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Refactor train#28

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TibbersHao wants to merge 49 commits intomainmlexchange/mlex_dlsia_segmentation_prototype:mainfrom refactor-trainmlexchange/mlex_dlsia_segmentation_prototype:refactor-trainCopy head branch name to clipboard

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Commits on Jun 28, 2024

• added functions to load yaml and validate params

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Commits on Jun 29, 2024

• added functions to initialize tiled dataset

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Commits on Jul 8, 2024

• added function for normalization, tensor conversion and qlty cropping

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Commits on Jul 15, 2024

• added DLSIA prefix for all model names

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Commits on Jul 18, 2024

• updated qlty version to 0.2.0

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• added function and tests for dataloader construction

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Commits on Jul 20, 2024

• temporary degrade to pydantic 1.10.15 to deal with old tiled catalog package compatibility

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• changed network names with DLSIA Prefix

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• changed model name

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• added training function and tests

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Commits on Jul 22, 2024

• added pytest folders

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• modified parameters and added tests for model training/saving

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• modified var name to specifically reflect to network name

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• added function and tests for model loading

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• added full inference function

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Commits on Jul 25, 2024

• pre-commit format fix

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Commits on Jul 27, 2024

• cleared unnecessary tests and added monkeypatch tests for device detection

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Commits on Jul 29, 2024

• trimmed one-line functions and got rid of unnecessary pytests

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Commits on Aug 2, 2024

• added utility functions for segmentation, breaking down big functions, added pytests

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Commits on Aug 14, 2024

• move dvc import inside loop to speed up process

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• enable pytest order as temp solution for dependency issues

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Commits on Aug 20, 2024

• rearrange fixtures

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Commits on Aug 22, 2024

• modified to local tiled server for testing purpose

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• fixed name mismatch

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• added dimension check for data_shape

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• fixed dimension mismatch when building network

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• format change

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• fixed model name mismatch

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Commits on Aug 23, 2024

• adjusments for full inference

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• pytest rearrangement and parameterization

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Commits on Aug 27, 2024

• trim fixture in test_3-train

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• format change

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Commits on Aug 28, 2024

• expanded pos tests, added neg tests, change to use session scope tmp dir

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Commits on Aug 29, 2024

• Merge branch 'main' into refactor-train

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• trim no longer used files and comments

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• format

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• update example uri in SPIN

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Commits on Aug 30, 2024

• Remove is_qlty parameter from TiledDataSet

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• Remove transform parameter from TiledDataSet

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Commits on Sep 3, 2024

• Move initialize_tiled_datasets to tiled_datasets

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Commits on Sep 6, 2024

• Refactor TiledDataset into TiledDataset and TiledMaskedDataset

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• 🐛 TiledDataset for partial inference was not covered in initialization

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• Temporarily pin starlette==0.38.2

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• Move mask node and mask_idx metadata access outside of datasets

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• Catching self-raised KeyError and from_uri Exceptions separately

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Commits on Sep 7, 2024

• 🐛 partial inference initialized TiledMaskedDataset

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• Merge pull request #32 from Wiebke/refactor-train-modifications-tiled-dataset

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Commits on Sep 27, 2024

• change default MSDNet final layer to None

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Commits on Oct 7, 2024

• remove final_layer to reduce future confusion

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