Update asset labels for cell meshes

[GianlucaFicarelli]

Implement:

• https://github.com/openbraininstitute/Ultraliser/issues/200
• https://github.com/openbraininstitute/Ultraliser/issues/211

and remove custom .h5 format for cell_surface_mesh, since not used and replaced by .glb.

In both staging and production there are only:

cell_surface_mesh                       | application/obj

EDIT based on the comments below, these asset labels have been added:

EntityType.cell_morphology -> AssetLabel.cell_surface_mesh -> ContentType.glb
EntityType.em_cell_mesh -> AssetLabel.cell_surface_mesh -> ContentType.glb
EntityType.em_cell_mesh -> AssetLabel.lod_cell_block -> directory

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

Flag	Coverage Δ
pytest	97.92% <100.00%> (+<0.01%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
app/db/types.py	99.46% <100.00%> (+<0.01%)	⬆️

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[jdcourcol]

I thought this:
content_type=ContentType.gltf_binary,

was for morphologies, not for em_cell_mesh.

[jdcourcol]

and for this:
AssetLabel.lod_mesh_block, I really want a documentation. There are multiple elements missings.

[GianlucaFicarelli]

I thought this: content_type=ContentType.gltf_binary,

was for morphologies, not for em_cell_mesh.

I understood from the linked tickets that the mesh itself can be represented as a single .obj or .glb, and that there can be a directory with many files in .glb format, representing small blocks.
@marwan-abdellah could you clarify?

AssetLabel.lod_mesh_block, I really want a documentation. There are multiple elements missings.

Agreed, but where should it go? The description in the asset label table is meant to be a short description, while for detailed specifications there should be a separate document (like for sonata specs, for example).
In either case I think we need @marwan-abdellah's help

[jdcourcol]

There are

• the use case where we start from a skeleton (so a morphology) and build a mesh, that I assumed was a single .glb . We would attach that .glb to the skeleton.
• the use case where we register a em_cell_mesh, this one has a directory with multiple lods each of them being glb.

[GianlucaFicarelli]

Considering the comment https://github.com/openbraininstitute/Ultraliser/issues/211#issuecomment-4066661627 and previous clarifications with @marwan-abdellah and @jdcourcol:

• for skeletonization in Ultraliser, the em_cell_mesh needs a single mesh file that has all the details of the mesh. It can be .obj or .glb, since they both contain the same information. We intend to allow .glb only, but we need to allow both the formats in entitycore until the existing assets have been migrated. The corresponding asset label is AssetLabel.cell_surface_mesh
• for the visualization, the em_cell_mesh needs LODs stored in a directory asset. Each LOD should not exceed 300kbytes, although there won't be a specific limit in entitycore. The format of the files in the directory needs to be documented (ticket https://github.com/openbraininstitute/Ultraliser/issues/205 ?). The corresponding asset label is AssetLabel.lod_mesh_block

@marwan-abdellah and @jdcourcol can you confirm the points above, and the changes in this PR?

[jdcourcol]

There is a 3rd bullet from my comment:

we start from a skeleton (so a morphology) and build a mesh, that I assumed was a single .glb . We would attach that .glb to the skeleton.

[mgeplf]

the entitycore side looks fine to me

[GianlucaFicarelli]

There is a 3rd bullet from my comment:

we start from a skeleton (so a morphology) and build a mesh, that I assumed was a single .glb . We would attach that .glb to the skeleton.

Clarified and updated the PR with a new asset label for the cell morphology:

• EntityType.cell_morphology -> AssetLabel.cell_surface_mesh -> ContentType.glb

Use case:

A morphology can be given to NeuroMorphoMesh to create a light but with nice triangulation and geometry to have beautiful visualization

The process to generate the mesh is the opposite of skeletonization.