Changelog¶

v0.2.0 ¶

What's Changed

Update backend filename when backend isn't created on replace by @talmo in #127
Update labels videos list on replace by @talmo in #128
Add video writing by @talmo in #129
- Add sio.VideoWriter: basic imageio-ffmpeg video writer with sensible H264 presets. This can be used as a context manager:
```
with sio.VideoWriter("video.mp4") as vw:
    for frame in video:
        vw(frame)
```
- Add sio.save_video: high-level video writing. This can be used to quickly write a set of frames or even a whole Video for easy (if inefficient) re-encoding:
```
bad_video = sio.load_video("unseekable.avi")
sio.save_video(bad_video, "seekable.mp4")
```
- Added IndexError in VideoBackend to enable sequence protocol for iteration over Videos:
```
for frame in video:
    pass
```
- Refactored sio.io.video to sio.io.video_reading.
Fixes to get JABS export to work with new data by @talmo in #132
Make skeleton nodes mutable by @talmo in #135
Add skeleton manipulation utilities by @talmo in #136
- Skeleton
  - __contains__(node: NodeOrIndex): Returns True if a node exists in the skeleton.
  - rebuild_cache(): Method allowing explicit regeneration of the caching attributes from the nodes.
  - Caching attributes are now named _name_to_node_cache and _node_to_ind_cache, better reflecting the mapping directionality.
  - require_node(node: NodeOrIndex, add_missing: bool = True): Returns a Node given a Node, int or str. If add_missing is True, the node is added or created, otherwise an IndexError is raised. This is helpful for flexibly converting between node representations with convenient existence handling.
  - add_nodes(list[Node | str]): Convenience method to add a list of nodes.
  - add_edges(edges: list[Edge | tuple[NodeOrIndex, NodeOrIndex]]): Convenience method to add a list of edges.
  - rename_nodes(name_map: dict[NodeOrIndex, str] | list[str]): Method to rename nodes either by specifying a potentially partial mapping from node(s) to new name(s), or a list of new names. Handles updating both the Node.name attributes and the cache.
  - rename_node(old_name: NodeOrIndex, new_name: str): Shorter syntax for renaming a single node.
  - remove_nodes(nodes: list[NodeOrIndex]): Method for removing nodes from the skeleton and updating caches. Does NOT update corresponding instances.
  - remove_node(node: NodeOrIndex): Shorter syntax for removing a single node.
  - reorder_nodes(new_order: list[NodeOrIndex]): Method for setting the order of the nodes within the skeleton with cache updating. Does NOT update corresponding instances.
- Instance/PredictedInstance
  - update_skeleton(): Updates the points attribute on the instance to reflect changes in the associated skeleton (removed nodes and reordering). This is called internally after updating the skeleton from the Labels level, but also exposed for more complex data manipulation workflows.
  - replace_skeleton(new_skeleton: Skeleton, node_map: dict[NodeOrIndex, NodeOrIndex] | None = None, rev_node_map: dict[NodeOrIndex, NodeOrIndex] | None = None): Method to replace the skeleton on the instance with optional capability to specify a node mapping so that data stored in the points attribute is retained and associated with the right nodes in the new skeleton. Mapping is specified in node_map from old to new nodes and defaults to mapping between node objects with the same name. rev_node_map maps new nodes to old nodes and is used internally when calling from the Labels level as it bypasses validation.
- Labels
  - instances: Convenience property that returns a generator that loops over all labeled frames and returns all instances. This can be lazily iterated over without having to construct a huge list of all the instances.
  - rename_nodes(name_map: dict[NodeOrIndex, str] | list[str], skeleton: Skeleton | None = None): Method to rename nodes in a specified skeleton within the labels.
  - remove_nodes(nodes: list[NodeOrIndex], skeleton: Skeleton | None = None): Method to remove nodes in a specified skeleton within the labels. This also updates all instances associated with the skeleton, removing point data for the removed nodes.
  - reorder_nodes(new_order: list[NodeOrIndex], skeleton: Skeleton | None = None): Method to reorder nodes in a specified skeleton within the labels. This also updates all instances associated with the skeleton, reordering point data for the nodes.
  - replace_skeleton(new_skeleton: Skeleton, old_skeleton: Skeleton | None = None, node_map: dict[NodeOrIndex, NodeOrIndex] | None = None): Method to replace a skeleton entirely within the labels, updating all instances associated with the old skeleton to use the new skeleton, optionally with node remapping to retain previous point data.
Add more checks for video seeking/reading failure by @talmo in #138
Fix HDF5Video edge cases by @talmo in #137
Docs changelog generation by @talmo in #130
Add Labels.extract, Labels.trim and Video.save by @talmo in #140
- LabeledFrame.frame_idx: Now always converted to int type.
- Video.close(): Now caches backend metadata to Video.backend_metadata to persist metadata on close.
- copy.deepcopy() now works on Video objects even if backend is open.
- Video.save(save_path: str | Path, frame_inds: list[int] | np.ndarray | None = None, video_kwargs: dict[str, Any] | None = None): Method to save a video file to an MP4 using VideoWriter with an optional subset of frames.
- Labels.extract(inds: list[int] | list[tuple[Video, int]] | np.ndarray, copy: bool = True): Add method to extract a subset of frames from the labels, optionally making a copy, and return a new Labels object.
- Labels.trim(save_path: str | Path, frame_inds: list[int] | np.ndarray, video: Video | int | None = None, video_kwargs: dict[str, Any] | None = None): Add method to extract a subset of the labels, write a video clip with the extracted friends, and adjust frame indices to match the clip.
Docs automation by @talmo in #141
Add more examples to docs by @talmo in #142

Full Changelog: v0.1.10...v0.2.0

v0.1.10 ¶

What's Changed

Fix embedded video lookup by @talmo in #122
Add better support for exporting and loading RGB videos from .pkg.slp files by @talmo in #125
Fix video indexing when embedding from labels that already have embedded data by @talmo in #126

Full Changelog: v0.1.9...v0.1.10

v0.1.9 ¶

What's Changed

Dependency management by @talmo in #118
- Drop av as a dependency since it's still a little buggy and doesn't have broad enough platform compatibility.
- Pin ndx-pose < 0.2.0 until #104 is merged in.
- Remove livecov dev tool as it was interfering with VSCode debugging.
Safer video loading from SLP by @talmo in #119
- Added sio.io.utils.is_file_accessible to check for readability by actually reading a byte. This catches permission and other esoteric filesystem errors (addresses #116).
- Explicit control over whether video files should be opened when loading labels with:sio.load_slp(..., open_videos=False)
- Explicit control over whether backend is auto-initialized when creating or using Video objects with Video(..., open_backend=False).
- More sanitization of filenames to posix/forward-slash safe forms when reading and writing SLP files.
Fix split calculation and allow for not embedding by @talmo in #120
- Fix: The function now correctly splits the labels into training, validation, and test sets based on the specified proportions (fixes #117). Previously, the validation fraction was being computed incorrectly in cases where its relative fraction was 1.0 after taking out the train split.
- Enhancement: Labels.make_training_splits(..., embed=False). Previously, the function would always embed the images, which could be slow for large projects. With this change, the embed parameter is introduced, allowing the user to choose whether to embed the images or save the labels with references to the source video files.

Full Changelog: v0.1.8...v0.1.9

v0.1.8 ¶

What's Changed

Fix docs by @talmo in #108
Support NumPy > 2.0 and Python 3.12 by @lochhh in #115

New Contributors

@lochhh made their first contribution in #115

Full Changelog: v0.1.7...v0.1.8

v0.1.7 ¶

What's Changed

Path sanitization hotfix by @talmo in #107

Full Changelog: v0.1.6...v0.1.7

v0.1.6 ¶

What's Changed

Grayscale property passthrough by @talmo in #99

Full Changelog: v0.1.5...v0.1.6

v0.1.5 ¶

What's Changed

Labels.split and Labels.make_training_splits by @talmo in #98

Full Changelog: v0.1.4...v0.1.5

v0.1.4 ¶

What's Changed

Add support for embedding images in .pkg.slp by @talmo in #91
- Saving SLP files with embedded images will re-save the embedded images.
- Embed images into SLP files with:
  - labels.save("labels.pkg.slp", embed="user") to embed frames with user-labeled instances (Instance)
  - labels.save("labels.pkg.slp", embed="user+suggestion") to embed frames with user-labeled instances and suggestion frames (useful for inference after training)
  - labels.save("labels.pkg.slp", embed="source") to restore the source video ("unembed")
Better reprs and QOL by @talmo in #96
- Better __repr__s for Skeleton, LabeledFrame, Labels, Instance, PredictedInstance
- Labels.append() and Labels.extend() to add LabeledFrames now will update Labels.tracks, Labels.skeletons and Labels.videos with contents.
- Labels.update() to manually update Labels.tracks, Labels.skeletons and Labels.videos with contents of Labels.labeled_frames and Labels.suggestions.
- Labels.replace_filenames(): multiple methods for replacing all video filenames across the project (#85).
- Skeleton.edge_names to return list of edges as tuples of string names
- Added docstrings to sio.load_video and related high level Video APIs to clarify supported file formats.
- Syntactic sugar: try to initialize video backend with Video(filename) construction (#94)

Note: This is a re-release of v0.1.3 which had a borked deployment.

Full Changelog: v0.1.2...v0.1.4

v0.1.3 ¶

What's Changed

Add support for embedding images in .pkg.slp by @talmo in #91
- Saving SLP files with embedded images will re-save the embedded images.
- Embed images into SLP files with:
  - labels.save("labels.pkg.slp", embed="user") to embed frames with user-labeled instances (Instance)
  - labels.save("labels.pkg.slp", embed="user+suggestion") to embed frames with user-labeled instances and suggestion frames (useful for inference after training)
  - labels.save("labels.pkg.slp", embed="source") to restore the source video ("unembed")
Better reprs and QOL by @talmo in #96
- Better __repr__s for Skeleton, LabeledFrame, Labels, Instance, PredictedInstance
- Labels.append() and Labels.extend() to add LabeledFrames now will update Labels.tracks, Labels.skeletons and Labels.videos with contents.
- Labels.update() to manually update Labels.tracks, Labels.skeletons and Labels.videos with contents of Labels.labeled_frames and Labels.suggestions.
- Labels.replace_filenames(): multiple methods for replacing all video filenames across the project (#85).
- Skeleton.edge_names to return list of edges as tuples of string names
- Added docstrings to sio.load_video and related high level Video APIs to clarify supported file formats.
- Syntactic sugar: try to initialize video backend with Video(filename) construction (#94)

Full Changelog: v0.1.2...v0.1.3

v0.1.2 ¶

What's Changed

Fix suggestions deserialization by @talmo in #95

Full Changelog: v0.1.1...v0.1.2

v0.1.1 ¶

What's Changed

Create docs pages by @talmo in #87
Add ImageVideo backend by @talmo in #88
Add SuggestionFrame by @talmo in #89
Implement ImageVideo support in SLP by @talmo in #90
Bump to v0.1.1 by @talmo in #93

Full Changelog: v0.1.0...v0.1.1

v0.1.0 ¶

What's Changed

Add skeleton utilities by @talmo in #76
- Skeleton.add_node: Add a node by name or object.
- Skeleton.add_edge: Add an edge by lists of names or objects.
- Skeleton.add_symmetry: Add a symmetry edge by lists of names or objects.
Update CI and versions by @talmo in #77
- Update dependency ranges (see below)
- Update action workflow versions
- Enable M1 mac runners
- Expand python version range to 3.7-3.12
  - Note: Python 3.7 is no longer tested in CI due to lack of conda-forge compatability.
- Enable pure conda-forge dependency setup
Bump to v0.1.0 by @talmo in #78
Fix multi-skeleton loading by @talmo in #79
- Fixes #71.
Add high level APIs by @talmo in #80
- Add load_video and load_file high level APIs (#48)
Labels QOL enhancements by @talmo in #81
- LabeledFrame.remove_predictions: Remove predicted instances from a labeled frame.
- LabeledFrame.remove_empty_instances: Remove instances with no visible points from a labeled frame.
- Labels.save: Instance-level convenience wrapper for sio.save_file.
- Labels.clean: Remove unused or empty frames, instances, videos, skeletons and tracks.
- Labels.remove_predictions: Remove predicted instances from all labeled frames (#69).
- Labels.__getitem__: Now supports lists, slices, numpy arrays, tuples of (Video, frame_idx) and Video.
Video QOL enhancements by @talmo in #82
- Video.is_open: Checks if the video exists and the backend is set.
- Video.open: Opens or restarts the backend for reading.
- Video.close: Closes the backend for reading.
- Video.exists: Check if the filename for the video exists.
- Video.replace_filename: Replace the filename and restart the backend.

Notes on dependency pins

ffmpeg < 6.1 due to imageio/imageio-ffmpeg#99
h5py >= 3.8.0 due to h5py/h5py#2118
python >= 3.8 due to h5py >= 3.8.0 (we still support python==3.7 via pip but this is not longer in CI)

Full Changelog: v0.0.14...v0.1.0

v0.0.14 ¶

What's Changed

Fix importing in Python 3.7 by @talmo in #75

Full Changelog: v0.0.13...v0.0.14

v0.0.13 ¶

What's Changed

Add sdist build by @talmo in #74

Full Changelog: v0.0.12...v0.0.13

v0.0.12 ¶

What's Changed

Add support for the Kumar Lab's JABS format by @SkepticRaven in #63
Fix multi-video serialization in SLP by @talmo in #72

New Contributors

@SkepticRaven made their first contribution in #63

Full Changelog: v0.0.11...v0.0.12

v0.0.11 ¶

What's Changed

Video handle persistence by @talmo in #64
Bump to 0.0.11 by @talmo in #66

Full Changelog: v0.0.10...v0.0.11

v0.0.10 ¶

This is a hotfix to get around installing in older environments with numpy <1.20.

What's Changed

Fallback on import newer numpy.testing module by @talmo in #65

Full Changelog: v0.0.9...v0.0.10

v0.0.9 ¶

What's Changed

Fix serialization for negative anchors metadata field in SLP files by @talmo in #59
Fix edge unpacking by @talmo in #60
Bump to v0.0.9 and update usage docs by @talmo in #61

Full Changelog: v0.0.8...v0.0.9

v0.0.8 ¶

What's Changed

Fix docstring for LabeledFrame.predicted_instances by @talmo in #43
Parse skeleton symmetries from SLP files by @talmo in #53
Add Labels.skeleton convenience attribute by @talmo in #54
Write SLP files by @talmo in #55
Create video backend automatically if filename exists. by @talmo in #56

Full Changelog: v0.0.7...v0.0.8

v0.0.7 ¶

What's Changed

Pin imageio version by @talmo in #39
Fix detection of embedded images when loading SLP files by @talmo in #40

Full Changelog: v0.0.6...v0.0.7

v0.0.6 ¶

What's Changed

Add from predicted parsing by @talmo in #37

Full Changelog: v0.0.5...v0.0.6

v0.0.5 ¶

What's Changed

Basic path resolution by @talmo in #36

Full Changelog: v0.0.4...v0.0.5

v0.0.4 ¶

What's Changed

Fix build by including readme correctly in pyproject.toml by @talmo in #34
Add Labels.find and Labels.video by @talmo in #35

Full Changelog: v0.0.3...v0.0.4

v0.0.3 ¶

What's Changed

Update CI by @talmo in #32
- Switch to using pyproject.toml alone instead of setup.cfg.
- Remove mypy type enforcement -- this is too strict for a library intended to be this flexible.
- Use micromamba in GitHub Actions workflow instead of miniconda
Video backends by @talmo in #31
- This PR implements the core video backends for media files, HDF5 and embedded images.
Bump version by @talmo in #33

Full Changelog: v0.0.2...v0.0.3

v0.0.2 ¶

What's Changed

Fix version and readme badge by @talmo in #19
Add NWB support III - provenance writing by @h-mayorquin in #17
Propagated extracted backend dict to video object by @h-mayorquin in #18
Change equality semantics for Points and Instances by @quantumdot in #21
Metadata not correctly propagated to nwb bug by @h-mayorquin in #23
Add LabelStudio project support by @quantumdot in #26
Add propagation of start time when writing nwbfile by @h-mayorquin in #29
Refactoring pre v0.0.2 by @talmo in #27
- High-level API cleaned up to load_nwb, save_nwb, load_labelstudio, save_labelstudio
- Basic NWB loading support
- Add Label Studio functionality for inferring nodes.

New Contributors

@quantumdot made their first contribution in #21

Full Changelog: v0.0.1...v0.0.2

v0.0.1 ¶

Initial stable release of the package.

What's Changed

Initial setup by @talmo in #1
Docstring linting and contributor guide by @talmo in #4
Create sleap-io structures by @davidasamy in #2
Read SLP files by @davidasamy in #3
Initial refactor by @talmo in #5
Performance fixes by @talmo in #6
Added dunder __repr__ to labels object by @h-mayorquin in #8
Add fix for PR CI and add a test by @talmo in #9
Add write utilities by @roomrys in #11
Add nwb support I by @h-mayorquin in #12
Add Labels.numpy and organize fixtures by @roomrys in #13
Add NWB support II by @h-mayorquin in #15
Add tests and functionality for loading provenance data by @h-mayorquin in #14
Build workflow by @talmo in #16

New Contributors

@talmo made their first contribution in #1
@davidasamy made their first contribution in #2
@h-mayorquin made their first contribution in #8
@roomrys made their first contribution in #11

Full Changelog: https://github.com/talmolab/sleap-io/commits/v0.0.1