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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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 | 142x 142x 142x 142x 142x 142x 2x 2x 2x 2x 2x 2x 16x 16x 3x 3x 2x 2x 16x 16x 2x 16x 16x 16x 2x 2x 16x 2x 2x 16x 2x 2x 2x 2x 2x 142x 2x 142x 142x 142x 142x 142x 142x 142x | import OHIF from '@ohif/core';
import i18n from '@ohif/i18n';
import { utilities as csUtils, Enums as csEnums } from '@cornerstonejs/core';
import dcmjs from 'dcmjs';
import { dicomWebUtils } from '@ohif/extension-default';
import { buildEcgModule } from './utils/ecgMetadata';
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) {
const dataSource = extensionManager.getActiveDataSource()[0];
// 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;
if (framesI < currentFrames) {
singleFrameInstance = instanceI;
currentFrames = framesI;
}
}
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,
others: instances, // all other level instances in the image Pyramid
instances,
othersFrameOfReferenceUID,
imageIds: instances.map(instance => instance.imageId),
getThumbnailSrc: dataSource.retrieve.getGetThumbnailSrc?.(
singleFrameInstance,
singleFrameInstance.imageId
),
label: SeriesDescription || `${i18n.t('Series')} ${SeriesNumber} - ${i18n.t('SM')}`,
};
// 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 E{
// 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,
};
}
/**
* DICOM Waveform SOP Class UIDs for ECG / cardiac electrophysiology.
* Reference: https://dicom.nema.org/medical/dicom/current/output/chtml/part04/sect_B.5.html
*/
const ECG_SOP_CLASS_UIDS = {
TWELVE_LEAD_ECG_WAVEFORM_STORAGE: '1.2.840.10008.5.1.4.1.1.9.1.1',
GENERAL_ECG_WAVEFORM_STORAGE: '1.2.840.10008.5.1.4.1.1.9.1.2',
AMBULATORY_ECG_WAVEFORM_STORAGE: '1.2.840.10008.5.1.4.1.1.9.1.3',
HEMODYNAMIC_WAVEFORM_STORAGE: '1.2.840.10008.5.1.4.1.1.9.2.1',
CARDIAC_ELECTROPHYSIOLOGY_WAVEFORM_STORAGE: '1.2.840.10008.5.1.4.1.1.9.3.1',
};
const ecgSopClassUids = Object.values(ECG_SOP_CLASS_UIDS);
const DicomEcgSOPClassHandlerId =
'@ohif/extension-cornerstone.sopClassHandlerModule.DicomEcgSopClassHandler';
function _getEcgDisplaySetsFromSeries(instances, servicesManager) {
const { userAuthenticationService } = servicesManager.services;
return instances.map(instance => {
const { Modality, SOPInstanceUID } = instance;
const { SeriesDescription, SeriesNumber, SeriesDate } = instance;
const { SeriesInstanceUID, StudyInstanceUID, SOPClassUID } = instance;
const imageId = instance.imageId;
// Register ECG metadata in the OHIF metadata provider so that
// Cornerstone's ECGViewport can retrieve it via metaData.get('ecgModule', imageId).
Iif (imageId) {
const ecgModule = buildEcgModule(instance, userAuthenticationService);
Iif (ecgModule) {
csUtils.genericMetadataProvider.addRaw(imageId, {
type: MetadataModules.ECG,
metadata: ecgModule,
});
}
}
return {
Modality,
displaySetInstanceUID: utils.guid(),
SeriesDescription,
SeriesNumber,
SeriesDate,
SOPInstanceUID,
SeriesInstanceUID,
StudyInstanceUID,
SOPClassHandlerId: DicomEcgSOPClassHandlerId,
SOPClassUID,
referencedImages: null,
measurements: null,
viewportType: csEnums.ViewportType.ECG,
instances: [instance],
instance,
thumbnailSrc: null,
isDerivedDisplaySet: false,
isLoaded: false,
sopClassUids: ecgSopClassUids,
numImageFrames: 0,
numInstances: 1,
imageIds: imageId ? [imageId] : [],
supportsWindowLevel: false,
label: SeriesDescription || 'ECG',
};
});
}
export function getDicomEcgSopClassHandler({ servicesManager }) {
const getDisplaySetsFromSeries = instances =>
_getEcgDisplaySetsFromSeries(instances, servicesManager);
return {
name: 'DicomEcgSopClassHandler',
sopClassUids: ecgSopClassUids,
getDisplaySetsFromSeries,
};
}
export function getSopClassHandlerModule(params) {
return [getDicomMicroscopySopClassHandler(params), getDicomEcgSopClassHandler(params)];
}
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