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fix(cornerstone-dicom-sr): Freehand SR hydration support (OHIF#3996)
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Co-authored-by: Ibrahim <[email protected]>
Co-authored-by: IbrahimCSAE <[email protected]>
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@igoroctaviano @IbrahimCSAE @thanh-nguyen-dang
3 people authored and thanh-nguyen-dang committed Apr 30, 2024
1 parent 00db1de commit bf1170b
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Showing 21 changed files with 356 additions and 227 deletions.
4 changes: 2 additions & 2 deletions extensions/cornerstone-dicom-seg/package.json
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Expand Up @@ -46,8 +46,8 @@
},
"dependencies": {
"@babel/runtime": "^7.20.13",
"@cornerstonejs/adapters": "^1.67.0",
"@cornerstonejs/core": "^1.67.0",
"@cornerstonejs/adapters": "^1.68.1",
"@cornerstonejs/core": "^1.68.1",
"@kitware/vtk.js": "29.7.0",
"react-color": "^2.19.3"
}
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6 changes: 3 additions & 3 deletions extensions/cornerstone-dicom-sr/package.json
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Expand Up @@ -46,9 +46,9 @@
},
"dependencies": {
"@babel/runtime": "^7.20.13",
"@cornerstonejs/adapters": "^1.67.0",
"@cornerstonejs/core": "^1.67.0",
"@cornerstonejs/tools": "^1.67.0",
"@cornerstonejs/adapters": "^1.68.1",
"@cornerstonejs/core": "^1.68.1",
"@cornerstonejs/tools": "^1.68.1",
"classnames": "^2.3.2"
}
}
49 changes: 44 additions & 5 deletions extensions/cornerstone-dicom-sr/src/getSopClassHandlerModule.ts
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@@ -1,6 +1,6 @@
import { SOPClassHandlerName, SOPClassHandlerId } from './id';
import { utils, classes, DisplaySetService, Types } from '@ohif/core';
import addMeasurement from './utils/addMeasurement';
import addDICOMSRDisplayAnnotation from './utils/addDICOMSRDisplayAnnotation';
import isRehydratable from './utils/isRehydratable';
import { adaptersSR } from '@cornerstonejs/adapters';

Expand Down Expand Up @@ -150,13 +150,37 @@ function _getDisplaySetsFromSeries(instances, servicesManager, extensionManager)
return [displaySet];
}

function _load(displaySet, servicesManager, extensionManager) {
async function _load(displaySet, servicesManager, extensionManager) {
const { displaySetService, measurementService } = servicesManager.services;
const dataSources = extensionManager.getDataSources();
const dataSource = dataSources[0];

const { ContentSequence } = displaySet.instance;

async function retrieveBulkData(obj, parentObj = null, key = null) {
for (const prop in obj) {
if (typeof obj[prop] === 'object' && obj[prop] !== null) {
await retrieveBulkData(obj[prop], obj, prop);
} else if (Array.isArray(obj[prop])) {
await Promise.all(obj[prop].map(item => retrieveBulkData(item, obj, prop)));
} else if (prop === 'BulkDataURI') {
const value = await dataSource.retrieve.bulkDataURI({
BulkDataURI: obj[prop],
StudyInstanceUID: displaySet.instance.StudyInstanceUID,
SeriesInstanceUID: displaySet.instance.SeriesInstanceUID,
SOPInstanceUID: displaySet.instance.SOPInstanceUID,
});
if (parentObj && key) {
parentObj[key] = new Float32Array(value);
}
}
}
}

if (displaySet.isLoaded !== true) {
await retrieveBulkData(ContentSequence);
}

displaySet.referencedImages = _getReferencedImagesList(ContentSequence);
displaySet.measurements = _getMeasurements(ContentSequence);

Expand Down Expand Up @@ -211,7 +235,7 @@ function _checkIfCanAddMeasurementsToDisplaySet(
return;
}

if (!newDisplaySet instanceof ImageSet) {
if ((!newDisplaySet) instanceof ImageSet) {
// This also filters out _this_ displaySet, as it is not an ImageSet.
return;
}
Expand Down Expand Up @@ -275,7 +299,22 @@ function _checkIfCanAddMeasurementsToDisplaySet(
}

if (_measurementReferencesSOPInstanceUID(measurement, SOPInstanceUID, frameNumber)) {
addMeasurement(measurement, imageId, newDisplaySet.displaySetInstanceUID);
const frame =
(measurement.coords[0].ReferencedSOPSequence &&
measurement.coords[0].ReferencedSOPSequence?.ReferencedFrameNumber) ||
1;

/** Add DICOMSRDisplay annotation for the SR viewport (only) */
addDICOMSRDisplayAnnotation(measurement, imageId, frame);

/** Update measurement properties */
measurement.loaded = true;
measurement.imageId = imageId;
measurement.displaySetInstanceUID = newDisplaySet.displaySetInstanceUID;
measurement.ReferencedSOPInstanceUID =
measurement.coords[0].ReferencedSOPSequence.ReferencedSOPInstanceUID;
measurement.frameNumber = frame;
delete measurement.coords;

unloadedMeasurements.splice(j, 1);
}
Expand All @@ -291,7 +330,7 @@ function _measurementReferencesSOPInstanceUID(measurement, SOPInstanceUID, frame
// Standard. But for now, we will support only one ReferenceFrameNumber.
const ReferencedFrameNumber =
(measurement.coords[0].ReferencedSOPSequence &&
measurement.coords[0].ReferencedSOPSequence[0]?.ReferencedFrameNumber) ||
measurement.coords[0].ReferencedSOPSequence?.ReferencedFrameNumber) ||
1;

if (frameNumber && Number(frameNumber) !== Number(ReferencedFrameNumber)) {
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2 changes: 1 addition & 1 deletion extensions/cornerstone-dicom-sr/src/index.tsx
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@@ -1,6 +1,6 @@
import React from 'react';
import getSopClassHandlerModule from './getSopClassHandlerModule';
import getHangingProtocolModule, { srProtocol } from './getHangingProtocolModule';
import { srProtocol } from './getHangingProtocolModule';
import onModeEnter from './onModeEnter';
import getCommandsModule from './commandsModule';
import preRegistration from './init';
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14 changes: 8 additions & 6 deletions extensions/cornerstone-dicom-sr/src/init.ts
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Original file line number Diff line number Diff line change
@@ -1,5 +1,4 @@
import {
addTool,
AngleTool,
annotation,
ArrowAnnotateTool,
Expand All @@ -9,6 +8,7 @@ import {
CircleROITool,
LengthTool,
PlanarFreehandROITool,
RectangleROITool,
} from '@cornerstonejs/tools';
import DICOMSRDisplayTool from './tools/DICOMSRDisplayTool';
import addToolInstance from './utils/addToolInstance';
Expand All @@ -19,24 +19,25 @@ import toolNames from './tools/toolNames';
* @param {object} configuration
*/
export default function init({ configuration = {} }: Types.Extensions.ExtensionParams): void {
addTool(DICOMSRDisplayTool);
addToolInstance(toolNames.SRLength, LengthTool, {});
addToolInstance(toolNames.DICOMSRDisplay, DICOMSRDisplayTool);
addToolInstance(toolNames.SRLength, LengthTool);
addToolInstance(toolNames.SRBidirectional, BidirectionalTool);
addToolInstance(toolNames.SREllipticalROI, EllipticalROITool);
addToolInstance(toolNames.SRCircleROI, CircleROITool);
addToolInstance(toolNames.SRArrowAnnotate, ArrowAnnotateTool);
addToolInstance(toolNames.SRAngle, AngleTool);
addToolInstance(toolNames.SRPlanarFreehandROI, PlanarFreehandROITool);
addToolInstance(toolNames.SRRectangleROI, RectangleROITool);

// TODO - fix the SR display of Cobb Angle, as it joins the two lines
addToolInstance(toolNames.SRCobbAngle, CobbAngleTool);
// TODO - fix the rehydration of Freehand, as it throws an exception
// on a missing polyline. The fix is probably in CS3D
addToolInstance(toolNames.SRPlanarFreehandROI, PlanarFreehandROITool);

// Modify annotation tools to use dashed lines on SR
const dashedLine = {
lineDash: '4,4',
};
annotation.config.style.setToolGroupToolStyles('SRToolGroup', {
[toolNames.DICOMSRDisplay]: dashedLine,
SRLength: dashedLine,
SRBidirectional: dashedLine,
SREllipticalROI: dashedLine,
Expand All @@ -45,6 +46,7 @@ export default function init({ configuration = {} }: Types.Extensions.ExtensionP
SRCobbAngle: dashedLine,
SRAngle: dashedLine,
SRPlanarFreehandROI: dashedLine,
SRRectangleROI: dashedLine,
global: {},
});
}
14 changes: 11 additions & 3 deletions extensions/cornerstone-dicom-sr/src/tools/DICOMSRDisplayTool.ts
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Expand Up @@ -22,14 +22,14 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
}

_getTextBoxLinesFromLabels(labels) {
// TODO -> max 3 for now (label + shortAxis + longAxis), need a generic solution for this!
// TODO -> max 5 for now (label + shortAxis + longAxis), need a generic solution for this!

const labelLength = Math.min(labels.length, 3);
const labelLength = Math.min(labels.length, 5);
const lines = [];

for (let i = 0; i < labelLength; i++) {
const labelEntry = labels[i];
lines.push(`${_labelToShorthand(labelEntry.label)}${labelEntry.value}`);
lines.push(`${_labelToShorthand(labelEntry.label)}: ${labelEntry.value}`);
}

return lines;
Expand Down Expand Up @@ -77,6 +77,7 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
toolName: this.getToolName(),
viewportId: enabledElement.viewport.id,
};
const { style: annotationStyle } = annotation.config;

for (let i = 0; i < filteredAnnotations.length; i++) {
const annotation = filteredAnnotations[i];
Expand All @@ -87,6 +88,10 @@ export default class DICOMSRDisplayTool extends AnnotationTool {

styleSpecifier.annotationUID = annotationUID;

const groupStyle = annotationStyle.getToolGroupToolStyles(this.toolGroupId)[
this.getToolName()
];

const lineWidth = this.getStyle('lineWidth', styleSpecifier, annotation);
const lineDash = this.getStyle('lineDash', styleSpecifier, annotation);
const color =
Expand All @@ -98,6 +103,7 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
color,
lineDash,
lineWidth,
...groupStyle,
};

Object.keys(renderableData).forEach(GraphicType => {
Expand Down Expand Up @@ -160,6 +166,7 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
const drawingOptions = {
color: options.color,
width: options.lineWidth,
lineDash: options.lineDash,
};
let allCanvasCoordinates = [];
renderableData.map((data, index) => {
Expand Down Expand Up @@ -307,6 +314,7 @@ export default class DICOMSRDisplayTool extends AnnotationTool {
{
color: options.color,
width: options.lineWidth,
lineDash: options.lineDash,
}
);
});
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47 changes: 15 additions & 32 deletions ...tone-dicom-sr/src/utils/addMeasurement.ts → .../src/utils/addDICOMSRDisplayAnnotation.ts
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@@ -1,15 +1,13 @@
import { vec3 } from 'gl-matrix';
import { Types, annotation } from '@cornerstonejs/tools';
import { metaData, utilities, Types as csTypes } from '@cornerstonejs/core';

import toolNames from '../tools/toolNames';
import SCOORD_TYPES from '../constants/scoordTypes';

const EPSILON = 1e-4;

const supportedLegacyCornerstoneTags = ['cornerstoneTools@^4.0.0'];

export default function addMeasurement(measurement, imageId, displaySetInstanceUID) {
// TODO -> Render rotated ellipse .
export default function addDICOMSRDisplayAnnotation(measurement, imageId, frameNumber) {
const toolName = toolNames.DICOMSRDisplay;

const measurementData = {
Expand All @@ -27,26 +25,25 @@ export default function addMeasurement(measurement, imageId, displaySetInstanceU
}

measurementData.renderableData[GraphicType].push(
_getRenderableData(GraphicType, GraphicData, imageId, measurement.TrackingIdentifier)
_getRenderableData(GraphicType, GraphicData, imageId)
);
});

// Use the metadata provider to grab its imagePlaneModule metadata
const imagePlaneModule = metaData.get('imagePlaneModule', imageId);

const annotationManager = annotation.state.getAnnotationManager();

// Create Cornerstone3D Annotation from measurement
const frameNumber =
(measurement.coords[0].ReferencedSOPSequence &&
measurement.coords[0].ReferencedSOPSequence[0]?.ReferencedFrameNumber) ||
1;

/**
* This annotation (DICOMSRDisplay) is only used by the SR viewport.
* This is used before the annotation is hydrated. If hydrated the measurement will be added
* to the measurement service and will be available for the other viewports.
*/
const SRAnnotation: Types.Annotation = {
annotationUID: measurement.TrackingUniqueIdentifier,
highlighted: false,
isLocked: false,
invalidated: false,
metadata: {
FrameOfReferenceUID: imagePlaneModule.frameOfReferenceUID,
toolName: toolName,
FrameOfReferenceUID: imagePlaneModule.frameOfReferenceUID,
referencedImageId: imageId,
},
data: {
Expand All @@ -58,28 +55,14 @@ export default function addMeasurement(measurement, imageId, displaySetInstanceU
TrackingUniqueIdentifier: measurementData.TrackingUniqueIdentifier,
renderableData: measurementData.renderableData,
},
frameNumber: frameNumber,
frameNumber,
},
};

const annotationManager = annotation.state.getAnnotationManager();
annotationManager.addAnnotation(SRAnnotation);

measurement.loaded = true;
measurement.imageId = imageId;
measurement.displaySetInstanceUID = displaySetInstanceUID;

// Remove the unneeded coord now its processed, but keep the SOPInstanceUID.
// NOTE: We assume that each SCOORD in the MeasurementGroup maps onto one frame,
// It'd be super weird if it didn't anyway as a SCOORD.
measurement.ReferencedSOPInstanceUID =
measurement.coords[0].ReferencedSOPSequence.ReferencedSOPInstanceUID;
measurement.frameNumber = frameNumber;
delete measurement.coords;
}

function _getRenderableData(GraphicType, GraphicData, imageId, TrackingIdentifier) {
const [cornerstoneTag, toolName] = TrackingIdentifier.split(':');

function _getRenderableData(GraphicType, GraphicData, imageId) {
let renderableData: csTypes.Point3[];

switch (GraphicType) {
Expand Down
32 changes: 16 additions & 16 deletions extensions/cornerstone-dicom-sr/src/viewports/OHIFCornerstoneSRViewport.tsx
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Expand Up @@ -125,6 +125,10 @@ function OHIFCornerstoneSRViewport(props) {
console.warn('More than one SOPClassUID in the same series is not yet supported.');
}

// if (!srDisplaySet.measurements || !srDisplaySet.measurements.length) {
// return;
// }

_getViewportReferencedDisplaySetData(
srDisplaySet,
newMeasurementSelected,
Expand Down Expand Up @@ -253,12 +257,16 @@ function OHIFCornerstoneSRViewport(props) {
* if it is hydrated we don't even use the SR viewport.
*/
useEffect(() => {
if (!srDisplaySet.isLoaded) {
srDisplaySet.load();
}
const numMeasurements = srDisplaySet.measurements.length;
setMeasurementCount(numMeasurements);
}, [srDisplaySet]);
const loadSR = async () => {
if (!srDisplaySet.isLoaded) {
await srDisplaySet.load();
}
const numMeasurements = srDisplaySet.measurements.length;
setMeasurementCount(numMeasurements);
updateViewport(measurementSelected);
};
loadSR();
}, [dataSource, srDisplaySet]);

/**
* Hook to update the tracking identifiers when the selected measurement changes or
Expand All @@ -275,19 +283,11 @@ function OHIFCornerstoneSRViewport(props) {
* Todo: what is this, not sure what it does regarding the react aspect,
* it is updating a local variable? which is not state.
*/
let isLocked = trackedMeasurements?.context?.trackedSeries?.length > 0;
const [isLocked, setIsLocked] = useState(trackedMeasurements?.context?.trackedSeries?.length > 0);
useEffect(() => {
isLocked = trackedMeasurements?.context?.trackedSeries?.length > 0;
setIsLocked(trackedMeasurements?.context?.trackedSeries?.length > 0);
}, [trackedMeasurements]);

/**
* Data fetching for the SR displaySet, which updates the measurements and
* also gets the referenced image displaySet that SR is based on.
*/
useEffect(() => {
updateViewport(measurementSelected);
}, [dataSource, srDisplaySet]);

useEffect(() => {
viewportActionCornersService.setComponents([
{
Expand Down
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