feat(Segmentation): Add contour representation for segmentations #384

sedghi · 2023-01-25T19:55:50Z

Continuing on the plan to add multiple representations for a segmentation, this PR adds the contour representation (read about representations here)

This PR add new geometryLoader which is supposed to deal with loading geometries and cache them. As the first geometry, this PR introduces contourSets and contours.

Since usually a set of contours represents an entity, a contourSet exists

Adding a contour representation is similar to adding a labelmap

First the geometry (in labelmap, the volume) should get added. For each contourSet a separate geometry is cached. This is a design decision that is intended to enabled converting of the geometry types to each other (contour -> closed surface and vice versa). As seen below each contourSet will get a geometryId that can later be used to construct a segmentation.

const promises = contourSets.map((contourSet) => {
  return geometryLoader.createAndCacheGeometry(contourSet.id, {
    type: GeometryType.CONTOUR,
    geometryData: contourSet as Types.PublicContourSetData,
  });
});

await Promise.all(promises);

A segmentation can get created

// Add the segmentations to state
  segmentation.addSegmentations([
    {
      segmentationId,
      representation: {
        // The type of segmentation
        type: csToolsEnums.SegmentationRepresentations.Contour,
        // The actual segmentation data, in the case of contour geometry
        //  this is a reference to the geometry data
        data: {
          geometryIds: contourSets.map({id}=>id)
        },
      },
    },
  ]);

A segmentation representation should get added

 await segmentation.addSegmentationRepresentations(toolGroupId, [
    {
      segmentationId,
      type: csToolsEnums.SegmentationRepresentations.Contour,
    },
  ]);

Demo

https://deploy-preview-384--cornerstone-3d-docs.netlify.app/live-examples/contoursegmentationrepresentation

PS: Kudos to @rodrigobasilio2022 for polydata experimentation with contours

netlify · 2023-01-25T19:55:55Z

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common/reviews/api/streaming-image-volume-loader.api.md

common/reviews/api/tools.api.md

packages/core/src/RenderingEngine/BaseVolumeViewport.ts

packages/core/src/RenderingEngine/StackViewport.ts

packages/core/src/RenderingEngine/Viewport.ts

packages/core/src/RenderingEngine/vtkClasses/vtkStreamingOpenGLVolumeMapper.js

jbocce · 2023-01-30T15:18:51Z

packages/core/src/RenderingEngine/BaseVolumeViewport.ts

@@ -536,7 +553,7 @@ abstract class BaseVolumeViewport extends Viewport implements IVolumeViewport {
      renderer
    );

-    vtkCamera.setIsPerformingCoordinateTransformation(false);
+    vtkCamera.setIsPerformingCoordinateTransformation?.(false);


I must be missing something, but I am trying to understand how setIsPerformingCoordinateTransformation is ever null such that the ?. is needed. Plesase help me here - what am I missing? :)

It is a custom method we add to our custom camera, so it might be possible that the other camera (vtkCamera) is used and hence we don't have it

wayfarer3130 · 2023-01-30T15:20:53Z

packages/core/src/RenderingEngine/vtkClasses/vtkStreamingOpenGLVolumeMapper.js

@@ -483,6 +500,107 @@ function vtkStreamingOpenGLVolumeMapper(publicAPI, model) {
        // mat3.transpose(keyMats.normalMatrix, keyMats.normalMatrix);
      }
    }
+
+    let lightNum = 0;


Could you extract this into a separate function, that you document what the behaviour is? I THINK I almost understand what is going on here, but it feels like separating this into a function with it's own function comment block would actually make it understandable and sufficiently documented that one could fix things later. Otherwise it is close to read only code after committed.

This is vtk.js source code we copied here (helps to keep it this way for future diffs). When we upgrade to vtk.js 26.x and one bug that I worked on is fixed, we can completely remove this setCameraShaderParameters

packages/core/src/cache/cache.ts

packages/tools/src/tools/displayTools/Contour/contourDisplay.ts

packages/docs/docs/concepts/cornerstone-core/geometryLoader.md

packages/core/src/RenderingEngine/VolumeViewport3D.ts

packages/core/src/cache/classes/Contour.ts

packages/tools/src/tools/base/BaseTool.ts

packages/core/src/cache/classes/Contour.ts

packages/core/src/cache/classes/ContourSet.ts

jbocce · 2023-01-30T16:40:33Z

packages/core/src/cache/classes/ContourSet.ts

+    return this.getPointsInAContour(contourIndex).length;
+  }
+
+  /**


Do you still want to keep these commented line?

Yes I guess it shows what is the overal plan

packages/tools/src/tools/displayTools/Contour/removeContourFromElement.ts

packages/tools/src/tools/displayTools/Contour/contourDisplay.ts

jbocce

Hey @sedghi. The changes overall look good. I like how contours parallel the label map segments. I have a bunch of comments, but nothing earth shattering. Looking forward to seeing a running example.

packages/core/src/types/IContourSet.ts

wayfarer3130

Other than the one comment to add a comment on the contour set, it looks good to me.

jbocce

One comment change should be done. Consider the others.

packages/core/src/utilities/actorCheck.ts

packages/core/src/RenderingEngine/Viewport.ts

packages/docs/docs/concepts/cornerstone-core/geometryLoader.md

jbocce · 2023-02-01T14:00:49Z

packages/core/src/utilities/actorCheck.ts

+ * @returns A boolean value.
+ */
+export function isImageActor(actorEntry: Types.ActorEntry): boolean {
+  return (


Consider removing the outer parentheses.

It is the prettier, so we can discuss it later.

packages/tools/src/store/ToolGroupManager/ToolGroup.ts

jbocce · 2023-02-01T14:36:03Z

utils/ExampleRunner/example-info.json

@@ -185,6 +185,10 @@
      "doubleClickWithStackAnnotationTools": {
        "name": "Double Click With Stack Annotation Tools",
        "description": "Demonstrates double click detection before/during/after using various annotation tools on a stack viewport."
+      },
+      "contourSegmentationRepresentation": {


Does it make sense to move this next to the label map example?

packages/tools/examples/contourSegmentationRepresentation/index.ts

jbocce

Remaining feedback is optional. Good stuff!

Ouwen · 2023-02-07T16:43:40Z

Hey not sure if this is appropriate forum for this, but just wanted to say that I really appreciate the level of documentation for this PR as it made it quite straightforward understand the design choice.

Awesome work on this!

longuto · 2023-07-26T08:21:50Z

How did the contourSets data come from ?

sedghi changed the title ~~[Draft] feat: Add contour representation in for segmentations~~ [Draft] feat: Add contour representation for segmentations Jan 25, 2023

sedghi marked this pull request as ready for review January 26, 2023 04:30

sedghi changed the title ~~[Draft] feat: Add contour representation for segmentations~~ feat: Add contour representation for segmentations Jan 26, 2023

sedghi requested review from jbocce and wayfarer3130 January 26, 2023 04:38

sedghi changed the title ~~feat: Add contour representation for segmentations~~ feat(Segmentation): Add contour representation for segmentations Jan 26, 2023

wayfarer3130 reviewed Jan 26, 2023

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sedghi force-pushed the feat/contour-representation branch from 0fb6b02 to 1f84a83 Compare February 1, 2023 13:57

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sedghi added 14 commits February 1, 2023 13:49

fix: polydata example should use the volume_3d viewport

32c50e0

refactor code for readability

fa0a5c3

fix: toolings for polydata and volume data

2515e31

add example to volume and polyline

4747830

final fixes

03e1c09

feat: add contour representation for segmentation

54e4c73

wip

3c7a721

make contour set a geometry

6be8534

remaining files

20f0cb0

apply review comments

93c4627

apply review comments

f784746

update tsconfig

f2bf860

apply review comments

889aa0c

apply review comments

d9cd7a8

sedghi force-pushed the feat/contour-representation branch from 1f84a83 to d9cd7a8 Compare February 1, 2023 18:49

fix build

6f6c5fa

sedghi merged commit 541a351 into main Feb 1, 2023

sedghi deleted the feat/contour-representation branch January 22, 2025 16:02

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feat(Segmentation): Add contour representation for segmentations #384

feat(Segmentation): Add contour representation for segmentations #384

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feat(Segmentation): Add contour representation for segmentations #384

feat(Segmentation): Add contour representation for segmentations #384

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