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Add Clear Control dataset support #114

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merged 17 commits into from
Apr 17, 2023
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@JoOkuma JoOkuma commented Apr 14, 2023

This PR implements the Clear Control dataset reader.

Besides a basic working functionality, the CC reader class provides the expected attributes of an array and a least recently used cache, so it just works with napari, and no zarr or dask is needed.

For example:

cc = ClearControlFOV(path, cache=True)
napari.view_image(cc)
napari.run()

NOTE: it's loaded just as an array, so there is no scaling according to metadata or splitting the channels into layers.

cc-dataset-demo.mp4

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JoOkuma commented Apr 17, 2023

Thanks @ziw-liu

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Code looks good to me! @JoOkuma you can decide whether the other 'public' functions in the module need to be in the documentation.

Didn't test this on any actual data though, but I trust your judgement on when to merge.

@ziw-liu ziw-liu added the enhancement New feature or request label Apr 17, 2023
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JoOkuma commented Apr 17, 2023

I'm not sure why Sphinx didn't document them automatically, maybe because there're properties (getters).
I'm fine the way it's.

I merged with main. I added ClearControl first on the documentation to keep it sorted alphabetically, but the list was not fully sorted, let me know if you prefer a different ordering.

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ziw-liu commented Apr 17, 2023

I added ClearControl first on the documentation to keep it sorted alphabetically, but the list was not fully sorted, let me know if you prefer a different ordering.

The current ordering is manual, listing the 'primary entry points' on the top. I think it may make sense to move all the one-microscope-specific formats (Dorado, PTI etc.) to a secondary node. But maybe we can deal with that in #112?

@JoOkuma JoOkuma merged commit e8afefb into czbiohub-sf:main Apr 17, 2023
@JoOkuma JoOkuma deleted the clearcontrol branch April 17, 2023 20:08
@ziw-liu ziw-liu mentioned this pull request May 31, 2023
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2 participants