Begin adding DICOM Segmentation handling to Cornerstone plugin via dcmjs

This commit is contained in:
Erik Ziegler 2019-01-30 16:51:54 +00:00
parent b93a677ef3
commit bf8f737fec
15 changed files with 346 additions and 83 deletions

8
.gitmodules vendored
View File

@ -6,10 +6,4 @@
url = git@github.com:OHIF/react-viewerbase.git
[submodule "Packages-react/react-cornerstone-viewport"]
path = Packages-react/react-cornerstone-viewport
url = git@github.com:cornerstonejs/react-cornerstone-viewport.git
[submodule "Packages-react/plugins/VTKPlugin"]
path = Packages-react/plugins/VTKPlugin
url = git@github.com:OHIF/VTKPlugin.git
[submodule "Packages-react/plugins/OpenLayersPlugin"]
path = Packages-react/plugins/OpenLayersPlugin
url = git@github.com:OHIF/OpenLayersPlugin.git
url = git@github.com:cornerstonejs/react-cornerstone-viewport.git

View File

@ -1,4 +1,4 @@
import React, { Component } from "react";
import React, { Component } from 'react';
import dicomParser from 'dicom-parser';
import TypedArrayProp from './TypedArrayProp';
@ -14,11 +14,10 @@ class DicomPDFViewport extends Component {
};
static propTypes = {
byteArray: TypedArrayProp.uint8,
byteArray: TypedArrayProp.uint8
};
renderPDF = (dataSet) => {
debugger;
renderPDF = dataSet => {
const sopClassUid = dataSet.string('x00080016');
if (sopClassUid !== SOP_CLASS_UIDS.ENCAPSULATED_PDF) {
@ -29,15 +28,15 @@ class DicomPDFViewport extends Component {
const offset = fileTag.dataOffset;
const remainder = offset + fileTag.length;
const pdfByteArray = dataSet.byteArray.slice(offset, remainder);
const PDF = new Blob([pdfByteArray], {type: 'application/pdf'});
const PDF = new Blob([pdfByteArray], { type: 'application/pdf' });
const fileURL = URL.createObjectURL(PDF);
this.setState({
fileURL
});
}
};
parseByteArray = (byteArray) => {
parseByteArray = byteArray => {
const options = {
untilTag: ''
};
@ -46,14 +45,14 @@ class DicomPDFViewport extends Component {
try {
dataSet = dicomParser.parseDicom(byteArray, options);
} catch(error) {
} catch (error) {
this.setState({
error
});
}
return dataSet
}
return dataSet;
};
componentDidMount() {
const dataSet = this.parseByteArray(this.props.byteArray);
@ -63,18 +62,22 @@ class DicomPDFViewport extends Component {
render() {
return (
<div className={'DicomPDFViewport'} style={{width: '100%', height: '100%'}}>
{this.state.fileURL &&
<object data={this.state.fileURL} type="application/pdf" width="100%" height="100%">
</object>
}
{this.state.error &&
<h2>{JSON.stringify(this.state.error)}</h2>
}
<div
className={'DicomPDFViewport'}
style={{ width: '100%', height: '100%' }}
>
{this.state.fileURL && (
<object
data={this.state.fileURL}
type="application/pdf"
width="100%"
height="100%"
/>
)}
{this.state.error && <h2>{JSON.stringify(this.state.error)}</h2>}
</div>
);
}
}
export default DicomPDFViewport;

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@ -1,5 +1,5 @@
import React, { Component } from "react";
import PropTypes from "prop-types";
import React, { Component } from 'react';
import PropTypes from 'prop-types';
import OHIF from 'ohif-core';
import OHIFComponentPlugin from './OHIFComponentPlugin.js';
import DicomPDFViewport from './DicomPDFViewport';
@ -10,13 +10,13 @@ class OHIFDicomPDFViewport extends Component {
static propTypes = {
studies: PropTypes.object,
displaySet: PropTypes.object,
viewportIndex: PropTypes.number,
viewportIndex: PropTypes.number
};
state = {
byteArray: null,
error: null
}
};
static id = 'DicomPDFViewportPDF';
@ -41,8 +41,9 @@ class OHIFDicomPDFViewport extends Component {
error
});
throw new Error(error);
});
throw new Error(error);
}
);
}
retrieveDicomData(studyInstanceUid, seriesInstanceUid, sopInstanceUid, wadoRoot, wadoUri, authorizationHeaders) {
@ -63,10 +64,10 @@ class OHIFDicomPDFViewport extends Component {
return (
<OHIFComponentPlugin {...pluginProps}>
{this.state.byteArray && <DicomPDFViewport byteArray={this.state.byteArray}/>}
{this.state.error &&
<h2>{JSON.stringify(this.state.error)}</h2>
}
{this.state.byteArray && (
<DicomPDFViewport byteArray={this.state.byteArray} />
)}
{this.state.error && <h2>{JSON.stringify(this.state.error)}</h2>}
</OHIFComponentPlugin>
);
}

@ -1 +1 @@
Subproject commit ede7e30e012174a0307f10e00b70e22bdfbe1b46
Subproject commit 8850a092a0b860bc9d423fcc49512567251fc47b

View File

@ -3,3 +3,5 @@ dist
node_modules
yarn.lock
yarn-error.log
src/sha.js
src/version.js

View File

@ -97,9 +97,9 @@
"classnames": "^2.2.6",
"cornerstone-core": "^2.2.8",
"cornerstone-math": "^0.1.8",
"cornerstone-tools": "3.0.0-b.1512",
"cornerstone-tools": "3.0.0-b.1679",
"cornerstone-wado-image-loader": "^2.2.3",
"dcmjs": "^0.3.0",
"dcmjs": "^0.3.2",
"dicom-parser": "^1.8.3",
"dicomweb-client": "^0.4.1",
"hammerjs": "^2.0.8",
@ -110,13 +110,13 @@
"oidc-client": "^1.6.1",
"prop-types": "^15.6.2",
"react-bootstrap-modal": "^4.2.0",
"react-cornerstone-viewport": "^0.1.8",
"react-cornerstone-viewport": "^0.1.9",
"react-dnd": "^7.0.2",
"react-dnd-html5-backend": "^7.0.2",
"react-redux": "^6.0.0",
"react-router": "^4.3.1",
"react-router-dom": "^4.3.1",
"react-viewerbase": "^0.2.1",
"react-viewerbase": "^0.2.4",
"redux": "^4.0.1",
"redux-oidc": "^3.1.0"
}

View File

@ -95,6 +95,13 @@ const defaultButtons = [
svgUrl: `${Icons}#icon-tools-measure-target`,
active: false
},
{
command: 'Brush',
type: 'tool',
text: 'Brush',
iconClasses: 'fa fa-circle',
active: false
},
{
command: 'reset',
type: 'command',

View File

@ -1,29 +1,48 @@
import React, { Component } from "react";
import PropTypes from "prop-types";
import React, { Component } from 'react';
import PropTypes from 'prop-types';
import OHIF from 'ohif-core';
import ConnectedCornerstoneViewport from './ConnectedCornerstoneViewport';
import OHIFComponentPlugin from '../OHIFComponentPlugin.js';
import cornerstoneTools from "cornerstone-tools";
import cornerstone from "cornerstone-core";
import cornerstoneTools from 'cornerstone-tools';
import cornerstone from 'cornerstone-core';
import './config';
import handleSegmentationStorage from './handleSegmentationStorage.js';
const { StackManager } = OHIF.utils;
// Create the synchronizer used to update reference lines
OHIF.viewer.updateImageSynchronizer = new cornerstoneTools.Synchronizer('cornerstonenewimage', cornerstoneTools.updateImageSynchronizer);
OHIF.viewer.updateImageSynchronizer = new cornerstoneTools.Synchronizer(
'cornerstonenewimage',
cornerstoneTools.updateImageSynchronizer
);
// Metadata configuration
const metadataProvider = new OHIF.cornerstone.MetadataProvider();
cornerstone.metaData.addProvider(metadataProvider.provider.bind(metadataProvider));
cornerstone.metaData.addProvider(
metadataProvider.provider.bind(metadataProvider)
);
StackManager.setMetadataProvider(metadataProvider);
const SOP_CLASSES = {
SEGMENTATION_STORAGE: '1.2.840.10008.5.1.4.1.1.66.4'
};
const specialCaseHandlers = {};
specialCaseHandlers[
SOP_CLASSES.SEGMENTATION_STORAGE
] = handleSegmentationStorage;
class OHIFCornerstoneViewportPlugin extends Component {
state = {
viewportData: null
};
static propTypes = {
studies: PropTypes.object,
displaySet: PropTypes.object,
viewportIndex: PropTypes.number,
viewportIndex: PropTypes.number
};
static id = 'CornerstoneViewportPlugin';
@ -39,9 +58,11 @@ class OHIFCornerstoneViewportPlugin extends Component {
static getCornerstoneStack(studies, studyInstanceUid, displaySetInstanceUid) {
// Create shortcut to displaySet
const study = studies.find(study => study.studyInstanceUid === studyInstanceUid);
const study = studies.find(
study => study.studyInstanceUid === studyInstanceUid
);
const displaySet = study.displaySets.find((set) => {
const displaySet = study.displaySets.find(set => {
return set.displaySetInstanceUid === displaySetInstanceUid;
});
@ -49,37 +70,104 @@ class OHIFCornerstoneViewportPlugin extends Component {
return StackManager.findOrCreateStack(study, displaySet);
}
static getPluginViewportData = (studies, studyInstanceUid, displaySetInstanceUid) => {
const currentStack = OHIFCornerstoneViewportPlugin.getCornerstoneStack(studies, studyInstanceUid, displaySetInstanceUid);
static getPluginViewportData = (
studies,
studyInstanceUid,
displaySetInstanceUid
) => {
const currentStack = OHIFCornerstoneViewportPlugin.getCornerstoneStack(
studies,
studyInstanceUid,
displaySetInstanceUid
);
// Clone the stack here so we don't mutate it later
const stack = Object.assign({}, currentStack);
stack.currentImageIdIndex = 0;
return stack;
};
getViewportData = async (
studies,
studyInstanceUid,
displaySetInstanceUid,
sopClassUid
) => {
let viewportData;
switch (sopClassUid) {
case SOP_CLASSES.SEGMENTATION_STORAGE:
const specialCaseHandler =
specialCaseHandlers[SOP_CLASSES.SEGMENTATION_STORAGE];
viewportData = await specialCaseHandler(
studies,
studyInstanceUid,
displaySetInstanceUid
);
break;
default:
const stack = OHIFCornerstoneViewportPlugin.getPluginViewportData(
studies,
studyInstanceUid,
displaySetInstanceUid
);
viewportData = {
studyInstanceUid,
displaySetInstanceUid,
stack
};
break;
}
return viewportData;
};
componentDidMount() {
const { studies, displaySet } = this.props.viewportData;
const {
studyInstanceUid,
displaySetInstanceUid,
sopClassUids
} = displaySet;
if (sopClassUids.length > 1) {
console.warn(
'More than one SOPClassUid in the same series is not yet supported.'
);
}
const sopClassUid = sopClassUids[0];
this.getViewportData(
studies,
studyInstanceUid,
displaySetInstanceUid,
sopClassUid
).then(viewportData => {
this.setState({
viewportData
});
});
}
render() {
const { viewportIndex } = this.props;
const { studies, displaySet } = this.props.viewportData;
const { studyInstanceUid, displaySetInstanceUid } = displaySet;
const stack = OHIFCornerstoneViewportPlugin.getPluginViewportData(studies, studyInstanceUid, displaySetInstanceUid);
const viewportData = {
studyInstanceUid,
displaySetInstanceUid,
stack
};
const { id, init, destroy } = OHIFCornerstoneViewportPlugin;
const pluginProps = { id, init, destroy };
return (
<OHIFComponentPlugin {...pluginProps}>
<ConnectedCornerstoneViewport viewportData={viewportData} viewportIndex={viewportIndex}/>
{this.state.viewportData && (
<ConnectedCornerstoneViewport
viewportData={this.state.viewportData}
viewportIndex={this.props.viewportIndex}
/>
)}
</OHIFComponentPlugin>
);
}
}
export default OHIFCornerstoneViewportPlugin;

View File

@ -0,0 +1,151 @@
import OHIF from 'ohif-core';
import cornerstoneTools from 'cornerstone-tools';
import * as dcmjs from 'dcmjs';
const { StackManager } = OHIF.utils;
function getDisplaySet(studies, studyInstanceUid, displaySetInstanceUid) {
const study = studies.find(
study => study.studyInstanceUid === studyInstanceUid
);
const displaySet = study.displaySets.find(set => {
return set.displaySetInstanceUid === displaySetInstanceUid;
});
return displaySet;
}
function getDisplaySetsBySeries(studies, studyInstanceUid, seriesInstanceUid) {
const study = studies.find(
study => study.studyInstanceUid === studyInstanceUid
);
return study.displaySets.filter(set => {
return set.seriesInstanceUid === seriesInstanceUid;
});
}
function getCornerstoneStack(studies, studyInstanceUid, displaySetInstanceUid) {
const study = studies.find(
study => study.studyInstanceUid === studyInstanceUid
);
// Create shortcut to displaySet
const displaySet = getDisplaySet(
studies,
studyInstanceUid,
displaySetInstanceUid
);
// Get stack from Stack Manager
const stack = StackManager.findOrCreateStack(study, displaySet);
// Clone the stack here so we don't mutate it later
const stackClone = Object.assign({}, stack);
stackClone.currentImageIdIndex = 0;
return stackClone;
}
function parseSeg(arrayBuffer, imageIds) {
return dcmjs.adapters.Cornerstone.Segmentation.readToolState(
imageIds,
arrayBuffer
);
}
function addSegMetadataToCornerstoneToolState(
segMetadata,
toolState,
displaySetInstanceUid
) {
cornerstoneTools.globalImageIdSpecificToolStateManager.restoreToolState(
toolState
);
const brushModule = cornerstoneTools.store.modules.brush;
for (let i = 0; i < segMetadata.length; i++) {
brushModule.setters.metadata(displaySetInstanceUid, i, segMetadata[i]);
}
}
function retrieveDicomData(wadoUri) {
// TODO: Authorization header depends on the server. If we ever have multiple servers
// we will need to figure out how / when to pass this information in.
return fetch(wadoUri, {
headers: OHIF.DICOMWeb.getAuthorizationHeader()
}).then(response => response.arrayBuffer());
}
async function handleSegmentationStorage(
studies,
studyInstanceUid,
displaySetInstanceUid
) {
const study = studies.find(
study => study.studyInstanceUid === studyInstanceUid
);
const displaySet = getDisplaySet(
studies,
studyInstanceUid,
displaySetInstanceUid
);
const segWadoUri = displaySet.images[0].getData().wadouri;
const arrayBuffer = await retrieveDicomData(segWadoUri);
const dicomData = dcmjs.data.DicomMessage.readFile(arrayBuffer);
const dataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(
dicomData.dict
);
dataset._meta = dcmjs.data.DicomMetaDictionary.namifyDataset(dicomData.meta);
const seriesInstanceUid = dataset.ReferencedSeriesSequence.SeriesInstanceUID;
const displaySets = getDisplaySetsBySeries(
studies,
studyInstanceUid,
seriesInstanceUid
);
if (displaySets.length > 1) {
console.warn(
'More than one display set with the same seriesInstanceUid. This is not supported yet...'
);
}
const referenceDisplaySet = displaySets[0];
const imageIds = referenceDisplaySet.images
.reverse()
.map(image => image.getImageId());
const results = parseSeg(arrayBuffer, imageIds);
if (!results) {
throw new Error('Fractional segmentations are not supported');
}
const { segMetadata, toolState } = results;
segMetadata.seriesInstanceUid = seriesInstanceUid;
addSegMetadataToCornerstoneToolState(
segMetadata,
toolState,
displaySetInstanceUid
);
const cachedStack = StackManager.findOrCreateStack(
study,
referenceDisplaySet
);
const stack = Object.assign({}, cachedStack);
stack.currentImageIdIndex = 0;
return {
studyInstanceUid,
displaySetInstanceUid,
stack
};
}
export default handleSegmentationStorage;

View File

@ -108,6 +108,24 @@ props.oidc = [
]
}; */
/*props.servers = {
"dicomWeb": [
{
"name": "DCM4CHEE",
"wadoUriRoot": "http://localhost:8080/dcm4chee-arc/aets/DCM4CHEE/wado",
"qidoRoot": "http://localhost:8080/dcm4chee-arc/aets/DCM4CHEE/rs",
"wadoRoot": "http://localhost:8080/dcm4chee-arc/aets/DCM4CHEE/rs",
"qidoSupportsIncludeField": true,
"imageRendering": "wadors",
"thumbnailRendering": "wadors",
"requestOptions": {
"requestFromBrowser": true,
"auth": "admin:admin"
}
}
]
};*/
/*
UI settings
Plugins

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@ -1 +1 @@
export default '298749821742198987421'
export default 'f06e629c2f2256576e7de5bda48124b3a808ab9b';

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@ -892,7 +892,7 @@
dependencies:
regenerator-runtime "^0.12.0"
"@babel/runtime@^7.0.0", "@babel/runtime@^7.1.2", "@babel/runtime@^7.2.0":
"@babel/runtime@^7.0.0", "@babel/runtime@^7.1.2", "@babel/runtime@^7.2.0", "@babel/runtime@^7.3.1":
version "7.3.1"
resolved "https://registry.yarnpkg.com/@babel/runtime/-/runtime-7.3.1.tgz#574b03e8e8a9898eaf4a872a92ea20b7846f6f2a"
integrity sha512-7jGW8ppV0ant637pIqAcFfQDDH1orEPGJb8aXfUozuCU3QqX7rX4DA8iwrbPrR1hcH0FTTHz47yQnk+bl5xHQA==
@ -1856,7 +1856,7 @@ babel-plugin-transform-react-remove-prop-types@0.4.20:
resolved "https://registry.yarnpkg.com/babel-plugin-transform-react-remove-prop-types/-/babel-plugin-transform-react-remove-prop-types-0.4.20.tgz#688bdea1e27ea0023775dea817fa2d3f8df8802b"
integrity sha512-bWQ8e7LsgdFpyHU/RabjDAjVhL7KLAJXEt0nb0LANFje8YAGA8RlZv88a72aCswOxELWULkYuJqfFoKgs58Tng==
babel-polyfill@>=6.9.1, babel-polyfill@^6.26.0:
babel-polyfill@>=6.9.1:
version "6.26.0"
resolved "https://registry.yarnpkg.com/babel-polyfill/-/babel-polyfill-6.26.0.tgz#379937abc67d7895970adc621f284cd966cf2153"
integrity sha1-N5k3q8Z9eJWXCtxiHyhM2WbPIVM=
@ -2969,10 +2969,10 @@ cornerstone-math@^0.1.6, cornerstone-math@^0.1.7, cornerstone-math@^0.1.8:
resolved "https://registry.yarnpkg.com/cornerstone-math/-/cornerstone-math-0.1.8.tgz#68ab1f9e4fdcd7c5cb23a0d2eb4263f9f894f1c5"
integrity sha512-x7NEQHBtVG7j1yeyj/aRoKTpXv1Vh2/H9zNLMyqYJDtJkNng8C4Q8M3CgZ1qer0Yr7eVq2x+Ynmj6kfOm5jXKw==
cornerstone-tools@3.0.0-b.1512:
version "3.0.0-b.1512"
resolved "https://registry.yarnpkg.com/cornerstone-tools/-/cornerstone-tools-3.0.0-b.1512.tgz#64e60709b7b638c08d201313a5748aa6f5145337"
integrity sha512-+lpoPJnTTkGq61XZzrNfAVhYJprBYqFZc++D0TgVUUOfAlXn5I016+cabfRQ/K65ecTfd8RitFK/LrIBUE7D2Q==
cornerstone-tools@3.0.0-b.1679:
version "3.0.0-b.1679"
resolved "https://registry.yarnpkg.com/cornerstone-tools/-/cornerstone-tools-3.0.0-b.1679.tgz#e97c4ddc5b229faeb625682412a7cfd77b9fc70c"
integrity sha512-t69w5lgS/eZQXdyEfLixWuGZbpspNmyhvu8af9cYQDQ445tchvBtSSD6h1u+5m1gXZvV4LxwBqD8rwZTpMzH9Q==
dependencies:
"@babel/runtime" "7.1.2"
cornerstone-math "^0.1.7"
@ -3404,13 +3404,14 @@ date-now@^0.1.4:
resolved "https://registry.yarnpkg.com/date-now/-/date-now-0.1.4.tgz#eaf439fd4d4848ad74e5cc7dbef200672b9e345b"
integrity sha1-6vQ5/U1ISK105cx9vvIAZyueNFs=
dcmjs@^0.3.0:
version "0.3.0"
resolved "https://registry.yarnpkg.com/dcmjs/-/dcmjs-0.3.0.tgz#d065a65b3df14d6028542760de6143f0acdc2ed0"
integrity sha512-k6La/q+ROPjoAPQCWIWd49XUGUzolLG6qJhEMdSAhYEa4WP6CLyjIgL1Ul2NqM7Vxyd74ydHi537AWxOtdSxmA==
dcmjs@^0.3.2:
version "0.3.2"
resolved "https://registry.yarnpkg.com/dcmjs/-/dcmjs-0.3.2.tgz#18bdcccd0083e01269c588fbbb019e44897b952e"
integrity sha512-6tA4A+22c6AK+5wqtU3cS1lNtEPEvndgeRdZfbuMJNC+OiPQFhPmK8+TrNF13ca9QWHUCyRT9mAfAMuio6GnEg==
dependencies:
babel-polyfill "^6.26.0"
babel-runtime "^6.26.0"
"@babel/polyfill" "^7.2.5"
"@babel/runtime" "^7.3.1"
loglevel "^1.6.1"
debug@*, debug@^4.0.0, debug@^4.0.1, debug@^4.1.0:
version "4.1.1"
@ -7362,7 +7363,7 @@ log-update@^2.3.0:
cli-cursor "^2.0.0"
wrap-ansi "^3.0.1"
loglevel@^1.4.1:
loglevel@^1.4.1, loglevel@^1.6.1:
version "1.6.1"
resolved "https://registry.yarnpkg.com/loglevel/-/loglevel-1.6.1.tgz#e0fc95133b6ef276cdc8887cdaf24aa6f156f8fa"
integrity sha1-4PyVEztu8nbNyIh82vJKpvFW+Po=
@ -10066,7 +10067,7 @@ react-bootstrap-modal@^4.2.0:
react-overlays "^0.8.0"
react-transition-group "^2.0.0"
react-cornerstone-viewport@^0.1.8:
react-cornerstone-viewport@^0.1.9:
version "0.1.9"
resolved "https://registry.yarnpkg.com/react-cornerstone-viewport/-/react-cornerstone-viewport-0.1.9.tgz#28cbf2ec3b13976f271e7cc30e6386c5d97e854c"
integrity sha512-demadfvFX9uOp+lV0wV6Pom6g3Dagdt/97m3mTAN7o236mCDVBn1SBHBkVIjOeKkkPmXIV2q0dlHuINsnlK4TA==
@ -10264,7 +10265,7 @@ react-transition-group@^2.0.0, react-transition-group@^2.2.0:
prop-types "^15.6.2"
react-lifecycles-compat "^3.0.4"
react-viewerbase@^0.2.1:
react-viewerbase@^0.2.4:
version "0.2.4"
resolved "https://registry.yarnpkg.com/react-viewerbase/-/react-viewerbase-0.2.4.tgz#c247cb39cfbf0db803475a8f35f7463a5a61e397"
integrity sha512-U50z7lCbgL4tAt/ZbkzAGAi5Q/RcPoT12XuRWy+jlq6oH+GtoQtLU7pA4DQkFAk73ebBYH6yL+2r296i8zDGTg==

@ -1 +0,0 @@
Subproject commit 2405290b1e5e80d13bae5358625463605eb83930

@ -1 +0,0 @@
Subproject commit dd8b3a7edddc5bc97af49bd4ceeb89c5f7d56dfb

@ -1 +1 @@
Subproject commit 1a66caa34d5a841ef414437a53093f7d22be840c
Subproject commit 59d177cb0e705441f58ce57d37a8122011522868