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import i18n from '@ohif/i18n';
import { metaData, eventTarget, utilities as csUtils } 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';
import { getSegmentationParserType } from './utils/segmentationConfig';
import {
getFrameIndexFromImageId,
isLocalSchemeImageId,
stripFrameFromImageId,
} from './utils/segLocalImageIds';
const sopClassUids = ['1.2.840.10008.5.1.4.1.1.66.4', '1.2.840.10008.5.1.4.1.1.66.7'];
const LABELMAP_SEG_SOP_CLASS_UID = '1.2.840.10008.5.1.4.1.1.66.7';
const loadPromises = {};
const SEG_LOAD_LOG_PREFIX = '[SEG load]';
// Max number of SEG frames fetched/decoded concurrently by the segmentation
// loader. Hard-coded to 16 for now; intended to become configurable (and to
// pair with the full-instance prefetch capability) in a follow-up.
const SEG_FRAME_DECODE_CONCURRENCY = 16;
function _normalizeImageId(imageId: string | string[] | undefined): string | undefined {
Iif (imageId == null) {
return undefined;
}
return Array.isArray(imageId) ? imageId[0] : imageId;
}
/**
* Expands a WADO-RS frame imageId (…/frames/1) into one imageId per frame.
* Multiframe SEG is stored as separate /frames/N resources on the server.
*/
function getFrameImageIds(segImageId: string, numberOfFrames: number): string[] {
const frameMatch = segImageId.match(/(.*\/frames\/)(\d+)(.*)$/);
Iif (!frameMatch || numberOfFrames <= 1) {
return [segImageId];
}
const prefix = frameMatch[1];
const suffix = frameMatch[3] || '';
const frameImageIds: string[] = [];
for (let frameNumber = 1; frameNumber <= numberOfFrames; frameNumber++) {
frameImageIds.push(`${prefix}${frameNumber}${suffix}`);
}
return frameImageIds;
}
function _getSegNumberOfFrames(instance: Record<string, unknown>): number {
const fromTag = Number(instance.NumberOfFrames);
if (fromTag > 0) {
return fromTag;
}
const perFrame = instance.PerFrameFunctionalGroupsSequence;
Iif (Array.isArray(perFrame) && perFrame.length > 0) {
return perFrame.length;
}
return 1;
}
function _ensureSegImageIdMetadataRegistered(
imageId: string | undefined,
instance: Record<string, unknown>
): void {
Iif (!imageId) {
return;
}
const metadataProvider = classes.MetadataProvider;
const StudyInstanceUID = instance.StudyInstanceUID as string | undefined;
const SeriesInstanceUID = instance.SeriesInstanceUID as string | undefined;
const SOPInstanceUID = (instance.SOPInstanceUID || instance.SopInstanceUID) as
| string
| undefined;
Iif (!StudyInstanceUID || !SeriesInstanceUID || !SOPInstanceUID) {
return;
}
metadataProvider.addImageIdToUIDs(imageId, {
StudyInstanceUID,
SeriesInstanceUID,
SOPInstanceUID,
frameNumber: getFrameIndexFromImageId(imageId),
});
}
/** Ensures metadataProvider.get('instance', imageId) resolves for frame-qualified local SEG ids. */
function _ensureSegInstanceMetadataAvailable(
imageId: string | undefined,
instance: Record<string, unknown>
): void {
Iif (!imageId) {
return;
}
_ensureSegImageIdMetadataRegistered(imageId, instance);
if (metaData.get('instance', imageId)) {
return;
}
const StudyInstanceUID = instance.StudyInstanceUID as string | undefined;
const SeriesInstanceUID = instance.SeriesInstanceUID as string | undefined;
const SOPInstanceUID = (instance.SOPInstanceUID || instance.SopInstanceUID) as
| string
| undefined;
const storedInstance =
StudyInstanceUID && SeriesInstanceUID && SOPInstanceUID
? DicomMetadataStore.getInstance(StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID)
: undefined;
classes.MetadataProvider.addCustomMetadata(
imageId,
'instance',
storedInstance || instance
);
}
function _getSegDataSource(extensionManager, instance: Record<string, unknown>) {
const StudyInstanceUID = instance.StudyInstanceUID as string | undefined;
const SeriesInstanceUID = instance.SeriesInstanceUID as string | undefined;
const SOPInstanceUID = (instance.SOPInstanceUID || instance.SopInstanceUID) as
| string
| undefined;
let localUrl: string | undefined;
if (StudyInstanceUID && SeriesInstanceUID && SOPInstanceUID) {
const storedInstance = DicomMetadataStore.getInstance(
StudyInstanceUID,
SeriesInstanceUID,
SOPInstanceUID
);
localUrl = storedInstance?.url as string | undefined;
}
localUrl = localUrl || (instance.url as string | undefined);
Iif (localUrl && isLocalSchemeImageId(localUrl)) {
const dicomLocal = extensionManager.getDataSources('dicomlocal');
Iif (dicomLocal?.[0]) {
return dicomLocal[0];
}
}
return extensionManager.getActiveDataSource()[0];
}
function _getSegImageIdFromInstance(
instance: Record<string, unknown>,
dataSource: { getImageIdsForInstance?: (args: { instance: unknown; frame?: number }) => unknown }
): string | undefined {
const numberOfFrames = _getSegNumberOfFrames(instance);
const frame = numberOfFrames > 1 ? 1 : undefined;
return _normalizeImageId(
dataSource.getImageIdsForInstance?.({ instance, frame }) as string | string[] | undefined
);
}
function _resolveFrameImageIds(
segImageIdStr: string,
instance: Record<string, unknown>,
dataSource: { getImageIdsForInstance?: (args: { instance: unknown; frame?: number }) => unknown }
): string[] {
const numberOfFrames = _getSegNumberOfFrames(instance);
const fromFrameUrl = getFrameImageIds(segImageIdStr, numberOfFrames);
if (fromFrameUrl.length > 1) {
return fromFrameUrl;
}
Iif (numberOfFrames <= 1) {
return [segImageIdStr];
}
const frameImageIds: string[] = [];
for (let frame = 1; frame <= numberOfFrames; frame++) {
const frameImageId = _normalizeImageId(
dataSource.getImageIdsForInstance?.({ instance, frame }) as string | string[] | undefined
);
Iif (frameImageId) {
frameImageIds.push(frameImageId);
}
}
return frameImageIds.length ? frameImageIds : [segImageIdStr];
}
function _logSegImageIds({
segDisplaySet,
segImageIdStr,
frameImageIds,
referencedImageIds,
}: {
segDisplaySet: AppTypes.DisplaySet;
segImageIdStr: string;
frameImageIds: string[];
referencedImageIds: string[];
}) {
const instance = segDisplaySet.instance as Record<string, unknown>;
const numberOfFrames = Number(instance?.NumberOfFrames) || 1;
log.debug(SEG_LOAD_LOG_PREFIX, 'Loading SEG pixel data', {
SOPInstanceUID: segDisplaySet.SOPInstanceUID,
SeriesInstanceUID: segDisplaySet.SeriesInstanceUID,
SOPClassUID: segDisplaySet.SOPClassUID,
NumberOfFrames: numberOfFrames,
segmentCount: Object.keys(segDisplaySet.segments || {}).length,
referencedDisplaySetInstanceUID: segDisplaySet.referencedDisplaySetInstanceUID,
referencedImageIdCount: referencedImageIds.length,
referencedImageIds,
segImageIdForMetadata: segImageIdStr,
frameImageIds,
loadSegFramesIndividually: frameImageIds.length > 1,
});
}
function _getDisplaySetsFromSeries(
instances,
servicesManager: AppTypes.ServicesManager,
extensionManager
) {
utils.sortStudyInstances(instances);
// Choose the LAST instance in the list as the most recently created one.
const instance = instances[instances.length - 1];
const {
StudyInstanceUID,
SeriesInstanceUID,
SOPInstanceUID,
SeriesDescription = '',
SeriesNumber,
SeriesDate,
StructureSetDate,
SOPClassUID,
FrameOfReferenceUID,
wadoRoot,
wadoUri,
wadoUriRoot,
imageId: predecessorImageId,
} = instance;
const displaySet = {
Modality: 'SEG',
loading: false,
isReconstructable: false,
displaySetInstanceUID: utils.guid(),
SeriesDescription,
SeriesNumber,
SeriesDate: SeriesDate || StructureSetDate || '',
SOPInstanceUID,
SeriesInstanceUID,
StudyInstanceUID,
SOPClassHandlerId,
SOPClassUID,
FrameOfReferenceUID,
referencedImages: null,
referencedSeriesInstanceUID: null,
referencedDisplaySetInstanceUID: null,
isDerivedDisplaySet: true,
isLoaded: false,
isHydrated: false,
segments: {},
sopClassUids,
instance,
predecessorImageId,
instances: [instance],
wadoRoot,
wadoUriRoot,
wadoUri,
isOverlayDisplaySet: true,
label: SeriesDescription || `${i18n.t('Series')} ${SeriesNumber} - ${i18n.t('SEG')}`,
};
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.getDisplaySetsForReferences(
instance.ReferencedSeriesSequence
);
Iif (referencedDisplaySets?.length > 1) {
console.warn(
'Segmentation does not currently handle references to multiple series, defaulting to first series'
);
}
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;
displaySet.isReconstructable = addedDisplaySet.isReconstructable;
displaySet.FrameOfReferenceUID = addedDisplaySet.FrameOfReferenceUID;
unsubscribe();
}
}
);
} else {
displaySet.referencedDisplaySetInstanceUID = referencedDisplaySet.displaySetInstanceUID;
displaySet.isReconstructable = referencedDisplaySet.isReconstructable;
displaySet.FrameOfReferenceUID = referencedDisplaySet.FrameOfReferenceUID;
}
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);
});
});
// Expose the in-flight load promise so observers (e.g. the viewport service
// waiting to attach the representation) can react to a load failure without
// re-invoking load().
segDisplaySet.loadingPromise = loadPromises[SOPInstanceUID];
return loadPromises[SOPInstanceUID];
}
async function _loadSegments({
extensionManager,
servicesManager,
segDisplaySet,
}: withAppTypes<{ segDisplaySet: AppTypes.DisplaySet }>) {
const { segmentationService, uiNotificationService, customizationService } =
servicesManager.services;
const instance = segDisplaySet.instance as Record<string, unknown>;
const dataSource = _getSegDataSource(extensionManager, instance);
const segImageIdStr = _getSegImageIdFromInstance(instance, dataSource);
Iif (!segImageIdStr) {
throw new Error(
'Could not get imageId for SEG instance (no local wadouri url and getImageIdsForInstance returned nothing).'
);
}
const referencedDisplaySet = servicesManager.services.displaySetService.getDisplaySetByUID(
segDisplaySet.referencedDisplaySetInstanceUID
);
Iif (!referencedDisplaySet) {
throw new Error('referencedDisplaySet is missing for SEG');
}
// Prefer cached stack imageIds (multiframe SEG fix #4890), then data source expansion.
let { imageIds } = referencedDisplaySet;
Iif (!imageIds?.length) {
imageIds = dataSource.getImageIdsForDisplaySet?.(referencedDisplaySet);
}
Iif (!imageIds?.length) {
imageIds = (referencedDisplaySet as { images?: { imageId: string }[] }).images?.map(
(img: { imageId: string }) => img.imageId
);
}
Iif (!imageIds?.length) {
throw new Error('referencedDisplaySet has no imageIds');
}
(segDisplaySet as AppTypes.DisplaySet & { referencedImageIds?: string[] }).referencedImageIds =
imageIds;
Iif (!referencedDisplaySet.imageIds?.length) {
referencedDisplaySet.imageIds = imageIds;
}
const frameImageIds = _resolveFrameImageIds(
segImageIdStr,
segDisplaySet.instance as Record<string, unknown>,
dataSource
);
const segImageIdForMetadata = isLocalSchemeImageId(segImageIdStr)
? stripFrameFromImageId(segImageIdStr)
: segImageIdStr;
_logSegImageIds({
segDisplaySet,
segImageIdStr: segImageIdForMetadata,
frameImageIds,
referencedImageIds: imageIds,
});
_ensureSegInstanceMetadataAvailable(segImageIdForMetadata, instance);
frameImageIds.forEach(id => _ensureSegInstanceMetadataAvailable(id, instance));
const tolerance = 0.001;
const onProgress = evt => {
const { percentComplete } = evt.detail;
segmentationService._broadcastEvent(segmentationService.EVENTS.SEGMENT_LOADING_COMPLETE, {
percentComplete,
});
};
eventTarget.addEventListener(Enums.Events.SEGMENTATION_LOAD_PROGRESS, onProgress);
// Fetch the whole SEG instance as a single Part 10 object and register its
// per-frame compressed pixels into the Cornerstone3D frame registry, so the
// per-frame loads below are served locally instead of one network request
// per frame: SEG frames are so small and numerous that one bulk fetch beats
// hundreds of tiny requests. Enabled by default; per-frame loading is the
// exception (loadMultiframeAsPart10: false in the data source config, or the
// cornerstone.segmentation.loadMultiframeAsPart10 customization). The
// prefetch is awaited until it completes OR fails — deliberately no timeout:
// a failed/unsupported instance fetch resolves quickly and falls back to
// per-frame, while a slow large fetch is still the fastest way to all frames.
const loadMultiframeAsPart10 =
(dataSource?.getConfig?.()?.loadMultiframeAsPart10 as boolean | undefined) ??
(customizationService?.getCustomization?.(
'cornerstone.segmentation.loadMultiframeAsPart10'
) as boolean | undefined) ??
true;
let prefetch;
if (loadMultiframeAsPart10) {
prefetch = dataSource.retrieve?.prefetchInstanceFrames?.({
instance,
imageId: segImageIdForMetadata,
});
if (prefetch?.done) {
await prefetch.done;
}
}
let results;
try {
results = await adaptersSEG.Cornerstone3D.Segmentation.createFromDicomSegImageId(
imageIds,
segImageIdForMetadata,
{
metadataProvider: metaData,
tolerance,
parserType: getSegmentationParserType(
segDisplaySet.SOPClassUID,
customizationService
),
frameImageIds,
concurrency: SEG_FRAME_DECODE_CONCURRENCY,
}
);
} finally {
eventTarget.removeEventListener(Enums.Events.SEGMENTATION_LOAD_PROGRESS, onProgress);
prefetch?.cancel?.();
}
let usedRecommendedDisplayCIELabValue = true;
const resultsTyped = results as {
segMetadata: { data: { rgba?: number[]; RecommendedDisplayCIELabValue?: number[] }[] };
};
resultsTyped.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);
const labelMapImageIds = (results as { labelMapImages?: { imageId: string }[][] })
.labelMapImages?.flat()
.map(image => image.imageId);
log.debug(SEG_LOAD_LOG_PREFIX, 'SEG parse complete', {
SOPInstanceUID: segDisplaySet.SOPInstanceUID,
labelMapImageCount: labelMapImageIds?.length ?? 0,
labelMapImageIds,
segmentIndices: Object.keys(segDisplaySet.segments || {}),
});
}
function _segmentationExists(segDisplaySet) {
return cstSegmentation.state.getSegmentation(segDisplaySet.displaySetInstanceUID);
}
function getSopClassHandlerModule(params: OhifTypes.Extensions.ExtensionParams) {
const { servicesManager, extensionManager } = params;
const getDisplaySetsFromSeries = instances => {
return _getDisplaySetsFromSeries(instances, servicesManager, extensionManager);
};
return [
{
name: 'dicom-seg',
sopClassUids,
getDisplaySetsFromSeries,
},
];
}
export default getSopClassHandlerModule;
|