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| 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 | 34x 34x 34x 34x 34x 34x 34x 34x 34x | import OHIF from '@ohif/core';
import { utilities as csUtils, Enums as csEnums } from '@cornerstonejs/core';
import dcmjs from 'dcmjs';
import { dicomWebUtils } from '@ohif/extension-default';
const { MetadataModules } = csEnums;
const { utils } = OHIF;
const { denaturalizeDataset } = dcmjs.data.DicomMetaDictionary;
const { transferDenaturalizedDataset, fixMultiValueKeys } = dicomWebUtils;
const SOP_CLASS_UIDS = {
VL_WHOLE_SLIDE_MICROSCOPY_IMAGE_STORAGE: '1.2.840.10008.5.1.4.1.1.77.1.6',
};
const SOPClassHandlerId =
'@ohif/extension-cornerstone.sopClassHandlerModule.DicomMicroscopySopClassHandler';
function _getDisplaySetsFromSeries(instances, servicesManager, extensionManager) {
// If the series has no instances, stop here
Iif (!instances || !instances.length) {
throw new Error('No instances were provided');
}
const instance = instances[0];
let singleFrameInstance = instance;
let currentFrames = +singleFrameInstance.NumberOfFrames || 1;
for (const instanceI of instances) {
const framesI = +instanceI.NumberOfFrames || 1;
Iif (framesI < currentFrames) {
singleFrameInstance = instanceI;
currentFrames = framesI;
}
}
let imageIdForThumbnail = null;
const dataSource = extensionManager.getActiveDataSource()[0];
Iif (singleFrameInstance) {
Iif (currentFrames == 1) {
// Not all DICOM server implementations support thumbnail service,
// So if we have a single-frame image, we will prefer it.
imageIdForThumbnail = singleFrameInstance.imageId;
}
Iif (!imageIdForThumbnail) {
// use the thumbnail service provided by DICOM server
imageIdForThumbnail = dataSource.getImageIdsForInstance({
instance: singleFrameInstance,
thumbnail: true,
});
}
}
const {
FrameOfReferenceUID,
SeriesDescription,
ContentDate,
ContentTime,
SeriesNumber,
StudyInstanceUID,
SeriesInstanceUID,
SOPInstanceUID,
SOPClassUID,
} = instance;
instances = instances.map(inst => {
// NOTE: According to DICOM standard a series should have a FrameOfReferenceUID
// When the Microscopy file was built by certain tool from multiple image files,
// each instance's FrameOfReferenceUID is sometimes different.
// Even though this means the file was not well formatted DICOM VL Whole Slide Microscopy Image,
// the case is so often, so let's override this value manually here.
//
// https://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.7.4.html#sect_C.7.4.1.1.1
inst.FrameOfReferenceUID = instance.FrameOfReferenceUID;
return inst;
});
const othersFrameOfReferenceUID = instances
.filter(v => v)
.map(inst => inst.FrameOfReferenceUID)
.filter((value, index, array) => array.indexOf(value) === index);
Iif (othersFrameOfReferenceUID.length > 1) {
console.warn(
'Expected FrameOfReferenceUID of difference instances within a series to be the same, found multiple different values',
othersFrameOfReferenceUID
);
}
const displaySet = {
plugin: 'microscopy',
Modality: 'SM',
viewportType: csEnums.ViewportType.WHOLE_SLIDE,
altImageText: 'Microscopy',
displaySetInstanceUID: utils.guid(),
SOPInstanceUID,
SeriesInstanceUID,
StudyInstanceUID,
FrameOfReferenceUID,
SOPClassHandlerId,
SOPClassUID,
SeriesDescription: SeriesDescription || 'Microscopy Data',
// Map ContentDate/Time to SeriesTime for series list sorting.
SeriesDate: ContentDate,
SeriesTime: ContentTime,
SeriesNumber,
firstInstance: singleFrameInstance, // top level instance in the image Pyramid
instance,
numImageFrames: 0,
numInstances: 1,
imageIdForThumbnail, // thumbnail image
others: instances, // all other level instances in the image Pyramid
instances,
othersFrameOfReferenceUID,
imageIds: instances.map(instance => instance.imageId),
};
// The microscopy viewer directly accesses the metadata already loaded, and
// uses the DICOMweb client library directly for loading, so it has to be
// provided here.
const dicomWebClient = dataSource.retrieve.getWadoDicomWebClient?.();
const instanceMap = new Map();
instances.forEach(instance => instanceMap.set(instance.imageId, instance));
if (dicomWebClient) {
const webClient = Object.create(dicomWebClient);
// This replaces just the dicom web metadata call with one which retrieves
// internally.
webClient.getDICOMwebMetadata = getDICOMwebMetadata.bind(webClient, instanceMap);
csUtils.genericMetadataProvider.addRaw(displaySet.imageIds[0], {
type: MetadataModules.WADO_WEB_CLIENT,
metadata: webClient,
});
} else {
// Might have some other way of getting the data in the future or internally?
// throw new Error('Unable to provide a DICOMWeb client library, microscopy will fail to view');
}
return [displaySet];
}
/**
* This method provides access to the internal DICOMweb metadata, used to avoid
* refetching the DICOMweb data. It gets assigned as a member function to the
* dicom web client.
*/
function getDICOMwebMetadata(instanceMap, imageId) {
const instance = instanceMap.get(imageId);
Iif (!instance) {
console.warn('Metadata not already found for', imageId, 'in', instanceMap);
return this.super.getDICOMwebMetadata(imageId);
}
return transferDenaturalizedDataset(
denaturalizeDataset(fixMultiValueKeys(instanceMap.get(imageId)))
);
}
export function getDicomMicroscopySopClassHandler({ servicesManager, extensionManager }) {
const getDisplaySetsFromSeries = instances => {
return _getDisplaySetsFromSeries(instances, servicesManager, extensionManager);
};
return {
name: 'DicomMicroscopySopClassHandler',
sopClassUids: [SOP_CLASS_UIDS.VL_WHOLE_SLIDE_MICROSCOPY_IMAGE_STORAGE],
getDisplaySetsFromSeries,
};
}
export function getSopClassHandlerModule(params) {
return [getDicomMicroscopySopClassHandler(params)];
}
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