fix(metadata): stop fabricating display metadata and add DICOM JSON converter
Replace the hand-built metadata subset in parseMeta with a VR-aware DICOM-to-DICOM-JSON converter. Window Center/Width, Rescale Intercept/Slope are only emitted when the source element exists; multi-values are preserved in source order. VOI/LUT, Presentation LUT and Pixel Padding tags are preserved and Pixel Data is excluded. - add src/dimse/dicomJson.ts (dictionary-aware converter) - rewrite src/dimse/parseMeta.ts to use the converter - add synthetic non-PHI DICOM writer and metadata tests - add npm test script (node:test + ts-node) and skipLibCheck
This commit is contained in:
padmanto
114
tests/dicomJson.test.ts
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114
tests/dicomJson.test.ts
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import { test } from 'node:test';
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import assert from 'node:assert/strict';
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import dicomParser, { Element } from 'dicom-parser';
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import { convertElementToJson, DicomJsonDataSet, parseDicomToJson } from '../src/dimse/dicomJson';
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import { buildMonochromeImage, Dataset } from './helpers/dicomWriter';
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const BASE_PIXELS = [0, 1, 2, 3, 4, 5, 6, 7];
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function crLike(extra: Dataset = [], bufferExtra: Partial<Parameters<typeof buildMonochromeImage>[0]> = {}) {
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return buildMonochromeImage({
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rows: 2,
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columns: 4,
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pixelData: BASE_PIXELS,
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extra,
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...bufferExtra,
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});
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}
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test('omits Window Center/Width when the source tags are absent', () => {
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const json = parseDicomToJson(crLike());
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assert.equal(json['00281050'], undefined);
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assert.equal(json['00281051'], undefined);
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});
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test('omits Rescale Intercept/Slope when the source tags are absent', () => {
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const json = parseDicomToJson(crLike());
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assert.equal(json['00281052'], undefined);
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assert.equal(json['00281053'], undefined);
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});
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test('preserves multi-valued Window Center/Width in source order', () => {
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const json = parseDicomToJson(crLike([
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{ tag: '00281050', vr: 'DS', value: '40\\400' },
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{ tag: '00281051', vr: 'DS', value: '80\\800' },
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]));
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assert.deepEqual(json['00281050'].Value, [40, 400]);
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assert.deepEqual(json['00281051'].Value, [80, 800]);
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});
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test('preserves rescale values when present', () => {
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const json = parseDicomToJson(crLike([
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{ tag: '00281052', vr: 'DS', value: '-1024' },
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{ tag: '00281053', vr: 'DS', value: '2' },
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]));
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assert.deepEqual(json['00281052'].Value, [-1024]);
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assert.deepEqual(json['00281053'].Value, [2]);
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});
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test('preserves VOI, LUT, presentation LUT and pixel padding metadata', () => {
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const json = parseDicomToJson(crLike([
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{ tag: '00281055', vr: 'LO', value: 'WINDOW' },
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{ tag: '00281056', vr: 'CS', value: 'LINEAR' },
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{ tag: '20500020', vr: 'CS', value: 'IDENTITY' },
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{ tag: '00280120', vr: 'US', value: 5 },
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{ tag: '00280121', vr: 'US', value: 10 },
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{
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tag: '00283010',
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vr: 'SQ',
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items: [
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[
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{ tag: '00283002', vr: 'US', value: [256, 0, 8] },
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{ tag: '00283006', vr: 'US', value: [1, 2, 3] },
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],
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],
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},
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]));
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assert.deepEqual(json['00281055'].Value, ['WINDOW']);
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assert.deepEqual(json['00281056'].Value, ['LINEAR']);
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assert.deepEqual(json['20500020'].Value, ['IDENTITY']);
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assert.deepEqual(json['00280120'].Value, [5]);
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assert.deepEqual(json['00280121'].Value, [10]);
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const sequence = json['00283010'];
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assert.equal(sequence.vr, 'SQ');
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const item = (sequence.Value as DicomJsonDataSet[])[0];
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assert.deepEqual(item['00283002'].Value, [256, 0, 8]);
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assert.deepEqual(item['00283006'].Value, [1, 2, 3]);
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});
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test('never emits Value: [undefined] for absent optional tags', () => {
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const json = parseDicomToJson(crLike());
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for (const [tag, element] of Object.entries(json)) {
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if (Array.isArray(element.Value)) {
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for (const value of element.Value) {
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assert.notEqual(value, undefined, `${tag} contains an undefined value`);
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}
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}
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}
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});
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test('excludes Pixel Data from metadata output', () => {
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const json = parseDicomToJson(crLike());
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assert.equal(json['7FE00010'], undefined);
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});
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test('falls back to the data dictionary when VR is not explicit', () => {
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const buffer = crLike([
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{ tag: '00281050', vr: 'DS', value: '40' },
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]);
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const dataSet = dicomParser.parseDicom(buffer);
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const explicit = dataSet.elements.x00281050;
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const implicitLike: Element = {
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tag: explicit.tag,
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length: explicit.length,
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dataOffset: explicit.dataOffset,
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};
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const json = convertElementToJson(dataSet, implicitLike);
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assert.equal(json.vr, 'DS');
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assert.deepEqual(json.Value, [40]);
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});
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174
tests/helpers/dicomWriter.ts
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174
tests/helpers/dicomWriter.ts
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/**
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* Minimal, dependency-free DICOM Part 10 writer used to build synthetic,
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* non-PHI fixtures for unit tests. Only the explicit VR little endian
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* transfer syntax is produced, which is enough to exercise the metadata
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* converter and native frame extraction.
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*/
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export interface VrElement {
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/** Tag in 'ggggeeee' hex form, e.g. '00281050'. */
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tag: string;
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vr: string;
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value?: string | number | number[] | Buffer;
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/** Sequence items, only used when vr === 'SQ'. Each item is itself a dataset. */
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items?: Dataset[];
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}
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export type Dataset = VrElement[];
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const LONG_VRS = new Set(['OB', 'OD', 'OF', 'OL', 'OV', 'OW', 'SQ', 'SV', 'UC', 'UN', 'UR', 'UT', 'UV']);
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const NUMERIC_VRS: Record<string, { width: number; write: (buf: Buffer, value: number, offset: number) => void }> = {
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US: { width: 2, write: (b, v, o) => b.writeUInt16LE(v, o) },
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SS: { width: 2, write: (b, v, o) => b.writeInt16LE(v, o) },
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UL: { width: 4, write: (b, v, o) => b.writeUInt32LE(v, o) },
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SL: { width: 4, write: (b, v, o) => b.writeInt32LE(v, o) },
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FL: { width: 4, write: (b, v, o) => b.writeFloatLE(v, o) },
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FD: { width: 8, write: (b, v, o) => b.writeDoubleLE(v, o) },
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};
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function paddingByte(vr: string): number {
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return vr === 'UI' ? 0x00 : 0x20;
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}
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function encodeValue(element: VrElement): Buffer {
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const { vr, value } = element;
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if (vr === 'SQ') {
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const items = Array.isArray(element.items) ? element.items : [];
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return Buffer.concat(items.map(encodeItem));
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}
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if (value === undefined) {
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return Buffer.alloc(0);
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}
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if (Buffer.isBuffer(value)) {
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return value;
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}
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if (NUMERIC_VRS[vr]) {
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const numbers = Array.isArray(value) ? value : [value as number];
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const { width, write } = NUMERIC_VRS[vr];
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const buffer = Buffer.alloc(numbers.length * width);
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numbers.forEach((number, index) => write(buffer, number, index * width));
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return buffer;
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}
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const text = Array.isArray(value) ? value.join('\\') : String(value);
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return Buffer.from(text, 'ascii');
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}
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function encodeItem(dataset: Dataset): Buffer {
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const body = encodeDataset(dataset);
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const header = Buffer.alloc(8);
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header.writeUInt16LE(0xfffe, 0);
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header.writeUInt16LE(0xe000, 2);
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header.writeUInt32LE(body.length, 4);
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return Buffer.concat([header, body]);
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}
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export function encodeElement(element: VrElement): Buffer {
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const group = Number.parseInt(element.tag.substring(0, 4), 16);
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const elementNumber = Number.parseInt(element.tag.substring(4, 8), 16);
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let value = encodeValue(element);
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if (value.length % 2 !== 0) {
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value = Buffer.concat([value, Buffer.from([paddingByte(element.vr)])]);
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}
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const isLong = LONG_VRS.has(element.vr);
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const header = Buffer.alloc(isLong ? 12 : 8);
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header.writeUInt16LE(group, 0);
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header.writeUInt16LE(elementNumber, 2);
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header.write(element.vr, 4, 2, 'ascii');
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if (isLong) {
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header.writeUInt32LE(value.length, 8);
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}
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else {
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header.writeUInt16LE(value.length, 6);
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}
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return Buffer.concat([header, value]);
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}
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export function encodeDataset(dataset: Dataset): Buffer {
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return Buffer.concat(dataset.map(encodeElement));
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}
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export interface Part10Options {
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transferSyntaxUID?: string;
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sopClassUID?: string;
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sopInstanceUID?: string;
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}
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export function buildPart10(dataset: Dataset, options: Part10Options = {}): Buffer {
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const transferSyntaxUID = options.transferSyntaxUID ?? '1.2.840.10008.1.2.1';
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const sopClassUID = options.sopClassUID ?? '1.2.840.10008.5.1.4.1.1.7';
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const sopInstanceUID = options.sopInstanceUID ?? '1.2.826.0.1.3680043.8.498.1';
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const metaElements: Dataset = [
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{ tag: '00020001', vr: 'OB', value: Buffer.from([0x00, 0x01]) },
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{ tag: '00020002', vr: 'UI', value: sopClassUID },
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{ tag: '00020003', vr: 'UI', value: sopInstanceUID },
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{ tag: '00020010', vr: 'UI', value: transferSyntaxUID },
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{ tag: '00020012', vr: 'UI', value: '1.2.826.0.1.3680043.8.498.1' },
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];
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const metaBody = encodeDataset(metaElements);
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const groupLength = encodeElement({ tag: '00020000', vr: 'UL', value: metaBody.length });
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const preamble = Buffer.alloc(128);
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const magic = Buffer.from('DICM', 'ascii');
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const datasetBytes = encodeDataset(dataset);
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return Buffer.concat([preamble, magic, groupLength, metaBody, datasetBytes]);
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}
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/** Build a synthetic single or multi frame MONOCHROME2 image. */
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export function buildMonochromeImage(options: {
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rows: number;
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columns: number;
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bitsAllocated?: number;
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samplesPerPixel?: number;
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numberOfFrames?: number;
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pixelData: number[];
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extra?: Dataset;
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transferSyntaxUID?: string;
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photometricInterpretation?: string;
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}): Buffer {
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const bitsAllocated = options.bitsAllocated ?? 8;
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const samplesPerPixel = options.samplesPerPixel ?? 1;
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const dataset: Dataset = [
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{ tag: '00080016', vr: 'UI', value: '1.2.840.10008.5.1.4.1.1.7' },
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{ tag: '00080018', vr: 'UI', value: '1.2.826.0.1.3680043.8.498.1' },
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{ tag: '00080060', vr: 'CS', value: 'CR' },
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{ tag: '0020000D', vr: 'UI', value: '1.2.826.0.1.3680043.8.498.100' },
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{ tag: '0020000E', vr: 'UI', value: '1.2.826.0.1.3680043.8.498.200' },
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{ tag: '00280002', vr: 'US', value: samplesPerPixel },
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{ tag: '00280004', vr: 'CS', value: options.photometricInterpretation ?? 'MONOCHROME2' },
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{ tag: '00280010', vr: 'US', value: options.rows },
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{ tag: '00280011', vr: 'US', value: options.columns },
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{ tag: '00280100', vr: 'US', value: bitsAllocated },
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{ tag: '00280101', vr: 'US', value: bitsAllocated },
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{ tag: '00280102', vr: 'US', value: bitsAllocated - 1 },
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{ tag: '00280103', vr: 'US', value: 0 },
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];
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if (options.numberOfFrames !== undefined) {
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dataset.push({ tag: '00280008', vr: 'IS', value: String(options.numberOfFrames) });
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}
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if (options.extra) {
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dataset.push(...options.extra);
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}
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const pixelData = bitsAllocated <= 8
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? Buffer.from(options.pixelData)
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: (() => {
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const buffer = Buffer.alloc(options.pixelData.length * 2);
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options.pixelData.forEach((value, index) => buffer.writeUInt16LE(value, index * 2));
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return buffer;
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})();
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dataset.push({ tag: '7FE00010', vr: bitsAllocated <= 8 ? 'OB' : 'OW', value: pixelData });
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return buildPart10(dataset, { transferSyntaxUID: options.transferSyntaxUID });
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}
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