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Porting create_empty_zarr to iohub #234

Merged
merged 38 commits into from
Sep 27, 2024
Merged

Porting create_empty_zarr to iohub #234

merged 38 commits into from
Sep 27, 2024

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edyoshikun
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@edyoshikun edyoshikun commented Jul 16, 2024 •
edited by talonchandler
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This PR adds shrimPy utility functions relevant to iohub listed below:

  • create_empty_zarr: enables the creation of an empty zarr
  • process_single_position: function that can apply a czyx in czyx out function to a zarr store.

TODO:

@edyoshikun edyoshikun mentioned this pull request Jul 16, 2024
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@mattersoflight
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mattersoflight commented Jul 16, 2024 •
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TODO:
Implement tests via hypothesis

@ziw-liu ziw-liu added enhancement New feature or request NGFF OME-NGFF (OME-Zarr format) labels Jul 17, 2024
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Heads up, I'll have a bunch of comments and edits here, WIP

@ieivanov ieivanov changed the base branch from main to mp_utils_port_v1 July 18, 2024 23:36
@ieivanov ieivanov changed the base branch from mp_utils_port_v1 to main July 18, 2024 23:41
ieivanov
ieivanov reviewed Jul 22, 2024
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P.S. I'm leaving a bunch of comments here so we can agree on the structure, but I'm also happy to implement some of these suggestions, I'm not asking others (Ed) to implement all of these.

JoOkuma
JoOkuma reviewed Jul 23, 2024
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The functions to process_ and transform_ the data could be made for general and work on arbitrary axes with some changes. We did this here in ultrack

Is it really necessary to have a function to process a single position?

From my POV, these "apply" functions should take an arbitrary BaseFOVMapping as input and write an ome-zarr.

We could write a wrapper of the BaseFOV that creates a "trivial" BaseFOVMapping that behaves as an HCS, so there's a single implementation for both cases and supporting multiple file types as input.

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ziw-liu and others added 2 commits July 31, 2024 11:33
@ziw-liu @JoOkuma @edyoshikun
Refactor NGFF module and migrate to Pydantic v2 (#233)
ee502b2 
* unify comment format

* fix typing and docstring

* create ngff sub-package
and refactor display util file

* refactor ngff meta file

* refactor ngff

* export transformation model

* fix type hint

* bump ome-zarr target in docstring

* migrate to pydantic v2

* isort

* fix validators

* remove union type

* fix dependency

* update docstring

* typing improvements

* Update iohub/ngff/models.py

Co-authored-by: Jordão Bragantini <[email protected]>

* fix style

* update module docstring to specify their content

---------

Co-authored-by: Jordão Bragantini <[email protected]>
@edyoshikun
improving docstring for functions and renaming input and output path …
7fc31a7 
…arguments to be more intuitive.
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ieivanov commented Aug 7, 2024

Related: czbiohub-sf/shrimPy#123

JoOkuma and others added 3 commits September 17, 2024 11:19
@JoOkuma @edyoshikun
Fixing pyramid scaling factor (#238)
9ba133a 
* Fixing pyramid scaling factor

* fix pyramid test

* fix test again
@ziw-liu @edyoshikun
Use annotation instead of field for tagged union (#244)
84f351c 
also removed non-standard axis
@edyoshikun
Export ImageArray from the ngff module (#245)
3304dac 
* adding the ImageArray

* precommit

* black
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@talonchandler talonchandler mentioned this pull request Sep 26, 2024
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talonchandler approved these changes Sep 26, 2024
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Ready to go from me!

@ieivanov ieivanov merged commit d6f7956 into main Sep 27, 2024
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@ieivanov ieivanov deleted the mp_utils_port branch September 27, 2024 20:55
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@talonchandler talonchandler talonchandler approved these changes

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@edyoshikun @mattersoflight @ieivanov @talonchandler @JoOkuma @ziw-liu