diff --git a/Dockerfile b/Dockerfile index 7c89bfe48..6c1e1fef7 100644 --- a/Dockerfile +++ b/Dockerfile @@ -73,6 +73,28 @@ RUN git clone https://github.com/AdaWorldAPI/lance-graph.git \ && git clone --depth 1 https://github.com/AdaWorldAPI/ndarray.git \ && git clone --depth 1 https://github.com/AdaWorldAPI/neo4j-rs.git +# CPU baseline: x86-64-v4 (the 4th microarch level — AVX-512F/BW/CD/DQ/VL on top +# of v3's AVX2+FMA). This is the compile FLOOR; it flips on `target_feature = +# "avx512f"`, so q2-ndarray's `simd.rs` dispatch selects its native `simd_avx512` +# backend (`__m512`/`__m512d`/`__m512i`) instead of the v3 AVX2 default. +# +# BF16 + AMX 16x16 tile GEMM are NOT gated by this flag — they ride q2-ndarray's +# CPU-AGNOSTIC runtime autodetect polyfill (`simd_caps()` + the AMX `arch_prctl` +# XTILEDATA enable + CPU-model detect). The polyfill opportunistically lights them +# up only when the *runtime* host actually has them, and always keeps the AVX2 / +# scalar paths it compiled in as fallback. So: AVX-512 = compile baseline here; +# BF16/AMX = runtime-detected; everything below v4 = polyfill fallback. +# +# ⚠ REQUIREMENT: a v4 floor makes the binary REQUIRE AVX-512 at run time — it +# SIGILLs on the first `__m512` op on a host without it (the PR #170 failure mode, +# one level up). The Railway *build* machine needs no AVX-512 (compiling != run), +# but the *deploy* host does. AMX additionally needs a Sapphire/Emerald/Granite +# Rapids Xeon at run time; on anything older the autodetect simply skips AMX (that +# is the agnostic polyfill working as intended, not an error). If a deploy target +# may lack AVX-512, drop this to `x86-64-v3` and rely on runtime dispatch for the +# AVX-512/AMX paths — one portable binary, same hot paths when the silicon allows. +ENV CARGO_BUILD_RUSTFLAGS="-C target-cpu=x86-64-v4" + # Build the q2 binary with embedded frontend WORKDIR /build/q2 RUN cargo build --release -p cockpit-server --features embed-cockpit,planner \ diff --git a/claude-notes/plans/2026-06-24-fma-torso-bodyparts3d-splat.md b/claude-notes/plans/2026-06-24-fma-torso-bodyparts3d-splat.md index d1e1e7b93..018070aa4 100644 --- a/claude-notes/plans/2026-06-24-fma-torso-bodyparts3d-splat.md +++ b/claude-notes/plans/2026-06-24-fma-torso-bodyparts3d-splat.md @@ -108,3 +108,112 @@ Validates the design before wiring it into the render. Next increments: (node_row-bounded + normal-oriented = crisp colours in the render) - [ ] animation: deform node anchors -> motion-skinned gaussians follow (Motion-Blender GS; the partonomy is the rig) + +## Best shading + lazylock + adaptive-FPS + SPL4 (branch claude/torso-shading) + +User: "best possible shading and lazylock buffering to mitigate batching", then +"adaptive framerate prediction + SIMD batching + v4", then the key insight: "the +Motion is fixed Rotation ... so it could easily prebuffer 270 frames for 90 FPS". +Scoping answers: framerate = BOTH (render-loop throttle now + codec P-frames as +the SPL4 motion track); PR scope = all of the above incl SPL4 in one push. + +### Infra fact ("GitHub uses Cargo not Dockerfile?") +q2 CI = pure Cargo+npm (`cargo fmt`/`xtask lint`/`clippy -D warnings`/`nextest`, +wasm-pack/npm). The only `docker` in CI is `docker image prune` (free runner disk). +The root `/Dockerfile` is Railway-deploy ONLY (`q2-cockpit` embeds the Vite cockpit, +clones lance-graph/ndarray/neo4j for the graph hot path). This splat feature does +not touch the Dockerfile. +- [x] **Dockerfile CPU baseline -> x86-64-v4** (user ask): `ENV + CARGO_BUILD_RUSTFLAGS="-C target-cpu=x86-64-v4"` before the cockpit-server + build. Flips `target_feature="avx512f"` so q2-ndarray's `simd.rs` picks the + native `simd_avx512` backend. BF16+AMX tile GEMM ride ndarray's runtime + autodetect polyfill (`simd_caps()` + AMX arch_prctl/model-detect) — not gated + by the flag, lit only when the host has them, AVX2/scalar fallback always + compiled. ⚠ v4 = AVX-512 REQUIRED at runtime (SIGILL otherwise, the PR#170 + mode one level up); AMX needs Sapphire/Emerald/Granite Rapids at runtime + (autodetect skips it otherwise = agnostic working as intended). Documented the + `x86-64-v3` fallback in the Dockerfile for non-AVX-512 deploy targets. + +### Shading (the lit look) — DONE +- [x] Render driver (scratchpad, ndarray 1.95, OUT of q2 workspace): shade AT + RECONSTRUCTION from the per-vertex normal already in SPL2 — hemisphere ambient + (sky/ground) + key diffuse (n·L, L fixed in WORLD so camera orbits a still + light = consistent turntable) + soft fill. Shading MULTIPLIES the flat palette + colour, so the codec-free per-structure colour story is intact. 20-frame + shaded turntable rendered (9s/frame) → JPEG (67 KB/frame) → + cockpit/public/torso-frames/. Verified in-cockpit: volumetric depth, colours + preserved, no Warhol blob. + +### Prebuffer = the answer to BOTH (A) and (B) [the user's insight] +The demo motion is a FIXED, periodic, deterministic camera rotation. So you neither +ADAPT the framerate nor PREDICT motion frame-by-frame — you PRECOMPUTE the closed +loop once and replay → every frame free → guaranteed 90 fps. This is exactly the +x265 GOP idea: a periodic camera path is a closed Group-of-Pictures; prebuffer the +GOP, replay forever. It is ALSO the honest SPL4 (B) motion source: the orbit is a +real known closed trajectory, so the 270 rotation steps ARE its P-frames — NO +synthetic breathing deformation needed (drop that demo). +- [ ] /torso turntable: bump FRAME_COUNT 20 → loop count over an exact 360° (frame + N == frame 0 for a seamless loop), 90 fps playback. Re-bake at the higher count + (background). Ship-size lever: 67 KB/frame × 270 ≈ 18 MB JPEG → offer WebM + encode (~3 MB) as the compaction. Mandatory here because CPU EWA splat is + 9s/frame — live render impossible; prebuffer is THE technique, not an optim. +- note: the live WebGL points view is already real-time; prebuffering full + framebuffers there is VRAM-prohibitive (270×810×1080×4 ≈ 945 MB) — so the + live-view win is lazylock + adaptive-FPS, and image-prebuffer stays on /torso. + +### Live views light up + lazylock + adaptive-FPS +- [ ] /torso-live (TorsoSplat) + /torso-map (TorsoMap): decode SPL2 `normal 3i8` + into an aNormal attribute (both skip it today); port hemisphere+diffuse+fill + into the FRAG. Same L → CPU frames and live WebGL agree. +- [ ] LazyLock build-once buffer: build geometry (pos+aColor+aNormal+aRow) ONCE; + mutate only via uniforms + draw-RANGE, never rebuild. +- [ ] Adaptive-FPS: EMA of rAF delta; over budget → shrink draw-range over the + Morton-ordered buffer (prefix = uniform spatial subsample) + drop pixelRatio; + recover when cheap; log active fraction (no silent decimation). + +### SPL4 — ship the codec (static I-frame real, motion track reserved) +- [ ] `spl_codec.py`: WRITE a real `.spl4` (helix-Morton order, per-node anchor + I-frame, motion-from-anchor + zig-zag residual, anchor-predicted palette colour + = 0 per-gaussian bytes, normals). Header `motion_track_count` (0 static) reserves + the P-frame slot without a format bump (RESERVE-DON'T-RECLAIM). +- [ ] TS `decodeSpl4`: inverse — reconstruct pos/normal/rgb/row at load; all 3 views + switch to SPL4. +- [ ] Fold deferred #55 nits: `import math` → module top; fix "round-trips it" + docstring; TorsoMap `ray.params.Points` mutate-not-replace. +- [ ] (B) motion track = orbit-as-motion P-frames (above); ship the FORMAT slot + + decode contract; the camera trajectory is the demonstrator (honest, not faked). + +### Verify + ship +- [ ] `cd cockpit && npm run build` (tsc clean); inspect shaded turntable + live + view; codec round-trip RMSE unchanged. Commit incrementally on + claude/torso-shading; ASK before push (GIT PUSH POLICY). + +## v4 — is_a-PRIMARY whole-body anatomical atlas (major pivot, 2026-06-24) + +Operator-driven pivot, several corrections of my assumptions: +1. **Use is_a, not part-of, for classification + names.** part-of is REGIONAL + (walk up a muscle -> chest wall -> thorax, never "muscular system") and its + names aren't canonical. is_a is the TYPE tree: every structure resolves up to + its canonical type (`pectoralis minor` -> ... -> `muscle organ`); is_a ships + canonical names; is_a's mesh set is a SUPERSET of part-of (2234 vs 1258 FJ, + +976) with finer organ segmentation (no single "aorta"/"heart" — split into + ascending/arch/descending/abdominal, each its own mesh). Downloaded the 142 MB + is_a obj package + the small is_a relation/name txts. +2. **container:identity / DN->GUID addressing.** tissue = walk the is_a TYPE tree + to the first type keyword (O(1), cached) = the DistinguishedName path, which + MATERIALISES to a numeric container:identity GUID (container = tissue class). + Stored per node: `tissue`, `is_a` (DN path, upper-ontology stripped), + `container`, `identity`, `guid`. +3. **Whole body is the goal — NO spatial torso filter.** Region focus (torso, an + organ) is a future SELECT -> CAMERA-ZOOM feature on the full-body splat, driven + O(1) by each node's centroid+bbox in the SoA, not a bake-time clip. +4. **Performance is the point.** Whole body = 602,341 gaussians / 1658 is_a + structures / 12.6 MB (414 arteries, 382 muscles, 221 veins, 203 bones, 126 + nerves, full viscera). The deliberate load that motivates lazylock + + adaptive-FPS (live views) and the prebuffered turntable (CPU EWA). +- bake = `bake_torso_splat.py` v4 (is_a-primary). Tissue atlas palette + depth-peel + opacity. Driver orientation fixed (+90 about X; head was landing down). +- [ ] re-render upright whole-body turntable -> /torso; live views already decode + the unchanged SPL2 (extra nodes.json fields are ignored) — light them + + lazylock + adaptive-FPS to show + mitigate the 602K load. +- research: `claude-notes/research/2026-06-24-torso-anatomy-coverage-gap.md`. diff --git a/claude-notes/research/2026-06-24-splat-on-substrate-jc-clam-cesium-hhtl.md b/claude-notes/research/2026-06-24-splat-on-substrate-jc-clam-cesium-hhtl.md new file mode 100644 index 000000000..ae67e5187 --- /dev/null +++ b/claude-notes/research/2026-06-24-splat-on-substrate-jc-clam-cesium-hhtl.md @@ -0,0 +1,227 @@ +# Splat render on substrate — jc / CLAM / cesium / HHTL (2026-06-24) + +> **Knowledge-transfer capture, written before it dilutes.** The q2 cockpit +> anatomy gaussian-splat render must **not hand-roll** sampling, footprint, +> anti-alias, or LOD. Every piece already exists — certified, closed-form, +> Jirak/jc-bounded — in the **ndarray + lance-graph substrate**. This doc maps +> the q2 render pipeline to the existing primitives **by exact path**, so the +> next session *cites* instead of re-deriving. Operator-directed: "implement all +> of the above and document before it dilutes citing the already existing." + +## CORRECTION (2026-06-24, cross-session full-read — read THIS before the rest) + +A parallel session's Opus readers read the `perturbation-sim` knowledge transfer +**fully** while this doc's first draft **synthesized**. They caught real +over-claims; the honest status: + +1. **The DOCUMENTED seam is cesium-wholesale, NOT hand-build-ClamTree.** The path + the docs prescribe: `Gaussian3D → SplatBatch → cesium-3dtiles-writer → cesium + SSE / HLOD / implicit-tiling → splat-render` + (`lance-graph/.claude/plans/cesium-osm-substrate-v1.md` D-OSM-5/6; + `3DGS-3D-Tiles-runtime-plan.md`). The "build a ClamTree, size each gaussian from + its leaf radius, hand to splat3d" path in the table below is a **SYNTHESIS** + (origin: the operator's "zwei Schenkel" framing + + `lance-graph/crates/bgz17/src/clam_bridge.rs:233-238` δ⁺/δ⁻ + `ndarray::hpc::clam`) + — **not** in this knowledge transfer. The docs' only ClamTree linkage is an + explicitly **[H], NOT-wired** CHAODA *anomaly-scoring* map over contingency + vectors — not a geometry tree whose leaf radius sizes a render gaussian. Treat + CLAM-reach-sizing as a CANDIDATE, not doc-prescribed. + +2. **HHTL is 3-tier in perturbation-sim** (TWIG = buses/leaf, HIP = basins + Kron/Schur-reduced, HEEL = cross-border super-graph; `METHODS.md:88`). The + 4-tier HEEL/HIP/TWIG/**LEAF** is the *datalake-traversal* instantiation + (data-block stages) — a different instance of "HHTL". + +3. **electrical-Morton = Morton over the resistance-distance SPECTRAL embedding, + never geography** (`METHODS.md:57`). That warning bites when you tile a + *semantic* metric (e.g. FMA system-distance) but cheat with geometry. For the + body's literal GEOMETRY, **geometric Morton is correct** — 3D Tiles does exactly + this; the geometry *is* the metric. The [S]-rhyme would be claiming a geometric + tile captures FMA *semantics*. + +4. **The CODE seam (does `cesium` ingest raw surfels or pre-built gaussians; does + `splat3d::Gaussian3D` take a full Σ or only scale+quat; does any existing + driver/test already wire surfels→cesium) is being settled by the other + session's Reader B.** DO NOT wire until that authoritative answer lands. The + table below is the candidate map, not the confirmed seam. + +**What both sessions agree survives:** the *front of the pipe* — BodyParts3D → +deterministic `part_of`/is_a system classification (colour) → per-triangle surfels +(`read_obj_tris`). The reinvention to delete is everything bolted on *after* it +(hand-rolled octree / fixed tangent / `lowdisc_indices` / `0.93`/`theta` / +CesiumJS-in-browser). + +## RESOLUTION (2026-06-24 PM — what q2 actually shipped: "opaque now, gaussian later") + +Three operator corrections landed in sequence and settled the q2 render: + +1. **"severe chubby halo effect"** → the disks were over-sized. +2. **"rather a triangle without gaussian at all than a ghostbuster pretending to do + gaussian splat"** → the soft-Gaussian look itself was rejected. +3. The other session's jc report confirmed the sizing fix (**k-NN metric Σ**, not + uniform stride). + +**The single durable finding: the ghost was the RENDERER, not the asset.** +`splat3d` composites soft-Gaussian alpha *tails* through the low-opacity translucent +surfels (skin 0.14 / flesh 0.45 depth-peel) → halo + fog. Swapping to an **opaque +z-buffer** on the *same bytes* — nearest surface wins, hard-edged disk, no alpha +accumulation — is crisp by construction. No re-bake was needed to kill the fog; the +fix was the compositing mode. (Pfister/Zwicker surfels, not a gaussian pretending.) + +**The marble fix (second, independent): sizing does NOT belong in the bake as a +hand-rolled `sqrt(stride)` bridge.** That uniform 4× over-inflation piled disks into +marbles. Replaced by **per-structure k-NN local spacing** (≈0.55× the 3-nearest +distance) — the same metric-Σ principle the substrate render path uses, computed in +the bake so the SPL3 asset is render-ready for the three.js cockpit (which has no +Σ-fit pass of its own). `scale_max` fell 0.037→0.0086 (4.3× smaller); disks tile. + +**SPL3 wire** (supersedes SPL2): body 22 B = pos 3f | normal 3i8 | rgb 3u8 | opacity +u8 | **scale u8** | node_row u16; header f32 = `scale_max` (per-surfel disk-radius +dequant ref: `scale_byte/255 * scale_max`). The opacity byte is a tissue-depth tag +the renderer uses to GATE the skin/flesh shell out (`uFloor`), not to fog. + +**The split (operator-chosen):** +- **Opaque now** — q2 owns it. All three cockpit views (`/torso`, `/torso-live`, + `/torso-map`) render opaque k-NN-sized surfels: crisp, ~40 ms/frame pure-Rust + preview, trivial three.js (opaque depth-tested points), no gaussian shader. +- **Gaussian later** — the other session owns it. Their certified path (jc::weyl + φ⁻¹ decimation + jc::ewa_sandwich_3d SPD cert on real surfels = 100 % valid, + min eigenvalue 9.88e-3 px² + Cesium SSE/HLOD `depth_cascade`) is the high-fidelity + offline render. q2 feeds it the **is_a classification it lacks** — + `crates/osint-bake/tools/export_isa_classification.py` → + `fma_isa_classification.json` (1658 concepts / 2234 meshes, FJ→tissue/system/GUID/DN), + reusing the same `tissue_of` walk so the two renders share one classifier. + +The convergence boundary held: **q2 = the is_a data + opaque preview; the other +session = the certified gaussian render.** Neither reimplements the other's half. + +## The anti-pattern this deletes (what was hand-rolled, wrongly) + +The scratchpad driver + `bake_torso_splat.py` reached the **"VR-paint iceberg"** +failure — per-vertex sampling at a **fixed tangent**, so each splat is an +isolated blob that doesn't reach its neighbours into the field (1–4 "hops" +instead of 5–12). Three hand-rolled guesses caused it, each superseded: + +| Hand-rolled (DELETE) | Why it's wrong | Substrate replacement | +|---|---|---| +| per-vertex + **fixed tangent** (`scale=[t,t,thin]`) | footprint not matched to local spacing → blobs/gaps | per-triangle surfel + **Σ fit to the neighbourhood** (`splat_neighborhood`) | +| `lowdisc_indices` (hand golden-ratio φ) in the bake | reinvents Weyl equidistribution | **`jc::weyl`** | +| `0.93` scale / `1.45–1.6` theta (trial-and-error) | iterate-until-it-looks-right | **cesium SSE** + **`jc::ewa_sandwich`** (closed-form, Jirak-bounded) | + +## The candidate pipeline (SYNTHESIS — see CORRECTION above; cesium-wholesale is the doc-prescribed seam) + +``` +per-triangle surfel ─→ CLAM reach ─→ jc::weyl sampling ─→ splat_neighborhood Σ-fit + ─→ ewa_coarsen (Morton-seam anti-alias) ─→ cesium SSE/HLOD (HHTL LOD) + ─→ jc::ewa_sandwich (certify J·Σ·Jᵀ SPD) ─→ render +``` + +| Stage | Primitive (what it does) | **Exact path** | +|---|---|---| +| per-triangle surfel | mean = centroid, normal = face normal — the correct *front* of the pipe | `q2: crates/osint-bake/tools/bake_torso_splat.py::read_obj_tris` | +| **metric reach** ("zwei Schenkel eines Dreiecks ergeben das dritte") | cover-tree radius via the δ⁺/δ⁻ triangle inequality (`δ⁺ = dist+radius`, `δ⁻ = max(0, dist−radius)`); `mean_leaf_radius` = local reach | `ndarray/src/hpc/clam.rs` (`Cluster::delta_plus` / `delta_minus`, `ClamTree::build_with_fn`, `mean_leaf_radius`) | +| **low-discrepancy sampling** | Weyl equidistribution (golden-ratio), the *certified* form of φ/R2 | `ndarray/crates/jc` → `jc::weyl` | +| **adaptive anisotropic footprint** | fit an SPD `Σ` to the local neighbourhood (metric-closeness-weighted covariance of neighbour offsets); `anisotropy = λ_max/λ_min` | `lance-graph/crates/perturbation-sim/src/splat.rs::splat_neighborhood` (2-D electrical ref); 3-D form in `ndarray/src/hpc/splat3d` (`Spd3::from_scale_quat`) | +| **Morton-seam anti-alias** (the Fujifilm-X / "irrational quorum" effect) | EWA pyramid coarsen down-weights spatially-distant (Morton-seam) cells, removing the seam aliasing a hard box-average introduces (test: box=34 → EWA=1) | `lance-graph/crates/perturbation-sim/src/splat.rs::ewa_coarsen` + `morton2` | +| **view-LOD** (HHTL screen-space error) | closed-form pixel error `sse_for_tile(geometric_error, distance, denom)`; `tile_meets_sse` decides refine/skip | `ndarray/crates/cesium/src/sse.rs`, `hlod.rs`, `implicit_tiling.rs` | +| **covariance certificate** | `J·Σ·Jᵀ` stays SPD across cascade hops (`prove_pillar_7`) | `ndarray/crates/jc` → `jc::ewa_sandwich`; `ndarray/src/hpc/pillar/ewa_sandwich_3d.rs` | +| **significance bound** | weak-dependence rate `n^(p/2−1)`, **NOT** classical IID Berry-Esseen | `I-NOISE-FLOOR-JIRAK` (lance-graph CLAUDE.md); Jirak 2016 (arXiv 1606.01617) | +| **HHTL cascade tiers** | HEEL/HIP/TWIG/LEAF certified traversal; tile↔data-block mapping | `lance-graph/.claude/plans/3DGS-HHTL-datalake-traversal-plan.md`; CANON node-key HEEL/HIP/TWIG u16 (lance-graph CLAUDE.md) | + +## Corrections to cite (do NOT re-derive these) + +1. **`jc::weyl` is Weyl *equidistribution*** (golden-ratio low-discrepancy + sampling), **not** the eigenvalue-perturbation inequality. The genuine + spectral-perturbation result (Weyl/Davis-Kahan on the Laplacian) lives in + `perturbation-sim` (`perturbation.rs`, `eigen.rs`). Source: + `perturbation-sim/README.md` § "Where it sits". +2. **Cesium is transcoded to ndarray, no WebGPU.** `ndarray/crates/cesium` + (`khr_gs`, `sse`, `hlod`, `implicit_tiling`, `to_cam_soa`, `arcgis_pbf`, + `osm_pbf`). It is **light** *because* the bounds (SSE, ewa_sandwich, Jirak) + are closed-form — no trial-and-error. +3. **HHTL coords = effective-resistance spectral Morton embedding** (electrical + distance, not geography) — `perturbation-sim/src/basin.rs` (Kron reduction + + Cheeger sweep `μ₂/2 ≤ h ≤ √(2μ₂)`). +4. **`perturbation-sim/splat.rs` is the 2-D power-grid instance** of this + magnitude-side algebra; the **3-D** instances are `ndarray::hpc::splat3d` + (EWA pillars) + `crates/cesium` (tiling) + `crates/jc` (weyl, ewa_sandwich). + Use splat.rs as the *reference shape* for the Σ-fit + ewa-coarsen; wire the + driver to the 3-D primitives. + +## Ownership boundary (read + consume, never reimplement) + +- **q2 bake** (`bake_torso_splat.py`): emit per-triangle surfels (centroid, + normal, tissue colour, opacity). The metric sizing is downstream, not here. +- **q2 driver** (scratchpad, ndarray 1.95 stable, OUT of the q2 workspace): + consume `ndarray::hpc::{clam, splat3d}` + `jc` + `cesium`. **No** hand-rolled + sizing constant survives. +- **Substrate** (`ndarray/crates/{jc,cesium}`, `ndarray/src/hpc/{clam,splat3d,pillar}`, + `lance-graph/crates/perturbation-sim`): owned by other sessions. **Read and + consume; never reimplement or modify** (architectural-compliance P0). + +## MESH PIVOT + Morton/gridlake synergy (2026-06-24 PM — the triangle-surface answer + substrate check) + +The opaque SURFEL render killed the fog but left "sequins" (discrete disks with gaps). +Operator: "connect to a triangle filled surface ... kurvenlineal over triangles +(Quadro/AutoCAD)" + "stay with highest quality, do NOT coarsen." The answer: render the +BodyParts3D OBJ FACES **filled** (`THREE.Mesh`, smooth Phong from the cell-averaged +per-vertex normals), not centroids-as-points. Filled triangle surfaces decisively beat +splats — solid ivory bone, red muscle, no sequins, no fog (the Open 3D Man material +aesthetic). The other session reached the same conclusion independently (601,922-tri +solid skeleton). + +- **Format:** SPM1 indexed mesh (vert 21 B [pos 3f|normal 3i8|rgb 3u8|opacity u8|node_row + u16] + tri 12 B [3× u32]); `crates/osint-bake/tools/bake_torso_mesh.py`. +- **Decimation:** vertex clustering, cell-averaged normals (= the smooth "curve-ruler"), + reuses the is_a tissue classifier. **Highest quality = cell 3.6 mm = 1.40M tris (29 MB)**; + web-weight coarsening (cell 5.5 mm = 831K) was REJECTED ("skull looks terrible"). +- **Render:** `cockpit/src/TorsoMesh.tsx` (live `THREE.Mesh`, two-sided Phong via + `gl_FrontFacing`, `uFloor` cuts the skin shell, S toggles). The preview driver gained a + filled-triangle Phong z-buffer rasterizer (SPM1) beside the surfel one. + +### Morton tile pyramid + simd_soa "gridlake" for the MESH ("shader batch synergies without the artifacts") + +Investigated ndarray read-only. **VERDICT: PARTIAL — the indexing/LOD substrate is +genuinely gaussian-free and reusable; the *render* half of splat3d is gaussian+alpha-blend +and gives nothing for opaque triangles.** + +GAUSSIAN-FREE + REUSABLE (no fog path, no `GaussianBatch`): +- `src/simd_soa.rs` `MultiLaneColumn` — fully general SoA carrier (`Arc<[u8]>`, 64-byte + aligned, zero-copy `iter_f32x16`/`iter_f64x8`/…). **Layout-only, zero geometry awareness.** + (The `#[derive(SoA)]` macro in `.claude/knowledge/hhtl-gridlake-pre-sprint-prompt.md` is + PLANNED, not shipped — only `MultiLaneColumn` + the 4 iterators exist today.) +- The Morton min/max **cascade pattern** in `examples/morton_cascade_probe.rs` (example, not + library API): Morton order makes each quadtree node a contiguous SoA range → flat min/max + reduction → prune a whole subtree. Adaptable to a spatial per-tile-bbox pyramid. +- `crates/cesium/src/{sse,hlod}.rs` — LIVE + tested + **geometry-agnostic** OGC 3D-Tiles + SSE (`sse_for_tile`) + HLOD `traverse_hlod` (ADD/REPLACE refine by screen-space error): + "which tiles at this distance" works unchanged for mesh tiles. (cesium is an oracle-only + non-default crate — lift the two modules, don't depend on it; `implicit_tiling.rs` Morton + decoder is all-commented scaffold.) +- `src/aabb.rs` — LIVE, generic, AVX-512 `aabb_intersect_batch` / `aabb_filter_by_distance` + — the batch frustum/box cull primitive. + +MUST BUILD consumer-side (none exists; the splat3d render path is gaussian + alpha-blend): +- A triangle→Morton-leaf tiler + per-tile bbox pyramid (the probe tiles 4×4 scalar cells, + not triangles). +- Generic `F32x16` vertex-projection + normal-transform kernels — the math is **inlined** in + the gaussian `splat3d/project.rs::project_chunk_x16`, not exposed; `Camera` (4×4 view + + pinhole intrinsics) exists and is general. +- An opaque Phong shade + z-buffer rasterizer — `splat3d/raster.rs` is the alpha-blend SH + compositor (the rejected fog path). + +So the synergy is real and **artifact-free at the substrate** (carrier + cascade + LOD + +cull), but a BUILD on top, not a wire-up: gaussian coupling is confined to +`splat3d/{gaussian,project,tile,raster,sh}.rs` + `cesium::to_cam_soa`, none of which the +mesh path must touch. Today's cockpit renders the 1.4M mesh on the GPU (three.js) where this +batching is moot; the gridlake/Morton path is the route to a NATIVE SIMD mesh rasterizer +(offline turntable / server render) if/when that is wanted. + +## Cross-refs + +- `claude-notes/research/2026-06-24-torso-anatomy-coverage-gap.md` — the is_a-primary + whole-body atlas (the geometry this renders). +- `claude-notes/plans/2026-06-24-fma-torso-bodyparts3d-splat.md` — the cockpit + pages + bake plan. +- lance-graph `crates/perturbation-sim/{README,METHODS,CLAM_CHAODA_FRAMING}.md` — + the magnitude-side algebra + the jc companion framing. diff --git a/claude-notes/research/2026-06-24-torso-anatomy-coverage-gap.md b/claude-notes/research/2026-06-24-torso-anatomy-coverage-gap.md new file mode 100644 index 000000000..9e383e98d --- /dev/null +++ b/claude-notes/research/2026-06-24-torso-anatomy-coverage-gap.md @@ -0,0 +1,97 @@ +# Torso anatomy coverage — structural gap analysis (2026-06-24) + +> Prompted by comparison against high-fidelity atlases (anatomytool.org "Open +> 3D Man", VOXEL-MAN inner-organs). Goal: understand what our BodyParts3D torso +> splat is MISSING in structure. We are NOT using their geometry — pure diagnostic. + +## Headline finding + +**The gaps are not a source gap — they are a ROOT-SELECTION gap.** We baked the +`FMA7181` "trunk" subtree = **178 of 1368 mesh-bearing concepts (13%)**. The +"missing" organs, vessels, and nerves are NOT absent from BodyParts3D; they are +in the download we already have, hanging off **sibling system branches** we +didn't include. + +BodyParts3D part-of tree = one root `FMA20394` "human body" (1368 mesh-concepts, +17,943 meshes). Its system branches: + +| mesh-concepts | FMA | branch | in our bake? | +|---:|---|---|---| +| 293 | FMA7161 | cardiovascular system (heart + arterial/venous trees) | ~3 (heart only) | +| 251 | FMA231424 | body proper (trunk wall + skeleton) | **most of our 178** | +| 141 | FMA7152 | alimentary system (liver, stomach, intestine, pancreas, esophagus) | 0 | +| 103 | FMA7154 | head | 0 (out of region) | +| 99 | FMA7482 | musculoskeletal system | partial | +| 92 | FMA7158 | respiratory system (lungs, bronchi, trachea) | 0 | +| 89 | FMA7157 | nervous system (brain, cord, named nerves) | 0 | +| 66/59 | FMA7185/6 | upper limbs | 0 (out of region) | +| 51/46 | FMA7187/8 | lower limbs | 0 (out of region) | +| 47 | FMA228642 | vasculature of body | 0 | +| 10 | FMA7159 | urinary system (kidneys, bladder, ureters) | 0 | +| 6 | FMA79063 | deep fascial system | 0 | +| 4 | FMA9668 | endocrine system | 0 | + +## Per-system probe (present in download / under trunk / baked) + +| system | mesh-concepts in download | under FMA7181 trunk | baked | +|---|---:|---:|---:| +| arteries (aorta/artery*) | 313 | 0 | 0 | +| veins (vena cava/vein*) | 102 | 2 | 2 | +| respiratory (lung+bronchi+trachea) | 64 | 0 | 0 | +| intestine | 27 | 0 | 0 | +| lumbar vertebrae | 12 | 0 | 0 | +| liver | 10 | 0 | 0 | +| pancreas | 6 | 0 | 0 | +| kidney | 2 | 0 | 0 | +| stomach / esophagus / gallbladder / sacrum | 1 each | 0 | 0 | +| diaphragm | 1 | 1 | **1** | +| spleen | **0** | 0 | 0 | + +## What's TRULY missing (vs. just un-baked) + +- **Almost nothing is a real source gap.** Organs, the 293-concept arterial + tree, the 89-concept nervous system — all present in the download, just under + sibling roots. Reachable for free. +- **Genuine source gaps** (where even full BodyParts3D < Open 3D Man): + - **spleen**: 0 meshes — actually absent. + - **fidelity / density**: BodyParts3D ships 99%-decimated meshes; peripheral + nerves are major-trunk-only (89 concepts = brain + cord + named nerves), not + the fine plexus threads the sculpted atlases show. Fascia/ligaments thin (6). + +## Why the trunk bake excluded them + +`FMA7181` "trunk" is a structural/wall decomposition: skeleton + body wall + +heart-in-mediastinum. It treats the cavities' contents as undivided bags +("content of abdomen", "content of posterior mediastinum" = single mesh blobs). +The actual organ meshes are reached via the **system** roots (cardiovascular / +respiratory / alimentary / urinary / nervous), which are spatially in the trunk +but topologically siblings of FMA7181. + +## Actionable conclusion + +To match the Open 3D Man's layered organs + vessels + nerves we do **not** need +their (NC/ND-licensed) geometry. We **expand the bake** to include the +thoraco-abdominal members of the organ/vessel/nerve systems (spatially filter +each system's meshes to the trunk bbox, union with the current 178). All free, +CC-BY, FMA-keyed, through the existing pipeline. We are currently rendering 13% +of the anatomy we already hold. + +Premium licensed geometry (VOXEL-MAN / Open 3D Man, bought commercially when the +project funds it) is only needed for the last mile: spleen, fine peripheral +nerves, and mesh fidelity — and it drops into the SAME geometry-agnostic pipeline +(OBJ + vn in), so it's a swap, not a rebuild. + +## Licensing note (for the PoC → commercial path) + +- **Gap analysis itself binds nothing** — studying any atlas to find gaps is not + use/redistribution. Free to look. +- **BodyParts3D is CC-BY**: commercial-safe, survives the PoC→commercial + transition with no relicensing landmine. This is a reason to build on it now. +- **VOXEL-MAN is CC BY-NC-ND**: ND blocks redistributing any *baked/modified* + form even non-commercially (a shared PoC demo = redistribution of a + derivative); NC blocks commercial. CC-ND is **not pay-to-unlock** — but UKE + Hamburg almost certainly dual-licenses (free CC for academic, separate paid + commercial license direct from the institution). "Pharma buys the license" + = that separate commercial contract, which is real and standard. +- Keep the pipeline geometry-agnostic so premium meshes drop in at + productization without touching the splat/codec/FMA-keying architecture. diff --git a/cockpit/public/fma_isa_classification.json b/cockpit/public/fma_isa_classification.json new file mode 100644 index 000000000..2462d19b4 --- /dev/null +++ b/cockpit/public/fma_isa_classification.json @@ -0,0 +1 @@ +{"attribution": "BodyParts3D, (c) The Database Center for Life Science. Current site licence: CC-BY 4.0; 2013 mesh files embed CC-BY-SA 2.1 Japan.", "source": "BodyParts3D 4.0 (DBCLS) is_a TYPE tree", "note": "join by FJ id; container:identity is the 8:8 GUID, is_a is the DN path", "concepts": 1658, "meshes": 2234, "classification": [{"fma": "FMA55077", "name": "pharyngeal raphe", "tissue": "flesh", "system": "integument", "is_a": "/integument/anatomical_boundary_entity/anatomical_line/pharyngeal_raphe", "container": 15, "identity": 0, "guid": 983040, "rgb": [189, 152, 142], "fj": ["FJ2749"]}, {"fma": "FMA75351", "name": "interventricular foramen", "tissue": "flesh", "system": "integument", "is_a": "/integument/anatomical_space/anatomical_conduit_space/interventricular_foramen", "container": 15, "identity": 1, "guid": 983041, "rgb": [201, 161, 151], "fj": ["FJ1752"]}, {"fma": "FMA54640", "name": "tongue", "tissue": "flesh", "system": "integument", "is_a": "/integument/heterogeneous_cluster/tongue", "container": 15, "identity": 2, "guid": 983042, "rgb": [193, 155, 146], "fj": ["FJ2761"]}, {"fma": "FMA55619", "name": "right pterygomandibular raphe", "tissue": "flesh", "system": "integument", "is_a": "/integument/anatomical_boundary_entity/anatomical_line/pterygomandibular_raphe/right_pterygomandibular_raphe", "container": 15, "identity": 3, "guid": 983043, "rgb": [206, 165, 155], "fj": ["FJ2756"]}, {"fma": "FMA55620", "name": "left pterygomandibular raphe", "tissue": "flesh", "system": "integument", "is_a": "/integument/anatomical_boundary_entity/anatomical_line/pterygomandibular_raphe/left_pterygomandibular_raphe", "container": 15, "identity": 4, "guid": 983044, "rgb": [198, 159, 149], "fj": ["FJ2744"]}, {"fma": "FMA63103", "name": "pancreatic duct tree", "tissue": "gland", "system": "alimentary", "is_a": "/alimentary/pancreatic_duct_tree", "container": 11, "identity": 0, "guid": 720896, "rgb": [197, 171, 143], "fj": ["FJ2630"]}, {"fma": "FMA71442", "name": "set of anterior cervical intertransversarii", "tissue": "flesh", "system": "integument", "is_a": "/integument/set_of_organs/musculature/set_of_anterior_cervical_intertransversarii", "container": 15, "identity": 5, "guid": 983045, "rgb": [203, 163, 153], "fj": ["FJ1549", "FJ1549M"]}, {"fma": "FMA71443", "name": "set of posterior cervical intertransversarii", "tissue": "flesh", "system": "integument", "is_a": "/integument/set_of_organs/musculature/set_of_posterior_cervical_intertransversarii", "container": 15, "identity": 6, "guid": 983046, "rgb": [195, 157, 147], "fj": ["FJ1553", "FJ1553M"]}, {"fma": "FMA11336", "name": "linea alba", "tissue": "flesh", "system": "integument", "is_a": "/integument/anatomical_junction/decussation/linea_alba", "container": 15, "identity": 7, "guid": 983047, "rgb": [207, 167, 156], "fj": ["FJ1448"]}, {"fma": "FMA11338", "name": "ileocecal junction", "tissue": "flesh", "system": "integument", "is_a": "/integument/anatomical_junction/zone_of_continuity/ileocecal_junction", "container": 15, "identity": 8, "guid": 983048, "rgb": [200, 160, 150], "fj": ["FJ2599"]}, {"fma": "FMA14542", "name": "appendix", "tissue": "flesh", "system": "integument", "is_a": "/integument/appendix", "container": 15, "identity": 9, "guid": 983049, "rgb": [192, 154, 145], "fj": ["FJ2565"]}, {"fma": "FMA15900", "name": "urinary bladder", "tissue": "kidney", "system": "urinary", "is_a": "/urinary/urinary_bladder", "container": 9, "identity": 0, "guid": 589824, "rgb": [154, 88, 82], "fj": ["FJ3149"]}, {"fma": "FMA19667", "name": "urethra", "tissue": "flesh", "system": "integument", "is_a": "/integument/urethra", "container": 15, "identity": 10, "guid": 983050, "rgb": [197, 158, 148], "fj": ["FJ3148"]}, {"fma": "FMA46442", "name": "tendinous arch of levator ani", "tissue": "flesh", "system": "integument", "is_a": "/integument/tendon/tendinous_arch_of_levator_ani", "container": 15, "identity": 11, "guid": 983051, "rgb": [189, 152, 143], "fj": ["FJ1465", "FJ1465M", "FJ2552", "FJ2553"]}, {"fma": "FMA58242", "name": "right lens", "tissue": "flesh", "system": "integument", "is_a": "/integument/lens/right_lens", "container": 15, "identity": 12, "guid": 983052, "rgb": [202, 162, 152], "fj": ["FJ1356"]}, {"fma": "FMA58243", "name": "left lens", "tissue": "flesh", "system": "integument", "is_a": "/integument/lens/left_lens", "container": 15, "identity": 13, "guid": 983053, "rgb": [194, 156, 146], "fj": ["FJ1305"]}, {"fma": "FMA58839", "name": "suspensory ligament of right lens", "tissue": "flesh", "system": "integument", "is_a": "/integument/suspensory_ligament_of_lens/suspensory_ligament_of_right_lens", "container": 15, "identity": 14, "guid": 983054, "rgb": [206, 166, 155], "fj": ["FJ1371"]}, {"fma": "FMA58840", "name": "suspensory ligament of left lens", "tissue": "flesh", "system": "integument", "is_a": "/integument/suspensory_ligament_of_lens/suspensory_ligament_of_left_lens", "container": 15, "identity": 15, "guid": 983055, "rgb": [199, 160, 150], "fj": ["FJ1320"]}, {"fma": "FMA59541", "name": "right lacrimal lake", "tissue": "flesh", "system": "integument", "is_a": "/integument/anatomical_space/anatomical_cavity/organ_cavity_subdivision/lacrimal_lake/right_lacrimal_lake", "container": 15, "identity": 16, "guid": 983056, "rgb": [191, 153, 144], "fj": ["FJ1352"]}, {"fma": "FMA59542", "name": "left lacrimal lake", "tissue": "flesh", "system": "integument", "is_a": "/integument/anatomical_space/anatomical_cavity/organ_cavity_subdivision/lacrimal_lake/left_lacrimal_lake", "container": 15, "identity": 17, "guid": 983057, "rgb": [203, 163, 153], "fj": ["FJ1301"]}, {"fma": "FMA61934", "name": "choroid plexus of cerebral hemisphere", "tissue": "nerve", "system": "nervous", "is_a": "/nervous/region_of_organ_component/region_of_wall_of_ventricular_system_of_neuraxis/choroid_plexus_of_cerebral_hemisphere", "container": 13, "identity": 0, "guid": 851968, "rgb": [222, 202, 86], "fj": ["FJ1755", "FJ1803"]}, {"fma": "FMA62008", "name": "hypothalamus", "tissue": "nerve", "system": "nervous", "is_a": "/nervous/organ_component_of_neuraxis/hypothalamus", "container": 13, "identity": 1, "guid": 851969, "rgb": [236, 214, 92], "fj": ["FJ1760", "FJ1808"]}, {"fma": "FMA62033", "name": "pineal body", "tissue": "nerve", "system": "nervous", "is_a": "/nervous/region_of_organ_component/circumventricular_organ_of_neuraxis/pineal_body", "container": 13, "identity": 2, "guid": 851970, "rgb": [228, 206, 88], "fj": ["FJ1795"]}, {"fma": "FMA63120", "name": "parenchyma of pancreas", "tissue": "gland", "system": "alimentary", "is_a": "/alimentary/parenchyma/parenchyma_of_pancreas", "container": 11, "identity": 1, "guid": 720897, "rgb": [200, 173, 145], "fj": ["FJ2629"]}, {"fma": "FMA63822", "name": "posterior intercostal arteries", "tissue": "flesh", "system": "integument", "is_a": "/integument/set_of_organ_parts/set_of_organ_regions/set_of_arteries/posterior_intercostal_arteries", "container": 15, "identity": 18, "guid": 983058, "rgb": [205, 165, 154], "fj": ["FJ1961", "FJ1975"]}, {"fma": "FMA70800", "name": "set of dorsal metacarpal arteries", "tissue": "flesh", "system": "integument", "is_a": "/integument/set_of_organ_parts/set_of_organ_regions/set_of_arteries/set_of_dorsal_metacarpal_arteries", "container": 15, "identity": 19, "guid": 983059, "rgb": [198, 159, 149], "fj": ["FJ2347", "FJ2348"]}, {"fma": "FMA70801", "name": "set of dorsal digital arteries", "tissue": "flesh", "system": "integument", "is_a": "/integument/set_of_organ_parts/set_of_organ_regions/set_of_arteries/set_of_dorsal_digital_arteries", "container": 15, "identity": 20, "guid": 983060, "rgb": [190, 153, 143], "fj": ["FJ2093", "FJ2197", "FJ2318", "FJ2346"]}, {"fma": "FMA70815", "name": "set of perforating arteries", "tissue": "flesh", "system": "integument", "is_a": "/integument/set_of_organ_parts/set_of_organ_regions/set_of_arteries/set_of_perforating_arteries", "container": 15, "identity": 21, "guid": 983061, "rgb": [202, 162, 152], "fj": ["FJ2090", "FJ2094", "FJ2127", "FJ2203"]}, {"fma": "FMA70821", "name": "set of common plantar digital arteries", "tissue": "flesh", "system": "integument", "is_a": "/integument/set_of_organ_parts/set_of_organ_regions/set_of_arteries/set_of_common_plantar_digital_arteries", "container": 15, "identity": 22, "guid": 983062, "rgb": [195, 156, 147], "fj": ["FJ2092", "FJ2196"]}, {"fma": "FMA70839", "name": "set of anterior intercostal veins", "tissue": "vein", "system": "cardiovascular", "is_a": "/cardiovascular/set_of_organ_parts/set_of_organ_regions/set_of_veins/set_of_anterior_intercostal_veins", "container": 4, "identity": 0, "guid": 262144, "rgb": [68, 99, 183], "fj": ["FJ1985", "FJ1994"]}, {"fma": "FMA70917", "name": "set of dorsal digital veins", "tissue": "vein", "system": "cardiovascular", "is_a": "/cardiovascular/set_of_organ_parts/set_of_organ_regions/set_of_veins/set_of_dorsal_digital_veins", "container": 4, "identity": 1, "guid": 262145, "rgb": [66, 95, 176], "fj": ["FJ2185", "FJ2198"]}, {"fma": "FMA70919", "name": "set of plantar digital veins", "tissue": "vein", "system": "cardiovascular", "is_a": "/cardiovascular/set_of_organ_parts/set_of_organ_regions/set_of_veins/set_of_plantar_digital_veins", "container": 4, "identity": 2, "guid": 262146, "rgb": [63, 91, 169], "fj": ["FJ2120", "FJ2175"]}, {"fma": "FMA70922", "name": "set of perforating veins", "tissue": "vein", "system": "cardiovascular", "is_a": "/cardiovascular/set_of_organ_parts/set_of_organ_regions/set_of_veins/set_of_perforating_veins", "container": 4, "identity": 3, "guid": 262147, "rgb": [67, 97, 180], "fj": ["FJ2100", "FJ2119", "FJ2138", "FJ2174", "FJ2192"]}, {"fma": "FMA71307", "name": "set of interspinales lumborum", "tissue": "flesh", "system": "integument", "is_a": "/integument/set_of_organs/musculature/musculature_of_subdivision_of_trunk/set_of_interspinales_lumborum", "container": 15, "identity": 23, "guid": 983063, "rgb": [196, 158, 148], "fj": ["FJ1550", "FJ1550M"]}, {"fma": "FMA71309", "name": "set of interspinales cervicis", "tissue": "flesh", "system": "integument", "is_a": "/integument/set_of_organs/musculature/musculature_of_subdivision_of_trunk/set_of_interspinales_cervicis", "container": 15, "identity": 24, "guid": 983064, "rgb": [189, 152, 142], "fj": ["FJ1552", "FJ1552M"]}, {"fma": "FMA7131", "name": "esophagus", "tissue": "gi", "system": "alimentary", "is_a": "/alimentary/esophagus", "container": 10, "identity": 0, "guid": 655360, "rgb": [203, 169, 132], "fj": ["FJ2563"]}, {"fma": "FMA7148", "name": "stomach", "tissue": "gi", "system": "alimentary", "is_a": "/alimentary/stomach", "container": 10, "identity": 1, "guid": 655361, "rgb": [195, 162, 127], "fj": ["FJ2564"]}, {"fma": "FMA71502", "name": "set of posterior temporal branches of lateral occipital artery", "tissue": "artery", "system": "cardiovascular", "is_a": "/cardiovascular/set_of_organ_parts/set_of_organ_regions/set_of_arteries/set_of_posterior_temporal_branches_of_lateral_occipital_artery", "container": 3, "identity": 0, "guid": 196608, "rgb": [208, 60, 53], "fj": ["FJ1719", "FJ1719M"]}, {"fma": "FMA71537", "name": "set of oesophageal branches of thoracic aorta", "tissue": "gi", "system": "alimentary", "is_a": "/alimentary/set_of_organ_parts/set_of_organ_regions/set_of_arteries/set_of_oesophageal_branches_of_thoracic_aorta", "container": 10, "identity": 2, "guid": 655362, "rgb": [200, 166, 130], "fj": ["FJ3431"]}, {"fma": "FMA71562", "name": "set of calcaneal branches of posterior tibial artery", "tissue": "artery", "system": "cardiovascular", "is_a": "/cardiovascular/set_of_organ_parts/set_of_organ_regions/set_of_arteries/set_of_calcaneal_branches_of_posterior_tibial_artery", "container": 3, "identity": 1, "guid": 196609, "rgb": [193, 55, 49], "fj": ["FJ2091", "FJ2195"]}, {"fma": "FMA71564", "name": "set of plantar digital arteries proper", "tissue": "flesh", "system": "integument", "is_a": "/integument/set_of_organ_parts/set_of_organ_regions/set_of_arteries/set_of_plantar_digital_arteries_proper", "container": 15, 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"/cardiovascular/organ_region/organ_segment/region_of_vascular_tree_organ/segment_of_venous_tree_organ/vein/systemic_vein/subdivision_of_superior_vena_caval_tree/subdivision_of_brachiocephalic_vein/subdivision_of_subclavian_vein/tributary_of_subclavian_vein/tributary_of_axillary_vein/tributary_of_brachial_vein/tributary_of_radial_vein/palmar_metacarpal_vein/left_palmar_metacarpal_vein", "container": 4, "identity": 220, "guid": 262364, "rgb": [63, 91, 168], "opacity": 0.96, "g_start": 392837, "g_count": 148, "fj": ["FJ2238", "FJ2320", "FJ2323"], "centroid": [0.339982326403678, -0.049835371978864076, -0.019411553712589482], "bbox": [[0.30766697885406086, -0.08674622479566015, -0.07805287415589797], [0.375575156677306, -0.02685080108462217, 0.03927930000234748]]}]} \ No newline at end of file diff --git a/cockpit/public/torso.splat b/cockpit/public/torso.splat index 519babe1d..fc839a813 100644 Binary files a/cockpit/public/torso.splat and b/cockpit/public/torso.splat differ diff --git a/cockpit/src/TorsoMap.tsx b/cockpit/src/TorsoMap.tsx index 55b6c0a58..8ac423951 100644 --- a/cockpit/src/TorsoMap.tsx +++ b/cockpit/src/TorsoMap.tsx @@ -1,12 +1,14 @@ // FMA torso · map view — the splat AS the GUID substrate. // -// Renders the same torso.splat (SPL2: real BodyParts3D geometry, per-vertex -// normal, per-gaussian node-row tag) but treats it as the value-tenant SoA it -// is: click a gaussian -> its node row -> O(1) into torso.nodes.json (the node -// SoA) -> the FMA structure's identity (concept id, name, partonomy path, -// gaussian range). Click a structure in the list -> its gaussians highlight. +// Renders the same torso.splat (SPL3: real BodyParts3D geometry, per-vertex normal, +// per-surfel node-row tag) but treats it as the value-tenant SoA it is: click a +// surfel -> its node row -> O(1) into torso.nodes.json (the node SoA) -> the FMA +// structure's identity (concept id, tissue, is_a DistinguishedName, container:identity +// GUID, gaussian range). Click a structure in the list -> its surfels highlight. // Geometry, graph, and splat are three tenants of one identity, switch-selected. // +// OPAQUE surfels (matches /torso-live): nearest surface wins, no soft-alpha fog. +// // Geometry: BodyParts3D, (c) The Database Center for Life Science (CC-BY 4.0 / // CC-BY-SA 2.1 JP). Attribution shown in-view. import { useEffect, useMemo, useRef, useState } from 'react'; @@ -19,74 +21,100 @@ interface NodeRow { name: string; depth: number; parent: number | null; - tiers: number[]; + tissue: string; + is_a: string; // DistinguishedName path (/system//) + container: number; + identity: number; + guid: number; // (container << 16) | identity rgb: [number, number, number]; g_start: number; g_count: number; centroid: [number, number, number] | null; } -interface NodesDoc { attribution: string; root: string; nodes: NodeRow[] } +interface NodesDoc { attribution: string; nodes: NodeRow[] } -interface Spl2 { +interface Spl3 { count: number; positions: Float32Array; - colors: Float32Array; // 0..1 rgb - rows: Float32Array; // node_row per gaussian + colors: Float32Array; // 0..1 rgb (flat per-structure tissue colour) + normals: Float32Array; // unit surface normal (drives lighting) + opacity: Float32Array; // 0..1 per-surfel (depth-peel tissue tag; gates skin/flesh) + scale: Float32Array; // per-surfel world disk radius (k-NN sized) + rows: Float32Array; // node_row per surfel (the O(1) switch key) } -function decodeSpl2(buf: ArrayBuffer): Spl2 { +// SPL3 body (22 B): pos 3f | normal 3i8 | rgb 3u8 | opacity u8 | scale u8 | node_row u16. +// Orientation: +90 about X, (x,y,z) -> (x,-z,y) — matches the bake/driver so the +// body stands head-up (BodyParts3D model +Z is superior). +function decodeSpl3(buf: ArrayBuffer): Spl3 { const dv = new DataView(buf); const magic = String.fromCharCode(dv.getUint8(0), dv.getUint8(1), dv.getUint8(2), dv.getUint8(3)); - if (magic !== 'SPL2') throw new Error(`bad magic "${magic}" (expected SPL2)`); + if (magic !== 'SPL3') throw new Error(`bad magic "${magic}" (expected SPL3)`); const count = dv.getUint32(4, true); + const scaleMax = dv.getFloat32(12, true); const off = 40; const positions = new Float32Array(count * 3); const colors = new Float32Array(count * 3); + const normals = new Float32Array(count * 3); + const opacity = new Float32Array(count); + const scale = new Float32Array(count); const rows = new Float32Array(count); for (let i = 0; i < count; i++) { - const b = off + i * 21; - // upright: (x,y,z) -> (x,z,-y) - positions[i * 3] = dv.getFloat32(b, true); - positions[i * 3 + 1] = dv.getFloat32(b + 8, true); - positions[i * 3 + 2] = -dv.getFloat32(b + 4, true); + const b = off + i * 22; + const x = dv.getFloat32(b, true), y = dv.getFloat32(b + 4, true), z = dv.getFloat32(b + 8, true); + positions[i * 3] = x; positions[i * 3 + 1] = -z; positions[i * 3 + 2] = y; + const nx = dv.getInt8(b + 12) / 127, ny = dv.getInt8(b + 13) / 127, nz = dv.getInt8(b + 14) / 127; + normals[i * 3] = nx; normals[i * 3 + 1] = -nz; normals[i * 3 + 2] = ny; colors[i * 3] = dv.getUint8(b + 15) / 255; colors[i * 3 + 1] = dv.getUint8(b + 16) / 255; colors[i * 3 + 2] = dv.getUint8(b + 17) / 255; - rows[i] = dv.getUint16(b + 19, true); + opacity[i] = dv.getUint8(b + 18) / 255; + scale[i] = (dv.getUint8(b + 19) / 255) * scaleMax; + rows[i] = dv.getUint16(b + 20, true); } - return { count, positions, colors, rows }; + return { count, positions, colors, normals, opacity, scale, rows }; } +// Lighting computed at the vertex from the baked surface normal — hemisphere ambient + +// key diffuse + soft fill, light fixed in object space. Per-surfel size = its own world +// radius projected to pixels (perspective-correct). OPAQUE: selection dims the rest by +// BRIGHTNESS (not alpha) so the picker stays crisp. const VERT = ` attribute vec3 aColor; +attribute vec3 aNormal; +attribute float aScale; attribute float aRow; uniform float uSelected; -uniform float uSize; +uniform float uFocalPx; varying vec3 vColor; -varying float vDim; void main() { - vColor = aColor; - vDim = (uSelected < 0.0 || abs(aRow - uSelected) < 0.5) ? 1.0 : 0.16; + vec3 n = normalize(aNormal); + const vec3 L = vec3(-0.401, 0.783, 0.476); + float ndl = max(dot(n, L), 0.0); + float hemi = 0.34 + 0.20 * (n.y * 0.5 + 0.5); + float fill = 0.12 * (-n.x * 0.5 + 0.5); + float shade = min(hemi + fill + 0.92 * ndl, 1.3); + bool sel = uSelected < 0.0 || abs(aRow - uSelected) < 0.5; + vColor = aColor * shade * (sel ? 1.0 : 0.18); vec4 mv = modelViewMatrix * vec4(position, 1.0); gl_Position = projectionMatrix * mv; - gl_PointSize = uSize * (1.0 / -mv.z); + gl_PointSize = max(2.0 * aScale * uFocalPx / max(-mv.z, 0.02), 1.5); }`; const FRAG = ` precision mediump float; varying vec3 vColor; -varying float vDim; void main() { vec2 c = gl_PointCoord - 0.5; if (dot(c, c) > 0.25) discard; - float a = smoothstep(0.25, 0.05, dot(c, c)); - gl_FragColor = vec4(vColor * vDim, a); + gl_FragColor = vec4(vColor, 1.0); }`; function mount( container: HTMLDivElement, - splat: Spl2, + splat: Spl3, onPick: (row: number) => void, apiRef: { current: { select: (row: number) => void } | null }, + onStats: (s: { fps: number; frac: number }) => void, ): () => void { let w = container.clientWidth || window.innerWidth; let h = container.clientHeight || window.innerHeight; @@ -99,15 +127,33 @@ function mount( renderer.setPixelRatio(Math.min(window.devicePixelRatio, 2)); container.appendChild(renderer.domElement); + // LazyLock: build the geometry ONCE; selection + throttle are uniforms / drawRange, + // never a rebuild. A shuffled index makes a drawRange prefix a uniform spatial + // subsample, so adaptive decimation thins evenly (not by structure order). const geom = new THREE.BufferGeometry(); geom.setAttribute('position', new THREE.BufferAttribute(splat.positions, 3)); geom.setAttribute('aColor', new THREE.BufferAttribute(splat.colors, 3)); + geom.setAttribute('aNormal', new THREE.BufferAttribute(splat.normals, 3)); + geom.setAttribute('aScale', new THREE.BufferAttribute(splat.scale, 1)); geom.setAttribute('aRow', new THREE.BufferAttribute(splat.rows, 1)); + const idx = new Uint32Array(splat.count); + for (let i = 0; i < splat.count; i++) idx[i] = i; + let s = 0x9e3779b9 >>> 0; + for (let i = splat.count - 1; i > 0; i--) { + s = (Math.imul(s, 1664525) + 1013904223) >>> 0; + const j = s % (i + 1); + const t = idx[i]; idx[i] = idx[j]; idx[j] = t; + } + geom.setIndex(new THREE.BufferAttribute(idx, 1)); + geom.setDrawRange(0, splat.count); + const focalPx = () => + renderer.domElement.height / (2 * Math.tan(THREE.MathUtils.degToRad(camera.fov) / 2)); const mat = new THREE.ShaderMaterial({ vertexShader: VERT, fragmentShader: FRAG, - uniforms: { uSelected: { value: -1 }, uSize: { value: 4.2 } }, - transparent: true, + uniforms: { uSelected: { value: -1 }, uFocalPx: { value: focalPx() } }, + transparent: false, // OPAQUE — crisp picker, no soft-alpha fog + depthTest: true, depthWrite: true, }); const points = new THREE.Points(geom, mat); @@ -137,8 +183,36 @@ function mount( apiRef.current = { select: (row: number) => { mat.uniforms.uSelected.value = row; } }; + // Adaptive-FPS: an EMA of the frame time predicts next-frame cost; over the 60fps + // budget we thin the draw range (uniform subsample) + drop pixelRatio BEFORE the + // stutter lands, and recover when frames are cheap. Active fraction is surfaced — + // never silent decimation. let raf = 0; - const tick = () => { raf = requestAnimationFrame(tick); controls.update(); renderer.render(scene, camera); }; + let ema = 16.6; + let last = performance.now(); + let active = splat.count; + let sinceStat = 0; + const tick = () => { + raf = requestAnimationFrame(tick); + const now = performance.now(); + ema = ema * 0.9 + (now - last) * 0.1; + last = now; + if (ema > 22 && active > splat.count * 0.2) { + active = Math.max(Math.round(splat.count * 0.2), Math.round(active * 0.9)); + } else if (ema < 15 && active < splat.count) { + active = Math.min(splat.count, Math.round(active * 1.05) + 2000); + } + geom.setDrawRange(0, active); + const pr = ema > 30 ? 1 : Math.min(window.devicePixelRatio, 2); + if (renderer.getPixelRatio() !== pr) renderer.setPixelRatio(pr); + mat.uniforms.uFocalPx.value = focalPx(); + controls.update(); + renderer.render(scene, camera); + if (++sinceStat >= 20) { + sinceStat = 0; + onStats({ fps: Math.round(1000 / Math.max(ema, 1)), frac: active / splat.count }); + } + }; tick(); const onResize = () => { w = container.clientWidth || window.innerWidth; h = container.clientHeight || window.innerHeight; @@ -152,19 +226,22 @@ function mount( }; } +const hex8 = (n: number) => '0x' + (n >>> 0).toString(16).padStart(8, '0'); + export function TorsoMap() { const ref = useRef(null); const apiRef = useRef<{ select: (row: number) => void } | null>(null); - const [splat, setSplat] = useState(null); + const [splat, setSplat] = useState(null); const [doc, setDoc] = useState(null); const [sel, setSel] = useState(null); const [error, setError] = useState(null); + const [stats, setStats] = useState<{ fps: number; frac: number } | null>(null); useEffect(() => { let cancelled = false; fetch('/torso.splat') .then((r) => { if (!r.ok) throw new Error(`HTTP ${r.status} torso.splat`); return r.arrayBuffer(); }) - .then((b) => !cancelled && setSplat(decodeSpl2(b))) + .then((b) => !cancelled && setSplat(decodeSpl3(b))) .catch((e) => !cancelled && setError(String(e))); fetch('/torso.nodes.json') .then((r) => (r.ok ? r.json() : null)) @@ -176,7 +253,7 @@ export function TorsoMap() { useEffect(() => { const c = ref.current; if (!c || !splat) return; - return mount(c, splat, (row) => setSel(row), apiRef); + return mount(c, splat, (row) => setSel(row), apiRef, setStats); }, [splat]); useEffect(() => { apiRef.current?.select(sel ?? -1); }, [sel]); @@ -220,23 +297,34 @@ export function TorsoMap() { click a structure — splat ↔ FMA, one node at one address {doc ? ` · ${owners.length} structures` : ''} + {splat && ( +
+ {splat.count.toLocaleString()} surfels + {stats ? ` · ${stats.fps} fps · ${Math.round(stats.frac * 100)}% drawn (adaptive)` : ''} +
+ )} {error && (
{error}
)} - {/* selected structure + partonomy path */} + {/* selected structure: identity (tissue + container:identity GUID + is_a DN) + partonomy */} {selNode && ( -
+
{selNode.name}
- {selNode.fma} · {selNode.g_count.toLocaleString()} gaussians · depth {selNode.depth} + {selNode.fma} · {selNode.g_count.toLocaleString()} surfels · depth {selNode.depth} +
+
+ {selNode.tissue} + {' · GUID '}{selNode.container}:{String(selNode.identity).padStart(4, '0')}{' '} + {hex8(selNode.guid)}
-
HHTL tiers [{selNode.tiers.join(', ')}]
+
{selNode.is_a}
{path.map((n, i) => (
setSel(n.row)}> diff --git a/cockpit/src/TorsoMesh.tsx b/cockpit/src/TorsoMesh.tsx new file mode 100644 index 000000000..201ea1727 --- /dev/null +++ b/cockpit/src/TorsoMesh.tsx @@ -0,0 +1,293 @@ +// FMA torso · live-orbit FILLED SMOOTH TRIANGLE MESH of REAL anatomy. +// +// Renders cockpit/public/torso.mesh — an indexed triangle surface vertex-cluster- +// decimated from the BodyParts3D is_a meshes, coloured per is_a tissue. Operator +// directive (2026-06-24): "connect to a triangle filled surface ... kurvenlineal over +// triangles (Quadro/AutoCAD)". So: filled THREE.Mesh, Gouraud/Phong smooth shading +// from the cell-averaged per-vertex normals — a solid CAD surface (ivory bone, red +// muscle, blue cartilage, ...), the Open 3D Man material-surface aesthetic. Triangle +// surfaces decisively beat the surfel splat (no sequins, no fog). +// +// Skin/flesh is cut away by default (uFloor) so the anatomy shows; press S to toggle +// the skin shell back (note: the BodyParts3D skin set is sparse, so the shell speckles). +// +// Geometry/data: BodyParts3D, (c) The Database Center for Life Science, +// licensed CC-BY 4.0. Attribution is shown in-view (required by the licence). +import { useEffect, useRef, useState } from 'react'; +import * as THREE from 'three'; +import { OrbitControls } from 'three/addons/controls/OrbitControls.js'; + +const PAGE_BG = 0x0a0e17; +const DEFAULT_FLOOR = 0.5; // gate skin (0.14) + flesh (0.45) out; keep muscle (0.55)+ + +interface Mesh { + vertCount: number; + triCount: number; + positions: Float32Array; + normals: Float32Array; + colors: Uint8Array; + opacity: Float32Array; + index: Uint32Array; +} + +// SPM1 wire (mirrors bake_torso_mesh.py): little-endian +// header 40 B: magic "SPM1" | vert_count u32 | tri_count u32 | node_count u32 +// | bbox_min 3f | bbox_max 3f +// vertex body vert_count x 21 B: pos 3f | normal 3i8 | rgb 3u8 | opacity u8 | node_row u16 +// index body tri_count x 12 B: 3x u32 (global vertex indices) +// Orientation +90 about X, (x,y,z) -> (x,-z,y), so the body stands head-up. +function decodeSpm1(buf: ArrayBuffer): Mesh { + const dv = new DataView(buf); + const magic = String.fromCharCode(dv.getUint8(0), dv.getUint8(1), dv.getUint8(2), dv.getUint8(3)); + if (magic !== 'SPM1') throw new Error(`bad magic "${magic}" (expected SPM1)`); + const vertCount = dv.getUint32(4, true); + const triCount = dv.getUint32(8, true); + const voff = 40; + const positions = new Float32Array(vertCount * 3); + const normals = new Float32Array(vertCount * 3); + const colors = new Uint8Array(vertCount * 3); + const opacity = new Float32Array(vertCount); + for (let i = 0; i < vertCount; i++) { + const b = voff + i * 21; + const x = dv.getFloat32(b, true), y = dv.getFloat32(b + 4, true), z = dv.getFloat32(b + 8, true); + positions[i * 3] = x; positions[i * 3 + 1] = -z; positions[i * 3 + 2] = y; + normals[i * 3] = dv.getInt8(b + 12) / 127; + normals[i * 3 + 1] = -dv.getInt8(b + 14) / 127; + normals[i * 3 + 2] = dv.getInt8(b + 13) / 127; + colors[i * 3] = dv.getUint8(b + 15); + colors[i * 3 + 1] = dv.getUint8(b + 16); + colors[i * 3 + 2] = dv.getUint8(b + 17); + opacity[i] = dv.getUint8(b + 18) / 255; + // node_row u16 at b+19 — used by the picker view, not here + } + const ioff = voff + vertCount * 21; + const index = new Uint32Array(triCount * 3); + for (let t = 0; t < triCount; t++) { + const b = ioff + t * 12; + index[t * 3] = dv.getUint32(b, true); + index[t * 3 + 1] = dv.getUint32(b + 4, true); + index[t * 3 + 2] = dv.getUint32(b + 8, true); + } + return { vertCount, triCount, positions, normals, colors, opacity, index }; +} + +interface Manifest { + attribution: string; + concepts: number; + verts: number; + tris: number; +} + +// Phong smooth shading: interpolate the cell-averaged world normal across each filled +// face, light per-pixel (hemisphere + key + fill, light fixed in world so the orbit +// stays consistently lit). The mesh is static (camera orbits), so aNormal IS the world +// normal. gl_FrontFacing flips it for the back side (clustered winding is inconsistent). +const VERT = ` +attribute vec3 aNormal; +attribute vec3 aColor; +attribute float aOpacity; +varying vec3 vNormal; +varying vec3 vColor; +varying float vOpacity; +void main() { + vNormal = aNormal; + vColor = aColor; + vOpacity = aOpacity; + gl_Position = projectionMatrix * modelViewMatrix * vec4(position, 1.0); +}`; +const FRAG = ` +precision mediump float; +uniform float uFloor; +varying vec3 vNormal; +varying vec3 vColor; +varying float vOpacity; +void main() { + if (vOpacity < uFloor) discard; // cut the skin/flesh shell + vec3 n = normalize(vNormal); + if (!gl_FrontFacing) n = -n; // two-sided + const vec3 L = vec3(-0.401, 0.783, 0.476); + float ndl = max(dot(n, L), 0.0); + float hemi = 0.34 + 0.20 * (n.y * 0.5 + 0.5); + float fill = 0.12 * (-n.x * 0.5 + 0.5); + float shade = min(hemi + fill + 0.92 * ndl, 1.3); + gl_FragColor = vec4(vColor * shade, 1.0); // OPAQUE solid surface +}`; + +function mount( + container: HTMLDivElement, + mesh: Mesh, + floorRef: { value: number }, + onStats: (s: { fps: number }) => void, +): () => void { + let w = container.clientWidth || window.innerWidth; + let h = container.clientHeight || window.innerHeight; + + const scene = new THREE.Scene(); + scene.background = new THREE.Color(PAGE_BG); + const camera = new THREE.PerspectiveCamera(45, w / h, 0.01, 100); + camera.position.set(0, 0.05, 3.0); + const renderer = new THREE.WebGLRenderer({ antialias: true }); + renderer.setSize(w, h); + renderer.setPixelRatio(Math.min(window.devicePixelRatio, 2)); + container.appendChild(renderer.domElement); + + const geom = new THREE.BufferGeometry(); + geom.setAttribute('position', new THREE.BufferAttribute(mesh.positions, 3)); + geom.setAttribute('aNormal', new THREE.BufferAttribute(mesh.normals, 3)); + geom.setAttribute('aColor', new THREE.BufferAttribute(mesh.colors, 3, true)); // u8 normalized + geom.setAttribute('aOpacity', new THREE.BufferAttribute(mesh.opacity, 1)); + geom.setIndex(new THREE.BufferAttribute(mesh.index, 1)); + const mat = new THREE.ShaderMaterial({ + vertexShader: VERT, + fragmentShader: FRAG, + uniforms: { uFloor: { value: floorRef.value } }, + side: THREE.DoubleSide, // clustered winding can be inconsistent + transparent: false, + depthTest: true, + depthWrite: true, + }); + const obj = new THREE.Mesh(geom, mat); + scene.add(obj); + + const controls = new OrbitControls(camera, renderer.domElement); + controls.enableDamping = true; + controls.dampingFactor = 0.08; + controls.autoRotate = true; + controls.autoRotateSpeed = 0.6; + controls.target.set(0, 0, 0); + controls.minDistance = 0.6; + controls.maxDistance = 12; + + // Adaptive-FPS: one indexed mesh is a single draw, so we can't subsample triangles + // like the point cloud — instead drop pixelRatio when the EMA frame-time slips, and + // recover when frames are cheap. 831K tris is one draw; this keeps it smooth. + let raf = 0; + let ema = 16.6; + let last = performance.now(); + let sinceStat = 0; + const tick = () => { + raf = requestAnimationFrame(tick); + const now = performance.now(); + ema = ema * 0.9 + (now - last) * 0.1; + last = now; + const pr = ema > 30 ? 1 : Math.min(window.devicePixelRatio, 2); + if (renderer.getPixelRatio() !== pr) renderer.setPixelRatio(pr); + mat.uniforms.uFloor.value = floorRef.value; + controls.update(); + renderer.render(scene, camera); + if (++sinceStat >= 20) { + sinceStat = 0; + onStats({ fps: Math.round(1000 / Math.max(ema, 1)) }); + } + }; + tick(); + + const onResize = () => { + w = container.clientWidth || window.innerWidth; + h = container.clientHeight || window.innerHeight; + camera.aspect = w / h; + camera.updateProjectionMatrix(); + renderer.setSize(w, h); + }; + const ro = new ResizeObserver(onResize); + ro.observe(container); + + return () => { + cancelAnimationFrame(raf); + ro.disconnect(); + controls.dispose(); + geom.dispose(); + mat.dispose(); + renderer.dispose(); + if (renderer.domElement.parentNode === container) { + container.removeChild(renderer.domElement); + } + }; +} + +export function TorsoMesh() { + const ref = useRef(null); + const [mesh, setMesh] = useState(null); + const [manifest, setManifest] = useState(null); + const [error, setError] = useState(null); + const [stats, setStats] = useState<{ fps: number } | null>(null); + const [skin, setSkin] = useState(false); + const floorRef = useRef({ value: DEFAULT_FLOOR }); + + // S toggles the skin/flesh shell (uFloor 0 <-> DEFAULT_FLOOR) without re-decoding. + useEffect(() => { + const onKey = (e: KeyboardEvent) => { + if (e.key === 's' || e.key === 'S') { + setSkin((v) => { + const nv = !v; + floorRef.current.value = nv ? 0.0 : DEFAULT_FLOOR; + return nv; + }); + } + }; + window.addEventListener('keydown', onKey); + return () => window.removeEventListener('keydown', onKey); + }, []); + + useEffect(() => { + let cancelled = false; + fetch('/torso.mesh') + .then((r) => { if (!r.ok) throw new Error(`HTTP ${r.status} fetching torso.mesh`); return r.arrayBuffer(); }) + .then((buf) => { if (!cancelled) setMesh(decodeSpm1(buf)); }) + .catch((e) => { if (!cancelled) setError(String(e)); }); + fetch('/torso.mesh.manifest.json') + .then((r) => (r.ok ? r.json() : null)) + .then((m) => { if (!cancelled && m) setManifest(m as Manifest); }) + .catch(() => {}); + return () => { cancelled = true; }; + }, []); + + useEffect(() => { + const container = ref.current; + if (!container || !mesh) return; + return mount(container, mesh, floorRef.current, setStats); + }, [mesh]); + + return ( +
+
+ +
+
FMA torso · solid surface
+
+ {manifest + ? `${manifest.tris.toLocaleString()} triangles · ${manifest.concepts} structures — real BodyParts3D geometry, drag to orbit` + : mesh + ? `${mesh.triCount.toLocaleString()} triangles — drag to orbit` + : error + ? '' + : 'loading torso.mesh…'} +
+ {stats && ( +
+ {stats.fps} fps · smooth Gouraud surface · S = skin {skin ? 'on' : 'off'} +
+ )} +
+ + {error && ( +
+ {error} +
+ run: python3 crates/osint-bake/tools/bake_torso_mesh.py … → cockpit/public/torso.mesh +
+
+ )} + + + +
+ {manifest?.attribution ?? 'BodyParts3D, (c) The Database Center for Life Science, licensed under CC Attribution 4.0 International'} +
+
+ ); +} diff --git a/cockpit/src/TorsoRender.tsx b/cockpit/src/TorsoRender.tsx index ecf20c4a6..8cf61a62e 100644 --- a/cockpit/src/TorsoRender.tsx +++ b/cockpit/src/TorsoRender.tsx @@ -1,19 +1,20 @@ -// FMA torso · splat3d CPU render (the "splat" page). +// FMA torso · opaque surfel turntable (the "splat render" page). // -// A turntable of frames rendered bake-side by ndarray::hpc::splat3d — the -// CPU-SIMD EWA gaussian-splat renderer (no GPU) — over the same torso.splat -// asset the /torso-live page orbits live. The frames are baked from real -// BodyParts3D anatomy (FMA-keyed meshes); see crates/osint-bake/tools/ -// bake_torso_splat.py + the scratchpad torso-render driver. +// A pre-rendered turntable of the OPAQUE surfel render (z-buffer, nearest surface +// wins — no soft-gaussian fog) over the same torso.splat asset the /torso-live page +// orbits live. Frames are rendered bake-side by the scratchpad torso-render driver +// over real BodyParts3D anatomy (FMA-keyed is_a meshes); see crates/osint-bake/tools/ +// bake_torso_splat.py. Skin/flesh is gated out so the crisp anatomy shows. // -// This is the "splat" companion to /torso-live's "live orbit": splat3d owns -// these pixels (the spine renders), three.js owns the live one. Same geometry. +// This is the offline companion to /torso-live's live orbit (same geometry); it is +// also the slot for the higher-fidelity CERTIFIED GAUSSIAN render (jc-SPD + Cesium +// SSE/HLOD, the substrate path) when that lands — "opaque now, gaussian later". // // Geometry: BodyParts3D, (c) The Database Center for Life Science, CC-BY 4.0. import { useEffect, useRef, useState } from 'react'; const FRAME_COUNT = 20; -const frameSrc = (i: number) => `/torso-frames/torso_${String(i).padStart(3, '0')}.jpg`; +const frameSrc = (i: number) => `/torso-frames/torso_${String(i).padStart(3, '0')}.png`; interface Manifest { attribution: string; @@ -87,10 +88,10 @@ export function TorsoRender() {
-
FMA torso · splat3d CPU render
+
FMA torso · opaque surfel turntable
- ndarray::hpc::splat3d (EWA, no GPU) - {manifest ? ` · ${manifest.gaussians.toLocaleString()} gaussians · ${manifest.concepts} structures` : ''} + z-buffer surfels (no GPU, no fog) + {manifest ? ` · ${manifest.gaussians.toLocaleString()} surfels · ${manifest.concepts} structures` : ''} {' · real BodyParts3D anatomy'}
diff --git a/cockpit/src/TorsoSplat.tsx b/cockpit/src/TorsoSplat.tsx index 0829b367d..69aecf61c 100644 --- a/cockpit/src/TorsoSplat.tsx +++ b/cockpit/src/TorsoSplat.tsx @@ -1,14 +1,18 @@ -// FMA torso · live-orbit gaussian splat of REAL anatomy. +// FMA torso · live-orbit OPAQUE surfel render of REAL anatomy. // -// Renders cockpit/public/torso.splat — a gaussian cloud baked from BodyParts3D -// (the FMA-keyed 3D mesh database; meshes live in one shared whole-body frame, -// so these are real anatomical coordinates, not a synthesized layout). The bake -// is crates/osint-bake/tools/bake_torso_splat.py over the FMA `part_of` subtree -// rooted at FMA7181 (trunk). Each of ~100 structures carries its own hue. +// Renders cockpit/public/torso.splat — per-triangle surfels baked from BodyParts3D +// (the FMA-keyed 3D mesh database; meshes live in one shared whole-body frame, so +// these are real anatomical coordinates). The bake is crates/osint-bake/tools/ +// bake_torso_splat.py over the is_a TYPE tree (every structure classified to its +// tissue, coloured per tissue, sized per-structure by k-NN local spacing). // -// This is the "live orbit" companion to the CPU splat3d render (/torso): same -// baked geometry, rendered live in WebGL with OrbitControls. Imperative three.js, -// modelled on OsintScene3D.tsx. +// OPAQUE, NOT a soft gaussian. Operator directive (2026-06-24): "rather a triangle +// without gaussian than a ghostbuster pretending to do gaussian splat." So each +// surfel is an opaque depth-tested disk — nearest surface wins, hard edge, NO alpha +// accumulation → no fog, no halo. The previous transparent soft-alpha point material +// was the ghost. `uFloor` gates the translucent skin/flesh shell out (press S to +// toggle) so the crisp anatomy underneath shows; see-inside is a select/clip move, +// never a fog. // // Geometry/data: BodyParts3D, (c) The Database Center for Life Science, // licensed CC-BY 4.0. Attribution is shown in-view (required by the licence). @@ -17,29 +21,32 @@ import * as THREE from 'three'; import { OrbitControls } from 'three/addons/controls/OrbitControls.js'; const PAGE_BG = 0x0a0e17; +const DEFAULT_FLOOR = 0.5; // gate skin (0.14) + flesh (0.45) out; keep muscle (0.55)+ -interface Spl1 { +interface Spl3 { count: number; - radius: number; + scaleMax: number; bboxMin: [number, number, number]; bboxMax: [number, number, number]; positions: Float32Array; colors: Uint8Array; + normals: Float32Array; + opacity: Float32Array; + scale: Float32Array; // per-surfel world disk radius (k-NN sized) } -// Decode the SPL2 wire (mirrors bake_torso_splat.py): little-endian -// header 40 B: magic "SPL2" | count u32 | node_count u32 | radius f32 +// Decode the SPL3 wire (mirrors bake_torso_splat.py): little-endian +// header 40 B: magic "SPL3" | count u32 | node_count u32 | scale_max f32 // | bbox_min 3f | bbox_max 3f -// body count x 21 B: pos 3f (12) | normal 3i8 (3) | rgb 3u8 (3) | opacity u8 (1) -// | node_row u16 (2) -// The live-orbit view renders points: it reads pos + rgb and ignores the normal -// and node-row tags (those drive the /torso splat3d render and the /torso-map view). -function decodeSpl1(buf: ArrayBuffer): Spl1 { +// body count x 22 B: pos 3f (12) | normal 3i8 (3) | rgb 3u8 (3) | opacity u8 (1) +// | scale u8 (1) | node_row u16 (2) +// scale dequantizes as scale_byte/255 * scale_max -> the surfel's world disk radius. +function decodeSpl3(buf: ArrayBuffer): Spl3 { const dv = new DataView(buf); const magic = String.fromCharCode(dv.getUint8(0), dv.getUint8(1), dv.getUint8(2), dv.getUint8(3)); - if (magic !== 'SPL2') throw new Error(`bad magic "${magic}" (expected SPL2)`); + if (magic !== 'SPL3') throw new Error(`bad magic "${magic}" (expected SPL3)`); const count = dv.getUint32(4, true); - const radius = dv.getFloat32(12, true); + const scaleMax = dv.getFloat32(12, true); const bboxMin: [number, number, number] = [ dv.getFloat32(16, true), dv.getFloat32(20, true), dv.getFloat32(24, true), ]; @@ -49,44 +56,83 @@ function decodeSpl1(buf: ArrayBuffer): Spl1 { const off = 40; const positions = new Float32Array(count * 3); const colors = new Uint8Array(count * 3); + const normals = new Float32Array(count * 3); + const opacity = new Float32Array(count); + const scale = new Float32Array(count); for (let i = 0; i < count; i++) { - const b = off + i * 21; - positions[i * 3] = dv.getFloat32(b, true); - positions[i * 3 + 1] = dv.getFloat32(b + 4, true); - positions[i * 3 + 2] = dv.getFloat32(b + 8, true); + const b = off + i * 22; + // upright: +90 about X, (x,y,z) -> (x,-z,y) (matches bake/driver); normals too. + const x = dv.getFloat32(b, true), y = dv.getFloat32(b + 4, true), z = dv.getFloat32(b + 8, true); + positions[i * 3] = x; positions[i * 3 + 1] = -z; positions[i * 3 + 2] = y; + normals[i * 3] = dv.getInt8(b + 12) / 127; + normals[i * 3 + 1] = -dv.getInt8(b + 14) / 127; + normals[i * 3 + 2] = dv.getInt8(b + 13) / 127; colors[i * 3] = dv.getUint8(b + 15); colors[i * 3 + 1] = dv.getUint8(b + 16); colors[i * 3 + 2] = dv.getUint8(b + 17); + opacity[i] = dv.getUint8(b + 18) / 255; + scale[i] = (dv.getUint8(b + 19) / 255) * scaleMax; } - return { count, radius, bboxMin, bboxMax, positions, colors }; + return { count, scaleMax, bboxMin, bboxMax, positions, colors, normals, opacity, scale }; } interface Manifest { attribution: string; - root_name: string; concepts: number; meshes: number; gaussians: number; } -// A soft round sprite so each gaussian reads as a splat, not a hard square. -function gaussianSprite(): THREE.CanvasTexture { - const s = 64; - const cv = document.createElement('canvas'); - cv.width = cv.height = s; - const ctx = cv.getContext('2d')!; - const g = ctx.createRadialGradient(s / 2, s / 2, 0, s / 2, s / 2, s / 2); - g.addColorStop(0, 'rgba(255,255,255,1)'); - g.addColorStop(0.5, 'rgba(255,255,255,0.85)'); - g.addColorStop(1, 'rgba(255,255,255,0)'); - ctx.fillStyle = g; - ctx.fillRect(0, 0, s, s); - const tex = new THREE.CanvasTexture(cv); - tex.needsUpdate = true; - return tex; -} +// Flat normal shading (hemisphere + diffuse + fill, light fixed in object space) — +// same recipe as the CPU driver so the views agree. The point size is the surfel's +// own world radius projected to pixels (perspective-correct), not a global size, so +// dense regions stay tight and the surface reads crisp. aOpacity drives the uFloor +// gate (skin/flesh dropped); the colour itself is opaque. +const VERT = ` +attribute vec3 aColor; +attribute vec3 aNormal; +attribute float aOpacity; +attribute float aScale; +uniform float uFocalPx; // viewportH / (2 tan(fov/2)) * pixelRatio +uniform float uFloor; // gate surfels below this opacity (skin/flesh shell) +uniform float uGain; // global size multiplier (user fine-tune) +varying vec3 vColor; +varying float vGate; +void main() { + vGate = aOpacity < uFloor ? -1.0 : 1.0; + vec3 n = normalize(aNormal); + const vec3 L = vec3(-0.401, 0.783, 0.476); + float ndl = max(dot(n, L), 0.0); + float hemi = 0.34 + 0.20 * (n.y * 0.5 + 0.5); + float fill = 0.12 * (-n.x * 0.5 + 0.5); + float shade = min(hemi + fill + 0.92 * ndl, 1.3); + vColor = aColor * shade; + vec4 mv = modelViewMatrix * vec4(position, 1.0); + gl_Position = projectionMatrix * mv; + // world disk diameter -> screen px; >= 1.5 px so no sub-pixel holes. + gl_PointSize = max(2.0 * aScale * uGain * uFocalPx / max(-mv.z, 0.02), 1.5); +}`; +// OPAQUE: hard-edged disk, alpha = 1. No transparency, no smoothstep tail. The depth +// buffer (depthTest + depthWrite) keeps the nearest surfel per pixel — that is the +// crispness. vGate < 0 discards the skin/flesh shell. +const FRAG = ` +precision mediump float; +varying vec3 vColor; +varying float vGate; +void main() { + if (vGate < 0.0) discard; + vec2 c = gl_PointCoord - 0.5; + if (dot(c, c) > 0.25) discard; + gl_FragColor = vec4(vColor, 1.0); +}`; -function mount(container: HTMLDivElement, splat: Spl1): () => void { +function mount( + container: HTMLDivElement, + splat: Spl3, + floorRef: { value: number }, + gainRef: { value: number }, + onStats: (s: { fps: number; frac: number }) => void, +): () => void { let w = container.clientWidth || window.innerWidth; let h = container.clientHeight || window.innerHeight; @@ -99,24 +145,41 @@ function mount(container: HTMLDivElement, splat: Spl1): () => void { renderer.setPixelRatio(Math.min(window.devicePixelRatio, 2)); container.appendChild(renderer.domElement); + // LazyLock: build the geometry ONCE; a shuffled index makes an adaptive drawRange + // prefix a uniform spatial subsample. Orientation is baked into the decode, so no + // points.rotation is needed (the body already stands head-up). const geom = new THREE.BufferGeometry(); geom.setAttribute('position', new THREE.BufferAttribute(splat.positions, 3)); - geom.setAttribute('color', new THREE.BufferAttribute(splat.colors, 3, true)); // u8 normalized - - const sprite = gaussianSprite(); - const mat = new THREE.PointsMaterial({ - size: Math.max(splat.radius * 3.4, 0.012), - sizeAttenuation: true, - vertexColors: true, - map: sprite, - alphaTest: 0.28, - transparent: true, + geom.setAttribute('aColor', new THREE.BufferAttribute(splat.colors, 3, true)); // u8 normalized + geom.setAttribute('aNormal', new THREE.BufferAttribute(splat.normals, 3)); + geom.setAttribute('aOpacity', new THREE.BufferAttribute(splat.opacity, 1)); + geom.setAttribute('aScale', new THREE.BufferAttribute(splat.scale, 1)); + const idx = new Uint32Array(splat.count); + for (let i = 0; i < splat.count; i++) idx[i] = i; + let s = 0x9e3779b9 >>> 0; + for (let i = splat.count - 1; i > 0; i--) { + s = (Math.imul(s, 1664525) + 1013904223) >>> 0; + const j = s % (i + 1); + const t = idx[i]; idx[i] = idx[j]; idx[j] = t; + } + geom.setIndex(new THREE.BufferAttribute(idx, 1)); + geom.setDrawRange(0, splat.count); + + const focalPx = () => + renderer.domElement.height / (2 * Math.tan(THREE.MathUtils.degToRad(camera.fov) / 2)); + const mat = new THREE.ShaderMaterial({ + vertexShader: VERT, + fragmentShader: FRAG, + uniforms: { + uFocalPx: { value: focalPx() }, + uFloor: { value: floorRef.value }, + uGain: { value: gainRef.value }, + }, + transparent: false, // OPAQUE — the ghost was the soft-alpha blend + depthTest: true, depthWrite: true, }); const points = new THREE.Points(geom, mat); - // BodyParts3D's long axis (superior-inferior) is model +Z; stand it upright so - // the torso's height maps to world +Y. - points.rotation.x = -Math.PI / 2; scene.add(points); const controls = new OrbitControls(camera, renderer.domElement); @@ -128,11 +191,36 @@ function mount(container: HTMLDivElement, splat: Spl1): () => void { controls.minDistance = 0.6; controls.maxDistance = 12; + // Adaptive-FPS: EMA of the frame time thins the draw range (uniform subsample) + + // drops pixelRatio before a stutter lands, recovering when frames are cheap. The + // fixed autorotate is deterministic, so this also stays smooth and predictable. let raf = 0; + let ema = 16.6; + let last = performance.now(); + let active = splat.count; + let sinceStat = 0; const tick = () => { raf = requestAnimationFrame(tick); + const now = performance.now(); + ema = ema * 0.9 + (now - last) * 0.1; + last = now; + if (ema > 22 && active > splat.count * 0.2) { + active = Math.max(Math.round(splat.count * 0.2), Math.round(active * 0.9)); + } else if (ema < 15 && active < splat.count) { + active = Math.min(splat.count, Math.round(active * 1.05) + 2000); + } + geom.setDrawRange(0, active); + const pr = ema > 30 ? 1 : Math.min(window.devicePixelRatio, 2); + if (renderer.getPixelRatio() !== pr) renderer.setPixelRatio(pr); + mat.uniforms.uFocalPx.value = focalPx(); // tracks pixelRatio + resize + mat.uniforms.uFloor.value = floorRef.value; + mat.uniforms.uGain.value = gainRef.value; controls.update(); renderer.render(scene, camera); + if (++sinceStat >= 20) { + sinceStat = 0; + onStats({ fps: Math.round(1000 / Math.max(ema, 1)), frac: active / splat.count }); + } }; tick(); @@ -152,7 +240,6 @@ function mount(container: HTMLDivElement, splat: Spl1): () => void { controls.dispose(); geom.dispose(); mat.dispose(); - sprite.dispose(); renderer.dispose(); if (renderer.domElement.parentNode === container) { container.removeChild(renderer.domElement); @@ -162,15 +249,34 @@ function mount(container: HTMLDivElement, splat: Spl1): () => void { export function TorsoSplat() { const ref = useRef(null); - const [splat, setSplat] = useState(null); + const [splat, setSplat] = useState(null); const [manifest, setManifest] = useState(null); const [error, setError] = useState(null); + const [stats, setStats] = useState<{ fps: number; frac: number } | null>(null); + const [skin, setSkin] = useState(false); + const floorRef = useRef({ value: DEFAULT_FLOOR }); + const gainRef = useRef({ value: 1.0 }); + + // S toggles the skin/flesh shell (uFloor 0 <-> DEFAULT_FLOOR) without re-decoding. + useEffect(() => { + const onKey = (e: KeyboardEvent) => { + if (e.key === 's' || e.key === 'S') { + setSkin((v) => { + const nv = !v; + floorRef.current.value = nv ? 0.0 : DEFAULT_FLOOR; + return nv; + }); + } + }; + window.addEventListener('keydown', onKey); + return () => window.removeEventListener('keydown', onKey); + }, []); useEffect(() => { let cancelled = false; fetch('/torso.splat') .then((r) => { if (!r.ok) throw new Error(`HTTP ${r.status} fetching torso.splat`); return r.arrayBuffer(); }) - .then((buf) => { if (!cancelled) setSplat(decodeSpl1(buf)); }) + .then((buf) => { if (!cancelled) setSplat(decodeSpl3(buf)); }) .catch((e) => { if (!cancelled) setError(String(e)); }); fetch('/torso.manifest.json') .then((r) => (r.ok ? r.json() : null)) @@ -182,7 +288,7 @@ export function TorsoSplat() { useEffect(() => { const container = ref.current; if (!container || !splat) return; - return mount(container, splat); + return mount(container, splat, floorRef.current, gainRef.current, setStats); }, [splat]); return ( @@ -190,16 +296,21 @@ export function TorsoSplat() {
-
FMA torso · gaussian splat
+
FMA torso · opaque surfels
{manifest - ? `${manifest.gaussians.toLocaleString()} gaussians · ${manifest.meshes} meshes · ${manifest.concepts} structures — real BodyParts3D geometry, drag to orbit` + ? `${manifest.gaussians.toLocaleString()} surfels · ${manifest.meshes} meshes · ${manifest.concepts} structures — real BodyParts3D geometry, drag to orbit` : splat - ? `${splat.count.toLocaleString()} gaussians — drag to orbit` + ? `${splat.count.toLocaleString()} surfels — drag to orbit` : error ? '' : 'loading torso.splat…'}
+ {stats && ( +
+ {stats.fps} fps · {Math.round(stats.frac * 100)}% drawn (adaptive) · S = skin {skin ? 'on' : 'off'} +
+ )}
{error && ( diff --git a/cockpit/src/main.tsx b/cockpit/src/main.tsx index 0b11700b2..8ab6c39e4 100644 --- a/cockpit/src/main.tsx +++ b/cockpit/src/main.tsx @@ -8,6 +8,7 @@ import { RenderPage, OrbitPage, FlightPage } from './RenderPage'; import { OsintScene3D } from './OsintScene3D'; import { OsintGraph } from './OsintGraph'; import { FmaGraph } from './FmaGraph'; +import { TorsoMesh } from './TorsoMesh'; import { TorsoSplat } from './TorsoSplat'; import { TorsoRender } from './TorsoRender'; import { TorsoMap } from './TorsoMap'; @@ -82,10 +83,12 @@ createRoot(document.getElementById('root')!).render( } /> {/* FMA anatomy slice — part-of basin × leaf-limited global type (dual membership) */} } /> - {/* FMA torso — real BodyParts3D anatomy as a gaussian splat, two ways: - /torso = splat3d CPU render (turntable), /torso-live = three.js orbit */} + {/* FMA torso — real BodyParts3D anatomy. /torso-live = filled smooth triangle + SURFACE (the hero: solid CAD-style anatomy); /torso = turntable; /torso-splat + = the opaque surfel point cloud (kept for comparison). */} } /> - } /> + } /> + } /> {/* FMA torso map — splat AS the GUID/value-tenant SoA: click a gaussian → its FMA node (O(1) switch into the node SoA) → label + partonomy ↔ graph */} } /> diff --git a/crates/osint-bake/tools/bake_torso_mesh.py b/crates/osint-bake/tools/bake_torso_mesh.py new file mode 100644 index 000000000..7b85cc3a4 --- /dev/null +++ b/crates/osint-bake/tools/bake_torso_mesh.py @@ -0,0 +1,235 @@ +#!/usr/bin/env python3 +"""Bake the REAL-anatomy torso as a FILLED, SMOOTH TRIANGLE MESH (not splats) — +operator directive 2026-06-24: "connect to a triangle filled surface ... kurvenlineal +over triangles (Quadro/AutoCAD)". The BodyParts3D OBJs are already triangulated with +per-vertex normals (`vn`); we vertex-cluster-decimate each mesh (averaging the normals +per cell = the smooth "curve-ruler" over the triangles) and emit ONE indexed mesh, +coloured per is_a tissue. Rendered filled + Gouraud/Phong it is a solid CAD surface +(ivory bone, red muscle, ...), matching the Open 3D Man material-surface aesthetic. + +Reuses bake_torso_splat's is_a classification (load_isa / tissue_of / isa_dn / colours) +so the mesh and the splat share ONE classifier. Geometry is the decimated triangle +surface; the splat bake stays the surfel/gaussian path. + +SPM1 wire (little-endian): + header 40 B: magic "SPM1" | vert_count u32 | tri_count u32 | node_count u32 + | bbox_min 3f | bbox_max 3f + vertex body vert_count x 21 B: pos 3f (12) | normal 3i8 (3) | rgb 3u8 (3) | opacity u8 (1) | node_row u16 (2) + index body tri_count x 12 B: 3x u32 (vertex indices, global) +Positions are normalised to [-1,1] (centre + uniform scale); orientation (x,-z,y) and +the i8-normal dequant happen in the renderer (cockpit/driver), same as SPL3. + +LICENCE: BodyParts3D, (c) The Database Center for Life Science. CC-BY 4.0 / CC-BY-SA 2.1 JP. + +Usage: python3 bake_torso_mesh.py [cell_mm] + cell_mm: vertex-cluster cell size in source mm (smaller = more triangles). Default 3.6 + ~= 600K triangles for the whole body. +""" +import collections +import json +import os +import struct +import sys + +from bake_torso_splat import ( + ATTRIBUTION, CONTAINER_ID, ISA_ROOT, SYSTEM_OF, TISSUE_OPACITY, + bfs, isa_dn, load_isa, tissue_color, tissue_of, +) + +CELL_MM_DEFAULT = 3.6 + + +def read_obj_mesh(path): + """Return (verts[(x,y,z)], normals[(nx,ny,nz)] aligned to verts, faces[(a,b,c)]). + BodyParts3D uses `f v//vn` with vn index == v index, so vn is 1:1 with v; if the + counts disagree we fall back to a +Z normal (rare).""" + vs, vn, faces = [], [], [] + with open(path, "rb") as f: + for ln in f: + if ln[:2] == b"v ": + p = ln.split(); vs.append((float(p[1]), float(p[2]), float(p[3]))) + elif ln[:3] == b"vn ": + p = ln.split(); vn.append((float(p[1]), float(p[2]), float(p[3]))) + elif ln[:2] == b"f ": + p = ln.split() + try: + idx = [int(t.split(b"/")[0]) - 1 for t in p[1:4]] + except (ValueError, IndexError): + continue + if len(idx) == 3 and all(0 <= k < len(vs) for k in idx): + faces.append((idx[0], idx[1], idx[2])) + ns = vn if len(vn) == len(vs) else [(0.0, 0.0, 1.0)] * len(vs) + return vs, ns, faces + + +def cluster_decimate(verts, normals, faces, inv_h, ox, oy, oz): + """Vertex clustering on a global grid (cell = 1/inv_h): collapse all verts in a cell + to one representative (mean position + mean normal), remap faces, drop degenerates. + Averaging the normals per cell keeps the surface SMOOTH (the curve-ruler effect).""" + cell_of = {} + acc = [] # [sx, sy, sz, nx, ny, nz, count] + remap = [0] * len(verts) + for i, (x, y, z) in enumerate(verts): + key = (int((x - ox) * inv_h), int((y - oy) * inv_h), int((z - oz) * inv_h)) + j = cell_of.get(key) + nx, ny, nz = normals[i] + if j is None: + j = len(acc); cell_of[key] = j + acc.append([x, y, z, nx, ny, nz, 1]) + else: + a = acc[j] + a[0] += x; a[1] += y; a[2] += z + a[3] += nx; a[4] += ny; a[5] += nz; a[6] += 1 + remap[i] = j + nv, nn = [], [] + for a in acc: + c = a[6] + nv.append((a[0] / c, a[1] / c, a[2] / c)) + nl = (a[3] * a[3] + a[4] * a[4] + a[5] * a[5]) ** 0.5 or 1.0 + nn.append((a[3] / nl, a[4] / nl, a[5] / nl)) + nf = [] + for (fa, fb, fc) in faces: + ra, rb, rc = remap[fa], remap[fb], remap[fc] + if ra != rb and rb != rc and ra != rc: + nf.append((ra, rb, rc)) + return nv, nn, nf + + +def main(scratch, out_path, cell_mm=CELL_MM_DEFAULT): + parent, children, name, elems, canon = load_isa(scratch) + order, depth = bfs(ISA_ROOT, children) + have = set(order) + isa_obj = os.path.join(scratch, "isa_BP3D_4.0_obj_99") + pof_obj = os.path.join(scratch, "partof", "partof_BP3D_4.0_obj_99") + + def obj_path(fj): + p = os.path.join(isa_obj, fj + ".obj") + return p if os.path.exists(p) else os.path.join(pof_obj, fj + ".obj") + + # deepest-first claim so the finest is_a type owns each shared mesh (mirrors the splat) + concepts = sorted((c for c in elems if c in have), key=lambda c: -depth[c]) + owner = {} + for c in concepts: + for fj in elems[c]: + owner.setdefault(fj, c) + meshes_of = collections.defaultdict(list) + for fj, c in owner.items(): + meshes_of[c].append(fj) + for v in meshes_of.values(): + v.sort() + kept = [c for c in order if c in meshes_of] + + inv_h = 1.0 / float(cell_mm) + tcache = {} + # global mesh accumulators + px, py, pz, nx, ny, nz, cr, cg, cb, cop, crow = ([] for _ in range(11)) + tris = [] # (a, b, c) global vertex indices + nodes = [] + ident_ctr = collections.Counter() + row_of = {c: r for r, c in enumerate(kept)} + + for c in kept: + r = row_of[c] + nm = canon.get(c, name.get(c, c)) + tissue = tissue_of(c, parent, name, canon, tcache) + col = tissue_color(tissue, r) + op_u8 = max(8, min(255, int(round(TISSUE_OPACITY[tissue] * 255)))) + container = CONTAINER_ID[tissue] + identity = ident_ctr[tissue] & 0xFFFF + ident_ctr[tissue] += 1 + v_start = len(px) + for fj in meshes_of[c]: + p = obj_path(fj) + if not os.path.exists(p): + continue + vs, ns, faces = read_obj_mesh(p) + if not faces: + continue + ox = min(v[0] for v in vs); oy = min(v[1] for v in vs); oz = min(v[2] for v in vs) + nv, nn, nf = cluster_decimate(vs, ns, faces, inv_h, ox, oy, oz) + base = len(px) + for (x, y, z), (ax, ay, az) in zip(nv, nn): + px.append(x); py.append(y); pz.append(z) + nx.append(ax); ny.append(ay); nz.append(az) + cr.append(col[0]); cg.append(col[1]); cb.append(col[2]) + cop.append(op_u8); crow.append(r) + for (a, b, cc) in nf: + tris.append((base + a, base + b, base + cc)) + pa, seen = parent.get(c), 0 + while pa is not None and pa not in row_of and seen < 24: + pa = parent.get(pa); seen += 1 + nodes.append({ + "row": r, "fma": c, "name": nm, "depth": depth[c], "parent": row_of.get(pa), + "tissue": tissue, "is_a": isa_dn(c, parent, name, tissue), + "container": container, "identity": identity, "guid": (container << 16) | identity, + "rgb": list(col), "opacity": round(TISSUE_OPACITY[tissue], 3), + "v_start": v_start, "v_count": len(px) - v_start, "fj": meshes_of[c], + }) + + if not px: + sys.exit("no geometry gathered") + + cx = (min(px) + max(px)) / 2; cy = (min(py) + max(py)) / 2; cz = (min(pz) + max(pz)) / 2 + half = max(max(px) - min(px), max(py) - min(py), max(pz) - min(pz)) / 2 or 1.0 + inv = 1.0 / half + for i in range(len(px)): + px[i] = (px[i] - cx) * inv; py[i] = (py[i] - cy) * inv; pz[i] = (pz[i] - cz) * inv + for nd in nodes: + s, c = nd["v_start"], nd["v_count"] + if c: + xs = px[s:s + c]; ys = py[s:s + c]; zs = pz[s:s + c] + nd["centroid"] = [sum(xs) / c, sum(ys) / c, sum(zs) / c] + nd["bbox"] = [[min(xs), min(ys), min(zs)], [max(xs), max(ys), max(zs)]] + else: + nd["centroid"] = None; nd["bbox"] = None + + nvert = len(px); ntri = len(tris) + bmin = (min(px), min(py), min(pz)); bmax = (max(px), max(py), max(pz)) + + def qi8(v): + return max(-127, min(127, int(round(v * 127)))) + + buf = bytearray() + buf += b"SPM1" + buf += struct.pack(" 3 else CELL_MM_DEFAULT) diff --git a/crates/osint-bake/tools/bake_torso_splat.py b/crates/osint-bake/tools/bake_torso_splat.py index eb8dd7726..9477c52cc 100644 --- a/crates/osint-bake/tools/bake_torso_splat.py +++ b/crates/osint-bake/tools/bake_torso_splat.py @@ -1,70 +1,151 @@ #!/usr/bin/env python3 -"""Bake the REAL-anatomy torso gaussian splat from BodyParts3D — v2: anisotropic -(surface normals) + per-node SoA with O(1) tenant tags. - -v1 emitted flat points (pos+rgb). v2 adds, in one pass over the meshes: - - the per-vertex SURFACE NORMAL (BodyParts3D OBJ ships `vn`) -> orientation, so - consumers can render oriented surface-tangent gaussians ("connect the dots") - instead of isotropic blobs; - - a per-gaussian NODE-ROW tag + a NODE SoA (one row per FMA structure) carrying - the value-tenants of that node's identity: fma id, name, partonomy depth + - HHTL tier-ranks, colour, the gaussian RANGE (start+count), and the OBJ-geometry - summary (centroid + bbox + FJ mesh handles). A consumer builds the "switch" - (identity -> row hashtable) once and reads any tenant in O(1). Geometry, graph, - and splat become three tenants of one identity. - -Source: BodyParts3D 4.0 (DBCLS), FMA-keyed OBJ meshes in one shared whole-body -frame. concept id == FMA id. Pairwise inputs (the user-supplied text files): - partof_inclusion_relation_list.txt FMA parent<->child (the partonomy / HHTL cascade) - partof_element_parts.txt FMA concept<->FJ mesh (geometry binding) - partof_parts_list_e.txt FMA<->repr-id<->name (labels) - partof_BP3D_4.0_obj_99/FJ####.obj meshes (v + vn, shared frame) +"""Bake the REAL-anatomy torso gaussian splat from BodyParts3D — v4: IS_A-PRIMARY +(canonical type + canonical name + the superset meshes), tissue-typed colour, +depth-peel opacity, DistinguishedName -> container:identity GUID. + +WHY is_a-primary (corrected 2026-06-24 — operator: "we NEED the is_a data; do NOT +assume the canonical name is in part-of"): part-of is a REGIONAL/containment +decomposition — walking UP from a muscle hits chest-wall -> thorax, never a +"muscular system", so it cannot classify tissue, and it carries non-canonical +regional names. is_a is the TYPE decomposition: every structure resolves UP to its +canonical type (`pectoralis minor` is_a -> ... -> `muscle organ`; `descending +aorta` is_a -> ... -> `artery`), is_a ships canonical names, AND its mesh set is a +SUPERSET of part-of's (2234 vs 1258 FJ, +976) with FINER organ segmentation (no +single "aorta"/"heart" concept — split into ascending/arch/descending/abdominal, +each its own mesh). So classification, names, and geometry all come from is_a. + +The is_a TYPE PATH is the DistinguishedName; it MATERIALISES to a numeric +container:identity GUID (8:8) — container = the tissue class (the deterministic, +"cesium-style" address), identity = the structure within it. Tissue resolution is +O(1) per structure (walk the is_a tree once, cache). + +part-of is used ONLY to define the torso ENVELOPE bbox (the body wall delimits the +thoraco-abdominal volume); any is_a structure whose centroid lies in that envelope +is kept -> a TORSO (organs + vessels + nerves), not the whole body with head+limbs. + +Colour stays FLAT PER STRUCTURE (codec anchor-prediction stays free); tissue colour +makes the palette MORE compressible (all arteries share one red). Depth-peel +opacity (muscle/wall translucent, deep organs/vessels/bone solid) lets inner +structures show through — the EWA renderer already alpha-composites. + +Source: BodyParts3D 4.0 (DBCLS), FMA-keyed OBJ in one shared whole-body frame. +Inputs (scratchpad): + isa_inclusion_relation_list.txt is_a TYPE tree (classification + canonical names) + isa_element_parts.txt is_a concept -> FJ mesh (+ name) + isa_parts_list_e.txt is_a concept -> canonical en name + isa_BP3D_4.0_obj_99/FJ####.obj the is_a meshes (superset; v + vn) + partof_inclusion_relation_list.txt + partof_element_parts.txt + partof obj + -> trunk (FMA7181) envelope bbox ONLY LICENCE / ATTRIBUTION (required): BodyParts3D, (c) The Database Center for Life -Science. The 2013 OBJ files embed CC-BY-SA 2.1 JP; the current DBCLS site relicenses -to CC-BY 4.0 -- both are carried below to be safe. +Science. CC-BY 4.0 (site) / CC-BY-SA 2.1 JP (2013 mesh files). Permissive / +commercial-safe (unlike the VOXEL-MAN / Open-3D-Man reference atlases, CC BY-NC-ND). -Outputs (cockpit/public/): - torso.splat SPL2 binary (hdr 40B: "SPL2"|count u32|node_count u32|radius f32| - bbox_min 3f|bbox_max 3f; body count*21B: - pos 3f|normal 3i8|rgb 3u8|opacity u8|node_row u16) - torso.nodes.json the node SoA (one row per FMA structure) - torso.manifest.json summary + attribution +Outputs (cockpit/public/): torso.splat (SPL2), torso.nodes.json (+ is_a DN, tissue, +container, identity, guid), torso.manifest.json. -Usage: python3 bake_torso_splat.py [root_fma] [budget] +Usage: python3 bake_torso_splat.py [budget] """ import collections -import colorsys import json import os import struct import sys -ROOT_DEFAULT = "FMA7181" # trunk (synonym: Torso) -BUDGET_DEFAULT = 250_000 +ISA_ROOT = "FMA62955" # is_a root "anatomical entity" +BUDGET_DEFAULT = 400_000 ATTRIBUTION = ("BodyParts3D, (c) The Database Center for Life Science. " "Current site licence: CC-BY 4.0; 2013 mesh files embed " "CC-BY-SA 2.1 Japan.") +# ── Tissue typing by walking the is_a TYPE tree (first keyword match up the chain +# wins). Exact, O(1) (cached). Order = most specific first. ─────────────────── +TYPEKEYS = [ + ("cartilage", ["cartilage"]), + ("bone", ["bone organ", "bone", "skeletal element"]), + ("muscle", ["muscle organ", "muscle"]), + ("heart", ["cardiac", "heart", "myocardi"]), + ("artery", ["arterial", "artery"]), + ("vein", ["venous", "vein"]), + ("nerve", ["nerve", "neuron", "neural", "ganglion", "spinal cord", "neuraxis"]), + ("lung", ["respiratory", "lung", "bronch", "alveol", "trachea", "larynx"]), + ("liver", ["hepatic", "liver"]), + ("kidney", ["renal", "kidney", "urinary", "ureter"]), + ("gi", ["alimentary", "gastrointestinal", "intestine", "stomach", "gastric", + "esophag", "digestive", "bowel"]), + ("gland", ["gland", "pancrea", "splen", "thymus", "endocrine"]), + ("vessel", ["vascular", "vessel"]), + ("viscus", ["viscus", "parenchymatous organ"]), + ("skin", ["skin", "integument", "dermis"]), +] +# Fallback on the structure's OWN canonical name (for is_a concepts whose type +# chain doesn't reach a keyword). +NAMEKEYS = [ + ("cartilage", ["cartilage"]), + ("muscle", ["muscle", "pectoralis", "oblique", "transversus", "diaphragm", + "sphincter", "psoas", "piriformis", "obturator"]), + ("bone", ["vertebra", "rib", "sternum", "clavicle", "scapula", "ilium", + "ischium", "pubis", "sacrum", "manubrium", "xiphoid"]), + ("artery", ["aorta", "artery", "arterial", "trunk"]), + ("vein", ["vein", "vena", "venous"]), + ("nerve", ["nerve", "plexus", "ganglion"]), + ("liver", ["liver", "hepatic"]), + ("kidney", ["kidney", "renal"]), + ("gi", ["stomach", "intestine", "colon", "esophagus", "duoden"]), +] +SYSTEM_OF = { + "artery": "cardiovascular", "vein": "cardiovascular", "heart": "cardiovascular", + "vessel": "cardiovascular", "lung": "respiratory", "gi": "alimentary", + "liver": "alimentary", "gland": "alimentary", "viscus": "viscera", + "kidney": "urinary", "nerve": "nervous", "bone": "musculoskeletal", + "cartilage": "musculoskeletal", "muscle": "musculoskeletal", + "skin": "integument", "flesh": "integument", +} +TISSUE_RGB = { + "bone": (230, 221, 196), "cartilage": (199, 209, 224), "muscle": (189, 96, 89), + "artery": (201, 58, 52), "vein": (66, 95, 176), "nerve": (226, 205, 88), + "heart": (168, 72, 71), "lung": (211, 152, 156), "liver": (139, 82, 76), + "kidney": (150, 86, 80), "gi": (201, 167, 131), "gland": (206, 179, 150), + "viscus": (188, 132, 120), "vessel": (180, 90, 110), "skin": (214, 178, 162), + "flesh": (199, 160, 150), +} +TISSUE_OPACITY = { + "skin": 0.14, "flesh": 0.45, "muscle": 0.55, "cartilage": 0.70, + "bone": 0.92, "heart": 0.90, "lung": 0.82, "liver": 0.92, "kidney": 0.92, + "gi": 0.90, "gland": 0.90, "viscus": 0.90, "artery": 0.96, "vein": 0.96, + "vessel": 0.94, "nerve": 0.97, +} +TISSUE_CONTAINERS = ["bone", "cartilage", "muscle", "artery", "vein", "vessel", + "heart", "lung", "liver", "kidney", "gi", "gland", "viscus", + "nerve", "skin", "flesh"] +CONTAINER_ID = {t: i for i, t in enumerate(TISSUE_CONTAINERS)} -def load_tree(bp_dir): + +def load_isa(d): parent, children, name = {}, collections.defaultdict(list), {} - with open(os.path.join(bp_dir, "partof_inclusion_relation_list.txt"), encoding="utf-8") as f: + with open(os.path.join(d, "isa_inclusion_relation_list.txt"), encoding="utf-8") as f: next(f) - for line in f: - p, pn, c, cn = line.rstrip("\n").split("\t") + for ln in f: + p, pn, c, cn = ln.rstrip("\n").split("\t") parent[c] = p children[p].append(c) name[p], name[c] = pn, cn elems = collections.defaultdict(list) - with open(os.path.join(bp_dir, "partof_element_parts.txt"), encoding="utf-8") as f: + with open(os.path.join(d, "isa_element_parts.txt"), encoding="utf-8") as f: + next(f) + for ln in f: + c, n, fj = ln.rstrip("\n").split("\t") + elems[c].append(fj) + name.setdefault(c, n) + canon = {} + with open(os.path.join(d, "isa_parts_list_e.txt"), encoding="utf-8") as f: next(f) - for line in f: - cid, _nm, fj = line.rstrip("\n").split("\t") - elems[cid].append(fj) + for ln in f: + col = ln.rstrip("\n").split("\t") + canon[col[0]] = col[-1] for v in children.values(): - v.sort() # deterministic sibling order -> stable tier ranks - return parent, children, name, elems + v.sort() + return parent, children, name, elems, canon def bfs(root, children): @@ -79,167 +160,325 @@ def bfs(root, children): return order, depth -def tier_ranks(node, parent, children): - """The sibling-rank chain root->node (the HHTL tier address / GUID content).""" - chain = [] - cur = node - while cur in parent: - sibs = children[parent[cur]] - chain.append(sibs.index(cur) + 1) # 1-based rank under parent - cur = parent[cur] - chain.reverse() - return chain - - -def read_obj_v_vn(path): - """Return parallel (positions, normals). BodyParts3D OBJ ships `vn`; faces are - `v//vn` with v_idx == vn_idx, so vertex i pairs with normal i.""" - vs, ns = [], [] +def read_obj_tris(path): + """One oriented SURFEL per triangle (the other session's technique): mean = + centroid, normal = face normal, r = mean centroid->vertex distance (so the disk + COVERS the triangle). Returns [(cx,cy,cz, nx,ny,nz, r)]. This is what reaches + into the field instead of leaving isolated per-vertex blobs.""" + vs = [] + out = [] with open(path, "rb") as f: for ln in f: if ln[:2] == b"v ": + p = ln.split(); vs.append((float(p[1]), float(p[2]), float(p[3]))) + elif ln[:2] == b"f ": p = ln.split() - vs.append((float(p[1]), float(p[2]), float(p[3]))) - elif ln[:3] == b"vn ": - p = ln.split() - ns.append((float(p[1]), float(p[2]), float(p[3]))) - if len(ns) != len(vs): - ns = [(0.0, 0.0, 1.0)] * len(vs) # fallback: no usable normals - return vs, ns + try: + ia = int(p[1].split(b"/")[0]) - 1 + ib = int(p[2].split(b"/")[0]) - 1 + ic = int(p[3].split(b"/")[0]) - 1 + except (ValueError, IndexError): + continue + if not (0 <= ia < len(vs) and 0 <= ib < len(vs) and 0 <= ic < len(vs)): + continue + a, b, c = vs[ia], vs[ib], vs[ic] + cx = (a[0] + b[0] + c[0]) / 3 + cy = (a[1] + b[1] + c[1]) / 3 + cz = (a[2] + b[2] + c[2]) / 3 + e1 = (b[0] - a[0], b[1] - a[1], b[2] - a[2]) + e2 = (c[0] - a[0], c[1] - a[1], c[2] - a[2]) + nx = e1[1] * e2[2] - e1[2] * e2[1] + ny = e1[2] * e2[0] - e1[0] * e2[2] + nz = e1[0] * e2[1] - e1[1] * e2[0] + nl = (nx * nx + ny * ny + nz * nz) ** 0.5 or 1.0 + r = (((cx - a[0]) ** 2 + (cy - a[1]) ** 2 + (cz - a[2]) ** 2) ** 0.5 + + ((cx - b[0]) ** 2 + (cy - b[1]) ** 2 + (cz - b[2]) ** 2) ** 0.5 + + ((cx - c[0]) ** 2 + (cy - c[1]) ** 2 + (cz - c[2]) ** 2) ** 0.5) / 3 + out.append((cx, cy, cz, nx / nl, ny / nl, nz / nl, r)) + return out + + +def lowdisc_indices(n, stride): + """Golden-ratio (R1) low-discrepancy subset of [0, n): ~n/stride indices, evenly + spread AND aperiodic — the cheapest 'Kurvenlineal / X-Trans' decorrelation. A + regular range(0,n,stride) picks every Nth vertex and BEATS against the mesh + tessellation (structured aliasing) and clumps on irregular meshes; the golden + step 1/phi never re-aligns (most-irrational continued fraction [1;1,1,...]), so + coverage is even with no periodic beat -> a smaller brush closes the surface + without tearing holes.""" + if stride <= 1 or n <= 1: + return range(n) + m = max(1, round(n / stride)) + g = 0.6180339887498949 # 1/phi + return sorted({min(n - 1, int(((i + 1) * g % 1.0) * n)) for i in range(m)}) + +def knn_radii(xs, ys, zs, k=3, factor=0.55): + """Per-surfel disk radius = `factor` * mean distance to the k nearest neighbours + within the SAME structure (the LOCAL sample spacing). This is the metric Sigma-fit + that REPLACES the hand-rolled sqrt(stride) bridge: dense regions get small disks, + sparse regions larger, with NO uniform over-inflation — so opaque disks TILE the + surface watertight (factor 0.55 -> ~10% overlap, crisp) instead of piling into + oversized marbles. Grid-hashed, ~O(n). Same principle the substrate render path + uses (k-NN metric Sigma); baked here so the SPL3 asset is render-ready for the + three.js cockpit consumer, which has no Sigma-fit pass of its own.""" + n = len(xs) + if n <= 1: + return [0.006] * n + x0, y0, z0 = min(xs), min(ys), min(zs) + span = max(max(xs) - x0, max(ys) - y0, max(zs) - z0) or 1.0 + cell = max(span / (n ** 0.5), 1e-4) # ~one surface-spacing per cell + inv = 1.0 / cell + grid = collections.defaultdict(list) -def concept_color(idx): - h = (idx * 0.6180339887498949) % 1.0 - r, g, b = colorsys.hsv_to_rgb(h, 0.34, 0.78) # muted pastel per structure - return (int(r * 255), int(g * 255), int(b * 255)) + def cellkey(i): + return (int((xs[i] - x0) * inv), int((ys[i] - y0) * inv), int((zs[i] - z0) * inv)) + + for i in range(n): + grid[cellkey(i)].append(i) + out = [cell * factor] * n + for i in range(n): + bx, by, bz = cellkey(i) + ds, ring = [], 1 + while len(ds) < k + 1 and ring <= 4: + ds = [] + for dx in range(-ring, ring + 1): + for dy in range(-ring, ring + 1): + for dz in range(-ring, ring + 1): + for j in grid.get((bx + dx, by + dy, bz + dz), ()): + if j != i: + ds.append((xs[i] - xs[j]) ** 2 + (ys[i] - ys[j]) ** 2 + + (zs[i] - zs[j]) ** 2) + ring += 1 + ds.sort() + kk = min(k, len(ds)) + if kk: + out[i] = factor * (sum(d ** 0.5 for d in ds[:kk]) / kk) + return out + + +def tissue_of(fma, parent, name, canon, cache): + """Walk the is_a TYPE chain to the first tissue keyword; fall back to the + structure's own canonical name; cache per fma (O(1) amortised).""" + if fma in cache: + return cache[fma] + cur, seen = fma, 0 + while cur is not None and seen < 24: + nm = name.get(cur, "").lower() + for t, keys in TYPEKEYS: + if any(k in nm for k in keys): + cache[fma] = t + return t + cur = parent.get(cur); seen += 1 + own = canon.get(fma, name.get(fma, "")).lower() + for t, keys in NAMEKEYS: + if any(k in own for k in keys): + cache[fma] = t + return t + cache[fma] = "flesh" + return "flesh" + + +# Generic FMA upper-ontology nodes carry no type signal — strip them so the DN +# reads as the meaningful type chain (/cardiovascular/artery/segment_of_artery/...). +DN_SKIP = { + "anatomical entity", "physical anatomical entity", "material anatomical entity", + "immaterial anatomical entity", "anatomical structure", "anatomical set", + "organ", "organ part", "organ component", "organ subdivision", "body part", + "cardinal organ part", "subdivision of cardinal organ part", "anatomical cluster", + "nonparenchymatous organ", "parenchymatous organ", "cavitated organ", + "organ with cavitated organ parts", "organ with organ cavity", "set", +} + + +def isa_dn(fma, parent, name, tissue): + """The is_a DistinguishedName path: /system//.""" + chain, cur, seen = [], fma, 0 + while cur is not None and seen < 24: + nm = name.get(cur, cur) + if nm.lower() not in DN_SKIP: + chain.append(nm) + cur = parent.get(cur); seen += 1 + body = "/".join(reversed(chain)).replace(" ", "_") + return f"/{SYSTEM_OF.get(tissue, 'body')}/{body}" -def main(bp_dir, obj_dir, out_path, root=ROOT_DEFAULT, budget=BUDGET_DEFAULT): - parent, children, name, elems = load_tree(bp_dir) - if root not in children and root not in name: - sys.exit(f"root {root} not in BodyParts3D part-of tree") - order, depth = bfs(root, children) - row_of = {fma: i for i, fma in enumerate(order)} +def tissue_color(tissue, idx): + r, g, b = TISSUE_RGB[tissue] + j = ((idx * 0.6180339887498949) % 1.0 - 0.5) * 0.10 + f = 1.0 + j + return (max(0, min(255, int(r * f))), max(0, min(255, int(g * f))), + max(0, min(255, int(b * f)))) - # claim each mesh to its DEEPEST owning concept (compound concepts list all - # descendant elements; deepest-first so leaves own their own meshes). + +def main(scratch, out_path, budget=BUDGET_DEFAULT): + parent, children, name, elems, canon = load_isa(scratch) + order, depth = bfs(ISA_ROOT, children) + have_depth = {c for c in order} + + isa_obj = os.path.join(scratch, "isa_BP3D_4.0_obj_99") + pof_obj = os.path.join(scratch, "partof", "partof_BP3D_4.0_obj_99") + + def obj_path(fj): + p = os.path.join(isa_obj, fj + ".obj") + return p if os.path.exists(p) else os.path.join(pof_obj, fj + ".obj") + + # concepts that carry meshes, ordered by is_a depth (deepest-first claiming so + # the FINEST type owns each mesh). + concepts = [c for c in elems if c in have_depth] + concepts_by_depth = sorted(concepts, key=lambda c: -depth[c]) owner = {} - for fma in sorted(order, key=lambda c: -depth[c]): - for fj in elems.get(fma, []): - owner.setdefault(fj, fma) + for c in concepts_by_depth: + for fj in elems[c]: + owner.setdefault(fj, c) meshes_of = collections.defaultdict(list) - for fj, fma in owner.items(): - meshes_of[fma].append(fj) + for fj, c in owner.items(): + meshes_of[c].append(fj) for v in meshes_of.values(): v.sort() - # pass 1: total vertex count -> global stride for the budget - total_v = 0 + # WHOLE BODY (operator 2026-06-24: "render the whole body, that's the goal; + # make a select -> camera-zoom later"). No spatial clip — every is_a structure + # with a mesh is baked. Region focus (torso, an organ) is a CAMERA move on the + # full-body splat, driven O(1) by each node's centroid+bbox in the SoA, not a + # bake-time filter. vcache = {} - for fma in order: - for fj in meshes_of.get(fma, []): - vs, ns = read_obj_v_vn(os.path.join(obj_dir, fj + ".obj")) - vcache[fj] = (vs, ns) - total_v += len(vs) + incl = collections.defaultdict(list) + total_v = 0 + owners_ordered = [c for c in order if c in meshes_of] + for c in owners_ordered: + for fj in meshes_of[c]: + p = obj_path(fj) + if not os.path.exists(p): + continue + tris = read_obj_tris(p) # one oriented surfel per triangle (the agreed front) + vcache[fj] = tris + incl[c].append(fj); total_v += len(tris) stride = max(1, round(total_v / budget)) - # pass 2: gather gaussians GROUPED by node (contiguous ranges) with the - # per-vertex normal; build node SoA rows. - gx, gy, gz, gnx, gny, gnz, gr, gg, gb, grow = ([] for _ in range(10)) + # pass 2: gather gaussians grouped by node; tissue colour + depth-peel opacity; + # is_a DN -> materialised container:identity GUID. + tcache = {} + gx, gy, gz, gnx, gny, gnz, gr, gg, gb, gop, grow = ([] for _ in range(11)) nodes = [] - for fma in order: - r = row_of[fma] - col = concept_color(r) + ident_ctr = collections.Counter() + row_of = {} + kept = [c for c in order if incl.get(c)] + for r, c in enumerate(kept): + row_of[c] = r + for c in kept: + r = row_of[c] + nm = canon.get(c, name.get(c, c)) + tissue = tissue_of(c, parent, name, canon, tcache) + col = tissue_color(tissue, r) + op_u8 = max(8, min(255, int(round(TISSUE_OPACITY[tissue] * 255)))) + container = CONTAINER_ID[tissue] + identity = ident_ctr[tissue] & 0xFFFF; ident_ctr[tissue] += 1 g_start = len(gx) - for fj in meshes_of.get(fma, []): - vs, ns = vcache[fj] - for k in range(0, len(vs), stride): - (x, y, z) = vs[k] - (nx, ny, nz) = ns[k] + for fj in incl[c]: + tris = vcache[fj] + for k in lowdisc_indices(len(tris), stride): + (x, y, z, nx, ny, nz, _rad) = tris[k] gx.append(x); gy.append(y); gz.append(z) gnx.append(nx); gny.append(ny); gnz.append(nz) gr.append(col[0]); gg.append(col[1]); gb.append(col[2]) - grow.append(r) - g_count = len(gx) - g_start + gop.append(op_u8); grow.append(r) + # nearest kept is_a ancestor -> parent row (the DN partonomy) + pa, seen = parent.get(c), 0 + while pa is not None and pa not in row_of and seen < 24: + pa = parent.get(pa); seen += 1 nodes.append({ - "row": r, "fma": fma, "name": name.get(fma, fma), "depth": depth[fma], - "parent": row_of.get(parent.get(fma)) if fma in parent else None, - "tiers": tier_ranks(fma, parent, children), - "rgb": list(col), "g_start": g_start, "g_count": g_count, - "fj": meshes_of.get(fma, []), + "row": r, "fma": c, "name": nm, "depth": depth[c], + "parent": row_of.get(pa), + "tissue": tissue, "is_a": isa_dn(c, parent, name, tissue), + "container": container, "identity": identity, + "guid": (container << 16) | identity, + "rgb": list(col), "opacity": round(TISSUE_OPACITY[tissue], 3), + "g_start": g_start, "g_count": len(gx) - g_start, + "fj": incl[c], }) if not gx: - sys.exit("no vertices gathered") + sys.exit("no vertices gathered (check the torso envelope / obj dirs)") - # recenter to centroid, uniform-normalize so max half-extent = 1 (normals, - # being directions under a recenter + uniform scale, stay valid). cx = (min(gx) + max(gx)) / 2; cy = (min(gy) + max(gy)) / 2; cz = (min(gz) + max(gz)) / 2 half = max(max(gx) - min(gx), max(gy) - min(gy), max(gz) - min(gz)) / 2 or 1.0 inv = 1.0 / half for i in range(len(gx)): gx[i] = (gx[i] - cx) * inv; gy[i] = (gy[i] - cy) * inv; gz[i] = (gz[i] - cz) * inv - - # per-node centroid + bbox in the normalized frame (the OBJ-geometry tenant). + # per-structure k-NN disk sizing (metric Sigma-fit; replaces the sqrt(stride) + # bridge). Computed on the NORMALISED coords so the radii are already in asset + # space. Each structure sized among its own surfels — no cross-tissue contamination. + gsc = [0.0] * len(gx) + for nd in nodes: + s, cnt = nd["g_start"], nd["g_count"] + gsc[s:s + cnt] = knn_radii(gx[s:s + cnt], gy[s:s + cnt], gz[s:s + cnt]) for nd in nodes: s, c = nd["g_start"], nd["g_count"] - if c == 0: - nd["centroid"] = None; nd["bbox"] = None - continue xs = gx[s:s + c]; ys = gy[s:s + c]; zs = gz[s:s + c] nd["centroid"] = [sum(xs) / c, sum(ys) / c, sum(zs) / c] nd["bbox"] = [[min(xs), min(ys), min(zs)], [max(xs), max(ys), max(zs)]] n = len(gx) bmin = (min(gx), min(gy), min(gz)); bmax = (max(gx), max(gy), max(gz)) - radius = 0.0035 + # SPL3: the header f32 is scale_max — the dequant reference for the per-gaussian + # scale byte. Use the 99th percentile of the disk radii (NOT the max) so a few + # giant triangles don't crush the precision of the bulk; the top 1% saturate at + # byte 255 (slightly under-sized, harmless). Robust quantization, not a tuned + # constant. Per-gaussian disk radius = scale_byte / 255 * scale_max. + ssort = sorted(gsc) + scale_max = ssort[min(len(ssort) - 1, int(round(0.99 * len(ssort))))] if ssort else 1.0 + scale_max = scale_max or 1.0 - def qi8(v): # normalize a normal component to a signed byte + def qi8(v): return max(-127, min(127, int(round(v * 127)))) buf = bytearray() - buf += b"SPL2" + buf += b"SPL3" buf += struct.pack(" 0), + "format": ("SPL3 (per-triangle surfels: pos 3f | normal 3i8 | rgb 3u8 | " + "opacity u8 | scale u8 | node_row u16 = 22 B; header f32 = " + "scale_max dequant ref); node SoA in torso.nodes.json"), + "build": "v4 is_a-primary (canonical type+name+meshes), tissue colour + depth-peel, DN->GUID", + "concepts": len(nodes), "meshes": len(owner), "gaussians": n, "stride": stride, + "scale_max": scale_max, "bbox_min": list(bmin), "bbox_max": list(bmax), + "tissues": dict(tissue_hist), } with open(os.path.join(pub, "torso.manifest.json"), "w", encoding="utf-8") as f: json.dump(manifest, f, indent=2) - owners = sum(1 for nd in nodes if nd["g_count"] > 0) - print(f"baked {out_path}: {n:,} gaussians, {len(nodes)} node rows " - f"({owners} own meshes), {len(owner)} meshes, stride {stride}", file=sys.stderr) - print(f" SPL2 {len(buf):,} B + torso.nodes.json + manifest", file=sys.stderr) + print(f"baked {out_path}: {n:,} gaussians, {len(nodes)} is_a structures, stride {stride}", + file=sys.stderr) + print(f" tissues: {dict(tissue_hist)}", file=sys.stderr) + print(f" scale_max {scale_max:.5f} (99th pct disk radius); SPL3 {len(buf):,} B " + f"+ torso.nodes.json + manifest", file=sys.stderr) if __name__ == "__main__": a = sys.argv - main(a[1], a[2], a[3], - a[4] if len(a) > 4 else ROOT_DEFAULT, - int(a[5]) if len(a) > 5 else BUDGET_DEFAULT) + main(a[1], a[2], int(a[3]) if len(a) > 3 else BUDGET_DEFAULT) diff --git a/crates/osint-bake/tools/export_isa_classification.py b/crates/osint-bake/tools/export_isa_classification.py new file mode 100644 index 000000000..16e872042 --- /dev/null +++ b/crates/osint-bake/tools/export_isa_classification.py @@ -0,0 +1,79 @@ +#!/usr/bin/env python3 +"""Export the FULL is_a tissue classification — every BodyParts3D is_a concept that +carries a mesh, mapped to {tissue, system, canonical name, is_a DistinguishedName, +container:identity GUID, rgb, FJ meshes}. + +CONVERGENCE ARTIFACT (2026-06-24, "opaque now, gaussian later"): the certified-gaussian +render session has the is_a MESHES (FJ####.obj) but not the is_a MAPPING (it has +part_of's inclusion tree, not is_a's). Join this table by FJ id to classify + colour + +GUID-address every mesh in that pipeline. It reuses bake_torso_splat's is_a tree walk +(`load_isa` + `tissue_of` + `isa_dn`) so the two renders share ONE classifier — no drift. + +Deepest-first claiming mirrors the bake: the FINEST is_a type owns each shared mesh. + +Source: BodyParts3D 4.0 (DBCLS). CC-BY 4.0 / CC-BY-SA 2.1 JP. + +Usage: python3 export_isa_classification.py +""" +import collections +import json +import sys + +from bake_torso_splat import ( + ATTRIBUTION, CONTAINER_ID, ISA_ROOT, SYSTEM_OF, + bfs, isa_dn, load_isa, tissue_color, tissue_of, +) + + +def main(scratch, out_path): + parent, children, name, elems, canon = load_isa(scratch) + order, depth = bfs(ISA_ROOT, children) + have = set(order) + + # deepest-first claim so the finest is_a type owns each shared mesh (mirrors the bake) + concepts = sorted((c for c in elems if c in have), key=lambda c: -depth[c]) + owner = {} + for c in concepts: + for fj in elems[c]: + owner.setdefault(fj, c) + meshes_of = collections.defaultdict(list) + for fj, c in owner.items(): + meshes_of[c].append(fj) + + tcache = {} + ident = collections.Counter() + rows = [] + for c in sorted(meshes_of, key=lambda c: (depth[c], c)): + tissue = tissue_of(c, parent, name, canon, tcache) + container = CONTAINER_ID[tissue] + identity = ident[tissue] & 0xFFFF + ident[tissue] += 1 + rows.append({ + "fma": c, + "name": canon.get(c, name.get(c, c)), + "tissue": tissue, + "system": SYSTEM_OF.get(tissue, "body"), + "is_a": isa_dn(c, parent, name, tissue), + "container": container, + "identity": identity, + "guid": (container << 16) | identity, + "rgb": list(tissue_color(tissue, len(rows))), + "fj": sorted(meshes_of[c]), + }) + + nmesh = sum(len(r["fj"]) for r in rows) + json.dump({ + "attribution": ATTRIBUTION, + "source": "BodyParts3D 4.0 (DBCLS) is_a TYPE tree", + "note": "join by FJ id; container:identity is the 8:8 GUID, is_a is the DN path", + "concepts": len(rows), "meshes": nmesh, + "classification": rows, + }, open(out_path, "w", encoding="utf-8")) + + hist = collections.Counter(r["tissue"] for r in rows) + print(f"{out_path}: {len(rows)} is_a concepts, {nmesh} meshes", file=sys.stderr) + print(f" tissues: {dict(hist)}", file=sys.stderr) + + +if __name__ == "__main__": + main(sys.argv[1], sys.argv[2])