package.json

@@ -7,6 +7,7 @@
     "start": "ts-node src/app.ts",
     "format": "npx prettier ./src",
     "build": "tsc --p ./tsconfig.json",
+    "test": "node --test -r ts-node/register/transpile-only tests/*.test.ts",
     "pkg:win": "npm run build && npx pkg --targets node16-win-x64 package.json"
   },
   "repository": {

src/dimse/dicomJson.ts

@@ -0,0 +1,286 @@
+import dicomParser, { DataSet, Element, readFixedString } from 'dicom-parser';
+import { get_element } from '@iwharris/dicom-data-dictionary';
+
+/**
+ * Minimal DICOM JSON model as defined by DICOM PS3.18 F.
+ * See https://dicom.nema.org/medical/dicom/current/output/chtml/part18/sect_F.2.html
+ */
+export interface DicomJsonElement {
+  vr: string;
+  Value?: unknown[];
+  InlineBinary?: string;
+  BulkDataURI?: string;
+}
+
+export type DicomJsonDataSet = Record<string, DicomJsonElement>;
+
+export interface DicomJsonOptions {
+  /**
+   * Include private (odd group) data elements. Defaults to false to keep
+   * responses small and to avoid leaking site-specific private data.
+   */
+  includePrivate?: boolean;
+}
+
+/** String VRs that map to a JSON array of strings. */
+const STRING_VRS = new Set([
+  'AE', 'AS', 'CS', 'DA', 'DT', 'LO', 'LT', 'SH', 'ST', 'TM', 'UC', 'UI', 'UR', 'UT',
+]);
+
+/** Numeric VRs and the byte-array parser reader used for each. */
+const NUMBER_VRS: Record<string, 'readUint16' | 'readInt16' | 'readUint32' | 'readInt32' | 'readFloat' | 'readDouble'> = {
+  US: 'readUint16',
+  SS: 'readInt16',
+  UL: 'readUint32',
+  SL: 'readInt32',
+  FL: 'readFloat',
+  FD: 'readDouble',
+};
+
+/** VRs whose payload is binary and must be encoded as InlineBinary/BulkDataURI. */
+const BINARY_VRS = new Set(['OB', 'OW', 'OF', 'OD', 'OL', 'OV', 'UN']);
+
+/** Pixel data and float pixel data are never part of the metadata response. */
+const EXCLUDED_TAGS = new Set(['7FE00010', '7FE00008', '7FE00009']);
+
+function formatKey(key: string): string {
+  return key.replace(/^x/i, '').toUpperCase();
+}
+
+function groupOf(tag: string): number {
+  return parseInt(tag.substring(0, 4), 16);
+}
+
+function isPrivateTag(tag: string): boolean {
+  return (groupOf(tag) & 0x0001) === 1;
+}
+
+function isExcludedTag(tag: string): boolean {
+  if (groupOf(tag) === 0x0002) {
+    return true;
+  }
+  if (EXCLUDED_TAGS.has(tag)) {
+    return true;
+  }
+  // Overlay data lives in groups 6000-60FF, element 3000.
+  const group = groupOf(tag);
+  if (group >= 0x6000 && group <= 0x60ff && tag.substring(4) === '3000') {
+    return true;
+  }
+  return false;
+}
+
+function resolveAmbiguousVr(vr: string, tag: string, dataSet: DataSet): string {
+  const options = vr.split(/\s+or\s+/i).map((v) => v.trim().toUpperCase());
+  if (options.length === 1) {
+    return options[0];
+  }
+  // Pixel Padding Value/Range Limit are US or SS depending on PixelRepresentation.
+  if ((tag === '00280120' || tag === '00280121') && options.includes('US') && options.includes('SS')) {
+    const pixelRepresentation = dataSet.uint16('x00280103');
+    return pixelRepresentation === 1 ? 'SS' : 'US';
+  }
+  return options[0];
+}
+
+function resolveVr(element: Element, tag: string, dataSet: DataSet): string {
+  let vr = element.vr;
+  if (!vr) {
+    const dictionaryEntry = get_element(tag);
+    if (dictionaryEntry) {
+      vr = dictionaryEntry.vr;
+    }
+  }
+  vr = (vr || 'UN').toUpperCase();
+  if (/\bor\b/i.test(vr)) {
+    vr = resolveAmbiguousVr(vr, tag, dataSet);
+  }
+  return vr;
+}
+
+function byteArrayParserFor(element: Element, dataSet: DataSet) {
+  return element.parser ?? dataSet.byteArrayParser;
+}
+
+function readBinary(dataSet: DataSet, element: Element): Buffer {
+  const byteArray = dataSet.byteArray;
+  if (Buffer.isBuffer(byteArray)) {
+    return byteArray.subarray(element.dataOffset, element.dataOffset + element.length);
+  }
+  return Buffer.from(byteArray.buffer, byteArray.byteOffset + element.dataOffset, element.length);
+}
+
+function stripTrailingNul(value: string): string {
+  let end = value.length;
+  while (end > 0 && value.charCodeAt(end - 1) === 0) {
+    end -= 1;
+  }
+  return value.slice(0, end);
+}
+
+function readStringValues(dataSet: DataSet, element: Element): string[] {
+  const raw = readFixedString(dataSet.byteArray, element.dataOffset, element.length);
+  const padded = stripTrailingNul(raw).replace(/ +$/g, '');
+  if (padded.length === 0) {
+    return [];
+  }
+  return padded.split('\\').map((value) => value.replace(/ +$/g, ''));
+}
+
+function parsePersonName(value: string): Record<string, string> {
+  const [alphabetic, ideographic, phonetic] = value.split('=');
+  const personName: Record<string, string> = {};
+  if (alphabetic) {
+    personName.Alphabetic = alphabetic;
+  }
+  if (ideographic) {
+    personName.Ideographic = ideographic;
+  }
+  if (phonetic) {
+    personName.Phonetic = phonetic;
+  }
+  return personName;
+}
+
+function readNumericValues(dataSet: DataSet, element: Element, vr: string): number[] {
+  const readerName = NUMBER_VRS[vr];
+  const reader = byteArrayParserFor(element, dataSet)[readerName];
+  const width = readerName === 'readFloat' || readerName === 'readInt32' || readerName === 'readUint32'
+    ? 4
+    : readerName === 'readDouble'
+      ? 8
+      : 2;
+  const count = Math.floor(element.length / width);
+  const values: number[] = [];
+  for (let i = 0; i < count; i += 1) {
+    values.push(reader(dataSet.byteArray, element.dataOffset + i * width));
+  }
+  return values;
+}
+
+function readAttributeTags(dataSet: DataSet, element: Element): string[] {
+  const parser = byteArrayParserFor(element, dataSet);
+  const count = Math.floor(element.length / 4);
+  const values: string[] = [];
+  for (let i = 0; i < count; i += 1) {
+    const offset = element.dataOffset + i * 4;
+    const group = parser.readUint16(dataSet.byteArray, offset);
+    const elementNumber = parser.readUint16(dataSet.byteArray, offset + 2);
+    values.push(
+      `${
+        group.toString(16).padStart(4, '0')
+      }${
+        elementNumber.toString(16).padStart(4, '0')}`.toUpperCase(),
+    );
+  }
+  return values;
+}
+
+function readDecimalStrings(dataSet: DataSet, element: Element): unknown[] {
+  return readStringValues(dataSet, element).map((value) => {
+    const parsed = Number(value);
+    return Number.isFinite(parsed) ? parsed : value;
+  });
+}
+
+function readIntegerStrings(dataSet: DataSet, element: Element): unknown[] {
+  return readStringValues(dataSet, element).map((value) => {
+    const parsed = Number.parseInt(value, 10);
+    return Number.isFinite(parsed) ? parsed : value;
+  });
+}
+
+function convertSequence(dataSet: DataSet, element: Element, options: DicomJsonOptions): DicomJsonElement {
+  const items: DicomJsonDataSet[] = [];
+  if (element.items) {
+    for (const item of element.items) {
+      if (item.dataSet) {
+        items.push(convertDataSetToJson(item.dataSet, options));
+      }
+    }
+  }
+  return { vr: 'SQ', Value: items };
+}
+
+/**
+ * Convert a parsed DICOM dataset into DICOM JSON (PS3.18 F).
+ *
+ * The conversion is VR aware: it uses the explicit VR stored on the element
+ * when available and falls back to the DICOM data dictionary otherwise. Absent
+ * attributes are never synthesized, so a source file without Window Center or
+ * Rescale tags will not gain fabricated values.
+ */
+export function convertElementToJson(
+  dataSet: DataSet,
+  element: Element,
+  options: DicomJsonOptions = {},
+): DicomJsonElement {
+  const tag = formatKey(element.tag);
+  const vr = resolveVr(element, tag, dataSet);
+
+  if (vr === 'SQ') {
+    return convertSequence(dataSet, element, options);
+  }
+
+  if (element.length === 0) {
+    return { vr, Value: [] };
+  }
+
+  if (vr === 'PN') {
+    return { vr, Value: readStringValues(dataSet, element).map(parsePersonName) };
+  }
+
+  if (vr === 'DS') {
+    return { vr, Value: readDecimalStrings(dataSet, element) };
+  }
+
+  if (vr === 'IS') {
+    return { vr, Value: readIntegerStrings(dataSet, element) };
+  }
+
+  if (vr === 'AT') {
+    return { vr, Value: readAttributeTags(dataSet, element) };
+  }
+
+  if (NUMBER_VRS[vr]) {
+    return { vr, Value: readNumericValues(dataSet, element, vr) };
+  }
+
+  if (STRING_VRS.has(vr)) {
+    return { vr, Value: readStringValues(dataSet, element) };
+  }
+
+  if (BINARY_VRS.has(vr)) {
+    return { vr, InlineBinary: readBinary(dataSet, element).toString('base64') };
+  }
+
+  // Unknown VR: fall back to an inline binary payload rather than guessing.
+  return { vr, InlineBinary: readBinary(dataSet, element).toString('base64') };
+}
+
+export function convertDataSetToJson(
+  dataSet: DataSet,
+  options: DicomJsonOptions = {},
+): DicomJsonDataSet {
+  const result: DicomJsonDataSet = {};
+  for (const key of Object.keys(dataSet.elements)) {
+    const element = dataSet.elements[key];
+    const tag = formatKey(key);
+    if (isExcludedTag(tag)) {
+      continue;
+    }
+    if (!options.includePrivate && isPrivateTag(tag)) {
+      continue;
+    }
+    result[tag] = convertElementToJson(dataSet, element, options);
+  }
+  return result;
+}
+
+export function parseDicomToJson(
+  buffer: Buffer | Uint8Array,
+  options: DicomJsonOptions = {},
+): DicomJsonDataSet {
+  const dataSet = dicomParser.parseDicom(buffer);
+  return convertDataSetToJson(dataSet, options);
+}

src/dimse/parseMeta.ts

@@ -1,144 +1,33 @@
 import { LoggerSingleton } from '../utils/logger';
 import { ConfParams, config } from '../utils/config';
 import { fileExists } from '../utils/fileHelper';
-import dicomParser from 'dicom-parser';
 import fs from 'fs';
 import path from 'path';
+import { DicomJsonDataSet, parseDicomToJson } from './dicomJson';
 
-interface ValueType {
-  Value: string[] | number[] | unknown[];
-  vr: string;
-}
-type ElementType = Record<string, ValueType>;
-
-function parseFile(filename: string): Promise<ElementType> {
+function parseFile(filename: string): Promise<DicomJsonDataSet> {
   const logger = LoggerSingleton.Instance;
-  return new Promise<ElementType>((resolve, reject) => {
+  return new Promise<DicomJsonDataSet>((resolve, reject) => {
     fileExists(filename).then((success: boolean) => {
       if (!success) {
         logger.error(`file does not exist: ${filename}`);
-        return reject();
+        return reject(new Error(`file does not exist: ${filename}`));
       }
 
-      fs.promises.readFile(filename).then((data: Uint8Array) => {
-        const dataset = dicomParser.parseDicom(data);
-
-        // parse additional needed attributes
-        const patientName = dataset.string('x00100010');
-        const patentID = dataset.string('x00100020');
-        const studyInstanceUID = dataset.string('x0020000d');
-        const studyDate = dataset.string('x00080020');
-        const studyTime = dataset.string('x00080030');
-        const seriesInstanceUID = dataset.string('x0020000e');
-        const seriesNumber = dataset.string('x00200011');
-        const sopInstanceUID = dataset.string('x00080018');
-        const sopClassUID = dataset.string('x00080016');
-        const bitsAllocated = dataset.uint16('x00280100');
-        const bitsStored = dataset.uint16('x00280101');
-        const highBit = dataset.uint16('x00280102');
-        const rows = dataset.uint16('x00280010');
-        const cols = dataset.uint16('x00280011');
-        const pixelSpacingString = dataset.string('x00280030');
-        const pixelSpacing = pixelSpacingString ? pixelSpacingString.split('\\').map((e: string) => parseFloat(e)) : [1, 1];
-        const modality = dataset.string('x00080060');
-        const samplesPerPixel = dataset.uint16('x00280002');
-        const photometricInterpretation = dataset.string('x00280004');
-        const pixelRepresentation = dataset.uint16('x00280103');
-        const windowCenter = dataset.string('x00281050');
-        const wc = windowCenter ? parseFloat(windowCenter.split('\\')[0]) : 40;
-        const windowWidth = dataset.string('x00281051');
-        const ww = windowWidth ? parseFloat(windowWidth.split('\\')[0]) : 80;
-        const rescaleIntercept = parseFloat(dataset.string('x00281052') || '1');
-        const rescaleSlope = parseFloat(dataset.string('x00281053') || '1');
-        const iopString = dataset.string('x00200037');
-        const iop = iopString ? iopString.split('\\').map((e: string) => parseFloat(e)) : null;
-        const ippString = dataset.string('x00200032');
-        const ipp = ippString ? ippString.split('\\').map((e: string) => parseFloat(e)) : null;
-        const instanceNumber = dataset.string('x00200013');
-        const sliceThickness = dataset.string('x00180050');
-        const sliceLocation = dataset.string('x00201041');
-
-        // TODO: buat ini dynamic berdasarkan includefields atau modality
-        // TODO: hapus tambahan di bawah ini yang tidak diperlukan
-
-        // MR-specific tags for overlay
-        const spacingBetweenSlices = dataset.string('x00180088');
-        const percentPhaseFieldOfView = dataset.string('x00180094');
-        const fovDimensionElement = dataset.elements.x00181149;
-        const fovDimension = fovDimensionElement ? [dataset.uint16('x00181149', 0), dataset.uint16('x00181149', 1)] : null;
-        const acquisitionMatrixElement = dataset.elements.x00181310;
-        const acquisitionMatrix = acquisitionMatrixElement
-          ? [dataset.uint16('x00181310', 0), dataset.uint16('x00181310', 1), dataset.uint16('x00181310', 2), dataset.uint16('x00181310', 3)]
-          : null;
-        const scanningSequence = dataset.string('x00180020');
-        const repetitionTime = dataset.string('x00180080');
-        const echoTime = dataset.string('x00180081');
-        const inversionTime = dataset.string('x00180082');
-        const receiveCoilName = dataset.string('x00181250');
-        const mrAcquisitionType = dataset.string('x00180023');
-        const phaseEncodingDirection = dataset.string('x00181312');
-        const numOfAverages = dataset.string('x00180083');
-        const echoTrainLength = dataset.string('x00180091');
-        const flipAngle = dataset.string('x00181314');
-        const pixelBandwidth = dataset.string('x00180095');
-        const acquisitionTime = dataset.string('x00080032');
-        const acquistionDurationTotal = dataset.string('x00189073'); // in seconds
-        const acquistionDurationPerFrame = dataset.string('x00189220'); // in ms
-        const parallelAcquisitionTechnique = dataset.string('x00189078');
-
-        // append to all results
-        const result: ElementType = {
-          '00100010': { Value: [{ Alphabetic: patientName }], vr: 'PN' },
-          '00100020': { Value: [patentID], vr: 'LO' },
-          '0020000D': { Value: [studyInstanceUID], vr: 'UI' },
-          '00080020': { Value: [studyDate], vr: 'DA' },
-          '00080030': { Value: [studyTime], vr: 'TM' },
-          '0020000E': { Value: [seriesInstanceUID], vr: 'UI' },
-          '00200011': { Value: [seriesNumber], vr: 'IS' },
-          '00080018': { Value: [sopInstanceUID], vr: 'UI' },
-          '00080016': { Value: [sopClassUID], vr: 'UI' },
-          '00080060': { Value: [modality], vr: 'CS' },
-          '00280002': { Value: [samplesPerPixel], vr: 'US' },
-          '00280004': { Value: [photometricInterpretation], vr: 'CS' },
-          '00280010': { Value: [rows], vr: 'US' },
-          '00280011': { Value: [cols], vr: 'US' },
-          '00280030': { Value: pixelSpacing, vr: 'DS' },
-          '00280100': { Value: [bitsAllocated], vr: 'US' },
-          '00280101': { Value: [bitsStored], vr: 'US' },
-          '00280102': { Value: [highBit], vr: 'US' },
-          '00280103': { Value: [pixelRepresentation], vr: 'US' },
-          '00281050': { Value: [wc], vr: 'DS' },
-          '00281051': { Value: [ww], vr: 'DS' },
-          '00281052': { Value: [rescaleIntercept], vr: 'DS' },
-          '00281053': { Value: [rescaleSlope], vr: 'DS' },
-          ...(iop && { '00200037': { Value: iop, vr: 'DS' } }),
-          ...(ipp && { '00200032': { Value: ipp, vr: 'DS' } }),
-          '00200013': { Value: [instanceNumber], vr: 'IS' },
-          '00180050': { Value: [sliceThickness], vr: 'DS' },
-          '00201041': { Value: [sliceLocation], vr: 'DS' },
-          '00180088': { Value: [spacingBetweenSlices], vr: 'DS' },
-          '00180094': { Value: [percentPhaseFieldOfView], vr: 'DS' },
-          ...(fovDimension && { '00181149': { Value: fovDimension, vr: 'IS' } }),
-          ...(acquisitionMatrix && { '00181310': { Value: acquisitionMatrix, vr: 'US' } }),
-          '00180020': { Value: [scanningSequence], vr: 'CS' },
-          '00180080': { Value: [repetitionTime], vr: 'DS' },
-          '00180081': { Value: [echoTime], vr: 'DS' },
-          '00180082': { Value: [inversionTime], vr: 'DS' },
-          '00181250': { Value: [receiveCoilName], vr: 'SH' },
-          '00180023': { Value: [mrAcquisitionType], vr: 'CS' },
-          '00181312': { Value: [phaseEncodingDirection], vr: 'CS' },
-          '00180083': { Value: [numOfAverages], vr: 'DS' },
-          '00180091': { Value: [echoTrainLength], vr: 'IS' },
-          '00181314': { Value: [flipAngle], vr: 'DS' },
-          '00180095': { Value: [pixelBandwidth], vr: 'DS' },
-          '00080032': { Value: [acquisitionTime], vr: 'TM' },
-          '00189073': { Value: [acquistionDurationTotal], vr: 'DS' },
-          '00189220': { Value: [acquistionDurationPerFrame], vr: 'FD' },
-          '00189078': { Value: [parallelAcquisitionTechnique], vr: 'CS' },
-        };
-
-        resolve(result);
-      });
+      fs.promises.readFile(filename)
+        .then((data: Uint8Array) => {
+          try {
+            resolve(parseDicomToJson(data));
+          }
+          catch (error) {
+            logger.error(`failed to parse metadata from ${filename}: ${error}`);
+            reject(error);
+          }
+        })
+        .catch((error: unknown) => {
+          logger.error(`failed to read ${filename}: ${error}`);
+          reject(error);
+        });
     });
   });
 }
@@ -147,7 +36,7 @@ export function parseMeta(json: object, studyInstanceUID: string, seriesInstance
   const logger = LoggerSingleton.Instance;
   logger.info(`parsing series ${seriesInstanceUID}`);
 
-  const parsing = new Array<Promise<ElementType>>();
+  const parsing = new Array<Promise<DicomJsonDataSet>>();
   const storagePath = config.get(ConfParams.STORAGE_PATH) as string;
   for (const [key] of Object.entries(json)) {
     const sopInstanceUid = json[key]['00080018'].Value[0];

tests/dicomJson.test.ts

@@ -0,0 +1,114 @@
+import { test } from 'node:test';
+import assert from 'node:assert/strict';
+import dicomParser, { Element } from 'dicom-parser';
+import { convertElementToJson, DicomJsonDataSet, parseDicomToJson } from '../src/dimse/dicomJson';
+import { buildMonochromeImage, Dataset } from './helpers/dicomWriter';
+
+const BASE_PIXELS = [0, 1, 2, 3, 4, 5, 6, 7];
+
+function crLike(extra: Dataset = [], bufferExtra: Partial<Parameters<typeof buildMonochromeImage>[0]> = {}) {
+  return buildMonochromeImage({
+    rows: 2,
+    columns: 4,
+    pixelData: BASE_PIXELS,
+    extra,
+    ...bufferExtra,
+  });
+}
+
+test('omits Window Center/Width when the source tags are absent', () => {
+  const json = parseDicomToJson(crLike());
+  assert.equal(json['00281050'], undefined);
+  assert.equal(json['00281051'], undefined);
+});
+
+test('omits Rescale Intercept/Slope when the source tags are absent', () => {
+  const json = parseDicomToJson(crLike());
+  assert.equal(json['00281052'], undefined);
+  assert.equal(json['00281053'], undefined);
+});
+
+test('preserves multi-valued Window Center/Width in source order', () => {
+  const json = parseDicomToJson(crLike([
+    { tag: '00281050', vr: 'DS', value: '40\\400' },
+    { tag: '00281051', vr: 'DS', value: '80\\800' },
+  ]));
+
+  assert.deepEqual(json['00281050'].Value, [40, 400]);
+  assert.deepEqual(json['00281051'].Value, [80, 800]);
+});
+
+test('preserves rescale values when present', () => {
+  const json = parseDicomToJson(crLike([
+    { tag: '00281052', vr: 'DS', value: '-1024' },
+    { tag: '00281053', vr: 'DS', value: '2' },
+  ]));
+
+  assert.deepEqual(json['00281052'].Value, [-1024]);
+  assert.deepEqual(json['00281053'].Value, [2]);
+});
+
+test('preserves VOI, LUT, presentation LUT and pixel padding metadata', () => {
+  const json = parseDicomToJson(crLike([
+    { tag: '00281055', vr: 'LO', value: 'WINDOW' },
+    { tag: '00281056', vr: 'CS', value: 'LINEAR' },
+    { tag: '20500020', vr: 'CS', value: 'IDENTITY' },
+    { tag: '00280120', vr: 'US', value: 5 },
+    { tag: '00280121', vr: 'US', value: 10 },
+    {
+      tag: '00283010',
+      vr: 'SQ',
+      items: [
+        [
+          { tag: '00283002', vr: 'US', value: [256, 0, 8] },
+          { tag: '00283006', vr: 'US', value: [1, 2, 3] },
+        ],
+      ],
+    },
+  ]));
+
+  assert.deepEqual(json['00281055'].Value, ['WINDOW']);
+  assert.deepEqual(json['00281056'].Value, ['LINEAR']);
+  assert.deepEqual(json['20500020'].Value, ['IDENTITY']);
+  assert.deepEqual(json['00280120'].Value, [5]);
+  assert.deepEqual(json['00280121'].Value, [10]);
+
+  const sequence = json['00283010'];
+  assert.equal(sequence.vr, 'SQ');
+  const item = (sequence.Value as DicomJsonDataSet[])[0];
+  assert.deepEqual(item['00283002'].Value, [256, 0, 8]);
+  assert.deepEqual(item['00283006'].Value, [1, 2, 3]);
+});
+
+test('never emits Value: [undefined] for absent optional tags', () => {
+  const json = parseDicomToJson(crLike());
+  for (const [tag, element] of Object.entries(json)) {
+    if (Array.isArray(element.Value)) {
+      for (const value of element.Value) {
+        assert.notEqual(value, undefined, `${tag} contains an undefined value`);
+      }
+    }
+  }
+});
+
+test('excludes Pixel Data from metadata output', () => {
+  const json = parseDicomToJson(crLike());
+  assert.equal(json['7FE00010'], undefined);
+});
+
+test('falls back to the data dictionary when VR is not explicit', () => {
+  const buffer = crLike([
+    { tag: '00281050', vr: 'DS', value: '40' },
+  ]);
+  const dataSet = dicomParser.parseDicom(buffer);
+  const explicit = dataSet.elements.x00281050;
+  const implicitLike: Element = {
+    tag: explicit.tag,
+    length: explicit.length,
+    dataOffset: explicit.dataOffset,
+  };
+
+  const json = convertElementToJson(dataSet, implicitLike);
+  assert.equal(json.vr, 'DS');
+  assert.deepEqual(json.Value, [40]);
+});

tests/helpers/dicomWriter.ts

@@ -0,0 +1,174 @@
+/**
+ * Minimal, dependency-free DICOM Part 10 writer used to build synthetic,
+ * non-PHI fixtures for unit tests. Only the explicit VR little endian
+ * transfer syntax is produced, which is enough to exercise the metadata
+ * converter and native frame extraction.
+ */
+
+export interface VrElement {
+  /** Tag in 'ggggeeee' hex form, e.g. '00281050'. */
+  tag: string;
+  vr: string;
+  value?: string | number | number[] | Buffer;
+  /** Sequence items, only used when vr === 'SQ'. Each item is itself a dataset. */
+  items?: Dataset[];
+}
+
+export type Dataset = VrElement[];
+
+const LONG_VRS = new Set(['OB', 'OD', 'OF', 'OL', 'OV', 'OW', 'SQ', 'SV', 'UC', 'UN', 'UR', 'UT', 'UV']);
+
+const NUMERIC_VRS: Record<string, { width: number; write: (buf: Buffer, value: number, offset: number) => void }> = {
+  US: { width: 2, write: (b, v, o) => b.writeUInt16LE(v, o) },
+  SS: { width: 2, write: (b, v, o) => b.writeInt16LE(v, o) },
+  UL: { width: 4, write: (b, v, o) => b.writeUInt32LE(v, o) },
+  SL: { width: 4, write: (b, v, o) => b.writeInt32LE(v, o) },
+  FL: { width: 4, write: (b, v, o) => b.writeFloatLE(v, o) },
+  FD: { width: 8, write: (b, v, o) => b.writeDoubleLE(v, o) },
+};
+
+function paddingByte(vr: string): number {
+  return vr === 'UI' ? 0x00 : 0x20;
+}
+
+function encodeValue(element: VrElement): Buffer {
+  const { vr, value } = element;
+
+  if (vr === 'SQ') {
+    const items = Array.isArray(element.items) ? element.items : [];
+    return Buffer.concat(items.map(encodeItem));
+  }
+
+  if (value === undefined) {
+    return Buffer.alloc(0);
+  }
+
+  if (Buffer.isBuffer(value)) {
+    return value;
+  }
+
+  if (NUMERIC_VRS[vr]) {
+    const numbers = Array.isArray(value) ? value : [value as number];
+    const { width, write } = NUMERIC_VRS[vr];
+    const buffer = Buffer.alloc(numbers.length * width);
+    numbers.forEach((number, index) => write(buffer, number, index * width));
+    return buffer;
+  }
+
+  const text = Array.isArray(value) ? value.join('\\') : String(value);
+  return Buffer.from(text, 'ascii');
+}
+
+function encodeItem(dataset: Dataset): Buffer {
+  const body = encodeDataset(dataset);
+  const header = Buffer.alloc(8);
+  header.writeUInt16LE(0xfffe, 0);
+  header.writeUInt16LE(0xe000, 2);
+  header.writeUInt32LE(body.length, 4);
+  return Buffer.concat([header, body]);
+}
+
+export function encodeElement(element: VrElement): Buffer {
+  const group = Number.parseInt(element.tag.substring(0, 4), 16);
+  const elementNumber = Number.parseInt(element.tag.substring(4, 8), 16);
+
+  let value = encodeValue(element);
+  if (value.length % 2 !== 0) {
+    value = Buffer.concat([value, Buffer.from([paddingByte(element.vr)])]);
+  }
+
+  const isLong = LONG_VRS.has(element.vr);
+  const header = Buffer.alloc(isLong ? 12 : 8);
+  header.writeUInt16LE(group, 0);
+  header.writeUInt16LE(elementNumber, 2);
+  header.write(element.vr, 4, 2, 'ascii');
+  if (isLong) {
+    header.writeUInt32LE(value.length, 8);
+  }
+  else {
+    header.writeUInt16LE(value.length, 6);
+  }
+  return Buffer.concat([header, value]);
+}
+
+export function encodeDataset(dataset: Dataset): Buffer {
+  return Buffer.concat(dataset.map(encodeElement));
+}
+
+export interface Part10Options {
+  transferSyntaxUID?: string;
+  sopClassUID?: string;
+  sopInstanceUID?: string;
+}
+
+export function buildPart10(dataset: Dataset, options: Part10Options = {}): Buffer {
+  const transferSyntaxUID = options.transferSyntaxUID ?? '1.2.840.10008.1.2.1';
+  const sopClassUID = options.sopClassUID ?? '1.2.840.10008.5.1.4.1.1.7';
+  const sopInstanceUID = options.sopInstanceUID ?? '1.2.826.0.1.3680043.8.498.1';
+
+  const metaElements: Dataset = [
+    { tag: '00020001', vr: 'OB', value: Buffer.from([0x00, 0x01]) },
+    { tag: '00020002', vr: 'UI', value: sopClassUID },
+    { tag: '00020003', vr: 'UI', value: sopInstanceUID },
+    { tag: '00020010', vr: 'UI', value: transferSyntaxUID },
+    { tag: '00020012', vr: 'UI', value: '1.2.826.0.1.3680043.8.498.1' },
+  ];
+  const metaBody = encodeDataset(metaElements);
+  const groupLength = encodeElement({ tag: '00020000', vr: 'UL', value: metaBody.length });
+
+  const preamble = Buffer.alloc(128);
+  const magic = Buffer.from('DICM', 'ascii');
+  const datasetBytes = encodeDataset(dataset);
+
+  return Buffer.concat([preamble, magic, groupLength, metaBody, datasetBytes]);
+}
+
+/** Build a synthetic single or multi frame MONOCHROME2 image. */
+export function buildMonochromeImage(options: {
+  rows: number;
+  columns: number;
+  bitsAllocated?: number;
+  samplesPerPixel?: number;
+  numberOfFrames?: number;
+  pixelData: number[];
+  extra?: Dataset;
+  transferSyntaxUID?: string;
+  photometricInterpretation?: string;
+}): Buffer {
+  const bitsAllocated = options.bitsAllocated ?? 8;
+  const samplesPerPixel = options.samplesPerPixel ?? 1;
+  const dataset: Dataset = [
+    { tag: '00080016', vr: 'UI', value: '1.2.840.10008.5.1.4.1.1.7' },
+    { tag: '00080018', vr: 'UI', value: '1.2.826.0.1.3680043.8.498.1' },
+    { tag: '00080060', vr: 'CS', value: 'CR' },
+    { tag: '0020000D', vr: 'UI', value: '1.2.826.0.1.3680043.8.498.100' },
+    { tag: '0020000E', vr: 'UI', value: '1.2.826.0.1.3680043.8.498.200' },
+    { tag: '00280002', vr: 'US', value: samplesPerPixel },
+    { tag: '00280004', vr: 'CS', value: options.photometricInterpretation ?? 'MONOCHROME2' },
+    { tag: '00280010', vr: 'US', value: options.rows },
+    { tag: '00280011', vr: 'US', value: options.columns },
+    { tag: '00280100', vr: 'US', value: bitsAllocated },
+    { tag: '00280101', vr: 'US', value: bitsAllocated },
+    { tag: '00280102', vr: 'US', value: bitsAllocated - 1 },
+    { tag: '00280103', vr: 'US', value: 0 },
+  ];
+
+  if (options.numberOfFrames !== undefined) {
+    dataset.push({ tag: '00280008', vr: 'IS', value: String(options.numberOfFrames) });
+  }
+
+  if (options.extra) {
+    dataset.push(...options.extra);
+  }
+
+  const pixelData = bitsAllocated <= 8
+    ? Buffer.from(options.pixelData)
+    : (() => {
+      const buffer = Buffer.alloc(options.pixelData.length * 2);
+      options.pixelData.forEach((value, index) => buffer.writeUInt16LE(value, index * 2));
+      return buffer;
+    })();
+  dataset.push({ tag: '7FE00010', vr: bitsAllocated <= 8 ? 'OB' : 'OW', value: pixelData });
+
+  return buildPart10(dataset, { transferSyntaxUID: options.transferSyntaxUID });
+}

tsconfig.json

@@ -69,6 +69,7 @@
     // "isolatedModules": true,                          /* Ensure that each file can be safely transpiled without relying on other imports. */
     // "allowSyntheticDefaultImports": true,             /* Allow 'import x from y' when a module doesn't have a default export. */
     "esModuleInterop": true,                             /* Emit additional JavaScript to ease support for importing CommonJS modules. This enables `allowSyntheticDefaultImports` for type compatibility. */
+    "skipLibCheck": true,                                /* Skip type checking of declaration files from dependencies. */
     // "preserveSymlinks": true,                         /* Disable resolving symlinks to their realpath. This correlates to the same flag in node. */
     "forceConsistentCasingInFileNames": true,            /* Ensure that casing is correct in imports. */