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Evaluate existing segementation#213

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ziw-liu wants to merge 64 commits intomainmehta-lab/VisCy:mainfrom segmentation-modulemehta-lab/VisCy:segmentation-moduleCopy head branch name to clipboard

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Commits on Oct 21, 2024

• caching dataloader

  

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• caching data module

  

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• black

  

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• ruff

  

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• Bump torch to 2.4.1 (#174)

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• adding timeout to ram_dataloader

  

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• bandaid to cached dataloader

  

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• fixing the dataloader using torch collate_fn

  

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• replacing dictionary with single array

  

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• loading prior to epoch 0

  

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• Revert "replacing dictionary with single array"

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• using multiprocessing manager

  

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• add sharded distributed sampler

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• add example script for ddp caching

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• format and lint

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Commits on Oct 22, 2024

• addding the custom distrb sampler to hcs_ram.py

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• adding sampler to val train dataloader

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• fix divisibility of the last shard

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• hcs_ram format and lint

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Commits on Oct 23, 2024

• data module that only crops and does not collate

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• wip: execute transforms on the GPU

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Commits on Oct 24, 2024

• path for if not ddp

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Commits on Oct 29, 2024

• fix randomness in inversion transform

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• add option to pop the normalization metadata

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Commits on Oct 30, 2024

• move gpu transform definition back to data module

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• add tiled crop transform for validation

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• add stack channel transform for gpu augmentation

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• fix typing

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• collate before sending to gpu

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• inherit gpu transforms for livecell dataset

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• update fcmae engine to apply per-dataset augmentations

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• format and lint hcs_ram

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Commits on Oct 31, 2024

• Merge branch 'simple-cache' into gpu-transform

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• fix abc type hint

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• update docstring style

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• disable grad for validation transforms

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• improve sample image logging in fcmae

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• fix dataset length when batch size is larger than the dataset

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• fix docstring

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• add option to disable normalization metadata

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• inherit gpu transform for ctmc

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• remove duplicate method overrride

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Commits on Nov 1, 2024

• update docstring for ctmc

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Commits on Nov 8, 2024

• Merge pull request #196 from mehta-lab/gpu-transform

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• Merge branch 'main' into simple-cache

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Commits on Nov 13, 2024

• allow skipping caching for large datasets

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• Merge branch 'main' into simple-cache

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Commits on Nov 14, 2024

• make the fcmae module compatible with image translation

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Commits on Nov 19, 2024

• remove prototype implementation

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• fix import path

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Commits on Dec 2, 2024

• Arbitrary prediction time transforms (#209)

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• add docstrings

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Commits on Dec 4, 2024

• wip: segmentation module

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• Merge branch 'main' into simple-cache

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• avoid casting

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• Merge branch 'simple-cache' into segmentation-module

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Commits on Dec 7, 2024

• update import path from iohub

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• make integer array in fixture

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• labels fixture

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• test segmentation metrics modules

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• less strings

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• test non-empty

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Commits on Dec 11, 2024

• select which wells to include in fit

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Commits on Jan 2, 2025

• Merge branch 'main' into segmentation-module

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