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feat: ROI threshold to consider two volumes for thresholding (corners…
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…tonejs#325)

* Adding ROI Threshold based on multiple volumes

* Add sliders for petVolume

* Refactoring threshold function parameters

* Working with LPS coords

* Running required checks

* Adding perfusion colormap

* Fix CI error in PR

* Fixing CI function parameter checking error

* Fixing CI error related to api change

* Removing unnecessary extra parameter

* Minor parameter adjustment

* Add test coverType option

* Add some comments

* Convert parameter in optional and set defaul value

* Convert parameter in optional and set defaul value

* Fixing CI errors

* Refactoring and comment threshold functions

* Refactoring code based on PR reviews

* Add spacing check between volumes in roi threshold

* fix build

Co-authored-by: Alireza <[email protected]>
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@rodrigobasilio2022 @sedghi
rodrigobasilio2022 and sedghi committed Jan 19, 2023
1 parent 30b0216 commit 4f943f7
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Showing 7 changed files with 563 additions and 91 deletions.
4 changes: 2 additions & 2 deletions common/reviews/api/tools.api.md
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Original file line number Diff line number Diff line change
Expand Up @@ -3551,7 +3551,7 @@ export class RectangleROIThresholdTool extends RectangleROITool {
}

// @public (undocumented)
function rectangleROIThresholdVolumeByRange(annotationUIDs: string[], segmentationVolume: Types_2.IImageVolume, referenceVolumes: Types_2.IImageVolume[], options: ThresholdRangeOptions_2): Types_2.IImageVolume;
function rectangleROIThresholdVolumeByRange(annotationUIDs: string[], segmentationVolume: Types_2.IImageVolume, thresholdVolumeInformation: ThresholdInformation_2[], options: ThresholdOptions): Types_2.IImageVolume;

// @public (undocumented)
export class RectangleROITool extends AnnotationTool {
Expand Down Expand Up @@ -4371,7 +4371,7 @@ type TextBoxHandle = {
};

// @public (undocumented)
function thresholdVolumeByRange(segmentationVolume: Types_2.IImageVolume, referenceVolume: Types_2.IImageVolume, options: ThresholdRangeOptions): Types_2.IImageVolume;
function thresholdVolumeByRange(segmentationVolume: Types_2.IImageVolume, thresholdVolumeInformation: ThresholdInformation[], options: ThresholdRangeOptions): Types_2.IImageVolume;

// @public (undocumented)
function throttle(func: Function, wait?: number, options?: {
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159 changes: 120 additions & 39 deletions packages/tools/examples/rectangleROIThreshold/index.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -12,9 +12,12 @@ import {
setTitleAndDescription,
addButtonToToolbar,
addSliderToToolbar,
addDropdownToToolbar,
setCtTransferFunctionForVolumeActor,
setPetColorMapTransferFunctionForVolumeActor,
} from '../../../../utils/demo/helpers';
import * as cornerstoneTools from '@cornerstonejs/tools';
import perfusionColorMap from './preset';

// This is for debugging purposes
console.warn(
Expand All @@ -41,7 +44,13 @@ const { ViewportType } = Enums;
// Define a unique id for the volume
const volumeName = 'CT_VOLUME_ID'; // Id of the volume less loader prefix
const volumeLoaderScheme = 'cornerstoneStreamingImageVolume'; // Loader id which defines which volume loader to use
const volumeId = `${volumeLoaderScheme}:${volumeName}`; // VolumeId with loader id + volume id

const ctVolumeName = 'CT_VOLUME_ID'; // Id of the volume less loader prefix
const ctVolumeId = `${volumeLoaderScheme}:${ctVolumeName}`; // VolumeId with loader id + volume id
const ptVolumeName = 'PT_VOLUME_ID';
const ptVolumeId = `${volumeLoaderScheme}:${ptVolumeName}`;
const volumeId = ptVolumeId;

const segmentationId = 'MY_SEGMENTATION_ID';
const toolGroupId = 'MY_TOOLGROUP_ID';

Expand Down Expand Up @@ -98,8 +107,27 @@ content.append(instructions);
// ============================= //

let numSlicesToProject = 3;
let lowerThreshold = 100;
let upperThreshold = 500;
let ctLowerThreshold = -900;
let ctUpperThreshold = -700;
const overwrite = true;

let ptLowerThreshold = 0;
let ptUpperThreshold = 5;
let overlapType = 0;

addDropdownToToolbar({
options: {
values: ['All voxels', 'Any voxel'],
defaultValue: 'Any voxel',
},
onSelectedValueChange: (selectedValue) => {
if (selectedValue === 'All voxels') {
overlapType = 1;
} else if (selectedValue === 'Any voxel') {
overlapType = 0;
}
},
});

addButtonToToolbar({
title: 'Execute threshold',
Expand All @@ -121,65 +149,84 @@ addButtonToToolbar({
return;
}

const { metadata } = annotation; // assuming they are all overlayed on the same toolGroup
const viewport = metadata.enabledElement.viewport as Types.IVolumeViewport;

const volumeActorInfo = viewport.getDefaultActor();

// Todo: this only works for volumeViewport
const { uid } = volumeActorInfo;
const referenceVolume = cache.getVolume(uid);
const ctVolume = cache.getVolume(ctVolumeId);
const ptVolume = cache.getVolume(ptVolumeId);
const segmentationVolume = cache.getVolume(segmentationId);

csToolsUtils.segmentation.rectangleROIThresholdVolumeByRange(
selectedAnnotationUIDs,
segmentationVolume,
[referenceVolume],
[
{ volume: ctVolume, lower: ctLowerThreshold, upper: ctUpperThreshold },
{ volume: ptVolume, lower: ptLowerThreshold, upper: ptUpperThreshold },
],
{
numSlicesToProject,
lower: lowerThreshold,
upper: upperThreshold,
overwrite: false,
overwrite,
overlapType,
}
);
},
});

addSliderToToolbar({
title: `Number of Slices to Segment: ${numSlicesToProject
.toString()
.padStart(4)}`,
range: [1, 5],
title: `#Slices to Segment: ${numSlicesToProject}`,
range: [1, 10],
defaultValue: numSlicesToProject,
onSelectedValueChange: (value) => {
numSlicesToProject = Number(value);
},
updateLabelOnChange: (value, label) => {
label.innerText = `Number of Slices to Segment: ${value}`;
label.innerText = `#Slices to Segment: ${value}`;
},
});

addSliderToToolbar({
title: `PT Lower Thresh: ${ptLowerThreshold}`,
range: [0, 10],
defaultValue: ptLowerThreshold,
onSelectedValueChange: (value) => {
ptLowerThreshold = Number(value);
},
updateLabelOnChange: (value, label) => {
label.innerText = `PT Lower Thresh: ${value}`;
},
});

addSliderToToolbar({
title: `PT Upper Thresh: ${ptUpperThreshold}`,
range: [0, 10],
defaultValue: ptUpperThreshold,
onSelectedValueChange: (value) => {
ptUpperThreshold = Number(value);
},
updateLabelOnChange: (value, label) => {
label.innerText = `PT Upper Thresh: ${value}`;
},
});

addSliderToToolbar({
title: `Lower Threshold: ${lowerThreshold}`,
range: [100, 400],
defaultValue: lowerThreshold,
title: `CT Lower Thresh: ${ctLowerThreshold}`,
range: [-1000, 1000],
defaultValue: ctLowerThreshold,
onSelectedValueChange: (value) => {
lowerThreshold = Number(value);
ctLowerThreshold = Number(value);
},
updateLabelOnChange: (value, label) => {
label.innerText = `Lower Threshold: ${value}`;
label.innerText = `CT Lower Thresh: ${value}`;
},
});

addSliderToToolbar({
title: `Upper Threshold: ${upperThreshold.toString().padStart(4)}`,
range: [500, 1000],
defaultValue: upperThreshold,
title: `CT Upper Thresh: ${ctUpperThreshold}`,
range: [-1000, 1000],
defaultValue: ctUpperThreshold,
onSelectedValueChange: (value) => {
upperThreshold = Number(value);
ctUpperThreshold = Number(value);
},
updateLabelOnChange: (value, label) => {
label.innerText = `Upper Threshold: ${value}`;
label.innerText = `CT Upper Thresh: ${value}`;
},
});

Expand Down Expand Up @@ -258,18 +305,32 @@ async function run() {
// hook instead of mouse buttons, it does not need to assign any mouse button.
toolGroup.setToolActive(StackScrollMouseWheelTool.toolName);

// Get Cornerstone imageIds for the source data and fetch metadata into RAM
const imageIds = await createImageIdsAndCacheMetaData({
StudyInstanceUID:
'1.3.6.1.4.1.14519.5.2.1.7009.2403.334240657131972136850343327463',
const wadoRsRoot = 'https://domvja9iplmyu.cloudfront.net/dicomweb';
const StudyInstanceUID =
'1.3.6.1.4.1.14519.5.2.1.7009.2403.871108593056125491804754960339';

// Get Cornerstone imageIds and fetch metadata into RAM
const ctImageIds = await createImageIdsAndCacheMetaData({
StudyInstanceUID,
SeriesInstanceUID:
'1.3.6.1.4.1.14519.5.2.1.7009.2403.367700692008930469189923116409',
wadoRsRoot,
});

const ptImageIds = await createImageIdsAndCacheMetaData({
StudyInstanceUID,
SeriesInstanceUID:
'1.3.6.1.4.1.14519.5.2.1.7009.2403.226151125820845824875394858561',
wadoRsRoot: 'https://d3t6nz73ql33tx.cloudfront.net/dicomweb',
'1.3.6.1.4.1.14519.5.2.1.7009.2403.780462962868572737240023906400',
wadoRsRoot,
});

// Define a volume in memory
const volume = await volumeLoader.createAndCacheVolume(volumeId, {
imageIds,
const ctVolume = await volumeLoader.createAndCacheVolume(ctVolumeId, {
imageIds: ctImageIds,
});
// Define a volume in memory
const ptVolume = await volumeLoader.createAndCacheVolume(ptVolumeId, {
imageIds: ptImageIds,
});

// Add some segmentations based on the source data volume
Expand Down Expand Up @@ -320,8 +381,9 @@ async function run() {
toolGroup.addViewport(viewportId2, renderingEngineId);
toolGroup.addViewport(viewportId3, renderingEngineId);

// Set the volume to load
volume.load();
// Set the volumes to load
ptVolume.load();
ctVolume.load();

// Set volumes on the viewports
await setVolumesForViewports(
Expand All @@ -330,6 +392,25 @@ async function run() {
[viewportId1, viewportId2, viewportId3]
);

await setVolumesForViewports(
renderingEngine,
[
{
volumeId: ctVolumeId,
callback: setCtTransferFunctionForVolumeActor,
},
{
volumeId: ptVolumeId,
callback: ({ volumeActor }) =>
setPetColorMapTransferFunctionForVolumeActor({
volumeActor,
preset: perfusionColorMap,
}),
},
],
[viewportId1, viewportId2, viewportId3]
);

// // Add the segmentation representation to the toolgroup
const segmentationRepresentationByUIDs =
await segmentation.addSegmentationRepresentations(toolGroupId, [
Expand Down
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