feat: crosshair mpr

This commit is contained in:
mozzie 2023-12-21 12:49:50 +08:00
parent c73fdb6a6d
commit ae02206a60
22 changed files with 1174 additions and 926 deletions

View File

@ -23,7 +23,6 @@
"js-cookie": "3.0.5",
"three": "0.156.1",
"path-to-regexp": "6.2.1",
"cornerstone-core": "2.6.1",
"dicom-parser": "1.8.21",
"@msgpack/msgpack": "3.0.0-beta2",
"pako": "2.1.0",
@ -32,8 +31,9 @@
"@cornerstonejs/core": "1.41.0",
"dcmjs": "0.30.0",
"dicomweb-client": "0.10.3",
"@cornerstonejs/tools": "3.0.2",
"@cornerstonejs/streaming-image-volume-loader": "1.41.0"
"@cornerstonejs/tools": "1.41.0",
"@cornerstonejs/streaming-image-volume-loader": "1.41.0",
"@cornerstonejs/calculate-suv": "1.1.0"
},
"devDependencies": {
"@babel/core": "^7.21.8",

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@ -0,0 +1,143 @@
[
"5.0.37",
[
"apple a14",
"14",
"a14 apple",
0,
[
[
2704,
1756,
120
]
]
],
[
"apple m1",
"1",
"apple m1",
0,
[
[
2880,
1800,
198
]
]
],
[
"apple m1 max",
"1",
"apple m1 max",
0,
[
[
3456,
2234,
556
]
]
],
[
"apple m1 pro",
"1",
"apple m1 pro",
0,
[
[
3024,
1964,
342
]
]
],
[
"apple m1 ultra",
"1",
"apple m1 ultra",
0,
[
[
5120,
2880,
437
]
]
],
[
"apple m2",
"2",
"apple m2",
0,
[
[
2880,
1800,
60
],
[
2940,
1912,
209
]
]
],
[
"apple m2 max",
"2",
"apple m2 max",
0,
[
[
3456,
2234,
120
]
]
],
[
"apple m2 pro",
"2",
"apple m2 pro",
0,
[
[
3024,
1964,
120
],
[
5120,
2880,
60
]
]
],
[
"apple m2 ultra",
"2",
"apple m2 ultra",
0,
[
[
5120,
2880,
60
]
]
],
[
"apple paravirtual device",
"",
"apple device paravirtual",
0,
[
[
1024,
768,
30
]
]
]
]

View File

@ -31,5 +31,5 @@ export const proxyMap: TProxyMap = {
target: "http://localhost:5000/",
changeOrigin: true,
pathRewrite: { "^/py": "" },
},
}
};

View File

@ -20,7 +20,7 @@ interface Configuration extends WebpackConfiguration {
devServer?: WebpackDevServerConfiguration;
}
const host = "127.0.0.1";
const host = "0.0.0.0";
const port = 9000;
// 合并公共配置,并添加开发环境配置

View File

@ -5,6 +5,9 @@ import cornerstoneDICOMImageLoader from "@cornerstonejs/dicom-image-loader";
import { getPixelSpacingInformation } from "./getPixelSpacingInformation";
import { convertMultiframeImageIds } from "./convertMultiframeImageIds";
import { removeInvalidTags } from "./removeInvalidTags";
import getPTImageIdInstanceMetadata from "./getPTImageIdInstanceMetadata";
import { calculateSUVScalingFactors } from "@cornerstonejs/calculate-suv";
import ptScalingMetaDataProvider from "./ptScalingMetaDataProvider";
const { DicomMetaDictionary } = dcmjs.data;
const { calibratedPixelSpacingMetadataProvider } = utilities;
@ -44,11 +47,22 @@ export const createImageIdsAndCacheMetaData = async (
console.log("modality", modality);
let imageIds = instances.map((instanceMetaData: any) => {
const seriesInstanceUID = instanceMetaData[SERIES_INSTANCE_UID].Value[0];
const sopInstanceUIDToUse =
const SeriesInstanceUID = instanceMetaData[SERIES_INSTANCE_UID].Value[0];
const SOPInstanceUIDToUse =
options.SOPInstanceUID || instanceMetaData[SOP_INSTANCE_UID].Value[0];
const imageId = `wadors:${options.wadoRsRoot}/studies/${options.StudyInstanceUID}/series/${seriesInstanceUID}/instances/${sopInstanceUIDToUse}/frames/1`;
const prefix = "wadors:";
const imageId =
prefix +
options.wadoRsRoot +
"/studies/" +
options.StudyInstanceUID +
"/series/" +
SeriesInstanceUID +
"/instances/" +
SOPInstanceUIDToUse +
"/frames/1";
cornerstoneDICOMImageLoader.wadors.metaDataManager.add(
imageId,
@ -62,6 +76,7 @@ export const createImageIdsAndCacheMetaData = async (
imageIds.forEach((imageId) => {
let instanceMetaData =
cornerstoneDICOMImageLoader.wadors.metaDataManager.get(imageId);
instanceMetaData = removeInvalidTags(instanceMetaData);
if (instanceMetaData) {
@ -81,8 +96,44 @@ export const createImageIdsAndCacheMetaData = async (
}
});
if (modality === "PT") {
const InstanceMetadataArray: any = [];
imageIds.forEach((imageId) => {
const instanceMetadata = getPTImageIdInstanceMetadata(imageId);
// TODO: Temporary fix because static-wado is producing a string, not an array of values
// (or maybe dcmjs isn't parsing it correctly?)
// It's showing up like 'DECY\\ATTN\\SCAT\\DTIM\\RAN\\RADL\\DCAL\\SLSENS\\NORM'
// but calculate-suv expects ['DECY', 'ATTN', ...]
if (typeof instanceMetadata.CorrectedImage === "string") {
instanceMetadata.CorrectedImage =
instanceMetadata.CorrectedImage.split("\\");
}
if (instanceMetadata) {
InstanceMetadataArray.push(instanceMetadata);
}
});
if (InstanceMetadataArray.length) {
try {
const suvScalingFactors = calculateSUVScalingFactors(
InstanceMetadataArray
);
InstanceMetadataArray.forEach((instanceMetadata, index) => {
ptScalingMetaDataProvider.addInstance(
imageIds[index],
suvScalingFactors[index]
);
});
} catch (error) {
console.log(error);
}
}
}
return imageIds;
} catch (error) {
console.log(error);
throw new Error("PACS 中数据不存在");
}
};

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@ -0,0 +1,211 @@
import { metaData } from "@cornerstonejs/core";
import type { InstanceMetadata } from "@cornerstonejs/calculate-suv";
export default function getPTImageIdInstanceMetadata(
imageId: string
): InstanceMetadata {
const petSequenceModule = metaData.get("petIsotopeModule", imageId);
const generalSeriesModule = metaData.get("generalSeriesModule", imageId);
const patientStudyModule = metaData.get("patientStudyModule", imageId);
const ptSeriesModule = metaData.get("petSeriesModule", imageId);
const ptImageModule = metaData.get("petImageModule", imageId);
if (!petSequenceModule) {
throw new Error("petSequenceModule metadata is required");
}
const radiopharmaceuticalInfo = petSequenceModule.radiopharmaceuticalInfo;
const { seriesDate, seriesTime, acquisitionDate, acquisitionTime } =
generalSeriesModule;
const { patientWeight } = patientStudyModule;
const { correctedImage, units, decayCorrection } = ptSeriesModule;
if (
seriesDate === undefined ||
seriesTime === undefined ||
patientWeight === undefined ||
acquisitionDate === undefined ||
acquisitionTime === undefined ||
correctedImage === undefined ||
units === undefined ||
decayCorrection === undefined ||
radiopharmaceuticalInfo.radionuclideTotalDose === undefined ||
radiopharmaceuticalInfo.radionuclideHalfLife === undefined ||
(radiopharmaceuticalInfo.radiopharmaceuticalStartDateTime === undefined &&
seriesDate === undefined &&
radiopharmaceuticalInfo.radiopharmaceuticalStartTime === undefined)
//
) {
throw new Error("required metadata are missing");
}
const instanceMetadata: InstanceMetadata = {
CorrectedImage: correctedImage,
Units: units,
RadionuclideHalfLife: radiopharmaceuticalInfo.radionuclideHalfLife,
RadionuclideTotalDose: radiopharmaceuticalInfo.radionuclideTotalDose,
DecayCorrection: decayCorrection,
PatientWeight: patientWeight,
SeriesDate: seriesDate,
SeriesTime: seriesTime,
AcquisitionDate: acquisitionDate,
AcquisitionTime: acquisitionTime,
};
if (
radiopharmaceuticalInfo.radiopharmaceuticalStartDateTime &&
radiopharmaceuticalInfo.radiopharmaceuticalStartDateTime !== undefined &&
typeof radiopharmaceuticalInfo.radiopharmaceuticalStartDateTime === "string"
) {
instanceMetadata.RadiopharmaceuticalStartDateTime =
radiopharmaceuticalInfo.radiopharmaceuticalStartDateTime;
}
if (
radiopharmaceuticalInfo.radiopharmaceuticalStartDateTime &&
radiopharmaceuticalInfo.radiopharmaceuticalStartDateTime !== undefined &&
typeof radiopharmaceuticalInfo.radiopharmaceuticalStartDateTime !== "string"
) {
const dateString = convertInterfaceDateToString(
radiopharmaceuticalInfo.radiopharmaceuticalStartDateTime
);
instanceMetadata.RadiopharmaceuticalStartDateTime = dateString;
}
if (
instanceMetadata.AcquisitionDate &&
instanceMetadata.AcquisitionDate !== undefined &&
typeof instanceMetadata.AcquisitionDate !== "string"
) {
const dateString = convertInterfaceDateToString(
instanceMetadata.AcquisitionDate
);
instanceMetadata.AcquisitionDate = dateString;
}
if (
instanceMetadata.SeriesDate &&
instanceMetadata.SeriesDate !== undefined &&
typeof instanceMetadata.SeriesDate !== "string"
) {
const dateString = convertInterfaceDateToString(
instanceMetadata.SeriesDate
);
instanceMetadata.SeriesDate = dateString;
}
if (
radiopharmaceuticalInfo.radiopharmaceuticalStartTime &&
radiopharmaceuticalInfo.radiopharmaceuticalStartTime !== undefined &&
typeof radiopharmaceuticalInfo.radiopharmaceuticalStartTime === "string"
) {
instanceMetadata.RadiopharmaceuticalStartTime =
radiopharmaceuticalInfo.radiopharmaceuticalStartTime;
}
if (
radiopharmaceuticalInfo.radiopharmaceuticalStartTime &&
radiopharmaceuticalInfo.radiopharmaceuticalStartTime !== undefined &&
typeof radiopharmaceuticalInfo.radiopharmaceuticalStartTime !== "string"
) {
const timeString = convertInterfaceTimeToString(
radiopharmaceuticalInfo.radiopharmaceuticalStartTime
);
instanceMetadata.RadiopharmaceuticalStartTime = timeString;
}
if (
instanceMetadata.AcquisitionTime &&
instanceMetadata.AcquisitionTime !== undefined &&
typeof instanceMetadata.AcquisitionTime !== "string"
) {
const timeString = convertInterfaceTimeToString(
instanceMetadata.AcquisitionTime
);
instanceMetadata.AcquisitionTime = timeString;
}
if (
instanceMetadata.SeriesTime &&
instanceMetadata.SeriesTime !== undefined &&
typeof instanceMetadata.SeriesTime !== "string"
) {
const timeString = convertInterfaceTimeToString(
instanceMetadata.SeriesTime
);
instanceMetadata.SeriesTime = timeString;
}
if (
ptImageModule.frameReferenceTime &&
ptImageModule.frameReferenceTime !== undefined
) {
instanceMetadata.FrameReferenceTime = ptImageModule.frameReferenceTime;
}
if (
ptImageModule.actualFrameDuration &&
ptImageModule.actualFrameDuration !== undefined
) {
instanceMetadata.ActualFrameDuration = ptImageModule.actualFrameDuration;
}
if (
patientStudyModule.patientSex &&
patientStudyModule.patientSex !== undefined
) {
instanceMetadata.PatientSex = patientStudyModule.patientSex;
}
if (
patientStudyModule.patientSize &&
patientStudyModule.patientSize !== undefined
) {
instanceMetadata.PatientSize = patientStudyModule.patientSize;
}
// Todo: add private tags
// if (
// dicomMetaData['70531000'] ||
// dicomMetaData['70531000'] !== undefined ||
// dicomMetaData['70531009'] ||
// dicomMetaData['70531009'] !== undefined
// ) {
// const philipsPETPrivateGroup: PhilipsPETPrivateGroup = {
// SUVScaleFactor: dicomMetaData['70531000'],
// ActivityConcentrationScaleFactor: dicomMetaData['70531009'],
// };
// instanceMetadata.PhilipsPETPrivateGroup = philipsPETPrivateGroup;
// }
// if (dicomMetaData['0009100d'] && dicomMetaData['0009100d'] !== undefined) {
// instanceMetadata.GEPrivatePostInjectionDateTime = dicomMetaData['0009100d'];
// }
return instanceMetadata;
}
function convertInterfaceTimeToString(time): string {
const hours = `${time.hours || "00"}`.padStart(2, "0");
const minutes = `${time.minutes || "00"}`.padStart(2, "0");
const seconds = `${time.seconds || "00"}`.padStart(2, "0");
const fractionalSeconds = `${time.fractionalSeconds || "000000"}`.padEnd(
6,
"0"
);
const timeString = `${hours}${minutes}${seconds}.${fractionalSeconds}`;
return timeString;
}
function convertInterfaceDateToString(date): string {
const month = `${date.month}`.padStart(2, "0");
const day = `${date.day}`.padStart(2, "0");
const dateString = `${date.year}${month}${day}`;
return dateString;
}
export { getPTImageIdInstanceMetadata };

View File

@ -2,10 +2,19 @@ import dicomParser from "dicom-parser";
import * as cornerstone from "@cornerstonejs/core";
import cornerstoneDICOMImageLoader from "@cornerstonejs/dicom-image-loader";
window.cornerstone = cornerstone;
export const initCornerstoneDICOMImageLoader = () => {
const { preferSizeOverAccuracy, useNorm16Texture } =
cornerstone.getConfiguration().rendering;
cornerstone.setConfiguration({
detectGPUConfig: {
benchmarksURL: "http://localhost:9000",
},
rendering: cornerstone.getConfiguration().rendering,
});
cornerstoneDICOMImageLoader.external.cornerstone = cornerstone;
cornerstoneDICOMImageLoader.external.dicomParser = dicomParser;
cornerstoneDICOMImageLoader.configure({
@ -16,8 +25,14 @@ export const initCornerstoneDICOMImageLoader = () => {
},
});
let maxWebWorkers = 1;
if (navigator.hardwareConcurrency) {
maxWebWorkers = Math.min(navigator.hardwareConcurrency, 7);
}
const config = {
maxWebWorkers: navigator.hardwareConcurrency ?? 7,
maxWebWorkers,
startWebWorkersOnDemand: false,
taskConfiguration: {
decodeTask: {

View File

@ -1,18 +1,17 @@
import { useEffect, useRef } from "react";
import initDemo from "./util/initDemo.js";
import {
Enums,
RenderingEngine,
Types,
Enums,
setVolumesForViewports,
volumeLoader,
getRenderingEngine,
} from "@cornerstonejs/core";
import { createImageIdsAndCacheMetaData } from "../CornerstoneDicomLoader/createImageIdsAndCacheMetaData";
import { initCornerstone } from "../CornerstoneDicomLoader/init";
import { useEffect, useRef } from "react";
import * as cornerstoneTools from "@cornerstonejs/tools";
import { PublicViewportInput } from "@cornerstonejs/core/dist/types/types";
import { setCtTransferFunctionForVolumeActor } from "./setCtTransferFunctionForVolumeActor";
interface CorsshairProps {
children?: JSX.Element;
}
import createImageIdsAndCacheMetaData from "./util/createImageIdsAndCacheMetaData";
import { PublicViewportInput } from "@cornerstonejs/core/dist/types/types/IViewport.js";
import setCtTransferFunctionForVolumeActor from "./util/setCtTransferFunctionForVolumeActor";
const {
ToolGroupManager,
@ -21,126 +20,185 @@ const {
StackScrollMouseWheelTool,
} = cornerstoneTools;
const toolGroupId = "MY_TOOLGROUP_ID";
const { ViewportType } = Enums;
interface CrosshairMprProps {
children?: JSX.Element;
}
const viewportId1 = "CT_AXIAL";
const viewportId2 = "CT_SAGITTAL";
const viewportId3 = "CT_CORONAL";
const toolGroupId = "group";
const viewportColors = {
[viewportId1]: "rgb(200, 0, 0)",
[viewportId2]: "rgb(200, 200, 0)",
[viewportId3]: "rgb(0, 200, 0)",
};
const viewportReferenceLineControllable = [
viewportId1,
viewportId2,
viewportId3,
];
const viewportReferenceLineDraggableRotatable = [
viewportId1,
viewportId2,
viewportId3,
];
const viewportReferenceLineSlabThicknessControlsOn = [
viewportId1,
viewportId2,
viewportId3,
];
// 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 renderingEngineId = "myRenderingEngine";
const viewportA = "CT_AXIAL";
const viewportB = "CT_SAGITTAL";
const viewportC = "CT_CORONAL";
function getReferenceLineColor(viewportId) {
return viewportColors[viewportId];
}
const viewportColors = {
[viewportA]: "rgb(200, 0, 0)",
[viewportB]: "rgb(200, 200, 0)",
[viewportC]: "rgb(0, 200, 0)",
};
function getReferenceLineControllable(viewportId) {
const index = viewportReferenceLineControllable.indexOf(viewportId);
return index !== -1;
}
const { ViewportType } = Enums;
function getReferenceLineDraggableRotatable(viewportId) {
const index = viewportReferenceLineDraggableRotatable.indexOf(viewportId);
return index !== -1;
}
const StudyInstanceUID =
"1.2.840.113564.345049290535.9692.637552042156233117.433089";
const SeriesInstanceUID =
"1.3.12.2.1107.5.1.4.76315.30000021042706150001900118311";
function getReferenceLineSlabThicknessControlsOn(viewportId) {
const index =
viewportReferenceLineSlabThicknessControlsOn.indexOf(viewportId);
return index !== -1;
}
export const Corsshair = (props: CorsshairProps) => {
const viewportA = useRef(null);
const viewportB = useRef(null);
const viewportC = useRef(null);
export const CrosshairMpr = (props: CrosshairMprProps) => {
const viewportId1Ref = useRef(null);
const viewportId2Ref = useRef(null);
const viewportId3Ref = useRef(null);
cornerstoneTools.addTool(StackScrollMouseWheelTool);
cornerstoneTools.addTool(CrosshairsTool);
const run = async () => {
await initCornerstone();
// Get Cornerstone imageIds and fetch metadata into RAM
initDemo();
// Get Cornerstone imageIds for the source data and fetch metadata into RAM
const imageIds = await createImageIdsAndCacheMetaData({
StudyInstanceUID,
SeriesInstanceUID,
StudyInstanceUID:
"1.2.840.113564.345049290535.9692.637552042156233117.433089",
SeriesInstanceUID:
"1.3.12.2.1107.5.1.4.76315.30000021042706150001900118311",
wadoRsRoot: "/dicom-web",
});
// Define a volume in memory
const volume = await volumeLoader.createAndCacheVolume(volumeId, {
imageIds,
});
console.log(volume)
// Instantiate a rendering engine
// const renderingEngine = new RenderingEngine(renderingEngineId);
const renderingEngineId = "myRenderingEngine";
const renderingEngine = new RenderingEngine(renderingEngineId);
// if (viewportA.current && viewportB.current && viewportC.current) {
// // Create the viewports
// const viewportInputArray: PublicViewportInput[] = [
// {
// viewportId: viewportA.current,
// type: ViewportType.ORTHOGRAPHIC,
// element: viewportA.current,
// defaultOptions: {
// orientation: Enums.OrientationAxis.AXIAL,
// background: [0, 0, 0],
// },
// },
// {
// viewportId: viewportB.current,
// type: ViewportType.ORTHOGRAPHIC,
// element: viewportB.current,
// defaultOptions: {
// orientation: Enums.OrientationAxis.SAGITTAL,
// background: [0, 0, 0],
// },
// },
// {
// viewportId: viewportC.current,
// type: ViewportType.ORTHOGRAPHIC,
// element: viewportC.current,
// defaultOptions: {
// orientation: Enums.OrientationAxis.CORONAL,
// background: [0, 0, 0],
// },
// },
// ];
// Create the viewports
const viewportInputArray: PublicViewportInput[] = [
{
viewportId: viewportId1,
type: ViewportType.ORTHOGRAPHIC,
element: viewportId1Ref.current!,
defaultOptions: {
orientation: Enums.OrientationAxis.AXIAL,
background: [0, 0, 0],
},
},
{
viewportId: viewportId2,
type: ViewportType.ORTHOGRAPHIC,
element: viewportId2Ref.current!,
defaultOptions: {
orientation: Enums.OrientationAxis.SAGITTAL,
background: [0, 0, 0],
},
},
{
viewportId: viewportId3,
type: ViewportType.ORTHOGRAPHIC,
element: viewportId3Ref.current!,
defaultOptions: {
orientation: Enums.OrientationAxis.CORONAL,
background: [0, 0, 0],
},
},
];
// renderingEngine.setViewports(viewportInputArray);
renderingEngine.setViewports(viewportInputArray);
// volume.load();
// Set the volume to load
volume.load();
// await setVolumesForViewports(
// renderingEngine,
// [
// {
// volumeId,
// callback: () => setCtTransferFunctionForVolumeActor,
// },
// ],
// [viewportA.current!, viewportB.current!, viewportC.current!]
// );
// Set volumes on the viewports
await setVolumesForViewports(
renderingEngine,
[
{
volumeId,
callback: setCtTransferFunctionForVolumeActor,
},
],
[viewportId1, viewportId2, viewportId3]
);
// // Render the image
// renderingEngine.renderViewports([
// viewportA.current!,
// viewportB.current!,
// viewportC.current!,
// ]);
// }
// Define tool groups to add the segmentation display tool to
const toolGroup = ToolGroupManager.createToolGroup(toolGroupId);
// For the crosshairs to operate, the viewports must currently be
// added ahead of setting the tool active. This will be improved in the future.
toolGroup.addViewport(viewportId1, renderingEngineId);
toolGroup.addViewport(viewportId2, renderingEngineId);
toolGroup.addViewport(viewportId3, renderingEngineId);
// Manipulation Tools
toolGroup.addTool(StackScrollMouseWheelTool.toolName);
// Add Crosshairs tool and configure it to link the three viewports
// These viewports could use different tool groups. See the PET-CT example
// for a more complicated used case.
toolGroup.addTool(CrosshairsTool.toolName, {
getReferenceLineColor,
getReferenceLineControllable,
getReferenceLineDraggableRotatable,
getReferenceLineSlabThicknessControlsOn,
});
toolGroup.setToolActive(CrosshairsTool.toolName, {
bindings: [{ mouseButton: 1 }],
});
// As the Stack Scroll mouse wheel is a tool using the `mouseWheelCallback`
// hook instead of mouse buttons, it does not need to assign any mouse button.
toolGroup.setToolActive(StackScrollMouseWheelTool.toolName);
renderingEngine.renderViewports([viewportId1, viewportId2, viewportId3]);
};
useEffect(() => {
run();
}, []);
return (
<div
style={{
display: "flex",
justifyContent: "space-evenly",
gap: 20,
height: 300,
}}
>
<div ref={viewportA}></div>
<div ref={viewportB}></div>
<div ref={viewportC}></div>
<div>
<div style={{ display: "flex", gap: 20 }}>
<div style={{ width: 300, height: 300 }} ref={viewportId1Ref}></div>
<div style={{ width: 300, height: 300 }} ref={viewportId2Ref}></div>
<div style={{ width: 300, height: 300 }} ref={viewportId3Ref}></div>
</div>
</div>
);
};

View File

@ -0,0 +1,65 @@
import { metaData } from '@cornerstonejs/core';
import cornerstoneDICOMImageLoader from '@cornerstonejs/dicom-image-loader';
/**
* preloads imageIds metadata in memory
**/
async function prefetchMetadataInformation(imageIdsToPrefetch) {
for (let i = 0; i < imageIdsToPrefetch.length; i++) {
await cornerstoneDICOMImageLoader.wadouri.loadImage(imageIdsToPrefetch[i])
.promise;
}
}
function getFrameInformation(imageId) {
if (imageId.includes('wadors:')) {
const frameIndex = imageId.indexOf('/frames/');
const imageIdFrameless =
frameIndex > 0 ? imageId.slice(0, frameIndex + 8) : imageId;
return {
frameIndex,
imageIdFrameless,
};
} else {
const frameIndex = imageId.indexOf('&frame=');
let imageIdFrameless =
frameIndex > 0 ? imageId.slice(0, frameIndex + 7) : imageId;
if (!imageIdFrameless.includes('&frame=')) {
imageIdFrameless = imageIdFrameless + '&frame=';
}
return {
frameIndex,
imageIdFrameless,
};
}
}
/**
* Receives a list of imageids possibly referring to multiframe dicom images
* and returns a list of imageid where each imageid referes to one frame.
* For each imageId representing a multiframe image with n frames,
* it will create n new imageids, one for each frame, and returns the new list of imageids
* If a particular imageid no refer to a mutiframe image data, it will be just copied into the new list
* @returns new list of imageids where each imageid represents a frame
*/
function convertMultiframeImageIds(imageIds) {
const newImageIds = [];
imageIds.forEach((imageId) => {
const { imageIdFrameless } = getFrameInformation(imageId);
const instanceMetaData = metaData.get('multiframeModule', imageId);
if (
instanceMetaData &&
instanceMetaData.NumberOfFrames &&
instanceMetaData.NumberOfFrames > 1
) {
const NumberOfFrames = instanceMetaData.NumberOfFrames;
for (let i = 0; i < NumberOfFrames; i++) {
const newImageId = imageIdFrameless + (i + 1);
newImageIds.push(newImageId);
}
} else {
newImageIds.push(imageId);
}
});
return newImageIds;
}
export { convertMultiframeImageIds, prefetchMetadataInformation };

View File

@ -0,0 +1,101 @@
import { api } from 'dicomweb-client';
import dcmjs from 'dcmjs';
import { utilities } from '@cornerstonejs/core';
import cornerstoneDICOMImageLoader from '@cornerstonejs/dicom-image-loader';
import getPixelSpacingInformation from './getPixelSpacingInformation';
import { convertMultiframeImageIds } from './convertMultiframeImageIds';
import removeInvalidTags from './removeInvalidTags';
const { DicomMetaDictionary } = dcmjs.data;
const { calibratedPixelSpacingMetadataProvider } = utilities;
/**
/**
* Uses dicomweb-client to fetch metadata of a study, cache it in cornerstone,
* and return a list of imageIds for the frames.
*
* Uses the app config to choose which study to fetch, and which
* dicom-web server to fetch it from.
*
* @returns {string[]} An array of imageIds for instances in the study.
*/
export default async function createImageIdsAndCacheMetaData({
StudyInstanceUID,
SeriesInstanceUID,
SOPInstanceUID = null,
wadoRsRoot,
client = null,
}) {
const SOP_INSTANCE_UID = '00080018';
const SERIES_INSTANCE_UID = '0020000E';
const MODALITY = '00080060';
const studySearchOptions = {
studyInstanceUID: StudyInstanceUID,
seriesInstanceUID: SeriesInstanceUID,
};
client = client || new api.DICOMwebClient({ url: wadoRsRoot });
let instances = await client.retrieveSeriesMetadata(studySearchOptions);
// if sop instance is provided we should filter the instances to only include the one we want
if (SOPInstanceUID) {
instances = instances.filter((instance) => {
return instance[SOP_INSTANCE_UID].Value[0] === SOPInstanceUID;
});
}
const modality = instances[0][MODALITY].Value[0];
let imageIds = instances.map((instanceMetaData) => {
const SeriesInstanceUID = instanceMetaData[SERIES_INSTANCE_UID].Value[0];
const SOPInstanceUIDToUse =
SOPInstanceUID || instanceMetaData[SOP_INSTANCE_UID].Value[0];
const prefix = 'wadors:';
const imageId =
prefix +
wadoRsRoot +
'/studies/' +
StudyInstanceUID +
'/series/' +
SeriesInstanceUID +
'/instances/' +
SOPInstanceUIDToUse +
'/frames/1';
cornerstoneDICOMImageLoader.wadors.metaDataManager.add(
imageId,
instanceMetaData
);
return imageId;
});
// if the image ids represent multiframe information, creates a new list with one image id per frame
// if not multiframe data available, just returns the same list given
imageIds = convertMultiframeImageIds(imageIds);
imageIds.forEach((imageId) => {
let instanceMetaData =
cornerstoneDICOMImageLoader.wadors.metaDataManager.get(imageId);
// It was using JSON.parse(JSON.stringify(...)) before but it is 8x slower
instanceMetaData = removeInvalidTags(instanceMetaData);
if (instanceMetaData) {
// Add calibrated pixel spacing
const metadata = DicomMetaDictionary.naturalizeDataset(instanceMetaData);
const pixelSpacing = getPixelSpacingInformation(metadata);
if (pixelSpacing) {
calibratedPixelSpacingMetadataProvider.add(imageId, {
rowPixelSpacing: parseFloat(pixelSpacing[0]),
columnPixelSpacing: parseFloat(pixelSpacing[1]),
});
}
}
});
return imageIds;
}

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@ -0,0 +1,136 @@
// See https://github.com/OHIF/Viewers/blob/94a9067fe3d291d30e25a1bda5913511388edea2/platform/core/src/utils/metadataProvider/getPixelSpacingInformation.js
export default function getPixelSpacingInformation(instance) {
// See http://gdcm.sourceforge.net/wiki/index.php/Imager_Pixel_Spacing
// TODO: Add Ultrasound region spacing
// TODO: Add manual calibration
// TODO: Use ENUMS from dcmjs
const projectionRadiographSOPClassUIDs = [
'1.2.840.10008.5.1.4.1.1.1', // CR Image Storage
'1.2.840.10008.5.1.4.1.1.1.1', // Digital X-Ray Image Storage for Presentation
'1.2.840.10008.5.1.4.1.1.1.1.1', // Digital X-Ray Image Storage for Processing
'1.2.840.10008.5.1.4.1.1.1.2', // Digital Mammography X-Ray Image Storage for Presentation
'1.2.840.10008.5.1.4.1.1.1.2.1', // Digital Mammography X-Ray Image Storage for Processing
'1.2.840.10008.5.1.4.1.1.1.3', // Digital Intra oral X-Ray Image Storage for Presentation
'1.2.840.10008.5.1.4.1.1.1.3.1', // Digital Intra oral X-Ray Image Storage for Processing
'1.2.840.10008.5.1.4.1.1.12.1', // X-Ray Angiographic Image Storage
'1.2.840.10008.5.1.4.1.1.12.1.1', // Enhanced XA Image Storage
'1.2.840.10008.5.1.4.1.1.12.2', // X-Ray Radiofluoroscopic Image Storage
'1.2.840.10008.5.1.4.1.1.12.2.1', // Enhanced XRF Image Storage
'1.2.840.10008.5.1.4.1.1.12.3', // X-Ray Angiographic Bi-plane Image Storage Retired
];
const {
PixelSpacing,
ImagerPixelSpacing,
SOPClassUID,
PixelSpacingCalibrationType,
PixelSpacingCalibrationDescription,
EstimatedRadiographicMagnificationFactor,
SequenceOfUltrasoundRegions,
} = instance;
const isProjection = projectionRadiographSOPClassUIDs.includes(SOPClassUID);
const TYPES = {
NOT_APPLICABLE: 'NOT_APPLICABLE',
UNKNOWN: 'UNKNOWN',
CALIBRATED: 'CALIBRATED',
DETECTOR: 'DETECTOR',
};
if (!isProjection) {
return PixelSpacing;
}
if (isProjection && !ImagerPixelSpacing) {
// If only Pixel Spacing is present, and this is a projection radiograph,
// PixelSpacing should be used, but the user should be informed that
// what it means is unknown
return {
PixelSpacing,
type: TYPES.UNKNOWN,
isProjection,
};
} else if (
PixelSpacing &&
ImagerPixelSpacing &&
PixelSpacing === ImagerPixelSpacing
) {
// If Imager Pixel Spacing and Pixel Spacing are present and they have the same values,
// then the user should be informed that the measurements are at the detector plane
return {
PixelSpacing,
type: TYPES.DETECTOR,
isProjection,
};
} else if (
PixelSpacing &&
ImagerPixelSpacing &&
PixelSpacing !== ImagerPixelSpacing
) {
// If Imager Pixel Spacing and Pixel Spacing are present and they have different values,
// then the user should be informed that these are "calibrated"
// (in some unknown manner if Pixel Spacing Calibration Type and/or
// Pixel Spacing Calibration Description are absent)
return {
PixelSpacing,
type: TYPES.CALIBRATED,
isProjection,
PixelSpacingCalibrationType,
PixelSpacingCalibrationDescription,
};
} else if (!PixelSpacing && ImagerPixelSpacing) {
let CorrectedImagerPixelSpacing = ImagerPixelSpacing;
if (EstimatedRadiographicMagnificationFactor) {
// Note that in IHE Mammo profile compliant displays, the value of Imager Pixel Spacing is required to be corrected by
// Estimated Radiographic Magnification Factor and the user informed of that.
// TODO: should this correction be done before all of this logic?
CorrectedImagerPixelSpacing = ImagerPixelSpacing.map(
(pixelSpacing) =>
pixelSpacing / EstimatedRadiographicMagnificationFactor
);
} else {
console.warn(
'EstimatedRadiographicMagnificationFactor was not present. Unable to correct ImagerPixelSpacing.'
);
}
return {
PixelSpacing: CorrectedImagerPixelSpacing,
isProjection,
};
} else if (
SequenceOfUltrasoundRegions &&
typeof SequenceOfUltrasoundRegions === 'object'
) {
const { PhysicalDeltaX, PhysicalDeltaY } = SequenceOfUltrasoundRegions;
const USPixelSpacing = [PhysicalDeltaX * 10, PhysicalDeltaY * 10];
return {
PixelSpacing: USPixelSpacing,
};
} else if (
SequenceOfUltrasoundRegions &&
Array.isArray(SequenceOfUltrasoundRegions) &&
SequenceOfUltrasoundRegions.length > 1
) {
console.warn(
'Sequence of Ultrasound Regions > one entry. This is not yet implemented, all measurements will be shown in pixels.'
);
} else if (isProjection === false && !ImagerPixelSpacing) {
// If only Pixel Spacing is present, and this is not a projection radiograph,
// we can stop here
return {
PixelSpacing,
type: TYPES.NOT_APPLICABLE,
isProjection,
};
}
console.warn(
'Unknown combination of PixelSpacing and ImagerPixelSpacing identified. Unable to determine spacing.'
);
}

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@ -0,0 +1,47 @@
import dicomParser from 'dicom-parser';
import * as cornerstone from '@cornerstonejs/core';
import * as cornerstoneTools from '@cornerstonejs/tools';
import cornerstoneDICOMImageLoader from '@cornerstonejs/dicom-image-loader';
window.cornerstone = cornerstone;
window.cornerstoneTools = cornerstoneTools;
const { preferSizeOverAccuracy, useNorm16Texture } =
cornerstone.getConfiguration().rendering;
export default function initCornerstoneDICOMImageLoader() {
// TODO: 此处非常的蛇皮
cornerstone.setUseSharedArrayBuffer(false)
cornerstone.setConfiguration({
detectGPUConfig: {
benchmarksURL: "http://localhost:9000"
}
})
cornerstoneDICOMImageLoader.external.cornerstone = cornerstone;
cornerstoneDICOMImageLoader.external.dicomParser = dicomParser;
cornerstoneDICOMImageLoader.configure({
useWebWorkers: true,
decodeConfig: {
convertFloatPixelDataToInt: false,
use16BitDataType: preferSizeOverAccuracy || useNorm16Texture,
},
});
let maxWebWorkers = 1;
if (navigator.hardwareConcurrency) {
maxWebWorkers = Math.min(navigator.hardwareConcurrency, 7);
}
var config = {
maxWebWorkers,
startWebWorkersOnDemand: false,
taskConfiguration: {
decodeTask: {
initializeCodecsOnStartup: false,
strict: false,
},
},
};
cornerstoneDICOMImageLoader.webWorkerManager.initialize(config);
}

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@ -0,0 +1,13 @@
import initProviders from './initProviders.js';
import initCornerstoneDICOMImageLoader from './initCornerstoneDICOMImageLoader';
import initVolumeLoader from './initVolumeLoader';
import { init as csRenderInit } from '@cornerstonejs/core';
import { init as csToolsInit } from '@cornerstonejs/tools';
export default async function initDemo() {
initProviders();
initCornerstoneDICOMImageLoader();
initVolumeLoader();
await csRenderInit();
await csToolsInit();
}

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@ -0,0 +1,17 @@
import * as cornerstone from '@cornerstonejs/core';
import ptScalingMetaDataProvider from './ptScalingMetaDataProvider';
const { calibratedPixelSpacingMetadataProvider } = cornerstone.utilities;
export default function initProviders() {
cornerstone.metaData.addProvider(
ptScalingMetaDataProvider.get.bind(ptScalingMetaDataProvider),
10000
);
cornerstone.metaData.addProvider(
calibratedPixelSpacingMetadataProvider.get.bind(
calibratedPixelSpacingMetadataProvider
),
11000
);
}

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@ -0,0 +1,19 @@
import { volumeLoader } from '@cornerstonejs/core';
import {
cornerstoneStreamingImageVolumeLoader,
cornerstoneStreamingDynamicImageVolumeLoader,
} from '@cornerstonejs/streaming-image-volume-loader';
export default function initVolumeLoader() {
volumeLoader.registerUnknownVolumeLoader(
cornerstoneStreamingImageVolumeLoader
);
volumeLoader.registerVolumeLoader(
'cornerstoneStreamingImageVolume',
cornerstoneStreamingImageVolumeLoader
);
volumeLoader.registerVolumeLoader(
'cornerstoneStreamingDynamicImageVolume',
cornerstoneStreamingDynamicImageVolumeLoader
);
}

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@ -0,0 +1,17 @@
import { utilities as csUtils } from '@cornerstonejs/core';
const scalingPerImageId = {};
function addInstance(imageId, scalingMetaData) {
const imageURI = csUtils.imageIdToURI(imageId);
scalingPerImageId[imageURI] = scalingMetaData;
}
function get(type, imageId) {
if (type === 'scalingModule') {
const imageURI = csUtils.imageIdToURI(imageId);
return scalingPerImageId[imageURI];
}
}
export default { addInstance, get };

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@ -0,0 +1,33 @@
/**
* Remove invalid tags from a metadata and return a new object.
*
* At this time it is only removing tags that has `null` or `undefined` values
* which is our main goal because that breaks when `naturalizeDataset(...)` is
* called.
*
* Validating the tag id using regex like /^[a-fA-F0-9]{8}$/ make it run
* +50% slower and looping through all characteres (split+every+Set or simple
* FOR+Set) double the time it takes to run. It is currently taking +12ms/1k
* images on average which can change depending on the machine.
*
* @param srcMetadata - source metadata
* @returns new metadata object without invalid tags
*/
function removeInvalidTags(srcMetadata) {
// Object.create(null) make it ~9% faster
const dstMetadata = Object.create(null);
const tagIds = Object.keys(srcMetadata);
let tagValue;
tagIds.forEach((tagId) => {
tagValue = srcMetadata[tagId];
if (tagValue !== undefined && tagValue !== null) {
dstMetadata[tagId] = tagValue;
}
});
return dstMetadata;
}
export { removeInvalidTags as default, removeInvalidTags };

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@ -1,20 +1,16 @@
import { VolumeActor } from "@cornerstonejs/core/dist/types/types";
const windowWidth = 400;
const windowCenter = 40;
const lower = windowCenter - windowWidth / 2.0;
const upper = windowCenter + windowWidth / 2.0;
export const ctVoiRange = { lower, upper };
const ctVoiRange = { lower, upper };
export const setCtTransferFunctionForVolumeActor = ({
volumeActor,
}: {
volumeActor: VolumeActor;
}) => {
export default function setCtTransferFunctionForVolumeActor({ volumeActor }) {
volumeActor
.getProperty()
.getRGBTransferFunction(0)
.setMappingRange(lower, upper);
};
}
export { ctVoiRange };

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@ -1,13 +1,13 @@
import { useEffect, useRef } from "react";
import { Enums, RenderingEngine, cache } from "@cornerstonejs/core";
import { initCornerstone } from "../CornerstoneDicomLoader/initCornerstoneDicomImageLoader";
import { initCornerstone } from "../CornerstoneDicomLoader/init";
import { createImageIdsAndCacheMetaData } from "../CornerstoneDicomLoader/createImageIdsAndCacheMetaData";
import {
IStackViewport,
PublicViewportInput,
} from "@cornerstonejs/core/dist/types/types";
interface VolumeViewerProps {
interface StackViewerProps {
children?: JSX.Element;
}
@ -21,7 +21,7 @@ const StudyInstanceUID =
const SeriesInstanceUID =
"1.3.12.2.1107.5.1.4.76315.30000021042706150001900118311";
export const VolumeViewer = (props: VolumeViewerProps) => {
export const StackViewer = (props: StackViewerProps) => {
const dicomRef = useRef(null);
const run = async () => {

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@ -1,7 +1,7 @@
import { Corsshair } from "./Crosshair";
import { CrosshairMpr } from "./Crosshair";
import { DiffViewer } from "./DiffViewer";
import { MprViewer } from "./MprViewer";
import { VolumeViewer } from "./VolumeViewer";
import { StackViewer } from "./StackViewer";
interface RootViewerProps {
children?: JSX.Element;
@ -10,7 +10,8 @@ interface RootViewerProps {
export const RootViewer = (props: RootViewerProps) => {
return (
<div>
<Corsshair />
<CrosshairMpr />
{/* <StackViewer /> */}
</div>
);
};

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