Bone meal merge attempt #2

ajensen1234 · 2023-05-23T19:00:17Z

We want to merge the changes from BoneMeal Senior project group into our working lab repository.

…builder

…s kept in place to prevent code from breaking while we negotiate.

… config.py

…py that I thought were in the previous commits.

…ntegration. Delete loss_manager.py following discussion in meeting this morning.

…SegmentationNetModule class. Adds support for selection of loss functions through config.py

…example

…class

…lab/Bone-Meal into builder_transformer_merger

Update README.md LGTM!

Builder transformer merger

…tement in JTMLDataset's setup method.

…n various architecture building files

…sions of the model are now saved during each fit.

…use of space.

…mmented out code in places.

Fix dataset and csvs. Implement ModelCheckpoint to save best model from whole fit session.

Engut and others added 30 commits January 29, 2023 09:59

Add hrt relevant files for builder

9ddedde

builder in running state

e9e6bb5

fixed issue with import statement in fit.py

c85fb48

Remove unused folder

e3a1ae4

deleted scripts/models/backbones/hrt/modules

4c28069

Merge branch 'builder' of https://github.com/BRIO-lab/Bone-Meal into …

bb6f6a1

…builder

Moved models and utils into lib directory

75784ef

added self.net dict to config.py

81548ec

added loss functions in loss.py and also fixed some file paths

0756b3e

Merge remote-tracking branch 'origin/builder' into builder

115353d

Add loss_manager.py from HRFormer repo.

ff1e74a

Annotate config.py and loss_manager.py

4607938

Added example dict for loss params

71fce1c

Delete redundant directory lib/models/modules.

09e92c4

Add hrnet backbone directory with files copied from scripts. Original…

e10ba75

…s kept in place to prevent code from breaking while we negotiate.

add import from new pose_hrnet_module to backbone_selector.py. Update…

81fee50

… config.py

Shifted a dict definition in config.py

bd7c33a

commit and push updates to config.py

982fb79

Preliminary changes to integrate hrnet into backbone selection scheme

df26d84

Add TODO annotation to pose_hrnet_module

74313bd

Committing relocation of lib for Module visibility in scripts

a41e8f2

Added format annotations to config.py. Committing changes to builder.…

c99af31

…py that I thought were in the previous commits.

Update modules in self.net

9e4fbbe

Alter config.py and loss_selector.py in preparation for final hrnet i…

6388280

…ntegration. Delete loss_manager.py following discussion in meeting this morning.

Add unit test main to loss_selector.py remove errored imports.

d020b38

Add call to LossSelector's get_loss method to the constructor of the …

2b8e057

…SegmentationNetModule class. Adds support for selection of loss functions through config.py

remove cache files that were staged by accident

a172b88

Delete deprecated files

9abced9

created skeleton code/framework for architecture builder

6589907

added comment about why there is no forward function unlike sasank's …

81a66ae

…example

curranzach and others added 30 commits March 2, 2023 16:25

Updated SegmentationNetModule training and HighResolutionTransformer …

55f7bba

…class

Merge branch 'builder_transformer_merger' of https://github.com/BRIO-…

042de7b

…lab/Bone-Meal into builder_transformer_merger

Alter builder taskflow to accommodate the backbones in hrt.py

b1f9f48

Fixed errors with previous build.

c97bf27

Merge pull request #2 from BRIO-lab/Engut-README-patch

d18585b

Update README.md LGTM!

Up to date working HPG code

f25dcb7

Merge pull request #4 from BRIO-lab/builder_transformer_merger

b6007d7

Builder transformer merger

added dataset changes and csv changes

e72c4ae

Experiencing bug while trying to run with albumentations

0b78579

Commiting pycache files

8c917e8

finish merge with remote

a10acac

Fixed issues with training using albumentations and the assertion sta…

9eae4f6

…tement in JTMLDataset's setup method.

Removed erroneous comment in HPG

406a9c8

Added a testing notebook for getting this Dataset bug.

a9e3f10

committing debug.py file

f4726d1

committing debug.py file

2d6c7f0

Added early stopping

5c35cb4

Commiting config.py before merge

c5e82e4

resolve conflicts in config.py

a86ba2d

Pushing my earlier work with Zach's stopping criteria

6209b52

Committing changes to the config prior to checking out bpr

ccc7e42

Commit work on comments in config

6e83fe2

Add ModelCheckpoint. Refactor pl callbacks in general. Add comments i…

4247871

…n various architecture building files

Committing config before pull

a626fd8

finishing pull via conflict resolution

c2a719b

Debugged issues with the ModelCheckpoint callback. Best and Final ver…

c244e33

…sions of the model are now saved during each fit.

Removed JTMLCallback validation_step logging with hpg to prevent over…

35576aa

…use of space.

Removed Early Stopping altogether. Added more comments and removed co…

1b4db15

…mmented out code in places.

Fixed logging issue with HRNet test results

5d6746c

Merge pull request #5 from BRIO-lab/fix_dataset_and_csvs

579c145

Fix dataset and csvs. Implement ModelCheckpoint to save best model from whole fit session.

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Bone meal merge attempt #2

Bone meal merge attempt #2

ajensen1234 commented May 23, 2023

Bone meal merge attempt #2

Are you sure you want to change the base?

Bone meal merge attempt #2

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ajensen1234 commented May 23, 2023