larvitar 2.0.5 → 2.0.7

package/imaging/loaders/nrrdLoader.ts

@@ -1,630 +0,0 @@
-/** @module loaders/nrrdLoader
- *  @desc This file provides functionalities for
- *        custom NRRD Loader
- */
-
-// external libraries
-import cornerstone from "cornerstone-core";
-import { default as cornerstoneDICOMImageLoader } from "cornerstone-wado-image-loader";
-import { each, clone, range, findKey, filter, pickBy } from "lodash";
-import { v4 as uuidv4 } from "uuid";
-import { ImageLoader } from "cornerstone-core";
-
-// internal libraries
-import {
-  getNormalOrientation,
-  getPixelRepresentation,
-  getTypedArrayFromDataType
-} from "../imageUtils";
-
-import {
-  getImageFrame,
-  getLarvitarImageTracker,
-  getLarvitarManager
-} from "./commonLoader";
-import type {
-  Image,
-  Instance,
-  Volume,
-  LarvitarManager,
-  ImageFrame,
-  ImageTracker,
-  MetaData
-} from "../types";
-import { DataSet } from "dicom-parser";
-
-// global module variables
-let customImageLoaderCounter = 0;
-
-/*
- * This module provides the following functions to be exported:
- * buildNrrdImage(volume, seriesId, custom_header)
- * getNrrdImageId(customLoaderName)
- * loadNrrdImage(imageId)
- * getImageIdFromSlice(sliceNumber, orientation)
- * getSliceNumberFromImageId(imageId, orientation)
- * getNrrdSerieDimensions()
- */
-
-type NrrdInputVolume = {
-  header: {
-    sizes: number[];
-    "space directions": number[][]; // a property with a space in the name ?? Seriously ??
-    "space origin": [number, number];
-    kinds: string[];
-    type: string;
-  };
-  data: Uint16Array; // TODO-ts: other typed arrays ?
-};
-
-export type NrrdSeries = {
-  currentImageIdIndex: number;
-  imageIds: string[];
-  instances: { [key: string]: Instance };
-  instanceUIDs: { [key: string]: string };
-  numberOfImages: number;
-  seriesDescription: string;
-  seriesUID: string;
-  customLoader: string;
-  nrrdHeader: NrrdHeader;
-  bytes: number;
-  dataSet?: DataSet;
-  metadata?: MetaData;
-  ecgData?: number[];
-};
-
-type NrrdHeader = {
-  volume: Volume;
-  intercept: number;
-  slope: number;
-  repr: string;
-  phase: string;
-  study_description: string;
-  series_description: string;
-  acquisition_date: string;
-  [imageId: string]: string | number | Volume | NrrdInstance; // TODO-ts: fix this: we need just NrrdInstance
-};
-
-type NrrdInstance = {
-  instanceUID: string;
-  seriesDescription: string;
-  seriesModality: string;
-  patientName: string;
-  bitsAllocated: number;
-  pixelRepresentation: string;
-};
-
-// TODO-ts: why it's different from cornerstone type ?
-// type Image = {
-//   imageId: string;
-//   rows: number;
-//   columns: number;
-//   minPixelValue: number;
-//   maxPixelValue: number;
-//   slope: number;
-//   intercept: number;
-//   windowCenter: number;
-//   windowWidth: number;
-//   render?: Function;
-//   getPixelData?: Function;
-//   getCanvas?: Function;
-//   color: boolean;
-//   columnPixelSpacing: number;
-//   rowPixelSpacing: number;
-//   invert: boolean;
-//   sizeInBytes: number;
-//   height: number;
-//   width: number;
-//   decodeTimeInMS?: number;
-//   webWorkerTimeInMS?: number;
-//   metadata: {[key: string]: MetadataValue};
-// }
-
-/**
- * Build the data structure for the provided image orientation
- * @instance
- * @function buildNrrdImage
- * @param {Object} volume The volume object
- * @param {String} seriesId The Id of the series
- * @param {Object} custom_header A custom header object
- * @return {Object} volume data
- */
-export const buildNrrdImage = function (
-  volume: NrrdInputVolume,
-  seriesId: string,
-  custom_header: NrrdHeader
-) {
-  //TODO-ts: better definition
-  let t0 = performance.now();
-  // standard image structure
-  let image: Partial<NrrdSeries> = {};
-  let manager = getLarvitarManager() as LarvitarManager;
-  let imageTracker = getLarvitarImageTracker() as ImageTracker;
-  image.currentImageIdIndex = 0;
-  image.imageIds = [];
-  image.instances = {};
-  image.numberOfImages = 0;
-  image.seriesDescription = "";
-  image.seriesUID = seriesId;
-
-  let header: Partial<NrrdHeader> = {};
-  header.volume = {} as Volume;
-  // need to extract header from nrrd file format
-  // sizes, spaceDirections and spaceOrigin
-
-  const index = volume.header.kinds[0] == "domain" ? 0 : 1;
-
-  let spacing_x = Math.sqrt(
-    volume.header["space directions"][index + 0][0] *
-      volume.header["space directions"][index + 0][0] +
-      volume.header["space directions"][index + 0][1] *
-        volume.header["space directions"][index + 0][1] +
-      volume.header["space directions"][index + 0][2] *
-        volume.header["space directions"][index + 0][2]
-  );
-  let spacing_y = Math.sqrt(
-    volume.header["space directions"][index + 1][0] *
-      volume.header["space directions"][index + 1][0] +
-      volume.header["space directions"][index + 1][1] *
-        volume.header["space directions"][index + 1][1] +
-      volume.header["space directions"][index + 1][2] *
-        volume.header["space directions"][index + 1][2]
-  );
-  let spacing_z = Math.sqrt(
-    volume.header["space directions"][index + 2][0] *
-      volume.header["space directions"][index + 2][0] +
-      volume.header["space directions"][index + 2][1] *
-        volume.header["space directions"][index + 2][1] +
-      volume.header["space directions"][index + 2][2] *
-        volume.header["space directions"][index + 2][2]
-  );
-  header.volume.rows = volume.header.sizes[index + 1];
-  header.volume.cols = volume.header.sizes[index + 0];
-  header.volume.numberOfSlices = volume.header.sizes[index + 2];
-  header.volume.imagePosition = volume.header["space origin"];
-  header.volume.pixelSpacing = [spacing_x, spacing_y];
-  header.volume.sliceThickness = spacing_z;
-  header.volume.repr =
-    volume.header.type[0].toUpperCase() + volume.header.type.slice(1);
-  header.volume.intercept = custom_header ? custom_header.intercept : 0;
-  header.volume.slope = custom_header ? custom_header.slope : 1;
-  header.volume.phase = custom_header ? custom_header.phase : "";
-  header.volume.study_description = custom_header
-    ? custom_header.study_description
-    : "";
-  header.volume.series_description = custom_header
-    ? custom_header.series_description
-    : "";
-  header.volume.acquisition_date = custom_header
-    ? custom_header.acquisition_date
-    : "";
-
-  let rows = volume.header.sizes[index + 1];
-  let cols = volume.header.sizes[index + 0];
-  let frames = volume.header.sizes[index + 2];
-  let iopArr = volume.header["space directions"][index + 0].concat(
-    volume.header["space directions"][index + 1]
-  );
-  if (iopArr.length !== 6) {
-    throw new Error("Invalid Image Orientation");
-  }
-  let iop = iopArr as [number, number, number, number, number, number];
-  let firstIpp = header.volume.imagePosition;
-  let w = getNormalOrientation(iop);
-  let ps = header.volume.pixelSpacing;
-  let thickness = header.volume.sliceThickness;
-  let intercept = header.volume.intercept;
-  let slope = header.volume.slope;
-
-  let metadata: Partial<Instance["metadata"]> = {
-    x00280010: rows, // Rows
-    x00280011: cols, // Columns
-    x00200037: iop, // ImageOrientationPatient
-    x00280030: ps, // PixelSpacing
-    x00180050: [thickness][0], // SliceThickness
-    x00281052: intercept ? [intercept] : [0],
-    x00281053: slope ? [slope] : [1],
-    x00200052: header.volume.imageIds
-      ? (header[header.volume.imageIds[0]] as NrrdInstance).instanceUID
-      : null,
-    x0008103e: header.volume.imageIds
-      ? (header[header.volume.imageIds[0]] as NrrdInstance).seriesDescription
-      : null,
-    x00080060: header.volume.imageIds
-      ? (header[header.volume.imageIds[0]] as NrrdInstance).seriesModality
-      : null,
-    x00100010: header.volume.imageIds
-      ? (header[header.volume.imageIds[0]] as NrrdInstance).patientName
-      : null,
-    x00280100: header.volume.imageIds
-      ? (header[header.volume.imageIds[0]] as NrrdInstance).bitsAllocated
-      : null,
-    x00280103: header.volume.imageIds
-      ? (header[header.volume.imageIds[0]] as NrrdInstance).pixelRepresentation
-      : null,
-    repr: header.volume.repr || null
-  };
-
-  // compute default ww/wl values here to use them also for resliced images
-  let minMax = cornerstoneDICOMImageLoader.getMinMax(volume.data);
-  let maxVoi =
-    minMax.max * (metadata.x00281053 as number[])[0] +
-    (metadata.x00281052 as number[])[0];
-  let minVoi =
-    minMax.min * (metadata.x00281053 as number[])[0] +
-    (metadata.x00281052 as number[])[0];
-  let ww = maxVoi - minVoi;
-  let wl = (maxVoi + minVoi) / 2;
-
-  metadata.x00280106 = minMax.min;
-  metadata.x00280107 = minMax.max;
-
-  // extract the pixelData of each frame, store the data into the image object
-  each(range(frames), function (sliceIndex: number) {
-    let sliceSize = rows * cols;
-    let sliceBuffer = volume.data.subarray(
-      sliceSize * sliceIndex,
-      sliceSize * (sliceIndex + 1)
-    );
-
-    if (!metadata) {
-      throw new Error("Metadata not found");
-    }
-
-    // @ts-ignore: TODO this is concepptually wrong, we already know the Pixel Representation
-    // (see above, line 241), this function just returns the same value again
-    let r = getPixelRepresentation(metadata);
-    let typedArray = getTypedArrayFromDataType(r);
-
-    if (!typedArray) {
-      throw new Error("Typed array not found");
-    }
-
-    let pixelData = new typedArray(sliceBuffer);
-    // assign these values to the metadata of all images
-    metadata.x00281050 = wl;
-    metadata.x00281051 = ww;
-
-    let imageId = getNrrdImageId("nrrdLoader");
-    if (!imageTracker) {
-      throw new Error("Image tracker not initialized");
-    }
-    imageTracker[imageId] = seriesId;
-
-    // store file references
-    image.imageIds!.push(imageId);
-    let frameMetadata: MetaData = clone(metadata);
-    frameMetadata.x00200032 = firstIpp.map(function (val, i) {
-      return val + thickness * sliceIndex * w[i];
-    });
-    image.instances![imageId] = {
-      instanceId: uuidv4(),
-      frame: sliceIndex,
-      metadata: frameMetadata,
-      pixelData: pixelData
-    };
-  });
-
-  let middleSlice = Math.floor(image.imageIds.length / 2);
-  image.currentImageIdIndex = middleSlice;
-  image.numberOfImages = image.imageIds.length;
-  // specify custom loader type and attach original header
-  image.customLoader = "nrrdLoader";
-  header.volume.imageIds = image.imageIds;
-  image.nrrdHeader = header as NrrdHeader;
-
-  if (!manager) {
-    throw new Error("Larvitar manager not initialized");
-  }
-
-  manager[seriesId] = image as NrrdSeries;
-
-  let t1 = performance.now();
-  console.log(`Call to buildNrrdImage took ${t1 - t0} milliseconds.`);
-  return image;
-};
-
-/**
- * Get the custom imageId from custom loader
- * @instance
- * @function getNrrdImageId
- * @param {String} customLoaderName The custom loader name
- * @return {String} the custom image id
- */
-export const getNrrdImageId = function (customLoaderName: string) {
-  let imageId = customLoaderName + "://" + customImageLoaderCounter;
-  customImageLoaderCounter++;
-  return imageId;
-};
-
-/**
- * Custom cornerstone image loader for nrrd files
- * @instance
- * @function loadNrrdImage
- * @param {String} imageId The image id
- * @return {Object} custom image object
- */
-export const loadNrrdImage: ImageLoader = function (imageId: string) {
-  let manager = getLarvitarManager() as LarvitarManager;
-  let imageTracker = getLarvitarImageTracker() as ImageTracker;
-  if (!manager || !imageTracker) {
-    throw new Error("Larvitar manager or image tracker not initialized");
-  }
-  let seriesId = imageTracker[imageId];
-  let instance = manager[seriesId].instances[imageId];
-  //@ts-ignore TODO-ts: fix this why is different typed array?
-  return createCustomImage(imageId, instance.metadata, instance.pixelData);
-};
-
-/**
- * Retrieve imageId for a slice in the given orientation
- * @instance
- * @function getImageIdFromSlice
- * @param {Integer} sliceNumber The image slice number
- * @param {String} orientation The orientation tag
- * @param {String} seriesId The series id
- * @return {String} image id
- */
-export const getImageIdFromSlice = function (
-  sliceNumber: number,
-  orientation: string,
-  seriesId: string
-) {
-  var prefix = "nrrdLoader://";
-  var serieImageTracker;
-  let imageTracker = getLarvitarImageTracker() as ImageTracker;
-
-  if (seriesId) {
-    serieImageTracker = pickBy(imageTracker, image => {
-      return image[0] == seriesId;
-    });
-  } else {
-    serieImageTracker = imageTracker;
-  }
-
-  var firstImageIdStr = findKey(serieImageTracker, entry => {
-    return entry[1] == orientation;
-  });
-
-  let firstImageId = firstImageIdStr?.split("//").pop();
-
-  if (firstImageId == undefined) {
-    console.error("cannot find imageId for orientation: " + orientation);
-    return "";
-  }
-
-  var imageIndex = parseInt(firstImageId) + parseInt(sliceNumber.toString());
-
-  var imageId = prefix.concat(imageIndex.toString());
-
-  return imageId;
-};
-
-/**
- * Retrieve slice number for a the given orientation
- * @instance
- * @function getSliceNumberFromImageId
- * @param {String} imageId The image slice id
- * @param {String} orientation The orientation tag
- * @param {String} seriesId The series id
- * @return {Integer} The image slice number
- */
-export const getSliceNumberFromImageId = function (
-  imageId: string,
-  orientation: string
-) {
-  let imageTracker = getLarvitarImageTracker() as ImageTracker;
-  var firstImageIdStr = findKey(imageTracker, entry => {
-    return entry[1] == orientation;
-  });
-
-  if (firstImageIdStr == undefined) {
-    console.error("cannot find imageId for orientation: " + orientation);
-    return 0;
-  }
-
-  var imageNumber = imageId.split("//").pop() || imageId;
-  let firstImageId = firstImageIdStr.split("//").pop();
-
-  if (firstImageId == undefined) {
-    console.error("cannot find imageId for orientation: " + orientation);
-    return 0;
-  }
-
-  var imageIndex = parseInt(imageNumber) - parseInt(firstImageId);
-
-  return imageIndex;
-};
-
-/**
- * Get series dimension for each view
- * @instance
- * @function getNrrdSerieDimensions
- * @return {Object} Series dimension for each view
- */
-export const getNrrdSerieDimensions = function () {
-  let imageTracker = getLarvitarImageTracker() as ImageTracker;
-  var dim_axial = filter(imageTracker, img => {
-    return img[1] == "axial";
-  });
-  var dim_coronal = filter(imageTracker, img => {
-    return img[1] == "coronal";
-  });
-  var dim_sagittal = filter(imageTracker, img => {
-    return img[1] == "sagittal";
-  });
-
-  return {
-    axial: [dim_coronal.length, dim_sagittal.length, dim_axial.length],
-    coronal: [dim_sagittal.length, dim_axial.length, dim_coronal.length],
-    sagittal: [dim_coronal.length, dim_axial.length, dim_sagittal.length]
-  };
-};
-
-/* Internal functions */
-
-/**
- * Create the custom image object for conrnestone from nrrd file
- * @instance
- * @function createCustomImage
- * @param {String} imageId The series id
- * @param {Object} metadata The metadata object
- * @param {Object} pixelData The pixelData object
- * @param {Object} dataSet The dataset
- * @return {String} The image id
- */
-let createCustomImage = function (
-  imageId: string,
-  metadata: MetaData,
-  pixelData: Uint8ClampedArray,
-  dataSet?: any
-) {
-  //TODO-ts check this
-  let canvas = window.document.createElement("canvas");
-  let lastImageIdDrawn = "";
-
-  let imageFrame = getImageFrame(metadata, dataSet) as ImageFrame;
-
-  // This function uses the pixelData received as argument without manipulating
-  // them: if the image is compressed, the decompress function should be called
-  // before creating the custom image object (like the multiframe case).
-  imageFrame.pixelData = pixelData;
-
-  let pixelSpacing = metadata.x00280030;
-  let rescaleIntercept = metadata.x00281052;
-  let rescaleSlope = metadata.x00281053;
-  let windowCenter = metadata.x00281050;
-  let windowWidth = metadata.x00281051;
-
-  function getSizeInBytes() {
-    let bytesPerPixel = Math.round(imageFrame.bitsAllocated / 8);
-    return (
-      imageFrame.rows *
-      imageFrame.columns *
-      bytesPerPixel *
-      imageFrame.samplesPerPixel
-    );
-  }
-
-  let image: Partial<Image> = {
-    imageId: imageId,
-    color: cornerstoneDICOMImageLoader.isColorImage(
-      imageFrame.photometricInterpretation
-    ),
-    columnPixelSpacing: pixelSpacing ? pixelSpacing[1] : undefined,
-    columns: imageFrame.columns,
-    height: imageFrame.rows,
-    intercept: rescaleIntercept ? (rescaleIntercept as number[])[0] : 0,
-    invert: imageFrame.photometricInterpretation === "MONOCHROME1",
-    minPixelValue: imageFrame.smallestPixelValue,
-    maxPixelValue: imageFrame.largestPixelValue,
-    render: undefined, // set below
-    rowPixelSpacing: pixelSpacing ? pixelSpacing[0] : undefined,
-    rows: imageFrame.rows,
-    sizeInBytes: getSizeInBytes(),
-    slope: rescaleSlope ? (rescaleSlope as number[])[0] : 1,
-    width: imageFrame.columns,
-    windowCenter: windowCenter ? (windowCenter as number[])[0] : undefined,
-    windowWidth: windowWidth ? (windowWidth as number[])[0] : undefined,
-    decodeTimeInMS: undefined,
-    webWorkerTimeInMS: undefined
-  };
-
-  // add function to return pixel data
-  image.getPixelData = function () {
-    if (!imageFrame.pixelData) {
-      console.warn('no pixel data for imageId "' + imageId);
-      return [];
-    }
-    return Array.from(imageFrame.pixelData);
-  };
-
-  // convert color space
-  if (image.color) {
-    // setup the canvas context
-    canvas.height = imageFrame.rows;
-    canvas.width = imageFrame.columns;
-
-    let context = canvas.getContext("2d");
-
-    if (!context) {
-      throw new Error("Unable to get canvas context");
-    }
-
-    let imageData = context.createImageData(
-      imageFrame.columns,
-      imageFrame.rows
-    );
-    cornerstoneDICOMImageLoader.convertColorSpace(imageFrame, imageData);
-
-    imageFrame.imageData = imageData;
-    imageFrame.pixelData = imageData.data;
-  }
-
-  // Setup the renderer
-  if (image.color) {
-    image.render = cornerstone.renderColorImage;
-    image.getCanvas = function () {
-      if (lastImageIdDrawn === imageId) {
-        return canvas;
-      }
-
-      canvas.height = image.rows || 0;
-      canvas.width = image.columns || 0;
-      let context = canvas.getContext("2d");
-      if (!context) {
-        throw new Error("Unable to get canvas context");
-      }
-      context.putImageData(imageFrame.imageData!, 0, 0);
-      lastImageIdDrawn = imageId;
-      return canvas;
-    };
-  } else {
-    image.render = undefined; // will be set at need in cornerstone render pipeline, see drawImageSync.js (line 44)
-  }
-
-  // calculate min/max if not supplied
-  if (image.minPixelValue === undefined || image.maxPixelValue === undefined) {
-    let minMax = cornerstoneDICOMImageLoader.getMinMax(pixelData);
-    image.minPixelValue = minMax.min;
-    image.maxPixelValue = minMax.max;
-  }
-
-  // set the ww/wc to cover the dynamic range of the image if no values are supplied
-  if (image.windowCenter === undefined || image.windowWidth === undefined) {
-    if (image.color) {
-      image.windowWidth = 255.0;
-      image.windowCenter = 127.5;
-    } else if (
-      image.maxPixelValue != null &&
-      image.minPixelValue != null &&
-      image.slope != null &&
-      image.intercept != null
-    ) {
-      let maxVoi = image.maxPixelValue * image.slope + image.intercept;
-      let minVoi = image.minPixelValue * image.slope + image.intercept;
-      image.windowWidth = maxVoi - minVoi;
-      image.windowCenter = (maxVoi + minVoi) / 2;
-    } else {
-      console.error(
-        "Unable to calculate default window width/center for imageId: " +
-          imageId
-      );
-    }
-  }
-
-  // Custom images does not have the "data" attribute becaouse their dataset is
-  // not available. The "metadata" attribute is used by the storeImageData
-  // function to store custom image pixelData and metadata.
-  image.metadata = metadata;
-
-  let promise: Promise<Image> = new Promise(function (resolve) {
-    resolve(image as Image);
-  });
-
-  // Return an object containing the Promise to cornerstone so it can setup callbacks to be
-  // invoked asynchronously for the success/resolve and failure/reject scenarios.
-  return {
-    promise
-  };
-};