Code

Parse multiplexing datasets#210

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tcompa merged 31 commits intomainfractal-analytics-platform/fractal-tasks-core:mainfrom multiplexing_parsingfractal-analytics-platform/fractal-tasks-core:multiplexing_parsingCopy head branch name to clipboardNov 21, 2022

+1,061-149

Commits

Commits on Nov 16, 2022

• BROKEN init create_zarr_structure_multiplex.py

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• Keep working on multiplex parsing

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Commits on Nov 17, 2022

• Sandbox multiplex / run example

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• Sandbox multiplex / run example

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• Update create_zarr_structure_multiplex.py prototype

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• Update create_zarr_structure_multiplex.py prototype

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• BROKEN make yokogawa parsing acquisition-aware

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• Provisionally allow yokogawa-to-zarr to work for both multiplex or standard datasets

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• .gitignore

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• Remove debug statements

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• Remove debug statements + style

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• Move define_omero_channels to specific module

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• Fix handling of zattrs

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• Validate OME-Zarr JSON schema

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• Multiple updates to multiplexing (notably: lib_read_fractal_metadata)

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Commits on Nov 18, 2022

• Update test to load manifest schema from fractal-common repo

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• Rename well->image in manifest and tests

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• Rename well->image in create_zarr_structure

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• Fix discover_acquisition_from_ome_zarr function

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• Fix import

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• Preliminary update to replicate_zarr_structure, to update plate/well/image metadata lists

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• Also store plate in metadata, im create_zarr_structure_multiplex, for consistence with other tasks

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• Rename well->image in one more test

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• Update 0.4.0 changelog

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Commits on Nov 21, 2022

• Add multiplex parsing to manifest

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• Improve docstring

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• Add zenodo_images_multiplex fixture

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• Add test for multiplex image-parsing

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• Include sphinx deps

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• Refactor lib_read_fractal_metadata functions + add docstrings

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• Fix docstrings of lib_read_fractal_metadata.py

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