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import dicomParser from 'dicom-parser';
import { utilities } from '@cornerstonejs/core';
import { imageIdToURI } from '../utils';
import DicomMetadataStore from '../services/DicomMetadataStore';
import fetchPaletteColorLookupTableData from '../utils/metadataProvider/fetchPaletteColorLookupTableData';
import toNumber from '../utils/toNumber';
import combineFrameInstance from '../utils/combineFrameInstance';
import formatPN from '../utils/formatPN';
const { calibratedPixelSpacingMetadataProvider, getPixelSpacingInformation } = utilities;
class MetadataProvider {
private readonly imageURIToUIDs: Map<string, any> = new Map();
// Can be used to store custom metadata for a specific type.
// For instance, the scaling metadata for PET can be stored here
// as type "scalingModule"
private readonly customMetadata: Map<string, any> = new Map();
addImageIdToUIDs(imageId, uids) {
Iif (!imageId) {
throw new Error('MetadataProvider::Empty imageId');
}
// This method is a fallback for when you don't have WADO-URI or WADO-RS.
// You can add instances fetched by any method by calling addInstance, and hook an imageId to point at it here.
// An example would be dicom hosted at some random site.
const imageURI = imageIdToURI(imageId);
this.imageURIToUIDs.set(imageURI, uids);
}
addCustomMetadata(imageId, type, metadata) {
const imageURI = imageIdToURI(imageId);
if (!this.customMetadata.has(type)) {
this.customMetadata.set(type, {});
}
this.customMetadata.get(type)[imageURI] = metadata;
}
_getInstance(imageId) {
Iif (!imageId) {
throw new Error('MetadataProvider::Empty imageId');
}
const uids = this.getUIDsFromImageID(imageId);
if (!uids) {
return;
}
const { StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID, frameNumber } = uids;
const instance = DicomMetadataStore.getInstance(
StudyInstanceUID,
SeriesInstanceUID,
SOPInstanceUID
);
Iif (!instance) {
return;
}
return (frameNumber && combineFrameInstance(frameNumber, instance)) || instance;
}
get(query, imageId, options = { fallback: false }) {
Iif (Array.isArray(imageId)) {
return;
}
const instance = this._getInstance(imageId);
if (query === INSTANCE) {
return instance;
}
// check inside custom metadata
if (this.customMetadata.has(query)) {
const customMetadata = this.customMetadata.get(query);
const imageURI = imageIdToURI(imageId);
if (customMetadata[imageURI]) {
return customMetadata[imageURI];
}
}
return this.getTagFromInstance(query, instance, options);
}
getTag(query, imageId, options) {
return this.get(query, imageId, options);
}
getInstance(imageId) {
return this.get(INSTANCE, imageId);
}
getTagFromInstance(naturalizedTagOrWADOImageLoaderTag, instance, options = { fallback: false }) {
if (!instance) {
return;
}
// If its a naturalized dcmjs tag present on the instance, return.
Iif (instance[naturalizedTagOrWADOImageLoaderTag]) {
return instance[naturalizedTagOrWADOImageLoaderTag];
}
// Maybe its a legacy dicomImageLoader tag then:
return this._getCornerstoneDICOMImageLoaderTag(naturalizedTagOrWADOImageLoaderTag, instance);
}
/**
* Adds a new handler for the given tag. The handler will be provided an
* instance object that it can read values from.
*/
public addHandler(wadoImageLoaderTag: string, handler) {
WADO_IMAGE_LOADER[wadoImageLoaderTag] = handler;
}
_getCornerstoneDICOMImageLoaderTag(wadoImageLoaderTag, instance) {
let metadata = WADO_IMAGE_LOADER[wadoImageLoaderTag]?.(instance);
if (metadata) {
return metadata;
}
switch (wadoImageLoaderTag) {
case WADO_IMAGE_LOADER_TAGS.GENERAL_SERIES_MODULE:
const { SeriesDate, SeriesTime } = instance;
let seriesDate;
let seriesTime;
if (SeriesDate) {
seriesDate = dicomParser.parseDA(SeriesDate);
}
if (SeriesTime) {
seriesTime = dicomParser.parseTM(SeriesTime);
}
metadata = {
modality: instance.Modality,
seriesInstanceUID: instance.SeriesInstanceUID,
seriesNumber: toNumber(instance.SeriesNumber),
studyInstanceUID: instance.StudyInstanceUID,
seriesDate,
seriesTime,
};
break;
case WADO_IMAGE_LOADER_TAGS.PATIENT_STUDY_MODULE:
metadata = {
patientAge: toNumber(instance.PatientAge),
patientSize: toNumber(instance.PatientSize),
patientWeight: toNumber(instance.PatientWeight),
};
break;
case WADO_IMAGE_LOADER_TAGS.PATIENT_DEMOGRAPHIC_MODULE:
metadata = {
patientSex: instance.PatientSex,
};
break;
case WADO_IMAGE_LOADER_TAGS.IMAGE_PIXEL_MODULE:
metadata = {
samplesPerPixel: toNumber(instance.SamplesPerPixel),
photometricInterpretation: instance.PhotometricInterpretation,
rows: toNumber(instance.Rows),
columns: toNumber(instance.Columns),
bitsAllocated: toNumber(instance.BitsAllocated),
bitsStored: toNumber(instance.BitsStored),
highBit: toNumber(instance.HighBit),
pixelRepresentation: toNumber(instance.PixelRepresentation),
planarConfiguration: toNumber(instance.PlanarConfiguration),
pixelAspectRatio: toNumber(instance.PixelAspectRatio),
smallestPixelValue: toNumber(instance.SmallestPixelValue),
largestPixelValue: toNumber(instance.LargestPixelValue),
redPaletteColorLookupTableDescriptor: toNumber(
instance.RedPaletteColorLookupTableDescriptor
),
greenPaletteColorLookupTableDescriptor: toNumber(
instance.GreenPaletteColorLookupTableDescriptor
),
bluePaletteColorLookupTableDescriptor: toNumber(
instance.BluePaletteColorLookupTableDescriptor
),
redPaletteColorLookupTableData: fetchPaletteColorLookupTableData(
instance,
'RedPaletteColorLookupTableData',
'RedPaletteColorLookupTableDescriptor'
),
greenPaletteColorLookupTableData: fetchPaletteColorLookupTableData(
instance,
'GreenPaletteColorLookupTableData',
'GreenPaletteColorLookupTableDescriptor'
),
bluePaletteColorLookupTableData: fetchPaletteColorLookupTableData(
instance,
'BluePaletteColorLookupTableData',
'BluePaletteColorLookupTableDescriptor'
),
};
break;
case WADO_IMAGE_LOADER_TAGS.VOI_LUT_MODULE:
const { WindowCenter, WindowWidth, VOILUTFunction } = instance;
if (WindowCenter == null || WindowWidth == null) {
return;
}
const windowCenter = Array.isArray(WindowCenter) ? WindowCenter : [WindowCenter];
const windowWidth = Array.isArray(WindowWidth) ? WindowWidth : [WindowWidth];
metadata = {
windowCenter: toNumber(windowCenter),
windowWidth: toNumber(windowWidth),
voiLUTFunction: VOILUTFunction,
};
break;
case WADO_IMAGE_LOADER_TAGS.MODALITY_LUT_MODULE:
const { RescaleIntercept, RescaleSlope } = instance;
// Early return if RescaleIntercept or RescaleSlope are not
// present (undefined) or explicitly set to null. We use loose
// equality in this case to check for *null* or *undefined*.
if (RescaleIntercept == null || RescaleSlope == null) {
return;
}
metadata = {
rescaleIntercept: toNumber(instance.RescaleIntercept),
rescaleSlope: toNumber(instance.RescaleSlope),
rescaleType: instance.RescaleType,
};
break;
case WADO_IMAGE_LOADER_TAGS.SOP_COMMON_MODULE:
metadata = {
sopClassUID: instance.SOPClassUID,
sopInstanceUID: instance.SOPInstanceUID,
};
break;
case WADO_IMAGE_LOADER_TAGS.PET_IMAGE_MODULE:
metadata = {
frameReferenceTime: instance.FrameReferenceTime,
actualFrameDuration: instance.ActualFrameDuration,
};
break;
case WADO_IMAGE_LOADER_TAGS.PET_ISOTOPE_MODULE:
const { RadiopharmaceuticalInformationSequence } = instance;
Iif (RadiopharmaceuticalInformationSequence) {
const RadiopharmaceuticalInformation = Array.isArray(
RadiopharmaceuticalInformationSequence
)
? RadiopharmaceuticalInformationSequence[0]
: RadiopharmaceuticalInformationSequence;
const { RadiopharmaceuticalStartTime, RadionuclideTotalDose, RadionuclideHalfLife } =
RadiopharmaceuticalInformation;
const radiopharmaceuticalInfo = {
radiopharmaceuticalStartTime: dicomParser.parseTM(RadiopharmaceuticalStartTime),
radionuclideTotalDose: RadionuclideTotalDose,
radionuclideHalfLife: RadionuclideHalfLife,
};
metadata = {
radiopharmaceuticalInfo,
};
}
break;
case WADO_IMAGE_LOADER_TAGS.OVERLAY_PLANE_MODULE:
const overlays = [];
for (let overlayGroup = 0x00; overlayGroup <= 0x1e; overlayGroup += 0x02) {
let groupStr = `60${overlayGroup.toString(16)}`;
if (groupStr.length === 3) {
groupStr = `600${overlayGroup.toString(16)}`;
}
const OverlayDataTag = `${groupStr}3000`;
const OverlayData = instance[OverlayDataTag];
if (!OverlayData) {
continue;
}
const OverlayRowsTag = `${groupStr}0010`;
const OverlayColumnsTag = `${groupStr}0011`;
const OverlayType = `${groupStr}0040`;
const OverlayOriginTag = `${groupStr}0050`;
const OverlayDescriptionTag = `${groupStr}0022`;
const OverlayLabelTag = `${groupStr}1500`;
const ROIAreaTag = `${groupStr}1301`;
const ROIMeanTag = `${groupStr}1302`;
const ROIStandardDeviationTag = `${groupStr}1303`;
const OverlayOrigin = instance[OverlayOriginTag];
let rows = 0;
if (instance[OverlayRowsTag] instanceof Array) {
// The DICOM VR for overlay rows is US (unsigned short).
const rowsInt16Array = new Uint16Array(instance[OverlayRowsTag][0]);
rows = rowsInt16Array[0];
} else {
rows = instance[OverlayRowsTag];
}
let columns = 0;
if (instance[OverlayColumnsTag] instanceof Array) {
// The DICOM VR for overlay columns is US (unsigned short).
const columnsInt16Array = new Uint16Array(instance[OverlayColumnsTag][0]);
columns = columnsInt16Array[0];
} else {
columns = instance[OverlayColumnsTag];
}
let x = 0;
let y = 0;
if (OverlayOrigin.length === 1) {
// The DICOM VR for overlay origin is SS (signed short) with a multiplicity of 2.
const originInt16Array = new Int16Array(OverlayOrigin[0]);
x = originInt16Array[0];
y = originInt16Array[1];
} else {
x = OverlayOrigin[0];
y = OverlayOrigin[1];
}
const overlay = {
rows: rows,
columns: columns,
type: instance[OverlayType],
x,
y,
pixelData: OverlayData,
description: instance[OverlayDescriptionTag],
label: instance[OverlayLabelTag],
roiArea: instance[ROIAreaTag],
roiMean: instance[ROIMeanTag],
roiStandardDeviation: instance[ROIStandardDeviationTag],
};
overlays.push(overlay);
}
metadata = {
overlays,
};
break;
case WADO_IMAGE_LOADER_TAGS.PATIENT_MODULE:
const { PatientName } = instance;
let patientName;
Iif (PatientName) {
patientName = formatPN(PatientName);
}
metadata = {
patientName,
patientId: instance.PatientID,
};
break;
case WADO_IMAGE_LOADER_TAGS.GENERAL_IMAGE_MODULE:
metadata = {
sopInstanceUID: instance.SOPInstanceUID,
instanceNumber: toNumber(instance.InstanceNumber),
lossyImageCompression: instance.LossyImageCompression,
lossyImageCompressionRatio: instance.LossyImageCompressionRatio,
lossyImageCompressionMethod: instance.LossyImageCompressionMethod,
};
break;
case WADO_IMAGE_LOADER_TAGS.GENERAL_STUDY_MODULE:
metadata = {
studyDescription: instance.StudyDescription,
studyDate: instance.StudyDate,
studyTime: instance.StudyTime,
accessionNumber: instance.AccessionNumber,
};
break;
case WADO_IMAGE_LOADER_TAGS.CINE_MODULE:
metadata = {
frameTime: instance.FrameTime,
numberOfFrames: instance.NumberOfFrames ? Number(instance.NumberOfFrames) : 1,
};
break;
case WADO_IMAGE_LOADER_TAGS.PET_SERIES_MODULE:
metadata = {
correctedImage: instance.CorrectedImage,
units: instance.Units,
decayCorrection: instance.DecayCorrection,
};
break;
case WADO_IMAGE_LOADER_TAGS.CALIBRATION_MODULE:
// map the DICOM tags to the cornerstone tags since cornerstone tags
// are camelCase and instance tags are all caps
metadata = {
sequenceOfUltrasoundRegions: instance.SequenceOfUltrasoundRegions?.map(region => {
return {
regionSpatialFormat: region.RegionSpatialFormat,
regionDataType: region.RegionDataType,
regionFlags: region.RegionFlags,
regionLocationMinX0: region.RegionLocationMinX0,
regionLocationMinY0: region.RegionLocationMinY0,
regionLocationMaxX1: region.RegionLocationMaxX1,
regionLocationMaxY1: region.RegionLocationMaxY1,
referencePixelX0: region.ReferencePixelX0,
referencePixelY0: region.ReferencePixelY0,
referencePixelPhysicalValueX: region.ReferencePixelPhysicalValueX,
referencePixelPhysicalValueY: region.ReferencePixelPhysicalValueY,
physicalUnitsXDirection: region.PhysicalUnitsXDirection,
physicalUnitsYDirection: region.PhysicalUnitsYDirection,
physicalDeltaX: region.PhysicalDeltaX,
physicalDeltaY: region.PhysicalDeltaY,
};
}),
};
break;
/**
* Below are the tags and not the modules since they are not really
* consistent with the modules above
*/
case 'temporalPositionIdentifier':
metadata = {
temporalPositionIdentifier: instance.TemporalPositionIdentifier,
};
break;
default:
return;
}
return metadata;
}
/**
* Retrieves the frameNumber information, depending on the url style
* wadors /frames/1
* wadouri &frame=1
* @param {*} imageId
* @returns
*/
getFrameInformationFromURL(imageId) {
function getInformationFromURL(informationString, separator) {
let result = '';
const splittedStr = imageId.split(informationString)[1];
if (splittedStr.includes(separator)) {
result = splittedStr.split(separator)[0];
} else {
result = splittedStr;
}
return result;
}
Iif (imageId.includes('/frames')) {
return getInformationFromURL('/frames', '/');
}
Iif (imageId.includes('&frame=')) {
return getInformationFromURL('&frame=', '&');
}
return;
}
getUIDsFromImageID(imageId) {
if (imageId.startsWith('wadors:')) {
const strippedImageId = imageId.split('/studies/')[1];
const splitImageId = strippedImageId.split('/');
return {
StudyInstanceUID: splitImageId[0], // Note: splitImageId[1] === 'series'
SeriesInstanceUID: splitImageId[2], // Note: splitImageId[3] === 'instances'
SOPInstanceUID: splitImageId[4],
frameNumber: splitImageId[6],
};
} else Iif (imageId.includes('?requestType=WADO')) {
const qs = queryString.parse(imageId);
return {
StudyInstanceUID: qs.studyUID,
SeriesInstanceUID: qs.seriesUID,
SOPInstanceUID: qs.objectUID,
frameNumber: qs.frameNumber,
};
}
// Maybe its a non-standard imageId
// check if the imageId starts with http:// or https:// using regex
// Todo: handle non http imageIds
let imageURI;
const urlRegex = /^(http|https|dicomfile):\/\//;
Iif (urlRegex.test(imageId)) {
imageURI = imageId;
} else {
imageURI = imageIdToURI(imageId);
}
// remove &frame=number from imageId
imageURI = imageURI.split('&frame=')[0];
const uids = this.imageURIToUIDs.get(imageURI);
const frameNumber = this.getFrameInformationFromURL(imageId) || '1';
Iif (uids && frameNumber !== undefined) {
return { ...uids, frameNumber };
}
return uids;
}
}
const metadataProvider = new MetadataProvider();
export default metadataProvider;
const WADO_IMAGE_LOADER = {
imagePlaneModule: instance => {
const { ImageOrientationPatient, ImagePositionPatient } = instance;
// Fallback for DX images.
// TODO: We should use the rest of the results of this function
// to update the UI somehow
const { PixelSpacing, type } = getPixelSpacingInformation(instance) || {};
let rowPixelSpacing;
let columnPixelSpacing;
let rowCosines;
let columnCosines;
let usingDefaultValues = false;
let isDefaultValueSetForRowCosine = false;
let isDefaultValueSetForColumnCosine = false;
let imageOrientationPatient;
if (PixelSpacing) {
[rowPixelSpacing, columnPixelSpacing] = PixelSpacing;
calibratedPixelSpacingMetadataProvider.add(instance.imageId, {
rowPixelSpacing: parseFloat(PixelSpacing[0]),
columnPixelSpacing: parseFloat(PixelSpacing[1]),
type,
});
} else E{
rowPixelSpacing = columnPixelSpacing = 1;
usingDefaultValues = true;
}
if (ImageOrientationPatient) {
rowCosines = toNumber(ImageOrientationPatient.slice(0, 3));
columnCosines = toNumber(ImageOrientationPatient.slice(3, 6));
imageOrientationPatient = toNumber(ImageOrientationPatient);
} else E{
rowCosines = [1, 0, 0];
columnCosines = [0, 1, 0];
imageOrientationPatient = [1, 0, 0, 0, 1, 0];
usingDefaultValues = true;
isDefaultValueSetForRowCosine = true;
isDefaultValueSetForColumnCosine = true;
}
const imagePositionPatient = toNumber(ImagePositionPatient) || [0, 0, 0];
Iif (!ImagePositionPatient) {
usingDefaultValues = true;
}
return {
frameOfReferenceUID: instance.FrameOfReferenceUID,
rows: toNumber(instance.Rows),
columns: toNumber(instance.Columns),
spacingBetweenSlices: toNumber(instance.SpacingBetweenSlices),
imageOrientationPatient,
rowCosines,
isDefaultValueSetForRowCosine,
columnCosines,
isDefaultValueSetForColumnCosine,
imagePositionPatient,
sliceThickness: toNumber(instance.SliceThickness),
sliceLocation: toNumber(instance.SliceLocation),
pixelSpacing: toNumber(PixelSpacing || 1),
rowPixelSpacing,
columnPixelSpacing,
usingDefaultValues,
};
},
};
const WADO_IMAGE_LOADER_TAGS = {
// dicomImageLoader specific
GENERAL_SERIES_MODULE: 'generalSeriesModule',
PATIENT_STUDY_MODULE: 'patientStudyModule',
IMAGE_PIXEL_MODULE: 'imagePixelModule',
VOI_LUT_MODULE: 'voiLutModule',
MODALITY_LUT_MODULE: 'modalityLutModule',
SOP_COMMON_MODULE: 'sopCommonModule',
PET_IMAGE_MODULE: 'petImageModule',
PET_ISOTOPE_MODULE: 'petIsotopeModule',
PET_SERIES_MODULE: 'petSeriesModule',
OVERLAY_PLANE_MODULE: 'overlayPlaneModule',
PATIENT_DEMOGRAPHIC_MODULE: 'patientDemographicModule',
// react-cornerstone-viewport specific
PATIENT_MODULE: 'patientModule',
GENERAL_IMAGE_MODULE: 'generalImageModule',
GENERAL_STUDY_MODULE: 'generalStudyModule',
CINE_MODULE: 'cineModule',
CALIBRATION_MODULE: 'calibrationModule',
};
const INSTANCE = 'instance';
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