Add method to download meshes

[markbader]

Description:

• This PR adds functionality to download meshes as .stl files.

Issues:

• fixes Download meshes from remote segmentations #1295

Todos:

Make sure to delete unnecessary points or to check all before merging:

• Updated Changelog

[github-actions]

☂️ Python Coverage

current status: ✅

Overall Coverage

Lines	Covered	Coverage	Threshold	Status
9291	7841	84%	80%	🟢

New Files

File	Coverage	Status
webknossos/webknossos/client/api_client/tracingstore_api_client.py	57%	🟢
TOTAL	57%	🟢

Modified Files

File	Coverage	Status
webknossos/webknossos/annotation/annotation.py	81%	🟢
webknossos/webknossos/client/api_client/init.py	100%	🟢
webknossos/webknossos/client/api_client/_abstract_api_client.py	94%	🟢
webknossos/webknossos/client/api_client/datastore_api_client.py	82%	🟢
webknossos/webknossos/client/api_client/models.py	100%	🟢
webknossos/webknossos/client/api_client/wk_api_client.py	89%	🟢
webknossos/webknossos/client/context.py	89%	🟢
webknossos/webknossos/dataset/dataset.py	85%	🟢
TOTAL	90%	🟢

updated for commit: 5f1733c by action🐍

[fm3]

Thanks for looking into this! I added a couple of comments.

Additionally: is there an exposed way to download meshes from datasets (without annotation?) Maybe a similar method could be added to wk.Dataset? On the other hand, I’d say the Tracingstore class with its download_mesh may not have to be user-facing.

What do you think?

[markbader]

What exactly should be downloaded from a dataset without annotation? I thought we always want to download a certain segment. Does a dataset have segments if there is no annotation?

[fm3]

Yes, this is somewhat specific to the webknossos terminology, but “on-disk” segmentation layers are not directly counted as annotations. Yes, volume annotation layers can have such segmentation layers as fallback layers, but no annotation object is required to see segments and their meshes. As long as a dataset has a layer of category segmentation, and a meshfile, this should be possible.

[markbader]

I am not sure if I understand it completely. I added the download_mesh method to the remote_dataset class.

As long as a dataset has a layer of category segmentation, and a meshfile, this should be possible.

Does this mean AdHoc meshes are not possible for a dataset with segmentation layer?

Another question is if downloading a mesh from a dataset is also possible with a tracing_id or just with the Datastore?

[fm3]

Does this mean AdHoc meshes are not possible for a dataset with segmentation layer?

AdHoc meshing is also possible, true, I missed that case in my post above.

Another question is if downloading a mesh from a dataset is also possible with a tracing_id or just with the Datastore?

Just with the datastore, not by tracing_id.

As discussed internally, I will take over this PR going forward. Thanks for your effort! I think it’s already very close to being complete.