Write anatomical orientation if available (RFC-4)#335
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Requires local install of https://github.com/melissalinkert/bioformats/commits/rfc-4 @ e31a392.
This should get moved to a 1.0-DEV test later.
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Closes #329. This depends upon an open Bio-Formats pull request (ome/bioformats#4454), so is a draft for now. This will also need to make use of the
1.0-DEVversion support and tests added in #330, as RFC-4 support should only be written with--ngff-version 1.0-DEV. I just didn't want to introduce conflicting commits here.As noted in #329, the general idea is that Bio-Formats proper implements most of RFC-4, including the controlled vocabulary therein. This pull request simply consumes axis orientations provided by Bio-Formats. The API defined in Bio-Formats and consumed here should be flexible enough to handle non-anatomical orientations, if that were to be added in a future RFC.
Basic tests make use of
FakeReader, but Analyze, Nifti, MINC, Bruker, Varian, and DICOM are all candidates for testing once we have suitable reference data (see #329 (comment)).I expect the build to fail here due to the need for ome/bioformats#4454. To test locally, check out that Bio-Formats branch, then
mvn clean package install, then./gradlew clean buildon this pull request's branch.