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Add Track when add Instance #1408

Merged
merged 1 commit into from
Jul 25, 2023
Merged

Add Track when add Instance #1408

merged 1 commit into from
Jul 25, 2023

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roomrys
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@roomrys roomrys commented Jul 24, 2023

Description

Previously, the Labels.add_instance method would add the track associated with the instance to the cache, but not to the Labels object itself. I did not verify this, but I am sure this is handled in the call sequence when SLEAP adds tracks; however, it makes the SLEAP API a bit difficult to use (leading to KeyErrors in the LabelsDataCache dictionaries).

This PR adds the Track associated with an Instance to the Labels.tracks list when calling Labels.add_instance.

Types of changes

  • Bugfix
  • New feature
  • Refactor / Code style update (no logical changes)
  • Build / CI changes
  • Documentation Update
  • Other (better API)

Does this address any currently open issues?

[list open issues here]

Outside contributors checklist

  • Review the guidelines for contributing to this repository
  • Read and sign the CLA and add yourself to the authors list
  • Make sure you are making a pull request against the develop branch (not main). Also you should start your branch off develop
  • Add tests that prove your fix is effective or that your feature works
  • Add necessary documentation (if appropriate)

Thank you for contributing to SLEAP!

❤️

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codecov bot commented Jul 24, 2023

Codecov Report

Merging #1408 (bcefd05) into develop (d173303) will increase coverage by 0.00%.
The diff coverage is 100.00%.

@@           Coverage Diff            @@
##           develop    #1408   +/-   ##
========================================
  Coverage    72.74%   72.74%           
========================================
  Files          133      133           
  Lines        23723    23722    -1     
========================================
  Hits         17257    17257           
+ Misses        6466     6465    -1
Files Changed Coverage Δ
sleap/io/dataset.py 83.66% <100.00%> (+0.08%) ⬆️

📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more

@roomrys roomrys marked this pull request as ready for review July 24, 2023 21:10
@roomrys roomrys requested a review from talmo July 24, 2023 22:01
talmo
talmo approved these changes Jul 24, 2023
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LGTM! Good code reuse on the get_track_occupancy call!

@roomrys roomrys merged commit 0afbb9b into develop Jul 25, 2023
@roomrys roomrys deleted the liezl/add-tracks-when-add-instance branch July 25, 2023 00:37
roomrys pushed a commit that referenced this pull request Sep 10, 2023
SLEAP 1.3.2
bbc43c1 
commit 734283a
Author: Liezl Maree <38435167+roomrys@users.noreply.github.com>
Date:   Sun Sep 10 08:19:36 2023 -0700

    Bump to 1.3.2 (#1482)

    * Bump to 1.3.2

    * Run manual build w/o pip upload

    * Use `importlib.resources` if available

    * Rebuild mac conda package

    * Lint

    * Build/upload pip wheel

    * Reset build_manual and up build number

commit e424501
Author: Liezl Maree <38435167+roomrys@users.noreply.github.com>
Date:   Sat Sep 9 10:32:29 2023 -0700

    Add pip extras (#1481)

    * Rename pip to pypi, add tensorflow

    * Move out jupyter requirements from dev

    * Add extras for conda/pip jupyter and dev

    * Rename `pip` extra to `pypi`

    * Add build_ci workflow

    * Install pip package using extras

    * Rerun notebooks with new pip wheel

    * Internal import after adding relative path to sys

    * Build develop docs on this branch

    * Add comments to setup.py extras

    * Update installation docs

    * Add wget bypass for apple silicon mambaforge

    * Create func to combine req

    * Italicize jupyter instead of bold

    ---------

    Co-authored-by: modularizer <modularizer@gmail.com>
    Co-authored-by: roomrys <>

commit 93ef288
Author: Shrivaths Shyam <52810689+shrivaths16@users.noreply.github.com>
Date:   Sat Sep 9 03:12:58 2023 +0530

    Limit max tracks via track-local queues (#1447)

    * Initial commit

    * format files

    * [wip] adding local deque for tracks

    * format files

    * [wip] adding local deque for tracks

    * [wip] Add max tracking for simpletracker

    * [wip] Add max tracking for simple tracker

    * [wip] add missing argument

    * [wip] Add and modify test functions

    * [wip] Add and modify test functions

    * Bug fix and refactoring code

    * [wip] Add max tracking for flow tracker.

    * [wip] Including suggested changes

    * [wip] refactor code

    * Add test function to check max tracks

    * Added suggestions and feedback

    * Prevent the creation of more than max tracks when we have unmatched detections

    * Add tests

    * Use maximum tracking by default when loading model via high level API

    * Lint

    * Fix integration test

    * Refactor max tracker tests

    * Add integration test for CLI

    * typo

    * Add max tracks to the tracking GUI

    * Update CLI docs and add examples

    ---------

    Co-authored-by: Talmo Pereira <talmo@princeton.edu>
    Co-authored-by: Talmo Pereira <talmo@salk.edu>

commit 64655d6
Author: DivyaSesh <64513125+gitttt-1234@users.noreply.github.com>
Date:   Wed Sep 6 09:50:35 2023 -0700

    Fix Auto-select GPU (#1474)

    * Fix Auto-select GPU

    * Format file

    * Add variable in init

    * Format files

    * Add small test to ensure environment variable is set

    * Make linter happy

    ---------

    Co-authored-by: roomrys <lmaree@ucsd.edu>

commit 0ef52cd
Author: Liezl Maree <38435167+roomrys@users.noreply.github.com>
Date:   Thu Aug 17 11:03:51 2023 -0700

    Migrate to `importlib_resources` backport (#1458)

    * Switch to  backport

    * Remove `pkg_resources`

    * Clean-up function (non-logical)

    * Make linter happy

    * Fix-up path for last few stragglers

    * Use `Path.as_posix` method instead of `str`

commit e0eebb2
Author: Liezl Maree <38435167+roomrys@users.noreply.github.com>
Date:   Tue Aug 15 13:10:06 2023 -0700

    Handle error message edge case when finding yaml paths (#1456)

commit 6858563
Author: Liezl Maree <38435167+roomrys@users.noreply.github.com>
Date:   Fri Aug 11 11:33:14 2023 -0700

    Add message if drag drop fails (#1451)

    * Fix drag and drop

    * Feedback when user drops invalid file type

    * Change wording on message

commit 88fdb68
Author: Liezl Maree <38435167+roomrys@users.noreply.github.com>
Date:   Fri Aug 11 11:27:57 2023 -0700

    Pin `tensorflow-hub<0.14.0` (#1446)

    * Pin pynwb 2.3.3

    * Remove pynwb pin, add comments

commit 4730788
Author: Talmo Pereira <talmo@salk.edu>
Date:   Fri Aug 11 10:52:09 2023 -0700

    Fix drag and drop (#1449)

commit 47f8096
Author: DivyaSesh <64513125+gitttt-1234@users.noreply.github.com>
Date:   Thu Aug 10 16:29:39 2023 -0700

    Add Option to Export CSV (#1438)

    * Add Option to Export CSV

    * Add Test Functions

    * Fomat Files

    * Change FormatID

commit 5ba6bc1
Author: Liezl Maree <38435167+roomrys@users.noreply.github.com>
Date:   Thu Aug 10 10:17:45 2023 -0700

    Add model folder to the unzip path (#1445)

    * Add model folder to the unzip path

    * Handle cases where zipped model either has no extra directory

    * Add test

    * Fix-up test and implementation

    * Manually lint

commit d61a184
Author: KevinZ0217 <96039456+KevinZ0217@users.noreply.github.com>
Date:   Wed Aug 9 14:47:21 2023 -0700

    Change the hotkey for exporting h5 analysis (#1444)

    * Change the hotkey for export h5 files to Ctrl+Alt+E

commit ad7529e
Author: KevinZ0217 <96039456+KevinZ0217@users.noreply.github.com>
Date:   Wed Aug 9 14:46:09 2023 -0700

    Add a button for copying model config to clipboard (#1433)

    * Add shortcur for export_analysis_current

    * Fix the linting issue

    * Add the button without copy method'

    * Add button for copying model config to clipboard

    * Fix linting by reformatting

    * Use Qtpy for clipboard rather than pyperclip

    * Pretty print model config json to clipboard and fix missing command

    * Fix the overwriting problem for dict object

    * Delete unnecessary print statement

    * Add a few comments & Remove unnecessary variables & remove unused function

commit 2611e7d
Author: Liezl Maree <38435167+roomrys@users.noreply.github.com>
Date:   Wed Aug 9 11:52:57 2023 -0700

    Improve error message for detecting video backend (#1441)

    * Improve error message for detecting video backend

    * Lint

    * Add small test

commit 1151a95
Author: Shrivaths Shyam <52810689+shrivaths16@users.noreply.github.com>
Date:   Wed Aug 2 17:08:38 2023 -0700

    Fix error thrown when last video is deleted  (#1421)

    * Handle None Video case during callbacks

    * format files

    * remove unused comments

    * Disable remove video button when there are no videos

    * Display default background when all videos are removed

    * Format files

    * Remove overlay error after removing last video

    * Redraw overlays on plot change (#1435)

    * Redraw overlays after changedPlot, changedPlot on reset

    * Update instance state on player reset

    ---------

    Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com>

commit 6002332
Author: Shrivaths Shyam <52810689+shrivaths16@users.noreply.github.com>
Date:   Mon Jul 31 13:28:53 2023 -0700

    Update status message on status bar (#1411)

    * Update status message on status bar

    * Update statusbar to show correct video count

    * remove additional conditional check

commit 3a01ef3
Author: Liezl Maree <38435167+roomrys@users.noreply.github.com>
Date:   Mon Jul 31 12:09:50 2023 -0700

    Correct GUI state emulation (#1422)

commit e94b516
Author: Liezl Maree <38435167+roomrys@users.noreply.github.com>
Date:   Thu Jul 27 12:11:41 2023 -0700

    Add video path and frame indices to metrics (#1396)

    * Add `Instance`s and `PredictedInstance`s to metrics

    * Add tests

    * Add frame/video info to metrics, wip: test writing

    * Fix metrics save test

commit b2ad203
Author: Liezl Maree <38435167+roomrys@users.noreply.github.com>
Date:   Thu Jul 27 12:08:19 2023 -0700

    Fix labels export for json (#1410)

    * wip: fix labels export for json

    * Add test for json.zip labels pkg

    * Add test for .slp labels pkg

    * Make linter happy

commit 90c012d
Author: KevinZ0217 <96039456+KevinZ0217@users.noreply.github.com>
Date:   Wed Jul 26 13:30:22 2023 -0700

    Add shortcut to export analysis for current video (#1414)

    * Add shortcur for export_analysis_current

    * Fix the linting issue

commit f9d0a22
Author: Shrivaths Shyam <52810689+shrivaths16@users.noreply.github.com>
Date:   Tue Jul 25 09:37:52 2023 -0700

    Modify compute OKS function (#1399)

    * Update compute OKS function

    * Update compute OKS function

    * Modify compute OKS function

    * Added suggested changes

    * Added further suggestions and comments

    * Added the permalink to the cocoeval function

    * Added permalink to cocoeval function

    ---------

    Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com>
    Co-authored-by: Talmo Pereira <talmo@salk.edu>

commit 904338c
Author: Liezl Maree <38435167+roomrys@users.noreply.github.com>
Date:   Tue Jul 25 06:34:25 2023 -0700

    Add `Video` to cache when adding `Track` (#1407)

    * Add `Video` to cache when adding `Track`

    * Use methods instead of rewriting code

    * Simplify code

commit 845214c
Author: DivyaSesh <64513125+gitttt-1234@users.noreply.github.com>
Date:   Mon Jul 24 21:20:02 2023 -0700

    Fix Remove Videos in Batch (#1406)

    * Fix Remove Videos in Batch

    * Remove Unused Testing Code

commit 0afbb9b
Author: Liezl Maree <38435167+roomrys@users.noreply.github.com>
Date:   Mon Jul 24 17:37:42 2023 -0700

    Add `Track` when add `Instance` (#1408)

commit d173303
Author: Liezl Maree <38435167+roomrys@users.noreply.github.com>
Date:   Mon Jul 24 08:25:09 2023 -0700

    Fix skeleton templates (#1404)

commit 0e7a372
Author: DivyaSesh <64513125+gitttt-1234@users.noreply.github.com>
Date:   Fri Jul 21 09:49:51 2023 -0700

    Fix panning bounding box (#1398)

commit fb61b6c
Author: Liezl Maree <38435167+roomrys@users.noreply.github.com>
Date:   Wed Jul 19 15:30:43 2023 -0700

    Fix `Filedialog` to work across (mac)OS (#1393)

    * Always use dir instead of directory

    * Wrap `FileDialog` methods for OS-specific calls

    * Clean-up os-specific wrapper to check for linux only

    * Lint

    * Fix test for non native `FileDialog`

commit 19cd2b5
Author: DivyaSesh <64513125+gitttt-1234@users.noreply.github.com>
Date:   Mon Jul 17 17:55:29 2023 -0700

    Add option to remove videos in batch (#1382)

    * add option to remove videos in batch

    * Add option to remove videos in batch

    * Add option to remove videos in batches

    * Modify Lint format

    * Add Test cases

    * Modify Test Cases for Removing Videos in Batch

    * Add Comment to test_docks

    * Remove commented line

    * Format files

commit 3b5c4ff
Author: Shrivaths Shyam <52810689+shrivaths16@users.noreply.github.com>
Date:   Fri Jul 14 17:06:58 2023 -0700

    Minor fix in computation of OKS (#1383)

    * fix compute oks

    * Update the oks fix

commit 1c2be11
Author: Liezl Maree <38435167+roomrys@users.noreply.github.com>
Date:   Thu Jul 6 14:44:01 2023 -0700

    Pin micromamba version (#1376)

    * Pin micromamba version

    * Add build number to pin
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@roomrys @talmo