Code

Refactor API for NGFF datasets#31

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ziw-liu merged 111 commits intomainczbiohub-sf/iohub:mainfrom ngff-datasetczbiohub-sf/iohub:ngff-datasetCopy head branch name to clipboardFeb 13, 2023

+1,862-1,446

Commits

Commits on Jan 21, 2023

• base class for ngff nodes

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Commits on Jan 23, 2023

• fix typo

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• sketch image container and position node

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Commits on Jan 26, 2023

• create new image in position

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• add docstrings

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• combine ome-zarr reader and writer

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• fix docstring length

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Commits on Jan 27, 2023

• append channel method

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• mixin class for file mode methods

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• handle metadata parsing in node classes

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• move ome-zarr-py and hypothesis to dev dependency

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• move hypothesis to dev dependency

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• match signature

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• fix constructors

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• fix metadata writing

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• fix default chunking

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• fix context manager

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• fix channel axis check

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• fix shape check

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• update OMEZarr example

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• rename ngff file

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• rename imports

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• showcase ImageArray.numpy()

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• update docstring

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• remove old writing code and add new well node

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• update well constructor and docstring

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• add row node

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• update docstring

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• elevate iterator

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• dummy metadata parsing for the row node

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• update docstrings

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• update example introduction

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• clarify read-only example

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• fix hcs metadata

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• add back dump metadata method as placeholder

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Commits on Jan 30, 2023

• plate node

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• fix typo

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• init plate meta in its own method

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• update docstring

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• replace old HCSWriter with a wrapper of plate node

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• remove reader adaptor

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• remove OMEZarrReader

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• update deprecation message

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• update docstring

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• rename example files

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• rearrange metadata attributes

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• fix plate metadata

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Commits on Jan 31, 2023

• fix metadata loading

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• update hcs example

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• fix omero metadata

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Commits on Feb 1, 2023

• rename test directory

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• rename test file

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Commits on Feb 2, 2023

• change error type

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• test util functions

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• fix linting and formatting

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• test OMEZarr

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• warning against invalid plate metadata

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• warn -> warning

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• warning against channel name not found

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• test HCSZarr.open()

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• handle missing axes and channel names

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• load axes from metadata if possible

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• fix check attribute logic

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• fix typo

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• test HCSZarr

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• return early if position is not found

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• match error type

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• restrict example count and loosen deadline

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• combine pytest commands

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• fix fixture call

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• remove unused import

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• update example comment

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• fix linting

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• fix linting

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• fix linting

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• Merge branch 'main' into ngff-dataset

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• Revert "Merge branch 'main' into ngff-dataset"

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• isort

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• Merge branch 'main' into ngff-dataset

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• remove empty files from merging

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• fix linting

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Commits on Feb 3, 2023

• Merge branch 'main' into ngff-dataset

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Commits on Feb 8, 2023

• simple refactors and an example that fails

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• revert wrong example changes

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• fix linting and formatting

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• simplify code

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• revert to conditional operator

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• Merge branch 'main' into ngff-dataset

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Commits on Feb 9, 2023

• use string as array key in examples

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• rename OMEZarr to OMEZarrFOV

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• Update docstrings

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• test append channel

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• check image shape with test

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Commits on Feb 10, 2023

• test create position

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• test well metadata

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• updated hcs_zarr example

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• Merge branch 'ngff-dataset' of https://github.com/czbiohub/iohub into ngff-dataset

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• move open store function to top level

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• rename open_store to aid auto-completion

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• wrap zarr.Group.tree() for ngff nodes

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• remove mixin and container classes

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• test against new api

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Commits on Feb 11, 2023

• update examples

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• refined examples and delete_channel stub

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• rename (ome_zarr -> singleFOV_zarr)

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• proposal for simplified API for tiled acquisition

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Commits on Feb 13, 2023

• Revert 3 commits

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• rename single fov example file

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• modify example store path and array name

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• edit HCS example

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• rename hcs example file

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