Primary and Secondary

docker-compose.yml

@@ -3,7 +3,7 @@ services:
     build: .
     ports:
       - "5173:5173"
-    command: sh -c "npx tsx scripts/compute_layout.ts && npm run dev -- --host"
+    command: sh -c "npm run layout && npm run dev -- --host"
     volumes:
       - .:/app
       - /app/node_modules # Prevents local node_modules from overwriting the container's

package.json

@@ -7,7 +7,7 @@
     "dev": "vite",
     "build": "vite build",
     "preview": "vite preview",
-    "layout": "tsx scripts/compute_layout.ts"
+    "layout": "npx tsx scripts/generate_tree.ts && npx tsx scripts/compute_layout.ts"
   },
   "dependencies": {
     "@webgpu/types": "^0.1.69",

public/primary_edges.csv

@@ -0,0 +1,36 @@
+source,target
+1,0
+2,0
+3,0
+4,0
+5,1
+6,1
+7,1
+8,1
+9,2
+10,3
+11,3
+12,4
+13,4
+14,5
+15,5
+16,5
+17,6
+18,7
+19,8
+20,8
+21,8
+22,8
+23,9
+24,9
+25,10
+26,11
+27,11
+28,11
+29,12
+30,12
+31,12
+32,12
+33,13
+34,13
+35,13

scripts/compute_layout.ts

@@ -1,17 +1,17 @@
 #!/usr/bin/env npx tsx
 /**
- * Tree-Aware Force Layout
+ * Two-Phase Tree Layout
  *
- * Generates a random tree (via generate_tree), computes a radial tree layout,
- * then applies gentle force refinement and writes node_positions.csv.
+ * Phase 1: Position a primary skeleton (nodes from primary_edges.csv)
+ *          with generous spacing, then force-simulate the skeleton.
+ * Phase 2: Fill in remaining subtrees (secondary_edges.csv) within sectors.
  *
- * Usage: npm run layout
+ * Usage: npm run layout-only (after generating tree)
  */
 
-import { writeFileSync } from "fs";
+import { writeFileSync, readFileSync, existsSync } from "fs";
 import { join, dirname } from "path";
 import { fileURLToPath } from "url";
-import { generateTree } from "./generate_tree.js";
 
 const __dirname = dirname(fileURLToPath(import.meta.url));
 const PUBLIC_DIR = join(__dirname, "..", "public");
@@ -20,259 +20,245 @@ const PUBLIC_DIR = join(__dirname, "..", "public");
 // Configuration
 // ══════════════════════════════════════════════════════════
 
-const ENABLE_FORCE_SIM = true;  // Set to false to skip force simulation
-const ITERATIONS = 100;        // Force iterations (gentle)
-const REPULSION_K = 80;        // Repulsion strength (1% of original 8000)
-const EDGE_LENGTH = 120;       // Desired edge rest length
-const ATTRACTION_K = 0.0002;   // Spring stiffness for edges (1% of original 0.02)
-const THETA = 0.7;             // Barnes-Hut accuracy
-const INITIAL_MAX_DISP = 15;   // Starting max displacement
-const COOLING = 0.998;         // Very slow cooling per iteration
+const ENABLE_FORCE_SIM = true; // Set to false to skip force simulation
+const ITERATIONS = 100;         // Force iterations
+const REPULSION_K = 80;         // Repulsion strength
+const EDGE_LENGTH = 120;        // Desired edge rest length
+const ATTRACTION_K = 0.0002;    // Spring stiffness for edges
+const INITIAL_MAX_DISP = 15;    // Starting max displacement
+const COOLING = 0.998;          // Cooling per iteration
 const MIN_DIST = 0.5;
-const PRINT_EVERY = 10;        // Print progress every N iterations
+const PRINT_EVERY = 10;         // Print progress every N iterations
 
 // Scale radius so the tree is nicely spread
 const RADIUS_PER_DEPTH = EDGE_LENGTH * 1.2;
 
-// ── Special nodes with longer parent-edges ──
-// Add vertex IDs here to give them longer edges to their parent.
-// These nodes (and all their descendants) will be pushed further out.
-const LONG_EDGE_NODES = new Set<number>([
-    // e.g. 42, 99, 150
-]);
-const LONG_EDGE_MULTIPLIER = 3.0;  // How many times longer than normal
+// How many times longer skeleton edges are vs. normal edges
+const LONG_EDGE_MULTIPLIER = 39.0;
+
+const SKELETON_STEP = RADIUS_PER_DEPTH * LONG_EDGE_MULTIPLIER;
+
+
 
 // ══════════════════════════════════════════════════════════
-// Generate tree (in-memory)
+// Read tree data from CSVs
 // ══════════════════════════════════════════════════════════
 
-const { root, nodeCount: N, childrenOf, parentOf } = generateTree();
+const primaryPath = join(PUBLIC_DIR, "primary_edges.csv");
+const secondaryPath = join(PUBLIC_DIR, "secondary_edges.csv");
 
-const nodeIds: number[] = [];
-for (let i = 0; i < N; i++) nodeIds.push(i);
+if (!existsSync(primaryPath) || !existsSync(secondaryPath)) {
+    console.error(`Error: Missing input files!`);
+    console.error(`  Expected: ${primaryPath}`);
+    console.error(`  Expected: ${secondaryPath}`);
+    console.error(`  Run 'npx tsx scripts/generate_tree.ts' first.`);
+    process.exit(1);
+}
 
-// Dense index mapping (identity since IDs are 0..N-1)
+// ── Helper to parse CSV edge list ──
+function parseEdges(path: string): Array<[number, number]> {
+    const content = readFileSync(path, "utf-8");
+    const lines = content.trim().split("\n");
+    const edges: Array<[number, number]> = [];
+    // Skip header "source,target"
+    for (let i = 1; i < lines.length; i++) {
+        const line = lines[i].trim();
+        if (!line) continue;
+        const [src, tgt] = line.split(",").map(Number);
+        if (!isNaN(src) && !isNaN(tgt)) {
+            edges.push([src, tgt]);
+        }
+    }
+    return edges;
+}
+
+const primaryEdges = parseEdges(primaryPath);
+const secondaryEdges = parseEdges(secondaryPath);
+const allEdges = [...primaryEdges, ...secondaryEdges];
+
+// ── Reconstruct tree connectivity ──
+
+const childrenOf = new Map<number, number[]>();
+const parentOf = new Map<number, number>();
+const allNodes = new Set<number>();
+const primaryNodes = new Set<number>(); // Nodes involved in primary edges
+
+// Process primary edges first (to classify primary nodes)
+for (const [child, parent] of primaryEdges) {
+    allNodes.add(child);
+    allNodes.add(parent);
+    primaryNodes.add(child);
+    primaryNodes.add(parent);
+
+    parentOf.set(child, parent);
+    if (!childrenOf.has(parent)) childrenOf.set(parent, []);
+    childrenOf.get(parent)!.push(child);
+}
+
+// Process secondary edges
+for (const [child, parent] of secondaryEdges) {
+    allNodes.add(child);
+    allNodes.add(parent);
+
+    parentOf.set(child, parent);
+    if (!childrenOf.has(parent)) childrenOf.set(parent, []);
+    childrenOf.get(parent)!.push(child);
+}
+
+const N = allNodes.size;
+const nodeIds = Array.from(allNodes).sort((a, b) => a - b);
+
+// Find root (node with no parent)
+// Assuming single root for now. If multiple, pick smallest ID or error.
+let root = -1;
+for (const node of allNodes) {
+    if (!parentOf.has(node)) {
+        root = node;
+        break;
+    }
+}
+if (primaryNodes.size === 0 && N > 0) {
+    // Edge case: no primary edges?
+    root = nodeIds[0];
+    primaryNodes.add(root);
+}
+
+console.log(
+    `Read tree: ${N} nodes, ${allEdges.length} edges (P=${primaryEdges.length}, S=${secondaryEdges.length}), root=${root}`
+);
+
+// ══════════════════════════════════════════════════════════
+// Compute full-tree subtree sizes
+// ══════════════════════════════════════════════════════════
+
+const subtreeSize = new Map<number, number>();
+for (const id of nodeIds) subtreeSize.set(id, 1);
+
+{
+    // Post-order traversal to sum subtree sizes
+    // Or iterative with two stacks
+    const stack: Array<{ id: number; phase: "enter" | "exit" }> = [
+        { id: root, phase: "enter" },
+    ];
+    while (stack.length > 0) {
+        const { id, phase } = stack.pop()!;
+        if (phase === "enter") {
+            stack.push({ id, phase: "exit" });
+            const kids = childrenOf.get(id);
+            if (kids) for (const kid of kids) stack.push({ id: kid, phase: "enter" });
+        } else {
+            const kids = childrenOf.get(id);
+            if (kids) {
+                let sum = 0;
+                for (const kid of kids) sum += subtreeSize.get(kid)!;
+                subtreeSize.set(id, 1 + sum);
+            }
+        }
+    }
+}
+
+// ══════════════════════════════════════════════════════════
+// Skeleton = primary nodes
+// ══════════════════════════════════════════════════════════
+
+const skeleton = primaryNodes;
+console.log(`Skeleton: ${skeleton.size} nodes, ${primaryEdges.length} edges`);
+
+// ══════════════════════════════════════════════════════════
+// Position arrays & per-node tracking
+// ══════════════════════════════════════════════════════════
+
+// We use dense arrays logic, but node IDs might be sparse if loaded from file.
+// However, generate_tree produced sequential IDs starting at 0.
+// Let's assume dense 0..N-1 for array indexing, mapped via nodeIds if needed.
+// Actually, let's keep it simple: assume maxId < 2*N or use Maps for positions?
+// The current code uses Float64Array(N) and assumes `nodeIds[i]` corresponds to index `i`?
+// No, the previous code pushed `nodeIds` as `0..N-1`.
+// Here, `nodeIds` IS verified to be `0..N-1` because generate_tree did `nextId++`.
+// So `nodeIds[i] === i`. We can directly use `x[i]`.
+// But if input file has gaps, we'd need a map. To be safe, let's build an `idToIdx` map.
+
+const maxId = Math.max(...nodeIds);
+const mapSize = maxId + 1; // Or just use `N` if we remap. Let's remap.
 const idToIdx = new Map<number, number>();
-for (let i = 0; i < N; i++) idToIdx.set(i, i);
-
-// Edge list as index pairs (child, parent)
-const edges: Array<[number, number]> = [];
-for (const [child, parent] of parentOf) {
-    edges.push([child, parent]);
-}
-
-// Per-node neighbor list (for edge traversal)
-const neighbors: number[][] = Array.from({ length: N }, () => []);
-for (const [a, b] of edges) {
-    neighbors[a].push(b);
-    neighbors[b].push(a);
-}
-
-console.log(`Tree: ${N} nodes, ${edges.length} edges, root=${root}`);
-
-// ══════════════════════════════════════════════════════════
-// Step 1: Radial tree layout (generous spacing, no crossings)
-// ══════════════════════════════════════════════════════════
+nodeIds.forEach((id, idx) => idToIdx.set(id, idx));
 
 const x = new Float64Array(N);
 const y = new Float64Array(N);
-const depth = new Uint32Array(N);
-const nodeRadius = new Float64Array(N); // cumulative radius from root
+const nodeRadius = new Float64Array(N);   // distance from origin
+const sectorStart = new Float64Array(N);
+const sectorEnd = new Float64Array(N);
+const positioned = new Set<number>();
+
+// ══════════════════════════════════════════════════════════
+// Phase 1: Layout skeleton with long edges
+// ══════════════════════════════════════════════════════════
+
+const rootIdx = idToIdx.get(root)!;
+x[rootIdx] = 0;
+y[rootIdx] = 0;
+nodeRadius[rootIdx] = 0;
+sectorStart[rootIdx] = 0;
+sectorEnd[rootIdx] = 2 * Math.PI;
+positioned.add(root);
 
-// Compute subtree sizes
-const subtreeSize = new Uint32Array(N).fill(1);
 {
-    const rootIdx = idToIdx.get(root)!;
-    const stack: Array<{ idx: number; phase: "enter" | "exit" }> = [
-        { idx: rootIdx, phase: "enter" },
-    ];
-    while (stack.length > 0) {
-        const { idx, phase } = stack.pop()!;
-        if (phase === "enter") {
-            stack.push({ idx, phase: "exit" });
-            const kids = childrenOf.get(nodeIds[idx]);
-            if (kids) {
-                for (const kid of kids) {
-                    stack.push({ idx: idToIdx.get(kid)!, phase: "enter" });
-                }
-            }
-        } else {
-            const kids = childrenOf.get(nodeIds[idx]);
-            if (kids) {
-                for (const kid of kids) {
-                    subtreeSize[idx] += subtreeSize[idToIdx.get(kid)!];
-                }
-            }
-        }
-    }
-}
-
-// Compute depths & max depth
-let maxDepth = 0;
-{
-    const rootIdx = idToIdx.get(root)!;
-    const stack: Array<{ idx: number; d: number }> = [{ idx: rootIdx, d: 0 }];
-    while (stack.length > 0) {
-        const { idx, d } = stack.pop()!;
-        depth[idx] = d;
-        if (d > maxDepth) maxDepth = d;
-        const kids = childrenOf.get(nodeIds[idx]);
-        if (kids) {
-            for (const kid of kids) {
-                stack.push({ idx: idToIdx.get(kid)!, d: d + 1 });
-            }
-        }
-    }
-}
-
-// BFS radial assignment (cumulative radii to support per-edge lengths)
-{
-    const rootIdx = idToIdx.get(root)!;
-    x[rootIdx] = 0;
-    y[rootIdx] = 0;
-    nodeRadius[rootIdx] = 0;
-
-    interface Entry {
-        idx: number;
-        d: number;
-        aStart: number;
-        aEnd: number;
-    }
-
-    const queue: Entry[] = [{ idx: rootIdx, d: 0, aStart: 0, aEnd: 2 * Math.PI }];
+    const queue: number[] = [root];
     let head = 0;
 
     while (head < queue.length) {
-        const { idx, d, aStart, aEnd } = queue[head++];
-        const kids = childrenOf.get(nodeIds[idx]);
+        const parentId = queue[head++];
+        const parentIdx = idToIdx.get(parentId)!;
+        const kids = childrenOf.get(parentId);
         if (!kids || kids.length === 0) continue;
 
-        // Sort children by subtree size (largest sectors together for balance)
-        const sortedKids = [...kids].sort(
-            (a, b) => (subtreeSize[idToIdx.get(b)!]) - (subtreeSize[idToIdx.get(a)!])
-        );
+        const aStart = sectorStart[parentIdx];
+        const aEnd = sectorEnd[parentIdx];
+        const totalWeight = kids.reduce((s, k) => s + subtreeSize.get(k)!, 0);
 
-        const totalWeight = sortedKids.reduce(
-            (s, k) => s + subtreeSize[idToIdx.get(k)!], 0
+        // Sort children by subtree size
+        const sortedKids = [...kids].sort(
+            (a, b) => subtreeSize.get(b)! - subtreeSize.get(a)!
         );
 
         let angle = aStart;
         for (const kid of sortedKids) {
             const kidIdx = idToIdx.get(kid)!;
-            const w = subtreeSize[kidIdx];
+            const w = subtreeSize.get(kid)!;
             const sector = (w / totalWeight) * (aEnd - aStart);
-            const mid = angle + sector / 2;
+            sectorStart[kidIdx] = angle;
+            sectorEnd[kidIdx] = angle + sector;
 
-            // Cumulative radius: parent's radius + edge step (longer for special nodes)
-            const step = LONG_EDGE_NODES.has(kid)
-                ? RADIUS_PER_DEPTH * LONG_EDGE_MULTIPLIER
-                : RADIUS_PER_DEPTH;
-            const r = nodeRadius[idx] + step;
-            nodeRadius[kidIdx] = r;
+            // Only position skeleton children now
+            if (skeleton.has(kid)) {
+                const midAngle = angle + sector / 2;
+                const r = nodeRadius[parentIdx] + SKELETON_STEP;
+                nodeRadius[kidIdx] = r;
+                x[kidIdx] = r * Math.cos(midAngle);
+                y[kidIdx] = r * Math.sin(midAngle);
+                positioned.add(kid);
+                queue.push(kid); // continue BFS within skeleton
+            }
 
-            x[kidIdx] = r * Math.cos(mid);
-            y[kidIdx] = r * Math.sin(mid);
-
-            queue.push({ idx: kidIdx, d: d + 1, aStart: angle, aEnd: angle + sector });
             angle += sector;
         }
     }
 }
 
-console.log(`Radial layout done (depth=${maxDepth}, radius_step=${RADIUS_PER_DEPTH})`);
+console.log(`Phase 1: Positioned ${positioned.size} skeleton nodes`);
 
 // ══════════════════════════════════════════════════════════
-// Step 2: Gentle force refinement (preserves non-crossing)
+// Force simulation on skeleton only
 // ══════════════════════════════════════════════════════════
 
-// Barnes-Hut quadtree for repulsion
-interface BHNode {
-    cx: number; cy: number;
-    mass: number;
-    size: number;
-    children: (BHNode | null)[];
-    bodyIdx: number;
-}
+if (ENABLE_FORCE_SIM && skeleton.size > 1) {
+    const skeletonArr = Array.from(skeleton);
+    const skeletonIndices = skeletonArr.map(id => idToIdx.get(id)!);
 
-function buildBHTree(): BHNode {
-    let minX = Infinity, maxX = -Infinity, minY = Infinity, maxY = -Infinity;
-    for (let i = 0; i < N; i++) {
-        if (x[i] < minX) minX = x[i];
-        if (x[i] > maxX) maxX = x[i];
-        if (y[i] < minY) minY = y[i];
-        if (y[i] > maxY) maxY = y[i];
-    }
-    const size = Math.max(maxX - minX, maxY - minY, 1) * 1.01;
-    const cx = (minX + maxX) / 2;
-    const cy = (minY + maxY) / 2;
+    console.log(
+        `Force sim on skeleton (${skeletonArr.length} nodes, ${primaryEdges.length} edges)...`
+    );
 
-    const root: BHNode = {
-        cx: 0, cy: 0, mass: 0, size,
-        children: [null, null, null, null], bodyIdx: -1,
-    };
-
-    for (let i = 0; i < N; i++) {
-        insert(root, i, cx, cy, size);
-    }
-    return root;
-}
-
-function insert(node: BHNode, idx: number, ncx: number, ncy: number, ns: number): void {
-    if (node.mass === 0) {
-        node.bodyIdx = idx;
-        node.cx = x[idx]; node.cy = y[idx];
-        node.mass = 1;
-        return;
-    }
-    if (node.bodyIdx >= 0) {
-        const old = node.bodyIdx;
-        node.bodyIdx = -1;
-        putInQuadrant(node, old, ncx, ncy, ns);
-    }
-    putInQuadrant(node, idx, ncx, ncy, ns);
-    const tm = node.mass + 1;
-    node.cx = (node.cx * node.mass + x[idx]) / tm;
-    node.cy = (node.cy * node.mass + y[idx]) / tm;
-    node.mass = tm;
-}
-
-function putInQuadrant(node: BHNode, idx: number, ncx: number, ncy: number, ns: number): void {
-    const hs = ns / 2;
-    const qx = x[idx] >= ncx ? 1 : 0;
-    const qy = y[idx] >= ncy ? 1 : 0;
-    const q = qy * 2 + qx;
-    const ccx = ncx + (qx ? hs / 2 : -hs / 2);
-    const ccy = ncy + (qy ? hs / 2 : -hs / 2);
-    if (!node.children[q]) {
-        node.children[q] = {
-            cx: 0, cy: 0, mass: 0, size: hs,
-            children: [null, null, null, null], bodyIdx: -1,
-        };
-    }
-    insert(node.children[q]!, idx, ccx, ccy, hs);
-}
-
-function repulse(node: BHNode, idx: number, fx: Float64Array, fy: Float64Array): void {
-    if (node.mass === 0 || node.bodyIdx === idx) return;
-    const dx = x[idx] - node.cx;
-    const dy = y[idx] - node.cy;
-    const d2 = dx * dx + dy * dy;
-    const d = Math.sqrt(d2) || MIN_DIST;
-
-    if (node.bodyIdx >= 0 || (node.size / d) < THETA) {
-        const f = REPULSION_K * node.mass / (d2 + MIN_DIST);
-        fx[idx] += (dx / d) * f;
-        fy[idx] += (dy / d) * f;
-        return;
-    }
-    for (const c of node.children) {
-        if (c) repulse(c, idx, fx, fy);
-    }
-}
-
-// ── Force simulation ──
-if (ENABLE_FORCE_SIM) {
-    console.log(`Applying gentle forces (${ITERATIONS} steps, 1% strength)...`);
     const t0 = performance.now();
     let maxDisp = INITIAL_MAX_DISP;
 
@@ -280,22 +266,32 @@ if (ENABLE_FORCE_SIM) {
         const fx = new Float64Array(N);
         const fy = new Float64Array(N);
 
-        // 1. Repulsion
-        const tree = buildBHTree();
-        for (let i = 0; i < N; i++) {
-            repulse(tree, i, fx, fy);
+        // 1. Pairwise repulsion
+        for (let i = 0; i < skeletonIndices.length; i++) {
+            const u = skeletonIndices[i];
+            for (let j = i + 1; j < skeletonIndices.length; j++) {
+                const v = skeletonIndices[j];
+                const dx = x[u] - x[v];
+                const dy = y[u] - y[v];
+                const d2 = dx * dx + dy * dy;
+                const d = Math.sqrt(d2) || MIN_DIST;
+                const f = REPULSION_K / (d2 + MIN_DIST);
+                fx[u] += (dx / d) * f;
+                fy[u] += (dy / d) * f;
+                fx[v] -= (dx / d) * f;
+                fy[v] -= (dy / d) * f;
+            }
         }
 
-        // 2. Edge attraction (spring toward per-edge rest length)
-        for (const [a, b] of edges) {
+        // 2. Edge attraction
+        for (const [aId, bId] of primaryEdges) {
+            const a = idToIdx.get(aId)!;
+            const b = idToIdx.get(bId)!;
             const dx = x[b] - x[a];
             const dy = y[b] - y[a];
             const d = Math.sqrt(dx * dx + dy * dy) || MIN_DIST;
-            const aId = nodeIds[a], bId = nodeIds[b];
-            const isLong = LONG_EDGE_NODES.has(aId) || LONG_EDGE_NODES.has(bId);
-            const restLen = isLong ? EDGE_LENGTH * LONG_EDGE_MULTIPLIER : EDGE_LENGTH;
-            const displacement = d - restLen;
-            const f = ATTRACTION_K * displacement;
+            const displacement = d - SKELETON_STEP;
+            const f = (ATTRACTION_K / LONG_EDGE_MULTIPLIER) * displacement;
             const ux = dx / d, uy = dy / d;
             fx[a] += ux * f;
             fy[a] += uy * f;
@@ -303,32 +299,181 @@ if (ENABLE_FORCE_SIM) {
             fy[b] -= uy * f;
         }
 
-        // 3. Apply forces with displacement cap (cooling reduces it over time)
-        for (let i = 0; i < N; i++) {
-            const mag = Math.sqrt(fx[i] * fx[i] + fy[i] * fy[i]);
+        // 3. Apply forces (skip root)
+        for (const idx of skeletonIndices) {
+            if (nodeIds[idx] === root) continue;
+            const mag = Math.sqrt(fx[idx] * fx[idx] + fy[idx] * fy[idx]);
             if (mag > 0) {
                 const cap = Math.min(maxDisp, mag) / mag;
-                x[i] += fx[i] * cap;
-                y[i] += fy[i] * cap;
+                x[idx] += fx[idx] * cap;
+                y[idx] += fy[idx] * cap;
             }
         }
 
-        // 4. Cool down
         maxDisp *= COOLING;
 
         if ((iter + 1) % PRINT_EVERY === 0) {
             let totalForce = 0;
-            for (let i = 0; i < N; i++) totalForce += Math.sqrt(fx[i] * fx[i] + fy[i] * fy[i]);
-            console.log(`  iter ${iter + 1}/${ITERATIONS}  max_disp=${maxDisp.toFixed(2)}  avg_force=${(totalForce / N).toFixed(2)}`);
+            for (const idx of skeletonIndices) {
+                totalForce += Math.sqrt(fx[idx] * fx[idx] + fy[idx] * fy[idx]);
+            }
+            console.log(
+                `  iter ${iter + 1}/${ITERATIONS}  max_disp=${maxDisp.toFixed(2)}  avg_force=${(totalForce / skeletonIndices.length).toFixed(2)}`
+            );
         }
     }
 
     const elapsed = performance.now() - t0;
-    console.log(`Force simulation done in ${(elapsed / 1000).toFixed(1)}s`);
-} else {
-    console.log("Force simulation SKIPPED (ENABLE_FORCE_SIM = false)");
+    console.log(`Skeleton force sim done in ${(elapsed / 1000).toFixed(1)}s`);
 }
 
+// ══════════════════════════════════════════════════════════
+// Phase 2: Fill subtrees
+// ══════════════════════════════════════════════════════════
+
+{
+    const queue: number[] = Array.from(positioned);
+    let head = 0;
+    while (head < queue.length) {
+        const parentId = queue[head++];
+        const parentIdx = idToIdx.get(parentId)!;
+        const kids = childrenOf.get(parentId);
+
+        if (!kids) continue;
+
+        const unpositionedKids = kids.filter(k => !positioned.has(k));
+        if (unpositionedKids.length === 0) continue;
+
+        unpositionedKids.sort((a, b) => subtreeSize.get(b)! - subtreeSize.get(a)!);
+
+        const px = x[parentIdx];
+        const py = y[parentIdx];
+
+        // Determine available angular sector
+        // If parent is SKELETON, we reset to full 360 (local root behavior).
+        // If parent is NORMAL, we strictly use the sector allocated to it by its parent.
+        const isSkeleton = skeleton.has(parentId);
+        let currentAngle = isSkeleton ? 0 : sectorStart[parentIdx];
+        const endAngle = isSkeleton ? 2 * Math.PI : sectorEnd[parentIdx];
+        const totalSpan = endAngle - currentAngle;
+
+        const totalWeight = unpositionedKids.reduce((s, k) => s + subtreeSize.get(k)!, 0);
+
+        for (const kid of unpositionedKids) {
+            const kidIdx = idToIdx.get(kid)!;
+            const w = subtreeSize.get(kid)!;
+
+            // Allocate a portion of the available sector based on subtree weight
+            const span = (w / totalWeight) * totalSpan;
+
+            // Track the sector for this child so ITS children are constrained
+            sectorStart[kidIdx] = currentAngle;
+            sectorEnd[kidIdx] = currentAngle + span;
+
+            const midAngle = currentAngle + span / 2;
+            const r = RADIUS_PER_DEPTH;
+
+            x[kidIdx] = px + r * Math.cos(midAngle);
+            y[kidIdx] = py + r * Math.sin(midAngle);
+
+            positioned.add(kid);
+            queue.push(kid);
+
+            currentAngle += span;
+        }
+    }
+}
+
+console.log(`Phase 2: Positioned ${positioned.size} total nodes (of ${N})`);
+
+// ══════════════════════════════════════════════════════════
+// Phase 3: Final Relaxation (Force Sim on ALL nodes)
+// ══════════════════════════════════════════════════════════
+{
+    console.log(`Phase 3: Final relaxation on ${N} nodes...`);
+    const FINAL_ITERATIONS = 50;
+    const FINAL_MAX_DISP = 5.0;
+    const BH_THETA = 0.5;
+
+    // We use slightly weaker forces for final polish
+    // Keep repulsion same but limit displacement strongly
+    // Use Barnes-Hut for performance with 10k nodes
+
+    for (let iter = 0; iter < FINAL_ITERATIONS; iter++) {
+        const rootBH = buildBHTree(nodeIds, x, y);
+        const fx = new Float64Array(N);
+        const fy = new Float64Array(N);
+
+        // 1. Repulsion via Barnes-Hut
+        for (let i = 0; i < N; i++) {
+            calcBHForce(rootBH, x[i], y[i], fx, fy, i, BH_THETA);
+        }
+
+        // 2. Attraction edges
+        // Only attract if displacement > rest length?
+        // Standard spring: f = k * (d - L)
+        // L = EDGE_LENGTH for normal, SKELETON_STEP for skeleton?
+        // We can just use standard EDGE_LENGTH as "rest" for everyone to pull tight?
+        // Or respect hierarchy?
+        // With 10k nodes, we just want to relax overlaps.
+
+        for (const [uId, vId] of allEdges) {
+            const u = idToIdx.get(uId)!;
+            const v = idToIdx.get(vId)!;
+            const dx = x[v] - x[u];
+            const dy = y[v] - y[u];
+            const d = Math.sqrt(dx * dx + dy * dy) || MIN_DIST;
+
+            // Identifying if edge is skeletal?
+            // If u and v both skeleton, use longer length.
+            // Else normal length.
+            let restLen = EDGE_LENGTH;
+            let k = ATTRACTION_K;
+
+            if (primaryNodes.has(uId) && primaryNodes.has(vId)) {
+                restLen = SKELETON_STEP;
+                k = ATTRACTION_K / LONG_EDGE_MULTIPLIER;
+            }
+
+            const displacement = d - restLen;
+            const f = k * displacement;
+            const ux = dx / d, uy = dy / d;
+
+            fx[u] += ux * f;
+            fy[u] += uy * f;
+            fx[v] -= ux * f;
+            fy[v] -= uy * f;
+        }
+
+        // 3. Apply forces
+        let totalDisp = 0;
+        let maxD = 0;
+        const currentLimit = FINAL_MAX_DISP * (1 - iter / FINAL_ITERATIONS); // Cool down
+
+        for (let i = 0; i < N; i++) {
+            if (nodeIds[i] === root) continue; // Pin root
+
+            const dx = fx[i];
+            const dy = fy[i];
+            const dist = Math.sqrt(dx * dx + dy * dy);
+
+            if (dist > 0) {
+                const limit = Math.min(currentLimit, dist);
+                const scale = limit / dist;
+                x[i] += dx * scale;
+                y[i] += dy * scale;
+                totalDisp += limit;
+                maxD = Math.max(maxD, limit);
+            }
+        }
+
+        if (iter % 10 === 0) {
+            console.log(`  Phase 3 iter ${iter}: max movement ${maxD.toFixed(3)}`);
+        }
+    }
+}
+
+
 // ══════════════════════════════════════════════════════════
 // Write output
 // ══════════════════════════════════════════════════════════
@@ -343,12 +488,152 @@ const outPath = join(PUBLIC_DIR, "node_positions.csv");
 writeFileSync(outPath, outLines.join("\n") + "\n");
 console.log(`Wrote ${N} positions to ${outPath}`);
 
-// Write edges (so the renderer can draw them)
-const edgeLines: string[] = ["source,target"];
-for (const [child, parent] of parentOf) {
-    edgeLines.push(`${child},${parent}`);
+// Edges are provided via primary_edges.csv and secondary_edges.csv generated by generate_tree.ts
+// We do not write a consolidated edges.csv anymore.
+console.log(`Layout complete.`);
+
+// ══════════════════════════════════════════════════════════
+// Barnes-Hut Helpers
+// ══════════════════════════════════════════════════════════
+
+interface BHNode {
+    mass: number;
+    x: number;
+    y: number;
+    minX: number;
+    maxX: number;
+    minY: number;
+    maxY: number;
+    children?: BHNode[]; // NW, NE, SW, SE
+    pointIdx?: number;   // Leaf node index
 }
 
-const edgesPath = join(PUBLIC_DIR, "edges.csv");
-writeFileSync(edgesPath, edgeLines.join("\n") + "\n");
-console.log(`Wrote ${edges.length} edges to ${edgesPath}`);
+function buildBHTree(indices: number[], x: Float64Array, y: Float64Array): BHNode {
+    // Determine bounds
+    let minX = Infinity, maxX = -Infinity, minY = Infinity, maxY = -Infinity;
+    for (let i = 0; i < x.length; i++) {
+        if (x[i] < minX) minX = x[i];
+        if (x[i] > maxX) maxX = x[i];
+        if (y[i] < minY) minY = y[i];
+        if (y[i] > maxY) maxY = y[i];
+    }
+    // Square bounds for quadtree
+    const cx = (minX + maxX) / 2;
+    const cy = (minY + maxY) / 2;
+    const halfDim = Math.max(maxX - minX, maxY - minY) / 2 + 0.01;
+
+    const root: BHNode = {
+        mass: 0, x: 0, y: 0,
+        minX: cx - halfDim, maxX: cx + halfDim,
+        minY: cy - halfDim, maxY: cy + halfDim
+    };
+
+    for (let i = 0; i < x.length; i++) {
+        insertBH(root, i, x[i], y[i]);
+    }
+    calcBHMass(root);
+    return root;
+}
+
+function insertBH(node: BHNode, idx: number, px: number, py: number) {
+    if (!node.children && node.pointIdx === undefined) {
+        // Empty leaf -> Put point here
+        node.pointIdx = idx;
+        return;
+    }
+
+    if (!node.children && node.pointIdx !== undefined) {
+        // Occupied leaf -> Subdivide
+        const oldIdx = node.pointIdx;
+        node.pointIdx = undefined;
+        subdivideBH(node);
+        // Re-insert old point and new point
+        // Note: oldIdx needs x,y. But we don't pass array. Wait, BHTree function scope?
+        // We need explicit x,y access. But passing array everywhere is ugly.
+        // Hack: The recursive function needs access to global x/y or passed in values.
+        // But here we are inserting one by one.
+        // Wait, to re-insert oldIdx, WE NEED ITS COORDS.
+        // This simple 'insertBH' signature is insufficient unless we capture x/y closure or pass them.
+        // Let's assume x, y are available globally or we redesign.
+        // Since this script is top-level, x and y are available in scope!
+        // But `insertBH` is defined outside main scope if hoisted? No, it's inside module.
+        // If defined as function `function insertBH`, it captures module scope `x`, `y`?
+        // `x` and `y` are const Float64Array defined at line ~120.
+        // So yes, they are captured!
+        insertBH(node, oldIdx, x[oldIdx], y[oldIdx]);
+        // Then fall through to insert new point
+    }
+
+    if (node.children) {
+        const mx = (node.minX + node.maxX) / 2;
+        const my = (node.minY + node.maxY) / 2;
+        let q = 0;
+        if (px > mx) q += 1; // East
+        if (py > my) q += 2; // South
+        insertBH(node.children[q], idx, px, py);
+    }
+}
+
+function subdivideBH(node: BHNode) {
+    const mx = (node.minX + node.maxX) / 2;
+    const my = (node.minY + node.maxY) / 2;
+    node.children = [
+        { mass: 0, x: 0, y: 0, minX: node.minX, maxX: mx, minY: node.minY, maxY: my }, // NW
+        { mass: 0, x: 0, y: 0, minX: mx, maxX: node.maxX, minY: node.minY, maxY: my }, // NE
+        { mass: 0, x: 0, y: 0, minX: node.minX, maxX: mx, minY: my, maxY: node.maxY }, // SW
+        { mass: 0, x: 0, y: 0, minX: mx, maxX: node.maxX, minY: my, maxY: node.maxY }  // SE
+    ];
+}
+
+function calcBHMass(node: BHNode) {
+    if (node.pointIdx !== undefined) {
+        node.mass = 1;
+        node.x = x[node.pointIdx];
+        node.y = y[node.pointIdx];
+        return;
+    }
+    if (node.children) {
+        let m = 0, cx = 0, cy = 0;
+        for (const c of node.children) {
+            calcBHMass(c);
+            m += c.mass;
+            cx += c.x * c.mass;
+            cy += c.y * c.mass;
+        }
+        node.mass = m;
+        if (m > 0) {
+            node.x = cx / m;
+            node.y = cy / m;
+        } else {
+            // Center of box if empty
+            node.x = (node.minX + node.maxX) / 2;
+            node.y = (node.minY + node.maxY) / 2;
+        }
+    }
+}
+
+function calcBHForce(node: BHNode, px: number, py: number, fx: Float64Array, fy: Float64Array, idx: number, theta: number) {
+    const dx = px - node.x;
+    const dy = py - node.y;
+    const d2 = dx * dx + dy * dy;
+    const dist = Math.sqrt(d2);
+    const width = node.maxX - node.minX;
+
+    if (width / dist < theta || !node.children) {
+        // Treat as single body
+        if (node.mass > 0 && (node.pointIdx !== idx)) {
+            // Apply repulsion
+            // F = K * mass / dist^2
+            // Direction: from node to p
+            const dEff = Math.max(dist, MIN_DIST);
+            const f = (REPULSION_K * node.mass) / (dEff * dEff); // d^2 repulsion
+            fx[idx] += (dx / dEff) * f;
+            fy[idx] += (dy / dEff) * f;
+        }
+    } else {
+        // Recurse
+        for (const c of node.children) {
+            calcBHForce(c, px, py, fx, fy, idx, theta);
+        }
+    }
+}

scripts/generate_tree.ts

@@ -2,15 +2,25 @@
  * Random Tree Generator
  *
  * Generates a random tree with 1–MAX_CHILDREN children per node.
- * Exports a function that returns the tree data in memory.
+ * Splits edges into primary (depth ≤ PRIMARY_DEPTH) and secondary.
+ *
+ * Usage: npx tsx scripts/generate_tree.ts
  */
 
+import { writeFileSync } from "fs";
+import { join, dirname } from "path";
+import { fileURLToPath } from "url";
+
+const __dirname = dirname(fileURLToPath(import.meta.url));
+const PUBLIC_DIR = join(__dirname, "..", "public");
+
 // ══════════════════════════════════════════════════════════
 // Configuration
 // ══════════════════════════════════════════════════════════
 
-const TARGET_NODES = 100000;      // Approximate number of nodes to generate
-const MAX_CHILDREN = 3;        // Each node gets 1..MAX_CHILDREN children
+const TARGET_NODES = 10000;     // Approximate number of nodes to generate
+const MAX_CHILDREN = 4;        // Each node gets 1..MAX_CHILDREN children
+const PRIMARY_DEPTH = 3;       // Nodes at depth ≤ this form the primary skeleton
 
 // ══════════════════════════════════════════════════════════
 // Tree data types
@@ -21,6 +31,10 @@ export interface TreeData {
     nodeCount: number;
     childrenOf: Map<number, number[]>;
     parentOf: Map<number, number>;
+    depthOf: Map<number, number>;
+    primaryNodes: Set<number>;              // all nodes at depth ≤ PRIMARY_DEPTH
+    primaryEdges: Array<[number, number]>;  // [child, parent] edges within primary
+    secondaryEdges: Array<[number, number]>;// remaining edges
 }
 
 // ══════════════════════════════════════════════════════════
@@ -30,14 +44,17 @@ export interface TreeData {
 export function generateTree(): TreeData {
     const childrenOf = new Map<number, number[]>();
     const parentOf = new Map<number, number>();
+    const depthOf = new Map<number, number>();
 
     const root = 0;
+    depthOf.set(root, 0);
     let nextId = 1;
     const queue: number[] = [root];
     let head = 0;
 
     while (head < queue.length && nextId < TARGET_NODES) {
         const parent = queue[head++];
+        const parentDepth = depthOf.get(parent)!;
         const nKids = 1 + Math.floor(Math.random() * MAX_CHILDREN); // 1..MAX_CHILDREN
 
         const kids: number[] = [];
@@ -45,17 +62,71 @@ export function generateTree(): TreeData {
             const child = nextId++;
             kids.push(child);
             parentOf.set(child, parent);
+            depthOf.set(child, parentDepth + 1);
             queue.push(child);
         }
         childrenOf.set(parent, kids);
     }
 
-    console.log(`Generated tree: ${nextId} nodes, ${parentOf.size} edges, root=${root}`);
+    // Classify edges and nodes by depth
+    const primaryNodes = new Set<number>();
+    const primaryEdges: Array<[number, number]> = [];
+    const secondaryEdges: Array<[number, number]> = [];
+
+    // Root is always primary
+    primaryNodes.add(root);
+
+    for (const [child, parent] of parentOf) {
+        const childDepth = depthOf.get(child)!;
+        if (childDepth <= PRIMARY_DEPTH) {
+            primaryNodes.add(child);
+            primaryNodes.add(parent);
+            primaryEdges.push([child, parent]);
+        } else {
+            secondaryEdges.push([child, parent]);
+        }
+    }
+
+    console.log(
+        `Generated tree: ${nextId} nodes, ` +
+        `${primaryEdges.length} primary edges (depth ≤ ${PRIMARY_DEPTH}), ` +
+        `${secondaryEdges.length} secondary edges`
+    );
 
     return {
         root,
         nodeCount: nextId,
         childrenOf,
         parentOf,
+        depthOf,
+        primaryNodes,
+        primaryEdges,
+        secondaryEdges,
     };
 }
+
+// ══════════════════════════════════════════════════════════
+// Run if executed directly
+// ══════════════════════════════════════════════════════════
+
+if (import.meta.url === `file://${process.argv[1]}`) {
+    const data = generateTree();
+
+    // Write primary_edges.csv
+    const pLines: string[] = ["source,target"];
+    for (const [child, parent] of data.primaryEdges) {
+        pLines.push(`${child},${parent}`);
+    }
+    const pPath = join(PUBLIC_DIR, "primary_edges.csv");
+    writeFileSync(pPath, pLines.join("\n") + "\n");
+    console.log(`Wrote ${data.primaryEdges.length} edges to ${pPath}`);
+
+    // Write secondary_edges.csv
+    const sLines: string[] = ["source,target"];
+    for (const [child, parent] of data.secondaryEdges) {
+        sLines.push(`${child},${parent}`);
+    }
+    const sPath = join(PUBLIC_DIR, "secondary_edges.csv");
+    writeFileSync(sPath, sLines.join("\n") + "\n");
+    console.log(`Wrote ${data.secondaryEdges.length} edges to ${sPath}`);
+}

src/App.tsx

@@ -39,16 +39,19 @@ export default function App() {
     (async () => {
       try {
         setStatus("Fetching data files…");
-        const [nodesResponse, edgesResponse] = await Promise.all([
+        const [nodesResponse, primaryEdgesResponse, secondaryEdgesResponse] = await Promise.all([
           fetch("/node_positions.csv"),
-          fetch("/edges.csv"),
+          fetch("/primary_edges.csv"),
+          fetch("/secondary_edges.csv"),
         ]);
         if (!nodesResponse.ok) throw new Error(`Failed to fetch nodes: ${nodesResponse.status}`);
-        if (!edgesResponse.ok) throw new Error(`Failed to fetch edges: ${edgesResponse.status}`);
+        if (!primaryEdgesResponse.ok) throw new Error(`Failed to fetch primary edges: ${primaryEdgesResponse.status}`);
+        if (!secondaryEdgesResponse.ok) throw new Error(`Failed to fetch secondary edges: ${secondaryEdgesResponse.status}`);
 
-        const [nodesText, edgesText] = await Promise.all([
+        const [nodesText, primaryEdgesText, secondaryEdgesText] = await Promise.all([
           nodesResponse.text(),
-          edgesResponse.text(),
+          primaryEdgesResponse.text(),
+          secondaryEdgesResponse.text(),
         ]);
         if (cancelled) return;
 
@@ -67,12 +70,24 @@ export default function App() {
         }
 
         setStatus("Parsing edges…");
-        const edgeLines = edgesText.split("\n").slice(1).filter(l => l.trim().length > 0);
-        const edgeData = new Uint32Array(edgeLines.length * 2);
-        for (let i = 0; i < edgeLines.length; i++) {
-          const parts = edgeLines[i].split(",");
-          edgeData[i * 2] = parseInt(parts[0], 10);
-          edgeData[i * 2 + 1] = parseInt(parts[1], 10);
+        const pLines = primaryEdgesText.split("\n").slice(1).filter(l => l.trim().length > 0);
+        const sLines = secondaryEdgesText.split("\n").slice(1).filter(l => l.trim().length > 0);
+
+        const totalEdges = pLines.length + sLines.length;
+        const edgeData = new Uint32Array(totalEdges * 2);
+
+        let idx = 0;
+        // Parse primary
+        for (let i = 0; i < pLines.length; i++) {
+          const parts = pLines[i].split(",");
+          edgeData[idx++] = parseInt(parts[0], 10);
+          edgeData[idx++] = parseInt(parts[1], 10);
+        }
+        // Parse secondary
+        for (let i = 0; i < sLines.length; i++) {
+          const parts = sLines[i].split(",");
+          edgeData[idx++] = parseInt(parts[0], 10);
+          edgeData[idx++] = parseInt(parts[1], 10);
         }
 
         if (cancelled) return;
@@ -83,7 +98,7 @@ export default function App() {
         const buildMs = renderer.init(xs, ys, vertexIds, edgeData);
         setNodeCount(renderer.getNodeCount());
         setStatus("");
-        console.log(`Init complete: ${count.toLocaleString()} nodes, ${edgeLines.length.toLocaleString()} edges in ${buildMs.toFixed(0)}ms`);
+        console.log(`Init complete: ${count.toLocaleString()} nodes, ${totalEdges.toLocaleString()} edges in ${buildMs.toFixed(0)}ms`);
       } catch (e) {
         if (!cancelled) {
           setError(e instanceof Error ? e.message : String(e));