Sleap

What's Changed

Highlights
* Added scaling functionality for both the instances and bounding box. by sean-afshar in https://github.com/talmolab/sleap/pull/1133
* Add Skeleton Templates by aaprasad in https://github.com/talmolab/sleap/pull/1122
* Resumable Training by jimzers in https://github.com/talmolab/sleap/pull/1130
* Tracking: robust assignment of the best score to an instance by getzze in https://github.com/talmolab/sleap/pull/1062
* Set max instances for top down models by sheridana in https://github.com/talmolab/sleap/pull/1070
* Flexibly resize input layer of `tf.keras.Model` upon loading trained model by roomrys in https://github.com/talmolab/sleap/pull/1084
* GUI Training: Use hidden params from loaded config by roomrys in https://github.com/talmolab/sleap/pull/1053
* Nix export of tracking results by jgrewe in https://github.com/talmolab/sleap/pull/1068
* Expose MoveNet to the Inference GUI by sheridana in https://github.com/talmolab/sleap/pull/1190
* Add option to "Add Videos..." from single image files by eberrigan in https://github.com/talmolab/sleap/pull/1183
* Add GUI and API option to remove unused tracks by roomrys in https://github.com/talmolab/sleap/pull/1210
* Add instance and track copy/pasting by talmo in https://github.com/talmolab/sleap/pull/1206
* Expose supervised ID models to GUI by sheridana in https://github.com/talmolab/sleap/pull/1213
* Ensure data format compatibility by roomrys in https://github.com/talmolab/sleap/pull/1222

Full Changelog

Documentation
* Change 'M1' to 'Apple Silicon' by roomrys in https://github.com/talmolab/sleap/pull/1188
* Update the Documentation badge by roomrys in https://github.com/talmolab/sleap/pull/1211

Enhancements
* GUI Training: Use hidden params from loaded config by roomrys in https://github.com/talmolab/sleap/pull/1053
* Add optional unragging arg to model export by sheridana in https://github.com/talmolab/sleap/pull/1054
* Tracking: robust assignment of the best score to an instance by getzze in https://github.com/talmolab/sleap/pull/1062
* Set max instances for top down models by sheridana in https://github.com/talmolab/sleap/pull/1070
* Flexibly resize input layer of `tf.keras.Model` upon loading trained model by roomrys in https://github.com/talmolab/sleap/pull/1084
* Add Option to Make Trail Shade Darker/Lighter by roomrys in https://github.com/talmolab/sleap/pull/1103
* Nix export of tracking results by jgrewe in https://github.com/talmolab/sleap/pull/1068
* Added scaling functionality for both the instances and bounding box. by sean-afshar in https://github.com/talmolab/sleap/pull/1133
* Add better error message for top down by roomrys in https://github.com/talmolab/sleap/pull/1121
* Add central padding to SizeMatcher by jiayinghsu in https://github.com/talmolab/sleap/pull/1129
* Added MoveNet as an external model reference by jiayinghsu in https://github.com/talmolab/sleap/pull/1141
* Resumable Training by jimzers in https://github.com/talmolab/sleap/pull/1130
* GenericTableModel/View improvements by jgrewe in https://github.com/talmolab/sleap/pull/1163
* Add Skeleton Templates by aaprasad in https://github.com/talmolab/sleap/pull/1122
* Add better error message for top down by roomrys in https://github.com/talmolab/sleap/pull/1121
* Add option of 2 for marker size by roomrys in https://github.com/talmolab/sleap/pull/1205
* Support new DLC multi-animal configs by roomrys in https://github.com/talmolab/sleap/pull/1204
* Expose MoveNet to the Inference GUI by sheridana in https://github.com/talmolab/sleap/pull/1190
* Add option to "Add Videos..." from single image files by eberrigan in https://github.com/talmolab/sleap/pull/1183
* Add GUI and API option to remove unused tracks by roomrys in https://github.com/talmolab/sleap/pull/1210
* Add instance and track copy/pasting by talmo in https://github.com/talmolab/sleap/pull/1206
* Expose supervised ID models to GUI by sheridana in https://github.com/talmolab/sleap/pull/1213
* Toggle grayscale of all videos using "Toggle Grayscale" button by roomrys in https://github.com/talmolab/sleap/pull/1215

Fixes
* Fix config option to `split_by_inds` by roomrys in https://github.com/talmolab/sleap/pull/1060
* Don't create instances during inference if no points were found by talmo in https://github.com/talmolab/sleap/pull/1073
* Add one-line fix to VideoWriterSkyvideo by roomrys in https://github.com/talmolab/sleap/pull/1082
* Fix parser for sleap-export by roomrys in https://github.com/talmolab/sleap/pull/1085
* Refactor commands to load project as `AppCommand`s by roomrys in https://github.com/talmolab/sleap/pull/1098
* Create signal that updates plot instead of removing and replotting items by roomrys in https://github.com/talmolab/sleap/pull/1134
* Fix symmetric skeletons (via table input) by roomrys in https://github.com/talmolab/sleap/pull/1136
* Fix body vs symmetry subgraph filtering by talmo in https://github.com/talmolab/sleap/pull/1142
* Handle changing backbones in training editor GUI by talmo in https://github.com/talmolab/sleap/pull/1140
* Hotfix for video save 1098 by roomrys in https://github.com/talmolab/sleap/pull/1148
* Update no-cuda-env to fix pillow errors by roomrys in https://github.com/talmolab/sleap/pull/1201
* Fix environment.yml by talmo in https://github.com/talmolab/sleap/pull/1202
* Fix typo in `Skeleton.__repr__` by roomrys in https://github.com/talmolab/sleap/pull/1200
* Split trainer cli function into two functions by roomrys in https://github.com/talmolab/sleap/pull/1197
* Threaded inference by talmo in https://github.com/talmolab/sleap/pull/1203
* Emit the signals to reset table views when data is empty by talmo in https://github.com/talmolab/sleap/pull/1207
* Ensure data format compatibility by roomrys in https://github.com/talmolab/sleap/pull/1222

New Contributors
* jgrewe made their first contribution in https://github.com/talmolab/sleap/pull/1068
* sean-afshar made their first contribution in https://github.com/talmolab/sleap/pull/1133
* eberrigan made their first contribution in https://github.com/talmolab/sleap/pull/1183

**Full Changelog**: https://github.com/talmolab/sleap/compare/v1.2.9...v1.3.0

Highlights
* Added scaling functionality for both the instances and bounding box. by sean-afshar in https://github.com/talmolab/sleap/pull/1133
* Add Skeleton Templates by aaprasad in https://github.com/talmolab/sleap/pull/1122
* Resumable Training by jimzers in https://github.com/talmolab/sleap/pull/1130
* Tracking: robust assignment of the best score to an instance by getzze in https://github.com/talmolab/sleap/pull/1062
* Set max instances for top down models by sheridana in https://github.com/talmolab/sleap/pull/1070
* Flexibly resize input layer of `tf.keras.Model` upon loading trained model by roomrys in https://github.com/talmolab/sleap/pull/1084
* GUI Training: Use hidden params from loaded config by roomrys in https://github.com/talmolab/sleap/pull/1053
* Nix export of tracking results by jgrewe in https://github.com/talmolab/sleap/pull/1068

Full changelog

Documentation
* Change 'M1' to 'Apple Silicon' by roomrys in https://github.com/talmolab/sleap/pull/1188

Enhancements
* GUI Training: Use hidden params from loaded config by roomrys in https://github.com/talmolab/sleap/pull/1053
* Add optional unragging arg to model export by sheridana in https://github.com/talmolab/sleap/pull/1054
* Tracking: robust assignment of the best score to an instance by getzze in https://github.com/talmolab/sleap/pull/1062
* Set max instances for top down models by sheridana in https://github.com/talmolab/sleap/pull/1070
* Flexibly resize input layer of `tf.keras.Model` upon loading trained model by roomrys in https://github.com/talmolab/sleap/pull/1084
* Add Option to Make Trail Shade Darker/Lighter by roomrys in https://github.com/talmolab/sleap/pull/1103
* Nix export of tracking results by jgrewe in https://github.com/talmolab/sleap/pull/1068
* Added scaling functionality for both the instances and bounding box. by sean-afshar in https://github.com/talmolab/sleap/pull/1133
* Add better error message for top down by roomrys in https://github.com/talmolab/sleap/pull/1121
* Add central padding to SizeMatcher by jiayinghsu in https://github.com/talmolab/sleap/pull/1129
* Added MoveNet as an external model reference by jiayinghsu in https://github.com/talmolab/sleap/pull/1141
* Resumable Training by jimzers in https://github.com/talmolab/sleap/pull/1130
* GenericTableModel/View improvements by jgrewe in https://github.com/talmolab/sleap/pull/1163
* Add Skeleton Templates by aaprasad in https://github.com/talmolab/sleap/pull/1122
* Add better error message for top down by roomrys in https://github.com/talmolab/sleap/pull/1121

Fixes
* Fix config option to `split_by_inds` by roomrys in https://github.com/talmolab/sleap/pull/1060
* Don't create instances during inference if no points were found by talmo in https://github.com/talmolab/sleap/pull/1073
* Add one-line fix to VideoWriterSkyvideo by roomrys in https://github.com/talmolab/sleap/pull/1082
* Fix parser for sleap-export by roomrys in https://github.com/talmolab/sleap/pull/1085
* Refactor commands to load project as `AppCommand`s by roomrys in https://github.com/talmolab/sleap/pull/1098
* Create signal that updates plot instead of removing and replotting items by roomrys in https://github.com/talmolab/sleap/pull/1134
* Fix symmetric skeletons (via table input) by roomrys in https://github.com/talmolab/sleap/pull/1136
* Fix body vs symmetry subgraph filtering by talmo in https://github.com/talmolab/sleap/pull/1142
* Handle changing backbones in training editor GUI by talmo in https://github.com/talmolab/sleap/pull/1140
* Hotfix for video save 1098 by roomrys in https://github.com/talmolab/sleap/pull/1148

New Contributors
* jgrewe made their first contribution in https://github.com/talmolab/sleap/pull/1068
* sean-afshar made their first contribution in https://github.com/talmolab/sleap/pull/1133

See the [Installation page](https://sleap.ai/installation.html) in the docs for more info.

Highlights
- Prefer user instances when calling Labels.numpy() (996)
- Add upper limit of the instance count in prediction score labeling suggestion method (981)
- Add more options to render video: wedges, palette, and distinctly color (998)
- Always draw user instances even if all nodes marked as not visible (1002)
- Add frame chunk method in labeling suggestions (1007)

Full changelog
Documentation
- Add sample movies to docs (992)
- Fix docs in Model_evaluation.ipynb (1034)

Enhancements
- Prefer user instances when calling Labels.numpy() (996)
- Add more options to render video: wedges, palette, and distinctly color (998)
- Add upper limit of the instance count in prediction score labeling suggestion method (981)
- Speed-up cache for multi-video projects (1017)
- Increase max number for target instances in simple tracker form (1037)
- Share usage data 1038
- Add frame chunk method in labeling suggestions (1007)

Fixes
- Fix printing of auto-selected GPU free memory (955)
- Fix add suggestions when target is current video (956)
- Fix `sleap-export` cli arg parsing (962)
- Fix cattr in Python 3.9 (967)
- Fix editing track name clears the old entry on double-click (980)
- Prune saved shifted instances (1001)
- Update suggestions upon video removal (1009)
- Correctly add .h5 extension to analysis files on Linux (1010)
- GUI Table: Do not set item value if same as current value (1022)
- Always draw user instances even if all nodes marked as not visible (1002)
- Shifted instances: make sure ref_instances is not empty (1029)
- Trails prefer user instances over predicted (1036)

See the [Installation page](https://sleap.ai/installation.html) in the docs for more info.

Full changelog
Fixes
- Add test and fix for GPU memory query (946, 949, 950)
- Fix sleap-export CLI and add docs (951)

See the [Installation page](https://sleap.ai/installation.html) in the docs for more info.

Highlights
- M1 Mac support (886)
- Fix shifted predictions on multi-resolution projects (902)
- Add GPU Memory Polling Function (911)
- Run sleap-track on video using index (920)

Full changelog
Documentation
- Add more documentation for nwb extension (861)
- Add conda downloads badge to README (869)
- Update link to contributing guideline
- Update CLA

Enhancements
- Integrate retracking into sleap-track (898)
- M1 Mac support (886)
- Run sleap-track on video using index (920)
- Use saved optical flow to use only on adjacent frames (870)
- Modify inference and centroid model to allow Bonsai ingestion (850)
- Append Unique Suggestions (874)
- Add GPU Memory Polling Function (911)

Fixes
- Add new track to linked predicted instance (879)
- Edit CI workflow to run on forked PRs
- Fix naming convention for sleap-convert (881)
- Fix cropping when rendering video (842)
- Fix shifted predictions on multi-resolution projects (902)
- Redraw plot to update trails after moving node (910)
- Force node to be placed w/in video (912)

See the [Installation page](https://sleap.ai/installation.html) in the docs for more info.

Highlights
N/A

Full changelog
Documentation
N/A

Enhancements
N/A

Fixes
- Fix conda packaging for `pynwb` and `ndx-pose` (860)