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Universal API implementations for Micro-Manager OME-TIFF and NDTiff #185

Merged
merged 79 commits into from
Mar 4, 2024
Merged

Universal API implementations for Micro-Manager OME-TIFF and NDTiff #185

merged 79 commits into from
Mar 4, 2024

Commits on Sep 1, 2023

  1. wip: draft mmstack ome-tiff fov

    @ziw-liu
    ziw-liu committed Sep 1, 2023
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  2. MM FOV base class

    @ziw-liu
    ziw-liu committed Sep 1, 2023
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  3. tests

    @ziw-liu
    ziw-liu committed Sep 1, 2023
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  4. bump tifffile

    @ziw-liu
    ziw-liu committed Sep 1, 2023
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  5. comment

    @ziw-liu
    ziw-liu committed Sep 1, 2023
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  6. fix indent after rebase

    @ziw-liu
    ziw-liu committed Sep 1, 2023
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Commits on Sep 2, 2023

  1. use get default

    @ziw-liu
    ziw-liu committed Sep 2, 2023
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  2. test pixel indexing

    @ziw-liu
    ziw-liu committed Sep 2, 2023
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  3. set MM metadata

    @ziw-liu
    ziw-liu committed Sep 2, 2023
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  4. style

    @ziw-liu
    ziw-liu committed Sep 2, 2023
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Commits on Feb 2, 2024

  1. update dependencies

    @ziw-liu
    ziw-liu committed Feb 2, 2024
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  2. Merge branch 'unified-api' into ometiff-uapi

    @ziw-liu
    ziw-liu committed Feb 2, 2024
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  3. add xarray

    @ziw-liu
    ziw-liu committed Feb 2, 2024
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Commits on Feb 6, 2024

  1. move old readers to the _deprecated namespace

    @ziw-liu
    ziw-liu committed Feb 6, 2024
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  2. uapi for ndtiff

    @ziw-liu
    ziw-liu committed Feb 6, 2024
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  3. refactor test setup to parametrize by dataset 

    use globals instead of fixtures since parametrization happens before fixture evaluation
    @ziw-liu
    ziw-liu committed Feb 6, 2024
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  4. convert mmstack

    @ziw-liu
    ziw-liu committed Feb 6, 2024
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  5. fix and test chunking

    @ziw-liu
    ziw-liu committed Feb 6, 2024
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Commits on Feb 7, 2024

  1. fix metadata conversion and test ndtiff

    @ziw-liu
    ziw-liu committed Feb 7, 2024
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Commits on Feb 8, 2024

  1. update cli

    @ziw-liu
    ziw-liu committed Feb 8, 2024
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  2. fix scaling

    @ziw-liu
    ziw-liu committed Feb 8, 2024
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  3. test 1.4 and incomplete ome-tiffs

    @ziw-liu
    ziw-liu committed Feb 8, 2024
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  4. move reader tests

    @ziw-liu
    ziw-liu committed Feb 8, 2024
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  5. deprecate reader tests

    @ziw-liu
    ziw-liu committed Feb 8, 2024
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  6. update deprecated tests

    @ziw-liu
    ziw-liu committed Feb 8, 2024
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  7. update ngff tests

    @ziw-liu
    ziw-liu committed Feb 8, 2024
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  8. isort

    @ziw-liu
    ziw-liu committed Feb 8, 2024
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  9. update black target to 3.10

    @ziw-liu
    ziw-liu committed Feb 8, 2024
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  10. lint

    @ziw-liu
    ziw-liu committed Feb 8, 2024
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  11. fix download paths

    @ziw-liu
    ziw-liu committed Feb 8, 2024
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  12. update docs references and theme

    @ziw-liu
    ziw-liu committed Feb 8, 2024
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  13. untrack autogenerated file

    @ziw-liu
    ziw-liu committed Feb 8, 2024
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  14. ignore execution time file

    @ziw-liu
    ziw-liu committed Feb 8, 2024
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  15. add github icon

    @ziw-liu
    ziw-liu committed Feb 8, 2024
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  16. update docstring

    @ziw-liu
    ziw-liu committed Feb 8, 2024
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  17. update docstring

    @ziw-liu
    ziw-liu committed Feb 8, 2024
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Commits on Feb 9, 2024

  1. show channel names and chunk size in info

    @ziw-liu
    ziw-liu committed Feb 9, 2024
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  2. print plate chunk size if verbose

    @ziw-liu
    ziw-liu committed Feb 9, 2024
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  3. fallback for pixel size

    @ziw-liu
    ziw-liu committed Feb 9, 2024
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  4. remove log level setting

    @ziw-liu
    ziw-liu committed Feb 9, 2024
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  5. do not filter logs and warnings in reader

    @ziw-liu
    ziw-liu committed Feb 9, 2024
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  6. avoid root logger

    @ziw-liu
    ziw-liu committed Feb 9, 2024
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  7. isort

    @ziw-liu
    ziw-liu committed Feb 9, 2024
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  8. set default logging level to INFO

    @ziw-liu
    ziw-liu committed Feb 9, 2024
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  9. format docstring

    @ziw-liu
    ziw-liu committed Feb 9, 2024
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  10. improve conversion messages

    @ziw-liu
    ziw-liu committed Feb 9, 2024
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  11. black

    @ziw-liu
    ziw-liu committed Feb 9, 2024
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  12. fix ome-tiff channel name indexing

    @ziw-liu
    ziw-liu committed Feb 9, 2024
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  13. fix ndtiff channel name indexing

    @ziw-liu
    ziw-liu committed Feb 9, 2024
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  14. update converter test

    @ziw-liu
    ziw-liu committed Feb 9, 2024
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Commits on Feb 12, 2024

  1. remove use of os.path in reader

    @ieivanov
    ieivanov committed Feb 12, 2024
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Commits on Feb 13, 2024

  1. expand _check_ndtiff checks

    @ieivanov
    ieivanov committed Feb 13, 2024
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Commits on Feb 15, 2024

  1. fix iteration

    @ziw-liu
    ziw-liu committed Feb 15, 2024
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  2. fix python 3.10 

    using `Path.glob(*/)` to get subdirs was added in 3.11
    @ziw-liu
    ziw-liu committed Feb 15, 2024
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  3. bump zarr version to include resizing fix 

    zarr-developers/zarr-python#1540
    @ziw-liu
    ziw-liu committed Feb 15, 2024
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  4. fix cli default

    @ziw-liu
    ziw-liu committed Feb 15, 2024
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  5. set log level with an environment variable

    @ziw-liu
    ziw-liu committed Feb 15, 2024
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  6. fix unset

    @ziw-liu
    ziw-liu committed Feb 15, 2024
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Commits on Feb 16, 2024

  1. catch non-existent page

    @ziw-liu
    ziw-liu committed Feb 16, 2024
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  2. implement fallback for incomplete channel names 

    workaround for the Dragonfly microscope where the multi-camera setup only has one channel name written
    @ziw-liu
    ziw-liu committed Feb 16, 2024
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  3. add debug logs

    @ziw-liu
    ziw-liu committed Feb 16, 2024
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  4. handle virtual frames

    @ziw-liu
    ziw-liu committed Feb 16, 2024
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  5. try reading pages from TiffFile directly

    @ziw-liu
    ziw-liu committed Feb 16, 2024
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  6. filter error logs about ImageJ metadata being broken 

    this is a known MM limitation when writing OME-TIFFs
    @ziw-liu
    ziw-liu committed Feb 16, 2024
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Commits on Feb 17, 2024

  1. fix regex

    @ziw-liu
    ziw-liu committed Feb 17, 2024
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Commits on Feb 21, 2024

  1. remove use of os.path in convert.py

    @ieivanov
    ieivanov committed Feb 21, 2024
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  2. better channel indexing in _get_summary_metadata

    @ieivanov
    ieivanov committed Feb 21, 2024
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  3. style

    @ieivanov
    ieivanov committed Feb 21, 2024
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Commits on Feb 22, 2024

  1. safer NoneType check

    @ziw-liu
    ziw-liu committed Feb 22, 2024
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  2. private default axis names for NDTiff

    @ziw-liu
    ziw-liu committed Feb 22, 2024
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  3. update documentation to reflect new entry point

    @ziw-liu
    ziw-liu committed Feb 22, 2024
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  4. add repr to MM FOV and dataset types

    @ziw-liu
    ziw-liu committed Feb 22, 2024
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  5. rename mm_meta and expose summary metadata

    @ziw-liu
    ziw-liu committed Feb 22, 2024
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Commits on Feb 28, 2024

  1. add MicroManagerFOVMapping.root

    @ziw-liu
    ziw-liu committed Feb 28, 2024
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  2. add MicroManagerFOVMapping.zyx_scale

    @ziw-liu
    ziw-liu committed Feb 28, 2024
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  3. add warning log for failed position grid

    @ziw-liu
    ziw-liu committed Feb 28, 2024
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  4. fix grid layout

    @ziw-liu
    ziw-liu committed Feb 28, 2024
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  5. suppress hypothesis flakiness

    @ziw-liu
    ziw-liu committed Feb 28, 2024
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  6. different health check suppression

    @ziw-liu
    ziw-liu committed Feb 28, 2024
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