Fixing pyramid scaling factor #238
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ziw-liu
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Aug 7, 2024
edyoshikun
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Sep 17, 2024
* Fixing pyramid scaling factor * fix pyramid test * fix test again
ieivanov
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Sep 27, 2024
* 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 <jordao.bragantini@czbiohub.org> * fix style * update module docstring to specify their content --------- Co-authored-by: Jordão Bragantini <jordao.bragantini@czbiohub.org> * 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 <67518483+ziw-liu@users.noreply.github.com> Co-authored-by: Jordão Bragantini <jordao.bragantini@czbiohub.org> Co-authored-by: Ivan Ivanov <ivan.ivanov@czbiohub.org> Co-authored-by: Talon Chandler <talonchandler@gmail.com>
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Hi, I noticed this bug a while ago, but the change was lost in #221
The spatial scaling should increase as we make the images smaller so they are all the same size.
This doesn't affect napari, but it does for other viewers (e.g. neuroglancer).