feat(seg): Improve Labelmap Statistics, Interpolation, and Threshold Configuration #1820

sedghi · 2025-02-10T15:07:02Z

This PR will:

Labelmap Statistics

makes it work on stack viewports too
moves the calculation to web worker to not block ui
moves it to a utility function instead of a brush strategy (we should be able to calculate stats on anything not just brush instances)

Sphere Brush

was broken on stack viewports now it is fixed

Interpolation

makes it work on stack viewports too
moves the calculation to web worker to not block ui
moves it to a utility function instead of a brush strategy (we should be able to calculate stats on anything not just brush instances)

THRESHOLD -> Strategy specific threshold

Previously, Brush tools using thresholding might have used a generic THRESHOLD property within their strategySpecificConfiguration. This PR introduces a shift towards more explicit and strategy-specific threshold configurations. Instead of a single THRESHOLD property (which is NOT a strategy), you'll now configure thresholds under properties named after the specific strategy itself (e.g., THRESHOLD_INSIDE_CIRCLE, THRESHOLD_INSIDE_SPHERE, THRESHOLD_INSIDE_SPHERE_WITH_ISLAND_REMOVAL).

It is now the app-level concern to make sure threshold is synced between different tool strategies if desired

{
    configuration: {
        activeStrategy: 'THRESHOLD_INSIDE_CIRCLE', 
        strategySpecificConfiguration: {
            THRESHOLD: { // Old generic THRESHOLD property
                threshold: [50, 200], // Example threshold range
            },
        },
    },
});

If your activeStrategy is 'THRESHOLD_INSIDE_CIRCLE', rename THRESHOLD to THRESHOLD_INSIDE_CIRCLE.
If your activeStrategy is 'THRESHOLD_INSIDE_SPHERE', rename THRESHOLD to THRESHOLD_INSIDE_SPHERE.
If your activeStrategy is 'THRESHOLD_INSIDE_SPHERE_WITH_ISLAND_REMOVAL', rename THRESHOLD to THRESHOLD_INSIDE_SPHERE_WITH_ISLAND_REMOVAL.

After (Example - Migrated Configuration):

{
     configuration: {
         activeStrategy: 'THRESHOLD_INSIDE_CIRCLE',
        strategySpecificConfiguration: {
            useCenterSegmentIndex: true,
            THRESHOLD_INSIDE_CIRCLE: { // Renamed to strategy-specific property
                threshold: [50, 200], // Threshold settings remain the same inside
            },
        },
    },
});

…or brush tools This commit introduces several improvements to the segmentation strategy configuration: - Updated strategy-specific configuration to use active strategy as key - Refactored dynamic threshold and threshold compositions to work with new configuration structure - Added support for stack and volume viewport strategy data handling - Simplified strategy data retrieval and configuration management - Removed deprecated configuration patterns

…at/new-seg-stuff

…provements - Introduced new `interpolateLabelmap` utility for advanced segmentation interpolation - Created `getOrCreateSegmentationVolume` helper function - Updated ITK image conversion utility to support custom scalar data - Refactored segmentation interpolation strategies - Simplified segmentation volume creation and management

- Introduced `calculateSpacingBetweenImageIds` utility for precise volume spacing calculation - Refactored `sortImageIdsAndGetSpacing` to use new spacing calculation method - Updated `generateVolumePropsFromImageIds` to generate default volume ID - Exported new spacing calculation utility in index

- Introduced `generateVolumeId` method to create deterministic volume IDs from image IDs - Added `getImageIdsForVolumeId` to retrieve image IDs associated with a volume - Implemented `_fnv1aHash` helper method for consistent ID generation - Created a new cache map `_imageIdsToVolumeIdCache` for tracking image-volume relationships

…generation - Updated `getOrCreateSegmentationVolume` to handle volume ID retrieval more robustly - Added support for generating volume IDs from labelmap image IDs - Simplified volume lookup and creation logic - Improved type safety with explicit type casting for representation data

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sedghi · 2025-02-10T16:01:08Z

@wayfarer3130, could you check out peerImport versus import? I'm having trouble getting the labelmapInterpolation example to work without await import. For some reason, running peerImport inside a web worker just isn't working.

packages/tools/src/workers/computeWorker.ts

- Added `peerImport` utility function to handle dynamic imports of optional modules - Updated `getItkImage`, `computeWorker`, and `polySegConverters` to use new peer import mechanism - Centralized module import strategy to improve modularity and flexibility

wayfarer3130 · 2025-02-13T14:30:31Z

packages/core/src/cache/cache.ts

+   * @param imageIds - Array of image IDs
+   * @returns A deterministic volume ID
+   */
+  public generateVolumeId(imageIds: string[]): string {


I love the idea, however I wonder if the hash length is sufficiently unique that we won't ever generate two hashes containing the same hash code? Would sha1 to 8 digits be better? That is natively encoded and is reasonably fast.
async function sha1(str) {
const enc = new TextEncoder();
const hash = await crypto.subtle.digest('SHA-1', enc.encode(str));
return Array.from(new Uint8Array(hash))
.map(v => v.toString(16).padStart(2, '0'))
.join('');
}

Also, does it need to be order invariant? Should the entries be sorted first?

Seems like crypto apis rely on secure context, so i guess we can't

packages/core/src/utilities/pointInShapeCallback.ts

packages/tools/examples/labelmapInterpolation/index.ts

packages/tools/examples/stackLabelmapSegmentation/index.ts

…at/new-seg-stuff

…tone3D into feat/new-seg-stuff

- Sort image URIs in volume ID generation for consistent hashing - Enhance scalar data update in VoxelManager to prevent side effects - Update labelmap interpolation to use active segment index - Deprecate labelmap interpolation strategy with warning

utils/demo/helpers/initDemo.js

wayfarer3130 · 2025-02-19T17:03:17Z

I'm seeing:
Warning: '@itk-wasm/morphological-contour-interpolation' module not found. Please install it separately.
when I try to run the example. Using the separate name strings doesn't seem to actually work. Is it ok if we just give it a chunk name for now and live with the fact that the binding is hard now? I don't really see a way to fix the workers other than importing them in some hand written wrapper library.

…at/new-seg-stuff

This commit introduces a new configuration mechanism to conditionally enable PolySeg and Labelmap Interpolation features: - Created a new `config.ts` module to manage global configuration - Updated initialization to set configuration options - Modified worker and import logic to respect configuration flags - Removed hardcoded example runner checks - Simplified dynamic import strategies for optional modules

wayfarer3130 · 2025-02-21T19:20:45Z

packages/labelmap-interpolation/src/workers/interpolationWorker.js

+import vtkDataArray from '@kitware/vtk.js/Common/Core/DataArray';
+
+/**
+ * Dynamically imports ITK WASM modules needed for labelmap interpolation


Could you add a comment that this doesn't currently allow the dynamic import?

sedghi · 2025-02-21T19:54:52Z

closing in favor of #1844

sedghi added 13 commits February 6, 2025 16:57

fix weridness

60b7b68

wip

7a0f940

Merge branch 'main' of github.com:cornerstonejs/cornerstone3D into fe…

9bb438e

…at/new-seg-stuff

wip

6cee10e

fix labelmapstatistics for stack viewport and make it in webworker

5a7a45c

interpolation with worker

351ea3e

publish events

1e31f70

api

f02f557

sedghi added 2 commits February 10, 2025 10:14

update

179dae6

fix suv peak stuff

58c8b84

sedghi changed the title ~~feat/new seg stuff~~ feat(seg): Improve Labelmap Statistics, Interpolation, and Threshold Configuration Feb 10, 2025

sedghi added 3 commits February 10, 2025 10:49

wip

c31c92a

fix

247441e

fix

2956942

sedghi requested a review from wayfarer3130 February 10, 2025 16:01

wayfarer3130 reviewed Feb 10, 2025

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sedghi added 2 commits February 11, 2025 12:13

update

2e93fb4

sedghi mentioned this pull request Feb 12, 2025

[Bug] Brushing Feature Malfunction When Switching Active Segments in THRESHOLD_INSIDE_CIRCLE strategy #1724

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wayfarer3130 reviewed Feb 13, 2025

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wayfarer3130 reviewed Feb 13, 2025

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wayfarer3130 reviewed Feb 13, 2025

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wayfarer3130 and others added 9 commits February 13, 2025 10:52

fix: Peer import using split to load wasm

f07e2fa

Merge branch 'main' of github.com:cornerstonejs/cornerstone3D into fe…

5d7e103

…at/new-seg-stuff

Merge branch 'feat/new-seg-stuff' of github.com:cornerstonejs/corners…

dfacfd6

…tone3D into feat/new-seg-stuff

fix

78986a7

remove composition

90d9fce

fix dynamic import

4551509

fix vite

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fix bundler issues

ace0183

wayfarer3130 reviewed Feb 19, 2025

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sedghi added 6 commits February 20, 2025 15:00

Merge branch 'main' of github.com:cornerstonejs/cornerstone3D into fe…

289cf2d

…at/new-seg-stuff

silent warning

20a6d88

works

880d3dc

fix

aa96ee4

fix

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wayfarer3130 reviewed Feb 21, 2025

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feat(seg): Improve Labelmap Statistics, Interpolation, and Threshold Configuration #1820

feat(seg): Improve Labelmap Statistics, Interpolation, and Threshold Configuration #1820

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feat(seg): Improve Labelmap Statistics, Interpolation, and Threshold Configuration #1820

feat(seg): Improve Labelmap Statistics, Interpolation, and Threshold Configuration #1820

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sedghi commented Feb 10, 2025 • edited Loading

Labelmap Statistics

Sphere Brush

Interpolation

THRESHOLD -> Strategy specific threshold

netlify bot commented Feb 10, 2025 • edited Loading

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