// distance finding algorithm import FloydWarshall from "./components/algorithms/FloydWarshall.js" /** * KamadaKawai positions the nodes initially based on * * "AN ALGORITHM FOR DRAWING GENERAL UNDIRECTED GRAPHS" * -- Tomihisa KAMADA and Satoru KAWAI in 1989 * * Possible optimizations in the distance calculation can be implemented. */ class KamadaKawai { /** * @param {Object} body * @param {number} edgeLength * @param {number} edgeStrength */ constructor(body, edgeLength, edgeStrength) { this.body = body; this.springLength = edgeLength; this.springConstant = edgeStrength; this.distanceSolver = new FloydWarshall(); } /** * Not sure if needed but can be used to update the spring length and spring constant * @param {Object} options */ setOptions(options) { if (options) { if (options.springLength) { this.springLength = options.springLength; } if (options.springConstant) { this.springConstant = options.springConstant; } } } /** * Position the system * @param {Array.} nodesArray * @param {Array.} edgesArray * @param {boolean} [ignoreClusters=false] */ solve(nodesArray, edgesArray, ignoreClusters = false) { // get distance matrix let D_matrix = this.distanceSolver.getDistances(this.body, nodesArray, edgesArray); // distance matrix // get the L Matrix this._createL_matrix(D_matrix); // get the K Matrix this._createK_matrix(D_matrix); // initial E Matrix this._createE_matrix(); // calculate positions let threshold = 0.01; let innerThreshold = 1; let iterations = 0; let maxIterations = Math.max(1000, Math.min(10 * this.body.nodeIndices.length, 6000)); let maxInnerIterations = 5; let maxEnergy = 1e9; let highE_nodeId = 0, dE_dx = 0, dE_dy = 0, delta_m = 0, subIterations = 0; while (maxEnergy > threshold && iterations < maxIterations) { iterations += 1; [highE_nodeId, maxEnergy, dE_dx, dE_dy] = this._getHighestEnergyNode(ignoreClusters); delta_m = maxEnergy; subIterations = 0; while (delta_m > innerThreshold && subIterations < maxInnerIterations) { subIterations += 1; this._moveNode(highE_nodeId, dE_dx, dE_dy); [delta_m, dE_dx, dE_dy] = this._getEnergy(highE_nodeId); } } } /** * get the node with the highest energy * @param {boolean} ignoreClusters * @returns {number[]} * @private */ _getHighestEnergyNode(ignoreClusters) { let nodesArray = this.body.nodeIndices; let nodes = this.body.nodes; let maxEnergy = 0; let maxEnergyNodeId = nodesArray[0]; let dE_dx_max = 0, dE_dy_max = 0; for (let nodeIdx = 0; nodeIdx < nodesArray.length; nodeIdx++) { let m = nodesArray[nodeIdx]; // by not evaluating nodes with predefined positions we should only move nodes that have no positions. if ((nodes[m].predefinedPosition === false || nodes[m].isCluster === true && ignoreClusters === true) || nodes[m].options.fixed.x === true || nodes[m].options.fixed.y === true) { let [delta_m,dE_dx,dE_dy] = this._getEnergy(m); if (maxEnergy < delta_m) { maxEnergy = delta_m; maxEnergyNodeId = m; dE_dx_max = dE_dx; dE_dy_max = dE_dy; } } } return [maxEnergyNodeId, maxEnergy, dE_dx_max, dE_dy_max]; } /** * calculate the energy of a single node * @param {Node.id} m * @returns {number[]} * @private */ _getEnergy(m) { let [dE_dx,dE_dy] = this.E_sums[m]; let delta_m = Math.sqrt(Math.pow(dE_dx, 2) + Math.pow(dE_dy, 2)); return [delta_m, dE_dx, dE_dy]; } /** * move the node based on it's energy * the dx and dy are calculated from the linear system proposed by Kamada and Kawai * @param {number} m * @param {number} dE_dx * @param {number} dE_dy * @private */ _moveNode(m, dE_dx, dE_dy) { let nodesArray = this.body.nodeIndices; let nodes = this.body.nodes; let d2E_dx2 = 0; let d2E_dxdy = 0; let d2E_dy2 = 0; let x_m = nodes[m].x; let y_m = nodes[m].y; let km = this.K_matrix[m]; let lm = this.L_matrix[m]; for (let iIdx = 0; iIdx < nodesArray.length; iIdx++) { let i = nodesArray[iIdx]; if (i !== m) { let x_i = nodes[i].x; let y_i = nodes[i].y; let kmat = km[i]; let lmat = lm[i]; let denominator = 1.0 / Math.pow(Math.pow(x_m - x_i, 2) + Math.pow(y_m - y_i, 2), 1.5); d2E_dx2 += kmat * (1 - lmat * Math.pow(y_m - y_i, 2) * denominator); d2E_dxdy += kmat * (lmat * (x_m - x_i) * (y_m - y_i) * denominator); d2E_dy2 += kmat * (1 - lmat * Math.pow(x_m - x_i, 2) * denominator); } } // make the variable names easier to make the solving of the linear system easier to read let A = d2E_dx2, B = d2E_dxdy, C = dE_dx, D = d2E_dy2, E = dE_dy; // solve the linear system for dx and dy let dy = (C / A + E / B) / (B / A - D / B); let dx = -(B * dy + C) / A; // move the node nodes[m].x += dx; nodes[m].y += dy; // Recalculate E_matrix (should be incremental) this._updateE_matrix(m); } /** * Create the L matrix: edge length times shortest path * @param {Object} D_matrix * @private */ _createL_matrix(D_matrix) { let nodesArray = this.body.nodeIndices; let edgeLength = this.springLength; this.L_matrix = []; for (let i = 0; i < nodesArray.length; i++) { this.L_matrix[nodesArray[i]] = {}; for (let j = 0; j < nodesArray.length; j++) { this.L_matrix[nodesArray[i]][nodesArray[j]] = edgeLength * D_matrix[nodesArray[i]][nodesArray[j]]; } } } /** * Create the K matrix: spring constants times shortest path * @param {Object} D_matrix * @private */ _createK_matrix(D_matrix) { let nodesArray = this.body.nodeIndices; let edgeStrength = this.springConstant; this.K_matrix = []; for (let i = 0; i < nodesArray.length; i++) { this.K_matrix[nodesArray[i]] = {}; for (let j = 0; j < nodesArray.length; j++) { this.K_matrix[nodesArray[i]][nodesArray[j]] = edgeStrength * Math.pow(D_matrix[nodesArray[i]][nodesArray[j]], -2); } } } /** * Create matrix with all energies between nodes * @private */ _createE_matrix() { let nodesArray = this.body.nodeIndices; let nodes = this.body.nodes; this.E_matrix = {}; this.E_sums = {}; for (let mIdx = 0; mIdx < nodesArray.length; mIdx++) { this.E_matrix[nodesArray[mIdx]] = []; } for (let mIdx = 0; mIdx < nodesArray.length; mIdx++) { let m = nodesArray[mIdx]; let x_m = nodes[m].x; let y_m = nodes[m].y; let dE_dx = 0; let dE_dy = 0; for (let iIdx = mIdx; iIdx < nodesArray.length; iIdx++) { let i = nodesArray[iIdx]; if (i !== m) { let x_i = nodes[i].x; let y_i = nodes[i].y; let denominator = 1.0 / Math.sqrt(Math.pow(x_m - x_i, 2) + Math.pow(y_m - y_i, 2)); this.E_matrix[m][iIdx] = [ this.K_matrix[m][i] * ((x_m - x_i) - this.L_matrix[m][i] * (x_m - x_i) * denominator), this.K_matrix[m][i] * ((y_m - y_i) - this.L_matrix[m][i] * (y_m - y_i) * denominator) ]; this.E_matrix[i][mIdx] = this.E_matrix[m][iIdx]; dE_dx += this.E_matrix[m][iIdx][0]; dE_dy += this.E_matrix[m][iIdx][1]; } } //Store sum this.E_sums[m] = [dE_dx, dE_dy]; } } /** * Update method, just doing single column (rows are auto-updated) (update all sums) * * @param {number} m * @private */ _updateE_matrix(m) { let nodesArray = this.body.nodeIndices; let nodes = this.body.nodes; let colm = this.E_matrix[m]; let kcolm = this.K_matrix[m]; let lcolm = this.L_matrix[m]; let x_m = nodes[m].x; let y_m = nodes[m].y; let dE_dx = 0; let dE_dy = 0; for (let iIdx = 0; iIdx < nodesArray.length; iIdx++) { let i = nodesArray[iIdx]; if (i !== m) { //Keep old energy value for sum modification below let cell = colm[iIdx]; let oldDx = cell[0]; let oldDy = cell[1]; //Calc new energy: let x_i = nodes[i].x; let y_i = nodes[i].y; let denominator = 1.0 / Math.sqrt(Math.pow(x_m - x_i, 2) + Math.pow(y_m - y_i, 2)); let dx = kcolm[i] * ((x_m - x_i) - lcolm[i] * (x_m - x_i) * denominator); let dy = kcolm[i] * ((y_m - y_i) - lcolm[i] * (y_m - y_i) * denominator); colm[iIdx] = [dx, dy]; dE_dx += dx; dE_dy += dy; //add new energy to sum of each column let sum = this.E_sums[i]; sum[0] += (dx-oldDx); sum[1] += (dy-oldDy); } } //Store sum at -1 index this.E_sums[m] = [dE_dx, dE_dy]; } } export default KamadaKawai;