larvitar 2.0.4 → 2.0.6

package/imaging/imageIo.ts

@@ -1,251 +0,0 @@
-/** @module imaging/imageIo
- *  @desc This file provides I/O functionalities on NRRD files and DICOM images
- */
-
-// external libraries
-import cornerstone from "cornerstone-core";
-import { forEach, find } from "lodash";
-
-// internal libraries
-import {
-  getMeanValue,
-  getDistanceBetweenSlices,
-  getTypedArrayFromDataType
-} from "./imageUtils";
-import store from "./imageStore";
-import { parse } from "./parsers/nrrd";
-import { checkMemoryAllocation } from "./monitors/memory";
-import { Series, Header, Volume, TypedArray } from "./types";
-
-/*
- * This module provides the following functions to be exported:
- * buildHeader(series)
- * getCachedPixelData(imageId)
- * buildData(series)
- * importNRRDImage(bufferArray)
- */
-
-/**
- * Build the image header from slices' metadata
- * @function buildHeader
- * @param {Object} series - Cornerstone series object
- * @returns {Object} header: image metadata
- */
-export const buildHeader = function (series: Series) {
-  let header: Partial<Header> = {};
-
-  forEach(series.imageIds, function (imageId: string) {
-    header[imageId] = series.instances[imageId].metadata;
-  });
-
-  let volume: Partial<Volume> = {};
-
-  volume.imageIds = series.imageIds;
-  volume.seriesId = series.instances[series.imageIds[0]].metadata.seriesUID;
-  volume.rows =
-    series.instances[series.imageIds[0]].metadata.rows ||
-    series.instances[series.imageIds[0]].metadata.x00280010;
-  volume.cols =
-    series.instances[series.imageIds[0]].metadata.cols ||
-    series.instances[series.imageIds[0]].metadata.x00280011;
-  volume.slope = series.instances[series.imageIds[0]].metadata.slope as number;
-  volume.repr = series.instances[series.imageIds[0]].metadata.repr as string;
-  volume.intercept = series.instances[series.imageIds[0]].metadata
-    .intercept as number;
-  volume.imagePosition = series.instances[series.imageIds[0]].metadata
-    .imagePosition as [number, number];
-  volume.numberOfSlices = series.imageIds.length;
-
-  // @ts-ignore
-  volume.imageOrientation = getMeanValue(
-    series,
-    "imageOrientation",
-    true
-  ) as number[];
-
-  // @ts-ignore
-  volume.pixelSpacing = getMeanValue(series, "pixelSpacing", true) as [
-    number,
-    number
-  ];
-  // volume.maxPixelValue = getMeanValue(series, "maxPixelValue", false);
-  // volume.minPixelValue = getMeanValue(series, "minPixelValue", false);
-  volume.sliceThickness = getDistanceBetweenSlices(series, 0, 1);
-
-  header.volume = volume as Volume;
-
-  return header as Header;
-};
-
-/**
- * Get cached pixel data
- * @function getCachedPixelData
- * @param {String} imageId - ImageId of the cached image
- * @returns {Promise} A promise which will resolve to a pixel data array or fail if an error occurs
- */
-
-export const getCachedPixelData = function (imageId: string) {
-  let cachedImage = find(cornerstone.imageCache.cachedImages, [
-    "imageId",
-    imageId
-  ]);
-  let promise = new Promise<number[]>((resolve, reject) => {
-    if (cachedImage && cachedImage.image) {
-      resolve(cachedImage.image.getPixelData());
-    } else {
-      cornerstone
-        .loadImage(imageId)
-        .then(image => resolve(image.getPixelData()))
-        .catch(err => reject(err));
-    }
-  });
-  return promise;
-};
-
-/**
- * Build the contiguous typed array from slices
- * @function buildData
- * @param {Object} series - Cornerstone series object
- * @param {Bool} useSeriesData - Flag to force using "series" data instead of cached ones
- * @returns {Array} Contiguous pixel array
- */
-export const buildData = function (series: Series, useSeriesData: boolean) {
-  if (checkMemoryAllocation(series.bytes)) {
-    let t0 = performance.now();
-    let repr = series.instances[series.imageIds[0]].metadata.repr;
-    let rows =
-      (series.instances[series.imageIds[0]].metadata.rows as number) ||
-      (series.instances[series.imageIds[0]].metadata.x00280010 as number);
-    let cols =
-      (series.instances[series.imageIds[0]].metadata.cols as number) ||
-      (series.instances[series.imageIds[0]].metadata.x00280011 as number);
-    let len = rows * cols * series.imageIds.length;
-
-    if (!repr) {
-      throw new Error("Image representation metadata not found");
-    }
-
-    let typedArray = getTypedArrayFromDataType(repr as string);
-
-    if (!typedArray) {
-      throw new Error("Image representation not supported");
-    }
-
-    let data = new typedArray(len);
-    let offsetData = 0;
-
-    // use input data or cached data
-    if (useSeriesData) {
-      forEach(series.imageIds, function (imageId: string) {
-        const sliceData = series.instances[imageId].pixelData;
-        if (sliceData) {
-          data.set(sliceData, offsetData);
-          offsetData += sliceData.length;
-        }
-      });
-      let t1 = performance.now();
-      console.log(`Call to buildData took ${t1 - t0} milliseconds.`);
-      return data;
-    } else {
-      store.addSeriesId(series.seriesUID, series.imageIds);
-      let image_counter = 0;
-      forEach(series.imageIds, function (imageId: string) {
-        getCachedPixelData(imageId).then((sliceData: number[]) => {
-          data.set(sliceData, offsetData);
-          offsetData += sliceData.length;
-          image_counter += 1;
-          if (image_counter == series.imageIds.length) {
-            let t1 = performance.now();
-            console.log(`Call to buildData took ${t1 - t0} milliseconds.`);
-            return data;
-          }
-        });
-      });
-    }
-  } else {
-    throw new Error("Data has not been builded: not enough memory");
-  }
-};
-
-/**
- * Build the contiguous typed array from slices (async version)
- * @function buildDataAsync
- * @param {Object} series - Cornerstone series object
- * @param {Number} time - Time(s) to wait for garbage collector
- * @param {Function} resolve - Promise resolve function
- * @param {Function} reject - Promise reject function
- */
-export const buildDataAsync = function (
-  series: Series,
-  time: number,
-  resolve: (response: TypedArray) => void,
-  reject: (response: string) => void
-) {
-  const memoryAllocation = checkMemoryAllocation(series.bytes);
-
-  if (memoryAllocation) {
-    let t0 = performance.now();
-    let repr = series.instances[series.imageIds[0]].metadata.repr;
-    let rows =
-      (series.instances[series.imageIds[0]].metadata.rows as number) ||
-      (series.instances[series.imageIds[0]].metadata.x00280010 as number);
-    let cols =
-      (series.instances[series.imageIds[0]].metadata.cols as number) ||
-      (series.instances[series.imageIds[0]].metadata.x00280011 as number);
-    let len = rows * cols * series.imageIds.length;
-
-    if (!repr) {
-      throw new Error("Image representation metadata not found");
-    }
-
-    let typedArray = getTypedArrayFromDataType(repr as string);
-
-    if (!typedArray) {
-      throw new Error("Image representation not supported");
-    }
-
-    let data = new typedArray(len);
-    let offsetData = 0;
-
-    let imageIds = series.imageIds.slice();
-    store.addSeriesId(series.seriesUID, series.imageIds);
-
-    function runFillPixelData(data: TypedArray) {
-      let imageId = imageIds.shift();
-      if (imageId) {
-        getCachedPixelData(imageId).then(sliceData => {
-          data.set(sliceData, offsetData);
-          offsetData += sliceData.length;
-          // this does the trick: delay next computation to next tick
-          setTimeout(() => {
-            runFillPixelData(data);
-          }, 0);
-        });
-      } else {
-        let t1 = performance.now();
-        console.log(`Call to buildDataAsync took ${t1 - t0} milliseconds.`);
-        resolve(data);
-      }
-    }
-    runFillPixelData(data);
-  } else if (time > 0) {
-    setTimeout(function () {
-      time = time - 5;
-      buildDataAsync(series, time, resolve, reject);
-    }, 5000);
-  } else {
-    reject("Data has not been builded: not enough memory");
-  }
-};
-
-/**
- * Import NRRD image from bufferArray
- * @function importNRRDImage
- * @param {ArrayBuffer} bufferArray - buffer array from nrrd file
- * @returns {Array} Parsed pixel data array
- */
-export const importNRRDImage = function (bufferArray: ArrayBuffer) {
-  // get the data
-  let volume = parse(bufferArray, { headerOnly: false });
-  return volume;
-};

package/imaging/imageLayers.ts

@@ -1,121 +0,0 @@
-/** @module imaging/imageLayers
- *  @desc This file provides functionalities for
- *        rendering image layers using cornerstone stack
- */
-
-// external libraries
-import cornerstone from "cornerstone-core";
-
-// internal libraries
-import { isElement } from "./imageUtils";
-import { Series } from "./types";
-
-/*
- * This module provides the following functions to be exported:
- * buildLayer(series, tag, options)
- * updateLayer(elementId, layerId, options)
- * getActiveLayer(elementId)
- * setActiveLayer(elementId, layerId)
- */
-
-/**
- * Build the image layers object
- * @function buildLayers
- * @param {Object} series - Cornerstone series object
- * @param {String} tag - Tag for the layer
- * @param {Object} options - layer options {opacity:float, colormap: str}
- * @returns {Object} Cornerstone layer object
- */
-export const buildLayer = function (
-  series: Series,
-  tag: string,
-  options: { opacity: number; colormap: string }
-) {
-  let layer = {
-    imageIds: series.imageIds,
-    currentImageIdIndex: Math.floor(series.imageIds.length / 2),
-    options: {
-      name: tag,
-      opacity: options?.opacity ? options?.opacity : 1.0,
-      visible: true,
-      viewport: {
-        colormap: options?.colormap ? options?.colormap : "gray"
-      }
-    }
-  };
-  return layer;
-};
-
-/**
- * Change the options of a layer
- * @instance
- * @function updateLayer
- * @param {String} elementId - The html div id used for rendering or its DOM HTMLElement
- * @param {string} layer - The layer id
- * @param {Object} options - The new layer's options
- */
-export const updateLayer = function (
-  elementId: string | HTMLElement,
-  layerId: string,
-  options: { opacity: number; colormap: string }
-) {
-  let element = isElement(elementId)
-    ? (elementId as HTMLElement)
-    : document.getElementById(elementId as string);
-  if (!element) {
-    console.log("not element");
-    return;
-  }
-  let layer = cornerstone.getLayer(element, layerId);
-  if (!layer.options) {
-    layer["options"] = {};
-  }
-  if (!layer.viewport) {
-    layer["viewport"] = {};
-  }
-  layer.options.opacity =
-    options.opacity != null ? options.opacity : layer.options.opacity;
-  layer.viewport.colormap = options.colormap
-    ? options.colormap
-    : layer.viewport.colormap;
-  cornerstone.updateImage(element);
-};
-
-/**
- * Get the active layer
- * @instance
- * @function getActiveLayer
- * @param {String} elementId - The html div id used for rendering or its DOM HTMLElement
- * @returns {Object} layer - The active layer object
- */
-export const getActiveLayer = function (elementId: string | HTMLElement) {
-  let element = isElement(elementId)
-    ? (elementId as HTMLElement)
-    : document.getElementById(elementId as string);
-  if (!element) {
-    console.log("not element");
-    return;
-  }
-  return cornerstone.getActiveLayer(element);
-};
-
-/**
- * Set the active layer
- * @instance
- * @function setActiveLayer
- * @param {String} elementId - The html div id used for rendering or its DOM HTMLElement
- * @param {String} layerId - The id of the layer
- */
-export const setActiveLayer = function (
-  elementId: string | HTMLElement,
-  layerId: string
-) {
-  let element = isElement(elementId)
-    ? (elementId as HTMLElement)
-    : document.getElementById(elementId as string);
-  if (!element) {
-    console.log("not element");
-    return;
-  }
-  cornerstone.setActiveLayer(element, layerId);
-};

package/imaging/imageLoading.ts

@@ -1,299 +0,0 @@
-/** @module imaging/imageLoading
- *  @desc This file provides functionalities for
- *        initialize, configure and update DICOMImageLoader
- */
-
-// external libraries
-import cornerstone from "cornerstone-core";
-import dicomParser from "dicom-parser";
-// import cornerstoneDICOMImageLoader from "@cornerstonejs/dicom-image-loader/dist/cornerstoneDICOMImageLoader.bundle.min.js";
-import { default as cornerstoneDICOMImageLoader } from "cornerstone-wado-image-loader";
-import cornerstoneWebImageLoader from "cornerstone-web-image-loader";
-import cornerstoneFileImageLoader from "cornerstone-file-image-loader";
-import { forEach } from "lodash";
-
-// internal libraries
-import store from "./imageStore";
-import { getSortedStack, getSortedUIDs } from "./imageUtils";
-import { loadNrrdImage } from "./loaders/nrrdLoader";
-import { loadReslicedImage } from "./loaders/resliceLoader";
-import { loadMultiFrameImage } from "./loaders/multiframeLoader";
-import { ImageObject, Instance, Series, StagedProtocol } from "./types";
-import { getLarvitarManager } from "./loaders/commonLoader";
-
-/**
- * Global standard configuration
- * @inner
- * @var {Object} globalConfig
- * @property {Number} maxWebWorkers - number of maximum web workers
- * @property {String} webWorkerPath - path to default DICOM web worker
- * @property {} - see https://github.com/cornerstonejs/cornerstoneDICOMImageLoader/blob/master/docs/WebWorkers.md
- */
-
-const MAX_CONCURRENCY = 6;
-const globalConfig = {
-  maxWebWorkers: Math.max(
-    Math.min(navigator.hardwareConcurrency - 1, MAX_CONCURRENCY),
-    1
-  ),
-  startWebWorkersOnDemand: true,
-  taskConfiguration: {
-    decodeTask: {
-      loadCodecsOnStartup: true,
-      initializeCodecsOnStartup: false,
-      strict: true
-    }
-  }
-};
-
-/*
- * This module provides the following functions to be exported:
- * initializeImageLoader(config)
- * initializeWebImageLoader()
- * initializeFileImageLoader()
- * registerNRRDImageLoader()
- * registerResliceLoader()
- * updateLoadedStack(seriesData, allSeriesStack)
- */
-
-/**
- * Configure DICOMImageLoader
- * @instance
- * @function initializeImageLoader
- * @param {Object} config - Custom config @default globalConfig
- */
-export const initializeImageLoader = function (config?: typeof globalConfig) {
-  let imageLoaderConfig = config ? config : globalConfig;
-  cornerstoneDICOMImageLoader.external.cornerstone = cornerstone;
-  cornerstoneDICOMImageLoader.external.dicomParser = dicomParser;
-  cornerstoneDICOMImageLoader.webWorkerManager.initialize(imageLoaderConfig);
-};
-
-/**
- * Configure cornerstoneWebImageLoader
- * @instance
- * @function initializeWebImageLoader
- */
-export const initializeWebImageLoader = function () {
-  cornerstoneWebImageLoader.external.cornerstone = cornerstone;
-  cornerstoneWebImageLoader.configure({
-    beforeSend: function () {
-      // add xhr as function arg
-      // Add custom headers here (e.g. auth tokens)
-      // xhr.setRequestHeader('x-auth-token', 'my auth token');
-    }
-  });
-};
-
-/**
- * Configure cornerstoneFileImageLoader
- * @instance
- * @function initializeFileImageLoader
- */
-export const initializeFileImageLoader = function () {
-  cornerstoneFileImageLoader.external.cornerstone = cornerstone;
-};
-
-/**
- * Register custom NRRD ImageLoader
- * @instance
- * @function registerNRRDImageLoader
- */
-export const registerNRRDImageLoader = function () {
-  cornerstone.registerImageLoader("nrrdLoader", loadNrrdImage);
-};
-
-/**
- * Register custom Reslice ImageLoader
- * @instance
- * @function registerResliceLoader
- */
-export const registerResliceLoader = function () {
-  cornerstone.registerImageLoader("resliceLoader", loadReslicedImage);
-};
-
-/**
- * Register custom MultiFrame ImageLoader
- * @instance
- * @function registerMultiFrameImageLoader
- */
-export const registerMultiFrameImageLoader = function () {
-  cornerstone.registerImageLoader("multiFrameLoader", loadMultiFrameImage);
-};
-
-/**
- * Update the allSeriesStack object using DICOMImageLoader fileManager
- * @instance
- * @function updateLoadedStack
- * @param {Object} seriesData - Cornerstone series object
- * @param {Object} allSeriesStack - Dict containing all series objects
- * @param {String} customId - Optional custom id to overwrite seriesUID as default one
- * @param {number} sliceIndex - Optional custom index to overwrite slice index as default one
- */
-export const updateLoadedStack = function (
-  seriesData: ImageObject,
-  allSeriesStack: ReturnType<typeof getLarvitarManager>,
-  customId?: string,
-  sliceIndex?: number
-) {
-  let lid = seriesData.metadata.larvitarSeriesInstanceUID;
-  let sid = seriesData.metadata.seriesUID;
-  let ssid = seriesData.metadata.studyUID;
-  let iid = seriesData.metadata.instanceUID as string;
-  let seriesDescription = seriesData.metadata.seriesDescription;
-  let numberOfSlices = seriesData.metadata["x00540081"]
-    ? seriesData.metadata["x00540081"]
-    : seriesData.metadata["x00201002"];
-  let numberOfFrames = seriesData.metadata["x00280008"];
-  let modality = seriesData.metadata["x00080060"];
-  let isMultiframe =
-    numberOfFrames && (numberOfFrames as number) > 1 ? true : false;
-  let numberOfTemporalPositions = seriesData.metadata["x00200105"];
-  let acquisitionNumberAttribute = seriesData.metadata["x00200012"];
-  let is4D = seriesData.metadata.is4D;
-  let waveform = seriesData.metadata.waveform;
-  let SOPUID = seriesData.metadata["x00080016"];
-  let isPDF = SOPUID == "1.2.840.10008.5.1.4.1.1.104.1" ? true : false;
-  let anonymized = seriesData.metadata.anonymized;
-
-  let color = cornerstoneDICOMImageLoader.isColorImage(
-    seriesData.metadata["x00280004"]
-  ) as boolean;
-  let id = customId || lid?.toString();
-
-  if (!id) {
-    throw new Error("Unique UID is not defined");
-  }
-
-  // Staged Protocol
-  // https://dicom.nema.org/dicom/2013/output/chtml/part17/sect_K.5.html
-  const numberOfStages = seriesData.metadata["x00082124"]; // Number of stages
-  const numberOfViews = seriesData.metadata["x0008212a"]; // Number of views in stage
-  const isStagedProtocol = numberOfStages ? true : false;
-
-  // initialize series stack
-  if (!allSeriesStack[id]) {
-    let series: Partial<Series> = {
-      currentImageIdIndex: 0,
-      imageIds: [], // (ordered)
-      instanceUIDs: {}, // instanceUID: imageId (ordered)
-      instances: {},
-      seriesDescription: seriesDescription as string,
-      larvitarSeriesInstanceUID: lid as string,
-      seriesUID: sid as string,
-      studyUID: ssid as string,
-      numberOfImages: is4D ? (acquisitionNumberAttribute as number) : 0,
-      numberOfSlices: numberOfSlices as number,
-      numberOfFrames: numberOfFrames as number,
-      numberOfTemporalPositions: numberOfTemporalPositions as number,
-      isMultiframe: isMultiframe,
-      waveform: waveform as boolean,
-      is4D: is4D as boolean,
-      isPDF: isPDF as boolean,
-      anonymized: anonymized as boolean,
-      modality: modality as string,
-      color: color,
-      bytes: 0
-    };
-    if (isStagedProtocol) {
-      const stageName = seriesData.metadata["x00082120"];
-      const stageNumber = seriesData.metadata["x00082122"];
-      const viewName = seriesData.metadata["x00082127"];
-      const viewNumber = seriesData.metadata["x00082128"];
-      const stagedProtocol: StagedProtocol = {
-        numberOfStages: numberOfStages as number,
-        numberOfViews: numberOfViews as number,
-        stageName: stageName ? (stageName as string).trim() : undefined,
-        stageNumber: stageNumber as number,
-        viewName: viewName ? (viewName as string).trim() : undefined,
-        viewNumber: viewNumber as number
-      };
-      series.stagedProtocol = stagedProtocol;
-    }
-    allSeriesStack[id] = series as Series;
-  }
-
-  // get instance number from metadata
-  const instanceNumber = seriesData.metadata["x00200013"];
-  const defaultMethod = instanceNumber ? "instanceNumber" : "imagePosition";
-  const sortMethods: Array<"imagePosition" | "contentTime" | "instanceNumber"> =
-    is4D ? [defaultMethod, "contentTime"] : [defaultMethod];
-
-  // if the parsed file is a new series instance, keep it
-
-  if (isMultiframe) {
-    allSeriesStack[id].bytes += seriesData.file.size;
-    allSeriesStack[id].dataSet = seriesData.dataSet;
-    allSeriesStack[id].metadata = seriesData.metadata;
-  } else if (isNewInstance(allSeriesStack[id].instances, iid!)) {
-    // generate an imageId for the file and store it
-    // in allSeriesStack imageIds array, used by
-    // DICOMImageLoader to display the stack of images
-    let imageId = cornerstoneDICOMImageLoader.wadouri.fileManager.add(
-      seriesData.file
-    ) as string;
-
-    if (sliceIndex !== undefined) {
-      allSeriesStack[id].imageIds[sliceIndex] = imageId;
-    } else {
-      allSeriesStack[id].imageIds.push(imageId);
-    }
-
-    if (is4D === false) {
-      allSeriesStack[id].numberOfImages =
-        (allSeriesStack[id].numberOfImages || 0) + 1;
-    }
-
-    allSeriesStack[id].bytes += seriesData.file.size;
-    // store needed instance tags
-    allSeriesStack[id].instances[imageId] = {
-      metadata: seriesData.metadata,
-      file: seriesData.file,
-      dataSet: seriesData.dataSet
-    };
-
-    if (isPDF === false) {
-      if (sliceIndex === undefined) {
-        // order images in stack
-        allSeriesStack[id].imageIds = getSortedStack(
-          allSeriesStack[id] as Series,
-          sortMethods,
-          true
-        );
-        // populate the ordered dictionary of instanceUIDs
-        allSeriesStack[id].instanceUIDs = getSortedUIDs(
-          allSeriesStack[id] as Series
-        );
-      } else {
-        allSeriesStack[id].instanceUIDs[iid] = imageId;
-      }
-      store.addSeriesId(id, allSeriesStack[id].imageIds);
-    } else {
-      allSeriesStack[id].instanceUIDs[iid] = imageId;
-      store.addSeriesId(id, allSeriesStack[id].imageIds);
-    }
-  }
-};
-
-/* Internal module functions */
-
-/**
- * Check if the instance is new or not
- * @inner
- * @function isNewInstance
- * @param {Object} instances - instances already loaded
- * @param {String} iid - instance uid to check
- * @return {Bool} True if is new instance, false if already present
- */
-let isNewInstance = function (
-  instances: { [key: string]: Instance },
-  iid: string
-) {
-  let isNewInstance = true;
-  forEach(instances, function (instance: Instance) {
-    if (instance.metadata.instanceUID === iid) {
-      isNewInstance = false;
-    }
-  });
-  return isNewInstance;
-};