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JPEG-2000 compression based refactoring #32
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Firstly, `NamedTemporaryFile` cannot be opened more than once on Windows; the implementation was effectively broken completely on the platform. Consequently, temporary file usage has been moved to `mkstemp()` and handled accordingly. Furthermore, the `out` argument to the JPEG-2000 codec `Codec.decode()` implementation was not being handled correctly causing visual corruption with certain workflows (noteably napari). As of this commit glymur 0.9.4 is required and the constructor based API is now in use.
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Refactors the codebase such that all compression is performed by imagecodecs using a JPEG-2000 codec for Zarr.
NOTE: Due to the Python 3.7+ requirements of some of the dependencies used in this PR and the availability of the iSyntax SDK for Python 3.7 currently being restricted to Windows it will only run on that platform.
This PR can be executed as regular isyntax2raw with the exception of the
--psnr
command line option. NOTE: This option is fed directly into imagecodecs and may need to be inversed depending on the version installed (--psnr=60
being equivalent to 40 PSNR). For example:Testing of the result can be performed on the same platform and Python environemnt with
napari
; assuming1.isyntax
has been converted to1.zarr
as above. For example:This testing with
napari
can happen on any platform with Python 3.7+ utilizing the JPEG-2000 Codec factored out and published to PyPI aszarr-jpeg2k
:Latest wheel: