larvitar 2.0.5 → 2.0.6

package/imaging/loaders/resliceLoader.ts

@@ -1,205 +0,0 @@
-/** @module loaders/resliceLoader
- *  @desc This file provides functionalities for
- *        custom Reslice Loader
- */
-
-// external libraries
-import cornerstone from "cornerstone-core";
-import { default as cornerstoneDICOMImageLoader } from "cornerstone-wado-image-loader";
-
-// internal libraries
-import {
-  getImageFrame,
-  getLarvitarImageTracker,
-  getLarvitarManager
-} from "./commonLoader";
-import type { Image, ImageFrame, MetaData } from "../types";
-
-/*
- * This module provides the following functions to be exported:
- * loadReslicedImage(imageId)
- */
-
-/**
- * Custom Loader for DICOMImageLoader
- * @instance
- * @function loadReslicedImage
- * @param {String} imageId The Id of the image
- * @returns {Object} custom image object
- */
-export const loadReslicedImage = function (imageId: string) {
-  let manager = getLarvitarManager();
-  let imageTracker = getLarvitarImageTracker();
-  let seriesId = imageTracker[imageId];
-  let instance = manager[seriesId].instances[imageId];
-  var reslicedPixeldata = instance.pixelData;
-  //@ts-ignore deprecated
-  return createCustomImage(imageId, instance.metadata, reslicedPixeldata);
-};
-
-/* 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 (
-  imageId: string,
-  metadata: MetaData,
-  pixelData: Uint8ClampedArray,
-  dataSet?: any // deprecated
-) {
-  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 as number[])[1]
-      : undefined,
-    columns: imageFrame.columns,
-    height: imageFrame.rows,
-    intercept: rescaleIntercept ? (rescaleIntercept as number) : 0,
-    invert: imageFrame.photometricInterpretation === "MONOCHROME1",
-    minPixelValue: imageFrame.smallestPixelValue,
-    maxPixelValue: imageFrame.largestPixelValue,
-    render: undefined, // set below
-    rowPixelSpacing: pixelSpacing ? (pixelSpacing as number[])[0] : undefined,
-    rows: imageFrame.rows,
-    sizeInBytes: getSizeInBytes(),
-    slope: rescaleSlope ? (rescaleSlope as number) : 1,
-    width: imageFrame.columns,
-    windowCenter: windowCenter ? (windowCenter as number) : undefined,
-    windowWidth: windowWidth ? (windowWidth as number) : 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 TODO check if this is really needed (see comment below)
-  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 to avoid erroneous calculation from getImageFrame function
-  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 &&
-      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;
-    } 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
-  };
-};

package/imaging/monitors/memory.ts

@@ -1,151 +0,0 @@
-/** @module monitors/memory
- *  @desc This file provides utility functions for
- *        monitoring memory usage
- */
-
-import {
-  getLarvitarManager,
-  removeSeriesFromLarvitarManager
-} from "../loaders/commonLoader";
-import { clearImageCache } from "../imageRendering";
-import store from "../imageStore";
-
-// Custom types for chrome
-interface Performance {
-  memory?: any;
-}
-
-// global module variables
-const backingMemory = 100 * 1048576; // 100 MB
-var customMemoryLimit: number | null = null;
-
-/*
- * This module provides the following functions to be exported:
- * checkAndClearMemory(bytes, [seriesUUIDs])
- * checkMemoryAllocation(bytes)
- * getUsedMemory()
- * getAvailableMemory()
- * setAvailableMemory()
- */
-
-/**
- * Check memory allocation and clear memory if needed
- * @instance
- * @function checkAndClearMemory
- * @param {Number} - Number of bytes to allocate
- * @param {Array} - Rendered Series ids
- */
-export const checkAndClearMemory = function (
-  bytes: number,
-  renderedSeriesIds: string[]
-) {
-  const isEnough = checkMemoryAllocation(bytes);
-  if (isEnough === false) {
-    const manager = getLarvitarManager();
-    // get all key of manager and create a list
-    const seriesIds = Object.keys(manager);
-    // create a list of non rendered series ids
-    const nonRenderedSeriesIds = seriesIds.filter(
-      seriesId => !renderedSeriesIds.includes(seriesId)
-    );
-    // remove non rendered series from manager
-    nonRenderedSeriesIds.forEach(seriesId => {
-      removeSeriesFromLarvitarManager(seriesId);
-      clearImageCache(seriesId);
-      store.removeSeriesId(seriesId);
-    });
-  }
-};
-
-/**
- * Check memory allocation and returns false if js Heap size has reached its limit
- * @instance
- * @function checkMemoryAllocation
- * @param {Number} - Number of bytes to allocate
- * @return {Boolean} - Returns a boolean flag to warn the user about memory allocation limit
- */
-export const checkMemoryAllocation = function (bytes: number) {
-  if (checkMemorySupport()) {
-    let usedMemory = getUsedMemory();
-    let availableMemory = getAvailableMemory();
-    let isEnough = availableMemory - bytes - usedMemory > 0 ? true : false;
-    if (!isEnough) {
-      console.log("Total Memory Available is: ", getMB(availableMemory), " MB");
-      console.log("Currently Used Memory is: ", getMB(usedMemory), " MB");
-      console.log(
-        "New memory requested allocation is: ",
-        getMB(usedMemory + bytes),
-        " MB"
-      );
-    }
-    return isEnough;
-  } else {
-    console.warn("Check Memory Allocation is not supported");
-    return true;
-  }
-};
-
-/**
- * Check performance.memory browser support and returns used Js Heap Size in Mb
- * @instance
- * @function getUsedMemory
- * @return {Number} - Returns used JSHeapSize in bytes or NaN if not supported
- */
-export const getUsedMemory = function () {
-  return checkMemorySupport()
-    ? (performance as Performance).memory.usedJSHeapSize
-    : NaN;
-};
-
-/**
- * Check performance.memory browser support and returns available Js Heap Size in Mb
- * @instance
- * @function getAvailableMemory
- * @return {Number} - Returns available JSHeapSize in bytes or NaN if not supported
- */
-export const getAvailableMemory = function () {
-  if (checkMemorySupport()) {
-    return customMemoryLimit
-      ? customMemoryLimit
-      : (performance as Performance).memory.jsHeapSizeLimit - backingMemory;
-  } else {
-    return NaN;
-  }
-};
-
-/**
- * Check performance.memory browser support and returns available Js Heap Size in Mb
- * @instance
- * @function setAvailableMemory
- * @param {Number} - Number of GB to set as maximum custom memory limit
- */
-export const setAvailableMemory = function (value: number) {
-  customMemoryLimit = value * 1024 * 1024 * 1024;
-};
-
-/* Internal module functions */
-
-/**
- * Check Browser support.
- * Firefox and Safari are not supported
- * See: https://developer.mozilla.org/en-US/docs/Web/API/Performance/memory
- * @instance
- * @function checkMemorySupport
- * @return {Boolean} - Returns memory object or false if not supported
- */
-const checkMemorySupport = function () {
-  return (performance as Performance).memory
-    ? (performance as Performance).memory
-    : false;
-};
-
-/**
- * Check Browser support.
- * @instance
- * @function getMB
- * @param {Number} bytes - Memory in bytes
- * @return {Number} - Memory in MB
- */
-const getMB = function (bytes: number) {
-  return bytes / 1048576;
-};

package/imaging/monitors/performance.ts

@@ -1,34 +0,0 @@
-/** @module monitors/performance
- *  @desc This file provides utility functions for
- *        monitoring performance usage
- */
-
-var PERFORMANCE_MONITOR = false;
-
-/**
- * Get performance monitor
- * @instance
- * @function getPerformanceMonitor
- * @returns {Boolean} - Performance monitor status
- */
-export const getPerformanceMonitor = function () {
-  return PERFORMANCE_MONITOR;
-};
-
-/**
- * Set performance monitor ON
- * @instance
- * @function activatePerformanceMonitor
- */
-export const activatePerformanceMonitor = function () {
-  PERFORMANCE_MONITOR = true;
-};
-
-/**
- * Set performance monitor OFF
- * @instance
- * @function deactivatePerformanceMonitor
- */
-export const deactivatePerformanceMonitor = function () {
-  PERFORMANCE_MONITOR = false;
-};

package/imaging/parsers/ecg.ts

@@ -1,54 +0,0 @@
-/** @module imaging/parsers/ecg
- *  @desc  This file provides functionalities for
- *         handling ECG signales in DICOM files
- */
-
-import { DataSet, Element } from "dicom-parser";
-import { getSeriesDataFromLarvitarManager } from "../loaders/commonLoader";
-
-/*
- * This module provides the following functions to be exported:
- * parseECG(dataSet, tag, nSampling)
- */
-
-/**
- * Generate an array of points representing the ECG signal
- * @instance
- * @function parseECG
- * @param {DataSet} dataSet - the DICOM dataset
- * @param {String} tag - the tag of the ECG signal
- * @param {Number} nSampling - the sampling rate
- * @returns {void}
- */
-export function parseECG(
-  seriesId: string,
-  dataSet: DataSet,
-  tag: string,
-  nSampling: number = 2
-): void {
-  const element: Element = dataSet.elements[tag];
-  let data: Uint8Array = dataSet.byteArray.slice(
-    element.dataOffset,
-    element.dataOffset + element.length
-  );
-  let points: number[] = [];
-  const nCountFrom: number = data.length / 2;
-  const nCountTo: number = Math.floor(0.5 + nCountFrom / nSampling);
-  let values: number[] = [];
-  let nFrom: number = 0;
-  for (let nTo: number = 0; nTo < nCountTo; nTo++) {
-    let v: number = data[nFrom] + 255 * data[nFrom + 1];
-    values.push(v);
-    nFrom += nSampling * 2;
-  }
-
-  const nMax: number = Math.max(...values);
-  const nMin: number = Math.min(...values);
-
-  for (let nTo: number = 0; nTo < nCountTo; nTo++) {
-    let data: number = ((values[nTo] - nMin) / (nMax - nMin)) * 100;
-    points.push(data);
-  }
-  let series = getSeriesDataFromLarvitarManager(seriesId);
-  series!.ecgData = points;
-}