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Refactor API for NGFF datasets #31

Merged
merged 111 commits into from
Feb 13, 2023
Merged

Refactor API for NGFF datasets #31

merged 111 commits into from
Feb 13, 2023

Commits on Jan 21, 2023

  1. base class for ngff nodes

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    ziw-liu committed Jan 21, 2023
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Commits on Jan 23, 2023

  1. fix typo

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    ziw-liu committed Jan 23, 2023
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  2. sketch image container and position node

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    ziw-liu committed Jan 23, 2023
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Commits on Jan 26, 2023

  1. create new image in position

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    ziw-liu committed Jan 26, 2023
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  2. add docstrings

    @ziw-liu
    ziw-liu committed Jan 26, 2023
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  3. combine ome-zarr reader and writer

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    ziw-liu committed Jan 26, 2023
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  4. fix docstring length

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    ziw-liu committed Jan 26, 2023
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Commits on Jan 27, 2023

  1. append channel method

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    ziw-liu committed Jan 27, 2023
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  2. mixin class for file mode methods

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    ziw-liu committed Jan 27, 2023
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  3. handle metadata parsing in node classes

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    ziw-liu committed Jan 27, 2023
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  4. move ome-zarr-py and hypothesis to dev dependency

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    ziw-liu committed Jan 27, 2023
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  5. move hypothesis to dev dependency

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    ziw-liu committed Jan 27, 2023
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  6. match signature

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    ziw-liu committed Jan 27, 2023
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  7. fix constructors

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    ziw-liu committed Jan 27, 2023
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  8. fix metadata writing

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    ziw-liu committed Jan 27, 2023
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  9. fix default chunking

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    ziw-liu committed Jan 27, 2023
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  10. fix context manager

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    ziw-liu committed Jan 27, 2023
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  11. fix channel axis check

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    ziw-liu committed Jan 27, 2023
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  12. fix shape check

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    ziw-liu committed Jan 27, 2023
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  13. update OMEZarr example

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    ziw-liu committed Jan 27, 2023
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  14. rename ngff file

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    ziw-liu committed Jan 27, 2023
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  15. rename imports

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    ziw-liu committed Jan 27, 2023
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  16. showcase ImageArray.numpy()

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  17. update docstring

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    ziw-liu committed Jan 27, 2023
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  18. remove old writing code and add new well node

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  19. update well constructor and docstring

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  20. add row node

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    ziw-liu committed Jan 27, 2023
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  21. update docstring

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  22. elevate iterator

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  23. dummy metadata parsing for the row node

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  24. update docstrings

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    ziw-liu committed Jan 27, 2023
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  25. update example introduction

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  26. clarify read-only example

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    ziw-liu committed Jan 27, 2023
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  27. fix hcs metadata

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    ziw-liu committed Jan 27, 2023
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  28. add back dump metadata method as placeholder

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    ziw-liu committed Jan 27, 2023
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Commits on Jan 30, 2023

  1. plate node

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    ziw-liu committed Jan 30, 2023
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  2. fix typo

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    ziw-liu committed Jan 30, 2023
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  3. init plate meta in its own method

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  4. update docstring

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    ziw-liu committed Jan 30, 2023
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  5. replace old HCSWriter with a wrapper of plate node

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  6. remove reader adaptor

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    ziw-liu committed Jan 30, 2023
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  7. remove OMEZarrReader

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    ziw-liu committed Jan 30, 2023
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  8. update deprecation message

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    ziw-liu committed Jan 30, 2023
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  9. update docstring

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    ziw-liu committed Jan 30, 2023
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  10. rename example files

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  11. rearrange metadata attributes

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    ziw-liu committed Jan 30, 2023
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  12. fix plate metadata

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    ziw-liu committed Jan 30, 2023
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Commits on Jan 31, 2023

  1. fix metadata loading

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    ziw-liu committed Jan 31, 2023
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  2. update hcs example

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    ziw-liu committed Jan 31, 2023
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  3. fix omero metadata

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    ziw-liu committed Jan 31, 2023
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Commits on Feb 1, 2023

  1. rename test directory

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  2. rename test file

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Commits on Feb 2, 2023

  1. change error type

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  2. test util functions

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  3. fix linting and formatting

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    ziw-liu committed Feb 2, 2023
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  4. test OMEZarr

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    ziw-liu committed Feb 2, 2023
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  5. warning against invalid plate metadata

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    ziw-liu committed Feb 2, 2023
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  6. warn -> warning

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  7. warning against channel name not found

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    ziw-liu committed Feb 2, 2023
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  8. test HCSZarr.open()

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  9. handle missing axes and channel names

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  10. load axes from metadata if possible

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  11. fix check attribute logic

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    ziw-liu committed Feb 2, 2023
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  12. fix typo

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    ziw-liu committed Feb 2, 2023
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  13. test HCSZarr

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  14. return early if position is not found

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  15. match error type

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  16. restrict example count and loosen deadline

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  17. combine pytest commands

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  18. fix fixture call

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  19. remove unused import

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  20. update example comment

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  21. fix linting

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  22. fix linting

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  23. fix linting

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  24. Merge branch 'main' into ngff-dataset

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  25. Revert "Merge branch 'main' into ngff-dataset" 

    This reverts commit c17b81e.
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  26. isort

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  27. Merge branch 'main' into ngff-dataset

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  28. remove empty files from merging

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  29. fix linting

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Commits on Feb 3, 2023

  1. Merge branch 'main' into ngff-dataset

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Commits on Feb 8, 2023

  1. simple refactors and an example that fails

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  2. revert wrong example changes

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  3. fix linting and formatting

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  4. simplify code

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  5. revert to conditional operator

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  6. Merge branch 'main' into ngff-dataset

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Commits on Feb 9, 2023

  1. use string as array key in examples

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  2. rename OMEZarr to OMEZarrFOV

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  3. Update docstrings

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  4. test append channel

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  5. check image shape with test

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Commits on Feb 10, 2023

  1. test create position

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  2. test well metadata

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  3. updated hcs_zarr example

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

    … ngff-dataset
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  5. move open store function to top level

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  6. rename open_store to aid auto-completion

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

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  8. remove mixin and container classes

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  9. test against new api

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Commits on Feb 11, 2023

  1. update examples

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  2. refined examples and delete_channel stub

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  3. rename (ome_zarr -> singleFOV_zarr)

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  4. proposal for simplified API for tiled acquisition

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Commits on Feb 13, 2023

  1. Revert 3 commits 

    This reverts commits 6d0ba4c,
b9516b1, 61237f9.
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  2. rename single fov example file

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  3. modify example store path and array name

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  4. edit HCS example

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  5. rename hcs example file

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