Import DLC with uniquebodyparts, add Tracks #1562
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Actionable comments generated: 3
Files ignored due to filter (3)
- tests/data/dlc/labeled-data/video/maudlc_testdata.csv
- tests/data/dlc/labeled-data/video/maudlc_testdata_v2.csv
- tests/data/dlc/maudlc_230_config.yaml
Files selected for processing (3)
- sleap/io/format/deeplabcut.py (5 hunks)
- sleap/nn/system.py (1 hunks)
- tests/io/test_formats.py (1 hunks)
Files skipped from review due to trivial changes (1)
- sleap/nn/system.py
Additional comments (Suppressed): 6
tests/io/test_formats.py (1)
- 235-242: The
test_maudlcfunction is parameterized with three different test data files. However, the functionreadis called only once inside the test function. This means that the same test will be run three times with different data, but only the results of the last run will be checked. If the intention is to run the test with each data file separately, thereadfunction call and subsequent assertions should be inside a loop that iterates over the test data files. If the intention is to run the test with all data files together, the test data files should be passed as a list to thereadfunction, assuming it supports this. Please verify the intended behavior.sleap/io/format/deeplabcut.py (5)
22-28: The import of
Trackfromsleap.instanceis new and is used later in the code to createTrackobjects for each animal. This change aligns with the PR summary which mentions the creation of Tracks with animal names.119-130: The
animal_nameslist has been replaced with atracksdictionary. This dictionary will storeTrackobjects for each animal, with the animal name as the key. This is a significant change and should be verified to ensure that it doesn't break any existing functionality that relies on theanimal_nameslist.178-210: The logic for creating instances has been updated to include the creation of
Trackobjects for each animal. This is a significant change and should be verified to ensure that it doesn't break any existing functionality that relies on the old instance creation logic.281-287: The code now checks for the presence of "uniquebodyparts" in the project data and adds them to the skeleton if they exist. This change aligns with the PR summary which mentions handling of unique body parts.
311-333: The logic for finding video files has been updated to handle different file extensions. This change aligns with the PR summary which mentions a bug fix related to assumptions about video file extensions.
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Actionable comments generated: 0
Files ignored due to filter (2)
- tests/data/dlc/labeled-data/video/CollectedData_LM.csv
- tests/data/dlc/madlc_230_config.yaml
Files selected for processing (2)
- sleap/io/format/deeplabcut.py (5 hunks)
- tests/io/test_formats.py (2 hunks)
Additional comments (Suppressed): 8
tests/io/test_formats.py (3)
198-202: The test data for
test_madlchas been reduced from three to two files. Ensure that this change does not affect the test's coverage and that all necessary scenarios are still being tested.234-241: A new test case
test_maudlchas been introduced. This test case reads labeled data from CSV files and asserts various properties of the data structure. It checks the skeleton node names, video filenames, frame coordinates, number of instances per frame, and track information. This is a good addition to the test suite as it increases the coverage of the code.242-303: The
test_maudlcfunction is well-structured and covers a wide range of assertions to ensure the correctness of the data structure. It checks the skeleton node names, video filenames, frame coordinates, number of instances per frame, and track information. This is a comprehensive test that should help catch any potential issues with the data structure.sleap/io/format/deeplabcut.py (5)
22-22: The import of
Dictfrom thetypingmodule is a new addition. Ensure that it is used appropriately in the code.119-130: The
tracksdictionary has been introduced to store tracks for each animal. This is a change from the previous version where animal names were stored in a list. This change seems to be in line with the new feature of creating Tracks with animal names.178-210: The logic for creating instances has been modified to use the
tracksdictionary. This is a significant change from the previous version where instances were created without tracks. Ensure that this change does not introduce any unexpected behavior.281-287: The
read()function has been updated to add nodes from the "uniquebodyparts" field if present. This is a new feature and should be tested thoroughly to ensure it works as expected.311-334: The logic for finding video files has been modified to handle different file extensions. This is a significant change from the previous version where only ".mp4" files were considered. Ensure that this change does not introduce any unexpected behavior.
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Actionable comments generated: 0
Files ignored due to filter (2)
- tests/data/dlc/labeled-data/video/CollectedData_LM.csv
- tests/data/dlc/madlc_230_config.yaml
Files selected for processing (2)
- sleap/io/format/deeplabcut.py (5 hunks)
- tests/io/test_formats.py (2 hunks)
Additional comments (Suppressed): 11
sleap/io/format/deeplabcut.py (5)
22-28: The import of
Trackfromsleap.instanceis new and is used for creating tracks for each animal. This is part of the new feature introduced in this PR.119-130: The
animal_nameslist has been replaced with atracksdictionary to store tracks for each animal. This is a significant change as it introduces the concept of tracks in the code.178-210: The logic for creating instances has been updated to use the
tracksdictionary. A new track is created for each animal if it doesn't exist already. This is a significant change as it introduces the concept of tracks in the code.281-287: The code now correctly parses the DLC config file to handle unique body parts that do not belong to any individual animal. This is part of the bug fix in this PR.
311-334: The code has been updated to handle video files with ".avi" extension, as the previous version only supported ".mp4" files. This is part of the bug fix in this PR.
tests/io/test_formats.py (6)
198-202: The new hunk has removed the "tests/data/dlc/madlc_230_config.yaml" from the test data. If this is intentional, ensure that the test case
test_madlcis still functioning as expected without this data. If it was removed by mistake, consider adding it back.234-240: The new hunk has added a new test case
test_maudlcwith three test data files. Ensure that these files exist and are in the correct format for the test case.249-255: The assertions are checking the properties of the labels object. Ensure that the expected values in the assertions match the actual values in the test data files.
257-263: The assertions are checking the number of labels and instances per frame. Ensure that the expected values in the assertions match the actual values in the test data files.
265-292: The assertions are checking the coordinates of the instances in the labels. Ensure that the expected values in the assertions match the actual values in the test data files.
295-303: The assertions are checking the properties of the tracks in the labels. Ensure that the expected values in the assertions match the actual values in the test data files.
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Thanks for the contribution @getzze! Looks like there's still a failing test related to the tracks, but just ping us when you're ready for review :) |
Codecov Report
@@ Coverage Diff @@
## develop #1562 +/- ##
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- Coverage 73.37% 73.36% -0.01%
===========================================
Files 134 134
Lines 23976 24009 +33
===========================================
+ Hits 17592 17614 +22
- Misses 6384 6395 +11
... and 3 files with indirect coverage changes 📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more |
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@talmo all the tests pass now, it's ready for reviewing. |
* 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 <52810689+shrivaths16@users.noreply.github.com> Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * 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 <38435167+roomrys@users.noreply.github.com> Co-authored-by: sidharth srinath <sidhumani22@gmail.com> * 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 <38435167+roomrys@users.noreply.github.com> * support loading slp files with non-compound types and str in metadata (#1566) Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * 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 <talmo@salk.edu> Co-authored-by: Talmo Pereira <talmo@princeton.edu> * 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 <berri104@gmail.com> * 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 <talmo@salk.edu> * 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 <38435167+roomrys@users.noreply.github.com> * Update .github/workflows/build.yml Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * 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 <38435167+roomrys@users.noreply.github.com> * 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 <keya@Keyas-MacBook-Air.local> * 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 <38435167+roomrys@users.noreply.github.com> * 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 <38435167+roomrys@users.noreply.github.com> * 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 <38435167+roomrys@users.noreply.github.com> * 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 <lmaree@ucsd.edu> Co-authored-by: roomrys <38435167+roomrys@users.noreply.github.com> * 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 <maxweinberg85@gmail.com> * 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 <talmo@salk.edu> --------- Co-authored-by: roomrys <lmaree@ucsd.edu> Co-authored-by: Talmo Pereira <talmo@salk.edu> * 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 <lmaree@ucsd.edu> Co-authored-by: Talmo Pereira <talmo@salk.edu> * Add imageio dependencies for pypi wheel (#1950) Add imagio dependencies for pypi wheel Co-authored-by: roomrys <lmaree@ucsd.edu> * Do not always color skeletons table black (#1952) Co-authored-by: roomrys <lmaree@ucsd.edu> * 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 <lmaree@ucsd.edu> * 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 <talmo@salk.edu> Co-authored-by: roomrys <38435167+roomrys@users.noreply.github.com> * 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 <52810689+shrivaths16@users.noreply.github.com> Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * 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 <talmo@salk.edu> * 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 <38435167+roomrys@users.noreply.github.com> * Update sleap/gui/dataviews.py Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * use pathlib instead of substrings * Update dataviews.py Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * Use Path instead of pathlib.Path and sort imports and remove unused imports * Use item.filename instead of getattr --------- Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * Make status bar dependent on UI mode (#2063) * remove bug for dark mode * fix toggle case --------- Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * 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 <talmo@salk.edu> * Add -c sleap/label/dev channel for win/linux - also trigger website build --------- Co-authored-by: Scott Yang <67733409+scott-yj-yang@users.noreply.github.com> Co-authored-by: Shrivaths Shyam <52810689+shrivaths16@users.noreply.github.com> Co-authored-by: getzze <getzze@gmail.com> Co-authored-by: Lili Karashchuk <krchtchk@gmail.com> Co-authored-by: Sidharth Srinath <69165889+ssrinath22@users.noreply.github.com> Co-authored-by: sidharth srinath <sidhumani22@gmail.com> Co-authored-by: Talmo Pereira <talmo@salk.edu> Co-authored-by: KevinZ0217 <96039456+KevinZ0217@users.noreply.github.com> Co-authored-by: Elizabeth <106755962+eberrigan@users.noreply.github.com> Co-authored-by: Talmo Pereira <talmo@princeton.edu> Co-authored-by: eberrigan <berri104@gmail.com> Co-authored-by: vaibhavtrip29 <82742234+vaibhavtrip29@users.noreply.github.com> Co-authored-by: Keya Loding <117320751+keyaloding@users.noreply.github.com> Co-authored-by: Keya Loding <keya@Keyas-MacBook-Air.local> Co-authored-by: Hajin Park <hajin1819@gmail.com> Co-authored-by: Elise Davis <elisemdavis02@gmail.com> Co-authored-by: gqcpm <63070177+gqcpm@users.noreply.github.com> Co-authored-by: Andrew Park <hep003@ucsd.edu> Co-authored-by: roomrys <lmaree@ucsd.edu> Co-authored-by: MweinbergUmass <143860933+MweinbergUmass@users.noreply.github.com> Co-authored-by: Max Weinberg <maxweinberg85@gmail.com> Co-authored-by: DivyaSesh <64513125+gitttt-1234@users.noreply.github.com> Co-authored-by: Felipe Parodi <53239931+felipe-parodi@users.noreply.github.com> Co-authored-by: croblesMed <carlosrobles00001@gmail.com>
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Hi there, I'm attempting to train a fresh SLEAP (single animal) model from my existing DLC labeled frames. The import appears to have worked beautifully! Nice job! However, I currently get the issue below, presumably because SLEAP is not expecting variations in the frame dimensions for the input images. I'm going to try the following hacks in the following order:
It'd be awesome if SLEAP could anticipate this issue and handle it gracefully. Traceback (most recent call last): |
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Hi @MHRosenberg, This is a pull request related to implementing aspects of the DLC import functionality, so not quite the right place for your bug report, but I did create an issue over here that you can follow: #2085 I'll continue the discussion over there. Thanks for the report! Cheers, Talmo |
Description
Importing Deeplabcut project with multiple animals failed because:
uniquebodypartslist. Unique body parts do not belong to any individual, so parsing the .csv file containing the labeled frames leads to key error of the type: Cannot find key ("animal", "unique_body_part"). Unique body parts belong to the "single" individual.In addition, this PR creates Tracks with the animal names (and "single" for the unique body parts), which is a new feature.
I added tests for importing Multiple animal DLC with uniquebodyparts.
Types of changes
Does this address any currently open issues?
#734
Outside contributors checklist
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Summary by CodeRabbit
summary()function, improving the readability of the code.test_maudlcto ensure the correct parsing and organization of data from CSV files.animal_nameslist with atracksdictionary for better data management.