Add option to export to CSV via sleap-convert and API #1730
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WalkthroughThis update introduces the capability to export analysis results in CSV format, enhancing the SLEAP project's data exporting functionalities. It streamlines the process for users needing CSV outputs for their tracking information, catering to broader analysis and integration needs, such as compatibility with external tools. Changes
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- sleap/io/convert.py (4 hunks)
- sleap/io/dataset.py (1 hunks)
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sleap/io/convert.py (3)
73-73: Consider adding a validation check for the 'analysis.csv' format to ensure that the necessary conditions for CSV export are met before proceeding with the conversion.
169-180: Ensure that thewrite_analysisfunction called for CSV export properly handles errors and exceptions, especially for file I/O operations.
165-184: > 📝 NOTEThis review was outside the diff hunks and was mapped to the diff hunk with the greatest overlap. Original lines [73-180]
Overall, the integration of the CSV export functionality appears well-implemented. However, consider adding unit tests to verify the correctness and robustness of the new feature.
Would you like assistance in creating unit tests for the CSV export functionality?
sleap/io/convert.py
Outdated
| @@ -105,6 +106,7 @@ def main(args: list = None): | |||
| """ | |||
| parser = create_parser() | |||
| args = parser.parse_args(args=args) | |||
| print(args) | |||
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Remove the debug print statement to maintain a clean and professional codebase.
- print(args)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.
Suggested change
| print(args) |
Comment on lines
+140
to
+145
| if "nix" in args.format: | ||
| out_suffix = "nix" | ||
| elif "csv" in args.format: | ||
| out_suffix = "csv" | ||
| else: | ||
| out_suffix = "h5" |
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Refactor the logic for determining the output file suffix into a separate function to improve code readability and maintainability.
+ def determine_output_suffix(format_arg: str) -> str:
+ if "nix" in format_arg:
+ return "nix"
+ elif "csv" in format_arg:
+ return "csv"
+ else:
+ return "h5"
- if "nix" in args.format:
- out_suffix = "nix"
- elif "csv" in args.format:
- out_suffix = "csv"
- else:
- out_suffix = "h5"
+ out_suffix = determine_output_suffix(args.format)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.
Suggested change
| if "nix" in args.format: | |
| out_suffix = "nix" | |
| elif "csv" in args.format: | |
| out_suffix = "csv" | |
| else: | |
| out_suffix = "h5" | |
| def determine_output_suffix(format_arg: str) -> str: | |
| if "nix" in format_arg: | |
| return "nix" | |
| elif "csv" in format_arg: | |
| return "csv" | |
| else: | |
| return "h5" | |
| out_suffix = determine_output_suffix(args.format) |
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## develop #1730 +/- ##
===========================================
+ Coverage 73.30% 74.12% +0.81%
===========================================
Files 134 134
Lines 24087 24456 +369
===========================================
+ Hits 17658 18127 +469
+ Misses 6429 6329 -100 ☔ View full report in Codecov by Sentry. |
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Actionable comments posted: 1
Actionable comments outside the diff hunks (11)
sleap/io/dataset.py (11)
Line range hint
55-55: Remove duplicate import ofCallable.- from typing import CallableThe
Callabletype is imported twice, which is unnecessary. Consider removing the duplicate import to clean up the code.
Line range hint
61-61: Remove unused importh5py.- import h5py as h5The
h5pymodule is imported but not used in the provided code. Removing unused imports helps to keep the codebase clean and maintainable.
Line range hint
68-68: Replace bareexceptwith specific exceptions.Using a bare
exceptcan catch unexpected exceptions, making debugging more difficult. It's better to catch specific exceptions to handle known error conditions.
Line range hint
69-69: Remove unused import_ForwardRef.- from typing import _ForwardRef as ForwardRef + passThe
_ForwardRefimport is unused in the provided code. Consider removing it to clean up the code.
Line range hint
304-314: Refactor lambda expressions to named functions.Using named functions instead of lambda expressions for complex logic can improve readability and maintainability.
- filter_func = lambda lf: video is None or lf.video == video + def filter_func(lf): + return video is None or lf.video == videoApply similar changes for other lambda expressions in this range.
Line range hint
854-854: Useisinstance()for type checks.Type checks should use
isinstance()for better readability and flexibility.- if type(key) != tuple: + if not isinstance(key, tuple):
Line range hint
2209-2209: Add missing import forglob.+ from glob import globThe
globfunction is used but not imported. Adding the missing import will resolve theUndefined name 'glob'issue.
Line range hint
2304-2304: Refine conditional check to useif not ret:.- if ret == False: + if not ret:Using
if not ret:is more Pythonic and concise for checking false conditions.
Line range hint
2407-2407: Define or importsleapfor theto_pipelinemethod.The
sleapnamespace is referenced but not defined or imported in the provided context. Ensure thatsleapis correctly imported or defined to avoid runtime errors.
Line range hint
2500-2500: Remove unused variablee.- except IndexError as e: + except IndexError:The variable
eis assigned in theexceptblock but never used. Removing it will clean up the code.
Line range hint
2502-2502: Correct the f-string without placeholders.- f"There are no videos in this project. No points matrix to return." + "There are no videos in this project. No points matrix to return."The f-string is used without any placeholders. Converting it to a regular string is more appropriate.
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- sleap/io/convert.py (3 hunks)
- sleap/io/dataset.py (1 hunks)
Files skipped from review as they are similar to previous changes (1)
- sleap/io/convert.py
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Actionable comments outside the diff hunks (1)
tests/io/test_convert.py (1)
Line range hint
100-100: Address unused variablelabels.The static analysis has identified that the local variable
labelsis assigned to but never used within thetest_sleap_formatfunction. This could potentially be an oversight or leftover from previous iterations of the code. Consider removing or utilizing this variable as appropriate to clean up the code and avoid confusion.- labels = min_labels_slp
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- tests/io/test_convert.py (2 hunks)
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tests/io/test_convert.py (2)
11-11: Add test cases for new CSV export functionality.The inclusion of
"analysis.csv"in the@pytest.mark.parametrizedecorator effectively extends the test coverage to include the new CSV export functionality. This is a positive change that ensures the feature is tested across its intended formats.
30-30: Refine logic for determining output file format.The updated logic in the
generate_filenamesfunction to prioritize"csv"over"nix"and"h5"based on theformatparameter is clear and aligns with the new feature's requirements. This change ensures that the correct file format is used for output files when exporting to CSV.
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Actionable comments outside the diff hunks (5)
tests/io/test_dataset.py (5)
Line range hint
13-13: The importsleap.io.legacy.load_labels_json_oldappears to be unused in this file.- from sleap.io.legacy import load_labels_json_old
Line range hint
117-119: Useis notfor object identity tests andnot infor membership tests to adhere to Python best practices.- assert not multi_skel_vid_labels.skeletons[0] is loaded_labels.skeletons[0] + assert multi_skel_vid_labels.skeletons[0] is not loaded_labels.skeletons[0] - assert not multi_skel_vid_labels.nodes[3] in loaded_labels.nodes + assert multi_skel_vid_labels.nodes[3] not in loaded_labels.nodes - assert not multi_skel_vid_labels.videos[0] is loaded_labels.videos[0] + assert multi_skel_vid_labels.videos[0] is not loaded_labels.videos[0]
Line range hint
690-690: The variablenew_labels_jsonis assigned but never used. Consider removing it if it's unnecessary.- new_labels_json = new_labels.to_dict()
Line range hint
706-706: Similar to a previous comment, the variablenew_labels_jsonis assigned but not used. Removing unnecessary variable assignments can improve code clarity.- new_labels_json = new_labels.to_dict()
Line range hint
1423-1423: The variabletrack_instsis assigned but never used. If the intention was to perform assertions or checks using this variable, ensure those are implemented. Otherwise, consider removing the assignment.- track_insts = [inst for inst in labels.instances() if inst.track == track]
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tests/io/test_dataset.py (3)
2-2: Consider grouping standard library imports together for better readability.
8-8: The addition ofget_nodes_as_np_stringsimport aligns with the new functionality for exporting to CSV. Ensure it's utilized effectively in the new test functions.
1573-1603: The new test functions for exporting to CSV files (test_export_csvandtest_exported_csv) are crucial for verifying the new CSV export functionality. Ensure comprehensive test coverage, including edge cases and error handling, to maintain robustness.
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Actionable comments outside the diff hunks (7)
tests/io/test_dataset.py (7)
Line range hint
13-13: Remove the unused import to clean up the code.- from sleap.io.legacy import load_labels_json_old
Line range hint
117-117: Useis notfor object identity tests.- assert not multi_skel_vid_labels.skeletons[0] is loaded_labels.skeletons[0] + assert multi_skel_vid_labels.skeletons[0] is not loaded_labels.skeletons[0]
Line range hint
118-118: Usenot infor membership tests.- assert not multi_skel_vid_labels.nodes[3] in loaded_labels.nodes + assert multi_skel_vid_labels.nodes[3] not in loaded_labels.nodes
Line range hint
119-119: Useis notfor object identity tests.- assert not multi_skel_vid_labels.videos[0] is loaded_labels.videos[0] + assert multi_skel_vid_labels.videos[0] is not loaded_labels.videos[0]
Line range hint
1423-1423: Remove the unused variable to clean up the code.- track_insts = [inst for inst in labels.instances() if inst.track == track]
Line range hint
690-690: The variablenew_labels_jsonis assigned but never used. Consider removing it if it's not needed.- new_labels_json = new_labels.to_dict()
Line range hint
706-706: The variablenew_labels_jsonis assigned but never used. Consider removing it if it's not needed.- new_labels_json = new_labels.to_dict()
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tests/io/test_dataset.py (1)
1576-1605: Ensure the CSV export tests verify the content of the CSV files.Consider adding assertions to check the actual content of the exported CSV files against expected values to ensure the export functionality works as intended.
talmo
requested changes
Apr 8, 2024
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LGTM, but can you also update the relevant part of the docs?
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Actionable comments outside the diff hunks (7)
tests/io/test_dataset.py (7)
Line range hint
13-13: Remove unused importsleap.io.legacy.load_labels_json_old.- import sleap.io.legacy.load_labels_json_old
Line range hint
117-117: Useis notfor object identity checks.- assert not multi_skel_vid_labels.skeletons[0] is loaded_labels.skeletons[0] + assert multi_skel_vid_labels.skeletons[0] is not loaded_labels.skeletons[0]
Line range hint
118-118: Usenot infor membership checks.- assert not multi_skel_vid_labels.nodes[3] in loaded_labels.nodes + assert multi_skel_vid_labels.nodes[3] not in loaded_labels.nodes
Line range hint
119-119: Useis notfor object identity checks.- assert not multi_skel_vid_labels.videos[0] is loaded_labels.videos[0] + assert multi_skel_vid_labels.videos[0] is not loaded_labels.videos[0]
Line range hint
690-690: Remove the unused variable assignment.- new_labels_json = new_labels.to_dict()
Line range hint
706-706: Remove the unused variable assignment.- new_labels_json = new_labels.to_dict()
Line range hint
1423-1423: Remove the unused variable assignment.- track_insts = [inst for inst in labels.instances() if inst.track == track]
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- docs/guides/cli.md (1 hunks)
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docs/guides/cli.md (1)
325-326: Consider clarifying the CSV format's capabilities or limitations.It would be helpful for users if the documentation included a brief description of what the CSV format includes or any limitations it might have compared to other formats. This could guide users in choosing the most appropriate format for their needs.
tests/io/test_dataset.py (2)
1576-1587: The test for CSV export functionality is correctly implemented.
1590-1602: The test for verifying the exported CSV content is correctly implemented.
talmo
approved these changes
Apr 9, 2024
roomrys
added a commit
that referenced
this pull request
Dec 19, 2024
* Remove no-op code from #1498 * Add options to set background color when exporting video (#1328) * implement #921 * simplified form / refractor * Add test function and update cli docs * Improve test function to check background color * Improve comments * Change background options to lowercase * Use coderabbitai suggested `fill` --------- Co-authored-by: Shrivaths Shyam <[email protected]> Co-authored-by: Liezl Maree <[email protected]> * Increase range on batch size (#1513) * Increase range on batch size * Set maximum to a factor of 2 * Set default callable for `match_lists_function` (#1520) * Set default for `match_lists_function` * Move test code to official tests * Check using expected values * Allow passing in `Labels` to `app.main` (#1524) * Allow passing in `Labels` to `app.main` * Load the labels object through command * Add warning when unable to switch back to CPU mode * Replace (broken) `--unrag` with `--ragged` (#1539) * Fix unrag always set to true in sleap-export * Replace unrag with ragged * Fix typos * Add function to create app (#1546) * Refactor `AddInstance` command (#1561) * Refactor AddInstance command * Add staticmethod wrappers * Return early from set_visible_nodes * Import DLC with uniquebodyparts, add Tracks (#1562) * Import DLC with uniquebodyparts, add Tracks * add tests * correct tests * Make the hdf5 videos store as int8 format (#1559) * make the hdf5 video dataset type as proper int8 by padding with zeros * add gzip compression * Scale new instances to new frame size (#1568) * Fix typehinting in `AddInstance` * brought over changes from my own branch * added suggestions * Ensured google style comments --------- Co-authored-by: roomrys <[email protected]> Co-authored-by: sidharth srinath <[email protected]> * Fix package export (#1619) Add check for empty videos * Add resize/scroll to training GUI (#1565) * Make resizable training GUI and add adaptive scroll bar * Set a maximum window size --------- Co-authored-by: Liezl Maree <[email protected]> * support loading slp files with non-compound types and str in metadata (#1566) Co-authored-by: Liezl Maree <[email protected]> * change inference pipeline option to tracking-only (#1666) change inference pipeline none option to tracking-only * Add ABL:AOC 2023 Workshop link (#1673) * Add ABL:AOC 2023 Workshop link * Trigger website build * Graceful failing with seeking errors (#1712) * Don't try to seek to faulty last frame on provider initialization * Catch seeking errors and pass * Lint * Fix IndexError for hdf5 file import for single instance analysis files (#1695) * Fix hdf5 read for single instance analysis files * Add test * Small test files * removing unneccessary fixtures * Replace imgaug with albumentations (#1623) What's the worst that could happen? * Initial commit * Fix augmentation * Update more deps requirements * Use pip for installing albumentations and avoid reinstalling OpenCV * Update other conda envs * Fix out of bounds albumentations issues and update dependencies (#1724) * Install albumentations using conda-forge in environment file * Conda install albumentations * Add ndx-pose to pypi requirements * Keep out of bounds points * Black * Add ndx-pose to conda install in environment file * Match environment file without cuda * Ordered dependencies * Add test * Delete comments * Add conda packages to mac environment file * Order dependencies in pypi requirements * Add tests with zeroes and NaNs for augmentation * Back * Black * Make comment one line * Add todo for later * Black * Update to new TensorFlow conda package (#1726) * Build conda package locally * Try 2.8.4 * Merge develop into branch to fix dependencies * Change tensorflow version to 2.7.4 in where conda packages are used * Make tensorflow requirements in pypi looser * Conda package has TensorFlow 2.7.0 and h5py and numpy installed via conda * Change tensorflow version in `environment_no_cuda.yml` to test using CI * Test new sleap/tensorflow package * Reset build number * Bump version * Update mac deps * Update to Arm64 Mac runners * pin `importlib-metadata` * Pin more stuff on mac * constrain `opencv` version due to new qt dependencies * Update more mac stuff * Patches to get to green * More mac skipping --------- Co-authored-by: Talmo Pereira <[email protected]> Co-authored-by: Talmo Pereira <[email protected]> * Fix CI on macosx-arm64 (#1734) * Build conda package locally * Try 2.8.4 * Merge develop into branch to fix dependencies * Change tensorflow version to 2.7.4 in where conda packages are used * Make tensorflow requirements in pypi looser * Conda package has TensorFlow 2.7.0 and h5py and numpy installed via conda * Change tensorflow version in `environment_no_cuda.yml` to test using CI * Test new sleap/tensorflow package * Reset build number * Bump version * Update mac deps * Update to Arm64 Mac runners * pin `importlib-metadata` * Pin more stuff on mac * constrain `opencv` version due to new qt dependencies * Update more mac stuff * Patches to get to green * More mac skipping * Re-enable mac tests * Handle GPU re-init * Fix mac build CI * Widen tolerance for movenet correctness test * Fix build ci * Try for manual build without upload * Try to reduce training CI time * Rework actions * Fix miniforge usage * Tweaks * Fix build ci * Disable manual build * Try merging CI coverage * GPU/CPU usage in tests * Lint * Clean up * Fix test skip condition * Remove scratch test --------- Co-authored-by: eberrigan <[email protected]> * Add option to export to CSV via sleap-convert and API (#1730) * Add csv as a format option * Add analysis to format * Add csv suffix to output path * Add condition for csv analysis file * Add export function to Labels class * delete print statement * lint * Add `analysis.csv` as parametrize input for `sleap-convert` tests * test `export_csv` method added to `Labels` class * black formatting * use `Path` to construct filename * add `analysis.csv` to cli guide for `sleap-convert` --------- Co-authored-by: Talmo Pereira <[email protected]> * Only propagate Transpose Tracks when propagate is checked (#1748) Fix always-propagate transpose tracks issue * View Hyperparameter nonetype fix (#1766) Pass config getter argument to fetch hyperparameters * Adding ragged metadata to `info.json` (#1765) Add ragged metadata to info.json file * Add batch size to GUI for inference (#1771) * Fix conda builds (#1776) * test conda packages in a test environment as part of CI * do not test sleap import using conda build * use github environment variables to define build path for each OS in the matrix and add print statements for testing * figure out paths one OS at a time * github environment variables work in subsequent steps not current step * use local builds first * print env info * try simple environment creation * try conda instead of mamba * fix windows build path * fix windows build path * add comment to reference pull request * remove test stage from conda build for macs and test instead by creating the environment in a workflow * test workflow by pushing to current branch * test conda package on macos runner * Mac build does not need nvidia channel * qudida and albumentations are conda installed now * add comment with original issue * use python 3.9 * use conda match specifications syntax * make print statements more readable for troubleshooting python versioning * clean up build file * update version for pre-release * add TODO * add tests for conda packages before uploading * update ci comments and branches * remove macos test of pip wheel since python 3.9 is not supported by setup-python action * Upgrade build actions for release (#1779) * update `build.yml` so it matches updates from `build_manual.yml` * test `build.yml` without uploading * test again using build_manual.yml * build pip wheel with Ubuntu and turn off caching so build.yml exactly matches build_manual.yml * `build.yml` on release only and upload * testing caching * `use-only-tar-bz2: true` makes environment unsolvable, change it back * Update .github/workflows/build_manual.yml Co-authored-by: Liezl Maree <[email protected]> * Update .github/workflows/build.yml Co-authored-by: Liezl Maree <[email protected]> * bump pre-release version * fix version for pre-release * run build and upload on release! * try setting `CACHE_NUMBER` to 1 with `use-only-tar-bz2` set to true * increasing the cache number to reset the cache does work when `use-only-tar-bz2` is set to true * publish and upload on release only --------- Co-authored-by: Liezl Maree <[email protected]> * Add ZMQ support via GUI and CLI (#1780) * Add ZMQ support via GUI and CLI, automatic port handler, separate utils module for the functions * Change menu name to match deleting predictions beyond max instance (#1790) Change menu and function names * Fix website build and remove build cache across workflows (#1786) * test with build_manual on push * comment out caching in build manual * remove cache step from builad manual since environment resolves when this is commented out * comment out cache in build ci * remove cache from build on release * remove cache from website build * test website build on push * add name to checkout step * update checkout to v4 * update checkout to v4 in build ci * remove cache since build ci works without it * update upload-artifact to v4 in build ci * update second chechout to v4 in build ci * update setup-python to v5 in build ci * update download-artifact to v4 in build ci * update checkout to v4 in build ci * update checkout to v4 in website build * update setup-miniconda to v3.0.3 in website build * update actions-gh-pages to v4 in website build * update actions checkout and setup-python in ci * update checkout action in ci to v4 * pip install lxml[html_clean] because of error message during action * add error message to website to explain why pip install lxml[html_clean] * remove my branch for pull request * Bump to 1.4.1a1 (#1791) * bump versions to 1.4.1a1 * we can change the version on the installation page since this will be merged into the develop branch and not main * Fix windows conda package upload and build ci (#1792) * windows OS is 2022 not 2019 on runner * upload windows conda build manually but not pypi build * remove comment and run build ci * change build manual back so that it doesn't upload * remove branch from build manual * update installation docs for 1.4.1a1 * Fix zmq inference (#1800) * Ensure that we always pass in the zmq_port dict to LossViewer * Ensure zmq_ports has correct keys inside LossViewer * Use specified controller and publish ports for first attempted addresses * Add test for ports being set in LossViewer * Add max attempts to find unused port * Fix find free port loop and add for controller port also * Improve code readablility and reuse * Improve error message when unable to find free port * Set selected instance to None after removal (#1808) * Add test that selected instance set to None after removal * Set selected instance to None after removal * Add `InstancesList` class to handle backref to `LabeledFrame` (#1807) * Add InstancesList class to handle backref to LabeledFrame * Register structure/unstructure hooks for InstancesList * Add tests for the InstanceList class * Handle case where instance are passed in but labeled_frame is None * Add tests relevant methods in LabeledFrame * Delegate setting frame to InstancesList * Add test for PredictedInstance.frame after complex merge * Add todo comment to not use Instance.frame * Add rtest for InstasnceList.remove * Use normal list for informative `merged_instances` * Add test for copy and clear * Add copy and clear methods, use normal lists in merge method * Bump to v1.4.1a2 (#1835) bump to 1.4.1a2 * Updated trail length viewing options (#1822) * updated trail length optptions * Updated trail length options in the view menu * Updated `prefs` to include length info from `preferences.yaml` * Added trail length as method of `MainWindow` * Updated trail length documentation * black formatting --------- Co-authored-by: Keya Loding <[email protected]> * Handle case when no frame selection for trail overlay (#1832) * Menu option to open preferences directory and update to util functions to pathlib (#1843) * Add menu to view preferences directory and update to pathlib * text formatting * Add `Keep visualizations` checkbox to training GUI (#1824) * Renamed save_visualizations to view_visualizations for clarity * Added Delete Visualizations button to the training pipeline gui, exposed del_viz_predictions config option to the user * Reverted view_ back to save_ and changed new training checkbox to Keep visualization images after training. * Fixed keep_viz config option state override bug and updated keep_viz doc description * Added test case for reading training CLI argument correctly * Removed unnecessary testing code * Creating test case to check for viz folder * Finished tests to check CLI argument reading and viz directory existence * Use empty string instead of None in cli args test * Use keep_viz_images false in most all test configs (except test to override config) --------- Co-authored-by: roomrys <[email protected]> * Allowing inference on multiple videos via `sleap-track` (#1784) * implementing proposed code changes from issue #1777 * comments * configuring output_path to support multiple video inputs * fixing errors from preexisting test cases * Test case / code fixes * extending test cases for mp4 folders * test case for output directory * black and code rabbit fixes * code rabbit fixes * as_posix errors resolved * syntax error * adding test data * black * output error resolved * edited for push to dev branch * black * errors fixed, test cases implemented * invalid output test and invalid input test * deleting debugging statements * deleting print statements * black * deleting unnecessary test case * implemented tmpdir * deleting extraneous file * fixing broken test case * fixing test_sleap_track_invalid_output * removing support for multiple slp files * implementing talmo's comments * adding comments * Add object keypoint similarity method (#1003) * Add object keypoint similarity method * fix max_tracking * correct off-by-one error * correct off-by-one error * Generate suggestions using max point displacement threshold (#1862) * create function max_point_displacement, _max_point_displacement_video. Add to yaml file. Create test for new function . . . will need to edit * remove unnecessary for loop, calculate proper displacement, adjusted tests accordingly * Increase range for displacement threshold * Fix frames not found bug * Return the latter frame index * Lint --------- Co-authored-by: roomrys <[email protected]> * Added Three Different Cases for Adding a New Instance (#1859) * implemented paste with offset * right click and then default will paste the new instance at the location of the cursor * modified the logics for creating new instance * refined the logic * fixed the logic for right click * refined logics for adding new instance at a specific location * Remove print statements * Comment code * Ensure that we choose a non nan reference node * Move OOB nodes to closest in-bounds position --------- Co-authored-by: roomrys <[email protected]> * Allow csv and text file support on sleap track (#1875) * initial changes * csv support and test case * increased code coverage * Error fixing, black, deletion of (self-written) unused code * final edits * black * documentation changes * documentation changes * Fix GUI crash on scroll (#1883) * Only pass wheelEvent to children that can handle it * Add test for wheelEvent * Fix typo to allow rendering videos with mp4 (Mac) (#1892) Fix typo to allow rendering videos with mp4 * Do not apply offset when double clicking a `PredictedInstance` (#1888) * Add offset argument to newInstance and AddInstance * Apply offset of 10 for Add Instance menu button (Ctrl + I) * Add offset for docks Add Instance button * Make the QtVideoPlayer context menu unit-testable * Add test for creating a new instance * Add test for "New Instance" button in `InstancesDock` * Fix typo in docstring * Add docstrings and typehinting * Remove unused imports and sort imports * Refactor video writer to use imageio instead of skvideo (#1900) * modify `VideoWriter` to use imageio with ffmpeg backend * check to see if ffmpeg is present * use the new check for ffmpeg * import imageio.v2 * add imageio-ffmpeg to environments to test * using avi format for now * remove SKvideo videowriter * test `VideoWriterImageio` minimally * add more documentation for ffmpeg * default mp4 for ffmpeg should be mp4 * print using `IMAGEIO` when using ffmpeg * mp4 for ffmpeg * use mp4 ending in test * test `VideoWriterImageio` with avi file extension * test video with odd size * remove redundant filter since imageio-ffmpeg resizes automatically * black * remove unused import * use logging instead of print statement * import cv2 is needed for resize * remove logging * Use `Video.from_filename` when structuring videos (#1905) * Use Video.from_filename when structuring videos * Modify removal_test_labels to have extension in filename * Use | instead of + in key commands (#1907) * Use | instead of + in key commands * Lint * Replace QtDesktop widget in preparation for PySide6 (#1908) * Replace to-be-depreciated QDesktopWidget * Remove unused imports and sort remaining imports * Remove unsupported |= operand to prepare for PySide6 (#1910) Fixes TypeError: unsupported operand type(s) for |=: 'int' and 'Option' * Use positional argument for exception type (#1912) traceback.format_exception has changed it's first positional argument's name from etype to exc in python 3.7 to 3.10 * Replace all Video structuring with Video.cattr() (#1911) * Remove unused AsyncVideo class (#1917) Remove unused AsyncVideo * Refactor `LossViewer` to use matplotlib (#1899) * use updated syntax for QtAgg backend of matplotlib * start add features to `MplCanvas` to replace QtCharts features in `LossViewer` (untested) * remove QtCharts imports and replace with MplCanvas * remove QtCharts imports and replace with MplCanvas * start using MplCanvas in LossViwer instead of QtCharts (untested) * use updated syntax * Uncomment all commented out QtChart * Add debug code * Refactor monitor to use LossViewer._init_series method * Add monitor only debug code * Add methods for setting up axes and legend * Add the matplotlib canvas to the widget * Resize axis with data (no log support yet) * Try using PathCollection for "batch" * Get "batch" plotting with ax.scatter (no log support yet) * Add log support * Add a _resize_axis method * Modify init_series to work for ax.plot as well * Use matplotlib to plot epoch_loss line * Add method _add_data_to_scatter * Add _add_data_to_plot method * Add docstring to _resize_axes * Add matplotlib plot for val_loss * Add matplotlib scatter for val_loss_best * Avoid errors with setting log scale before any positive values * Add x and y axes labels * Set title (removing html tags) * Add legend * Adjust positioning of plot * Lint * Leave MplCanvas unchanged * Removed unused training_monitor.LossViewer * Resize fonts * Move legend outside of plot * Add debug code for montitor aesthetics * Use latex formatting to bold parts of title * Make axes aesthetic * Add midpoint grid lines * Set initial limits on x and y axes to be 0+ * Ensure x axis minimum is always resized to 0+ * Adjust plot to account for plateau patience title * Add debug code for plateau patience title line * Lint * Set thicker line width * Remove unused import * Set log axis on initialization * Make tick labels smaller * Move plot down a smidge * Move ylabel left a bit * Lint * Add class LossPlot * Refactor LossViewer to use LossPlot * Remove QtCharts code * Remove debug codes * Allocate space for figure items based on item's size * Refactor LossPlot to use underscores for internal methods * Ensure y_min, y_max not equal Otherwise we get an unnecessary teminal message: UserWarning: Attempting to set identical bottom == top == 3.0 results in singular transformations; automatically expanding. self.axes.set_ylim(y_min, y_max) --------- Co-authored-by: roomrys <[email protected]> Co-authored-by: roomrys <[email protected]> * Refactor `LossViewer` to use underscores for internal method names (#1919) Refactor LossViewer to use underscores for internal method names * Manually handle `Instance.from_predicted` structuring when not `None` (#1930) * Use `tf.math.mod` instead of `%` (#1931) * Option for Max Stride to be 128 (#1941) Co-authored-by: Max Weinberg <[email protected]> * Add discussion comment workflow (#1945) * Add a bot to autocomment on workflow * Use github markdown warning syntax * Add a multiline warning * Change happy coding to happy SLEAPing Co-authored-by: Talmo Pereira <[email protected]> --------- Co-authored-by: roomrys <[email protected]> Co-authored-by: Talmo Pereira <[email protected]> * Add comment on issue workflow (#1946) * Add workflow to test conda packages (#1935) * Add missing imageio-ffmpeg to meta.ymls (#1943) * Update installation docs 1.4.1 (#1810) * [wip] Updated installation docs * Add tabs for different OS installations * Move installation methods to tabs * Use tabs.css * FIx styling error (line under last tab in terminal hint) * Add installation instructions before TOC * Replace mamba with conda * Lint * Find good light colors not switching when change dark/light themes * Get color scheme switching with dark/light toggle button * Upgrade website build dependencies * Remove seemingly unneeded dependencies from workflow * Add myst-nb>=0.16.0 lower bound * Trigger dev website build * Fix minor typo in css * Add miniforge and one-liner installs for package managers --------- Co-authored-by: roomrys <[email protected]> Co-authored-by: Talmo Pereira <[email protected]> * Add imageio dependencies for pypi wheel (#1950) Add imagio dependencies for pypi wheel Co-authored-by: roomrys <[email protected]> * Do not always color skeletons table black (#1952) Co-authored-by: roomrys <[email protected]> * Remove no module named work error (#1956) * Do not always color skeletons table black * Remove offending (possibly unneeded) line that causes the no module named work error to print in terminal * Remove offending (possibly unneeded) line that causes the no module named work error to print in terminal * Remove accidentally added changes * Add (failing) test to ensure menu-item updates with state change * Reconnect callback for menu-item (using lambda) * Add (failing) test to ensure menu-item updates with state change Do not assume inital state * Reconnect callback for menu-item (using lambda) --------- Co-authored-by: roomrys <[email protected]> * Add `normalized_instance_similarity` method (#1939) * Add normalize function * Expose normalization function * Fix tests * Expose object keypoint sim function * Fix tests * Handle skeleton decoding internally (#1961) * Reorganize (and add) imports * Add (and reorganize) imports * Modify decode_preview_image to return bytes if specified * Implement (minimally tested) replace_jsonpickle_decode * Add support for using idx_to_node map i.e. loading from Labels (slp file) * Ignore None items in reduce_list * Convert large function to SkeletonDecoder class * Update SkeletonDecoder.decode docstring * Move decode_preview_image to SkeletonDecoder * Use SkeletonDecoder instead of jsonpickle in tests * Remove unused imports * Add test for decoding dict vs tuple pystates * Handle skeleton encoding internally (#1970) * start class `SkeletonEncoder` * _encoded_objects need to be a dict to add to * add notebook for testing * format * fix type in docstring * finish classmethod for encoding Skeleton as a json string * test encoded Skeleton as json string by decoding it * add test for decoded encoded skeleton * update jupyter notebook for easy testing * constraining attrs in dev environment to make sure decode format is always the same locally * encode links first then encode source then target then type * save first enconding statically as an input to _get_or_assign_id so that we do not always get py/id * save first encoding statically * first encoding is passed to _get_or_assign_id * use first_encoding variable to determine if we should assign a py/id * add print statements for debugging * update notebook for easy testing * black * remove comment * adding attrs constraint to show this passes for certain attrs version only * add import * switch out jsonpickle.encode * oops remove import * can attrs be unconstrained? * forgot comma * pin attrs for testing * test Skeleton from json, template, with symmetries, and template * use SkeletonEncoder.encode * black * try removing None values in EdgeType reduced * Handle case when nodes are replaced by integer indices from caller * Remove prototyping notebook * Remove attrs pins * Remove sort keys (which flips the neccessary ordering of our py/ids) * Do not add extra indents to encoded file * Only append links after fully encoded (fat-finger) * Remove outdated comment * Lint --------- Co-authored-by: Talmo Pereira <[email protected]> Co-authored-by: roomrys <[email protected]> * Pin ndx-pose<0.2.0 (#1978) * Pin ndx-pose<0.2.0 * Typo * Sort encoded `Skeleton` dictionary for backwards compatibility (#1975) * Add failing test to check that encoded Skeleton is sorted * Sort Skeleton dictionary before encoding * Remove unused import * Disable comment bot for now * Fix COCO Dataset Loading for Invisible Keypoints (#2035) Update coco.py # Fix COCO Dataset Loading for Invisible Keypoints ## Issue When loading COCO datasets, keypoints marked as invisible (flag=0) are currently skipped and later placed randomly within the instance's bounding box. However, in COCO format, these keypoints may still have valid coordinate information that should be preserved (see toy_dataset for expected vs. current behavior). ## Changes Modified the COCO dataset loading logic to: - Check if invisible keypoints (flag=0) have non-zero coordinates - If coordinates are (0,0), skip the point (existing behavior) - If coordinates are not (0,0), create the point at those coordinates but mark it as not visible - Maintain existing behavior for visible (flag=2) and labeled * Lint * Add tracking score as seekbar header options (#2047) * Add `tracking_score` as a constructor arg for `PredictedInstance` * Add `tracking_score` to ID models * Add fixture with tracking scores * Add tracking score to seekbar header * Add bonsai guide for sleap docs (#2050) * [WIP] Add bonsai guide page * Add more information to the guide with images * add branch for website build * Typos * fix links * Include suggestions * Add more screenshots and refine the doc * Remove branch from website workflow * Completed documentation edits from PR made by reviewer + review bot. --------- Co-authored-by: Shrivaths Shyam <[email protected]> Co-authored-by: Liezl Maree <[email protected]> * Don't mark complete on instance scaling (#2049) * Add check for instances with track assigned before training ID models (#2053) * Add menu item for deleting instances beyond frame limit (#1797) * Add menu item for deleting instances beyond frame limit * Add test function to test the instances returned * typos * Update docstring * Add frame range form * Extend command to use frame range --------- Co-authored-by: Talmo Pereira <[email protected]> * Highlight instance box on hover (#2055) * Make node marker and label sizes configurable via preferences (#2057) * Make node marker and label sizes configurable via preferences * Fix test * Enable touchpad pinch to zoom (#2058) * Fix import PySide2 -> qtpy (#2065) * Fix import PySide2 -> qtpy * Remove unnecessary print statements. * Add channels for pip conda env (#2067) * Add channels for pypi conda env * Trigger dev website build * Separate the video name and its filepath columns in `VideoTablesModel` (#2052) * add option to show video names with filepath * add doc * new feature added successfully * delete unnecessary code * remove attributes from video object * Update dataviews.py * remove all properties * delete toggle option * remove video show * fix the order of the columns * remove options * Update sleap/gui/dataviews.py Co-authored-by: Liezl Maree <[email protected]> * Update sleap/gui/dataviews.py Co-authored-by: Liezl Maree <[email protected]> * use pathlib instead of substrings * Update dataviews.py Co-authored-by: Liezl Maree <[email protected]> * Use Path instead of pathlib.Path and sort imports and remove unused imports * Use item.filename instead of getattr --------- Co-authored-by: Liezl Maree <[email protected]> * Make status bar dependent on UI mode (#2063) * remove bug for dark mode * fix toggle case --------- Co-authored-by: Liezl Maree <[email protected]> * Bump version to 1.4.1 (#2062) * Bump version to 1.4.1 * Trigger conda/pypi builds (no upload) * Trigger website build * Add dev channel to installation instructions --------- Co-authored-by: Talmo Pereira <[email protected]> * Add -c sleap/label/dev channel for win/linux - also trigger website build --------- Co-authored-by: Scott Yang <[email protected]> Co-authored-by: Shrivaths Shyam <[email protected]> Co-authored-by: getzze <[email protected]> Co-authored-by: Lili Karashchuk <[email protected]> Co-authored-by: Sidharth Srinath <[email protected]> Co-authored-by: sidharth srinath <[email protected]> Co-authored-by: Talmo Pereira <[email protected]> Co-authored-by: KevinZ0217 <[email protected]> Co-authored-by: Elizabeth <[email protected]> Co-authored-by: Talmo Pereira <[email protected]> Co-authored-by: eberrigan <[email protected]> Co-authored-by: vaibhavtrip29 <[email protected]> Co-authored-by: Keya Loding <[email protected]> Co-authored-by: Keya Loding <[email protected]> Co-authored-by: Hajin Park <[email protected]> Co-authored-by: Elise Davis <[email protected]> Co-authored-by: gqcpm <[email protected]> Co-authored-by: Andrew Park <[email protected]> Co-authored-by: roomrys <[email protected]> Co-authored-by: MweinbergUmass <[email protected]> Co-authored-by: Max Weinberg <[email protected]> Co-authored-by: DivyaSesh <[email protected]> Co-authored-by: Felipe Parodi <[email protected]> Co-authored-by: croblesMed <[email protected]>
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Description
analysis.csvas an option for exporting a csv usingsleap-convertCLIexport_csvfunction toLabelsclass for exporting a csv using the APITypes of changes
Does this address any currently open issues?
#1713
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