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Facemap Pose Estimation Inference #24

Merged
merged 185 commits into from
Nov 15, 2023
Merged

Facemap Pose Estimation Inference #24

merged 185 commits into from
Nov 15, 2023

Commits on Aug 14, 2023

  1. index on main: 10550ad Merge pull request datajoint#23 from kabilar/main

    @sidhulyalkar
    sidhulyalkar committed Aug 14, 2023
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  2. WIP on main: 10550ad Merge pull request datajoint#23 from kabilar/main

    @sidhulyalkar
    sidhulyalkar committed Aug 14, 2023
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Commits on Aug 15, 2023

  1. add facemap model table and update facemap processing to trigger face… 

    …map pose inference
    @sidhulyalkar
    sidhulyalkar committed Aug 15, 2023
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Commits on Aug 18, 2023

  1. start to add implementation of facemap processing

    @sidhulyalkar
    sidhulyalkar committed Aug 18, 2023
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  2. add model inference step

    @sidhulyalkar
    sidhulyalkar committed Aug 18, 2023
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Commits on Aug 21, 2023

  1. update model dict save to h5py format

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    sidhulyalkar committed Aug 21, 2023
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Commits on Sep 8, 2023

  1. add new facial_pose_model file allowing to run model inference

    @sidhulyalkar
    sidhulyalkar committed Sep 8, 2023
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  2. formatting

    @sidhulyalkar
    sidhulyalkar committed Sep 8, 2023
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  3. revert fbe changes

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    sidhulyalkar committed Sep 8, 2023
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Commits on Sep 14, 2023

  1. change facemap_output_dir to pose_estimation_output_dir

    @sidhulyalkar
    sidhulyalkar committed Sep 14, 2023
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  2. change idx from model_name to model_id

    @sidhulyalkar
    sidhulyalkar committed Sep 14, 2023
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  3. fetch model_file

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    sidhulyalkar committed Sep 14, 2023
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  4. change to fetch1

    @sidhulyalkar
    sidhulyalkar committed Sep 14, 2023
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  5. copy facemap output to specified output dir

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    sidhulyalkar committed Sep 14, 2023
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  6. use vid name to specify output model and metadata files

    @sidhulyalkar
    sidhulyalkar committed Sep 14, 2023
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  7. fix nested array

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    sidhulyalkar committed Sep 14, 2023
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  8. remove bbox from pose object definition

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    sidhulyalkar committed Sep 14, 2023
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Commits on Sep 15, 2023

  1. add test video files for debugging

    @sidhulyalkar
    sidhulyalkar committed Sep 15, 2023
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  2. save files as posix

    @sidhulyalkar
    sidhulyalkar committed Sep 15, 2023
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  3. save vids as posix for insertion into pose object

    @sidhulyalkar
    sidhulyalkar committed Sep 15, 2023
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  4. test using video_name instead of full path

    @sidhulyalkar
    sidhulyalkar committed Sep 15, 2023
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  5. revert to use full video path

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    sidhulyalkar committed Sep 15, 2023
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  6. add list around filenames

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    sidhulyalkar committed Sep 15, 2023
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  7. fix load from output .h5

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    sidhulyalkar committed Sep 15, 2023
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  8. formatting

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    sidhulyalkar committed Sep 15, 2023
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  9. switch back to video files specified in fbe.VR

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    sidhulyalkar committed Sep 15, 2023
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  10. change model output dir to fbe.VR video root directory

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    sidhulyalkar committed Sep 15, 2023
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Commits on Sep 16, 2023

  1. set output to load from video root dir

    @sidhulyalkar
    sidhulyalkar committed Sep 16, 2023
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Commits on Sep 18, 2023

  1. use shutil to copy files

    @sidhulyalkar
    sidhulyalkar committed Sep 18, 2023
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  2. remove pathlib3x from import

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    sidhulyalkar committed Sep 18, 2023
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  3. update body_part insertion key

    @sidhulyalkar
    sidhulyalkar committed Sep 18, 2023
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  4. refactor to load results before rerunning processing to solve lost tr… 

    …ansaction issue
    @sidhulyalkar
    sidhulyalkar committed Sep 18, 2023
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  5. minor formatting

    @sidhulyalkar
    sidhulyalkar committed Sep 18, 2023
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  6. rename total_frame_count

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    sidhulyalkar committed Sep 18, 2023
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  7. set body_part to varchar(32)

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    sidhulyalkar committed Sep 18, 2023
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Commits on Sep 19, 2023

  1. add key to bodyparposition entry

    @sidhulyalkar
    sidhulyalkar committed Sep 19, 2023
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  2. fix syntax

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    sidhulyalkar committed Sep 19, 2023
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  3. add key to each element of body_part_position_entry

    @sidhulyalkar
    sidhulyalkar committed Sep 19, 2023
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  4. modify BodyPartPosition to inherit from BodyPart as opposed to Facema… 

    …pModel.BodyPart
    @sidhulyalkar
    sidhulyalkar committed Sep 19, 2023
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  5. add body_part_key to bodypart_pos_entry

    @sidhulyalkar
    sidhulyalkar committed Sep 19, 2023
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  6. switch to fetch1

    @sidhulyalkar
    sidhulyalkar committed Sep 19, 2023
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  7. inherit from FacemapModel.BodyPart

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  8. modify body_position_entries

    @sidhulyalkar
    sidhulyalkar committed Sep 19, 2023
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  9. bugfix

    @sidhulyalkar
    sidhulyalkar committed Sep 19, 2023
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  10. fix typo

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    sidhulyalkar committed Sep 19, 2023
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  11. add get_tracectory class method

    @sidhulyalkar
    sidhulyalkar committed Sep 19, 2023
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  12. add pandas import

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    sidhulyalkar committed Sep 19, 2023
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  13. query bodypartposition with recording id

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    sidhulyalkar committed Sep 19, 2023
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  14. fetch as_dict =True

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    sidhulyalkar committed Sep 19, 2023
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  15. fetch1 to fetch

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    sidhulyalkar committed Sep 19, 2023
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Commits on Sep 20, 2023

  1. modify fetching of results

    @sidhulyalkar
    sidhulyalkar committed Sep 20, 2023
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  2. convert ndarray to list

    @sidhulyalkar
    sidhulyalkar committed Sep 20, 2023
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  3. fix typo

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    sidhulyalkar committed Sep 20, 2023
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  4. fetch to fetch1

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    sidhulyalkar committed Sep 20, 2023
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  5. rename paramset_key to model_id

    @sidhulyalkar
    sidhulyalkar committed Sep 20, 2023
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  6. add bbox optional input param

    @sidhulyalkar
    sidhulyalkar committed Sep 20, 2023
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  7. specify facemap_model_schema_name to be a string

    @sidhulyalkar
    sidhulyalkar committed Sep 20, 2023
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  8. minor fixes

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    sidhulyalkar committed Sep 20, 2023
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  9. add facemap pose estimation -- run inference notebook

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Commits on Sep 21, 2023

  1. modify activate parameter outputs

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  2. remove notebook for now

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    sidhulyalkar committed Sep 21, 2023
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  3. remove unused imports

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    sidhulyalkar committed Sep 21, 2023
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Commits on Sep 25, 2023

  1. add insert_model classfunction

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    sidhulyalkar committed Sep 25, 2023
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Commits on Sep 26, 2023

  1. add symlinks for video files to output dir

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    sidhulyalkar committed Sep 26, 2023
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  2. remove output results copy

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    sidhulyalkar committed Sep 26, 2023
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  3. add class method for pose estimation task generation

    @sidhulyalkar
    sidhulyalkar committed Sep 26, 2023
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  4. update comments

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    sidhulyalkar committed Sep 26, 2023
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  5. add automated video recording insertion

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    sidhulyalkar committed Sep 26, 2023
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Commits on Sep 27, 2023

  1. Add bbox default if None

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    sidhulyalkar committed Sep 27, 2023
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  2. keep list of videos for run input as_posix

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    sidhulyalkar committed Sep 27, 2023
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  3. remove video recording classmethod

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    sidhulyalkar committed Sep 27, 2023
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Commits on Sep 30, 2023

  1. add facial pose estimation training

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    sidhulyalkar committed Sep 30, 2023
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  2. support single video

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    sidhulyalkar committed Sep 30, 2023
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  3. comment second training approach

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Commits on Oct 1, 2023

  1. bugfix

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    sidhulyalkar committed Oct 1, 2023
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  2. remove add objects from imported schema activate

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    sidhulyalkar committed Oct 1, 2023
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  3. fix typo training to train

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    sidhulyalkar committed Oct 1, 2023
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  4. modify training task table definition

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  5. update comments

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    sidhulyalkar committed Oct 1, 2023
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  6. fix comment

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    sidhulyalkar committed Oct 1, 2023
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  7. change smallblob to tinyblob typo

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Commits on Oct 2, 2023

  1. add facemap task insertion class method

    @sidhulyalkar
    sidhulyalkar committed Oct 2, 2023
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  2. fix output dir

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    sidhulyalkar committed Oct 2, 2023
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Commits on Oct 4, 2023

  1. restructure keypoints file

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    sidhulyalkar committed Oct 4, 2023
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  2. modify keypoints file loading from fileset

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  3. modify insert_facemap_training task class function

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  4. modify facemap training task insert

    @sidhulyalkar
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  5. modify training task insertion key

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  6. call infer output dir as class method

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  7. fix rename typo

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    sidhulyalkar committed Oct 4, 2023
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  8. fix typo

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    sidhulyalkar committed Oct 4, 2023
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  9. set training task attribute values to None

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  10. update FacemapModelTrainingTask comment

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  11. change blob from none type

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    sidhulyalkar committed Oct 4, 2023
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  12. set smallints to null default value

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  13. update renamed variable file_set_id in FacemapModelTraining

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  14. fix typo

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    sidhulyalkar committed Oct 4, 2023
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  15. change File to KeypointsFile in ref

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  16. update facemap pose object to be named pose, and facemap_pose will re… 

    …fer to imported schema
    @sidhulyalkar
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  17. fix typo

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    sidhulyalkar committed Oct 4, 2023
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  18. rename refined_model_id to retrain_model_id

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    sidhulyalkar committed Oct 4, 2023
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Commits on Oct 5, 2023

  1. change model_id fetch

    @sidhulyalkar
    sidhulyalkar committed Oct 5, 2023
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  2. fix model id none fetch

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    sidhulyalkar committed Oct 5, 2023
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Commits on Oct 6, 2023

  1. store model reference in model training table

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    sidhulyalkar committed Oct 6, 2023
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  2. bugfix

    @sidhulyalkar
    sidhulyalkar committed Oct 6, 2023
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  3. comment out alternate approach

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    sidhulyalkar committed Oct 6, 2023
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Commits on Oct 10, 2023

  1. modify to use save_model

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    sidhulyalkar committed Oct 10, 2023
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Commits on Oct 12, 2023

  1. revert cross val cahnges, switch to new branch

    @sidhulyalkar
    sidhulyalkar committed Oct 12, 2023
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Commits on Oct 23, 2023

  1. update body part contents:

    @sidhulyalkar
    sidhulyalkar committed Oct 23, 2023
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  2. fetch fileset paths using key

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    sidhulyalkar committed Oct 23, 2023
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  3. remove alternate cv model training

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    sidhulyalkar committed Oct 23, 2023
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  4. update comment

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  5. update keypoints loading bodyparts

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    sidhulyalkar committed Oct 23, 2023
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  6. update comments

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  7. update model insertion

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  8. set bbox to null

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  9. update load trigger commentA

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    sidhulyalkar committed Oct 23, 2023
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  10. update task generation to be based on vrec_key

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    sidhulyalkar committed Oct 23, 2023
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  11. update load, remove check that files exist, now FnF error will be thrown

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    sidhulyalkar committed Oct 23, 2023
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  12. rename files

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  13. change facemap_pose to facemap_inference

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  14. mkae keypointsFile part table a 1 to 1 mapping

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  15. update comment

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  16. refactor pose estimation task definition, remove unneeded attributes

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    sidhulyalkar committed Oct 23, 2023
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Commits on Oct 27, 2023

  1. Update element_facemap/facemap_inference.py 

    Co-authored-by: Kushal Bakshi <52367253+kushalbakshi@users.noreply.github.com>
    @sidhulyalkar @kushalbakshi
    sidhulyalkar and kushalbakshi authored Oct 27, 2023
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  2. Update element_facemap/facemap_inference.py 

    Co-authored-by: Kushal Bakshi <52367253+kushalbakshi@users.noreply.github.com>
    @sidhulyalkar @kushalbakshi
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  3. Update element_facemap/facemap_inference.py 

    Co-authored-by: Kushal Bakshi <52367253+kushalbakshi@users.noreply.github.com>
    @sidhulyalkar @kushalbakshi
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  4. Update element_facemap/facemap_inference.py 

    Co-authored-by: Kushal Bakshi <52367253+kushalbakshi@users.noreply.github.com>
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  5. Update element_facemap/facemap_inference.py 

    Co-authored-by: Kushal Bakshi <52367253+kushalbakshi@users.noreply.github.com>
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    sidhulyalkar and kushalbakshi authored Oct 27, 2023
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  6. Update element_facemap/facemap_inference.py 

    Co-authored-by: Kushal Bakshi <52367253+kushalbakshi@users.noreply.github.com>
    @sidhulyalkar @kushalbakshi
    sidhulyalkar and kushalbakshi authored Oct 27, 2023
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  7. Update element_facemap/facemap_inference.py 

    Co-authored-by: Kushal Bakshi <52367253+kushalbakshi@users.noreply.github.com>
    @sidhulyalkar @kushalbakshi
    sidhulyalkar and kushalbakshi authored Oct 27, 2023
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  8. Update element_facemap/facemap_inference.py 

    Co-authored-by: Kushal Bakshi <52367253+kushalbakshi@users.noreply.github.com>
    @sidhulyalkar @kushalbakshi
    sidhulyalkar and kushalbakshi authored Oct 27, 2023
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  9. clean u[ load trigger logic to reduce _load_facemap_result function c… 

    …alls
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    sidhulyalkar committed Oct 27, 2023
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  10. merge suggestions

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  11. change self to cls

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    sidhulyalkar committed Oct 27, 2023
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  12. modify comments

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  13. change root dit imports

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    sidhulyalkar committed Oct 27, 2023
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  14. update infer_output_dir, inserts

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  15. remove multivideo comment

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    sidhulyalkar committed Oct 27, 2023
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Commits on Oct 30, 2023

  1. update comment to remove Session and VideoRecording unneeded dependen… 

    …cies
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Commits on Oct 31, 2023

  1. modify image_data loading to convert images to grayscale before runni… 

    …ng through model training
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  2. modify output_dir to be unique for each run

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  3. modify pose estimation task insertion

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    sidhulyalkar committed Oct 31, 2023
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  4. add docstrings and modify PoseEstimationTask defintion

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  5. update formatting

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  6. add back in selected_frame_ind

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  7. modify retrained model id to be specified as varchar

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  8. add RetrainedModelFile table to store rel file path of model

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Commits on Nov 1, 2023

  1. update train task insertionA

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  2. add relative file path to FacemapModel table for RetrainModel part ta… 

    …ble reference
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  3. remove varchar specification for .proj attributes

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  4. set retrain model id to have a none default value

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  5. set retrain model id to have a null default value

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  6. specify retrain model id to be nullable

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  7. remove model_id fetch

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  8. update to not allow user to specify model id

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    sidhulyalkar committed Nov 1, 2023
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  9. small bugfix

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    sidhulyalkar committed Nov 1, 2023
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  10. remove relative_filepath option for model table

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    sidhulyalkar committed Nov 1, 2023
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  11. switch to store file attachment in part table

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    sidhulyalkar committed Nov 1, 2023
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  12. fix typo

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    sidhulyalkar committed Nov 1, 2023
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  13. modify RetrainedModelFile insert

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  14. modify retrained file insert

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  15. move part table insert after insert into facemapProcessing

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  16. update RetrainedModelFile insert

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  17. modify RetrainedModelFile part table to store model_id as link to mod… 

    …el table
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  18. modify refined_model_name -> refined_model_prefix

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    sidhulyalkar committed Nov 1, 2023
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  19. rename var and update comment

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    sidhulyalkar committed Nov 1, 2023
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  20. update comment

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  21. add print for when paramset exists

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  22. update refine_model_prefix in task insertion

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  23. fix typo

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Commits on Nov 3, 2023

  1. modify refined_model_prefix to be a prefix

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  2. Update element_facemap/facemap_train.py 

    Co-authored-by: Thinh Nguyen <thinh@datajoint.com>
    @sidhulyalkar @ttngu207
    sidhulyalkar and ttngu207 authored Nov 3, 2023
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  3. Update element_facemap/facemap_train.py 

    Co-authored-by: Thinh Nguyen <thinh@datajoint.com>
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  4. modify infer_output_dir to be a class function

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  5. Merge branch 'new_facemap_integration_test' of https://github.com/sid… 

    …hulyalkar/element-facemap into new_facemap_integration_test
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  6. Update facemap_inference.py

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Commits on Nov 4, 2023

  1. update refined_model_prefix -> refined_model_name (prefixed to output… 

    …_dir.stem)
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  2. train_output_dir -> training_output_dir

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  3. model_description -> varchar(1000)

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  4. facemap_inference.FacemapModel.proj(retrain_model_id=‘model_id’) # li… 

    …nk to facemap model table --> make into a secondary attr
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Commits on Nov 6, 2023

  1. modify design to make base_model_id required, with expectation that d… 

    …efault model is intially inserted
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  2. remove unused model_id from insert_pose_estimation_task

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    sidhulyalkar committed Nov 6, 2023
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  3. update infer_output_dir to pull model_id from key

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Commits on Nov 8, 2023

  1. remove training

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    sidhulyalkar committed Nov 8, 2023
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