Do not support linking to existing BDV/XML images in Fiji Project Creator

[tischi]

@constantinpape @martinschorb @jhennies @K-Meech

Currently we have in the JAVA API:

 public void addBdvFormatImage ( SpimData spimData, String imageName, String datasetName,
                                    ProjectCreator.ImageType imageType, ProjectCreator.AddMethod addMethod, String uiSelectionGroup, ImageDataFormat imageDataFormat, boolean exclusive ) throws SpimDataException, IOException {

This is for "adding/linking" to already existing BDV/XML images.

To simplify the code and it's maintenance I would like to remove this and only support linking to already existing OME-Zarr.

OK?

[constantinpape]

I think that's fine.

[K-Meech]

Hi @tischi - do you mean you only want to support moving/copying/linking to ome-zarr and remove all support for n5? Do you also want to remove n5 support for adding images currently open in ImageJ?

[tischi]

@K-Meech Yes, OME-Zarr only would be the easiest and also long term the best strategy (fingers crossed).

[tischi]

The point is that all the code for the XML based formats needs to be maintained by us and it is quite complex. If we only use OME-Zarr we can now rely a lot on the new n5 libraries.

Essentially I could delete 90% of the code in mobie-io and around 50% of the code in the ProjectCreator. This will make further maintenance much easier, which is essential given that we have very limited developers to work on the mobie Java code.

[K-Meech]

@tischi - sure, that makes sense! My only concern would be that people who have existing n5 projects would no longer be able to edit / add to them via the project creator. So it would be good to give people some warning that this will be removed e.g. getting in touch with the main users / making a post on image.sc etc ?

[tischi]

@K-Meech good point, do you know such people? Could you write such a forum post and ping them?

[martinschorb]

It would probably affect 97% of the volume-EM projects

[K-Meech]

@tischi I'm not sure who is using this at the moment, beyond the volume EM folks as @martinschorb said. You could consider adding a deprecation warning for a few months that gets printed when the project creator is opened?

[tischi]

It would probably affect 97% of the volume-EM projects

@martinschorb Why are there so many non-OME-Zarr data?

[martinschorb]

Janelia runs N5 and historically we mostly created N5 as well. But your changes would only affect the creator? If so and the restriction is to no longer being able to add new sources, I guess that's fine. Python would still allow it...

[tischi]

Yes, this will only affect the Fiji project creator and Fiji project editor.

Otherwise there still is full support for many file formats, including XML/N5 and XML/HFD5.

[martinschorb]

Then from my side nothing speaks against going ahead with the cleanup.