New Mesh File Support #6491

leowe · 2022-09-22T13:50:59Z

URL of deployed dev instance (used for testing):

https://newmeshfilesupport.webknossos.xyz

Steps to test:

Use a mesh file with the new format and use "Show precomputed mesh" for a segment in webknossos

Issues:

fixes Support new Mesh File Format #5830

Remove Draco dummy route & functions

(Please delete unneeded items, merge only when none are left open)

Updated (unreleased) changelog
Needs datastore update after deployment
Ready for review

…nossos into new-mesh-file-support

…ithub

philippotto · 2022-10-04T17:12:17Z

@daniel-wer I think you can already review the PR. For the lighting part, I'm still waiting for other feedback, but that code isn't really critical anyway. For the version comparison with 2, I'm a bit hesitant, since I know that there are already mesh files in circulation with v=2. So, maybe it's alright to leave the comparison at >= 2. What do you think?

daniel-wer

Nice work, I will report back after testing 👍

frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts

daniel-wer · 2022-10-05T08:04:59Z

frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts

-      meshFileName,
-      id,
-    );
+    // todo: should actually check against 3, but some new mesh files


For the version comparison with 2, I'm a bit hesitant, since I know that there are already mesh files in circulation with v=2. So, maybe it's alright to leave the comparison at >= 2. What do you think?

Are we talking about many (or important) mesh files with version 2? Otherwise, I would lean towards bumping the comparison to 3 and assert that the mesh file version is neither 1 nor 2. This would make the code easier to understand and forfeit the need to explain that everything is named v3 but some mesh files have v2. Also we would need to make sure that there exists a test dataset that has a mesh file with the correct version 3.

frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts

frontend/javascripts/types/api_flow_types.ts

public/wasm/draco_wasm_wrapper.js

…rty (the latter won't exist for newer mesh files, as it was redundant)

daniel-wer

The mesh loading with new and old mesh file formats worked very well 👍

I only noticed one issue during testing. When opening a sharing link that included an active mesh file, for example, this one: https://newmeshfilesupport.webknossos.xyz/annotations/633d73740100009b005f634a#%7B%22position%22:%5B3517,3800,1025%5D,%22mode%22:%22orthogonal%22,%22zoomStep%22:1,%22stateByLayer%22:%7B%22071103ab-b959-4d83-9538-d7512ad225c9%22:%7B%22meshInfo%22:%7B%22meshFileName%22:%22meshfile_v3%22,%22meshes%22:%5B%7B%22segmentId%22:58624,%22seedPosition%22:%5B3436,3687,1025%5D,%22isPrecomputed%22:true,%22meshFileName%22:%22meshfile_v3%22%7D%5D%7D%7D%7D%7D

the other mesh file is activated, not the "meshfile_v3". (The mesh that is encoded in the URL as well is loaded using the correct mesh file!)

… in sharing link

philippotto · 2022-10-05T14:05:42Z

the other mesh file is activated, not the "meshfile_v3". (The mesh that is encoded in the URL as well is loaded using the correct mesh file!)

good catch! I fixed it now :) if you give your final "go", I'd merge this 🚢

daniel-wer

LGTM, please see the code suggestions to fix a remaining typo. 👍

daniel-wer · 2022-10-05T14:10:27Z

frontend/javascripts/oxalis/controller/scene_controller.ts

-    // light2.position.set(-1, -1, -1).normalize();
-    // this.isosurfacesRootGroup.add(light2);
+    const AMBIENT_INTENSITY = 30;
+    const DIRECTIONAL_INTENSITRY = 5;


Suggested change

const DIRECTIONAL_INTENSITRY = 5;

const DIRECTIONAL_INTENSITY = 5;

daniel-wer · 2022-10-05T14:10:35Z

frontend/javascripts/oxalis/controller/scene_controller.ts

+
+    const ambientLight = new THREE.AmbientLight(2105376, AMBIENT_INTENSITY);
+
+    const directionalLight = new THREE.DirectionalLight(16777215, DIRECTIONAL_INTENSITRY);


Suggested change

const directionalLight = new THREE.DirectionalLight(16777215, DIRECTIONAL_INTENSITRY);

const directionalLight = new THREE.DirectionalLight(16777215, DIRECTIONAL_INTENSITY);

daniel-wer · 2022-10-05T14:10:45Z

frontend/javascripts/oxalis/controller/scene_controller.ts

+    directionalLight.position.z = 1;
+    directionalLight.position.normalize();
+
+    const directionalLight2 = new THREE.DirectionalLight(16777215, DIRECTIONAL_INTENSITRY);


Suggested change

const directionalLight2 = new THREE.DirectionalLight(16777215, DIRECTIONAL_INTENSITRY);

const directionalLight2 = new THREE.DirectionalLight(16777215, DIRECTIONAL_INTENSITY);

frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts

…write the existing key), as this is important when an existing precomputed mesh is changed to an ad-hoc one (the same was already done when adding precomputed meshes)

…jects-created * 'master' of github.com:scalableminds/webknossos: (337 commits) Fix docs for the annotation download file format (#6546) Added total runtime information to VX reports (#6543) fix VX report for completed + skipped tasks (#6540) Avoid allocating spire uint objects during apply agglomerate (#6532) Explore remote N5 datasets (#6520) Fix MeshChunk byteOffset (Long, not Int) (#6536) update browserslist (#6505) Support new Mesh File (v3) (#6491) makes workflow_yamlContent optional (#6518) Always return 404 for Failures in Zarr Streaming (#6515) Poll wk version to notify during upgrade (#6451) add script which extracts newest changelog and creates GH release for it (#6504) release 22.10.0 (#6500) voxel³ -> voxel (#6501) Allow task type summary to identify task type when creating tasks in bulk (#6486) Fix sql evolution 090 (defer not null constraint) (#6498) SQL schema cleanup (#6492) Fix validation of layer selection when trying to start globalization of floodfills (#6497) Add "shift + w" shortcut to cycle backwards through tools (#6493) Fix filtering for public datasets in dataset table (#6496) ...

leowe and others added 2 commits September 22, 2022 15:50

refactor Hdf5Access

dba08ec

Merge branch 'master' into new-mesh-file-support

7426496

fm3 assigned leowe Sep 22, 2022

leowe and others added 27 commits September 22, 2022 19:30

add first new mesh file functionality

c9aecb7

finished basic functionality

1f60390

write new routes

4190440

add small todo

ca0690c

add dummy draco route

0865d99

remove draco file from binaryData

56cd3f7

add dummy loading of draco encoded file

786129c

add dummy draco file

a71efdf

add draco loader

220a97a

change response from dummyDracoFile

b931cda

remove println

e214ee0

Merge branch 'master' into new-mesh-file-support

01a6d0c

reformat

610a331

Merge branch 'master' into new-mesh-file-support

006e7a4

add changelog entry

ef11d68

add formatVersion als parameter in URL

877a85e

rename chunkdatarequest and add custom writes to vec3float

8e60a9d

use new mesh v3 api

72e325d

temporary workaround for mapping name with empty string

de2c466

Merge branch 'new-mesh-file-support' of github.com:scalableminds/webk…

5aa3ee8

…nossos into new-mesh-file-support

adapt frontend to backend changes

8b55ab4

add new api modules

a8bfbac

remove the dummy draco file code again

65081e9

fix addition

8839007

use DRACOLoader from threejs package

d269280

Merge branch 'new-mesh-file-support' of github.com:scalableminds/webk…

023d7ed

…nossos into new-mesh-file-support

use wasm for draco decoding

d506a52

philippotto added 3 commits October 4, 2022 17:06

refactor maybeFetchMeshFiles to be a saga

9e4bd54

avoid redundant fetches of mesh files for the same layer

e658ada

add draco decoder wasm to repo and use that instead of depending on g…

286325b

…ithub

philippotto requested a review from daniel-wer October 4, 2022 17:10

daniel-wer reviewed Oct 5, 2022

View reviewed changes

philippotto added 5 commits October 5, 2022 10:54

integrate some PR feedback

4358f83

simplify maybeFetchMeshFiles saga

96c0934

clean up version handling

fb33b56

read artifact_schema_version from mesh files instead of version prope…

e8902f5

…rty (the latter won't exist for newer mesh files, as it was redundant)

re-add support for v1 and v2 mesh files

122b1bd

daniel-wer reviewed Oct 5, 2022

View reviewed changes

philippotto added 3 commits October 5, 2022 15:38

clean up lighting

2c2e23a

fix enabling of corresponding mesh file when loading meshes specified…

378b29a

… in sharing link

fix linting

6ef6faf

set opacity to 100% for non-passive meshes

978b493

daniel-wer approved these changes Oct 5, 2022

View reviewed changes

fix typo

466a12f

philippotto enabled auto-merge (squash) October 5, 2022 14:24

philippotto disabled auto-merge October 5, 2022 14:24

philippotto enabled auto-merge (squash) October 5, 2022 14:24

always add an isosurface object when loading ad-hoc (will simply over…

c08a8a9

…write the existing key), as this is important when an existing precomputed mesh is changed to an ad-hoc one (the same was already done when adding precomputed meshes)

philippotto merged commit ea424ac into master Oct 5, 2022

philippotto deleted the new-mesh-file-support branch October 5, 2022 15:05

fm3 restored the new-mesh-file-support branch October 12, 2022 08:04

fm3 deleted the new-mesh-file-support branch October 12, 2022 08:05

philippotto restored the new-mesh-file-support branch October 18, 2022 07:58

fm3 deleted the new-mesh-file-support branch January 27, 2023 10:15

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New Mesh File Support #6491

New Mesh File Support #6491

leowe commented Sep 22, 2022 •

edited by daniel-wer

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philippotto commented Oct 4, 2022

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daniel-wer Oct 5, 2022

daniel-wer Oct 5, 2022

	const DIRECTIONAL_INTENSITRY = 5;
	const DIRECTIONAL_INTENSITY = 5;


		const ambientLight = new THREE.AmbientLight(2105376, AMBIENT_INTENSITY);

		const directionalLight = new THREE.DirectionalLight(16777215, DIRECTIONAL_INTENSITRY);

	const directionalLight2 = new THREE.DirectionalLight(16777215, DIRECTIONAL_INTENSITRY);
	const directionalLight2 = new THREE.DirectionalLight(16777215, DIRECTIONAL_INTENSITY);

New Mesh File Support #6491

New Mesh File Support #6491

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leowe commented Sep 22, 2022 • edited by daniel-wer Loading

URL of deployed dev instance (used for testing):

Steps to test:

Issues:

philippotto commented Oct 4, 2022

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leowe commented Sep 22, 2022 •

edited by daniel-wer

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