Allow to specify mask during inference when using a custom workflow

[daniel-wer]

See https://github.com/scalableminds/voxelytics/pull/3872 for context. (Needs to be deployed together)

Also the template was currently incomplete due to https://github.com/scalableminds/voxelytics/pull/3800 which I fixed by adding the datastore_url to the template (/cc @MatthisCl).

URL of deployed dev instance (used for testing):

• https://___.webknossos.xyz

Steps to test:

• I tested this
• Can be tested using a local worker (voxelytics branch use-mask-from-annotation) by adding a mask config to the template (under the datasource_config key) when doing neuron inferral using a custom workflow (create an annotation with some brush strokes first and copy the annotation link):

        mask:
          url: <annotation_url>
          segmentation_name: Volume
          mag: [1, 1, 1]

---

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

• Updated changelog
• Removed dev-only changes like prints and application.conf edits
• Considered common edge cases

[coderabbitai]

📝 Walkthrough

Walkthrough

The pull request introduces a comprehensive restructuring of the configuration in the default-predict-workflow-template.ts file. The changes involve expanding the datasource_config from a single line to a detailed object with multiple properties such as name, type, scale, data_dir, path, color_name, wkw_resolution, and bounding_box. A new datastore_url property is also added to the publish_dataset_meshes configuration, providing more granular control over data source and dataset publishing settings.

Changes

File	Change Summary
frontend/javascripts/oxalis/view/action-bar/default-predict-workflow-template.ts	- Expanded datasource_config from single line to detailed object - Added nested bounding_box with topleft and size properties - Introduced new datastore_url in configuration
CHANGELOG.unreleased.md	- Updated changelog with new features and fixes, including dataset volume display, performance optimizations, and bounding box tool enhancements - Fixed template for neuron inferral using a custom workflow

Possibly related PRs

• Fix: Use forwardRef for scrollable virtualized tree #8186: This PR modifies the ScrollableVirtualizedTree component, which is relevant to the changes in the main PR that involve detailed configurations for the predict task, as both involve enhancements to tree structures and data handling.
• Relax bounding box requirements for model training #8222: This PR relaxes bounding box requirements for model training, which relates to the changes in the main PR that define a more detailed structure for bounding boxes in the datasource_config.
• Allow selective segment visibility regardless of proofreading tool #8281: This PR introduces selective segment visibility, which is relevant as it enhances the user interface for managing segment visibility, similar to how the main PR enhances the configuration for data sources and bounding boxes.
• Call triggers/reload with fallback layer name #8298: This PR addresses issues with reloading data for segmentation layers, which connects to the main PR's focus on improving configurations related to data handling and bounding boxes.

Suggested labels

documentation

Suggested reviewers

• philippotto

Poem

🐰 Config rabbit hops with glee,
Expanding structures, setting free
Datasource details, neat and bright
Bounding boxes taking flight!
Workflow template, now complete ✨

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[coderabbitai]

Actionable comments posted: 1

🧹 Nitpick comments (1)

frontend/javascripts/oxalis/view/action-bar/default-predict-workflow-template.ts (1)

33-33: LGTM! Consider documenting the datastore_url field

The addition of datastore_url is well-placed and follows the template's pattern. However, since this is a template that users will need to configure, consider adding a comment explaining the expected format and purpose of the datastore_url.

+    # URL of the datastore where the dataset will be published
     datastore_url: TO_BE_SET_BY_WORKER

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[coderabbitai]

Actionable comments posted: 0

🧹 Nitpick comments (1)

CHANGELOG.unreleased.md (1)

47-47: Enhance the changelog entry with more specific details.

While the entry correctly references the PR, it could be more informative for users by explicitly mentioning the added capability to specify masks during inference. Consider expanding it to:

-Fixed the template for neuron inferral using a custom workflow. [#8312](https://github.com/scalableminds/webknossos/pull/8312)
+Fixed the template for neuron inferral using a custom workflow to support mask specification during inference. [#8312](https://github.com/scalableminds/webknossos/pull/8312)

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[MatthisCl]

Nice, i did an inference run with a mask on my local webknossos and it worked, lgtm 👍

Only thing i was a bit confused about was dataset: # your dataset here in the template, shouldn't that always be dataset: predict:prediction on default?

[daniel-wer]

Thank you!

Only thing i was a bit confused about was dataset: # your dataset here in the template, shouldn't that always be dataset: predict:prediction on default?

The assumption is that most users would add their own tasks in between the predict and publish, for example to perform a segmentation with custom parameters or so. That's why this field is left to be filled out by the user :)