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feat(Segmentation): download RTSS from Labelmap(#3692)

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Co-authored-by: Alireza <ar.sedghi@gmail.com>
This commit is contained in:
dxlinandAlireza authored and GitHub committed 2023-10-06 15:00:04 -04:00
1 parent eab42c1032
commit 40673f64b3
22 files changed
+177 -429
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extensions/cornerstone-dicom-seg/package.json
+3 -1
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@@ -44,7 +44,9 @@
},
"dependencies": {
"@babel/runtime": "^7.20.13",
"@cornerstonejs/tools": "^1.19.4",
"@cornerstonejs/tools": "^1.20.1",
"@cornerstonejs/adapters": "^1.20.1",
"@kitware/vtk.js": "27.3.1",
"react-color": "^2.19.3"
}
}
extensions/cornerstone-dicom-seg/src/commandsModule.ts
+55 -3
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@@ -2,9 +2,16 @@ import dcmjs from 'dcmjs';
import { createReportDialogPrompt } from '@ohif/extension-default';
import { ServicesManager, Types } from '@ohif/core';
import { cache, metaData } from '@cornerstonejs/core';
import { segmentation as cornerstoneToolsSegmentation } from '@cornerstonejs/tools';
import { adaptersSEG, helpers } from '@cornerstonejs/adapters';
import { DicomMetadataStore } from '@ohif/core';
import {
segmentation as cornerstoneToolsSegmentation,
Enums as cornerstoneToolsEnums,
} from '@cornerstonejs/tools';
import { adaptersRT, helpers, adaptersSEG } from '@cornerstonejs/adapters';
import { classes, DicomMetadataStore } from '@ohif/core';
import vtkImageMarchingSquares from '@kitware/vtk.js/Filters/General/ImageMarchingSquares';
import vtkDataArray from '@kitware/vtk.js/Common/Core/DataArray';
import vtkImageData from '@kitware/vtk.js/Common/DataModel/ImageData';
import {
updateViewportsForSegmentationRendering,
@@ -12,12 +19,20 @@ import {
getTargetViewport,
} from './utils/hydrationUtils';
const { datasetToBlob } = dcmjs.data;
const {
Cornerstone3D: {
Segmentation: { generateLabelMaps2DFrom3D, generateSegmentation },
},
} = adaptersSEG;
const {
Cornerstone3D: {
RTSS: { generateRTSSFromSegmentations },
},
} = adaptersRT;
const { downloadDICOMData } = helpers;
const commandsModule = ({
@@ -348,6 +363,40 @@ const commandsModule = ({
return naturalizedReport;
},
/**
* Converts segmentations into RTSS for download.
* This sample function retrieves all segentations and passes to
* cornerstone tool adapter to convert to DICOM RTSS format. It then
* converts dataset to downloadable blob.
*
*/
downloadRTSS: ({ segmentationId }) => {
const segmentations = segmentationService.getSegmentation(segmentationId);
const vtkUtils = {
vtkImageMarchingSquares,
vtkDataArray,
vtkImageData,
};
const RTSS = generateRTSSFromSegmentations(
segmentations,
classes.MetadataProvider,
DicomMetadataStore,
cache,
cornerstoneToolsEnums,
vtkUtils
);
try {
const reportBlob = datasetToBlob(RTSS);
//Create a URL for the binary.
const objectUrl = URL.createObjectURL(reportBlob);
window.location.assign(objectUrl);
} catch (e) {
console.warn(e);
}
},
};
const definitions = {
@@ -372,6 +421,9 @@ const commandsModule = ({
storeSegmentation: {
commandFn: actions.storeSegmentation,
},
downloadRTSS: {
commandFn: actions.downloadRTSS,
},
};
return {
extensions/cornerstone-dicom-seg/src/panels/PanelSegmentation.tsx
+8 -1
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@@ -1,7 +1,7 @@
import { createReportAsync } from '@ohif/extension-default';
import React, { useEffect, useState, useCallback } from 'react';
import PropTypes from 'prop-types';
import { SegmentationGroupTable } from '@ohif/ui';
import { SegmentationGroupTable, LegacyButtonGroup, LegacyButton } from '@ohif/ui';
import callInputDialog from './callInputDialog';
import callColorPickerDialog from './colorPickerDialog';
@@ -215,6 +215,12 @@ export default function PanelSegmentation({
}
};
const onSegmentationDownloadRTSS = segmentationId => {
commandsManager.runCommand('downloadRTSS', {
segmentationId,
});
};
return (
<>
<div className="ohif-scrollbar flex min-h-0 flex-auto select-none flex-col justify-between overflow-auto">
@@ -227,6 +233,7 @@ export default function PanelSegmentation({
onSegmentationClick={onSegmentationClick}
onSegmentationDelete={onSegmentationDelete}
onSegmentationDownload={onSegmentationDownload}
onSegmentationDownloadRTSS={onSegmentationDownloadRTSS}
storeSegmentation={storeSegmentation}
onSegmentationEdit={onSegmentationEdit}
onSegmentClick={onSegmentClick}
extensions/cornerstone-dicom-seg/src/panels/SegmentationToolbox.tsx
+15 -15
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@@ -10,9 +10,9 @@ const TOOL_TYPES = {
SPHERE_BRUSH: 'SphereBrush',
CIRCULAR_ERASER: 'CircularEraser',
SPHERE_ERASER: 'SphereEraser',
CIRCLE_SCISSOR: 'CircleScissor',
RECTANGLE_SCISSOR: 'RectangleScissor',
SPHERE_SCISSOR: 'SphereScissor',
CIRCLE_SHAPE: 'CircleScissor',
RECTANGLE_SHAPE: 'RectangleScissor',
SPHERE_SHAPE: 'SphereScissor',
THRESHOLD_CIRCULAR_BRUSH: 'ThresholdCircularBrush',
THRESHOLD_SPHERE_BRUSH: 'ThresholdSphereBrush',
};
@@ -31,7 +31,7 @@ const initialState = {
brushSize: 15,
mode: 'CircularEraser', // Can be 'CircularEraser' or 'SphereEraser'
},
Scissors: {
Shapes: {
brushSize: 15,
mode: 'CircleScissor', // E.g., 'CircleScissor', 'RectangleScissor', or 'SphereScissor'
},
@@ -301,24 +301,24 @@ function SegmentationToolbox({ servicesManager, extensionManager }) {
],
},
{
name: 'Scissor',
icon: 'icon-tool-scissor',
name: 'Shapes',
icon: 'icon-tool-shape',
disabled: !toolsEnabled,
active:
state.activeTool === TOOL_TYPES.CIRCLE_SCISSOR ||
state.activeTool === TOOL_TYPES.RECTANGLE_SCISSOR ||
state.activeTool === TOOL_TYPES.SPHERE_SCISSOR,
onClick: () => setToolActive(TOOL_TYPES.CIRCLE_SCISSOR),
state.activeTool === TOOL_TYPES.CIRCLE_SHAPE ||
state.activeTool === TOOL_TYPES.RECTANGLE_SHAPE ||
state.activeTool === TOOL_TYPES.SPHERE_SHAPE,
onClick: () => setToolActive(TOOL_TYPES.CIRCLE_SHAPE),
options: [
{
name: 'Mode',
type: 'radio',
value: state.Scissors.mode,
id: 'scissor-mode',
value: state.Shapes.mode,
id: 'shape-mode',
values: [
{ value: TOOL_TYPES.CIRCLE_SCISSOR, label: 'Circle' },
{ value: TOOL_TYPES.RECTANGLE_SCISSOR, label: 'Rectangle' },
{ value: TOOL_TYPES.SPHERE_SCISSOR, label: 'Sphere' },
{ value: TOOL_TYPES.CIRCLE_SHAPE, label: 'Circle' },
{ value: TOOL_TYPES.RECTANGLE_SHAPE, label: 'Rectangle' },
{ value: TOOL_TYPES.SPHERE_SHAPE, label: 'Sphere' },
],
onChange: value => setToolActive(value),
},
extensions/cornerstone-dicom-sr/package.json
+3 -3
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@@ -44,9 +44,9 @@
},
"dependencies": {
"@babel/runtime": "^7.20.13",
"@cornerstonejs/adapters": "^1.19.4",
"@cornerstonejs/core": "^1.19.4",
"@cornerstonejs/tools": "^1.19.4",
"@cornerstonejs/adapters": "^1.20.1",
"@cornerstonejs/core": "^1.20.1",
"@cornerstonejs/tools": "^1.20.1",
"classnames": "^2.3.2"
}
}
extensions/cornerstone/package.json
+5 -5
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@@ -36,7 +36,7 @@
"@cornerstonejs/codec-libjpeg-turbo-8bit": "^1.2.2",
"@cornerstonejs/codec-openjpeg": "^1.2.2",
"@cornerstonejs/codec-openjph": "^2.4.2",
"@cornerstonejs/dicom-image-loader": "^1.19.4",
"@cornerstonejs/dicom-image-loader": "^1.20.1",
"@ohif/core": "3.7.0-beta.101",
"@ohif/ui": "3.7.0-beta.101",
"dcmjs": "^0.29.6",
@@ -52,10 +52,10 @@
},
"dependencies": {
"@babel/runtime": "^7.20.13",
"@cornerstonejs/adapters": "^1.19.4",
"@cornerstonejs/core": "^1.19.4",
"@cornerstonejs/streaming-image-volume-loader": "^1.19.4",
"@cornerstonejs/tools": "^1.19.4",
"@cornerstonejs/adapters": "^1.20.1",
"@cornerstonejs/core": "^1.20.1",
"@cornerstonejs/streaming-image-volume-loader": "^1.20.1",
"@cornerstonejs/tools": "^1.20.1",
"@kitware/vtk.js": "27.3.1",
"html2canvas": "^1.4.1",
"lodash.debounce": "4.0.8",
extensions/measurement-tracking/package.json
+2 -2
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@@ -30,8 +30,8 @@
"start": "yarn run dev"
},
"peerDependencies": {
"@cornerstonejs/core": "^1.19.4",
"@cornerstonejs/tools": "^1.19.4",
"@cornerstonejs/core": "^1.20.1",
"@cornerstonejs/tools": "^1.20.1",
"@ohif/core": "3.7.0-beta.101",
"@ohif/extension-cornerstone-dicom-sr": "3.7.0-beta.101",
"@ohif/ui": "3.7.0-beta.101",
extensions/tmtv/src/utils/dicomRTAnnotationExport/RTStructureSet/RTSSReport.js
-235
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@@ -1,235 +0,0 @@
import AnnotationToPointData from './measurements/AnnotationToPointData';
import dcmjs from 'dcmjs';
import { DicomMetadataStore } from '@ohif/core';
const { DicomMetaDictionary } = dcmjs.data;
export default class RTSSReport {
constructor() {}
/**
* Convert handles to RTSSReport report object containing the dcmjs dicom dataset.
*
* Note: The tool data needs to be formatted in a specific way, and currently
* it is limited to the RectangleROIStartEndTool in the Cornerstone.
*
* @param annotations Array of Cornerstone tool annotation data
* @param metadataProvider Metadata provider
* @param options report generation options
* @returns Report object containing the dataset
*/
static generateReport(annotations, metadataProvider, options) {
let dataset = initializeDataset(annotations, metadataProvider);
annotations.forEach((annotation, index) => {
const ContourSequence = AnnotationToPointData.convert(
annotation,
index,
metadataProvider,
options
);
dataset.StructureSetROISequence.push(
getStructureSetModule(annotation, index, metadataProvider)
);
dataset.ROIContourSequence.push(ContourSequence);
dataset.RTROIObservationsSequence.push(
getRTROIObservationsSequence(annotation, index, metadataProvider)
);
// ReferencedSeriesSequence
// Todo: handle more than one series
dataset.ReferencedSeriesSequence = getReferencedSeriesSequence(
annotation,
index,
metadataProvider
);
// ReferencedFrameOfReferenceSequence
dataset.ReferencedFrameOfReferenceSequence = getReferencedFrameOfReferenceSequence(
annotation,
metadataProvider,
dataset
);
});
const fileMetaInformationVersionArray = new Uint8Array(2);
fileMetaInformationVersionArray[1] = 1;
const _meta = {
FileMetaInformationVersion: {
Value: [fileMetaInformationVersionArray.buffer],
vr: 'OB',
},
TransferSyntaxUID: {
Value: ['1.2.840.10008.1.2.1'],
vr: 'UI',
},
ImplementationClassUID: {
Value: [DicomMetaDictionary.uid()], // TODO: could be git hash or other valid id
vr: 'UI',
},
ImplementationVersionName: {
Value: ['dcmjs'],
vr: 'SH',
},
};
dataset._meta = _meta;
return dataset;
}
/**
* Generate Cornerstone tool state from dataset
* @param {object} dataset dataset
* @param {object} hooks
* @param {function} hooks.getToolClass Function to map dataset to a tool class
* @returns
*/
static generateToolState(dataset, hooks = {}) {
// Todo
console.warn('RTSSReport.generateToolState not implemented');
}
}
function initializeDataset(annotations, metadataProvider) {
const rtSOPInstanceUID = DicomMetaDictionary.uid();
// get the first annotation data
const { referencedImageId: imageId, FrameOfReferenceUID } = annotations[0].metadata;
const { studyInstanceUID } = metadataProvider.get('generalSeriesModule', imageId);
const patientModule = getPatientModule(imageId, metadataProvider);
const rtSeriesModule = getRTSeriesModule(imageId, metadataProvider);
return {
StructureSetROISequence: [],
ROIContourSequence: [],
RTROIObservationsSequence: [],
ReferencedSeriesSequence: [],
ReferencedFrameOfReferenceSequence: [],
...patientModule,
...rtSeriesModule,
StudyInstanceUID: studyInstanceUID,
SOPClassUID: '1.2.840.10008.5.1.4.1.1.481.3', // RT Structure Set Storage
SOPInstanceUID: rtSOPInstanceUID,
Manufacturer: 'dcmjs',
Modality: 'RTSTRUCT',
FrameOfReferenceUID,
PositionReferenceIndicator: '',
StructureSetLabel: '',
StructureSetName: '',
ReferringPhysicianName: '',
OperatorsName: '',
StructureSetDate: DicomMetaDictionary.date(),
StructureSetTime: DicomMetaDictionary.time(),
};
}
function getPatientModule(imageId, metadataProvider) {
const generalSeriesModule = metadataProvider.get('generalSeriesModule', imageId);
const generalStudyModule = metadataProvider.get('generalStudyModule', imageId);
const patientStudyModule = metadataProvider.get('patientStudyModule', imageId);
const patientModule = metadataProvider.get('patientModule', imageId);
const patientDemographicModule = metadataProvider.get('patientDemographicModule', imageId);
return {
Modality: generalSeriesModule.modality,
PatientID: patientModule.patientId,
PatientName: patientModule.patientName,
PatientBirthDate: '',
PatientAge: patientStudyModule.patientAge,
PatientSex: patientDemographicModule.patientSex,
PatientWeight: patientStudyModule.patientWeight,
StudyDate: generalStudyModule.studyDate,
StudyTime: generalStudyModule.studyTime,
StudyID: 'ToDo',
AccessionNumber: generalStudyModule.accessionNumber,
};
}
function getReferencedFrameOfReferenceSequence(toolData, metadataProvider, dataset) {
const { referencedImageId: imageId, FrameOfReferenceUID } = toolData.metadata;
const instance = metadataProvider.get('instance', imageId);
const { SeriesInstanceUID } = instance;
const { ReferencedSeriesSequence } = dataset;
return [
{
FrameOfReferenceUID,
RTReferencedStudySequence: [
{
ReferencedSOPClassUID: dataset.SOPClassUID,
ReferencedSOPInstanceUID: dataset.SOPInstanceUID,
RTReferencedSeriesSequence: [
{
SeriesInstanceUID,
ContourImageSequence: [...ReferencedSeriesSequence[0].ReferencedInstanceSequence],
},
],
},
],
},
];
}
function getReferencedSeriesSequence(toolData, index, metadataProvider) {
// grab imageId from toolData
const { referencedImageId: imageId } = toolData.metadata;
const instance = metadataProvider.get('instance', imageId);
const { SeriesInstanceUID, StudyInstanceUID } = instance;
const ReferencedSeriesSequence = [];
if (SeriesInstanceUID) {
const series = DicomMetadataStore.getSeries(StudyInstanceUID, SeriesInstanceUID);
const ReferencedSeries = {
SeriesInstanceUID,
ReferencedInstanceSequence: [],
};
series.instances.forEach(instance => {
const { SOPInstanceUID, SOPClassUID } = instance;
ReferencedSeries.ReferencedInstanceSequence.push({
ReferencedSOPClassUID: SOPClassUID,
ReferencedSOPInstanceUID: SOPInstanceUID,
});
});
ReferencedSeriesSequence.push(ReferencedSeries);
}
return ReferencedSeriesSequence;
}
function getRTSeriesModule(imageId, metadataProvider) {
return {
SeriesInstanceUID: DicomMetaDictionary.uid(), // generate a new series instance uid
SeriesNumber: '99', // Todo:: what should be the series number?
};
}
function getStructureSetModule(toolData, index, metadataProvider) {
const { FrameOfReferenceUID } = toolData.metadata;
return {
ROINumber: index + 1,
ROIName: `Todo: name ${index + 1}`,
ROIDescription: `Todo: description ${index + 1}`,
ROIGenerationAlgorithm: 'Todo: algorithm',
ReferencedFrameOfReferenceUID: FrameOfReferenceUID,
};
}
function getRTROIObservationsSequence(toolData, index, metadataProvider) {
return {
ObservationNumber: index + 1,
ReferencedROINumber: index + 1,
RTROIInterpretedType: 'Todo: type',
ROIInterpreter: 'Todo: interpreter',
};
}
extensions/tmtv/src/utils/dicomRTAnnotationExport/RTStructureSet/dicomRTAnnotationExport.js
+7 -3
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@@ -1,12 +1,16 @@
import RTSSReport from './RTSSReport';
import dcmjs from 'dcmjs';
import { classes } from '@ohif/core';
import { classes, DicomMetadataStore } from '@ohif/core';
import { adaptersSEG } from '@cornerstonejs/adapters';
const { datasetToBlob } = dcmjs.data;
const metadataProvider = classes.MetadataProvider;
export default function dicomRTAnnotationExport(annotations) {
const dataset = RTSSReport.generateReport(annotations, metadataProvider);
const dataset = adaptersSEG.Cornerstone3D.RTStruct.RTSS.generateRTSSFromAnnotations(
annotations,
metadataProvider,
DicomMetadataStore
);
const reportBlob = datasetToBlob(dataset);
//Create a URL for the binary.
extensions/tmtv/src/utils/dicomRTAnnotationExport/RTStructureSet/measurements/AnnotationToPointData.js
-53
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@@ -1,53 +0,0 @@
import RectangleROIStartEndThreshold from './RectangleROIStartEndThreshold';
function validateAnnotation(annotation) {
if (!annotation?.data) {
throw new Error('Tool data is empty');
}
if (!annotation.metadata || annotation.metadata.referenceImageId) {
throw new Error('Tool data is not associated with any imageId');
}
}
class AnnotationToPointData {
constructor() {}
static convert(annotation, index, metadataProvider) {
validateAnnotation(annotation);
const { toolName } = annotation.metadata;
const toolClass = AnnotationToPointData.TOOL_NAMES[toolName];
if (!toolClass) {
throw new Error(`Unknown tool type: ${toolName}, cannot convert to RTSSReport`);
}
// Each toolData should become a list of contours, ContourSequence
// contains a list of contours with their pointData, their geometry
// type and their length.
const ContourSequence = toolClass.getContourSequence(annotation, metadataProvider);
// Todo: random rgb color for now, options should be passed in
const color = [
Math.floor(Math.random() * 255),
Math.floor(Math.random() * 255),
Math.floor(Math.random() * 255),
];
return {
ReferencedROINumber: index + 1,
ROIDisplayColor: color,
ContourSequence,
};
}
static register(toolClass) {
AnnotationToPointData.TOOL_NAMES[toolClass.toolName] = toolClass;
}
}
AnnotationToPointData.TOOL_NAMES = {};
AnnotationToPointData.register(RectangleROIStartEndThreshold);
export default AnnotationToPointData;
extensions/tmtv/src/utils/dicomRTAnnotationExport/RTStructureSet/measurements/RectangleROIStartEndThreshold.js
-51
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@@ -1,51 +0,0 @@
// comment
class RectangleROIStartEndThreshold {
constructor() {}
static getContourSequence(toolData, metadataProvider) {
const { data } = toolData;
const { projectionPoints, projectionPointsImageIds } = data.cachedStats;
return projectionPoints.map((point, index) => {
const ContourData = getPointData(point);
const ContourImageSequence = getContourImageSequence(
projectionPointsImageIds[index],
metadataProvider
);
return {
NumberOfContourPoints: ContourData.length / 3,
ContourImageSequence,
ContourGeometricType: 'CLOSED_PLANAR',
ContourData,
};
});
}
}
RectangleROIStartEndThreshold.toolName = 'RectangleROIStartEndThreshold';
function getPointData(points) {
// Since this is a closed contour, the order of the points is important.
// re-order the points to be in the correct order clockwise
// Spread to make sure Float32Arrays are converted to arrays
const orderedPoints = [...points[0], ...points[1], ...points[3], ...points[2]];
const pointsArray = orderedPoints.flat();
// reduce the precision of the points to 2 decimal places
const pointsArrayWithPrecision = pointsArray.map(point => {
return point.toFixed(2);
});
return pointsArrayWithPrecision;
}
function getContourImageSequence(imageId, metadataProvider) {
const sopCommon = metadataProvider.get('sopCommonModule', imageId);
return {
ReferencedSOPClassUID: sopCommon.sopClassUID,
ReferencedSOPInstanceUID: sopCommon.sopInstanceUID,
};
}
export default RectangleROIStartEndThreshold;