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import { metaData, triggerEvent, eventTarget } from '@cornerstonejs/core';
import { CONSTANTS, segmentation as cstSegmentation } from '@cornerstonejs/tools';
import { adaptersSEG, Enums } from '@cornerstonejs/adapters';
import { SOPClassHandlerId } from './id';
import { dicomlabToRGB } from './utils/dicomlabToRGB';
const sopClassUids = ['1.2.840.10008.5.1.4.1.1.66.4'];
const loadPromises = {};
function _getDisplaySetsFromSeries(
instances,
servicesManager: AppTypes.ServicesManager,
extensionManager
) {
const instance = instances[0];
const {
StudyInstanceUID,
SeriesInstanceUID,
SOPInstanceUID,
SeriesDescription,
SeriesNumber,
SeriesDate,
SOPClassUID,
wadoRoot,
wadoUri,
wadoUriRoot,
} = instance;
const displaySet = {
Modality: 'SEG',
loading: false,
isReconstructable: true, // by default for now since it is a volumetric SEG currently
displaySetInstanceUID: utils.guid(),
SeriesDescription,
SeriesNumber,
SeriesDate,
SOPInstanceUID,
SeriesInstanceUID,
StudyInstanceUID,
SOPClassHandlerId,
SOPClassUID,
referencedImages: null,
referencedSeriesInstanceUID: null,
referencedDisplaySetInstanceUID: null,
isDerivedDisplaySet: true,
isLoaded: false,
isHydrated: false,
segments: {},
sopClassUids,
instance,
instances: [instance],
wadoRoot,
wadoUriRoot,
wadoUri,
isOverlayDisplaySet: true,
};
const referencedSeriesSequence = instance.ReferencedSeriesSequence;
Iif (!referencedSeriesSequence) {
console.error('ReferencedSeriesSequence is missing for the SEG');
return;
}
const referencedSeries = referencedSeriesSequence[0] || referencedSeriesSequence;
displaySet.referencedImages = instance.ReferencedSeriesSequence.ReferencedInstanceSequence;
displaySet.referencedSeriesInstanceUID = referencedSeries.SeriesInstanceUID;
const { displaySetService } = servicesManager.services;
const referencedDisplaySets = displaySetService.getDisplaySetsForSeries(
displaySet.referencedSeriesInstanceUID
);
const referencedDisplaySet = referencedDisplaySets[0];
if (!referencedDisplaySet) {
// subscribe to display sets added which means at some point it will be available
const { unsubscribe } = displaySetService.subscribe(
displaySetService.EVENTS.DISPLAY_SETS_ADDED,
({ displaySetsAdded }) => {
// here we can also do a little bit of search, since sometimes DICOM SEG
// does not contain the referenced display set uid , and we can just
// see which of the display sets added is more similar and assign it
// to the referencedDisplaySet
const addedDisplaySet = displaySetsAdded[0];
if (addedDisplaySet.SeriesInstanceUID === displaySet.referencedSeriesInstanceUID) {
displaySet.referencedDisplaySetInstanceUID = addedDisplaySet.displaySetInstanceUID;
unsubscribe();
}
}
);
} else {
displaySet.referencedDisplaySetInstanceUID = referencedDisplaySet.displaySetInstanceUID;
}
displaySet.load = async ({ headers }) =>
await _load(displaySet, servicesManager, extensionManager, headers);
return [displaySet];
}
function _load(
segDisplaySet,
servicesManager: AppTypes.ServicesManager,
extensionManager,
headers
) {
const { SOPInstanceUID } = segDisplaySet;
const { segmentationService } = servicesManager.services;
if (
(segDisplaySet.loading || segDisplaySet.isLoaded) &&
loadPromises[SOPInstanceUID] &&
_segmentationExists(segDisplaySet)
) {
return loadPromises[SOPInstanceUID];
}
segDisplaySet.loading = true;
// We don't want to fire multiple loads, so we'll wait for the first to finish
// and also return the same promise to any other callers.
loadPromises[SOPInstanceUID] = new Promise(async (resolve, reject) => {
if (!segDisplaySet.segments || Object.keys(segDisplaySet.segments).length === 0) {
try {
await _loadSegments({
extensionManager,
servicesManager,
segDisplaySet,
headers,
});
} catch (e) {
segDisplaySet.loading = false;
return reject(e);
}
}
segmentationService
.createSegmentationForSEGDisplaySet(segDisplaySet)
.then(() => {
segDisplaySet.loading = false;
resolve();
})
.catch(error => {
segDisplaySet.loading = false;
reject(error);
});
});
return loadPromises[SOPInstanceUID];
}
async function _loadSegments({
extensionManager,
servicesManager,
segDisplaySet,
headers,
}: withAppTypes) {
const utilityModule = extensionManager.getModuleEntry(
'@ohif/extension-cornerstone.utilityModule.common'
);
const { segmentationService, uiNotificationService } = servicesManager.services;
const { dicomLoaderService } = utilityModule.exports;
const arrayBuffer = await dicomLoaderService.findDicomDataPromise(segDisplaySet, null, headers);
const referencedDisplaySet = servicesManager.services.displaySetService.getDisplaySetByUID(
segDisplaySet.referencedDisplaySetInstanceUID
);
Iif (!referencedDisplaySet) {
throw new Error('referencedDisplaySet is missing for SEG');
}
let { imageIds } = referencedDisplaySet;
Iif (!imageIds) {
// try images
const { images } = referencedDisplaySet;
imageIds = images.map(image => image.imageId);
}
// Todo: what should be defaults here
const tolerance = 0.001;
eventTarget.addEventListener(Enums.Events.SEGMENTATION_LOAD_PROGRESS, evt => {
const { percentComplete } = evt.detail;
segmentationService._broadcastEvent(segmentationService.EVENTS.SEGMENT_LOADING_COMPLETE, {
percentComplete,
});
});
const results = await adaptersSEG.Cornerstone3D.Segmentation.createFromDICOMSegBuffer(
imageIds,
arrayBuffer,
{ metadataProvider: metaData, tolerance }
);
let usedRecommendedDisplayCIELabValue = true;
results.segMetadata.data.forEach((data, i) => {
if (i > 0) {
data.rgba = data.RecommendedDisplayCIELabValue;
if (data.rgba) {
data.rgba = dicomlabToRGB(data.rgba);
} else E{
usedRecommendedDisplayCIELabValue = false;
data.rgba = CONSTANTS.COLOR_LUT[i % CONSTANTS.COLOR_LUT.length];
}
}
});
Iif (!usedRecommendedDisplayCIELabValue) {
// Display a notification about the non-utilization of RecommendedDisplayCIELabValue
uiNotificationService.show({
title: 'DICOM SEG import',
message:
'RecommendedDisplayCIELabValue not found for one or more segments. The default color was used instead.',
type: 'warning',
duration: 5000,
});
}
Object.assign(segDisplaySet, results);
}
function _segmentationExists(segDisplaySet) {
return cstSegmentation.state.getSegmentation(segDisplaySet.displaySetInstanceUID);
}
function getSopClassHandlerModule({ servicesManager, extensionManager }) {
const getDisplaySetsFromSeries = instances => {
return _getDisplaySetsFromSeries(instances, servicesManager, extensionManager);
};
return [
{
name: 'dicom-seg',
sopClassUids,
getDisplaySetsFromSeries,
},
];
}
export default getSopClassHandlerModule;
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