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PaulHaxPaulHax
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fix: reset ITK-wasm worker before loading labelmaps in session restore
The singleton ITK-wasm worker accumulates WASM heap across readImage calls. When loading a session with a large base image (~361MB) followed by a labelmap (~180MB), the heap can exceed 2GB. Emscripten's ccall returns pointers as signed i32, so pointers >2^31 wrap negative, causing RangeError. Reset the worker before deserializing segment groups to give each labelmap read a fresh WASM heap, preventing the overflow.
1 parent 529e212 commit 75fa6c9

3 files changed

Lines changed: 184 additions & 0 deletions

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‎src/io/import/processors/restoreStateFile.ts‎

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@@ -20,6 +20,7 @@ import { useViewStore } from '@/src/store/views';
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import { useViewConfigStore } from '@/src/store/view-configs';
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import { migrateManifest } from '@/src/io/state-file/migrations';
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import { useMessageStore } from '@/src/store/messages';
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import { resetWorker } from '@/src/io/itk/worker';
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type LeafSource =
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| { type: 'uri'; uri: string; name: string; mime?: string }
@@ -136,6 +137,12 @@ export async function completeStateFileRestore(
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useViewConfigStore().deserializeAll(manifest, stateIDToStoreID);
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// Reset the ITK-wasm worker to free accumulated WASM heap from loading
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// base images. Without this, loading large labelmaps on the same worker
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// can push the heap past 2GB, causing signed pointer overflow in
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// Emscripten's ccall (pointers > 2^31 wrap negative).
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await resetWorker();
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const segmentGroupIDMap = await useSegmentGroupStore().deserialize(
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manifest,
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stateFiles,

‎src/io/itk/worker.ts‎

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@@ -33,6 +33,14 @@ export function getWorker() {
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return webWorker;
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}
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export async function resetWorker() {
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if (webWorker) {
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webWorker.terminate();
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webWorker = null;
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}
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await ensureWorker();
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}
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export function getDicomSeriesWorkerPool() {
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return readDicomSeriesWorkerPool;
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}

‎tests/specs/session-large-uri-base.e2e.ts‎

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@@ -0,0 +1,169 @@
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import * as fs from 'node:fs';
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import * as path from 'node:path';
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import * as zlib from 'node:zlib';
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import { cleanuptotal } from 'wdio-cleanuptotal-service';
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import { volViewPage } from '../pageobjects/volview.page';
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import { writeManifestToFile } from './utils';
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import { DOWNLOAD_TIMEOUT, TEMP_DIR } from '../../wdio.shared.conf';
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const writeBufferToFile = async (data: Buffer, fileName: string) => {
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const filePath = path.join(TEMP_DIR, fileName);
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await fs.promises.writeFile(filePath, data);
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cleanuptotal.addCleanup(async () => {
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if (fs.existsSync(filePath)) fs.unlinkSync(filePath);
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});
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return filePath;
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};
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const createNiftiGz = (
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dimX: number,
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dimY: number,
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dimZ: number,
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datatype: number,
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bitpix: number
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) => {
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const bytesPerVoxel = bitpix / 8;
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const header = Buffer.alloc(352);
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header.writeInt32LE(348, 0);
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header.writeInt16LE(3, 40);
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header.writeInt16LE(dimX, 42);
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header.writeInt16LE(dimY, 44);
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header.writeInt16LE(dimZ, 46);
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header.writeInt16LE(1, 48);
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header.writeInt16LE(1, 50);
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header.writeInt16LE(1, 52);
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header.writeInt16LE(datatype, 70);
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header.writeInt16LE(bitpix, 72);
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header.writeFloatLE(1, 76);
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header.writeFloatLE(1, 80);
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header.writeFloatLE(1, 84);
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header.writeFloatLE(1, 88);
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header.writeFloatLE(352, 108);
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header.writeFloatLE(1, 112);
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header.writeInt16LE(1, 254);
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header.writeFloatLE(1, 280);
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header.writeFloatLE(0, 284);
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header.writeFloatLE(0, 288);
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header.writeFloatLE(0, 292);
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header.writeFloatLE(0, 296);
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header.writeFloatLE(1, 300);
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header.writeFloatLE(0, 304);
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header.writeFloatLE(0, 308);
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header.writeFloatLE(0, 312);
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header.writeFloatLE(0, 316);
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header.writeFloatLE(1, 320);
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header.writeFloatLE(0, 324);
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header.write('n+1\0', 344, 'binary');
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const imageData = Buffer.alloc(dimX * dimY * dimZ * bytesPerVoxel);
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return zlib.gzipSync(Buffer.concat([header, imageData]), { level: 1 });
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};
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/**
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* Regression test for session restore with large base image + labelmap.
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*
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* Scenario: Int16 1024×1024×172 base image loaded via URI, with a UInt8
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* labelmap of the same dimensions. On the shared ITK-wasm worker, base
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* image processing grew the WASM heap to ~1721MB. Loading the labelmap
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* on the same worker pushed it past 2GB, causing signed pointer overflow
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* in Emscripten's ccall (output pointers > 2^31 wrap negative →
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* RangeError: Start offset -N is outside the bounds).
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*
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* Fix: reset the ITK-wasm worker before deserializing labelmaps to
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* prevent heap accumulation.
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*/
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describe('Session with large URI base and labelmap', function () {
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this.timeout(180_000);
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it('loads large base image with labelmap without errors', async () => {
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const prefix = `session-large-${Date.now()}`;
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const baseFileName = `${prefix}-base-i16.nii.gz`;
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const labelmapFileName = `${prefix}-labelmap-u8.nii.gz`;
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// Int16 1024×1024×172 = 361MB raw
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await writeBufferToFile(
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createNiftiGz(1024, 1024, 172, 4, 16),
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baseFileName
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);
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// UInt8 labelmap same dimensions = 180MB raw
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await writeBufferToFile(
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createNiftiGz(1024, 1024, 172, 2, 8),
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labelmapFileName
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);
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const manifest = {
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version: '6.1.0',
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dataSources: [
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{ id: 0, type: 'uri', uri: `/tmp/${baseFileName}` },
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{ id: 1, type: 'uri', uri: `/tmp/${labelmapFileName}` },
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],
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labelMaps: [
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{
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id: 'seg-1',
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dataSourceId: 1,
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metadata: {
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name: 'Annotation',
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parentImage: '0',
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segments: {
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order: [1],
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byValue: {
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'1': {
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value: 1,
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name: 'Label 1',
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color: [255, 0, 0, 255],
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visible: true,
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},
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},
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},
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},
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},
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],
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};
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const manifestFileName = `${prefix}-manifest.volview.json`;
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await writeManifestToFile(manifest, manifestFileName);
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const rangeErrors: string[] = [];
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const onLogEntry = (logEntry: { text: string | null }) => {
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const text = logEntry.text ?? '';
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if (text.includes('RangeError')) {
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rangeErrors.push(text);
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}
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};
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browser.on('log.entryAdded', onLogEntry);
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try {
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await volViewPage.open(`?urls=[tmp/${manifestFileName}]`);
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await volViewPage.waitForViews(DOWNLOAD_TIMEOUT * 6);
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expect(rangeErrors).toEqual([]);
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const notifications = await volViewPage.getNotificationsCount();
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expect(notifications).toEqual(0);
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// Verify segment group loaded
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const annotationsTab = await $(
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'button[data-testid="module-tab-Annotations"]'
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);
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await annotationsTab.click();
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const segmentGroupsTab = await $('button.v-tab*=Segment Groups');
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await segmentGroupsTab.waitForClickable();
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await segmentGroupsTab.click();
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await browser.waitUntil(
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async () => {
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const segmentGroups = await $$('.segment-group-list .v-list-item');
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return (await segmentGroups.length) >= 1;
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},
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{
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timeout: DOWNLOAD_TIMEOUT,
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timeoutMsg: 'Segment group not found after session restore',
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}
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);
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} finally {
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browser.off('log.entryAdded', onLogEntry);
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}
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});
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});

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