Refactor to take out problematic dependencies #8
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This pull request fixes 1 alert when merging 2d951e7 into dbd442a - view on LGTM.com fixed alerts:
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This pull request fixes 1 alert when merging 4d2a259 into dbd442a - view on LGTM.com fixed alerts:
Heads-up: LGTM.com's PR analysis will be disabled on the 5th of December, and LGTM.com will be shut down ⏻ completely on the 16th of December 2022. Please enable GitHub code scanning, which uses the same CodeQL engine ⚙️ that powers LGTM.com. For more information, please check out our post on the GitHub blog. |
Context
Currently, the input for frc calculation is the image filepath rather than the array containing image data, which makes Quoll harder to implement as a Napari plugin. Also, the filepath reading from Miplib uses pims which can complicate installation due to Java dependencies.
Changes
Quoll now creates miplib Image objects directly from the image data, which is extracted from a Quoll Image object. The Quoll Image object only accepts .tiffs and .mrcs at the moment, rather than the wide range accepted from BioFormats through pims, though the installation of dependencies is easier. This change also makes Quoll more easily compatible with Napari plugin implementations.
Still need to have a look at the pyproject.toml and see how we can install a more minimal version of miplib that does not require the many + large dependencies we do not use and/or have trouble with: these include jpype1, pims, SimpleITK, psf, ...