Create volume annotations #1340

brokkoli71 · 2025-07-22T16:01:16Z

Description:

Volume Annotations can be created and modified

Issues:

fixes Create volume annotations #1318

Todos:

How to test uploading volume annotation to wk?
Memory Store
is the created volume annotation zip correct?
fix slow tests

Todos Documentation:

Updated Changelog
Updated Documentation
Added / Updated Tests

to test

# Conflicts: # webknossos/webknossos/annotation/annotation.py

…est_edited_volume_annotation_upload_download

webknossos/webknossos/annotation/annotation.py

brokkoli71 · 2025-08-10T10:19:31Z

webknossos/webknossos/annotation/annotation.py

+                f"Unsupported volume layer edit mode: {volume_layer_edit_mode}"
+            )
+
+    def export_to_dataset(


VolumeLayer.export_to_dataset is extracted from Annotation.export_volume_layer_to_dataset

webknossos/webknossos/annotation/annotation.py

…mes to disk

# Conflicts: # webknossos/tests/cassettes/test_annotation/test_annotation_upload_download_roundtrip.yml # webknossos/tests/cassettes/test_annotation/test_bounding_box_roundtrip.yml

…tible with tensorstore (?)

github-actions · 2025-08-31T14:28:40Z

☂️ Python Coverage

current status: ✅

Overall Coverage

Lines	Covered	Coverage	Threshold	Status
9435	7925	84%	80%	🟢

New Files

File	Coverage	Status
webknossos/webknossos/annotation/volume_layer.py	98%	🟢
TOTAL	98%	🟢

Modified Files

File	Coverage	Status
webknossos/webknossos/annotation/annotation.py	79%	🟢
webknossos/webknossos/client/api_client/wk_api_client.py	89%	🟢
webknossos/webknossos/dataset/view.py	89%	🟢
TOTAL	86%	🟢

updated for commit: 533f7de by action🐍

webknossos/examples/calculate_segment_sizes.py

normanrz · 2025-09-02T07:45:07Z

webknossos/examples/learned_segmenter.py

This one could be rewritten to actually use the new create-annotation feature.

webknossos/webknossos/annotation/annotation.py

webknossos/examples/WIP/offline_merger_mode.py

Co-authored-by: Tom Herold <tom.herold@scalableminds.com>

# Conflicts: # webknossos/tests/cassettes/test_annotation/test_annotation_upload_download_roundtrip.yml # webknossos/tests/cassettes/test_annotation/test_bounding_box_roundtrip.yml

normanrz

I think this looks really nice! Thanks for building this.

webknossos/webknossos/annotation/volume_layer.py

# Conflicts: # webknossos/tests/cassettes/test_annotation/test_annotation_upload_download_roundtrip.yml # webknossos/tests/cassettes/test_annotation/test_bounding_box_roundtrip.yml

brokkoli71 added 7 commits July 16, 2025 17:07

make VolumeLayer non-protected

007243d

add VolumeLayer.edit contextmanager

f7deda1

Merge branch 'master' into create-volume-annotations

69daad3

format

9e80718

lint

cd63d9f

add @pytest.mark.use_proxay

96cfa07

to test

format

6481415

This was referenced Jul 25, 2025

The import of volume annotations in Zarr 3 format is not specification compliant scalableminds/webknossos#8604

Open

Configurable Zarr3 codecs #1343

Merged

brokkoli71 added 9 commits July 29, 2025 14:20

Merge branch 'refs/heads/master' into create-volume-annotations

a7e8211

Merge branch 'refs/heads/master' into create-volume-annotations

c6cf61e

# Conflicts: # webknossos/webknossos/annotation/annotation.py

rechunk mags with Zarr3Config to have expected volume annotations format

892773a

Enum for VolumeLayerEditMode

d85c715

test_edit_volume_annotation, test_save_edited_volume_annotation and t…

487a1c5

…est_edited_volume_annotation_upload_download

format and lint

393e9ee

Merge branch 'master' into create-volume-annotations

f76231e

edited annotation uploadable

82cc58c

Merge branch 'master' into create-volume-annotations

88c5220

brokkoli71 self-assigned this Aug 9, 2025

brokkoli71 commented Aug 10, 2025

View reviewed changes

webknossos/webknossos/annotation/annotation.py Outdated Show resolved Hide resolved

brokkoli71 commented Aug 10, 2025

View reviewed changes

webknossos/webknossos/annotation/annotation.py Outdated Show resolved Hide resolved

brokkoli71 added 4 commits August 12, 2025 13:32

set zarr3 datatype for wk.Annotation.download

32542c1

implement VolumeLayerEditMode.MEMORY

cab2679

get voxel_size from nml

70f3b0d

init zip when creating volume layer

e7871d6

brokkoli71 commented Aug 17, 2025

View reviewed changes

webknossos/webknossos/annotation/annotation.py Outdated Show resolved Hide resolved

brokkoli71 added 3 commits August 29, 2025 12:13

store volume layer in zip of zips and save downloaded annotation volu…

94e1626

…mes to disk

use volume_layers_root argument of Annotation.download

7b7e6fa

Merge branch 'master' into create-volume-annotations

c9bc2ca

# Conflicts: # webknossos/tests/cassettes/test_annotation/test_annotation_upload_download_roundtrip.yml # webknossos/tests/cassettes/test_annotation/test_bounding_box_roundtrip.yml

update cassettes

b44b14a

brokkoli71 marked this pull request as ready for review August 29, 2025 11:22

brokkoli71 added 3 commits August 31, 2025 14:11

load editing layer into tensorstore, as MemoryFileSystem is not compa…

15d526b

…tible with tensorstore (?)

typing and format

c103a9f

avoid tensorstore array memory path collision

286fd80

normanrz reviewed Sep 2, 2025

View reviewed changes

hotzenklotz reviewed Sep 2, 2025

View reviewed changes

webknossos/examples/WIP/offline_merger_mode.py Outdated Show resolved Hide resolved

brokkoli71 and others added 12 commits September 5, 2025 11:22

rename nml to skeleton in offline_merger_mode.py

bbfc7a3

Co-authored-by: Tom Herold <tom.herold@scalableminds.com>

replace volume_layers_root with temp dir and incorporate further review

ff05931

Merge branch 'master' into create-volume-annotations

635dcc0

# Conflicts: # webknossos/tests/cassettes/test_annotation/test_annotation_upload_download_roundtrip.yml # webknossos/tests/cassettes/test_annotation/test_bounding_box_roundtrip.yml

fix format mistakes

cd58e96

update cassettes

3b5fb00

extract VolumeLayer to volume_layer.py

f628748

update cassette

aa66ed8

faster VolumeLayer.edit with SequentialExecutor

76bf92a

improve test_edit_volume_annotation

93e9272

document changes

e8c157c

update learned_segmenter.py to use VolumeLayer.edit

e77a40f

lint

e56cc7e

normanrz approved these changes Sep 15, 2025

View reviewed changes

webknossos/webknossos/annotation/volume_layer.py Show resolved Hide resolved

brokkoli71 added 2 commits September 15, 2025 21:59

VolumeLayer.edit kw-only

ccdb188

Merge branch 'master' into create-volume-annotations

533f7de

# Conflicts: # webknossos/tests/cassettes/test_annotation/test_annotation_upload_download_roundtrip.yml # webknossos/tests/cassettes/test_annotation/test_bounding_box_roundtrip.yml

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brokkoli71 commented Jul 22, 2025 •

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Description:

Issues:

Todos:

Todos Documentation:

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brokkoli71 Aug 10, 2025

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☂️ Python Coverage

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normanrz Sep 2, 2025

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brokkoli71 commented Jul 22, 2025 •

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github-actions bot commented Aug 31, 2025 •

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