Merge pull request #59 from AdaWorldAPI/claude/charming-johnson-ufstpw

fma: (place:tissue) render convergence + /fma-body cockpit + 1M SoA scan PoC

Author: AdaWorldAPI

cockpit/public/fma_body.mesh

@@ -0,0 +1 @@
+{"source":"BodyParts3D 4.0 (DBCLS) is_a OBJ, vertex-cluster decimated","attribution":"BodyParts3D, (c) The Database Center for Life Science, CC-BY 4.0 / CC-BY-SA 2.1 JP","format":"SPM1; opacity byte = LAYER id (1 skin·2 muscle·3 organ·4 skeleton·5 vessel·6 nerve·7 connective·8 other)","verts":329478,"tris":744742,"cell_mm":3.6,"layers":{"vessel":496,"organ":270,"skeleton":231,"other":202,"muscle":57,"skin":2}}

cockpit/public/fma_body.mesh.manifest.json

@@ -0,0 +1,298 @@
+// /fma-body — MY full-body FMA viewer (additive to the other session's /torso*).
+//
+// Renders cockpit/public/fma_body.mesh (baked by `fma`'s cockpit_bake) — the same SPM1
+// indexed triangle surface the cockpit already decodes, but the per-vertex `opacity`
+// byte carries a clean LAYER id (1 skin · 2 muscle · 3 organ · 4 skeleton · 5 vessel ·
+// 6 nerve · 7 connective · 8 other). So the viewer can TOGGLE each layer with a button,
+// and switch the whole body between SOLID and TRANSPARENT. Color is the converged
+// `tissue` byte (is_a); geometry is real BodyParts3D, vertex-cluster decimated.
+//
+// This does not touch /torso, /torso-live, /torso-splat, /torso-map (#57/#58).
+//
+// Geometry/data: BodyParts3D, (c) The Database Center for Life Science, CC-BY 4.0.
+import { useEffect, useRef, useState } from 'react';
+import * as THREE from 'three';
+import { OrbitControls } from 'three/addons/controls/OrbitControls.js';
+
+const PAGE_BG = 0x0a0e17;
+
+// layer id (opacity byte) → label + swatch. id 0 unused; index = id.
+const LAYERS: { id: number; name: string; color: string }[] = [
+  { id: 1, name: 'skin', color: '#dba88a' },
+  { id: 2, name: 'muscle', color: '#bd5c57' },
+  { id: 3, name: 'organ', color: '#cc9484' },
+  { id: 4, name: 'skeleton', color: '#ebe0c7' },
+  { id: 5, name: 'vessel', color: '#cc3838' },
+  { id: 6, name: 'nerve', color: '#ebd152' },
+  { id: 7, name: 'connective', color: '#e0dbcc' },
+  { id: 8, name: 'other', color: '#9696a0' },
+];
+
+interface Mesh {
+  vertCount: number;
+  triCount: number;
+  positions: Float32Array;
+  normals: Float32Array;
+  colors: Uint8Array;
+  layer: Float32Array; // per-vertex layer id (from the opacity byte)
+  index: Uint32Array;
+}
+
+// SPM1 (little-endian): header 40 B | vert 21 B [pos 3f|normal 3i8|rgb 3u8|opacity u8|
+// node_row u16] | index 12 B. Orientation (x,y,z)->(-x,z,y): proper rotation (det +1),
+// head-up in three.js Y-up — identical to TorsoMesh so both viewers agree.
+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 layer = 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);
+    layer[i] = dv.getUint8(b + 18); // opacity byte = LAYER id
+  }
+  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, layer, index };
+}
+
+// Per-layer visibility via uEnabled[9] (indexed by the vertex layer id) + a global alpha
+// for the solid↔transparent switch. Phong smooth shade, two-sided.
+const VERT = `
+attribute vec3 aNormal;
+attribute vec3 aColor;
+attribute float aLayer;
+varying vec3 vNormal;
+varying vec3 vColor;
+varying float vLayer;
+void main() {
+  vNormal = aNormal;
+  vColor = aColor;
+  vLayer = aLayer;
+  gl_Position = projectionMatrix * modelViewMatrix * vec4(position, 1.0);
+}`;
+const FRAG = `
+precision mediump float;
+uniform float uEnabled[9];
+uniform float uAlpha;
+varying vec3 vNormal;
+varying vec3 vColor;
+varying float vLayer;
+void main() {
+  int li = int(vLayer + 0.5);
+  if (li < 0 || li > 8 || uEnabled[li] < 0.5) discard;   // layer toggled off
+  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, uAlpha);
+}`;
+
+interface RenderState {
+  enabled: Float32Array; // length 9, indexed by layer id
+  alpha: number;
+  transparent: boolean;
+}
+
+function mount(container: HTMLDivElement, mesh: Mesh, st: RenderState, 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));
+  geom.setAttribute('aLayer', new THREE.BufferAttribute(mesh.layer, 1));
+  geom.setIndex(new THREE.BufferAttribute(mesh.index, 1));
+  const mat = new THREE.ShaderMaterial({
+    vertexShader: VERT,
+    fragmentShader: FRAG,
+    uniforms: { uEnabled: { value: st.enabled }, uAlpha: { value: st.alpha } },
+    side: THREE.DoubleSide,
+    transparent: st.transparent,
+    depthWrite: !st.transparent,
+  });
+  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;
+
+  let raf = 0;
+  let ema = 16.6;
+  let last = performance.now();
+  let sinceStat = 0;
+  let wasTransparent = st.transparent;
+  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.uEnabled.value = st.enabled;
+    mat.uniforms.uAlpha.value = st.alpha;
+    if (st.transparent !== wasTransparent) {
+      mat.transparent = st.transparent;
+      mat.depthWrite = !st.transparent;
+      mat.needsUpdate = true;
+      wasTransparent = st.transparent;
+    }
+    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 FmaBody() {
+  const ref = useRef<HTMLDivElement>(null);
+  const [mesh, setMesh] = useState<Mesh | null>(null);
+  const [error, setError] = useState<string | null>(null);
+  const [stats, setStats] = useState<{ fps: number } | null>(null);
+  // skin off by default (so the anatomy shows); everything else on.
+  const [on, setOn] = useState<Record<number, boolean>>({ 1: false, 2: true, 3: true, 4: true, 5: true, 6: true, 7: true, 8: true });
+  const [transparent, setTransparent] = useState(false);
+  // shared, mutation-friendly render state (read every frame by the GL loop).
+  const stRef = useRef<RenderState>({ enabled: new Float32Array([0, 0, 1, 1, 1, 1, 1, 1, 1]), alpha: 1, transparent: false });
+
+  // push React state → the GL render state each change.
+  useEffect(() => {
+    const e = new Float32Array(9);
+    for (let i = 1; i <= 8; i++) e[i] = on[i] ? 1 : 0;
+    stRef.current.enabled = e;
+    stRef.current.transparent = transparent;
+    stRef.current.alpha = transparent ? 0.42 : 1.0;
+  }, [on, transparent]);
+
+  useEffect(() => {
+    let cancelled = false;
+    fetch('/fma_body.mesh')
+      .then((r) => { if (!r.ok) throw new Error(`HTTP ${r.status} fetching fma_body.mesh`); return r.arrayBuffer(); })
+      .then((buf) => { if (!cancelled) setMesh(decodeSpm1(buf)); })
+      .catch((e) => { if (!cancelled) setError(String(e)); });
+    return () => { cancelled = true; };
+  }, []);
+
+  useEffect(() => {
+    const container = ref.current;
+    if (!container || !mesh) return;
+    return mount(container, mesh, stRef.current, setStats);
+  }, [mesh]);
+
+  const btn = (active: boolean): React.CSSProperties => ({
+    padding: '5px 11px',
+    borderRadius: 6,
+    border: `1px solid ${active ? '#5a7fa8' : '#2a3242'}`,
+    background: active ? '#16202e' : '#0e1219',
+    color: active ? '#cdd9e5' : '#6a7686',
+    font: '12px ui-monospace, monospace',
+    cursor: 'pointer',
+  });
+
+  return (
+    <div style={{ position: 'fixed', inset: 0, background: '#0a0e17', overflow: 'hidden' }}>
+      <div ref={ref} style={{ position: 'absolute', inset: 0 }} />
+
+      <div style={{ position: 'absolute', top: 12, left: 16, color: '#cdd9e5', font: '13px ui-monospace, monospace', pointerEvents: 'none' }}>
+        <div style={{ fontSize: 15, color: '#fff' }}>FMA body · (place:tissue) layers</div>
+        <div style={{ opacity: 0.7 }}>
+          {mesh ? `${mesh.triCount.toLocaleString()} triangles · drag to orbit` : error ? '' : 'loading fma_body.mesh…'}
+        </div>
+        {stats && <div style={{ opacity: 0.5, marginTop: 2 }}>{stats.fps} fps · solid surface, layer-gated by the converged key</div>}
+      </div>
+
+      {/* layer toggles + solid/transparent */}
+      <div style={{ position: 'absolute', top: 12, right: 16, display: 'flex', flexDirection: 'column', gap: 8, alignItems: 'flex-end' }}>
+        <div style={{ display: 'flex', gap: 6, flexWrap: 'wrap', justifyContent: 'flex-end', maxWidth: 360 }}>
+          {LAYERS.map((l) => (
+            <button key={l.id} style={btn(on[l.id])} onClick={() => setOn((p) => ({ ...p, [l.id]: !p[l.id] }))}>
+              <span style={{ display: 'inline-block', width: 8, height: 8, borderRadius: 4, background: l.color, marginRight: 6, verticalAlign: 'middle' }} />
+              {l.name}
+            </button>
+          ))}
+        </div>
+        <button style={btn(transparent)} onClick={() => setTransparent((v) => !v)}>
+          {transparent ? 'transparent' : 'solid'} ⇄
+        </button>
+        <div style={{ display: 'flex', gap: 14, font: '12px ui-monospace, monospace', marginTop: 2 }}>
+          <a href="/torso-live" style={{ color: '#7fa6c4', textDecoration: 'none' }}>/torso-live →</a>
+          <a href="/fma" style={{ color: '#7fa6c4', textDecoration: 'none' }}>/fma graph →</a>
+        </div>
+      </div>
+
+      {error && (
+        <div style={{ position: 'absolute', top: '46%', width: '100%', textAlign: 'center', color: '#ff8095', font: '13px ui-monospace, monospace' }}>
+          {error}
+          <div style={{ opacity: 0.7, marginTop: 6 }}>
+            bake: <code>cargo run -p fma --bin cockpit_bake -- &lt;parts&gt; &lt;element_parts&gt; &lt;converged.tsv&gt; cockpit/public/fma_body.mesh</code>
+          </div>
+        </div>
+      )}
+
+      <div style={{ position: 'absolute', bottom: 10, left: 16, color: '#5a6b7e', font: '10px ui-monospace, monospace', maxWidth: '70%', pointerEvents: 'none' }}>
+        BodyParts3D, (c) The Database Center for Life Science, licensed under CC Attribution 4.0 International
+      </div>
+    </div>
+  );
+}

cockpit/src/FmaBody.tsx

@@ -12,6 +12,7 @@ import { TorsoMesh } from './TorsoMesh';
 import { TorsoSplat } from './TorsoSplat';
 import { TorsoRender } from './TorsoRender';
 import { TorsoMap } from './TorsoMap';
+import { FmaBody } from './FmaBody';
 import { ReasoningPage } from './ReasoningPage';
 import { ErrorBoundary } from './components/ErrorBoundary';
 import './styles/cockpit.css';
@@ -92,6 +93,10 @@ createRoot(document.getElementById('root')!).render(
           {/* 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 */}
           <Route path="/torso-map" element={<TorsoMap />} />
+          {/* MY full-body FMA viewer — solid triangle surface gated per (place:tissue)
+              LAYER (skin/muscle/organ/skeleton/vessel/nerve buttons) + solid↔transparent.
+              Additive; reads cockpit/public/fma_body.mesh; never touches /torso* (#57/#58). */}
+          <Route path="/fma-body" element={<FmaBody />} />
           {/* The Palantir JSON-graph cockpit (221 aiwar nodes) stays reachable
               at /palantir and as the catch-all for its own sub-routes. */}
           <Route path="/palantir" element={<PalantirApp />} />