Porting `create_empty_zarr` to iohub by edyoshikun · Pull Request #234 · czbiohub-sf/iohub

edyoshikun · 2024-07-16T21:38:29Z

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:

Add docstring documentation to functions
~~Decide on the processing BaseFOV vs Position level~~ moved to Position should be a subclass of BaseFOV #249
Names of the functions
Hypothesis testing

…aming and functions.

mattersoflight · 2024-07-16T23:15:05Z

TODO:
Implement tests via hypothesis

ieivanov · 2024-07-18T21:20:24Z

Heads up, I'll have a bunch of comments and edits here, WIP

ieivanov · 2024-07-23T01:14:58Z

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

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.

* 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 <jordao.bragantini@czbiohub.org> * fix style * update module docstring to specify their content --------- Co-authored-by: Jordão Bragantini <jordao.bragantini@czbiohub.org>

…arguments to be more intuitive.

ieivanov · 2024-08-07T23:58:16Z

Related: czbiohub-sf/biahub#78

* Fixing pyramid scaling factor * fix pyramid test * fix test again

also removed non-standard axis

* adding the ImageArray * precommit * black

talonchandler

Ready to go from me!

edyoshikun added 2 commits July 16, 2024 11:48

initial commit with added docs prior to refactoring to simplify the n…

4386d32

…aming and functions.

considering varying t_idx_in and out

a5bca81

edyoshikun mentioned this pull request Jul 16, 2024

Porting_ip_funcs czbiohub-sf/shrimPy#153

Closed

template for hypothesis

6edd790

ziw-liu added enhancement labels Jul 17, 2024

ieivanov changed the base branch from main to mp_utils_port_v1 July 18, 2024 23:36

ieivanov changed the base branch from mp_utils_port_v1 to main July 18, 2024 23:41

ieivanov mentioned this pull request Jul 19, 2024

Moving code from shrimPy to biahub czbiohub-sf/biahub#1

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ieivanov reviewed Jul 22, 2024

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ziw-liu and others added 2 commits July 31, 2024 11:33

improving docstring for functions and renaming input and output path …

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…arguments to be more intuitive.

JoOkuma and others added 3 commits September 17, 2024 11:19

Fixing pyramid scaling factor (#238)

9ba133a

* Fixing pyramid scaling factor * fix pyramid test * fix test again

Use annotation instead of field for tagged union (#244)

84f351c

also removed non-standard axis

Export ImageArray from the ngff module (#245)

3304dac

* adding the ImageArray * precommit * black

edyoshikun commented Sep 17, 2024

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renaming method arguments to have consistent naming structure

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talonchandler added 2 commits September 19, 2024 20:12

update import

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typing

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talonchandler reviewed Sep 20, 2024

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docs typos

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ieivanov and others added 3 commits September 20, 2024 11:18

fix process_single_position iterator @talonchandler @edyoshikun

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update apply_transform... docstring

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compatibility with minimal deskew w/ @edyoshikun

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talonchandler mentioned this pull request Sep 20, 2024

biahub deskew depends on submitit and iohub's parallelization utilities czbiohub-sf/biahub#5

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7 tasks

ieivanov and others added 10 commits September 20, 2024 16:48

pretty flat_iterable

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adding new tests

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create_empty test without testing channel names

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fixing the create_empty_zarr extra indentation

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-attempt to fix apply_transform_test. @ieivanov revert if needed

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fixed apply_transform_czyx

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debug pytest

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fixing the test for create_empty_plate pytest

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synchronize log messages

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docs improvements

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talonchandler mentioned this pull request Sep 26, 2024

Position should be a subclass of BaseFOV #249

Open

talonchandler added 4 commits September 26, 2024 13:57

improved docs and typing for Callable func

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remove commented slurmkit fix

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delete unused function

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Merge branch 'main' into mp_utils_port

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talonchandler approved these changes Sep 26, 2024

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ieivanov merged commit d6f7956 into main Sep 27, 2024

ieivanov deleted the mp_utils_port branch September 27, 2024 20:55

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edyoshikun commented Jul 16, 2024 •

edited by talonchandler

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