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feat(segmentGroups): support overlapping segments in SEG files
Each component in the image to convert is a non overlapping labelmap. Create another segment group for each component of image to convert. closes #672
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,56 @@ | ||
| import { describe, it, expect } from 'vitest'; | ||
| import vtkImageData from '@kitware/vtk.js/Common/DataModel/ImageData'; | ||
| import vtkDataArray from '@kitware/vtk.js/Common/Core/DataArray'; | ||
| import vtkImageExtractComponentsFilter from '../imageExtractComponentsFilter'; | ||
|
|
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| describe('vtkImageExtractComponentsFilter', () => { | ||
| it('should extract specified components', () => { | ||
| // Create an image data with known scalar components | ||
| const imageData = vtkImageData.newInstance(); | ||
| imageData.setDimensions([2, 2, 1]); | ||
|
|
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| // Create scalar data with 3 components per voxel | ||
| const scalars = vtkDataArray.newInstance({ | ||
| numberOfComponents: 3, | ||
| values: new Uint8Array([ | ||
| // Voxel 0 | ||
| 10, 20, 30, | ||
| // Voxel 1 | ||
| 40, 50, 60, | ||
| // Voxel 2 | ||
| 70, 80, 90, | ||
| // Voxel 3 | ||
| 100, 110, 120, | ||
| ]), | ||
| }); | ||
|
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| imageData.getPointData().setScalars(scalars); | ||
|
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| // Create the filter and set components to extract | ||
| const extractComponentsFilter = | ||
| vtkImageExtractComponentsFilter.newInstance(); | ||
| extractComponentsFilter.setComponents([0, 2]); // Extract components 0 and 2 | ||
| extractComponentsFilter.setInputData(imageData); | ||
| extractComponentsFilter.update(); | ||
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| const outputData = extractComponentsFilter.getOutputData(); | ||
| const outputScalars = outputData.getPointData().getScalars(); | ||
| const outputValues = outputScalars.getData(); | ||
|
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| // Expected output | ||
| const expectedValues = new Uint8Array([ | ||
| // Voxel 0 | ||
| 10, 30, | ||
| // Voxel 1 | ||
| 40, 60, | ||
| // Voxel 2 | ||
| 70, 90, | ||
| // Voxel 3 | ||
| 100, 120, | ||
| ]); | ||
|
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| // Check if output matches expected values | ||
| expect(outputScalars.getNumberOfComponents()).toBe(2); | ||
| expect(outputValues).toEqual(expectedValues); | ||
| }); | ||
| }); |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,86 @@ | ||
| /* eslint-disable no-param-reassign */ | ||
| import macro from '@kitware/vtk.js/macro'; | ||
| import vtkImageData from '@kitware/vtk.js/Common/DataModel/ImageData'; | ||
| import vtkDataArray from '@kitware/vtk.js/Common/Core/DataArray'; | ||
|
|
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| function vtkImageExtractComponentsFilter(publicAPI, model) { | ||
| model.classHierarchy.push('vtkImageExtractComponentsFilter'); | ||
|
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| publicAPI.requestData = (inData, outData) => { | ||
| const inputData = inData[0]; | ||
| const outputData = vtkImageData.newInstance(); | ||
|
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| const components = model.components; | ||
| if (!components || !Array.isArray(components) || components.length === 0) { | ||
| throw Error('No components specified for extraction.'); | ||
| } | ||
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| const inputScalars = inputData.getPointData().getScalars(); | ||
| const numInputComponents = inputScalars.getNumberOfComponents(); | ||
| components.forEach((c) => { | ||
| if (c < 0) { | ||
| throw Error('Component index must be greater than or equal to 0.'); | ||
| } | ||
| if (c >= numInputComponents) { | ||
| throw Error( | ||
| 'Component index must be less than the number of components in the input data.' | ||
| ); | ||
| } | ||
| }); | ||
|
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| outputData.shallowCopy(inputData); | ||
|
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| const inputArray = inputScalars.getData(); | ||
| const numPixels = inputArray.length / numInputComponents; | ||
|
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| const outputNumComponents = components.length; | ||
| const outputArray = new inputArray.constructor( | ||
| numPixels * outputNumComponents | ||
| ); | ||
|
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| for (let pixel = 0; pixel < numPixels; pixel++) { | ||
| for (let c = 0; c < components.length; c++) { | ||
| outputArray[pixel * outputNumComponents + c] = | ||
| inputArray[pixel * numInputComponents + components[c]]; | ||
| } | ||
| } | ||
|
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| outputData.getPointData().setScalars( | ||
| vtkDataArray.newInstance({ | ||
| numberOfComponents: outputNumComponents, | ||
| values: outputArray, | ||
| }) | ||
| ); | ||
|
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| outData[0] = outputData; | ||
| }; | ||
| } | ||
|
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| const DEFAULT_VALUES = { | ||
| components: [], | ||
| }; | ||
|
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| // ---------------------------------------------------------------------------- | ||
|
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| export function extend(publicAPI, model, initialValues = {}) { | ||
| Object.assign(model, DEFAULT_VALUES, initialValues); | ||
|
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| macro.obj(publicAPI, model); | ||
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| macro.algo(publicAPI, model, 1, 1); | ||
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| macro.setGet(publicAPI, model, ['components']); | ||
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| vtkImageExtractComponentsFilter(publicAPI, model); | ||
| } | ||
|
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| // ---------------------------------------------------------------------------- | ||
|
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| export const newInstance = macro.newInstance( | ||
| extend, | ||
| 'vtkImageExtractComponentsFilter' | ||
| ); | ||
|
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| // ---------------------------------------------------------------------------- | ||
|
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| export default { newInstance, extend }; |
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