larvitar 2.0.4 → 2.0.6

package/imaging/imageReslice.ts

@@ -1,87 +0,0 @@
-/** @module imaging/imageReslice
- *  @desc  This file provides functionalities for
- *         image reslice in orthogonal directions
- */
-
-// external libraries
-import { v4 as uuidv4 } from "uuid";
-import { each } from "lodash";
-
-// internal libraries
-import { getReslicedMetadata, getReslicedPixeldata } from "./imageUtils";
-import {
-  getLarvitarImageTracker,
-  getLarvitarManager
-} from "./loaders/commonLoader";
-import store from "./imageStore";
-import { Series } from "./types";
-
-/*
- * This module provides the following functions to be exported:
- * resliceSeries(seriesId, seriesData, orientation)
- */
-
-/**
- * Reslice a serie from native orientation to coronal or sagittal orientation
- * @instance
- * @function resliceSeries
- * @param {Object} seriesData the original series data
- * @param {String} orientation the reslice orientation [coronal or sagittal]
- * @returns {Promise} - Return a promise which will resolve when data is available
- */
-export function resliceSeries(
-  seriesData: Series,
-  orientation: "axial" | "coronal" | "sagittal"
-) {
-  let reslicePromise = new Promise(resolve => {
-    let reslicedSeries: Partial<Series> = {};
-    let reslicedSeriesId = uuidv4();
-    let reslicedMetaData = getReslicedMetadata(
-      reslicedSeriesId,
-      "axial",
-      orientation,
-      seriesData,
-      "resliceLoader"
-    );
-
-    reslicedSeries.imageIds = reslicedMetaData.imageIds;
-    // @ts-ignore fix incompatibilities between these types
-    reslicedSeries.instances = reslicedMetaData.instances;
-
-    reslicedSeries.currentImageIdIndex = Math.floor(
-      reslicedSeries.imageIds.length / 2
-    );
-
-    function computeReslice(
-      seriesData: Series,
-      reslicedSeriesId: string,
-      reslicedSeries: Series
-    ) {
-      let t0 = performance.now();
-      let imageTracker = getLarvitarImageTracker();
-      let manager = getLarvitarManager();
-      each(reslicedSeries.imageIds, function (imageId: string) {
-        reslicedSeries.instances[imageId].pixelData = getReslicedPixeldata(
-          imageId,
-          seriesData,
-          reslicedSeries
-        ) as Uint16Array;
-        imageTracker[imageId] = reslicedSeriesId;
-      });
-      store.addSeriesId(reslicedSeriesId, reslicedSeries.imageIds);
-      reslicedSeries.numberOfImages = reslicedSeries.imageIds.length;
-      reslicedSeries.seriesUID = reslicedSeriesId;
-      reslicedSeries.seriesDescription = seriesData.seriesDescription;
-      reslicedSeries.orientation = orientation;
-      manager[reslicedSeriesId] = reslicedSeries;
-      //@ts-ignore deprecated
-      manager[seriesData.seriesUID][orientation] = reslicedSeriesId;
-      let t1 = performance.now();
-      console.log(`Call to resliceSeries took ${t1 - t0} milliseconds.`);
-      resolve(reslicedSeries);
-    }
-    // reslice the data
-    computeReslice(seriesData, reslicedSeriesId, reslicedSeries as Series);
-  });
-  return reslicePromise;
-}

package/imaging/imageStore.ts

@@ -1,487 +0,0 @@
-/** @module imaging/imageStore
- *  @desc This file provides functionalities
- *        for data config store.
- */
-
-// external libraries
-import { get as _get, cloneDeep as _cloneDeep } from "lodash";
-
-type StoreSeries = { imageIds: string[]; progress: number };
-
-type Store = {
-  colormapId: string;
-  errorLog: string; // TODO review this, should be an array?
-  leftActiveTool?: string;
-  rightActiveTool?: string;
-  series: { [seriesUID: string]: StoreSeries };
-  viewports: { [key: string]: typeof DEFAULT_VIEWPORT };
-  // fallback for any other field
-  [key: string]: any;
-};
-
-type SetPayload =
-  | ["errorLog" | "leftActiveTool" | "rightActiveTool", string]
-  | [
-      "isColor" | "isMultiframe" | "isPDF" | "isTimeserie" | "ready",
-      string,
-      boolean
-    ]
-  | [
-      (
-        | "progress"
-        | "loading"
-        | "minPixelValue"
-        | "maxPixelValue"
-        | "minSliceId"
-        | "maxSliceId"
-        | "minTimeId"
-        | "maxTimeId"
-        | "rotation"
-        | "scale"
-        | "sliceId"
-        | "timeId"
-        | "thickness"
-      ),
-      string,
-      number
-    ]
-  | ["timestamp", string, number | undefined]
-  | ["pendingSliceId", string, number | undefined]
-  | ["timestamps" | "timeIds", string, number[]]
-  | [
-      "contrast" | "dimensions" | "spacing" | "translation",
-      string,
-      number,
-      number
-    ]
-  | [
-      "defaultViewport",
-      string,
-      number,
-      number,
-      number,
-      number,
-      number,
-      number,
-      boolean
-    ];
-
-// Larvitar store object
-let STORE: Store;
-
-// Data listeners
-let storeListener: ((data: Store) => {}) | undefined = undefined;
-const seriesListeners = {} as {
-  [seriesId: string]: (data: StoreSeries) => {};
-};
-const viewportsListeners = {} as {
-  [elementId: string]: (data: typeof DEFAULT_VIEWPORT) => {};
-};
-
-// default initial store object
-const INITIAL_STORE_DATA: Store = {
-  colormapId: "gray",
-  errorLog: "",
-  leftActiveTool: undefined,
-  rightActiveTool: undefined,
-  series: {},
-  viewports: {}
-};
-
-// default viewport object
-export const DEFAULT_VIEWPORT: {
-  loading: number;
-  ready: boolean;
-  minSliceId: number;
-  maxSliceId: number;
-  sliceId: number;
-  pendingSliceId?: number;
-  minTimeId: number;
-  maxTimeId: number;
-  timeId: number;
-  timestamp: number;
-  timestamps: number[];
-  timeIds: number[];
-  rows: number;
-  cols: number;
-  spacing_x: number;
-  spacing_y: number;
-  thickness: number;
-  minPixelValue: number;
-  maxPixelValue: number;
-  isColor: boolean;
-  isMultiframe: boolean;
-  isTimeserie: boolean;
-  isPDF: boolean;
-  viewport: {
-    scale: number;
-    rotation: number;
-    translation: {
-      x: number;
-      y: number;
-    };
-    voi: {
-      windowCenter: number;
-      windowWidth: number;
-    };
-    // redundant fields ?
-    rows: number;
-    cols: number;
-    spacing_x: number;
-    spacing_y: number;
-    thickness: number;
-  };
-  default: {
-    scale: number;
-    rotation: number;
-    translation: {
-      x: number;
-      y: number;
-    };
-    voi: {
-      windowCenter: number;
-      windowWidth: number;
-      invert: boolean;
-    };
-  };
-} = {
-  loading: 0, // from 0 to 100 (%)
-  ready: false, // true when currentImageId is rendered
-  minSliceId: 0,
-  maxSliceId: 0,
-  sliceId: 0,
-  pendingSliceId: undefined,
-  minTimeId: 0,
-  maxTimeId: 0,
-  timeId: 0,
-  timestamp: 0,
-  timestamps: [],
-  timeIds: [],
-  rows: 0,
-  cols: 0,
-  spacing_x: 0.0,
-  spacing_y: 0.0,
-  thickness: 0.0,
-  minPixelValue: 0,
-  maxPixelValue: 0,
-  isColor: false,
-  isMultiframe: false,
-  isTimeserie: false,
-  isPDF: false,
-  viewport: {
-    scale: 0.0,
-    rotation: 0.0,
-    translation: {
-      x: 0.0,
-      y: 0.0
-    },
-    voi: {
-      windowCenter: 0.0,
-      windowWidth: 0.0
-    },
-    // redundant fields ?
-    rows: 0,
-    cols: 0,
-    spacing_x: 0.0,
-    spacing_y: 0.0,
-    thickness: 0.0
-  },
-  default: {
-    scale: 0.0,
-    rotation: 0.0,
-    translation: {
-      x: 0.0,
-      y: 0.0
-    },
-    voi: {
-      windowCenter: 0.0,
-      windowWidth: 0.0,
-      invert: false
-    }
-  }
-};
-
-export type Viewport = typeof DEFAULT_VIEWPORT;
-
-// Trigger store listeners
-const triggerStoreListener = (data: Store) =>
-  storeListener ? storeListener(data) : undefined;
-
-const triggerViewportListener = (elementId: string) => {
-  if (viewportsListeners[elementId] && STORE?.viewports[elementId]) {
-    viewportsListeners[elementId](STORE.viewports[elementId]);
-  }
-};
-
-const triggerSeriesListener = (seriesId: string) => {
-  if (seriesListeners[seriesId] && STORE?.series[seriesId]) {
-    seriesListeners[seriesId](STORE.series[seriesId]);
-  }
-};
-
-/**
- * Set a value into store
- * @function setValue
- * @param {Object} data - The data object
- */
-const setValue = (store: Store, data: SetPayload) => {
-  let field = data[0];
-  const k = data[1];
-  let [_1, _2, ...v] = data;
-
-  const viewport = store.viewports[k];
-
-  // assign values
-  switch (field) {
-    case "progress":
-      if (!store.series[k]) {
-        return;
-      }
-      store.series[k][field] = (v as [number])[0];
-      triggerSeriesListener(k);
-      break;
-
-    case "isColor":
-    case "isMultiframe":
-    case "isPDF":
-    case "isTimeserie":
-    case "ready":
-      if (!viewport) {
-        return;
-      }
-      viewport[field] = (v as [boolean])[0];
-      triggerViewportListener(k);
-      break;
-
-    case "loading":
-    case "minPixelValue":
-    case "maxPixelValue":
-    case "minSliceId":
-    case "maxSliceId":
-    case "minTimeId":
-    case "maxTimeId":
-    case "sliceId":
-    case "pendingSliceId":
-    case "timeId":
-    case "timestamp":
-      if (!viewport) {
-        return;
-      }
-      viewport[field] = (v as [number])[0];
-      triggerViewportListener(k);
-      break;
-
-    case "timestamps":
-    case "timeIds":
-      if (!viewport) {
-        return;
-      }
-      viewport[field] = (v as [[number]])[0];
-      triggerViewportListener(k);
-      break;
-
-    case "rotation":
-    case "scale":
-      if (!viewport) {
-        return;
-      }
-      viewport.viewport[field] = (v as [number])[0];
-      triggerViewportListener(k);
-      break;
-
-    case "thickness":
-      if (!viewport) {
-        return;
-      }
-      viewport[field] = (v as [number])[0];
-      viewport.viewport[field] = (v as [number])[0];
-      triggerViewportListener(k);
-      break;
-
-    case "translation":
-      if (!viewport) {
-        return;
-      }
-      v = v as [number, number];
-      viewport.viewport[field] = { x: v[0], y: v[1] };
-      triggerViewportListener(k);
-      break;
-
-    case "contrast":
-      if (!viewport) {
-        return;
-      }
-      v = v as [number, number];
-      viewport.viewport.voi.windowWidth = v[0];
-      viewport.viewport.voi.windowCenter = v[1];
-      triggerViewportListener(k);
-      break;
-
-    case "dimensions":
-      if (!viewport) {
-        return;
-      }
-      v = v as [number, number];
-      viewport.rows = v[0];
-      viewport.cols = v[1];
-      viewport.viewport.rows = v[0];
-      viewport.viewport.cols = v[1];
-      triggerViewportListener(k);
-      break;
-
-    case "spacing":
-      if (!viewport) {
-        return;
-      }
-      v = v as [number, number];
-      viewport.spacing_x = v[0];
-      viewport.spacing_y = v[1];
-      viewport.viewport.spacing_x = v[0];
-      viewport.viewport.spacing_y = v[1];
-      triggerViewportListener(k);
-      break;
-
-    case "defaultViewport":
-      if (!viewport) {
-        return;
-      }
-      v = v as [number, number, number, number, number, number, boolean];
-      viewport.default.scale = v[0];
-      viewport.default.rotation = v[1];
-      viewport.default.translation.x = v[2];
-      viewport.default.translation.y = v[3];
-      viewport.default.voi.windowWidth = v[4];
-      viewport.default.voi.windowCenter = v[5];
-      viewport.default.voi.invert = v[6];
-      triggerViewportListener(k);
-      break;
-
-    default:
-      store[field] = k;
-      break;
-  }
-};
-
-/**
- * Instancing the store
- */
-const setup = (data = _cloneDeep(INITIAL_STORE_DATA)) => {
-  /**
-   * Create the Proxy handler object
-   * @param  {String} name The namespace
-   * @param  {Object} data The data object
-   * @return {Object}      The Proxy handler
-   */
-  const handler: ProxyHandler<Store> = {
-    get: (obj, prop: string) => {
-      if (prop === "_isProxy") return true;
-      if (
-        ["object", "array"].includes(
-          Object.prototype.toString.call(obj[prop]).slice(8, -1).toLowerCase()
-        ) &&
-        !obj[prop]._isProxy
-      ) {
-        obj[prop] = new Proxy<Store>(obj[prop], handler);
-      }
-      return obj[prop];
-    },
-    set: (obj, prop: string, value) => {
-      // console.warn("SET", obj, prop, value);
-      if (obj[prop] === value) return true;
-      obj[prop] = value;
-      triggerStoreListener(data);
-      return true;
-    },
-    deleteProperty: (obj, prop: string) => {
-      delete obj[prop];
-      triggerStoreListener(data);
-      return true;
-    }
-  };
-
-  return new Proxy<Store>(data, handler);
-};
-
-const initializeStore = () => {
-  STORE = setup();
-};
-
-const validateStore = () => {
-  if (!STORE) {
-    throw "Larvitar store does not exists. Initialize it with the 'initializeStore' function.";
-  }
-};
-
-export const set = (payload: SetPayload) => {
-  validateStore();
-  setValue(STORE!, payload);
-};
-
-export default {
-  initialize: initializeStore,
-  // add/remove viewports
-  addViewport: (name: string) => {
-    validateStore();
-    STORE!.viewports[name] = _cloneDeep(DEFAULT_VIEWPORT);
-  },
-  deleteViewport: (name: string) => {
-    validateStore();
-    delete STORE!.viewports[name];
-  },
-  // add/remove series instances ids
-  addSeriesId: (seriesId: string, imageIds: string[]) => {
-    validateStore();
-    if (!STORE!.series[seriesId]) {
-      STORE!.series[seriesId] = {} as StoreSeries;
-    }
-    STORE!.series[seriesId].imageIds = imageIds;
-    triggerSeriesListener(seriesId);
-  },
-  removeSeriesId: (seriesId: string) => {
-    validateStore();
-    delete STORE!.series[seriesId];
-  },
-  resetSeriesIds: () => {
-    validateStore();
-    STORE!.series = {};
-  },
-  // expose useful sets
-  setSliceId: (elementId: string, imageIndex: number) => {
-    set(["sliceId", elementId, imageIndex]);
-  },
-  setPendingSliceId: (elementId: string, imageIndex: number) => {
-    set(["pendingSliceId", elementId, imageIndex]);
-  },
-  setMaxSliceId: (elementId: string, imageIndex: number) => {
-    set(["maxSliceId", elementId, imageIndex]);
-  },
-  // get
-  get: (props: string | string[]) => {
-    validateStore();
-    return _get(STORE, props);
-  },
-  // watch store
-  addStoreListener: (listener: (data: Store) => {}) =>
-    (storeListener = listener),
-  removeStoreListener: () => (storeListener = undefined),
-  // watch single viewport
-  addViewportListener: (
-    elementId: string,
-    listener: (data: typeof DEFAULT_VIEWPORT) => {}
-  ) => {
-    viewportsListeners[elementId] = listener;
-  },
-  removeViewportListener: (elementId: string) => {
-    delete viewportsListeners[elementId];
-  },
-  // watch single series
-  addSeriesListener: (
-    seriesId: string,
-    listener: (data: StoreSeries) => {}
-  ) => {
-    seriesListeners[seriesId] = listener;
-  },
-  removeSeriesListener: (seriesId: string) => {
-    delete seriesListeners[seriesId];
-  }
-};