122 lines
3.8 KiB
JavaScript
122 lines
3.8 KiB
JavaScript
import OHIF from '@ohif/core';
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const { utils } = OHIF;
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const SOP_CLASS_UIDS = {
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VL_WHOLE_SLIDE_MICROSCOPY_IMAGE_STORAGE: '1.2.840.10008.5.1.4.1.1.77.1.6',
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};
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const SOPClassHandlerId =
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'@ohif/extension-dicom-microscopy.sopClassHandlerModule.DicomMicroscopySopClassHandler';
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function _getDisplaySetsFromSeries(instances, servicesManager, extensionManager) {
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// If the series has no instances, stop here
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if (!instances || !instances.length) {
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throw new Error('No instances were provided');
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}
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const instance = instances[0];
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let singleFrameInstance = instance;
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let currentFrames = +singleFrameInstance.NumberOfFrames || 1;
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for (const instanceI of instances) {
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const framesI = +instanceI.NumberOfFrames || 1;
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if (framesI < currentFrames) {
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singleFrameInstance = instanceI;
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currentFrames = framesI;
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}
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}
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let imageIdForThumbnail = null;
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if (singleFrameInstance) {
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if (currentFrames == 1) {
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// Not all DICOM server implementations support thumbnail service,
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// So if we have a single-frame image, we will prefer it.
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imageIdForThumbnail = singleFrameInstance.imageId;
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}
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if (!imageIdForThumbnail) {
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// use the thumbnail service provided by DICOM server
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const dataSource = extensionManager.getActiveDataSource()[0];
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imageIdForThumbnail = dataSource.getImageIdsForInstance({
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instance: singleFrameInstance,
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thumbnail: true,
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});
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}
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}
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const {
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FrameOfReferenceUID,
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SeriesDescription,
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ContentDate,
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ContentTime,
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SeriesNumber,
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StudyInstanceUID,
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SeriesInstanceUID,
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SOPInstanceUID,
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SOPClassUID,
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} = instance;
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instances = instances.map(inst => {
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// NOTE: According to DICOM standard a series should have a FrameOfReferenceUID
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// When the Microscopy file was built by certain tool from multiple image files,
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// each instance's FrameOfReferenceUID is sometimes different.
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// Even though this means the file was not well formatted DICOM VL Whole Slide Microscopy Image,
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// the case is so often, so let's override this value manually here.
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//
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// https://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.7.4.html#sect_C.7.4.1.1.1
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inst.FrameOfReferenceUID = instance.FrameOfReferenceUID;
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return inst;
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});
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const othersFrameOfReferenceUID = instances
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.filter(v => v)
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.map(inst => inst.FrameOfReferenceUID)
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.filter((value, index, array) => array.indexOf(value) === index);
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if (othersFrameOfReferenceUID.length > 1) {
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console.warn(
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'Expected FrameOfReferenceUID of difference instances within a series to be the same, found multiple different values',
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othersFrameOfReferenceUID
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);
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}
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const displaySet = {
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plugin: 'microscopy',
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Modality: 'SM',
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altImageText: 'Microscopy',
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displaySetInstanceUID: utils.guid(),
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SOPInstanceUID,
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SeriesInstanceUID,
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StudyInstanceUID,
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FrameOfReferenceUID,
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SOPClassHandlerId,
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SOPClassUID,
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SeriesDescription: SeriesDescription || 'Microscopy Data',
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// Map ContentDate/Time to SeriesTime for series list sorting.
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SeriesDate: ContentDate,
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SeriesTime: ContentTime,
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SeriesNumber,
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firstInstance: singleFrameInstance, // top level instance in the image Pyramid
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instance,
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numImageFrames: 0,
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numInstances: 1,
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imageIdForThumbnail, // thumbnail image
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others: instances, // all other level instances in the image Pyramid
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othersFrameOfReferenceUID,
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};
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return [displaySet];
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}
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export default function getDicomMicroscopySopClassHandler({ servicesManager, extensionManager }) {
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const getDisplaySetsFromSeries = instances => {
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return _getDisplaySetsFromSeries(instances, servicesManager, extensionManager);
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};
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return {
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name: 'DicomMicroscopySopClassHandler',
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sopClassUids: [SOP_CLASS_UIDS.VL_WHOLE_SLIDE_MICROSCOPY_IMAGE_STORAGE],
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getDisplaySetsFromSeries,
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};
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}
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