larvitar 2.0.4 → 2.0.6

package/imaging/imageTags.ts

@@ -1,609 +0,0 @@
-// external libraries
-import TAG_DICT from "./dataDictionary.json";
-//Changed data dictionary using:
-//regex "\((\d+),(\d+)\)"
-//"x$1$2"
-//now tag are in format "x00000000"
-import { convertBytes } from "dicom-character-set";
-import { DataSet, Element } from "dicom-parser";
-import type { MetaDataTypes } from "./MetaDataTypes"; //custom type created as tag-type. { "x0000000":string, ...}
-/*
- * This module provides the following functions to be exported:
- * parseTag(dataSet, propertyName, element)
- * getDICOMTagCode(code)
- * getDICOMTag(code)
- * isStringVr(vr)
- * parseDateTag(tagValue)
- * parseDateTimeTag(tagValue)
- * parseTimeTag(tagValue)
- * parsePatientNameTag(tagValue)
- * parseAgeTag(tagValue)
- * parseDICOMFileIDTag(tagValue)
- * getTagValue(dataSet, tag)
- * formatDate(date)
- * formatDateTime(date)
- * isValidDate(d)
- */
-
-/**
- * Convert date from dicom tag
- * @instance
- * @function formatDate
- * @param {Date} dicomDate - A date from a DICOM tag
- * @return {String} - The human readable date
- */
-let formatDate = function (date: string) {
-  let yyyy = date.slice(0, 4);
-  let mm = date.slice(4, 6);
-  let dd = date.slice(6, 8);
-  return (
-    yyyy + "-" + (mm[1] ? mm : "0" + mm[0]) + "-" + (dd[1] ? dd : "0" + dd[0])
-  );
-};
-
-/**
- * Convert datetime from dicom tag
- * @instance
- * @function formatDateTime
- * @param {Date} dicomDateTime - A dateTime from a DICOM tag
- * @return {String} - The human readable dateTime
- */
-let formatDateTime = function (date: string) {
-  let yyyy = date.slice(0, 4);
-  let mm = date.slice(4, 6);
-  let dd = date.slice(6, 8);
-  let hh = date.slice(8, 10);
-  let m = date.slice(10, 12);
-  let ss = date.slice(12, 14);
-
-  return (
-    yyyy +
-    "-" +
-    (mm[1] ? mm : "0" + mm[0]) +
-    "-" +
-    (dd[1] ? dd : "0" + dd[0]) +
-    "/" +
-    hh +
-    ":" +
-    m +
-    ":" +
-    ss
-  );
-};
-
-/**
- * Check if argument is a valid Date Object
- * @instance
- * @function isValidDate
- * @param {Date} d - The date object to be checked
- * @return {Boolean} - Boolean result
- */
-const isValidDate = function (d: Date) {
-  return d instanceof Date && !isNaN(d.getTime());
-};
-
-/**
- * Parse a dicom date tag into human readable format
- * @instance
- * @function parseDateTag
- * @param {String} tagValue - The string to be parsed
- * @return {String} - The parsed result
- */
-const parseDateTag = function (tagValue: string) {
-  if (!tagValue) return "";
-  const year = tagValue.substring(0, 4);
-  const month = tagValue.substring(4, 6);
-  const day = tagValue.substring(6, 8);
-  const date = new Date(parseInt(year), parseInt(month) - 1, parseInt(day));
-  if (isValidDate(date) === true) {
-    return date.toISOString();
-  } else {
-    return tagValue;
-  }
-};
-
-/**
- * Parse a dicom datetime tag into human readable format
- * @instance
- * @function parseDateTimeTag
- * @param {String} tagValue - The string to be parsed
- * @return {String} - The parsed result
- */
-const parseDateTimeTag = function (tagValue: string) {
-  if (!tagValue) return "";
-  const year = tagValue.substring(0, 4);
-  const month = tagValue.substring(4, 6);
-  const day = tagValue.substring(6, 8);
-  const hour = tagValue.substring(8, 10);
-  const min = tagValue.substring(10, 12);
-  const sec = tagValue.substring(12, 14);
-  // const msec = tagValue.substring(15, 21);
-  const date = new Date(
-    parseInt(year),
-    parseInt(month) - 1,
-    parseInt(day),
-    parseInt(hour),
-    parseInt(min),
-    parseInt(sec),
-    parseInt(sec)
-  );
-  if (isValidDate(date) === true) {
-    return date.toISOString();
-  } else {
-    return tagValue;
-  }
-};
-
-/**
- * Parse a dicom time tag into human readable format
- * @instance
- * @function parseTimeTag
- * @param {String} tagValue - The string to be parsed
- * @return {String} - The parsed result
- */
-const parseTimeTag = function (tagValue: string) {
-  if (!tagValue) return "";
-  let hour = tagValue.substring(0, 2);
-  let min = tagValue.substring(2, 4);
-  let sec = tagValue.substring(4, 6);
-  let msec = tagValue.substring(7, 13) ? tagValue.substring(7, 13) : "0";
-  let result = hour + ":" + min + ":" + sec + "." + msec;
-  return result;
-};
-
-/**
- * Parse a dicom patient tag into human readable format
- * @instance
- * @function parsePatientNameTag
- * @param {String} tagValue - The string to be parsed
- * @return {String} - The parsed result
- */
-const parsePatientNameTag = function (tagValue: string) {
-  if (!tagValue) return "";
-  return tagValue.replace(/\^/gi, " ");
-};
-
-/**
- * Parse a dicom age tag into human readable format
- * @instance
- * @function parseAgeTag
- * @param {String} tagValue - The string to be parsed
- * @return {String} - The parsed result
- */
-const parseAgeTag = function (tagValue: string) {
-  if (!tagValue) return "";
-  let regs = /(\d{3})(D|W|M|Y)/gim.exec(tagValue);
-  if (regs) {
-    return parseInt(regs[1]) + " " + regs[2];
-  } else {
-    return "";
-  }
-};
-
-/**
- * Parse a dicom fileID tag into human readable format
- * @instance
- * @function parseDICOMFileIDTag
- * @param {String} tagValue - The string to be parsed
- * @return {String} - The parsed result
- */
-const parseDICOMFileIDTag = function (tagValue: string) {
-  // The DICOM File Service does not specify any "separator" between
-  // the Components of the File ID. This is a Value Representation issue that
-  // may be addressed in a specific manner by each Media Format Layer.
-  // In DICOM IODs, File ID Components are generally handled as multiple
-  // Values and separated by "backslashes".
-  // There is no requirement that Media Format Layers use this separator.
-  if (!tagValue) return "";
-  // @ts-ignore //TODO this can't work!
-  return tagValue.split("\\").join(path.sep);
-};
-
-/**
- * Check if argument is a string of concatenated vrs
- * @instance
- * @function isStringVr
- * @param {String} vr - The string to be checked
- * @return {Boolean} - Boolean result
- */
-const isStringVr = function (vr: string) {
-  // vr can be a string of concatenated vrs
-  vr = vr || "";
-  vr = vr.split("|")[0];
-
-  if (
-    vr === "AT" ||
-    vr === "FL" ||
-    vr === "FD" ||
-    vr === "OB" ||
-    vr === "OF" ||
-    vr === "OW" ||
-    vr === "SI" ||
-    vr === "SL" || // signed long
-    vr === "SQ" ||
-    vr === "SS" ||
-    vr === "UL" ||
-    vr === "US"
-  ) {
-    return false;
-  }
-  return true;
-};
-
-/**
- * Get the dicom tag code from dicom image
- * @instance
- * @function getDICOMTagCode
- * @param {String} dicomTag - The original DICOM tag code
- * @return {String} - The human readable DICOM tag code
- */
-/*function getDICOMTagCode(code: string) {
-  let re = /x(\w{4})(\w{4})/;
-  let result = re.exec(code);
-  if (!result) {
-    return code;
-  }
-  let newCode = "(" + result[1] + "," + result[2] + ")";
-  newCode = newCode.toUpperCase();
-  return newCode;
-}*/
-//This function is not necessary animore because dataDictionary contains tags in format "x00000000"
-
-/**
- * Get the dicom tag from dicom tag code
- * @instance
- * @function getDICOMTag
- * @param {String} dicomTagCode - The original DICOM tag code
- * @return {String} - The human readable DICOM tag
- */
-function getDICOMTag(code: string) {
-  let newCode = code;
-
-  if (!Object.keys(TAG_DICT).includes(newCode)) {
-    console.debug(`Invalid tag key: ${newCode}`);
-    return null;
-  }
-  // force type to keyof typeof TAG_DICT after having checked that it is a valid key
-  let tag = TAG_DICT[newCode as keyof typeof TAG_DICT];
-  return tag;
-}
-
-/**
- * Parse a DICOM Tag according to its type
- * @instance
- * @function parseTag
- * @param {Object} dataSet - The parsed dataset object from dicom parser
- * @param {String} propertyName - The tag name
- * @param {Object} element - The parsed dataset element
- * @return {String} - The DICOM Tag value
- */
-export function parseTag<T>(
-  dataSet: DataSet,
-  propertyName: string, //x0000000 string
-  element: Element // TODO-ts better type @szanchi
-) {
-  // GET VR
-  var tagData = dataSet.elements[propertyName];
-  var vr = tagData?.vr;
-  if (!vr) {
-    // use dicom dict to get VR
-    var tag = getDICOMTag(propertyName);
-    //From now on tag is an object of datadictionary.json (TAG_TYPE) and tag.tag is rapresented as "x0000000"
-    //so propertyname= tag.tag=keyof MetaDataTypes
-    if (tag && tag.vr) {
-      vr = tag.vr;
-    } else {
-      return element;
-    }
-  }
-
-  var valueIn;
-  var valueOut;
-
-  if (isStringVr(vr)) {
-    // We ask the dataset to give us the element's data in string form.
-    // Most elements are strings but some aren't so we do a quick check
-    // to make sure it actually has all ascii characters so we know it is
-    // reasonable to display it.
-    let TAG = propertyName as keyof MetaDataTypes;
-    var str = dataSet.string(propertyName);
-    if (str === undefined) {
-      return undefined;
-    } else {
-      // the string will be undefined if the element is present but has no data
-      // (i.e. attribute is of type 2 or 3) so we only display the string if it has
-      // data. Note that the length of the element will be 0 to indicate "no data"
-      // so we don't put anything here for the value in that case.
-      valueIn = str;
-      valueOut = str as MetaDataTypes[typeof TAG];
-    }
-
-    // A string of characters representing an Integer in base-10 (decimal),
-    // shall contain only the characters 0 - 9, with an optional leading "+" or "-".
-    // It may be padded with leading and/or trailing spaces. Embedded spaces
-    // are not allowed. The integer, n, represented shall be in the range:
-    // -231 <= n <= (231 - 1).
-    if (vr === "IS") {
-      valueOut = parseInt(valueIn);
-    }
-    // A string of characters representing either a fixed point number
-    // or a floating point number. A fixed point number shall contain only
-    // the characters 0-9 with an optional leading "+" or "-" and an optional "."
-    // to mark the decimal point. A floating point number shall be conveyed
-    // as defined in ANSI X3.9, with an "E" or "e" to indicate the start
-    // of the exponent. Decimal Strings may be padded with leading or trailing spaces.
-    // Embedded spaces are not allowed.
-    else if (vr === "DS") {
-      valueIn = valueIn.split("\\").map(Number);
-      if (propertyName == "x00281050" || propertyName == "x00281051") {
-        valueOut = valueIn.length > 0 ? valueIn[0] : valueIn;
-      } else {
-        valueOut = valueIn.length == 1 ? valueIn[0] : valueIn;
-      }
-    }
-    // A string of characters of the format YYYYMMDD; where YYYY shall contain year,
-    // MM shall contain the month, and DD shall contain the day,
-    // interpreted as a date of the Gregorian calendar system.
-    else if (vr === "DA") {
-      valueOut = parseDateTag(valueIn);
-    }
-    // A concatenated date-time character string in the format:
-    // YYYYMMDDHHMMSS.FFFFFF
-    else if (vr === "DT") {
-      valueOut = parseDateTimeTag(valueIn);
-    }
-    // A string of characters of the format HHMMSS.FFFFFF; where HH contains hours
-    // (range "00" - "23"), MM contains minutes (range "00" - "59"),
-    // SS contains seconds (range "00" - "60"), and FFFFFF contains a fractional
-    // part of a second as small as 1 millionth of a second (range "000000" - "999999").
-    else if (vr === "TM") {
-      valueOut = parseTimeTag(valueIn);
-    }
-    // Specific Character Set (0008,0005) identifies the Character Set that expands or
-    // replaces the Basic Graphic Set (ISO 646) for values of Data Elements that have
-    // Value Representation of SH, LO, ST, PN, LT, UC or UT.
-    // If the Attribute Specific Character Set (0008,0005) is not present or has only
-    // a single value, Code Extension techniques are not used. Defined Terms for the
-    // Attribute Specific Character Set (0008,0005), when single valued, are derived
-    // from the International Registration Number as per ISO 2375
-    // (e.g., ISO_IR 100 for Latin alphabet No. 1).
-    // See https://github.com/radialogica/dicom-character-set
-    else if (
-      vr == "PN" ||
-      vr == "SH" ||
-      vr == "LO" ||
-      vr == "ST" ||
-      vr == "LT" ||
-      vr == "UC" ||
-      vr == "UT"
-    ) {
-      // get character set
-      let characterSet = dataSet.string("x00080005");
-
-      if (characterSet) {
-        let data = dataSet.elements[propertyName];
-        let arr: Uint8Array | null = new Uint8Array(
-          dataSet.byteArray.buffer,
-          data.dataOffset,
-          data.length
-        );
-        // try to convert bytes
-        // if raises invalid character set
-        // catch error
-        try {
-          valueOut = convertBytes(characterSet, arr, {
-            vr: vr
-          });
-        } catch (error) {
-          console.warn("Invalid Character Set: " + characterSet);
-          valueOut = "Invalid Character Set: " + characterSet;
-        }
-        arr = null;
-      }
-      if (vr == "PN") {
-        // PatientName tag value is: "LastName^FirstName^MiddleName".
-        // Spaces inside each name component are permitted. If you don't know
-        // any of the three components, just leave it empty.
-        // Actually you may even append a name prefix (^professor) and
-        // a name suffix (^senior) so you have a maximum of 5 components.
-        valueOut = parsePatientNameTag(valueIn);
-      }
-      valueOut = valueOut.replace(/\0/g, ""); // remove null char (\u0000)
-    }
-    // A string of characters with one of the following formats
-    // -- nnnD, nnnW, nnnM, nnnY; where nnn shall contain the number of days for D,
-    // weeks for W, months for M, or years for Y.
-    else if (vr == "AS") {
-      valueOut = parseAgeTag(valueIn);
-    }
-
-    // A string of characters with leading or trailing spaces (20H) being non-significant.
-    else if (vr === "CS") {
-      if (propertyName === "x00041500") {
-        valueOut = parseDICOMFileIDTag(valueIn);
-      } else {
-        valueOut = valueIn.split("\\").join(", ");
-      }
-    }
-  } else if (vr === "US") {
-    valueOut = dataSet.uint16(propertyName);
-  } else if (vr === "SS") {
-    valueOut = dataSet.int16(propertyName);
-  } else if (vr === "US|SS") {
-    valueOut = dataSet.int16(propertyName);
-  } else if (vr === "UL") {
-    valueOut = dataSet.uint32(propertyName);
-  } else if (vr === "SL") {
-    valueOut = dataSet.int32(propertyName);
-  } else if (vr == "FD") {
-    valueOut = dataSet.double(propertyName);
-  } else if (vr == "FL") {
-    // check if there are multiple values
-    if (propertyName === "x00186060") {
-      // RWaveTimeVector
-      let index = 0;
-      let rWaveTimeVector: number[] = [];
-      while (dataSet.float(propertyName, index)) {
-        let value = dataSet.float(propertyName, index);
-        // push value in array if is bigger than previous value
-        if (index > 0 && value && value < rWaveTimeVector[index - 1]) {
-          break;
-        }
-        if (value) {
-          rWaveTimeVector.push(value);
-        }
-        index++;
-      }
-      valueOut = rWaveTimeVector;
-    } else {
-      valueOut = dataSet.float(propertyName);
-    }
-  } else if (
-    vr === "OB" ||
-    vr === "OW" ||
-    vr === "OW|OB" ||
-    vr === "US|OW" ||
-    vr === "UN" ||
-    vr === "OF" ||
-    vr === "UT"
-  ) {
-    // If it is some other length and we have no string
-    if (element.length === 2) {
-      valueOut =
-        "binary data of length " +
-        element.length +
-        " as uint16: " +
-        dataSet.uint16(propertyName);
-    } else if (element.length === 4) {
-      valueOut =
-        "binary data of length " +
-        element.length +
-        " as uint32: " +
-        dataSet.uint32(propertyName);
-    } else {
-      valueOut = tagData;
-    }
-  } else if (vr === "AT") {
-    var group = dataSet.uint16(propertyName, 0);
-    if (group) {
-      var groupHexStr = ("0000" + group.toString(16)).substr(-4);
-      var elm = dataSet.uint16(propertyName, 1);
-      var elmHexStr = elm
-        ? ("0000" + elm.toString(16)).substr(-4)
-        : "0000".substr(-4);
-      valueOut = "x" + groupHexStr + elmHexStr;
-    } else {
-      valueOut = "";
-    }
-  }
-  //seems it is not used TODO-ts sm
-  /*else if (vr === "SQ") {
-    // parse the nested tags and returns metadata in array of metadata. 
-    var subTags = map(element, function (obj) {
-      return map(obj, function (v : Element, k : string) {
-        let TAG= k as keyof MetaDataTypes;
-        return parseTag<MetaDataTypes[typeof TAG]>(dataSet, k, v);
-      });
-    });
-
-    valueOut = subTags;
-  }*/
-  else {
-    // If it is some other length and we have no string
-    valueOut = "no display code for VR " + vr;
-  }
-
-  return valueOut as T;
-}
-
-/**
- * Extract tag value according to its value rapresentation, see
- * {@link http://dicom.nema.org/dicom/2013/output/chtml/part05/sect_6.2.html}
- * @instance
- * @function getTagValue
- * @param {Object} dataSet - the dataset
- * @param {String} tag - the desired tag key
- * @return {Number | Array | String} - the desired tag value
- */
-export const getTagValue = function (dataSet: DataSet, tag: string) {
-  let tagObj = getDICOMTag(tag);
-  // tag value rapresentation
-  if (!tagObj) {
-    return null;
-  }
-  let vr = tagObj.vr;
-
-  // parse value according to vr map
-  let vrParsingMap: {
-    [key: string]: () => any;
-  } = {
-    // Date
-    // string of characters of the format YYYYMMDD; where YYYY shall contain year,
-    // MM shall contain the month, and DD shall contain the day,
-    // interpreted as a date of the Gregorian calendar system.
-    DA: function () {
-      let dateString = dataSet.string(tag);
-      return dateString ? formatDate(dateString) : "";
-    },
-    // Decimal String
-    // A string of characters representing either a fixed point number
-    // or a floating point number.
-    DS: function () {
-      if (!dataSet) {
-        return null;
-      }
-      let tag_str = dataSet.string(tag);
-      let array = tag_str ? tag_str.split("\\").map(Number) : null;
-      if (!array) {
-        return null;
-      }
-      return array.length === 1 ? array[0] : array;
-    },
-    // Date Time
-    // A concatenated date-time character string in the format:
-    // YYYYMMDDHHMMSS.FFFFFF&ZZXX
-    DT: function () {
-      let dateString = dataSet.string(tag);
-      return dateString ? formatDateTime(dateString) : "";
-    },
-    // Person Name
-    // A character string encoded using a 5 component convention.
-    // The character code 5CH (the BACKSLASH "\" in ISO-IR 6) shall
-    // not be present, as it is used as the delimiter between values
-    // in multiple valued data elements. The string may be padded
-    // with trailing spaces. For human use, the five components
-    // in their order of occurrence are: family name complex,
-    // given name complex, middle name, name prefix, name suffix.
-    PN: function () {
-      let tag_str = dataSet.string(tag);
-      let pn = tag_str ? tag_str.split("^") : null;
-      if (!pn) {
-        return null;
-      }
-
-      let pns = [pn[3], pn[0], pn[1], pn[2], pn[4]];
-      return pns.join(" ").trim();
-    },
-    // Signed Short
-    // Signed binary integer 16 bits long in 2's complement form
-    SS: function () {
-      return dataSet.uint16(tag);
-    },
-    // Unique Identifier
-    // A character string containing a UID that is used to uniquely
-    // identify a wide letiety of items. The UID is a series of numeric
-    // components separated by the period "." character.
-    UI: function () {
-      return dataSet.string(tag);
-    },
-    // Unsigned Short
-    // Unsigned binary integer 16 bits long.
-    US: function () {
-      return dataSet.uint16(tag);
-    },
-    "US|SS": function () {
-      return dataSet.uint16(tag);
-    }
-  };
-  return vrParsingMap[vr] ? vrParsingMap[vr]() : dataSet.string(tag);
-};