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feat: visualize overlapping segments in cornerstone (#2185)

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* feat: visualize overlapping segments

load multiple labelMaps (splitted by dcmjs because overlapping) in a segmentations [IDC2164]

Dynamically update active labelmap [IDC2164]

Co-authored-by: Davide Punzo <punzodavide@hotmail.it>
Co-authored-by: Igor Octaviano <igoroctaviano@gmail.com>
This commit is contained in:
Davide Punzo 2020-12-10 11:04:27 +01:00 committed by GitHub
parent a7a5a359dc
commit 29fceacee9
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
15 changed files with 182 additions and 136 deletions
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2
extensions/cornerstone/package.json
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@ -36,7 +36,7 @@
"cornerstone-math": "^0.1.8",
"cornerstone-tools": "^4.20.1",
"cornerstone-wado-image-loader": "^3.1.0",
"dcmjs": "0.16.5",
"dcmjs": "0.17.0",
"dicom-parser": "^1.8.3",
"hammerjs": "^2.0.8",
"prop-types": "^15.6.2",

2
extensions/dicom-html/package.json
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@ -29,7 +29,7 @@
},
"peerDependencies": {
"@ohif/core": "^0.50.0",
"dcmjs": "0.16.5",
"dcmjs": "0.17.0",
"prop-types": "^15.6.2",
"react": "^16.8.6",
"react-dom": "^16.8.6"

2
extensions/dicom-rt/package.json
View File

@ -31,7 +31,7 @@
"@ohif/core": "^0.50.0",
"cornerstone-core": "^2.2.8",
"cornerstone-tools": "^4.20.1",
"dcmjs": "0.16.5",
"dcmjs": "0.17.0",
"gl-matrix": "^3.3.0",
"prop-types": "^15.6.2",
"react": "^16.8.6",

2
extensions/dicom-segmentation/package.json
View File

@ -31,7 +31,7 @@
"@ohif/core": "^0.50.0",
"cornerstone-core": "^2.2.8",
"cornerstone-tools": "^4.20.1",
"dcmjs": "0.16.5",
"dcmjs": "0.17.0",
"prop-types": "^15.6.2",
"react": "^16.8.6",
"react-dom": "^16.8.6"

32
extensions/dicom-segmentation/src/components/SegmentationPanel/SegmentationPanel.js
View File

@ -159,12 +159,12 @@ const SegmentationPanel = ({
const labelmapList = getLabelmapList(
brushStackState,
firstImageId,
activeViewport
activeViewport,
);
const segmentList = getSegmentList(
labelmap3D,
firstImageId,
brushStackState
brushStackState,
);
setState(state => ({
...state,
@ -292,10 +292,13 @@ const SegmentationPanel = ({
const sameSegment = state.selectedSegment === segmentNumber;
const setCurrentSelectedSegment = () => {
const activeViewport = viewports[activeIndex];
_setActiveSegment(
firstImageId,
segmentNumber,
labelmap3D.activeSegmentIndex
labelmap3D.activeSegmentIndex,
activeViewport
);
updateState('selectedSegment', sameSegment ? null : segmentNumber);
@ -640,7 +643,7 @@ const _getReferencedSegDisplaysets = (StudyInstanceUID, SeriesInstanceUID) => {
* @param {*} activeSegmentIndex
* @returns
*/
const _setActiveSegment = (firstImageId, segmentIndex, activeSegmentIndex) => {
const _setActiveSegment = (firstImageId, segmentIndex, activeSegmentIndex, activeViewport) => {
if (segmentIndex === activeSegmentIndex) {
log.info(`${activeSegmentIndex} is already the active segment`);
return;
@ -653,8 +656,27 @@ const _setActiveSegment = (firstImageId, segmentIndex, activeSegmentIndex) => {
brushStackState.labelmaps3D[brushStackState.activeLabelmapIndex];
labelmap3D.activeSegmentIndex = segmentIndex;
refreshViewports();
/**
* Activates the correct label map if clicked segment
* does not belong to the active labelmap
*/
const { StudyInstanceUID } = activeViewport;
const studyMetadata = studyMetadataManager.get(StudyInstanceUID);
const allDisplaySets = studyMetadata.getDisplaySets();
let newLabelmapIndex = brushStackState.activeLabelmapIndex;
allDisplaySets.forEach(displaySet => {
if (displaySet.labelmapSegments) {
Object.keys(displaySet.labelmapSegments).forEach(labelmapIndex => {
if (displaySet.labelmapSegments[labelmapIndex].includes(segmentIndex)) {
newLabelmapIndex = labelmapIndex;
}
});
}
});
brushStackState.activeLabelmapIndex = newLabelmapIndex;
refreshViewports();
return segmentIndex;
};

84
extensions/dicom-segmentation/src/getOHIFDicomSegSopClassHandler.js
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@ -1,6 +1,11 @@
import { MODULE_TYPES, utils } from '@ohif/core';
import loadSegmentation from './loadSegmentation';
import getSourceDisplaySet from './getSourceDisplaySet';
import OHIF from '@ohif/core';
import dcmjs from 'dcmjs';
const { DicomLoaderService } = OHIF.utils;
const { DicomMessage, DicomMetaDictionary } = dcmjs.data;
// TODO: Should probably use dcmjs for this
const SOP_CLASS_UIDS = {
@ -16,7 +21,7 @@ export default function getSopClassHandlerModule({ servicesManager }) {
id: 'OHIFDicomSegSopClassHandler',
type: MODULE_TYPES.SOP_CLASS_HANDLER,
sopClassUIDs,
getDisplaySetFromSeries: function(
getDisplaySetFromSeries: function (
series,
study,
dicomWebClient,
@ -46,7 +51,6 @@ export default function getSopClassHandlerModule({ servicesManager }) {
StudyInstanceUID,
FrameOfReferenceUID,
authorizationHeaders,
metadata,
isDerived: true,
referencedDisplaySetUID: null, // Assigned when loaded.
labelmapIndex: null, // Assigned when loaded.
@ -58,15 +62,85 @@ export default function getSopClassHandlerModule({ servicesManager }) {
metadata,
};
segDisplaySet.getSourceDisplaySet = function(studies) {
segDisplaySet.getSourceDisplaySet = function (studies) {
return getSourceDisplaySet(studies, segDisplaySet);
};
segDisplaySet.load = function(referencedDisplaySet, studies) {
return loadSegmentation(segDisplaySet, referencedDisplaySet, studies);
segDisplaySet.load = async function (referencedDisplaySet, studies) {
segDisplaySet.isLoaded = true;
const { StudyInstanceUID } = referencedDisplaySet;
const segArrayBuffer = await DicomLoaderService.findDicomDataPromise(
segDisplaySet,
studies
);
const dicomData = DicomMessage.readFile(segArrayBuffer);
const dataset = DicomMetaDictionary.naturalizeDataset(dicomData.dict);
dataset._meta = DicomMetaDictionary.namifyDataset(dicomData.meta);
const imageIds = _getImageIdsForDisplaySet(
studies,
StudyInstanceUID,
referencedDisplaySet.SeriesInstanceUID
);
return new Promise((resolve, reject) => {
let results;
try {
results = _parseSeg(segArrayBuffer, imageIds);
} catch (error) {
segDisplaySet.isLoaded = false;
segDisplaySet.loadError = true;
reject(error);
}
const { labelmapBufferArray, segMetadata, segmentsOnFrame, segmentsOnFrameArray } = results;
if (labelmapBufferArray.length > 1) {
for (let i = 0; i < labelmapBufferArray.length; ++i) {
loadSegmentation(imageIds, segDisplaySet, labelmapBufferArray[i], segMetadata, segmentsOnFrame, segmentsOnFrameArray[i]);
}
} else {
loadSegmentation(imageIds, segDisplaySet, labelmapBufferArray[0], segMetadata, segmentsOnFrame, []);
}
segDisplaySet.labelmapIndex = 0;
resolve();
});
};
return segDisplaySet;
},
};
}
function _parseSeg(arrayBuffer, imageIds) {
return dcmjs.adapters.Cornerstone.Segmentation.generateToolState(
imageIds,
arrayBuffer,
cornerstone.metaData
);
}
function _getImageIdsForDisplaySet(
studies,
StudyInstanceUID,
SeriesInstanceUID
) {
const study = studies.find(
study => study.StudyInstanceUID === StudyInstanceUID
);
const displaySets = study.displaySets.filter(displaySet => {
return displaySet.SeriesInstanceUID === SeriesInstanceUID;
});
if (displaySets.length > 1) {
console.warn(
'More than one display set with the same SeriesInstanceUID. This is not supported yet...'
);
// TODO -> We could make check the instance list and see if any match?
// Do we split the segmentation into two cornerstoneTools segmentations if there are images in both series?
// ^ Will that even happen?
}
const referencedDisplaySet = displaySets[0];
return referencedDisplaySet.images.map(image => image.getImageId());
}

157
extensions/dicom-segmentation/src/loadSegmentation.js
View File

@ -1,92 +1,62 @@
import OHIF from '@ohif/core';
import dcmjs from 'dcmjs';
import cornerstone from 'cornerstone-core';
import cornerstoneTools from 'cornerstone-tools';
const { DicomLoaderService } = OHIF.utils;
export default async function loadSegmentation(
imageIds,
segDisplaySet,
referencedDisplaySet,
studies
labelmapBuffer,
segMetadata,
segmentsOnFrame,
labelmapSegments
) {
const { StudyInstanceUID } = referencedDisplaySet;
const { setters } = cornerstoneTools.getModule('segmentation');
// Set here is loading is asynchronous.
// If this function throws its set back to false.
segDisplaySet.isLoaded = true;
// TODO: Could define a color LUT based on colors in the SEG.
const labelmapIndex = _getNextLabelmapIndex(imageIds[0]);
const colorLUTIndex = _makeColorLUTAndGetIndex(segMetadata);
const segArrayBuffer = await DicomLoaderService.findDicomDataPromise(
segDisplaySet,
studies
setters.labelmap3DByFirstImageId(
imageIds[0],
labelmapBuffer,
labelmapIndex,
segMetadata,
imageIds.length,
segmentsOnFrame,
colorLUTIndex
);
const dicomData = dcmjs.data.DicomMessage.readFile(segArrayBuffer);
const dataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(
dicomData.dict
);
if (!segDisplaySet.labelmapSegments) {
segDisplaySet.labelmapSegments = {};
}
dataset._meta = dcmjs.data.DicomMetaDictionary.namifyDataset(dicomData.meta);
/**
* Cache each labelmap segments.
* This data is used to determine the active label map when a given segment is activated/clicked.
*/
segDisplaySet.labelmapSegments[labelmapIndex] = labelmapSegments.length ? Array.from(new Set(labelmapSegments.filter(a => !!a).reduce((a, b) => a.concat(b)))) : [];
segDisplaySet.labelmapIndex = labelmapIndex;
const imageIds = _getImageIdsForDisplaySet(
studies,
StudyInstanceUID,
referencedDisplaySet.SeriesInstanceUID
);
return new Promise((resolve, reject) => {
let results;
try {
results = _parseSeg(segArrayBuffer, imageIds);
} catch (error) {
segDisplaySet.isLoaded = false;
segDisplaySet.loadError = true;
reject(error);
}
const { labelmapBuffer, segMetadata, segmentsOnFrame } = results;
const { setters } = cornerstoneTools.getModule('segmentation');
// TODO: Could define a color LUT based on colors in the SEG.
const labelmapIndex = _getNextLabelmapIndex(imageIds[0]);
const colorLUTIndex = _makeColorLUTAndGetIndex(segMetadata);
setters.labelmap3DByFirstImageId(
imageIds[0],
labelmapBuffer,
labelmapIndex,
segMetadata,
imageIds.length,
segmentsOnFrame,
colorLUTIndex
);
segDisplaySet.labelmapIndex = labelmapIndex;
/*
* TODO: Improve the way we notify parts of the app that depends on segs to be loaded.
*
* Currently we are using a non-ideal implementation through a custom event to notify the segmentation panel
* or other components that could rely on loaded segmentations that
* the segments were loaded so that e.g. when the user opens the panel
* before the segments are fully loaded, the panel can subscribe to this custom event
* and update itself with the new segments.
*
* This limitation is due to the fact that the cs segmentation module is an object (which will be
* updated after the segments are loaded) that React its not aware of its changes
* because the module object its not passed in to the panel component as prop but accessed externally.
*
* Improving this event approach to something reactive that can be tracked inside the react lifecycle,
* allows us to easily watch the module or the segmentations loading process in any other component
* without subscribing to external events.
*/
console.log('Segmentation loaded.');
const event = new CustomEvent('extensiondicomsegmentationsegloaded');
document.dispatchEvent(event);
resolve(labelmapIndex);
});
/*
* TODO: Improve the way we notify parts of the app that depends on segs to be loaded.
*
* Currently we are using a non-ideal implementation through a custom event to notify the segmentation panel
* or other components that could rely on loaded segmentations that
* the segments were loaded so that e.g. when the user opens the panel
* before the segments are fully loaded, the panel can subscribe to this custom event
* and update itself with the new segments.
*
* This limitation is due to the fact that the cs segmentation module is an object (which will be
* updated after the segments are loaded) that React its not aware of its changes
* because the module object its not passed in to the panel component as prop but accessed externally.
*
* Improving this event approach to something reactive that can be tracked inside the react lifecycle,
* allows us to easily watch the module or the segmentations loading process in any other component
* without subscribing to external events.
*/
console.log('Segmentation loaded.');
const event = new CustomEvent('extensiondicomsegmentationsegloaded');
document.dispatchEvent(event);
}
function _getNextLabelmapIndex(firstImageId) {
@ -172,38 +142,3 @@ function _getNextColorLUTIndex() {
return colorLUTIndex;
}
function _parseSeg(arrayBuffer, imageIds) {
return dcmjs.adapters.Cornerstone.Segmentation.generateToolState(
imageIds,
arrayBuffer,
cornerstone.metaData
);
}
function _getImageIdsForDisplaySet(
studies,
StudyInstanceUID,
SeriesInstanceUID
) {
const study = studies.find(
study => study.StudyInstanceUID === StudyInstanceUID
);
const displaySets = study.displaySets.filter(displaySet => {
return displaySet.SeriesInstanceUID === SeriesInstanceUID;
});
if (displaySets.length > 1) {
console.warn(
'More than one display set with the same SeriesInstanceUID. This is not supported yet...'
);
// TODO -> We could make check the instance list and see if any match?
// Do we split the segmentation into two cornerstoneTools segmentations if there are images in both series?
// ^ Will that even happen?
}
const referencedDisplaySet = displaySets[0];
return referencedDisplaySet.images.map(image => image.getImageId());
}

2
extensions/dicom-tag-browser/package.json
View File

@ -28,7 +28,7 @@
},
"peerDependencies": {
"@ohif/core": "^2.6.0",
"dcmjs": "0.16.5",
"dcmjs": "0.17.0",
"react": "^16.8.6"
},
"dependencies": {

2
extensions/vtk/package.json
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@ -35,7 +35,7 @@
"cornerstone-core": "^2.2.8",
"cornerstone-tools": "^4.20.1",
"cornerstone-wado-image-loader": "^3.1.0",
"dcmjs": "0.16.5",
"dcmjs": "0.17.0",
"dicom-parser": "^1.8.3",
"i18next": "^17.0.3",
"i18next-browser-languagedetector": "^3.0.1",

13
extensions/vtk/src/OHIFVTKViewport.js
View File

@ -72,7 +72,7 @@ class OHIFVTKViewport extends Component {
};
static defaultProps = {
onScroll: () => {},
onScroll: () => { },
};
static id = 'OHIFVTKViewport';
@ -159,6 +159,15 @@ class OHIFVTKViewport extends Component {
const { activeLabelmapIndex } = brushStackState;
const labelmap3D = brushStackState.labelmaps3D[activeLabelmapIndex];
if (brushStackState.labelmaps3D.length > 1 && this.props.viewportIndex === 0) {
const { UINotificationService } = this.props.servicesManager.services;
UINotificationService.show({
title: 'Overlapping Segmentation Found',
message: 'Overlapping segmentations cannot be displayed when in MPR mode',
type: 'info',
});
}
this.segmentsDefaultProperties = labelmap3D.segmentsHidden.map(
isHidden => {
return { visible: !isHidden };
@ -354,7 +363,7 @@ class OHIFVTKViewport extends Component {
if (
displaySet.displaySetInstanceUID !==
prevDisplaySet.displaySetInstanceUID ||
prevDisplaySet.displaySetInstanceUID ||
displaySet.SOPInstanceUID !== prevDisplaySet.SOPInstanceUID ||
displaySet.frameIndex !== prevDisplaySet.frameIndex
) {

2
platform/core/package.json
View File

@ -39,7 +39,7 @@
"dependencies": {
"@babel/runtime": "^7.5.5",
"ajv": "^6.10.0",
"dcmjs": "0.16.5",
"dcmjs": "0.17.0",
"dicomweb-client": "^0.6.0",
"immer": "6.0.2",
"isomorphic-base64": "^1.0.2",

4
platform/ui/src/contextProviders/SnackbarProvider.js
View File

@ -37,6 +37,10 @@ const SnackbarProvider = ({ children, service }) => {
return null;
}
if (options.type === 'error') {
console.error(options.error);
}
const newItem = {
...DEFAULT_OPTIONS,
...options,

2
platform/viewer/package.json
View File

@ -68,7 +68,7 @@
"cornerstone-math": "^0.1.8",
"cornerstone-tools": "^4.20.1",
"cornerstone-wado-image-loader": "^3.1.0",
"dcmjs": "0.16.5",
"dcmjs": "0.17.0",
"dicom-parser": "^1.8.3",
"dicomweb-client": "^0.4.4",
"hammerjs": "^2.0.8",

3
platform/viewer/src/components/ViewportGrid/ViewportGrid.js
View File

@ -12,7 +12,7 @@ import EmptyViewport from './EmptyViewport.js';
const { loadAndCacheDerivedDisplaySets } = utils;
const ViewportGrid = function(props) {
const ViewportGrid = function (props) {
const {
activeViewportIndex,
availablePlugins,
@ -48,6 +48,7 @@ const ViewportGrid = function(props) {
title: 'Error loading derived display set:',
message: error.message,
type: 'error',
error,
autoClose: false,
});
});

9
yarn.lock
View File

@ -6619,14 +6619,15 @@ dateformat@^3.0.0:
resolved "https://registry.yarnpkg.com/dateformat/-/dateformat-3.0.3.tgz#a6e37499a4d9a9cf85ef5872044d62901c9889ae"
integrity sha512-jyCETtSl3VMZMWeRo7iY1FL19ges1t55hMo5yaam4Jrsm5EPL89UQkoQRyiI+Yf4k8r2ZpdngkV8hr1lIdjb3Q==
dcmjs@0.16.5:
version "0.16.5"
resolved "https://registry.yarnpkg.com/dcmjs/-/dcmjs-0.16.5.tgz#05aa0c8d539a4d5777f996b9b796932d1f848993"
integrity sha512-Y92KAx4JSfev79xjYhaukQZjWgyJlaHnXSTdbtkGkJAHERjIakgHcCIPmACuVmtW/nHViTu04zIGAB0pmZ4GaA==
dcmjs@0.17.0:
version "0.17.0"
resolved "https://registry.yarnpkg.com/dcmjs/-/dcmjs-0.17.0.tgz#dbfd6db3efd2936f9bead9c902b7db396f64e9f5"
integrity sha512-7JnNqNWXqjGyspLRwKM4nn+TU/+w3iMl9boU4eHrr831M4crMWWIiSQDejpOnfDT9+opqyeaYcNkiekr7p6TFg==
dependencies:
"@babel/polyfill" "^7.8.3"
"@babel/runtime" "^7.8.4"
gl-matrix "^3.1.0"
lodash.clonedeep "^4.5.0"
loglevelnext "^3.0.1"
ndarray "^1.0.19"