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import { MetadataModules } from '../enums';
import type { Point3 } from '../types';
import { peerImport } from '../init';
import * as metaData from '../metaData';
import microscopyViewportCss from '../constants/microscopyViewportCss';
import imageIdToURI from './imageIdToURI';
export interface WSIImageMetadataSource {
NumberOfFrames?: number;
TotalPixelMatrixColumns: number;
TotalPixelMatrixRows: number;
ImageOrientationSlide?: number[];
ImagedVolumeWidth?: number;
ImagedVolumeHeight?: number;
ImagedVolumeDepth?: number;
TotalPixelMatrixOriginSequence?: Array<{
XOffsetInSlideCoordinateSystem?: number;
YOffsetInSlideCoordinateSystem?: number;
ZOffsetInSlideCoordinateSystem?: number;
}>;
['00080008']?: {
Value?: string[];
};
['00200052']?: {
Value?: string[];
};
isMultiframe?: unknown;
frameNumber?: unknown;
[key: string]: unknown;
}
export interface WSIImageVolumeLike extends WSIImageMetadataSource {
ImageType: string[];
}
export interface WSIClientLike {
getDICOMwebMetadata(imageId: string): WSIImageMetadataSource;
}
export interface WSIMapViewLike {
getCenter(): [number, number];
getExtent?(): number[];
getProjection(): {
getExtent(): number[];
};
getResolution(): number;
getResolutionForZoom?(zoom: number): number;
getRotation(): number;
getZoom(): number;
setCenter(center: [number, number]): void;
setResolution?(resolution: number): void;
setRotation(rotation: number): void;
setZoom(zoom: number): void;
}
export interface WSIMapLike {
getView(): WSIMapViewLike;
getViewport(): HTMLElement;
on(eventName: string, handler: () => void): void;
render(): void;
un(eventName: string, handler: () => void): void;
updateSize?(): void;
}
export interface WSIViewerLike {
cleanup?(): void;
deactivateDragPanInteraction(): void;
getAffine(): unknown;
getMap(): WSIMapLike;
render(args: { container: HTMLElement }): void;
}
export interface WSITransformUtilitiesLike {
applyInverseTransform(args: {
coordinate: [number, number];
affine: unknown;
}): [number, number];
applyTransform(args: {
coordinate: [number, number];
affine: unknown;
}): [number, number];
}
export interface DicomMicroscopyViewerLike {
metadata: {
VLWholeSlideMicroscopyImage: new (args: {
metadata: WSIImageMetadataSource;
}) => WSIImageVolumeLike;
};
utils?: WSITransformUtilitiesLike;
viewer: {
VolumeImageViewer: new (args: {
client: unknown;
metadata: WSIImageVolumeLike[];
controls: string[];
retrieveRendered: boolean;
bindings: Record<string, unknown>;
}) => WSIViewerLike;
};
}
export interface WSIImageDataMetadata {
bitsAllocated: number;
numberOfComponents: number;
origin: Point3;
direction: number[];
dimensions: [number, number, number];
spacing: [number, number, number];
hasPixelSpacing: boolean;
numVoxels: number;
imagePlaneModule: Record<string, unknown>;
}
export interface LoadedWSIData {
volumeImages: WSIImageVolumeLike[];
metadataDicomweb: WSIImageMetadataSource[];
metadata: WSIImageDataMetadata;
frameOfReferenceUID: string | null;
imageURISet: Set<string>;
}
const overlayCssId = 'wsiViewportOverlayCss';
export async function getDicomMicroscopyViewer(): Promise<DicomMicroscopyViewerLike> {
return peerImport(
'dicom-microscopy-viewer'
) as Promise<DicomMicroscopyViewerLike>;
}
export function addWSIMiniNavigationOverlayCss() {
if (document.getElementById(overlayCssId)) {
return;
}
const overlayCss = document.createElement('style');
overlayCss.innerText = microscopyViewportCss;
overlayCss.setAttribute('id', overlayCssId);
document.getElementsByTagName('head')[0].append(overlayCss);
}
export function getWSIImageDataMetadata(args: {
metadataDicomweb: WSIImageMetadataSource[];
imageIds: string[];
imageIndex?: number;
}): WSIImageDataMetadata {
const { metadataDicomweb, imageIds, imageIndex = 0 } = args;
const maxImage = metadataDicomweb.reduce((currentMax, image) => {
return currentMax?.NumberOfFrames < image.NumberOfFrames
? image
: currentMax;
});
const {
TotalPixelMatrixColumns: columns,
TotalPixelMatrixRows: rows,
ImageOrientationSlide,
ImagedVolumeWidth: width,
ImagedVolumeHeight: height,
ImagedVolumeDepth: depth,
} = maxImage;
const imagePlaneModule = metaData.get(
MetadataModules.IMAGE_PLANE,
imageIds[imageIndex]
);
let rowCosines = ImageOrientationSlide.slice(0, 3);
let columnCosines = ImageOrientationSlide.slice(3, 6);
if (rowCosines == null || columnCosines == null) {
rowCosines = [1, 0, 0] as Point3;
columnCosines = [0, 1, 0] as Point3;
}
const rowCosineVec = vec3.fromValues(
rowCosines[0],
rowCosines[1],
rowCosines[2]
);
const colCosineVec = vec3.fromValues(
columnCosines[0],
columnCosines[1],
columnCosines[2]
);
const scanAxisNormal = vec3.create();
vec3.cross(scanAxisNormal, rowCosineVec, colCosineVec);
const {
XOffsetInSlideCoordinateSystem = 0,
YOffsetInSlideCoordinateSystem = 0,
ZOffsetInSlideCoordinateSystem = 0,
} = maxImage.TotalPixelMatrixOriginSequence?.[0] || {};
const origin = [
XOffsetInSlideCoordinateSystem,
YOffsetInSlideCoordinateSystem,
ZOffsetInSlideCoordinateSystem,
] as Point3;
const xSpacing = width / columns;
const ySpacing = height / rows;
const zSpacing = depth;
const xVoxels = columns;
const yVoxels = rows;
const zVoxels = 1;
return {
bitsAllocated: 8,
numberOfComponents: 3,
origin,
direction: [...rowCosineVec, ...colCosineVec, ...scanAxisNormal],
dimensions: [xVoxels, yVoxels, zVoxels],
spacing: [xSpacing, ySpacing, zSpacing],
hasPixelSpacing: !!(width && height),
numVoxels: xVoxels * yVoxels * zVoxels,
imagePlaneModule,
};
}
export async function loadWSIData(args: {
imageIds: string[];
client: WSIClientLike;
dicomMicroscopyViewer?: DicomMicroscopyViewerLike;
}): Promise<LoadedWSIData> {
const { imageIds, client, dicomMicroscopyViewer } = args;
const DicomMicroscopyViewer =
dicomMicroscopyViewer || (await getDicomMicroscopyViewer());
let frameOfReferenceUID: string | null = null;
const metadataDicomweb = imageIds.map((imageId) => {
const imageMetadata = client.getDICOMwebMetadata(imageId);
Object.defineProperty(imageMetadata, 'isMultiframe', {
value: imageMetadata.isMultiframe,
enumerable: false,
});
Object.defineProperty(imageMetadata, 'frameNumber', {
value: undefined,
enumerable: false,
});
const imageType = imageMetadata['00080008']?.Value;
if (imageType?.length === 1) {
imageMetadata['00080008'].Value = imageType[0].split('\\');
}
const imageFrameOfReference = imageMetadata['00200052']?.Value?.[0];
if (!frameOfReferenceUID) {
frameOfReferenceUID = imageFrameOfReference;
} else if (imageFrameOfReference !== frameOfReferenceUID) {
imageMetadata['00200052'].Value = [frameOfReferenceUID];
}
return imageMetadata;
});
const volumeImages: WSIImageVolumeLike[] = [];
metadataDicomweb.forEach((metadata) => {
const image =
new DicomMicroscopyViewer.metadata.VLWholeSlideMicroscopyImage({
metadata,
});
const imageFlavor = image.ImageType[2];
if (imageFlavor === 'VOLUME' || imageFlavor === 'THUMBNAIL') {
volumeImages.push(image);
}
});
return {
volumeImages,
metadataDicomweb,
metadata: getWSIImageDataMetadata({
metadataDicomweb: volumeImages,
imageIds,
}),
frameOfReferenceUID,
imageURISet: new Set(imageIds.map((imageId) => imageIdToURI(imageId))),
};
}
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