larvitar 2.0.4 → 2.0.6

package/imaging/loaders/multiframeLoader.ts

@@ -1,435 +0,0 @@
-/** @module loaders/multiframeLoader
- *  @desc This file is a custom DICOM loader for multiframe images
- */
-
-// external libraries
-import { default as cornerstoneDICOMImageLoader } from "cornerstone-wado-image-loader";
-import { each, range } from "lodash";
-
-// internal libraries
-import {
-  getImageFrame,
-  getLarvitarImageTracker,
-  getLarvitarManager
-} from "./commonLoader";
-import { parseDataSet } from "../imageParsing";
-import type {
-  Image,
-  ImageFrame,
-  LarvitarManager,
-  MetaData,
-  Series
-} from "../types";
-
-// global module variables
-let customImageLoaderCounter = 0;
-
-// Local cache used to store multiframe datasets to avoid reading and parsing
-// the whole file to show a single frame.
-let multiframeDatasetCache: { [key: string]: Series | null } | null = null;
-/*
- * This module provides the following functions to be exported:
- * loadMultiFrameImage(elementId)
- * buildMultiFrameImage(seriesId, serie)
- * getMultiFrameImageId(customLoaderName)
- * clearMultiFrameCache()
- */
-
-/**
- * Custom MultiFrame Loader Function
- * @export
- * @function loadMultiFrameImage
- * @param {String} imageId - ImageId tag
- * @returns {Function} Custom Image Creation Function
- */
-export const loadMultiFrameImage = function (imageId: string) {
-  let parsedImageId = cornerstoneDICOMImageLoader.wadouri.parseImageId(imageId);
-  let rootImageId = parsedImageId.scheme + ":" + parsedImageId.url;
-  let imageTracker = getLarvitarImageTracker();
-  let seriesId = imageTracker[rootImageId];
-  let manager = getLarvitarManager() as LarvitarManager;
-  if (multiframeDatasetCache === null) {
-    multiframeDatasetCache = {};
-  }
-
-  if (multiframeDatasetCache[rootImageId]) {
-    multiframeDatasetCache[rootImageId] = multiframeDatasetCache[rootImageId];
-  } else if (manager) {
-    multiframeDatasetCache[rootImageId] = manager[seriesId] as Series;
-  } else {
-    throw new Error("No multiframe dataset found for seriesId: " + seriesId);
-  }
-
-  let metadata =
-    multiframeDatasetCache[rootImageId]?.instances[imageId].metadata;
-  return createCustomImage(rootImageId, imageId, parsedImageId.frame, metadata);
-};
-
-/**
- * Build the multiframe layout in the larvitar Manager
- * @export
- * @function buildMultiFrameImage
- * @param {String} seriesId - SeriesId tag
- * @param {Object} serie - parsed serie object
- */
-export const buildMultiFrameImage = function (seriesId: string, serie: Series) {
-  let t0 = performance.now();
-  let manager = getLarvitarManager();
-  let imageTracker = getLarvitarImageTracker();
-  let numberOfFrames = serie.metadata!.numberOfFrames!;
-  let frameTime = serie.metadata!.frameTime;
-  let frameDelay = serie.metadata!.frameDelay ? serie.metadata!.frameDelay : 0;
-  let rWaveTimeVector = serie.metadata!.rWaveTimeVector;
-  let sopInstanceUID = serie.metadata!["x00080018"] as string;
-  let dataSet = serie.dataSet;
-  let imageId = getMultiFrameImageId("multiFrameLoader");
-  imageTracker[imageId] = seriesId;
-
-  // check if manager exists for this seriesId
-  if (!manager[seriesId]) {
-    manager[seriesId] = serie;
-    manager[seriesId].imageIds = [];
-    manager[seriesId].instances = {};
-  }
-
-  each(range(numberOfFrames as number), function (frameNumber) {
-    let frameImageId = imageId + "?frame=" + frameNumber;
-    // EXTRACT MULTIFRAME METADATA (x52009230) Per-frame Functional Groups Sequence
-    let frameMetadata = { ...serie.metadata! };
-
-    parseDataSet(dataSet!, frameMetadata, {
-      tags: ["x52009230"],
-      frameId: frameNumber
-    });
-
-    // TODO-ts REMOVE "AS" WHEN METADATA VALUES ARE TYPED
-    // store file references
-    const managerSeriesId = manager[seriesId] as Series;
-    managerSeriesId.seriesUID = seriesId;
-    managerSeriesId.studyUID = serie.metadata!["x0020000d"] as string;
-    managerSeriesId.modality = serie.metadata!["x00080060"] as string;
-    managerSeriesId.color = cornerstoneDICOMImageLoader.isColorImage(
-      serie.metadata!["x00280004"]
-    );
-
-    managerSeriesId.isMultiframe = true;
-    managerSeriesId.currentImageIdIndex = 0;
-    managerSeriesId.numberOfFrames = numberOfFrames;
-    managerSeriesId.frameTime = frameTime;
-    managerSeriesId.frameDelay = frameDelay;
-    managerSeriesId.rWaveTimeVector = rWaveTimeVector;
-    managerSeriesId.numberOfImages = undefined;
-    managerSeriesId.bytes = serie.bytes;
-    managerSeriesId.imageIds.push(frameImageId);
-    managerSeriesId.instanceUIDs[sopInstanceUID] = imageId;
-    managerSeriesId.instances[frameImageId] = {
-      instanceId: sopInstanceUID,
-      frame: frameNumber,
-      metadata: frameMetadata
-    };
-    managerSeriesId.dataSet = dataSet || null;
-    managerSeriesId.seriesDescription = serie.metadata!
-      .seriesDescription as string;
-  });
-
-  let t1 = performance.now();
-  console.log(`Call to buildMultiFrameImage took ${t1 - t0} milliseconds.`);
-};
-
-/**
- * Get the custom imageId from custom loader
- * @instance
- * @function getMultiFrameImageId
- * @param {String} customLoaderName The custom loader name
- * @return {String} the custom image id
- */
-export const getMultiFrameImageId = function (customLoaderName: string) {
-  let imageId = customLoaderName + "://" + customImageLoaderCounter;
-  customImageLoaderCounter++;
-  return imageId;
-};
-
-/**
- * Clear the multiframe cache
- * @instance
- * @function clearMultiFrameCache
- * @param {String} seriesId - SeriesId tag
- */
-export const clearMultiFrameCache = function (seriesId: string) {
-  each(multiframeDatasetCache, function (image, imageId) {
-    if (!image) {
-      return;
-    }
-    if (seriesId == image.seriesUID || !seriesId) {
-      if (image.dataSet) {
-        // @ts-ignore: modify external type ?
-        image.dataSet.byteArray = null;
-      }
-      image.dataSet = null;
-      image.elements = null;
-      each(image.instances, function (instance) {
-        // @ts-ignore: is needed to clear the cache ?
-        instance.metadata = null;
-      });
-      // @ts-ignore: is needed to clear the cache ?
-      image.instances = null;
-      multiframeDatasetCache![imageId] = null;
-      delete multiframeDatasetCache![imageId];
-    }
-  });
-  if (!seriesId) {
-    multiframeDatasetCache = null;
-  }
-};
-
-/* Internal module functions */
-
-/**
- * Create the custom image object for cornerstone from custom image
- * @instance
- * @function createCustomImage
- * @param {String} imageId The Id of the image
- * @param {Object} metadata the metadata object
- * @param {Object} pixelData pixel data object
- * @param {Object} dataSet dataset object
- * @returns {Object} custom image object
- */
-let createCustomImage = function (
-  id: string,
-  imageId: string,
-  frameIndex: number,
-  metadata?: MetaData
-) {
-  let options: { [key: string]: any } = {}; //TODO-ts change any to proper type when available
-  // always preScale the pixel array unless it is asked not to
-  options.preScale = {
-    enabled:
-      options.preScale && options.preScale.enabled !== undefined
-        ? options.preScale.enabled
-        : false
-  };
-
-  if (multiframeDatasetCache === null || !multiframeDatasetCache[id]) {
-    throw new Error("No multiframe dataset found for id: " + id);
-  }
-
-  let dataSet = (multiframeDatasetCache as { [key: string]: Series })[id]
-    .dataSet;
-
-  if (!dataSet) {
-    throw new Error("No dataset found for id: " + id);
-  }
-
-  let pixelDataElement = dataSet.elements.x7fe00010;
-  // Extract pixelData of the required frame
-  let pixelData: number[];
-  try {
-    if (pixelDataElement.encapsulatedPixelData) {
-      pixelData = cornerstoneDICOMImageLoader.wadouri.getEncapsulatedImageFrame(
-        dataSet,
-        frameIndex
-      );
-    } else {
-      pixelData = cornerstoneDICOMImageLoader.wadouri.getUncompressedImageFrame(
-        dataSet,
-        frameIndex
-      );
-    }
-  } catch (error) {
-    throw new Error("No pixel data for id: " + id);
-  }
-
-  if (!metadata) {
-    throw new Error("No metadata for id: " + id);
-  }
-
-  let imageFrame = getImageFrame(metadata, dataSet);
-  let transferSyntax = dataSet.string("x00020010");
-
-  let canvas = window.document.createElement("canvas");
-  // Get the scaling parameters from the metadata
-  if (options.preScale.enabled) {
-    const scalingParameters = cornerstoneDICOMImageLoader.getScalingParameters(
-      cornerstone.metaData,
-      imageId
-    );
-
-    if (scalingParameters) {
-      options.preScale = {
-        ...options.preScale,
-        scalingParameters
-      };
-    }
-  }
-
-  const decodePromise = cornerstoneDICOMImageLoader.decodeImageFrame(
-    imageFrame,
-    transferSyntax,
-    pixelData,
-    canvas,
-    options
-  );
-
-  let promise: Promise<Image> = new Promise((resolve, reject) => {
-    decodePromise.then(function handleDecodeResponse(imageFrame: 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).
-      setPixelDataType(imageFrame);
-
-      let pixelSpacing = metadata.x00280030 ? metadata.x00280030 : 1.0;
-      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 as number[])[1]
-          ? (pixelSpacing as number[])[1]
-          : (pixelSpacing as number), // check for specific spacing value
-        columns: imageFrame.columns,
-        data: dataSet ? dataSet : undefined,
-        height: imageFrame.rows,
-        floatPixelData: undefined,
-        intercept: (rescaleIntercept as number)
-          ? (rescaleIntercept as number)
-          : 0,
-        invert: imageFrame.photometricInterpretation === "MONOCHROME1",
-        minPixelValue: imageFrame.smallestPixelValue,
-        maxPixelValue: imageFrame.largestPixelValue,
-        render: undefined, // set below
-        rowPixelSpacing: (pixelSpacing as number[])[0]
-          ? (pixelSpacing as number[])[0]
-          : (pixelSpacing as number), // check for specific spacing value
-        rows: imageFrame.rows,
-        sizeInBytes: getSizeInBytes(),
-        slope: (rescaleSlope as number) ? (rescaleSlope as number) : 1,
-        width: imageFrame.columns,
-        windowCenter: windowCenter as number,
-        windowWidth: windowWidth as number,
-        decodeTimeInMS: undefined, // TODO
-        loadTimeInMS: undefined // TODO
-      };
-      // add function to return pixel data
-      image.getPixelData = function () {
-        if (imageFrame.pixelData === undefined) {
-          throw new Error("No pixel data for image " + imageId);
-        }
-        return Array.from(imageFrame.pixelData);
-      };
-
-      // convert color space if not isJPEGBaseline8BitColor
-      let isJPEGBaseline8BitColor =
-        cornerstoneDICOMImageLoader.isJPEGBaseline8BitColor(
-          imageFrame,
-          transferSyntax
-        );
-
-      if (image.color && !isJPEGBaseline8BitColor) {
-        // 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.getCanvas = function () {
-          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);
-          return canvas;
-        };
-      }
-
-      // 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;
-          image.windowCenter = 128;
-        } else if (
-          image.maxPixelValue &&
-          image.minPixelValue &&
-          image.slope &&
-          image.intercept
-        ) {
-          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;
-        }
-      }
-
-      resolve(image as Image);
-    }, reject);
-  });
-
-  // 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
-  };
-};
-
-/**
- * This is an override of the cornerstoneDICOMImageLoader setPixelDataType function
- * @instance
- * @function setPixelDataType
- * @param {Object} imageFrame The Id of the image
- */
-const setPixelDataType = function (imageFrame: ImageFrame) {
-  if (imageFrame.bitsAllocated === 16) {
-    if (imageFrame.pixelRepresentation === 0) {
-      imageFrame.pixelData = new Uint16Array(
-        imageFrame.pixelData as Uint16Array
-      );
-    } else {
-      imageFrame.pixelData = new Int16Array(imageFrame.pixelData as Int16Array);
-    }
-  } else {
-    imageFrame.pixelData = new Uint8Array(imageFrame.pixelData as Uint8Array);
-  }
-};