeplabcut/pose_estimation_tensorflow/core/evaluate.py
* Improve snapshots_to_evaluate docstring * Get training_iterations from snapshot_name * Rename trainingsiterations -> training_iterations
* Create get_available_requested_snapshots for obtaining specified snapshot names (new feature). * Create get_snapshots_by_index to handle the original implementation. * Minor improvements and fixes
* Add snapshots_to_evaluate parameter to multi-animal evaluation * Minor renaming
* add evaluate_by_snapshot branch for testing purposes
* Better typehint for int or str * Raise IndexError instead of ValueError
* Add list_sorted_existing_snapshots to auxiliaryfunctions.py. * Update several files to use the newly refactored function. * Preserve same exception handling, albeit with modified message to be more general and concise.
* Add new snapshot auxiliary function usage. * Preserve continuation of loop if no snapshots are found.
* Update name for all usages * Minor change to function docstring * Remove redundant sorting in evaluate_multianimal.py
* Test snapshots present and returned in order * Test snapshots not found
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@n-poulsen and @jeylau let's prioritize this -- I think it's a great addition, and can be worked into DLC3.0 |
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Made some minor linting changes, tested on single + multi-animal projects. Looks good to me (as soon as tests pass)!
Great PR, thanks @Tetra-quark!
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* Add feature to evaluate network for specfic, named snapshots. (#2508) * Add snapshot selection option to evaluate_network while preserving existing functionality. - Replace snapindex with more explicit snapshot_name. snapshotindex from config is used to identify the snapshot name instead. - Refactor logic for snapshotindex allowed values. Add limit to negative index values. * Update evaluate.py - Replace snapshots_to_evaluate numpy indexing with list loop - Raise error if no snapshots are found * Add snapshots_to_evaluate docstring * Remove unused distance function * Update evaluate.py * Improve snapshots_to_evaluate docstring * Get training_iterations from snapshot_name * Rename trainingsiterations -> training_iterations * Improve snapshot_to_evaluate typehint and docstring. * Refactor evaluate.py * Create get_available_requested_snapshots for obtaining specified snapshot names (new feature). * Create get_snapshots_by_index to handle the original implementation. * Minor improvements and fixes * Add tests for new snapshot functions in evaluate.py * Update evaluate_multianimal.py * Add snapshots_to_evaluate parameter to multi-animal evaluation * Minor renaming * Update python-package.yml * add evaluate_by_snapshot branch for testing purposes * Add snapshots_to_evaluate usage in testscript.py * Update get_snapshots_by_index function * Better typehint for int or str * Raise IndexError instead of ValueError * Add get_snapshots_by_index tests to test_evaluate.py * Update return_evaluate_network_data function with get_snapshots_by_index usage * Fix potential reference before assignment by raising ValueError * Refactor getting existing snapshot file names as sorted list. * Add list_sorted_existing_snapshots to auxiliaryfunctions.py. * Update several files to use the newly refactored function. * Preserve same exception handling, albeit with modified message to be more general and concise. * Refactor evaluate_multianimal.py * Add new snapshot auxiliary function usage. * Preserve continuation of loop if no snapshots are found. * Remove indentation level. * Rename list_sorted_exisiting_snapshots -> get_snapshots_in_folder * Update name for all usages * Minor change to function docstring * Remove redundant sorting in evaluate_multianimal.py * Port numpy array to list (not performance critical) * Add get_snapshots_from_folder tests * Test snapshots present and returned in order * Test snapshots not found * Fix deprecated function names * Improve snapshots_to_evaluate test in testscript.py * Correct spelling * Add per_keypoint_evaluation to evaluate_multianimal_full function call (woops!) * minor linting --------- Co-authored-by: Mackenzie Mathis <mathis@rowland.harvard.edu> Co-authored-by: Niels Poulsen <niels.poulsen@epfl.ch> * fixed file dialog not showing uppercase file extension video files (#2645) * fixed file dialog not showing uppercase file extension video files * bug fix: no shuffle_change slot in main window * bug fix --------- Co-authored-by: Niels Poulsen <niels.poulsen@epfl.ch> Co-authored-by: Mackenzie Mathis <mathis@rowland.harvard.edu> --------- Co-authored-by: jkopp <32641315+Tetra-quark@users.noreply.github.com> Co-authored-by: Mackenzie Mathis <mathis@rowland.harvard.edu> Co-authored-by: Terry Park <58895710+park-jsdev@users.noreply.github.com>
MMathisLab
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* Add feature to evaluate network for specfic, named snapshots. (#2508) * Add snapshot selection option to evaluate_network while preserving existing functionality. - Replace snapindex with more explicit snapshot_name. snapshotindex from config is used to identify the snapshot name instead. - Refactor logic for snapshotindex allowed values. Add limit to negative index values. * Update evaluate.py - Replace snapshots_to_evaluate numpy indexing with list loop - Raise error if no snapshots are found * Add snapshots_to_evaluate docstring * Remove unused distance function * Update evaluate.py * Improve snapshots_to_evaluate docstring * Get training_iterations from snapshot_name * Rename trainingsiterations -> training_iterations * Improve snapshot_to_evaluate typehint and docstring. * Refactor evaluate.py * Create get_available_requested_snapshots for obtaining specified snapshot names (new feature). * Create get_snapshots_by_index to handle the original implementation. * Minor improvements and fixes * Add tests for new snapshot functions in evaluate.py * Update evaluate_multianimal.py * Add snapshots_to_evaluate parameter to multi-animal evaluation * Minor renaming * Update python-package.yml * add evaluate_by_snapshot branch for testing purposes * Add snapshots_to_evaluate usage in testscript.py * Update get_snapshots_by_index function * Better typehint for int or str * Raise IndexError instead of ValueError * Add get_snapshots_by_index tests to test_evaluate.py * Update return_evaluate_network_data function with get_snapshots_by_index usage * Fix potential reference before assignment by raising ValueError * Refactor getting existing snapshot file names as sorted list. * Add list_sorted_existing_snapshots to auxiliaryfunctions.py. * Update several files to use the newly refactored function. * Preserve same exception handling, albeit with modified message to be more general and concise. * Refactor evaluate_multianimal.py * Add new snapshot auxiliary function usage. * Preserve continuation of loop if no snapshots are found. * Remove indentation level. * Rename list_sorted_exisiting_snapshots -> get_snapshots_in_folder * Update name for all usages * Minor change to function docstring * Remove redundant sorting in evaluate_multianimal.py * Port numpy array to list (not performance critical) * Add get_snapshots_from_folder tests * Test snapshots present and returned in order * Test snapshots not found * Fix deprecated function names * Improve snapshots_to_evaluate test in testscript.py * Correct spelling * Add per_keypoint_evaluation to evaluate_multianimal_full function call (woops!) * minor linting --------- Co-authored-by: Mackenzie Mathis <mathis@rowland.harvard.edu> Co-authored-by: Niels Poulsen <niels.poulsen@epfl.ch> * fixed file dialog not showing uppercase file extension video files (#2645) * fixed file dialog not showing uppercase file extension video files * bug fix: no shuffle_change slot in main window * bug fix --------- Co-authored-by: Niels Poulsen <niels.poulsen@epfl.ch> Co-authored-by: Mackenzie Mathis <mathis@rowland.harvard.edu> --------- Co-authored-by: jkopp <32641315+Tetra-quark@users.noreply.github.com> Co-authored-by: Mackenzie Mathis <mathis@rowland.harvard.edu> Co-authored-by: Terry Park <58895710+park-jsdev@users.noreply.github.com>
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Adds a feature to pass a list of snapshot names snapshots_to_evaluate to the evaluate_network function as an alternative to using the snapshotindex parameter in the main config.yaml file.
The new parameter allows multiple, explicitly named snapshots to be evaluated where previously only a single snapshot or "all" could be chosen.
This pull request closes #2356.
Overview of changes:
Example usage: