SVR 3D viewer: memory safety + offline tumor segmentation (ONNX)

[blader]

Summary

This PR hardens the SVR 3D volume workflow for power-user (large maxVolumeDim) cases by reducing peak allocations, making GPU usage budget-aware, and tightening segmentation tooling so it fails safely instead of crashing the tab.

It also upgrades seeded 3D region-growing segmentation to be interactive (live tolerance preview + ROI guidance), so you can iterate quickly without committing labels on every slider tweak.

Key user-visible changes:

• The 3D viewer now has a GPU-budgeted render LOD path (Auto) that can downsample render textures to fit a configurable budget.
• Label rendering no longer allocates full-size zero buffers when labels are disabled.
• Seeded 3D region grow no longer allocates a full-volume mask.
• Seeded 3D region grow now supports auto-preview updates (debounced + cancellable) while adjusting tolerance/target, and supports an ROI box (guide or hard) drawn on the slice inspector.
• ONNX tumor segmentation is preflight-guarded for huge volumes (blocked by default with an explicit unsafe override).
• The legacy SVR 3D modal is now a thin wrapper around the shared 3D viewer so improvements apply everywhere.

What’s in this PR

SVR + 3D viewer memory/stability

• GPU-budgeted render LOD (Auto quality): compute a render plan that chooses render dims + texture mode (f32 vs u8) to fit a budget.
• Label texture allocation is lazy: keep a 1×1×1 placeholder texture when labels are disabled/missing; allocate full 3D label texture only when needed.
• Downsample labels for rendering when render LOD is active (nearest) so label overlays don’t force full-res GPU allocations.
• Single code path for 3D viewing: SvrVolume3DModal now renders SvrVolume3DViewer instead of maintaining a separate WebGL implementation.

Interactive seeded 3D region growing (seed + live tolerance + ROI)

• Slice inspector interactions:
  • Click to set the seed voxel.
  • Drag to draw an ROI box (interpreted as an axis-aligned 3D box spanning the full depth along the current inspector axis).
• Controls:
  • Auto preview toggle.
  • ROI mode selector: guide (default) vs hard.
  • Outside scale slider (enabled in guide mode) to tighten tolerance outside the ROI.
  • Target label + tolerance changes trigger auto-preview re-grows (debounced; in-flight grows are cancelled for responsiveness).
• Clear seed / clear seg cancels in-flight grows and resets preview bookkeeping.

regionGrow3D updates

• Sparse: regionGrow3D() returns a Uint32Array of voxel indices and uses a 1-bit visited bitset (avoids Uint8Array(nvox) masks).
• Multi-seed: added optional seedIndices?: Uint32Array so users can grow multiple disjoint islands in one operation.
• ROI support: added optional roi?: { min/max, mode: "hard" | "guide", outsideToleranceScale? }:
  • hard: never accepts voxels outside ROI.
  • guide: accepts outside ROI only if the intensity falls within a tighter (seed-centered) range derived from outsideToleranceScale.
• Added unit coverage for ROI hard/guide + multi-seed behavior (tests/segmentation3d.test.ts).

ONNX preflight guardrail

• Full-res ONNX runs are blocked by default when the estimated logits tensor size exceeds a conservative budget. Users can opt in via an “unsafe full-res ONNX” checkbox.
• This prevents accidental multi-hundred-MiB to multi-GiB allocations on large volumes.

Tooling

• Added Prettier (config + scripts) for consistent formatting:
  • npm run prettier / npm run prettier:check

Implementation notes

Render LOD plumbing

• Render planning + resampling utilities were factored into frontend/src/utils/svr/renderLod.ts.
• The viewer builds a render texture payload via a single helper (buildRenderVolumeTexData) with periodic yields for responsiveness.

regionGrow3D memory model

• Prior implementation allocated mask = new Uint8Array(nvox).
• New implementation:
  • visited: Uint32Array((nvox + 31) >>> 5) (1 bit/voxel)
  • queue: Uint32Array(maxVoxels) which is also returned as indices.subarray(0, count)
  • Viewer applies the label by iterating the sparse indices list.

Live preview label overlay

• The viewer keeps a single working labels buffer and replaces the previous preview by restoring a sparse list of previous values (prevIndices + prevValues) before applying the next preview.
• This avoids copying a full Uint8Array(nvox) per slider move.

ONNX preflight

• Preflight uses a lower-bound estimate (float32 logits with C=4 channels) and blocks by default above a conservative logits budget.
• This is intentionally strict for stability; users can re-run SVR at lower resolution/ROI, or opt into unsafe full-res ONNX.

How to test

From frontend/:

• npm run lint
• npm run test

Manual (SVR 3D viewer):

• Open the 3D viewer and expand the Segmentation panel.
• Click in the slice inspector to place a seed.
• With Auto preview enabled, adjust tolerance/target and confirm the segmentation updates.
• Drag an ROI box; try guide vs hard modes; adjust outside scale and confirm it controls leakage outside the ROI.

Notable unit coverage includes:

• 3D segmentation utils (tests/segmentation3d.test.ts)
• ONNX wrappers (tests/onnxTumorSegmentation.test.ts, tests/onnxLogitsToLabels.test.ts)

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Project	Deployment	Actions	Updated (UTC)
miraviewer	Ready	Preview, Comment	Feb 4, 2026 5:26am