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Arcadia-Science / readlif

Leica Image Format (LIF) file reader for Python
GNU General Public License v3.0
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feature/add-support-for-reading-from-buffers #16

Closed evamaxfield closed 3 years ago

evamaxfield commented 3 years ago

Hey @nimne, I am finally getting around to upgrading the aicsimageio 4.x LifReader to use the new readlif==0.4.x.

AICSImageIO 4.x promises support for local and remote file reading and writing, and in trying to use readlif noticed you are handling bare pathlikes. Just a simple addition + tests for conditional routing of buffer support.

Thanks again for your work on this library! Hoping to get the aicsimageio LifReader all handled soon.

evamaxfield commented 3 years ago

Looks like the only tests that are failing are the "full_test" suites because I don't have the GitHub Secrets for your file server. Everything else looks good though. :slightly_smiling_face:

evamaxfield commented 3 years ago

By the way, is there any chance you have a mosaic LIF file that I could use for testing? I see there are tests for it where you download the file, but can I get that file or a similar example file to toss into our test set?

nimne commented 3 years ago

I'm still learning Github actions, apparently the secrets don't load on pull requests - so it's trying to use an empty environment variable, causing a failure. I was trying to solve the problem of having huge image files in the repo for testing, but the bugs aren't worked out yet!

Thanks for the additions, they look great! I'll get this merged and tag it is 0.5.0 - it should be on pypi by the end of the day.

There is a tiled file linked in the thread here: https://forum.image.sc/t/tilling-issue-with-lif-file/26843 although it's quite large. It should be possible to only keep a few images as an example using the Leica software. Unfortunately, I don't have access to a Leica scope / software at the moment to make a minimal example.

I'm glad that this is useful for the aicsimageio project.