Refactor NGFF module and migrate to Pydantic v2 #233
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and refactor display util file
ziw-liu
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@ziw-liu should you update the dependencies to |
JoOkuma
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Jul 19, 2024
Co-authored-by: Jordão Bragantini <[email protected]>
ieivanov
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Jul 22, 2024
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I think this looks good, free free to merge when you're happy with it. Somewhere could you give more details on what belongs in ngff.models, ngff.nodes, and ngff.display? Is there a parallel to structures in the TIFF data readers? With the Universal API, do you think we can also achieve similar code structure?
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JoOkuma
approved these changes
Jul 29, 2024
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@ziw-liu sorry, I forgot to approve after my review. |
See f718d73.
What structure are you envisioning? I organized NGFF files here so that on the top level ( |
edyoshikun
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Jul 31, 2024
* 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]>
ieivanov
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* initial commit with added docs prior to refactoring to simplify the naming and functions. * considering varying t_idx_in and out * template for hypothesis * Refactor NGFF module and migrate to Pydantic v2 (#233) * 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]> * improving docstring for functions and renaming input and output path arguments to be more intuitive. * Fixing pyramid scaling factor (#238) * Fixing pyramid scaling factor * fix pyramid test * fix test again * Use annotation instead of field for tagged union (#244) also removed non-standard axis * Export `ImageArray` from the `ngff` module (#245) * adding the ImageArray * precommit * black * renaming method arguments to have consistent naming structure * flake8 * refactor _calculate_zyx_chunk_size * use input_store_path and output_store_path throughout * style * rename and clean up time indices * update time_indices documentation * add processing for channel indices * fix syntax and move ngff_utils.py to ngff/utils.py * update import * typing * docs typos * fix process_single_position iterator @talonchandler @edyoshikun * update apply_transform... docstring * compatibility with minimal deskew w/ @edyoshikun * pretty flat_iterable * adding new tests * create_empty test without testing channel names * fixing the create_empty_zarr extra indentation * -attempt to fix apply_transform_test. @ieivanov revert if needed * fixed apply_transform_czyx * debug pytest * fixing the test for create_empty_plate pytest * synchronize log messages * docs improvements * improved docs and typing for Callable func * remove commented slurmkit fix * delete unused function --------- Co-authored-by: Ziwen Liu <[email protected]> Co-authored-by: Jordão Bragantini <[email protected]> Co-authored-by: Ivan Ivanov <[email protected]> Co-authored-by: Talon Chandler <[email protected]>
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(Breaking) Moved the NGFF files to a subpackage.
Migrate to Pydantic v2. Downstream packages need to use the
v1namespace as shown in mehta-lab/recOrder@13ca75e.This PR is laying the ground work for the upcoming NGFF UAPI implementation. But the diff is significant enough so I'd like to get it reviewed first.