Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Globalize Floodfill Script #461

Merged
merged 33 commits into from
Nov 26, 2021
Merged

Globalize Floodfill Script #461

merged 33 commits into from
Nov 26, 2021

Conversation

youri-k
Copy link
Contributor

@youri-k youri-k commented Oct 21, 2021 •
edited by philippotto
Loading

Description:

  • execute script to merge segmentation layer and volume annotation
  • globalizes all floodfill operations that were cut short by the wK frontend

Issues:

Todos:

  • Updated Changelog

@philippotto
Copy link
Member

@youri-k How is the performance coming along? :) Do you think, the PR is already reviewable?

@youri-k youri-k changed the title [WIP] Globalize Floodfill Script Globalize Floodfill Script Nov 4, 2021
@youri-k youri-k marked this pull request as ready for review November 4, 2021 09:24
philippotto
philippotto requested changes Nov 5, 2021
View reviewed changes
Copy link
Member

@philippotto philippotto left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

cool stuff :) I left some comments and could you also push the test case you wrote for this? even if it's not really polished, it would be good to have it in the repository.

webknossos/webknossos/geometry/bounding_box.py Outdated Show resolved Hide resolved
webknossos/script-collection/globalize_floodfill.py Outdated Show resolved Hide resolved
webknossos/script-collection/globalize_floodfill.py Show resolved Hide resolved
webknossos/script-collection/globalize_floodfill.py Outdated Show resolved Hide resolved
webknossos/script-collection/globalize_floodfill.py Outdated Show resolved Hide resolved
webknossos/script-collection/globalize_floodfill.py Outdated Show resolved Hide resolved
webknossos/script-collection/globalize_floodfill.py Outdated Show resolved Hide resolved
webknossos/script-collection/globalize_floodfill.py Outdated Show resolved Hide resolved
webknossos/script-collection/globalize_floodfill.py Outdated Show resolved Hide resolved
webknossos/script-collection/globalize_floodfill.py Outdated Show resolved Hide resolved
@philippotto philippotto self-assigned this Nov 18, 2021
@philippotto
Merge branch 'master' of github.com:scalableminds/webknossos-libs int…
0065d64 
…o globalize-floodfill
@philippotto
integrate some PR feedback
a15c5ae
@philippotto
chmod +x, make parameters required and make logging less verbose
919b216
@philippotto
merge volume data by FS copy + apply strategy, floodfill over 1024-ch…
de337a5 
…unks and optimize that
@philippotto
clean up merge code
542dc7d
@philippotto
implement FastVec3Int via subclassing
eb911d4
@philippotto
auto-compute bottomright in bounding box for performance reasons
c95d1ab
@philippotto
get rid of FastVec3Int by using a fast staticmethod instead
f664445
@philippotto
convert old wkw api usages in globalize_flood_fill to new dataset api…
13f9d4f 
… and also use Vec3Int everywhere
@philippotto
run full script
8897b56
@philippotto
auto-select correct chunk size
f66814b
@philippotto
rename some variables
40c95e5
@philippotto
don't use print
5f53814
@philippotto
remove 'slow' comments
9698e87
@philippotto
remove mag_headers logging
d7a688e
@philippotto
implement redownsample; fix instantiation of Vec3Int
9fff34f
@philippotto
format
f549df3
@philippotto
typing
9094b7c
@philippotto philippotto enabled auto-merge (squash) November 26, 2021 13:30
@philippotto philippotto merged commit 9c63ca6 into master Nov 26, 2021
@philippotto philippotto deleted the globalize-floodfill branch November 26, 2021 14:55
hotzenklotz added a commit that referenced this pull request Nov 30, 2021
@hotzenklotz
Merge branch 'master' of github.com:scalableminds/webknossos-libs int…
99cf7b6 
…o update_demos

* 'master' of github.com:scalableminds/webknossos-libs:
  Update changelogs for release v0.8.23 (#493)
  Resolve path when symlinking layer and make_relative is False (#492)
  Globalize Floodfill Script (#461)
  Bump pillow from 8.2.0 to 8.3.2 in /wkcuber (#488)
  Add websites metadata to pyproject.toml (#485)
@philippotto philippotto mentioned this pull request Dec 7, 2021
Merged
1 task
@philippotto philippotto mentioned this pull request Jan 6, 2022
Merged
1 task
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@philippotto philippotto philippotto approved these changes

Assignees

@philippotto philippotto

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

Implement Script that can globalize a local flood-fill operation
2 participants
@youri-k @philippotto