Add feature to evaluate network for specfic, named snapshots. #2508
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…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
Tetra-quark
changed the title
Tetra-quark
changed the title
Member
|
@n-poulsen and @jeylau let's prioritize this -- I think it's a great addition, and can be worked into DLC3.0 |
n-poulsen
approved these changes
Jul 5, 2024
Contributor
n-poulsen
left a comment
n-poulsen
left a comment
There was a problem hiding this comment.
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!
MMathisLab
added a commit
that referenced
this pull request
Jul 16, 2024
* 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 <[email protected]> Co-authored-by: Niels Poulsen <[email protected]> * 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 <[email protected]> Co-authored-by: Mackenzie Mathis <[email protected]> --------- Co-authored-by: jkopp <[email protected]> Co-authored-by: Mackenzie Mathis <[email protected]> Co-authored-by: Terry Park <[email protected]>
MMathisLab
added a commit
that referenced
this pull request
Jul 19, 2024
* 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 <[email protected]> Co-authored-by: Niels Poulsen <[email protected]> * 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 <[email protected]> Co-authored-by: Mackenzie Mathis <[email protected]> --------- Co-authored-by: jkopp <[email protected]> Co-authored-by: Mackenzie Mathis <[email protected]> Co-authored-by: Terry Park <[email protected]>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Adds a feature to pass a list of snapshot names
snapshots_to_evaluateto theevaluate_networkfunction as an alternative to using thesnapshotindexparameter in the mainconfig.yamlfile.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:
snapshots_to_evaluateparameter to both single and multi-animal evaluation.get_available_requested_snapshotsto handle thesnapshots_to_evaluateparameter.get_snapshots_by_indexto refactor existingsnapshotindexfrom config file functionality.get_snapshots_from_folderto refactor getting an ordered list of snapshots from the train folder.testscript.pyto usesnapshots_to_evaluateinevaluate_network(however in doing so I have disabled thesnapshotindexmethod, both should be in the test ideally).Example usage: