@graphty/layout 1.2.4 → 1.2.6

package/dist/src/algorithms/optimization/kamada-kawai-solver.d.ts

@@ -1,32 +0,0 @@
-/**
- * Kamada-Kawai layout algorithm optimization functions
- */
-import { Graph } from '../../types';
-import { DistanceMap } from './types';
-/**
- * Compute all-pairs shortest path distances for the graph
- *
- * @param G - NetworkX graph
- * @param weight - Edge attribute for weight
- * @returns Dictionary of dictionaries of shortest path distances
- */
-export declare function _computeShortestPathDistances(G: Graph, weight: string): DistanceMap;
-/**
- * Solve the Kamada-Kawai layout optimization problem
- *
- * @param distMatrix - Matrix of desired distances between nodes
- * @param positions - Initial node positions
- * @param dim - Dimension of layout
- * @returns Optimized node positions
- */
-export declare function _kamadaKawaiSolve(distMatrix: number[][], positions: number[][], dim: number): number[][];
-/**
- * Cost function and gradient for Kamada-Kawai layout algorithm
- *
- * @param posVec - Flattened position array
- * @param invDist - Inverse distance matrix
- * @param meanWeight - Weight for centering positions
- * @param dim - Dimension of layout
- * @returns Array with [cost, gradient]
- */
-export declare function _kamadaKawaiCostfn(posVec: number[], invDist: number[][], meanWeight: number, dim: number): [number, number[]];

package/dist/src/algorithms/optimization/kamada-kawai-solver.js

@@ -1,176 +0,0 @@
-/**
- * Kamada-Kawai layout algorithm optimization functions
- */
-import { _lbfgsDirection } from './lbfgs';
-import { _backtrackingLineSearch } from './line-search';
-import { getNodesFromGraph, getEdgesFromGraph } from '../../utils/graph';
-/**
- * Compute all-pairs shortest path distances for the graph
- *
- * @param G - NetworkX graph
- * @param weight - Edge attribute for weight
- * @returns Dictionary of dictionaries of shortest path distances
- */
-export function _computeShortestPathDistances(G, weight) {
-    const distances = {};
-    const nodes = getNodesFromGraph(G);
-    const edges = getEdgesFromGraph(G);
-    // Initialize distances with direct edges
-    for (const node of nodes) {
-        distances[node] = {};
-        distances[node][node] = 0;
-        for (const other of nodes) {
-            if (node !== other) {
-                distances[node][other] = Infinity;
-            }
-        }
-    }
-    // Add direct edges
-    for (const [source, target] of edges) {
-        // In a real implementation, we would get the weight from the graph
-        // For now, assume weight = 1 or use weight attribute if available
-        let edgeWeight = 1;
-        if (G.getEdgeData) {
-            edgeWeight = G.getEdgeData(source, target, weight) || 1;
-        }
-        distances[source][target] = edgeWeight;
-        distances[target][source] = edgeWeight; // Assuming undirected graph
-    }
-    // Floyd-Warshall algorithm for all-pairs shortest paths
-    for (const k of nodes) {
-        for (const i of nodes) {
-            for (const j of nodes) {
-                if (distances[i][k] + distances[k][j] < distances[i][j]) {
-                    distances[i][j] = distances[i][k] + distances[k][j];
-                }
-            }
-        }
-    }
-    return distances;
-}
-/**
- * Solve the Kamada-Kawai layout optimization problem
- *
- * @param distMatrix - Matrix of desired distances between nodes
- * @param positions - Initial node positions
- * @param dim - Dimension of layout
- * @returns Optimized node positions
- */
-export function _kamadaKawaiSolve(distMatrix, positions, dim) {
-    // Implementation of L-BFGS optimization for Kamada-Kawai
-    const nNodes = positions.length;
-    const meanWeight = 1e-3;
-    // Convert distances to inverse distances (with protection against division by zero)
-    const invDistMatrix = distMatrix.map(row => row.map(d => d === 0 ? 0 : 1 / (d + 1e-3)));
-    // Flatten positions for optimization
-    let posVec = positions.flat();
-    // Optimization parameters
-    const maxIter = 500;
-    const gtol = 1e-5;
-    const m = 10; // L-BFGS memory size
-    // Implement a simplified L-BFGS-B algorithm
-    let alpha = 1.0;
-    const oldValues = [];
-    const oldGrads = [];
-    for (let iter = 0; iter < maxIter; iter++) {
-        // Calculate cost and gradient
-        const [cost, grad] = _kamadaKawaiCostfn(posVec, invDistMatrix, meanWeight, dim);
-        // Compute search direction using L-BFGS approximation
-        const direction = _lbfgsDirection(grad, oldValues, oldGrads, m);
-        // Simple line search for step size
-        alpha = _backtrackingLineSearch(posVec, direction, cost, grad, (x) => _kamadaKawaiCostfn(x, invDistMatrix, meanWeight, dim)[0], alpha);
-        // Save current position and gradient for next iteration
-        const oldPos = [...posVec];
-        // Update position
-        for (let i = 0; i < posVec.length; i++) {
-            posVec[i] += alpha * direction[i];
-        }
-        // Calculate new gradient
-        const [, newGrad] = _kamadaKawaiCostfn(posVec, invDistMatrix, meanWeight, dim);
-        // Update L-BFGS memory
-        oldValues.push(posVec.map((val, i) => val - oldPos[i]));
-        oldGrads.push(newGrad.map((val, i) => val - grad[i]));
-        // Keep only m most recent updates
-        if (oldValues.length > m) {
-            oldValues.shift();
-            oldGrads.shift();
-        }
-        // Check convergence
-        const gradNorm = Math.sqrt(newGrad.reduce((sum, g) => sum + g * g, 0));
-        if (gradNorm < gtol) {
-            break;
-        }
-    }
-    // Reshape result back into positions array
-    const result = [];
-    for (let i = 0; i < nNodes; i++) {
-        result.push(posVec.slice(i * dim, (i + 1) * dim));
-    }
-    return result;
-}
-/**
- * Cost function and gradient for Kamada-Kawai layout algorithm
- *
- * @param posVec - Flattened position array
- * @param invDist - Inverse distance matrix
- * @param meanWeight - Weight for centering positions
- * @param dim - Dimension of layout
- * @returns Array with [cost, gradient]
- */
-export function _kamadaKawaiCostfn(posVec, invDist, meanWeight, dim) {
-    const nNodes = invDist.length;
-    const positions = [];
-    // Reshape flat vector into positions array
-    for (let i = 0; i < nNodes; i++) {
-        positions.push(posVec.slice(i * dim, (i + 1) * dim));
-    }
-    // Calculate cost
-    let cost = 0;
-    // Add mean position penalty term
-    const sumPos = Array(dim).fill(0);
-    for (let i = 0; i < nNodes; i++) {
-        for (let d = 0; d < dim; d++) {
-            sumPos[d] += positions[i][d];
-        }
-    }
-    cost += 0.5 * meanWeight * sumPos.reduce((sum, val) => sum + val * val, 0);
-    // Add distance penalty terms
-    for (let i = 0; i < nNodes; i++) {
-        for (let j = i + 1; j < nNodes; j++) {
-            // Calculate actual distance
-            const diff = positions[i].map((val, d) => val - positions[j][d]);
-            const distance = Math.sqrt(diff.reduce((sum, d) => sum + d * d, 0));
-            // Add penalty for difference between actual and ideal distance
-            const idealInvDist = invDist[i][j];
-            const offset = distance * idealInvDist - 1.0;
-            cost += 0.5 * offset * offset;
-        }
-    }
-    // Calculate gradient
-    const grad = new Array(posVec.length).fill(0);
-    // Add gradient of mean position penalty
-    for (let i = 0; i < nNodes; i++) {
-        for (let d = 0; d < dim; d++) {
-            grad[i * dim + d] += meanWeight * sumPos[d];
-        }
-    }
-    // Add gradient of distance penalties
-    for (let i = 0; i < nNodes; i++) {
-        for (let j = i + 1; j < nNodes; j++) {
-            // Calculate actual distance and direction
-            const diff = positions[i].map((val, d) => val - positions[j][d]);
-            const distance = Math.sqrt(diff.reduce((sum, d) => sum + d * d, 0)) || 1e-10;
-            const direction = diff.map(d => d / distance);
-            // Calculate contribution to gradient
-            const idealInvDist = invDist[i][j];
-            const offset = distance * idealInvDist - 1.0;
-            for (let d = 0; d < dim; d++) {
-                const force = idealInvDist * offset * direction[d];
-                grad[i * dim + d] += force;
-                grad[j * dim + d] -= force;
-            }
-        }
-    }
-    return [cost, grad];
-}
-//# sourceMappingURL=kamada-kawai-solver.js.map

package/dist/src/algorithms/optimization/kamada-kawai-solver.js.map

@@ -1 +0,0 @@
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package/dist/src/algorithms/optimization/lbfgs.d.ts

@@ -1,13 +0,0 @@
-/**
- * L-BFGS optimization utilities
- */
-/**
- * Compute the search direction using L-BFGS approximation
- *
- * @param grad - Current gradient
- * @param sList - List of position differences (s_k)
- * @param yList - List of gradient differences (y_k)
- * @param m - Memory size
- * @returns Direction vector
- */
-export declare function _lbfgsDirection(grad: number[], sList: number[][], yList: number[][], m: number): number[];

package/dist/src/algorithms/optimization/lbfgs.js

@@ -1,56 +0,0 @@
-/**
- * L-BFGS optimization utilities
- */
-/**
- * Compute the search direction using L-BFGS approximation
- *
- * @param grad - Current gradient
- * @param sList - List of position differences (s_k)
- * @param yList - List of gradient differences (y_k)
- * @param m - Memory size
- * @returns Direction vector
- */
-export function _lbfgsDirection(grad, sList, yList, m) {
-    if (sList.length === 0) {
-        // First iteration - use negative gradient
-        return grad.map(g => -g);
-    }
-    const q = grad.slice();
-    const alpha = Array(sList.length).fill(0);
-    const rho = [];
-    // Compute rho values
-    for (let i = 0; i < sList.length; i++) {
-        const s = sList[i];
-        const y = yList[i];
-        rho.push(1 / y.reduce((sum, val, j) => sum + val * s[j], 0));
-    }
-    // Forward pass
-    for (let i = sList.length - 1; i >= 0; i--) {
-        const s = sList[i];
-        alpha[i] = rho[i] * s.reduce((sum, val, j) => sum + val * q[j], 0);
-        for (let j = 0; j < q.length; j++) {
-            q[j] -= alpha[i] * yList[i][j];
-        }
-    }
-    // Scale initial Hessian approximation
-    let gamma = 1;
-    if (sList.length > 0 && yList.length > 0) {
-        const y = yList[yList.length - 1];
-        const s = sList[sList.length - 1];
-        gamma = s.reduce((sum, val, i) => sum + val * y[i], 0) /
-            y.reduce((sum, val) => sum + val * val, 0);
-    }
-    // Initialize direction with scaled negative gradient
-    const direction = q.map(val => -gamma * val);
-    // Backward pass
-    for (let i = 0; i < sList.length; i++) {
-        const s = sList[i];
-        const y = yList[i];
-        const beta = rho[i] * y.reduce((sum, val, j) => sum + val * direction[j], 0);
-        for (let j = 0; j < direction.length; j++) {
-            direction[j] += s[j] * (alpha[i] - beta);
-        }
-    }
-    return direction;
-}
-//# sourceMappingURL=lbfgs.js.map

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package/dist/src/algorithms/optimization/line-search.d.ts

@@ -1,15 +0,0 @@
-/**
- * Line search optimization utilities
- */
-/**
- * Backtracking line search to find step size
- *
- * @param x - Current position
- * @param direction - Search direction
- * @param f - Function value at current position
- * @param grad - Gradient at current position
- * @param func - Function to evaluate cost
- * @param alpha0 - Initial step size
- * @returns Optimal step size
- */
-export declare function _backtrackingLineSearch(x: number[], direction: number[], f: number, grad: number[], func: (x: number[]) => number, alpha0: number): number;

package/dist/src/algorithms/optimization/line-search.js

@@ -1,37 +0,0 @@
-/**
- * Line search optimization utilities
- */
-/**
- * Backtracking line search to find step size
- *
- * @param x - Current position
- * @param direction - Search direction
- * @param f - Function value at current position
- * @param grad - Gradient at current position
- * @param func - Function to evaluate cost
- * @param alpha0 - Initial step size
- * @returns Optimal step size
- */
-export function _backtrackingLineSearch(x, direction, f, grad, func, alpha0) {
-    const c1 = 1e-4;
-    const c2 = 0.9;
-    const initialSlope = grad.reduce((sum, g, i) => sum + g * direction[i], 0);
-    if (initialSlope >= 0) {
-        return 1e-8; // Direction is not a descent direction
-    }
-    let alpha = alpha0;
-    const maxIter = 20;
-    for (let i = 0; i < maxIter; i++) {
-        // Try step
-        const newX = x.map((val, i) => val + alpha * direction[i]);
-        const newF = func(newX);
-        // Check sufficient decrease condition (Armijo condition)
-        if (newF <= f + c1 * alpha * initialSlope) {
-            return alpha;
-        }
-        // Reduce step size
-        alpha *= c2;
-    }
-    return alpha; // Return last alpha even if not optimal
-}
-//# sourceMappingURL=line-search.js.map

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package/dist/src/algorithms/optimization/types.d.ts

@@ -1,5 +0,0 @@
-/**
- * Type definitions for optimization algorithms
- */
-import { Node } from '../../types';
-export type DistanceMap = Record<Node, Record<Node, number>>;

package/dist/src/algorithms/optimization/types.js

@@ -1,5 +0,0 @@
-/**
- * Type definitions for optimization algorithms
- */
-export {};
-//# sourceMappingURL=types.js.map

package/dist/src/algorithms/optimization/types.js.map

@@ -1 +0,0 @@
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package/dist/src/algorithms/planarity/check.d.ts

@@ -1,17 +0,0 @@
-/**
- * Main planarity checking function
- */
-import { Graph, Node, Edge, Embedding } from '../../types';
-/**
- * Check if graph is planar using a simplified version of Boyer-Myrvold algorithm.
- * Returns planarity and embedding information.
- *
- * @param G - Graph
- * @param nodes - List of nodes
- * @param edges - List of edges
- * @returns Object containing isPlanar flag and embedding
- */
-export declare function checkPlanarity(G: Graph, nodes: Node[], edges: Edge[]): {
-    isPlanar: boolean;
-    embedding: Embedding | null;
-};

package/dist/src/algorithms/planarity/check.js

@@ -1,30 +0,0 @@
-/**
- * Main planarity checking function
- */
-import { isK5, isK33 } from './special-graphs';
-import { lrPlanarityTest } from './lr-test';
-import { createTriangulationEmbedding } from './embedding';
-/**
- * Check if graph is planar using a simplified version of Boyer-Myrvold algorithm.
- * Returns planarity and embedding information.
- *
- * @param G - Graph
- * @param nodes - List of nodes
- * @param edges - List of edges
- * @returns Object containing isPlanar flag and embedding
- */
-export function checkPlanarity(G, nodes, edges) {
-    // For small graphs (n <= 4), all are planar
-    if (nodes.length <= 4) {
-        return { isPlanar: true, embedding: createTriangulationEmbedding(nodes, edges) };
-    }
-    // For K5 (complete graph with 5 nodes) and K3,3 (complete bipartite with 3,3 nodes)
-    // these are not planar by Kuratowski's theorem
-    if (isK5(nodes, edges) || isK33(nodes, edges)) {
-        return { isPlanar: false, embedding: null };
-    }
-    // For other graphs, use LR algorithm (Left-Right Planarity Test)
-    const result = lrPlanarityTest(nodes, edges);
-    return result;
-}
-//# sourceMappingURL=check.js.map

package/dist/src/algorithms/planarity/check.js.map

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package/dist/src/algorithms/planarity/embedding.d.ts

@@ -1,29 +0,0 @@
-/**
- * Embedding functions for planar graphs
- */
-import { Node, Edge, Embedding, PositionMap } from '../../types';
-/**
- * Create a triangulation-based embedding for a planar graph
- *
- * @param nodes - List of nodes
- * @param edges - List of edges
- * @returns Embedding object
- */
-export declare function createTriangulationEmbedding(nodes: Node[], edges: Edge[]): Embedding;
-/**
- * Find a simple cycle in the graph (for outer face)
- *
- * @param nodes - List of nodes
- * @param edges - List of edges
- * @param adjMap - Adjacency map
- * @returns Cycle as array of nodes, or null if none found
- */
-export declare function findCycle(nodes: Node[], edges: Edge[], adjMap: Record<Node, Set<Node>>): Node[] | null;
-/**
- * Convert a combinatorial embedding to node positions
- *
- * @param embedding - The embedding object
- * @param nodes - List of nodes
- * @returns Dictionary mapping nodes to positions
- */
-export declare function combinatorialEmbeddingToPos(embedding: Embedding, nodes: Node[]): PositionMap;

package/dist/src/algorithms/planarity/embedding.js

@@ -1,179 +0,0 @@
-/**
- * Embedding functions for planar graphs
- */
-/**
- * Create a triangulation-based embedding for a planar graph
- *
- * @param nodes - List of nodes
- * @param edges - List of edges
- * @returns Embedding object
- */
-export function createTriangulationEmbedding(nodes, edges) {
-    // Create a simple embedding using the incremental approach
-    const embedding = {
-        nodeOrder: [...nodes],
-        faceList: [],
-        nodePositions: {}
-    };
-    // Create a map of adjacent nodes
-    const adjMap = {};
-    for (const node of nodes) {
-        adjMap[node] = new Set();
-    }
-    for (const [u, v] of edges) {
-        adjMap[u].add(v);
-        adjMap[v].add(u);
-    }
-    // Create outer face as a cycle (if possible)
-    const outerFace = findCycle(nodes, edges, adjMap) || nodes;
-    embedding.faceList.push(outerFace);
-    // Position nodes on a convex polygon (outer face)
-    const n = outerFace.length;
-    for (let i = 0; i < n; i++) {
-        const angle = 2 * Math.PI * i / n;
-        embedding.nodePositions[outerFace[i]] = [Math.cos(angle), Math.sin(angle)];
-    }
-    // Position interior nodes using barycentric coordinates
-    const interiorNodes = nodes.filter(node => !embedding.nodePositions[node]);
-    for (const node of interiorNodes) {
-        const neighbors = Array.from(adjMap[node]);
-        if (neighbors.length === 0) {
-            // Isolated node, place at center
-            embedding.nodePositions[node] = [0, 0];
-        }
-        else {
-            // Average position of neighbors that have positions
-            let xSum = 0, ySum = 0, count = 0;
-            for (const neighbor of neighbors) {
-                if (embedding.nodePositions[neighbor]) {
-                    xSum += embedding.nodePositions[neighbor][0];
-                    ySum += embedding.nodePositions[neighbor][1];
-                    count++;
-                }
-            }
-            if (count > 0) {
-                // Place slightly away from center to avoid overlaps
-                const jitter = 0.1 * Math.random();
-                embedding.nodePositions[node] = [
-                    xSum / count + jitter * (Math.random() - 0.5),
-                    ySum / count + jitter * (Math.random() - 0.5)
-                ];
-            }
-            else {
-                // No neighbors have positions yet, place randomly inside unit circle
-                const r = 0.5 * Math.random();
-                const angle = 2 * Math.PI * Math.random();
-                embedding.nodePositions[node] = [r * Math.cos(angle), r * Math.sin(angle)];
-            }
-        }
-    }
-    return embedding;
-}
-/**
- * Find a simple cycle in the graph (for outer face)
- *
- * @param nodes - List of nodes
- * @param edges - List of edges
- * @param adjMap - Adjacency map
- * @returns Cycle as array of nodes, or null if none found
- */
-export function findCycle(nodes, edges, adjMap) {
-    if (nodes.length === 0)
-        return null;
-    if (nodes.length <= 2)
-        return nodes; // Not a real cycle but handle it
-    // Try to find a Hamiltonian cycle for simplicity (for small graphs)
-    if (nodes.length <= 8) {
-        const visited = new Set();
-        const path = [];
-        function hamiltonianCycleDFS(node) {
-            path.push(node);
-            visited.add(node);
-            if (path.length === nodes.length) {
-                // Check if it's a cycle (last node connects to first)
-                if (adjMap[node].has(path[0])) {
-                    return true;
-                }
-                // Not a cycle
-                visited.delete(node);
-                path.pop();
-                return false;
-            }
-            for (const neighbor of adjMap[node]) {
-                if (!visited.has(neighbor)) {
-                    if (hamiltonianCycleDFS(neighbor)) {
-                        return true;
-                    }
-                }
-            }
-            visited.delete(node);
-            path.pop();
-            return false;
-        }
-        if (hamiltonianCycleDFS(nodes[0])) {
-            return path;
-        }
-    }
-    // Fallback: try to find any cycle using DFS
-    const visited = new Set();
-    const parent = {};
-    let cycleFound = null;
-    function findCycleDFS(node, parentNode) {
-        visited.add(node);
-        for (const neighbor of adjMap[node]) {
-            if (neighbor === parentNode)
-                continue;
-            if (visited.has(neighbor)) {
-                // Found a cycle
-                cycleFound = constructCycle(node, neighbor, parent);
-                return true;
-            }
-            parent[neighbor] = node;
-            if (findCycleDFS(neighbor, node)) {
-                return true;
-            }
-        }
-        return false;
-    }
-    function constructCycle(u, v, parent) {
-        const cycle = [v, u];
-        let current = u;
-        while (parent[current] !== undefined && parent[current] !== v) {
-            current = parent[current];
-            cycle.push(current);
-        }
-        return cycle;
-    }
-    // Try to find a cycle
-    for (const node of nodes) {
-        if (!visited.has(node)) {
-            parent[node] = null;
-            if (findCycleDFS(node, null)) {
-                break;
-            }
-        }
-    }
-    return cycleFound || nodes; // Fallback to all nodes if no cycle found
-}
-/**
- * Convert a combinatorial embedding to node positions
- *
- * @param embedding - The embedding object
- * @param nodes - List of nodes
- * @returns Dictionary mapping nodes to positions
- */
-export function combinatorialEmbeddingToPos(embedding, nodes) {
-    const pos = {};
-    // Use the positions from the embedding
-    for (const node of nodes) {
-        if (embedding.nodePositions[node]) {
-            pos[node] = embedding.nodePositions[node];
-        }
-        else {
-            // Fallback for any nodes without positions
-            pos[node] = [0, 0];
-        }
-    }
-    return pos;
-}
-//# sourceMappingURL=embedding.js.map

package/dist/src/algorithms/planarity/embedding.js.map

@@ -1 +0,0 @@
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package/dist/src/algorithms/planarity/index.d.ts

@@ -1,7 +0,0 @@
-/**
- * Re-export all planarity algorithms
- */
-export { checkPlanarity } from './check';
-export { isK5, isK33, tryFindBipartitePartition } from './special-graphs';
-export { lrPlanarityTest } from './lr-test';
-export { createTriangulationEmbedding, findCycle, combinatorialEmbeddingToPos } from './embedding';