add ROIs to OME-TIFF export

[mtbc]

Try exporting then importing an image with ROIs and make sure that the ROIs are preserved. Of course, this preserves only the properties defined in ROI.xsd. Also check that https://ci.openmicroscopy.org/job/OMERO-DEV-merge-integration-java/lastCompletedBuild/testngreports/integration/ExporterTest/ passes.

Still does not work for mask ROIs, sorry @imunro.

--no-rebase

[jburel]

@mtbc: sorry I didn't have time with the various meetings to review it.
I will do that tomorrow am

[jburel]

one think to review, outside the scope of this PR is the stylesheets to downgrade to be sure that the ROIs can be preserved during the process

[jburel]

Tested the following:

• Export image with a roi with shapes propagated across z
• Export image with several rois
• Export image with rois and annotation on shape

The tests passed.
Something to consider now, ability to pass a parameter to export or not the rois
we now have images with a large number of images so the user should be able to decide to add them or not.

I export to a previous schema (2013), The rois are exported but ref for annotation to the wrong schema
This is outside the scope of this PR and will need investigation

[jburel]

Another parameter that we could consider passing will be the compression used for data

[mtbc]

The annotation schema version bug is interesting. I wonder who might know about that. Definitely worth noting.

For this PR, any more testing required?

[joshmoore]

one think to review, outside the scope of this PR is the stylesheets to downgrade to be sure that the ROIs can be preserved during the process

https://trello.com/c/CQMxBS71/21-downgrading-rois

Something to consider now, ability to pass a parameter to export or not the rois

https://trello.com/c/lKfhVnjW/22-skip-rois-in-export

The rois are exported but ref for annotation to the wrong schema

https://trello.com/c/83il07Mv/23-annotation-ref-version

Another parameter that we could consider passing will be the compression used for data

That's probably more along the lines of https://trello.com/c/d2OqpHCq/14-export-import-decide-api

Anything else or just waiting on the release of Bio-Formats 5.1.4?

[jburel]

@mtbc: I think I have an idea for the schema issue and stylesheet
Nothing I can think of for now
but all the points can be addressed in follow up PR
certainly a good start
I have not yet tested annotation on ROI, only on shape

[jburel]

for annotation on shape:

<Shape>....
<AnnotationRef xmlns="http://www.openmicroscopy.org/Schemas/SA/2015-01" ID="urn:lsid:export.openmicroscopy.org:Annotation:73e8e6ff-d6fe-4c12-8397-3af0d1d901d2_12801:219647"/></Shape>

for annotation on roi:

</Shape></Union><AnnotationRef xmlns="http://www.openmicroscopy.org/Schemas/SA/2015-01" ID="urn:lsid:export.openmicroscopy.org:Annotation:73e8e6ff-d6fe-4c12-8397-3af0d1d901d2_12801:219647"/></ROI>

Both options are working

[jburel]

happy to have it merged when we decide

[joshmoore]

👍 Merging to allow schema changes to be built on top.