larvitar 2.0.5 → 2.0.7

package/imaging/imageParsing.ts

@@ -1,444 +0,0 @@
-/** @module imaging/imageParsing
- *  @desc  This file provides functionalities for parsing DICOM image files
- */
-
-// external libraries
-import { DataSet, parseDicom } from "dicom-parser";
-import { forEach, each, has, pick } from "lodash";
-import { v4 as uuidv4 } from "uuid";
-
-// internal libraries
-import { getPixelRepresentation, randomId } from "./imageUtils";
-import { parseTag } from "./imageTags";
-import { updateLoadedStack } from "./imageLoading";
-import { checkMemoryAllocation } from "./monitors/memory";
-import { ImageObject, Instance, MetaData, Series } from "./types";
-import { getLarvitarManager } from "./loaders/commonLoader";
-import type { MetaDataTypes } from "./MetaDataTypes";
-import { NrrdSeries } from "./loaders/nrrdLoader";
-
-// global module variables
-var t0: number; // t0 variable for timing debugging purpose
-
-/*
- * This module provides the following functions to be exported:
- * readFiles(fileList)
- * readFile(file)
- * parseDataSet(dataSet, metadata, customFilter)
- * clearImageParsing(seriesStack)
- */
-
-/**
- * Reset series stack object and its internal data
- * @instance
- * @function clearImageParsing
- * @param {Object} seriesStack - Parsed series stack object
- */
-export const clearImageParsing = function (
-  seriesStack: ReturnType<typeof getLarvitarManager> | null
-) {
-  each(seriesStack, function (stack: Series | NrrdSeries) {
-    each(stack.instances, function (instance: Instance) {
-      if (instance.dataSet) {
-        // @ts-ignore
-        instance.dataSet.byteArray = null;
-      }
-      instance.dataSet = null;
-      instance.file = null;
-      // @ts-ignore
-      instance.metadata = null;
-    });
-  });
-  seriesStack = null;
-};
-
-/**
- * Read dicom files and return allSeriesStack object
- * @instance
- * @function readFiles
- * @param {Array} entries - List of file objects
- * @returns {Promise} - Return a promise which will resolve to a image object list or fail if an error occurs
- */
-export const readFiles = function (entries: File[]) {
-  return parseFiles(entries);
-};
-
-/**
- * Read a single dicom file and return parsed object
- * @instance
- * @function readFile
- * @param {File} entry - File object
- * @returns {Promise} - Return a promise which will resolve to a image object or fail if an error occurs
- */
-export const readFile = function (entry: File) {
-  return parseFile(entry);
-};
-
-/* Internal module functions */
-
-//This type is used to instantiate metadata and nested objects in imageParsing in order to allow dynamic setting
-//of MetaDataTypes objects' properties.
-//In other words, metadata : ExtendedMetaDataTypes is useful and substitutes metadata : MetaDataTypes when metadata values
-//aren't called explicitly using metadata['xGGGGEEEEE']
-//and are instead called using TAG as a variable (i.e. metadata[TAG]).
-//It is important to highlight that even if we set metadata[TAG]=tagValue; whose type (of tagValue) is the correct one (returned by ParseTag).
-//if we then extract x=metadata[TAG]; we obtain tagValue : unknown and a casting with : MetaDataType[typeof TAG] is necessary.
-
-type ExtendedMetaDataTypes = MetaDataTypes & {
-  [key: string]: unknown;
-};
-
-/**
- * Parse metadata from dicom parser dataSet object
- * @instance
- * @function parseDataSet
- * @param {Object} dataSet - dicom parser dataSet object
- * @param {Object} metadata - Initialized metadata object
- * @param {Array} customFilter - Optional filter: {tags:[], frameId: 0}
- */
-// This function iterates through dataSet recursively and store tag values into metadata object
-
-export const parseDataSet = function (
-  dataSet: DataSet,
-  metadata: ExtendedMetaDataTypes,
-  customFilter?: { tags: string[]; frameId: number }
-) {
-  // customFilter= {tags:[], frameId:xxx}
-  // the dataSet.elements object contains properties for each element parsed.  The name of the property
-  // is based on the elements tag and looks like 'xGGGGEEEE' where GGGG is the group number and EEEE is the
-  // element number both with lowercase hexadecimal letters.  For example, the Series Description DICOM element 0008,103E would
-  // be named 'x0008103e'.  Here we iterate over each property (element) so we can build a string describing its
-  // contents to add to the output array
-  try {
-    let elements = dataSet.elements;
-
-    customFilter && has(customFilter, "tags")
-      ? pick(dataSet.elements, customFilter.tags)
-      : dataSet.elements;
-    for (let propertyName in elements) {
-      let element = elements[propertyName]; //metadata
-      const TAG = propertyName as keyof ExtendedMetaDataTypes;
-      // Here we check for Sequence items and iterate over them if present. items will not be set in the
-      // element object for elements that don't have SQ VR type.  Note that implicit little endian
-      // sequences will are currently not parsed.
-      if (element.items) {
-        let nestedArray: MetaDataTypes[] = [];
-
-        // iterates over nested elements (nested metadata)
-        element.items.forEach(function (item) {
-          let nestedObject: ExtendedMetaDataTypes = {};
-          for (let nestedPropertyName in item.dataSet!.elements) {
-            let TAG_tagValue = nestedPropertyName as keyof MetaDataTypes;
-
-            let tagValue = parseTag<MetaDataTypes[typeof TAG_tagValue]>(
-              item.dataSet!,
-              nestedPropertyName,
-              item.dataSet!.elements[nestedPropertyName]
-            );
-
-            let TAG_nested = nestedPropertyName as keyof ExtendedMetaDataTypes;
-            nestedObject[TAG_nested] = tagValue;
-            //see MetaDataTypes.ts last property to understand how this dynamic value setting is possible
-          }
-          nestedArray.push(nestedObject);
-        });
-        metadata[TAG] = nestedArray;
-      } else {
-        let TAG_tagValue = propertyName as keyof MetaDataTypes;
-        let tagValue = parseTag<MetaDataTypes[typeof TAG_tagValue]>(
-          dataSet,
-          propertyName,
-          element
-        );
-        let TAG = propertyName as keyof ExtendedMetaDataTypes;
-        // identify duplicated tags (keep the first occurency and store the others in another tag eg x00280010_uuid)
-        if (metadata[TAG] !== undefined) {
-          console.debug(
-            `Identified duplicated tag "${propertyName}", values are:`,
-            metadata[TAG],
-            tagValue
-          );
-          let TAG_uuidv4 = (propertyName +
-            "_" +
-            uuidv4()) as keyof ExtendedMetaDataTypes;
-          metadata[TAG_uuidv4] = tagValue;
-        } else {
-          metadata[TAG] = tagValue;
-        }
-      }
-    }
-  } catch (err) {
-    console.log(err);
-  }
-};
-
-/**
- * Manage the parsing process waiting for the parsed object before proceeding with the next parse request
- * @inner
- * @function parseNextFile
- * @param {Array} parsingQueue - Array of queued files to be parsed
- * @param {Object} allSeriesStack - Series stack object to be populated
- * @param {string} uuid - Series uuid to be used if series instance uuid is missing
- * @param {Function} resolve - Promise resolve function
- * @param {Function} reject - Promise reject function
- */
-let parseNextFile = function (
-  parsingQueue: File[],
-  allSeriesStack: ReturnType<typeof getLarvitarManager>,
-  uuid: string,
-  resolve: Function,
-  reject: Function
-) {
-  // initialize t0 on first file of the queue
-  if (
-    Object.keys(allSeriesStack).length === 0 &&
-    allSeriesStack.constructor === Object
-  ) {
-    t0 = performance.now();
-  }
-
-  if (parsingQueue.length === 0) {
-    let t1 = performance.now();
-    console.log(`Call to readFiles took ${t1 - t0} milliseconds.`);
-    resolve(allSeriesStack);
-    return;
-  }
-
-  // remove and return first item from queue
-  let file = parsingQueue.shift() as File | undefined | null;
-
-  if (!file) {
-    console.warn("File is undefined or null");
-    return;
-  }
-
-  // Check if there is enough memory to parse the file
-  if (checkMemoryAllocation(file.size) === false) {
-    // do not parse the file and stop parsing
-    clearImageParsing(allSeriesStack);
-    let t1 = performance.now();
-    console.log(`Call to readFiles took ${t1 - t0} milliseconds.`);
-    file = null;
-    reject("Available memory is not enough");
-    return;
-  } else {
-    // parse the file and wait for results
-    parseFile(file)
-      .then((seriesData: ImageObject | null) => {
-        // use generated series uid if not found in dicom file
-        seriesData!.metadata.seriesUID = seriesData!.metadata.seriesUID || uuid;
-        // add file to cornerstoneDICOMImageLoader file manager
-        updateLoadedStack(seriesData!, allSeriesStack);
-        // proceed with the next file to parse
-        parseNextFile(parsingQueue, allSeriesStack, uuid, resolve, reject);
-        seriesData = null;
-        file = null;
-      })
-      .catch(err => {
-        console.error(err);
-        parseNextFile(parsingQueue, allSeriesStack, uuid, resolve, reject);
-        file = null;
-      });
-  }
-};
-
-/**
- * Push files in queue and start parsing next file
- * @inner
- * @function parseFiles
- * @param {Array} fileList - Array of file objects
- * @returns {Promise} - Return a promise which will resolve to a image object list or fail if an error occurs
- */
-const parseFiles = function (fileList: File[]) {
-  let allSeriesStack = {};
-  let parsingQueue: File[] = [];
-
-  forEach(fileList, function (file: File) {
-    if (!file.name.startsWith(".") && !file.name.startsWith("DICOMDIR")) {
-      parsingQueue.push(file);
-    }
-  });
-  return new Promise((resolve, reject) => {
-    const uuid = uuidv4();
-    parseNextFile(parsingQueue, allSeriesStack, uuid, resolve, reject);
-  });
-};
-
-/**
- * Parse a single DICOM File (metaData and pixelData)
- * @inner
- * @function parseFile
- * @param {File} file - File object to be parsed
- * @returns {Promise} - Return a promise which will resolve to a image object or fail if an error occurs
- */
-const parseFile = function (file: File) {
-  const parsePromise = new Promise<ImageObject>((resolve, reject) => {
-    let reader = new FileReader();
-    reader.onload = function () {
-      let arrayBuffer = reader.result;
-      // Here we have the file data as an ArrayBuffer.
-      // dicomParser requires as input a Uint8Array so we create that here.
-
-      if (!arrayBuffer || typeof arrayBuffer === "string") {
-        reject("Error reading file");
-        return;
-      }
-
-      let byteArray: Uint8Array | null = new Uint8Array(arrayBuffer);
-      let dataSet;
-
-      // this try-catch is used to handle non-DICOM files: log error but continue parsing the other files
-      try {
-        dataSet = parseDicom(byteArray);
-        byteArray = null;
-        let metadata: MetaData = {};
-        parseDataSet(dataSet, metadata);
-
-        let temporalPositionIdentifier = metadata["x00200100"]; // Temporal order of a dynamic or functional set of Images.
-        let numberOfTemporalPositions = metadata["x00200105"]; // Total number of temporal positions prescribed.
-        const is4D =
-          temporalPositionIdentifier !== undefined &&
-          (numberOfTemporalPositions as number) > 1
-            ? true
-            : false;
-
-        let modality = metadata["x00080060"] as string;
-        let singleFrameModalities = [
-          "CR",
-          "DX",
-          "MG",
-          "PX",
-          "RF",
-          "XA",
-          "US",
-          "IVUS",
-          "OCT"
-        ];
-        // US XA RF IVUS OCT DX CR PX MG
-        // Overwrite SOPInstanceUID to manage single stack images (US, XA).
-        // Usually different SeriesInstanceUID means different series and that value
-        // is used into the application to group different instances into the same series,
-        // but if a DICOM file contains a multiframe series, then the SeriesInstanceUID
-        // can be shared by other files of the same study.
-        // In these cases, the SOPInstanceUID (unique) is used as SeriesInstanceUID.
-        let uniqueId = singleFrameModalities.includes(modality)
-          ? metadata["x00080018"]
-          : metadata["x0020000e"];
-        let seriesInstanceUID = metadata["x0020000e"];
-        let pixelSpacing = metadata["x00280030"];
-        let imageOrientation = metadata["x00200037"];
-        let imagePosition = metadata["x00200032"];
-        let sliceThickness = metadata["x00180050"];
-        let numberOfFrames = metadata["x00280008"];
-        let isMultiframe = (numberOfFrames as number) > 1 ? true : false;
-        let waveform = metadata["x50003000"] ? true : false;
-
-        if (dataSet.warnings.length > 0) {
-          // warnings
-          reject(dataSet.warnings);
-        } else {
-          let pixelDataElement = dataSet.elements.x7fe00010;
-          let SOPUID = metadata["x00080016"];
-          if (pixelDataElement) {
-            // done, pixelDataElement found
-            let instanceUID = metadata["x00080018"] || randomId();
-            let imageObject: Partial<ImageObject> = {
-              // data needed for rendering
-              file: file,
-              dataSet: dataSet
-            };
-            imageObject.metadata = metadata as MetaData;
-            imageObject.metadata.anonymized = false;
-            imageObject.metadata.larvitarSeriesInstanceUID = uniqueId;
-            imageObject.metadata.sopClassUID = metadata["x00080016"];
-            imageObject.metadata.seriesUID = seriesInstanceUID;
-            imageObject.metadata.instanceUID = instanceUID;
-            imageObject.metadata.studyUID = metadata["x0020000d"];
-            imageObject.metadata.accessionNumber = metadata["x00080050"];
-            imageObject.metadata.studyDescription = metadata["x00081030"];
-            imageObject.metadata.patientName = metadata["x00100010"] as string;
-            imageObject.metadata.patientBirthdate = metadata["x00100030"];
-            imageObject.metadata.seriesDescription = metadata[
-              "x0008103e"
-            ] as string;
-            imageObject.metadata.seriesDate = metadata["x00080021"];
-            imageObject.metadata.seriesModality = metadata["x00080060"]
-              ?.toString()
-              .toLowerCase();
-            imageObject.metadata.intercept = metadata["x00281052"];
-            imageObject.metadata.slope = metadata["x00281053"];
-            imageObject.metadata.pixelSpacing = pixelSpacing;
-            imageObject.metadata.sliceThickness = sliceThickness;
-            imageObject.metadata.imageOrientation = imageOrientation;
-            imageObject.metadata.imagePosition = imagePosition;
-            imageObject.metadata.rows = metadata["x00280010"];
-            imageObject.metadata.cols = metadata["x00280011"];
-            imageObject.metadata.numberOfSlices = metadata["x00540081"]
-              ? metadata["x00540081"] // number of slices
-              : metadata["x00201002"]; // number of instances
-            imageObject.metadata.numberOfFrames = numberOfFrames;
-            if (isMultiframe) {
-              imageObject.metadata.frameTime = metadata["x00181063"];
-              imageObject.metadata.frameDelay = metadata["x00181066"];
-              if (metadata["x00186060"]) {
-                imageObject.metadata.rWaveTimeVector = metadata["x00186060"];
-              }
-            }
-            imageObject.metadata.isMultiframe = isMultiframe;
-            if (is4D) {
-              imageObject.metadata.temporalPositionIdentifier =
-                metadata["x00200100"];
-              imageObject.metadata.numberOfTemporalPositions =
-                metadata["x00200105"];
-              imageObject.metadata.contentTime = metadata["x00080033"];
-            }
-            imageObject.metadata.is4D = is4D;
-            imageObject.metadata.waveform = waveform;
-            imageObject.metadata.windowCenter = metadata["x00281050"];
-            imageObject.metadata.windowWidth = metadata["x00281051"];
-            imageObject.metadata.minPixelValue = metadata["x00280106"];
-            imageObject.metadata.maxPixelValue = metadata["x00280107"];
-            imageObject.metadata.length = pixelDataElement.length;
-            imageObject.metadata.repr = getPixelRepresentation(dataSet);
-            resolve(imageObject as ImageObject);
-          } else if (SOPUID == "1.2.840.10008.5.1.4.1.1.104.1") {
-            let pdfObject: Partial<ImageObject> = {
-              // data needed for rendering
-              file: file,
-              dataSet: dataSet
-            };
-            pdfObject.metadata = metadata;
-            pdfObject.metadata.larvitarSeriesInstanceUID = uniqueId;
-            pdfObject.metadata.seriesUID = seriesInstanceUID;
-            pdfObject.instanceUID =
-              metadata["x00080018"]?.toString() || randomId();
-            pdfObject.metadata.studyUID = metadata["x0020000d"];
-            pdfObject.metadata.accessionNumber = metadata["x00080050"];
-            pdfObject.metadata.studyDescription = metadata["x00081030"];
-            pdfObject.metadata.patientName = metadata["x00100010"] as string;
-            pdfObject.metadata.patientBirthdate = metadata["x00100030"];
-            pdfObject.metadata.seriesDate = metadata["x00080021"];
-            pdfObject.metadata.seriesModality = metadata["x00080060"]
-              ?.toString()
-              .toLowerCase();
-            pdfObject.metadata.mimeType = metadata["x00420012"];
-            pdfObject.metadata.is4D = false;
-            pdfObject.metadata.numberOfFrames = 0;
-            pdfObject.metadata.numberOfSlices = 0;
-            pdfObject.metadata.numberOfTemporalPositions = 0;
-            resolve(pdfObject as ImageObject);
-          } else {
-            // done, no pixelData
-            reject("no pixelData");
-          }
-        }
-      } catch (err) {
-        reject(
-          `Larvitar: can not read file "${file.name}" \nParsing error: ${err}`
-        );
-      }
-    };
-    reader.readAsArrayBuffer(file);
-  });
-  return parsePromise;
-};

package/imaging/imagePresets.ts

@@ -1,156 +0,0 @@
-/** @module imaging/imagePresets
- *  @desc  This file provides functionalities for
- *         image presets for ww and wc
- */
-
-// external libraries
-import cornerstone from "cornerstone-core";
-import { each, find } from "lodash";
-
-// internal libraries
-import { set as setStore } from "./imageStore";
-
-/**
- * Object used to list image presets
- * @object
- */
-const IMAGE_PRESETS = [
-  { name: "CT: Abdomen", ww: 350, wl: 50 },
-  { name: "CT: Bone", ww: 2500, wl: 500 },
-  { name: "CT: Cerebrum", ww: 80, wl: 0 },
-  { name: "CT: Covid-19", ww: 240, wl: -860 },
-  { name: "CT: Liver", ww: 150, wl: 50 },
-  { name: "CT: Lung", ww: 1500, wl: -500 },
-  { name: "CT: Mediastinum", ww: 300, wl: 50 },
-  { name: "CT: Pelvis", ww: 400, wl: 40 }
-];
-
-/*
- * This module provides the following functions to be exported:
- * getImagePresets()
- * setImagePreset(name)
- * setImageCustomPreset(viewportNames, customValues)
- */
-
-/**
- * Get Image presets object
- * @instance
- * @function getImagePresets
- */
-export const getImagePresets = function () {
-  return IMAGE_PRESETS;
-};
-
-/**
- * Set Image presets
- * @instance
- * @function setImagePreset
- * @param {Array} viewportNames - List of viewports where to apply preset
- * @param {String} preset - The image preset name or the preset object
- */
-export const setImagePreset = function (
-  viewportNames: string[],
-  preset: string | (typeof IMAGE_PRESETS)[0]
-) {
-  if (!Array.isArray(viewportNames)) {
-    console.error(
-      "Invalid parameter, viewportNames has to be an array of viewport names."
-    );
-    return;
-  }
-  let image_preset =
-    typeof preset === "string" ? find(IMAGE_PRESETS, { name: preset }) : preset;
-
-  if (!image_preset) {
-    console.error("Invalid image preset");
-    return;
-  }
-
-  each(viewportNames, function (viewportName: string) {
-    let element = document.getElementById(viewportName);
-    let enabledElement;
-
-    if (!element) {
-      console.warn("No element with id", viewportName);
-      return;
-    }
-
-    try {
-      enabledElement = cornerstone.getEnabledElement(element);
-    } catch {
-      console.warn("No enabledElement with id", viewportName);
-      return;
-    }
-
-    let viewport = cornerstone.getViewport(element);
-
-    if (!viewport) {
-      console.warn("No viewport with id", viewportName);
-      return;
-    }
-
-    viewport.voi.windowWidth = image_preset!.ww;
-    viewport.voi.windowCenter = image_preset!.wl;
-    cornerstone.setViewport(element, viewport);
-    // sync ww and wc values in store
-    setStore([
-      "contrast",
-      viewportName,
-      viewport.voi.windowWidth,
-      viewport.voi.windowCenter
-    ]);
-  });
-};
-
-/**
- * Set Image presets
- * @instance
- * @function setImageCustomPreset
- * @param {Array} viewportNames - List of viewports where to apply preset
- * @param {Object} customValues - {wl: value, ww: value}
- */
-export const setImageCustomPreset = function (
-  viewportNames: string[],
-  customValues: { wl: number; ww: number }
-) {
-  if (!Array.isArray(viewportNames)) {
-    console.error(
-      "Invalid parameter, viewportNames has to be an array of viewport names."
-    );
-    return;
-  }
-  each(viewportNames, function (viewportName: string) {
-    let element = document.getElementById(viewportName);
-    let enabledElement;
-
-    if (!element) {
-      console.warn("No element with id", viewportName);
-      return;
-    }
-
-    try {
-      enabledElement = cornerstone.getEnabledElement(element);
-    } catch {
-      console.warn("No enabledElement with id", viewportName);
-      return;
-    }
-
-    let viewport = cornerstone.getViewport(element);
-
-    if (!viewport) {
-      console.warn("No viewport with id", viewportName);
-      return;
-    }
-
-    viewport.voi.windowWidth = customValues.ww;
-    viewport.voi.windowCenter = customValues.wl;
-    cornerstone.setViewport(element, viewport);
-    // sync ww and wc values in store
-    setStore([
-      "contrast",
-      viewportName,
-      viewport.voi.windowWidth,
-      viewport.voi.windowCenter
-    ]);
-  });
-};