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import { Events as EVENTS, MetadataModules } from '../enums';
import {
IWSIViewport,
WSIViewportProperties,
Point3,
Point2,
ICamera,
WSIViewportInput,
VOIRange,
} from '../types';
import * as metaData from '../metaData';
import { Transform } from './helpers/cpuFallback/rendering/transform';
import Viewport from './Viewport';
import { getOrCreateCanvas } from './helpers';
import { EPSILON } from '../constants';
import { triggerEvent } from '../utilities';
const _map = Symbol.for('map');
const EVENT_POSTRENDER = 'postrender';
/**
* An object representing a single stack viewport, which is a camera
* looking into an internal scene, and an associated target output `canvas`.
*/
class WSIViewport extends Viewport implements IWSIViewport {
public modality;
// Viewport Data
protected imageIds: string[];
readonly uid;
readonly renderingEngineId: string;
private frameOfReferenceUID: string;
// First is some specific metadata on the current image
protected metadata;
// Then the metadata array containing the dicomweb metadata definitions
protected metadataDicomweb;
private microscopyElement: HTMLDivElement;
protected map;
private internalCamera = {
rotation: 0,
centerIndex: [0, 0],
extent: [0, -2, 1, -1],
xSpacing: 1,
ySpacing: 1,
resolution: 1,
zoom: 1,
};
private viewer;
/**
* The VOI Range is used to apply contrast/brightness adjustments to the image.
*/
private voiRange: VOIRange = {
lower: 0,
upper: 255,
};
constructor(props: WSIViewportInput) {
super({
...props,
canvas: props.canvas || getOrCreateCanvas(props.element),
});
this.renderingEngineId = props.renderingEngineId;
this.element.setAttribute('data-viewport-uid', this.id);
this.element.setAttribute(
'data-rendering-engine-uid',
this.renderingEngineId
);
// Need to set the top level position as relative to make nested items
// use absolute positioning internally.
this.element.style.position = 'relative';
this.microscopyElement = document.createElement('div');
this.microscopyElement.id = crypto.randomUUID();
this.microscopyElement.innerText = 'Initial';
this.microscopyElement.style.background = 'grey';
this.microscopyElement.style.width = '100%';
this.microscopyElement.style.height = '100%';
this.microscopyElement.style.position = 'absolute';
this.microscopyElement.style.left = '0';
this.microscopyElement.style.top = '0';
const cs3dElement = this.element.firstElementChild;
cs3dElement.insertBefore(this.microscopyElement, cs3dElement.childNodes[1]);
this.addEventListeners();
this.resize();
}
public static get useCustomRenderingPipeline() {
return true;
}
private addEventListeners() {
this.canvas.addEventListener(
EVENTS.ELEMENT_DISABLED,
this.elementDisabledHandler
);
}
private removeEventListeners() {
this.canvas.removeEventListener(
EVENTS.ELEMENT_DISABLED,
this.elementDisabledHandler
);
}
private elementDisabledHandler() {
this.removeEventListeners();
}
private getImageDataMetadata(imageIndex = 0) {
const maxImage = this.metadataDicomweb.reduce((maxImage, image) => {
return maxImage?.NumberOfFrames < image.NumberOfFrames ? image : maxImage;
});
const {
TotalPixelMatrixColumns: columns,
TotalPixelMatrixRows: rows,
ImageOrientationSlide,
ImagedVolumeWidth: width,
ImagedVolumeHeight: height,
ImagedVolumeDepth: depth,
} = maxImage;
const imagePlaneModule = metaData.get(
MetadataModules.IMAGE_PLANE,
this.imageIds[imageIndex]
);
let rowCosines = ImageOrientationSlide.slice(0, 3);
let columnCosines = ImageOrientationSlide.slice(3, 6);
// if null or undefined
if (rowCosines == null || columnCosines == null) {
rowCosines = <Point3>[1, 0, 0];
columnCosines = <Point3>[0, 1, 0];
}
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,
];
const xSpacing = width / columns;
const ySpacing = height / rows;
const xVoxels = columns;
const yVoxels = rows;
const zSpacing = depth;
const zVoxels = 1;
this.hasPixelSpacing = !!(width && height);
return {
bitsAllocated: 8,
numComps: 3,
origin,
direction: [...rowCosineVec, ...colCosineVec, ...scanAxisNormal],
dimensions: [xVoxels, yVoxels, zVoxels],
spacing: [xSpacing, ySpacing, zSpacing],
hasPixelSpacing: this.hasPixelSpacing,
numVoxels: xVoxels * yVoxels * zVoxels,
imagePlaneModule,
};
}
// Sets the frame number - note according to DICOM, this is 1 based
public async setFrameNumber(frame: number) {
// No-op right now, not sure what this will be
}
public setProperties(props: WSIViewportProperties) {
// No-op - todo implement this
}
public getProperties = (): WSIViewportProperties => {
return {};
};
public resetProperties() {
this.setProperties({});
}
protected getScalarData() {
return null;
}
public getImageData() {
const { metadata } = this;
const spacing = metadata.spacing;
return {
dimensions: metadata.dimensions,
spacing,
numComps: 3,
origin: metadata.origin,
direction: metadata.direction,
metadata: { Modality: this.modality },
getScalarData: () => this.getScalarData(),
imageData: {
getDirection: () => metadata.direction,
getDimensions: () => metadata.dimensions,
getRange: () => [0, 255],
getScalarData: () => this.getScalarData(),
getSpacing: () => metadata.spacing,
worldToIndex: (point: Point3) => {
const canvasPoint = this.worldToCanvas(point);
const pixelCoord = this.canvasToIndex(canvasPoint);
return [pixelCoord[0], pixelCoord[1], 0];
},
indexToWorld: (point: Point3) => {
const canvasPoint = this.indexToCanvas([point[0], point[1]]);
return this.canvasToWorld(canvasPoint);
},
},
hasPixelSpacing: this.hasPixelSpacing,
calibration: this.calibration,
preScale: {
scaled: false,
},
};
}
/**
* Checks to see if the imageURI is currently being displayed. The imageURI
* may contain frame numbers according to the DICOM standard format, which
* will be stripped to compare the base image URI, and then the values used
* to check if that frame is currently being displayed.
*
* The DICOM standard allows for comma separated values as well, however,
* this is not supported here, with only a single range or single value
* being tested.
*
* For a single value, the time range +/- 5 frames is permitted to allow
* the detection to actually succeed when nearby without requiring an exact
* time frame to be matched.
*
* @param imageURI - containing frame number or range.
* @returns
*/
public hasImageURI(imageURI: string) {
// TODO - implement this
return true;
}
public setCamera(camera: ICamera): void {
const previousCamera = this.getCamera();
const { parallelScale, focalPoint } = camera;
const view = this.getView();
const { xSpacing } = this.internalCamera;
if (parallelScale) {
const worldToCanvasRatio = this.element.clientHeight / parallelScale;
const resolution = 1 / xSpacing / worldToCanvasRatio;
view.setResolution(resolution);
}
if (focalPoint) {
const newCanvas = this.worldToCanvas(focalPoint);
const newIndex = this.canvasToIndex(newCanvas);
view.setCenter(newIndex);
}
const updatedCamera = this.getCamera();
this.triggerCameraModifiedEventIfNecessary(previousCamera, updatedCamera);
}
/**
* This function returns the imageID associated with either the current
* frame being displayed, or the range of frames being played. This may not
* correspond to any particular imageId that has imageId metadata, as the
* format is one of:
* `<DICOMweb URI>/frames/<Start Frame>(-<End Frame>)?`
* or
* `<Other URI>[?&]frameNumber=<Start Frame>(-<EndFrame>)?`
* for a URL parameter.
*
* @returns an imageID for video
*/
public getCurrentImageId() {
return this.imageIds[0];
}
public getFrameNumber() {
return 1;
}
public getCamera(): ICamera {
this.refreshRenderValues();
const { resolution, xSpacing } = this.internalCamera;
const canvasToWorldRatio = resolution * xSpacing;
const canvasCenter: Point2 = [
this.element.clientWidth / 2,
this.element.clientHeight / 2,
];
const focalPoint = this.canvasToWorld(canvasCenter);
return {
parallelProjection: true,
focalPoint,
position: focalPoint,
viewUp: [0, -1, 0],
parallelScale: this.element.clientHeight * canvasToWorldRatio, // Reverse zoom direction back
viewPlaneNormal: [0, 0, 1],
};
}
public resetCamera = (): boolean => {
return true;
};
/**
* Gets the number of slices - this will be the number of focal planes,
* and not hte actual number of slices in the image sets.
*/
public getNumberOfSlices = (): number => {
return 1;
};
/**
* Need to return this as a function to prevent webpack from munging it.
*/
private getImportPath() {
return '/dicom-microscopy-viewer/dicomMicroscopyViewer.min.js';
}
/**
* The FOR for whole slide imaging is the frame of reference in the DICOM
* metadata, and should be the same for all slices being viewed.
*/
public getFrameOfReferenceUID = (): string => {
return this.frameOfReferenceUID;
};
public resize = (): void => {
const canvas = this.canvas;
const { clientWidth, clientHeight } = canvas;
// Set the canvas to be same resolution as the client.
if (canvas.width !== clientWidth || canvas.height !== clientHeight) {
canvas.width = clientWidth;
canvas.height = clientHeight;
}
this.refreshRenderValues();
};
/**
* Converts a VideoViewport canvas coordinate to a video coordinate.
*
* @param canvasPosition - to convert to world
* @returns World position
*/
public canvasToWorld = (canvasPos: Point2): Point3 => {
if (!this.metadata) {
return;
}
// compute the pixel coordinate in the image
const [px, py] = this.canvasToIndex(canvasPos);
// convert pixel coordinate to world coordinate
const { origin, spacing, direction } = this.getImageData();
const worldPos = vec3.fromValues(0, 0, 0);
// Calculate size of spacing vector in normal direction
const iVector = direction.slice(0, 3) as Point3;
const jVector = direction.slice(3, 6) as Point3;
// Calculate the world coordinate of the pixel
vec3.scaleAndAdd(worldPos, origin, iVector, px * spacing[0]);
vec3.scaleAndAdd(worldPos, worldPos, jVector, py * spacing[1]);
return [worldPos[0], worldPos[1], worldPos[2]] as Point3;
};
/**
* Converts and [x,y] video coordinate to a Cornerstone3D VideoViewport.
*
* @param worldPos - world coord to convert to canvas
* @returns Canvas position
*/
public worldToCanvas = (worldPos: Point3): Point2 => {
if (!this.metadata) {
return;
}
const { spacing, direction, origin } = this.metadata;
const iVector = direction.slice(0, 3) as Point3;
const jVector = direction.slice(3, 6) as Point3;
const diff = vec3.subtract([0, 0, 0], worldPos, origin);
const indexPoint: Point2 = [
vec3.dot(diff, iVector) / spacing[0],
vec3.dot(diff, jVector) / spacing[1],
];
// pixel to canvas
const canvasPoint = this.indexToCanvas(indexPoint);
return canvasPoint;
};
/**
* This is a wrapper for setWSI to allow generic behaviour
*/
public setDataIds(imageIds: string[]) {
const webClient = metaData.get(MetadataModules.WEB_CLIENT, imageIds[0]);
if (!webClient) {
throw new Error(
`To use setDataIds on WSI data, you must provide metaData.webClient for ${imageIds[0]}`
);
}
this.setWSI(imageIds, webClient);
}
public async setWSI(imageIds: string[], client) {
this.microscopyElement.style.background = 'red';
this.microscopyElement.innerText = 'Loading';
this.imageIds = imageIds;
// Import the straight module so that webpack doesn't touch it.
await import(/* webpackIgnore: true */ this.getImportPath());
const DicomMicroscopyViewer = (window as any).dicomMicroscopyViewer;
this.frameOfReferenceUID = null;
const metadataDicomweb = this.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 frameOfReference = imageMetadata['00200052']?.Value?.[0];
if (!this.frameOfReferenceUID) {
this.frameOfReferenceUID = frameOfReference;
} else if (frameOfReference !== this.frameOfReferenceUID) {
imageMetadata['00200052'].Value = [this.frameOfReferenceUID];
}
return imageMetadata;
});
const volumeImages = [];
metadataDicomweb.forEach((m) => {
const image =
new DicomMicroscopyViewer.metadata.VLWholeSlideMicroscopyImage({
metadata: m,
});
const imageFlavor = image.ImageType[2];
if (imageFlavor === 'VOLUME' || imageFlavor === 'THUMBNAIL') {
volumeImages.push(image);
}
});
this.metadataDicomweb = volumeImages;
// Construct viewer instance
const viewer = new DicomMicroscopyViewer.viewer.VolumeImageViewer({
client,
metadata: volumeImages,
controls: [],
bindings: {},
});
// Render viewer instance in the "viewport" HTML element
viewer.render({ container: this.microscopyElement });
this.metadata = this.getImageDataMetadata();
viewer.deactivateDragPanInteraction();
this.viewer = viewer;
this.map = viewer[_map];
this.map.on(EVENT_POSTRENDER, this.postrender);
this.resize();
this.microscopyElement.innerText = '';
Object.assign(this.microscopyElement.style, {
'--ol-partial-background-color': 'rgba(127, 127, 127, 0.7)',
'--ol-foreground-color': '#000000',
'--ol-subtle-foreground-color': '#000',
'--ol-subtle-background-color': 'rgba(78, 78, 78, 0.5)',
background: 'none',
});
}
public postrender = () => {
this.refreshRenderValues();
triggerEvent(this.element, EVENTS.IMAGE_RENDERED, {
element: this.element,
viewportId: this.id,
viewport: this,
renderingEngineId: this.renderingEngineId,
});
};
/**
* Scrolls the image - for WSI, this changes the zoom ratio since different
* images are used to represent different zoom levels, although this also
* allows fractional zoom levels
*/
public scroll(delta: number) {
const camera = this.getCamera();
this.setCamera({
parallelScale: camera.parallelScale * (1 + 0.1 * delta),
});
}
public getRotation = () => 0;
protected canvasToIndex = (canvasPos: Point2): Point2 => {
const transform = this.getTransform();
transform.invert();
return transform.transformPoint(canvasPos);
};
protected indexToCanvas = (indexPos: Point2): Point2 => {
const transform = this.getTransform();
return transform.transformPoint(indexPos);
};
/** This can be implemented later when multi-slice WSI is supported */
public getSliceIndex() {
return 0;
}
/**
* Gets the internal OpenLayers view object being rendered
* Note this is not typeds right now, but might add typing later.
*/
getView() {
if (!this.viewer) {
return;
}
// TODO - use a native method rather than accessing internals directly
const map = this.viewer[_map];
// TODO - remove the globals setter
const anyWindow = window as unknown as Record<string, unknown>;
anyWindow.map = map;
anyWindow.viewer = this.viewer;
anyWindow.view = map?.getView();
anyWindow.wsi = this;
return map?.getView();
}
/**
* Updates the internal camera rendering values from the underlying open layers
* data.
*/
private refreshRenderValues() {
const view = this.getView();
if (!view) {
return;
}
const resolution = view.getResolution();
if (!resolution || resolution < EPSILON) {
return;
}
// The location of the center right now
const centerIndex = view.getCenter();
const extent = view.getProjection().getExtent();
const rotation = view.getRotation();
const zoom = view.getZoom();
const {
metadata: {
spacing: [xSpacing, ySpacing],
},
} = this;
// this means that each unit (pixel) in the world (video) would be
// represented by n pixels in the canvas.
const worldToCanvasRatio = 1 / resolution / xSpacing;
Object.assign(this.internalCamera, {
extent,
centerIndex,
worldToCanvasRatio,
xSpacing,
ySpacing,
resolution,
rotation,
zoom,
});
}
public customRenderViewportToCanvas = () => {
// console.log('TODO - custom render');
};
public getZoom() {
return this.getView()?.getZoom();
}
public setZoom(zoom: number) {
this.getView()?.setZoom(zoom);
}
/**
* The transform here is from index to canvas points, so this takes
* into account the scaling applied and the center location, but nothing to do
* with world coordinate transforms.
* Note that the 'index' values are often negative values with respect to the overall
* image area, as that is what is used internally for the view.
*
* @returns A transform from index to canvas points
*/
protected getTransform() {
this.refreshRenderValues();
const { centerIndex: center, resolution, rotation } = this.internalCamera;
const halfCanvas = [this.canvas.width / 2, this.canvas.height / 2];
const transform = new Transform();
// Translate to the center of the canvas (move origin of the transform
// to the center of the canvas)
transform.translate(halfCanvas[0], halfCanvas[1]);
// Difference in sign for x/y to account for screen coordinates
transform.rotate(rotation);
transform.scale(1 / resolution, -1 / resolution);
transform.translate(-center[0], -center[1]);
return transform;
}
public getReferenceId(): string {
return `imageId:${this.getCurrentImageId()}`;
}
public getCurrentImageIdIndex() {
return 0;
}
}
export default WSIViewport;
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