Code

Add feature extractors#6

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kaczmarj merged 25 commits intomainSBU-BMI/SpinPath:mainfrom ref/extractorsSBU-BMI/SpinPath:ref/extractorsCopy head branch name to clipboardJan 13, 2025

Commits

Commits on Nov 30, 2024

• modularize extractors + install timm

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• use len instead of shape for num patches

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• add virchow2 and hoptimus0

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• mypy, please ignore timm

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• use extractor.run

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Commits on Jan 9, 2025

• do not cache tissue mask or coords

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• add encoders hibou, kaiko, phikon, phikonv2, provgigapath, virchow

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• mypy: ignore transformers

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• sort imports

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• set abmil model to eval mode

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• update model inference func

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• replace deprectated torchvision transforms funcs

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• add Resize to hoptimus0 transform

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• add --quantize option

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Commits on Jan 13, 2025

• do not squeeze embeddings

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• add --quantize to runlocal

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• remove unused type:ignore commment

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• add transformers as dependency

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• test python3.12

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• run mypy with python 3.12

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• set zarr<3.0.0 and rm tifffile and imagecodecs

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• ignore complicated numpy typing issues

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• reformat with ruff

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• use env var to force cpu usage

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• in windows, set SPINPATH_FORCE_CPU

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