render client refactoring and clean-up

[trautmane]

Hi,

The render java and spark clients have accumulated over the years. I'd like to remove any clients that are no longer used or needed and then reorganize the remaining clients into logical sub-packages.

I thought I'd reach out to the relatively small community I think uses render to see what, if any, clients are still being used.

If you or your group/lab uses render, I'd greatly appreciate it if you would add a comment to this issue with answers to the following questions:

1. Does your group or lab still use render and if so ... ?
2. Which java and spark clients do you use (e.g. java TilePairClient, spark N5Client, ...)?
3. Which branch(es) or tag(s) do you use (e.g. master, ibeam_msem, ...)?
4. Which viewer(s) do you use (e.g. neuroglancer, CATMAID, ...)?

I'm tagging the community I know of here:
@fcollman @RussTorres @sharmishtaa @mahaling @djkapner @perlman
@khaledkhairy @nishantshakya @catherinerajendran
@martinschorb

Of course, I'd be happy to hear from anyone else who is using render.

Hope you all are well,
Eric

[nishantshakya]

1. Yes
2. a) Java (BoxClient, MipMapClient, RenderSectionClient)
   b) Spark (N5Client, BoxClient, MipMapClient)
3. master for Java clients, ibeam_msem for Spark clients
4. Catmaid, Neuroglancer

@catherinerajendran should be able to list other clients, missing from my project, but used by other projects in the lab.

[catherinerajendran]

Hi Eric, Java clients: TilePairClient, SIFTPointMatchClient Branch: master Viewer: Catmaid, Neuroglancer, OpenSeaDragon (ArgbRenderer for RGB images and ByteRenderer for grayscale images) Best, Catherine

…

On Thu, Dec 14, 2023 at 4:32 PM Nishant Shakya ***@***.***> wrote: 1. Yes 2. a) Java (BoxClient, MipMapClient, RenderSectionClient) b) Spark (N5Client, BoxClient, MipMapClient) 3. master for Java clients, ibeam_msem for Spark clients 4. Catmaid, Neuroglancer @catherinerajendran <https://github.com/catherinerajendran> should be able to list other clients, missing from my project, but used by other projects in the lab. — Reply to this email directly, view it on GitHub <#164 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEHZVIXA53BU3U6XUXLRVVLYJN47JAVCNFSM6AAAAABAVRFPIKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNJWHAYTQNBVGU> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[RussTorres]

Great to hear from you Eric!

1. Yes!
2. These are the ones we use extensively in day-to-day processing tasks, though we do support and access more than these as part of render-python and asap-modules.

Java:

• org.janelia.render.client.ImportJsonClient
• org.janelia.render.client.TilePairClient
• org.janelia.render.client.CoordinateClient
• org.janelia.alignment.Render (thank you for legacy support -- will update soon)
• org.janelia.render.client.RenderSectionClient (though we are mostly changing this in favor of manipulating renderparameters and using the Render client)
• org.janelia.render.client.PointMatchClient

Spark:

• org.janelia.render.client.spark.SIFTPointMatchClient

3. mostly using the RussTorres s3_urihandler branch, which is closest to tag v2.0.2 -- we are planning to move to a more modern version when we implement some additional infrastructure changes.
4. neuroglancer, particularly with links populated by a custom vizrelay configuration

Thank you,
Russel

[martinschorb]

Hi Eric,

1. Yes!
2. we mostly access the Java Client scripts (ImportJsonClient, TilePairClient, MipMapClient,...) through render-python and asap-modules
   in addition: Spark: SIFTPointMatchClient, N5Client
3. ibeam_msem
4. BDV/MoBIE, hoping for OME_Zarr support soon.

Thanks for you countless efforts!