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MVP here we come #2

Merged
merged 14 commits into from
Mar 10, 2022
Merged

MVP here we come #2

merged 14 commits into from
Mar 10, 2022

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CBroz1
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@CBroz1 CBroz1 commented Mar 4, 2022

Commits

Changes

  • README: add note on dependency conflict numpy==1.2
  • dlc.py:
    • remove arg for get_dlc_processed_dir
    • Add note on scorer_legacy
    • add docstrings
    • add note on continue from prev snapshot
    • add set shuffle/trainindex/maxiters to int for model training make
    • BodyPart.insert_new - refactor logic for yaml type check
    • Model.insert_new_model - refactor config yaml type check
      • Add scorer legacy check
      • add dlc version insertion
      • add body part description arg
    • ModelEvaluation - make items nullable bc saw eval that didn't return some value
      • refactor config yaml type check
    • PoseEstimationTask - permit estimation paramset to pass to analyze_videos
      • Type set to string for concatenating output dir
      • add insert helper function
    • PoseEstimation - permit output_dir as fullpath, per 'relative' arg in task table
      • permit passing analyze_videos params
  • dlc_reader:
    • add conditional logic for if passed the output dir instead of project dir
    • assumes output dir is under project dir
    • do_pose_estimation - permit args passed from PoseEstimationTask.params

CBroz1 and others added 7 commits February 3, 2022 09:10
@CBroz1
Merge from CBroz1/dev
738999d 
Recent work
@CBroz1
Update element_deeplabcut/dlc.py
046064d 
Co-authored-by: Thinh Nguyen <[email protected]>
@CBroz1
Merge pull request #3 from CBroz1/dev
b498a02 
Add functions to link tables
@CBroz1
Merge pull request #4 from ttngu207/main
1d990db 
prototype revision no 2
@CBroz1
PEP8
aa4961e
@CBroz1
See details - long list
cef65ed 
README: add note on dependency conflict numpy==1.2

dlc schema:
- remove arg for get_dlc_processed_dir
- Add note on scorer_legacy
- add docstrings
- add note on continue from prev snapshot
- add set shuffle/trainindex/maxiters to int for model training make
- BodyPart.insert_new - refactor logic for yaml type check
- Model.insert_new_model - refactor config yaml type check
    - Add scorer legacy check
    - add dlc version insertion
    - add body part description arg
- ModelEvaluation - make items nullable bc saw eval that didn't return some value
    - refactor config yaml type check
- PoseEstimationTask - permit estimation paramset to pass to analyze_videos
    - Type set to string for concatenating output dir
    - add insert helper function
- PoseEstimation - permit output_dir as fullpath, per 'relative' arg in task table
    - permit passing analyze_videos params

dlc_reader:
- add conditional logic for if passed the output dir instead of project dir
- assumes output dir is under project dir
- do_pose_estimation - permit args passed from PoseEstimationTask.params
@CBroz1
update diagram
88eb82f
ttngu207
ttngu207 reviewed Mar 8, 2022
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I've added a number of comments/suggestions, please review

CBroz1
CBroz1 commented Mar 8, 2022
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Had some follow-up questions

@CBroz1
Rebasing
3c8ff44 
PEP8
README: add note on dependency conflict numpy==1.2
/images/: update diagram
dlc schema:
- remove arg for get_dlc_processed_dir
- Add note on scorer_legacy
- add docstrings
- add note on continue from prev snapshot
- add set shuffle/trainindex/maxiters to int for model training make
- add `TrainingVideo` table for training instead of `VideoRecording`
    - `LabeledFrame` -> `File` generalizable part table
- BodyPart.insert_new
    - refactor logic for yaml type check
    - separate BodyPart functions - return list then insert
- Model.insert_new_model - refactor config yaml type check
    - Add scorer legacy check
    - add dlc version insertion
- ModelEvaluation - make items nullable bc saw eval that didn't return some value
    - refactor config yaml type check
- PoseEstimationTask - permit estimation paramset to pass to analyze_videos
    - Type set to string for concatenating output dir
    - add insert helper function
- PoseEstimation - permit output_dir as fullpath, per 'relative' arg in task table
    - permit passing analyze_videos params
    - permit null analyze_video_param
dlc_reader:
- prev had separate output dir and project dir... removing
- do_pose_estimation - permit args passed from PoseEstimationTask.params
- adjust yml_path in reader to remove dlc_dir.parent
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CBroz1 commented Mar 9, 2022

Ran through full pipeline here - Made some tweaks to resolve dlc_reader issue, where DLC expects the project path when generating pose estimation.

@CBroz1 CBroz1 requested a review from ttngu207 March 9, 2022 21:59
@ttngu207 ttngu207 merged commit 015843a into ttngu207:main Mar 10, 2022
ttngu207 pushed a commit that referenced this pull request Oct 6, 2023
@CBroz1
Merge pull request #2 from CBroz1/dev
8095081 
Update schema split: `train`, `model`
ttngu207 pushed a commit that referenced this pull request Oct 6, 2023
Merge pull request #2 from CBroz1/main
981415c 
Pushing from `cbroz1:dev` discussion to `datajoint:main`
ttngu207 pushed a commit that referenced this pull request Sep 20, 2024
@kushalbakshi
Merge pull request #2 from ttngu207/iub-lulab
353315d 
Add computed table `LabeledVideo`
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@CBroz1 @ttngu207