POC: bring viv-dicomweb-test work into SLIM and add basic bulk annotations support by igoroctaviano · Pull Request #381 · ImagingDataCommons/slim

igoroctaviano · 2026-04-08T00:46:20Z

Summary

POC port of viv-dicomweb-test into SLIM: Viv + Deck.gl slide viewing on dedicated /viv/... routes plus bulk simple annotations (polygons) wired through the same DICOMweb + DMV decode path as OpenLayers.

DMV: feat: export bulk annotation and graphic-fetch APIs for Viv / non-OpenLayers consumers dicom-microscopy-viewer#237

What changed (vs `master`)

Verified against feat/viv-loader ↔ master in the Slim repo (18 files, ~4.3k insertions).

Routing: New React Router paths that mirror existing case URLs but prefix /viv: /viv/studies/:studyInstanceUID/* and the GCP Healthcare store variant. ParametrizedCaseViewer passes isVivRoute and optional vivSettings from config when the pathname starts with /viv/.
src/viv/ module: dicomLoader.ts (DICOMweb tiling + DMV integration), VivSlideViewport.tsx, loadBulkAnnotationLayers.ts, vivDisplayDefaults.ts, README.md. Includes request abort/cancel handling and viewport work (incl. 8-bit SM tile positioning).
UI integration: CaseViewer.tsx switches the slide viewport to VivSlideViewport on Viv routes, adds VivSettingsDrawer and an annotation rail wired to AnnotationGroupList, and adjusts study URLs so navigation stays under /viv/….
Dependencies: @deck.gl/*, @vivjs/layers, @vivjs/loaders, @luma.gl/*; dicomweb-client raised to ^0.11.2 (plus types/dicomweb-client). Overrides pin Deck versions; bun.lock updated.
Build: craco.config.js — Babel transpilation for node_modules under @deck.gl, @luma.gl, @math.gl, @probe.gl, @hms-dbmi/viv.
DICOM web client hook: DicomWebManager.applyToPrimaryDicomwebClient so Viv tiles can attach to the primary store’s requestHooks (same XHR pipeline as VolumeImageViewer).
Config types: AppConfig.d.ts — optional vivSettings (selections, channelsVisible, contrastLimits, colors, initialViewState). There is no useViv flag; Viv is strictly /viv/... URLs.
ICC profiles: iccProfilesPreference.ts and updates in SlideViewer.tsx so ICC enable/disable persists (fixes ICC behavior with the Viv path).
Types: types/dicom-microscopy-viewer/index.d.ts extended for DMV APIs the Viv loader uses.
App.tsx: registers the Viv routes.

Branch & local setup

SLIM branch: feat/viv-loader.
POC still expects a linked dicom-microscopy-viewer checkout with Viv-facing API changes until a matching release is published. From DMV (correct branch): bun link. From the Slim checkout: bun link dicom-microscopy-viewer, then bun install if needed. bun unlink dicom-microscopy-viewer in Slim restores registry installs. Details: src/viv/README.md.

How to test

Add this server URL: https://proxy.imaging.datacommons.cancer.gov/current/viewer-only-no-downloads-see-tinyurl-dot-com-slash-3j3d9jyp/dicomWeb
Open the Viv-prefixed study URL (same study/series as before, /viv after the origin):

http://localhost:3000/viv/studies/2.25.106918873973188798943205935727506273925/series/1.3.6.1.4.1.5962.99.1.1088146757.1503397867.1637470719301.2.0
(Optional) In public/config/*.js, set vivSettings for channel/contrast/colors/initialViewState on /viv/....
Toggle annotation group visibility. Expect a long first pass while every polygon is built (~23 s in one run); after that, pan/zoom stays responsive and memory behaved better than earlier OpenLayers attempts for this POC.

Possible TODO's

deepsource-io · 2026-04-08T00:47:10Z

DeepSource Code Review

We reviewed changes in 736739e...da60454 on this pull request. Below is the summary for the review, and you can see the individual issues we found as inline review comments.

See full review on DeepSource ↗

PR Report Card

Overall Grade	Security Reliability Complexity Hygiene

Code Review Summary

Analyzer	Status	Updated (UTC)	Details
JavaScript		Aug 24, 2026 8:26p.m.	Review ↗

Important

AI Review is run only on demand for your team. We're only showing results of static analysis review right now. To trigger AI Review, comment @deepsourcebot review on this thread.

igoroctaviano · 2026-04-14T18:39:04Z

@fedorov, now you can test this using /viv
e.g.
Compare http://localhost:3000/viv/studies/2.25.302737996345872783571112300080988167697/series/1.3.6.1.4.1.5962.99.1.1354739488.2060999382.1637737312032.2.0
with http://localhost:3000/studies/2.25.302737996345872783571112300080988167697/series/1.3.6.1.4.1.5962.99.1.1354739488.2060999382.1637737312032.2.0

fedorov · 2026-05-07T15:07:03Z

@igoroctaviano it would be helpful to indicate somewhere (in the "info" panel perhaps?) whether given instance is using viv or not.

I deployed the viewer with useViv: true at https://andrey-slim-test.web.app/studies/2.25.147491078891690248552488589436202370211/series/1.3.6.1.4.1.5962.99.1.1471805016.1464679391.1637854377560.2.0, and I have no clue if it worked and what backend is being used!

igoroctaviano · 2026-05-07T15:15:05Z

PR description outdated. Just use the viv route before /studies

sonarqubecloud · 2026-05-07T15:44:59Z

Quality Gate passed

Issues
46 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
2.4% Duplication on New Code

See analysis details on SonarQube Cloud

fedorov · 2026-05-20T20:26:45Z

Here's a quick dashboard to click through studies that have ANN series: https://datastudio.google.com/reporting/83a69414-337a-4ef4-ad54-4fc22b53f843/page/p1jyF/edit

sonarqubecloud · 2026-06-05T17:57:47Z

Quality Gate passed

Issues
104 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.3% Duplication on New Code

See analysis details on SonarQube Cloud

github-actions · 2026-07-13T23:22:40Z

Visit the preview URL for this PR (updated for commit da60454):

https://idc-external-006--pr381-feat-viv-loader-yhpb45gm.web.app

_{(expires Mon, 31 Aug 2026 20:29:44 GMT)}

_{🔥 via Firebase Hosting GitHub Action 🌎}

_{Sign: 88aacecd98ba54d2f9c8d201a9444e43d1ad8307}

github-actions · 2026-08-14T12:16:06Z

📦 Firebase Preview - Using Published DMV

This preview is using the published dicom-microscopy-viewer from package.json:


Version	`^0.48.23`

github-actions · 2026-08-14T13:00:41Z

📦 Firebase Preview - Using Published DMV

This preview is using the published dicom-microscopy-viewer from package.json:


Version	`^0.48.23`

github-actions · 2026-08-14T13:26:42Z

📦 Firebase Preview - Using Published DMV

This preview is using the published dicom-microscopy-viewer from package.json:


Version	`^0.48.23`

github-actions · 2026-08-14T13:37:44Z

📦 Firebase Preview - Using Published DMV

This preview is using the published dicom-microscopy-viewer from package.json:


Version	`^0.48.23`

github-actions · 2026-08-14T13:45:00Z

📦 Firebase Preview - Using Published DMV

This preview is using the published dicom-microscopy-viewer from package.json:


Version	`^0.48.23`

github-actions · 2026-08-14T14:33:10Z

📦 Firebase Preview - Using Published DMV

This preview is using the published dicom-microscopy-viewer from package.json:


Version	`^0.48.23`

github-actions · 2026-08-14T14:41:52Z

📦 Firebase Preview - Using Published DMV

This preview is using the published dicom-microscopy-viewer from package.json:


Version	`^0.48.23`

github-actions · 2026-08-14T14:48:50Z

📦 Firebase Preview - Using Published DMV

This preview is using the published dicom-microscopy-viewer from package.json:


Version	`^0.48.23`

github-actions · 2026-08-14T14:52:36Z

📦 Firebase Preview - Using Published DMV

This preview is using the published dicom-microscopy-viewer from package.json:


Version	`^0.48.23`

github-actions · 2026-08-14T14:56:11Z

📦 Firebase Preview - Using Published DMV

This preview is using the published dicom-microscopy-viewer from package.json:


Version	`^0.48.23`

github-actions · 2026-08-14T15:00:59Z

📦 Firebase Preview - Using Published DMV

This preview is using the published dicom-microscopy-viewer from package.json:


Version	`^0.48.23`

github-actions · 2026-08-14T16:54:14Z

📦 Firebase Preview - Using Published DMV

This preview is using the published dicom-microscopy-viewer from package.json:


Version	`^0.48.23`

Fix correctness, concurrency, and structural issues found in the feat/viv-loader review: - Infer OF (not OL) for PointCoordinatesData when DICOM JSON omits VR; harden Range streaming against ignored Range headers / 416 EOF; stop silently completing truncated downloads; remove POLYLINE off-by-one phantom vertices; keep finite zero coordinates as valid. - Deduplicate prefix emission into bulkPrefixEmitter and coordinate transform/validity helpers into annotationCoords (shared with the center-out worker kernel). Transfer only first-vertex XY to the worker. - Make DicomLoader ICC sync single-flight and dispose-guarded; promise- memoize viewer creation; LRU + generation-guard the tile cache; skip out-of-range synthetic dyadic tiles; suppress only bridged tile aborts. - Extract bulk-annotation orchestration into useVivBulkAnnotations with per-group hydrate generations, error-phase reporting, constant scatter accessors, and binary streaming centroid data; shrink VivSlideViewport. - Apply persisted ICC preference on classic slide switch; reset viv annotation panel state on series change; restore sidebar contrast under disabled antd menu items; purify preference reads and share one storage listener; fix craco @vivjs include and TypedArray typings; tune the XHR retry hook (idempotent methods only, shorter backoff).

Track in-flight hydrates as uid→dispatchGen ownership so a hydrate that settles after a fast hide→show can no longer delete the newer hydrate's marker, clear its streamed artifacts, or spawn a concurrent duplicate. Also: clear pending done/error timers on fresh progress reports; epoch- guard the tile-throttle batch counter across series resets; invalidate graphic caches when the catalog effect restarts; defer legacy LOD threshold key deletion until the first preference write.

Validate buffered Range-ignored payloads against graphicIndex (same truncation throw as the streaming routes), cap mid-stream HTTP 200 restarts, and match Range EOF only via status 416 or explicit wording. Widen fetchGraphicIndex to Int32Array|Uint32Array and normalize at the call site. Terminate the center-out worker with a sentinel error that skips the sync mega-sort fallback. Replace the Boolean(aborted) lint hit with a helper that re-reads AbortSignal after await.

Add a Cursor rule and CONTRIBUTING note that explanatory comments use /** */ rather than // (tooling directives excepted). Convert explanatory comments in the Viv bulk-annotation path and the retry hook to that style.

When dicomweb-client attaches an HTTP status, only retry 429/5xx so 416 EOF and rejected 206 no longer burn multi-second backoff. After a partial stream paint fails, own the error instead of monolithic re-emit that duplicates layer ids.

Catalog effect cleanup previously bumped gens without clearing the in-flight Map, so a stale settle could reinstall graphicCache after invalidate. Also restore empty-response as Range EOF and JSDoc the fetchGraphicIndex OL note.

Capture the in-flight Set for effect cleanups and include annotationDeckRef in the redraw layout effect deps so CRA CI stops treating warnings as errors.

- Return undefined explicitly in useEffect (VivBulkAnnotationLoadIndicator) - Simplify boolean returns and rename short variables (iccProfilesPreference) - Rename short variables to descriptive names (vivBulkLodPreference, dicomLoader) - Use template literal for worker source (centerOutAnnotationOrder) - Reorder variable declarations to avoid used-before-defined (centerOutAnnotationOrder) - Add skipcq for valid patterns (CaseViewer default import, void operator) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

- Reorder settle/onMessage/onError to fix used-before-defined (JS-0357) - Rename short variables: v→viewerRecord, m→affineMatrix, b→imageBits, s→imageSpp, r→ratio for JS-C1002 - Add explicit return at end of _ensureTileDecodeReady (JS-0045) - Change SyntheticDyadicPixelSource.getRaster to use Promise.reject (JS-0116) - Add skipcq comments for intentional patterns (JS-0105, JS-R1005) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

- Use function declarations instead of let+assignment for hoisting (JS-0242) - Rename short variables: v→indexValue, o→api, r→result (JS-C1002) - Add skipcq for dcmjs namespace import (JS-C1003) - Add skipcq for high-complexity functions (JS-R1005) - Use regular strings instead of template literals where no interpolation (JS-R1004) - Use property shorthand for annotationGroupWrapper (JS-0240) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

- Replace Math.random() with crypto.getRandomValues() for retry jitter (S2245) - Remove identical conditional branches in isMultipart check (S3923) - Remove unnecessary void operators in useEffect dependencies (S3735) - Extract duplicate ensureCapacity to createPayloadBuffer helper (S4144) - Add skipcq comment for getRaster interface compliance (JS-0105) - Convert template strings without interpolations to regular strings (JS-R1004) - Rename single-letter variables to descriptive names (JS-C1002) - Remove unnecessary async keyword from function returning promise (JS-0116) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

The e2e visual regression workflow is for testing bulk annotation rendering, which belongs in the feat/bump-dmv-bulk-ann branch (PR #405), not in this viv-loader branch. This branch doesn't have the e2e test infrastructure (build:e2e, test:e2e scripts). Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

- Remove e2e-visual.yml workflow (belongs in PR #405, not this branch) - Add skipcq for void operator usage (JS-0098) - Add skipcq for high complexity functions (JS-R1005): - buildPointLayersFromGraphicData - buildPathLayersFromGraphicData - loadBulkAnnotationMetadataAndJobs - Rename short variables (JS-C1002): - g→typedGeom, t→geomType - b→bulkApi - d→typedDataset - Use regular strings instead of template literals (JS-R1004) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

- Move skipcq comment directly above void statement (JS-0098) - Fix more template strings without interpolation (JS-R1004) - Remove async from deprecated function that doesn't await (JS-0116) - Add skipcq for buildStyledBulkOverlayLayers complexity (JS-R1005) - Rename `a` to `alpha` for opacity calculation (JS-C1002) - Add skipcq for delete statements on ref-tracked dynamic keys (JS-0320) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Add skipcq comments for void statements (JS-0098), delete operations on dynamic keys (JS-0320), and cleanup function returns (JS-0045). Rename short variable names: a -> alpha, g -> geom (JS-C1002). Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

- Add skipcq for delete operations in loops (JS-0320) - Add skipcq for useEffect cleanup functions (JS-0045) - Rename short variables: r -> obj, w/h -> width/height, z -> tileZ, a/b -> spacingX/spacingY, t -> ratio/factor (JS-C1002) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

- Rename short variables: d -> displayOpts, w/h -> width/height, v -> viv, z -> zoom, t -> tgt (JS-C1002) - Add skipcq for void statements on fire-and-forget async ops (JS-0098) - Add skipcq for useEffect cleanup functions (JS-0045) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

The lockfile was missing the entry for dicomweb-client@0.10.3 which is a transitive dependency from dicom-microscopy-viewer. This caused CI failures with ERR_PNPM_LOCKFILE_MISSING_DEPENDENCY. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

sonarqubecloud · 2026-08-24T20:26:59Z

Quality Gate passed

Issues
52 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.3% Duplication on New Code

See analysis details on SonarQube Cloud

github-actions · 2026-08-24T20:29:14Z

📦 Firebase Preview - Using Published DMV

This preview is using the published dicom-microscopy-viewer from package.json:


Version	`^0.48.24`

igoroctaviano requested a review from fedorov April 8, 2026 00:54

igoroctaviano added 9 commits August 24, 2026 17:19

Add viv loader

3f51fe4

Improve viewport displaying

4eac4c0

Fixing 8-bit: Rendering images correctly (wrong position)

3cb9955

Fixing 8-bit: Rendering images correctly (correct position)

da8b189

Add request abort

1c8ed29

Working: Bulk ann (polygons)

a386f08

Working: Bulk ann (polygons)

476e6b1

Linting

08cf693

Linting and padding

6f3a061

igoroctaviano and others added 26 commits August 24, 2026 17:21

Adjust stroke

d69cc61

Adjust stroke

74d7840

Address errors

49821d2

Address errors

8d28d2f

Update point vs polygon defaults

2bce40c

docs: prefer JSDoc block comments for explanations

d18c16b

Add a Cursor rule and CONTRIBUTING note that explanatory comments use /** */ rather than // (tooling directives excepted). Convert explanatory comments in the Viv bulk-annotation path and the retry hook to that style.

fix(viv): drop hydrate ownership on catalog invalidation

5a4bff5

Catalog effect cleanup previously bumped gens without clearing the in-flight Map, so a stale settle could reinstall graphicCache after invalidate. Also restore empty-response as Range EOF and JSDoc the fetchGraphicIndex OL note.

ci: retrigger checks after master merge

5ec2544

fix: silence react-hooks exhaustive-deps CI failures in viv bulk hook

8685860

Capture the in-flight Set for effect cleanups and include annotationDeckRef in the redraw layout effect deps so CRA CI stops treating warnings as errors.

fix(viv): add eslint-disable for intentional useMemo dependencies

1b69445

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

fix(viv): place eslint-disable before dependency array

de13151

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

igoroctaviano force-pushed the feat/viv-loader branch from d0f9fef to 7f76ce1 Compare August 24, 2026 20:22

fix(deps): regenerate lockfile to remove duplicate entries

da60454

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Uh oh!

Conversation

igoroctaviano commented Apr 8, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Summary

What changed (vs master)

Branch & local setup

How to test

Possible TODO's

Uh oh!

deepsource-io Bot commented Apr 8, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

DeepSource Code Review

PR Report Card

Code Review Summary

Uh oh!

igoroctaviano commented Apr 14, 2026

Uh oh!

fedorov commented May 7, 2026

Uh oh!

igoroctaviano commented May 7, 2026

Uh oh!

sonarqubecloud Bot commented May 7, 2026

Quality Gate passed

Uh oh!

fedorov commented May 20, 2026

Uh oh!

sonarqubecloud Bot commented Jun 5, 2026

Quality Gate passed

Uh oh!

github-actions Bot commented Jul 13, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

github-actions Bot commented Aug 14, 2026

📦 Firebase Preview - Using Published DMV

Uh oh!

github-actions Bot commented Aug 14, 2026

📦 Firebase Preview - Using Published DMV

Uh oh!

github-actions Bot commented Aug 14, 2026

📦 Firebase Preview - Using Published DMV

Uh oh!

github-actions Bot commented Aug 14, 2026

📦 Firebase Preview - Using Published DMV

Uh oh!

github-actions Bot commented Aug 14, 2026

📦 Firebase Preview - Using Published DMV

Uh oh!

github-actions Bot commented Aug 14, 2026

📦 Firebase Preview - Using Published DMV

Uh oh!

github-actions Bot commented Aug 14, 2026

📦 Firebase Preview - Using Published DMV

Uh oh!

github-actions Bot commented Aug 14, 2026

📦 Firebase Preview - Using Published DMV

Uh oh!

github-actions Bot commented Aug 14, 2026

📦 Firebase Preview - Using Published DMV

Uh oh!

github-actions Bot commented Aug 14, 2026

📦 Firebase Preview - Using Published DMV

Uh oh!

github-actions Bot commented Aug 14, 2026

📦 Firebase Preview - Using Published DMV

Uh oh!

github-actions Bot commented Aug 14, 2026

📦 Firebase Preview - Using Published DMV

Uh oh!

sonarqubecloud Bot commented Aug 24, 2026

Quality Gate passed

Uh oh!

github-actions Bot commented Aug 24, 2026

📦 Firebase Preview - Using Published DMV

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

igoroctaviano commented Apr 8, 2026 •

edited

Loading

What changed (vs `master`)

deepsource-io Bot commented Apr 8, 2026 •

edited

Loading

github-actions Bot commented Jul 13, 2026 •

edited

Loading