mirror of https://gitee.com/bigwinds/arangodb
GraphViewer: ModularityJoiner is now independet from the nodes, just relying on edges. Did speed up setup process as iteration is only over connected nodes
This commit is contained in:
Michael Hackstein
parent
2b7bb78fa6
commit
2d16ac415e
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@ -27,17 +27,16 @@
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/// @author Copyright 2011-2013, triAGENS GmbH, Cologne, Germany
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////////////////////////////////////////////////////////////////////////////////
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function ModularityJoiner(nodes, edges) {
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function ModularityJoiner(edges) {
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"use strict";
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if (nodes === undefined) {
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throw "Nodes have to be given.";
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}
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if (edges === undefined) {
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throw "Edges have to be given.";
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}
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var matrix = null,
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backwardMatrix,
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degrees = null,
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m = 0,
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revM = 0,
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a = null,
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@ -149,11 +148,19 @@ function ModularityJoiner(nodes, edges) {
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makeAdjacencyMatrix = function() {
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matrix = {};
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backwardMatrix = {};
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degrees = {};
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_.each(edges, function (e) {
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var s = e.source._id,
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t = e.target._id;
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matrix[s] = matrix[s] || {};
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matrix[s][t] = (matrix[s][t] || 0) + 1;
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backwardMatrix[t] = backwardMatrix[t] || {};
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backwardMatrix[t][s] = (backwardMatrix[t][s] || 0) + 1;
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degrees[s] = degrees[s] || {_in: 0, _out:0};
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degrees[t] = degrees[t] || {_in: 0, _out:0};
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degrees[s]._out++;
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degrees[t]._in++;
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});
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m = edges.length;
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revM = 1/m;
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@ -162,76 +169,42 @@ function ModularityJoiner(nodes, edges) {
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makeInitialDegrees = function() {
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a = {};
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_.each(nodes, function (n) {
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a[n._id] = {
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_in: n._inboundCounter / m,
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_out: n._outboundCounter / m
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_.each(degrees, function (n, id) {
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a[id] = {
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_in: n._in / m,
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_out: n._out / m
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};
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});
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return a;
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},
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makeInitialDQBKP = function() {
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dQ = {};
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_.each(nodes, function(n1) {
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var s = n1._id;
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_.each(nodes, function(n2) {
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var t = n2._id,
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ast;
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if (matrix[s] && matrix[s][t]) {
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ast = matrix[s][t];
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} else {
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ast = 0;
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}
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if (s < t) {
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dQ[s] = dQ[s] || {};
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dQ[s][t] = (dQ[s][t] || 0) + ast * revM - a[s]._in * a[t]._out;
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return;
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}
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if (t < s) {
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dQ[t] = dQ[t] || {};
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dQ[t][s] = (dQ[t][s] || 0) + ast * revM - a[s]._in * a[t]._out;
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return;
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}
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});
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});
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},
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notConnectedPenalty = function(s, t) {
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return a[s]._out * a[t]._in + a[s]._in * a[t]._out;
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},
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neighbors = function(sID) {
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var outbound = _.keys(matrix[sID] || {}),
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inbound = _.keys(backwardMatrix[sID] || {});
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return _.union(outbound, inbound);
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},
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makeInitialDQ = function() {
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dQ = {};
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_.each(nodes, function(n1) {
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var s = n1._id;
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_.each(nodes, function(n2) {
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var t = n2._id,
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ast = 0,
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_.each(matrix, function(tars, s) {
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var bw = backwardMatrix[s] || {},
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keys = neighbors(s);
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_.each(keys, function(t) {
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var ast = (tars[t] || 0),
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value;
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if (t <= s) {
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return;
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}
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if (matrix[s] && matrix[s][t]) {
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ast += matrix[s][t];
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}
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if (matrix[t] && matrix[t][s]) {
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ast += matrix[t][s];
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}
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if (ast === 0) {
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return;
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}
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ast += (bw[t] || 0);
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value = ast * revM - notConnectedPenalty(s, t);
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if (value > 0) {
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setDQVal(s, t, value);
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}
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return;
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});
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});
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});
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},
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makeInitialHeap = function() {
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heap = {};
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@ -239,53 +212,6 @@ function ModularityJoiner(nodes, edges) {
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return heap;
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},
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updateDQAndHeapBKP = function (low, high) {
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_.each(dQ, function (list, s) {
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if (s < low) {
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list[low] += list[high];
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delete list[high];
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if (heap[s] === low || heap[s] === high) {
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setHeapToMaxInList(list, s);
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} else {
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if (dQ[s][heap[s]] < list[low]) {
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heap[s] = low;
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}
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}
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return;
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}
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if (s === low) {
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delete list[high];
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if (_.isEmpty(list)) {
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delete dQ[s];
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delete heap[s];
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return;
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}
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_.each(list, function(v, k) {
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if (k < high) {
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list[k] += dQ[k][high];
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delete dQ[k][high];
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return;
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}
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if (high < k) {
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list[k] += dQ[high][k];
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return;
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}
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return;
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});
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setHeapToMaxInList(list, s);
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return;
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}
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if (_.isEmpty(list)) {
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delete dQ[s];
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delete heap[s];
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}
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return;
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});
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delete dQ[high];
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delete heap[high];
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},
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// i < j && i != j != k
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updateDQAndHeapValue = function (i, j, k) {
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var val;
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@ -335,8 +261,6 @@ function ModularityJoiner(nodes, edges) {
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});
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},
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////////////////////////////////////
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// getters //
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////////////////////////////////////
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@ -430,21 +354,6 @@ function ModularityJoiner(nodes, edges) {
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// Evaluate value of community by distance //
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//////////////////////////////////////////////
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neighbors = function(sID) {
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var neigh = [];
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_.each(edges, function(e) {
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if (e.source._id === sID) {
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neigh.push(e.target._id);
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return;
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}
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if (e.target._id === sID) {
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neigh.push(e.source._id);
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return;
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}
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});
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return neigh;
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},
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floatDistStep = function(dist, depth, todo) {
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if (todo.length === 0) {
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return true;
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@ -462,7 +371,7 @@ function ModularityJoiner(nodes, edges) {
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floatDist = function(sID) {
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var dist = {};
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_.each(_.pluck(nodes, "_id"), function(n) {
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_.each(matrix, function(u, n) {
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dist[n] = Number.POSITIVE_INFINITY;
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});
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dist[sID] = 0;
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@ -500,10 +409,6 @@ function ModularityJoiner(nodes, edges) {
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}
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return val;
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};
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if (nodes.length === 0 || edges.length === 0) {
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isRunning = false;
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throw "Load some nodes first.";
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}
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setup();
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best = getBest();
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while (best !== null) {
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@ -63,21 +63,15 @@
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describe('setup process', function() {
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it('should throw an error if no nodes are given', function() {
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expect(function() {
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var s = new ModularityJoiner();
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}).toThrow("Nodes have to be given.");
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});
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it('should throw an error if no edges are given', function() {
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expect(function() {
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var s = new ModularityJoiner([]);
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var s = new ModularityJoiner();
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}).toThrow("Edges have to be given.");
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});
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it('should not throw an error if mandatory information is given', function() {
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expect(function() {
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var s = new ModularityJoiner([], []);
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var s = new ModularityJoiner([]);
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}).not.toThrow();
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});
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@ -104,7 +98,7 @@
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}
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},
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w = new WebWorkerWrapper(ModularityJoiner, cb, n, e);
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w = new WebWorkerWrapper(ModularityJoiner, cb, e);
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});
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waitsFor(function() {
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@ -129,7 +123,7 @@
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beforeEach(function () {
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nodes = [];
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edges = [];
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joiner = new ModularityJoiner(nodes, edges);
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joiner = new ModularityJoiner(edges);
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testNetFour = function() {
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helper.insertSimpleNodes(nodes, ["0", "1", "2", "3"]);
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edges.push(helper.createSimpleEdge(nodes, 0, 1));
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@ -685,7 +679,7 @@
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});
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*/
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});
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/*
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describe('checking the zachary karate club', function() {
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beforeEach(function() {
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@ -819,19 +813,18 @@
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});
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it('should be able to find communities', function() {
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/*
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correct acc to: NMCM09
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Red:
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21,23,24,19,27,16,30,33,34,29,15,9,31
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White:
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25, 26, 28, 32
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Green:
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5, 6, 7, 11, 17
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Blue:
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1, 2, 3, 4, 10, 14, 20, 22, 18, 13, 12
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*/
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/////////////////////////////////////////////////////
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/// correct acc to: NMCM09 //
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/// Red: //
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/// 21,23,24,19,27,16,30,33,34,29,15,9,31 //
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/// White: //
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/// 25, 26, 28, 32 //
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/// Green: //
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/// 5, 6, 7, 11, 17 //
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/// Blue: //
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/// 1, 2, 3, 4, 10, 14, 20, 22, 18, 13, 12 //
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/////////////////////////////////////////////////////
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this.addMatchers({
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toContainKarateClubCommunities: function() {
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var c1 = [
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@ -893,7 +886,7 @@
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});
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});
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*/
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describe('checking consistency after join', function() {
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beforeEach(function() {
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@ -1085,17 +1078,17 @@
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// This is the max. number of nodes for the admin UI
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// However the format is realy unlikely in the adminUI
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/*
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it('should be able to handle 3000 nodes', function() {
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var start = (new Date()).getTime();
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var i, best, nodeCount = 3000;
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var start = (new Date()).getTime(),
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i, best, nodeCount = 3000, diff;
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helper.insertNSimpleNodes(nodes, nodeCount);
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helper.insertClique(nodes, edges, [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]);
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for (i = 11; i < nodeCount; i++) {
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edges.push(helper.createSimpleEdge(nodes, i - 1, i));
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edges.push(helper.createSimpleEdge(nodes, i, i - 2));
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}
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var diff = (new Date()).getTime() - start;
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diff = (new Date()).getTime() - start;
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console.log("Runtime Fill:", diff, "ms");
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start = (new Date()).getTime();
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joiner.setup();
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@ -1103,17 +1096,15 @@
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console.log("Runtime Setup:", diff, "ms");
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start = (new Date()).getTime();
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best = joiner.getBest();
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var step = 0;
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while (best !== null) {
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joiner.joinCommunity(best);
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best = joiner.getBest();
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step++;
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}
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diff = (new Date()).getTime() - start;
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console.log("Runtime Compute:", diff, "ms");
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});
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*/
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// This is what we expect in the Admin UI
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it('should be able to handle few large satelites', function() {
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var start = (new Date()).getTime(),
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@ -1603,37 +1594,37 @@
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});
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/*
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it('should be able to handle 10000 nodes', function() {
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var start = (new Date()).getTime();
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var i, best, nodeCount = 10000;
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helper.insertNSimpleNodes(nodes, nodeCount);
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helper.insertClique(nodes, edges, [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]);
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for (i = 11; i < nodeCount; i++) {
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edges.push(helper.createSimpleEdge(nodes, i - 1, i));
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edges.push(helper.createSimpleEdge(nodes, i, i - 2));
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}
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var diff = (new Date()).getTime() - start;
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console.log("Runtime Fill:", diff, "ms");
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start = (new Date()).getTime();
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joiner.setup();
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diff = (new Date()).getTime() - start;
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console.log("Runtime Setup:", diff, "ms");
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start = (new Date()).getTime();
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best = joiner.getBest();
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var step = 0;
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while (best !== null) {
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joiner.joinCommunity(best);
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best = joiner.getBest();
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step++;
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}
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diff = (new Date()).getTime() - start;
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console.log("Runtime Compute:", diff, "ms");
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});
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*/
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});
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/*
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it('should be able to handle 10000 nodes', function() {
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var start = (new Date()).getTime();
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var i, best, nodeCount = 10000;
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helper.insertNSimpleNodes(nodes, nodeCount);
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helper.insertClique(nodes, edges, [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]);
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for (i = 11; i < nodeCount; i++) {
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edges.push(helper.createSimpleEdge(nodes, i - 1, i));
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edges.push(helper.createSimpleEdge(nodes, i, i - 2));
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}
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var diff = (new Date()).getTime() - start;
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console.log("Runtime Fill:", diff, "ms");
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start = (new Date()).getTime();
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joiner.setup();
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diff = (new Date()).getTime() - start;
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console.log("Runtime Setup:", diff, "ms");
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start = (new Date()).getTime();
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best = joiner.getBest();
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var step = 0;
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while (best !== null) {
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joiner.joinCommunity(best);
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best = joiner.getBest();
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step++;
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}
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diff = (new Date()).getTime() - start;
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console.log("Runtime Compute:", diff, "ms");
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});
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*/
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});
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/*
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