gitnexus 1.2.6 → 1.2.8

package/vendor/leiden/utils.cjs

@@ -1,392 +1,392 @@
-/**
- * Graphology Leiden Utils
- * ========================
- *
- * Miscellaneous utilities used by the Leiden algorithm.
- *
- * Vendored from: https://github.com/graphology/graphology/tree/master/src/communities-leiden
- * License: MIT
- */
-var SparseMap = require('mnemonist/sparse-map');
-var createRandom = require('pandemonium/random').createRandom;
-
-function addWeightToCommunity(map, community, weight) {
- var currentWeight = map.get(community);
-
- if (typeof currentWeight === 'undefined') currentWeight = 0;
-
- currentWeight += weight;
-
- map.set(community, currentWeight);
-}
-
-function UndirectedLeidenAddenda(index, options) {
- options = options || {};
-
- var rng = options.rng || Math.random;
- var randomness = 'randomness' in options ? options.randomness : 0.01;
-
- this.index = index;
- this.random = createRandom(rng);
- this.randomness = randomness;
- this.rng = rng;
-
- var NodesPointerArray = index.counts.constructor;
- var WeightsArray = index.weights.constructor;
-
- var order = index.C;
- this.resolution = index.resolution;
-
- // Used to group nodes by communities
- this.B = index.C;
- this.C = 0;
- this.communitiesOffsets = new NodesPointerArray(order);
- this.nodesSortedByCommunities = new NodesPointerArray(order);
- this.communitiesBounds = new NodesPointerArray(order + 1);
-
- // Used to merge nodes subsets
- this.communityWeights = new WeightsArray(order);
- this.degrees = new WeightsArray(order);
- this.nonSingleton = new Uint8Array(order);
- this.externalEdgeWeightPerCommunity = new WeightsArray(order);
- this.belongings = new NodesPointerArray(order);
- this.neighboringCommunities = new SparseMap(WeightsArray, order);
- this.cumulativeIncrement = new Float64Array(order);
- this.macroCommunities = null;
-}
-
-UndirectedLeidenAddenda.prototype.groupByCommunities = function () {
- var index = this.index;
-
- var n, i, c, b, o;
-
- n = 0;
- o = 0;
-
- for (i = 0; i < index.C; i++) {
- c = index.counts[i];
-
- if (c !== 0) {
- this.communitiesBounds[o++] = n;
- n += c;
- this.communitiesOffsets[i] = n;
- }
- }
-
- this.communitiesBounds[o] = n;
-
- o = 0;
-
- for (i = 0; i < index.C; i++) {
- b = index.belongings[i];
- o = --this.communitiesOffsets[b];
- this.nodesSortedByCommunities[o] = i;
- }
-
- this.B = index.C - index.U;
- this.C = index.C;
-};
-
-UndirectedLeidenAddenda.prototype.communities = function () {
- var communities = new Array(this.B);
-
- var i, j, community, start, stop;
-
- for (i = 0; i < this.B; i++) {
- start = this.communitiesBounds[i];
- stop = this.communitiesBounds[i + 1];
- community = [];
-
- for (j = start; j < stop; j++) {
- community.push(j);
- }
-
- communities[i] = community;
- }
-
- return communities;
-};
-
-UndirectedLeidenAddenda.prototype.mergeNodesSubset = function (start, stop) {
- var index = this.index;
- var currentMacroCommunity =
- index.belongings[this.nodesSortedByCommunities[start]];
- var neighboringCommunities = this.neighboringCommunities;
-
- var totalNodeWeight = 0;
-
- var i, j, w;
- var ei, el, et;
-
- // Initializing singletons
- for (j = start; j < stop; j++) {
- i = this.nodesSortedByCommunities[j];
-
- this.belongings[i] = i;
- this.nonSingleton[i] = 0;
- this.degrees[i] = 0;
- totalNodeWeight += index.loops[i] / 2;
-
- this.communityWeights[i] = index.loops[i];
- this.externalEdgeWeightPerCommunity[i] = 0;
-
- ei = index.starts[i];
- el = index.starts[i + 1];
-
- for (; ei < el; ei++) {
- et = index.neighborhood[ei];
- w = index.weights[ei];
-
- this.degrees[i] += w;
-
- if (index.belongings[et] !== currentMacroCommunity) continue;
-
- totalNodeWeight += w;
- this.externalEdgeWeightPerCommunity[i] += w;
- this.communityWeights[i] += w;
- }
- }
-
- var microDegrees = this.externalEdgeWeightPerCommunity.slice();
-
- var s, ri, ci;
- var order = stop - start;
-
- var degree,
- bestCommunity,
- qualityValueIncrement,
- maxQualityValueIncrement,
- totalTransformedQualityValueIncrement,
- targetCommunity,
- targetCommunityDegree,
- targetCommunityWeight;
-
- var r, lo, hi, mid, chosenCommunity;
-
- ri = this.random(start, stop - 1);
-
- for (s = start; s < stop; s++, ri++) {
- j = start + (ri % order);
-
- i = this.nodesSortedByCommunities[j];
-
- if (this.nonSingleton[i] === 1) {
- continue;
- }
-
- if (
- this.externalEdgeWeightPerCommunity[i] <
- this.communityWeights[i] *
- (totalNodeWeight / 2 - this.communityWeights[i]) *
- this.resolution
- ) {
- continue;
- }
-
- this.communityWeights[i] = 0;
- this.externalEdgeWeightPerCommunity[i] = 0;
-
- neighboringCommunities.clear();
- neighboringCommunities.set(i, 0);
-
- degree = 0;
-
- ei = index.starts[i];
- el = index.starts[i + 1];
-
- for (; ei < el; ei++) {
- et = index.neighborhood[ei];
-
- if (index.belongings[et] !== currentMacroCommunity) continue;
-
- w = index.weights[ei];
-
- degree += w;
-
- addWeightToCommunity(neighboringCommunities, this.belongings[et], w);
- }
-
- bestCommunity = i;
- maxQualityValueIncrement = 0;
- totalTransformedQualityValueIncrement = 0;
-
- for (ci = 0; ci < neighboringCommunities.size; ci++) {
- targetCommunity = neighboringCommunities.dense[ci];
- targetCommunityDegree = neighboringCommunities.vals[ci];
- targetCommunityWeight = this.communityWeights[targetCommunity];
-
- if (
- this.externalEdgeWeightPerCommunity[targetCommunity] >=
- targetCommunityWeight *
- (totalNodeWeight / 2 - targetCommunityWeight) *
- this.resolution
- ) {
- qualityValueIncrement =
- targetCommunityDegree -
- ((degree + index.loops[i]) *
- targetCommunityWeight *
- this.resolution) /
- totalNodeWeight;
-
- if (qualityValueIncrement > maxQualityValueIncrement) {
- bestCommunity = targetCommunity;
- maxQualityValueIncrement = qualityValueIncrement;
- }
-
- if (qualityValueIncrement >= 0)
- totalTransformedQualityValueIncrement += Math.exp(
- qualityValueIncrement / this.randomness
- );
- }
-
- this.cumulativeIncrement[ci] = totalTransformedQualityValueIncrement;
- }
-
- if (
- totalTransformedQualityValueIncrement < Number.MAX_VALUE &&
- totalTransformedQualityValueIncrement < Infinity
- ) {
- r = totalTransformedQualityValueIncrement * this.rng();
- lo = -1;
- hi = neighboringCommunities.size + 1;
-
- while (lo < hi - 1) {
- mid = (lo + hi) >>> 1;
-
- if (this.cumulativeIncrement[mid] >= r) hi = mid;
- else lo = mid;
- }
-
- chosenCommunity = neighboringCommunities.dense[hi];
- } else {
- chosenCommunity = bestCommunity;
- }
-
- this.communityWeights[chosenCommunity] += degree + index.loops[i];
-
- ei = index.starts[i];
- el = index.starts[i + 1];
-
- for (; ei < el; ei++) {
- et = index.neighborhood[ei];
-
- if (index.belongings[et] !== currentMacroCommunity) continue;
-
- targetCommunity = this.belongings[et];
-
- if (targetCommunity === chosenCommunity) {
- this.externalEdgeWeightPerCommunity[chosenCommunity] -=
- microDegrees[et];
- } else {
- this.externalEdgeWeightPerCommunity[chosenCommunity] +=
- microDegrees[et];
- }
- }
-
- if (chosenCommunity !== i) {
- this.belongings[i] = chosenCommunity;
- this.nonSingleton[chosenCommunity] = 1;
- this.C--;
- }
- }
-
- var microCommunities = this.neighboringCommunities;
- microCommunities.clear();
-
- for (j = start; j < stop; j++) {
- i = this.nodesSortedByCommunities[j];
- microCommunities.set(this.belongings[i], 1);
- }
-
- return microCommunities.dense.slice(0, microCommunities.size);
-};
-
-UndirectedLeidenAddenda.prototype.refinePartition = function () {
- this.groupByCommunities();
-
- this.macroCommunities = new Array(this.B);
-
- var i, start, stop, mapping;
-
- var bounds = this.communitiesBounds;
-
- for (i = 0; i < this.B; i++) {
- start = bounds[i];
- stop = bounds[i + 1];
-
- mapping = this.mergeNodesSubset(start, stop);
- this.macroCommunities[i] = mapping;
- }
-};
-
-UndirectedLeidenAddenda.prototype.split = function () {
- var index = this.index;
- var isolates = this.neighboringCommunities;
-
- isolates.clear();
-
- var i, community, isolated;
-
- for (i = 0; i < index.C; i++) {
- community = this.belongings[i];
-
- if (i !== community) continue;
-
- isolated = index.isolate(i, this.degrees[i]);
- isolates.set(community, isolated);
- }
-
- for (i = 0; i < index.C; i++) {
- community = this.belongings[i];
-
- if (i === community) continue;
-
- isolated = isolates.get(community);
- index.move(i, this.degrees[i], isolated);
- }
-
- var j, macro;
-
- for (i = 0; i < this.macroCommunities.length; i++) {
- macro = this.macroCommunities[i];
-
- for (j = 0; j < macro.length; j++) macro[j] = isolates.get(macro[j]);
- }
-};
-
-UndirectedLeidenAddenda.prototype.zoomOut = function () {
- var index = this.index;
- this.refinePartition();
- this.split();
-
- var newLabels = index.zoomOut();
-
- var macro, leader, follower;
-
- var i, j;
-
- for (i = 0; i < this.macroCommunities.length; i++) {
- macro = this.macroCommunities[i];
- leader = newLabels[macro[0]];
-
- for (j = 1; j < macro.length; j++) {
- follower = newLabels[macro[j]];
- index.expensiveMove(follower, leader);
- }
- }
-};
-
-UndirectedLeidenAddenda.prototype.onlySingletons = function () {
- var index = this.index;
-
- var i;
-
- for (i = 0; i < index.C; i++) {
- if (index.counts[i] > 1) return false;
- }
-
- return true;
-};
-
-exports.addWeightToCommunity = addWeightToCommunity;
-exports.UndirectedLeidenAddenda = UndirectedLeidenAddenda;
+/**
+ * Graphology Leiden Utils
+ * ========================
+ *
+ * Miscellaneous utilities used by the Leiden algorithm.
+ *
+ * Vendored from: https://github.com/graphology/graphology/tree/master/src/communities-leiden
+ * License: MIT
+ */
+var SparseMap = require('mnemonist/sparse-map');
+var createRandom = require('pandemonium/random').createRandom;
+
+function addWeightToCommunity(map, community, weight) {
+ var currentWeight = map.get(community);
+
+ if (typeof currentWeight === 'undefined') currentWeight = 0;
+
+ currentWeight += weight;
+
+ map.set(community, currentWeight);
+}
+
+function UndirectedLeidenAddenda(index, options) {
+ options = options || {};
+
+ var rng = options.rng || Math.random;
+ var randomness = 'randomness' in options ? options.randomness : 0.01;
+
+ this.index = index;
+ this.random = createRandom(rng);
+ this.randomness = randomness;
+ this.rng = rng;
+
+ var NodesPointerArray = index.counts.constructor;
+ var WeightsArray = index.weights.constructor;
+
+ var order = index.C;
+ this.resolution = index.resolution;
+
+ // Used to group nodes by communities
+ this.B = index.C;
+ this.C = 0;
+ this.communitiesOffsets = new NodesPointerArray(order);
+ this.nodesSortedByCommunities = new NodesPointerArray(order);
+ this.communitiesBounds = new NodesPointerArray(order + 1);
+
+ // Used to merge nodes subsets
+ this.communityWeights = new WeightsArray(order);
+ this.degrees = new WeightsArray(order);
+ this.nonSingleton = new Uint8Array(order);
+ this.externalEdgeWeightPerCommunity = new WeightsArray(order);
+ this.belongings = new NodesPointerArray(order);
+ this.neighboringCommunities = new SparseMap(WeightsArray, order);
+ this.cumulativeIncrement = new Float64Array(order);
+ this.macroCommunities = null;
+}
+
+UndirectedLeidenAddenda.prototype.groupByCommunities = function () {
+ var index = this.index;
+
+ var n, i, c, b, o;
+
+ n = 0;
+ o = 0;
+
+ for (i = 0; i < index.C; i++) {
+ c = index.counts[i];
+
+ if (c !== 0) {
+ this.communitiesBounds[o++] = n;
+ n += c;
+ this.communitiesOffsets[i] = n;
+ }
+ }
+
+ this.communitiesBounds[o] = n;
+
+ o = 0;
+
+ for (i = 0; i < index.C; i++) {
+ b = index.belongings[i];
+ o = --this.communitiesOffsets[b];
+ this.nodesSortedByCommunities[o] = i;
+ }
+
+ this.B = index.C - index.U;
+ this.C = index.C;
+};
+
+UndirectedLeidenAddenda.prototype.communities = function () {
+ var communities = new Array(this.B);
+
+ var i, j, community, start, stop;
+
+ for (i = 0; i < this.B; i++) {
+ start = this.communitiesBounds[i];
+ stop = this.communitiesBounds[i + 1];
+ community = [];
+
+ for (j = start; j < stop; j++) {
+ community.push(j);
+ }
+
+ communities[i] = community;
+ }
+
+ return communities;
+};
+
+UndirectedLeidenAddenda.prototype.mergeNodesSubset = function (start, stop) {
+ var index = this.index;
+ var currentMacroCommunity =
+ index.belongings[this.nodesSortedByCommunities[start]];
+ var neighboringCommunities = this.neighboringCommunities;
+
+ var totalNodeWeight = 0;
+
+ var i, j, w;
+ var ei, el, et;
+
+ // Initializing singletons
+ for (j = start; j < stop; j++) {
+ i = this.nodesSortedByCommunities[j];
+
+ this.belongings[i] = i;
+ this.nonSingleton[i] = 0;
+ this.degrees[i] = 0;
+ totalNodeWeight += index.loops[i] / 2;
+
+ this.communityWeights[i] = index.loops[i];
+ this.externalEdgeWeightPerCommunity[i] = 0;
+
+ ei = index.starts[i];
+ el = index.starts[i + 1];
+
+ for (; ei < el; ei++) {
+ et = index.neighborhood[ei];
+ w = index.weights[ei];
+
+ this.degrees[i] += w;
+
+ if (index.belongings[et] !== currentMacroCommunity) continue;
+
+ totalNodeWeight += w;
+ this.externalEdgeWeightPerCommunity[i] += w;
+ this.communityWeights[i] += w;
+ }
+ }
+
+ var microDegrees = this.externalEdgeWeightPerCommunity.slice();
+
+ var s, ri, ci;
+ var order = stop - start;
+
+ var degree,
+ bestCommunity,
+ qualityValueIncrement,
+ maxQualityValueIncrement,
+ totalTransformedQualityValueIncrement,
+ targetCommunity,
+ targetCommunityDegree,
+ targetCommunityWeight;
+
+ var r, lo, hi, mid, chosenCommunity;
+
+ ri = this.random(start, stop - 1);
+
+ for (s = start; s < stop; s++, ri++) {
+ j = start + (ri % order);
+
+ i = this.nodesSortedByCommunities[j];
+
+ if (this.nonSingleton[i] === 1) {
+ continue;
+ }
+
+ if (
+ this.externalEdgeWeightPerCommunity[i] <
+ this.communityWeights[i] *
+ (totalNodeWeight / 2 - this.communityWeights[i]) *
+ this.resolution
+ ) {
+ continue;
+ }
+
+ this.communityWeights[i] = 0;
+ this.externalEdgeWeightPerCommunity[i] = 0;
+
+ neighboringCommunities.clear();
+ neighboringCommunities.set(i, 0);
+
+ degree = 0;
+
+ ei = index.starts[i];
+ el = index.starts[i + 1];
+
+ for (; ei < el; ei++) {
+ et = index.neighborhood[ei];
+
+ if (index.belongings[et] !== currentMacroCommunity) continue;
+
+ w = index.weights[ei];
+
+ degree += w;
+
+ addWeightToCommunity(neighboringCommunities, this.belongings[et], w);
+ }
+
+ bestCommunity = i;
+ maxQualityValueIncrement = 0;
+ totalTransformedQualityValueIncrement = 0;
+
+ for (ci = 0; ci < neighboringCommunities.size; ci++) {
+ targetCommunity = neighboringCommunities.dense[ci];
+ targetCommunityDegree = neighboringCommunities.vals[ci];
+ targetCommunityWeight = this.communityWeights[targetCommunity];
+
+ if (
+ this.externalEdgeWeightPerCommunity[targetCommunity] >=
+ targetCommunityWeight *
+ (totalNodeWeight / 2 - targetCommunityWeight) *
+ this.resolution
+ ) {
+ qualityValueIncrement =
+ targetCommunityDegree -
+ ((degree + index.loops[i]) *
+ targetCommunityWeight *
+ this.resolution) /
+ totalNodeWeight;
+
+ if (qualityValueIncrement > maxQualityValueIncrement) {
+ bestCommunity = targetCommunity;
+ maxQualityValueIncrement = qualityValueIncrement;
+ }
+
+ if (qualityValueIncrement >= 0)
+ totalTransformedQualityValueIncrement += Math.exp(
+ qualityValueIncrement / this.randomness
+ );
+ }
+
+ this.cumulativeIncrement[ci] = totalTransformedQualityValueIncrement;
+ }
+
+ if (
+ totalTransformedQualityValueIncrement < Number.MAX_VALUE &&
+ totalTransformedQualityValueIncrement < Infinity
+ ) {
+ r = totalTransformedQualityValueIncrement * this.rng();
+ lo = -1;
+ hi = neighboringCommunities.size + 1;
+
+ while (lo < hi - 1) {
+ mid = (lo + hi) >>> 1;
+
+ if (this.cumulativeIncrement[mid] >= r) hi = mid;
+ else lo = mid;
+ }
+
+ chosenCommunity = neighboringCommunities.dense[hi];
+ } else {
+ chosenCommunity = bestCommunity;
+ }
+
+ this.communityWeights[chosenCommunity] += degree + index.loops[i];
+
+ ei = index.starts[i];
+ el = index.starts[i + 1];
+
+ for (; ei < el; ei++) {
+ et = index.neighborhood[ei];
+
+ if (index.belongings[et] !== currentMacroCommunity) continue;
+
+ targetCommunity = this.belongings[et];
+
+ if (targetCommunity === chosenCommunity) {
+ this.externalEdgeWeightPerCommunity[chosenCommunity] -=
+ microDegrees[et];
+ } else {
+ this.externalEdgeWeightPerCommunity[chosenCommunity] +=
+ microDegrees[et];
+ }
+ }
+
+ if (chosenCommunity !== i) {
+ this.belongings[i] = chosenCommunity;
+ this.nonSingleton[chosenCommunity] = 1;
+ this.C--;
+ }
+ }
+
+ var microCommunities = this.neighboringCommunities;
+ microCommunities.clear();
+
+ for (j = start; j < stop; j++) {
+ i = this.nodesSortedByCommunities[j];
+ microCommunities.set(this.belongings[i], 1);
+ }
+
+ return microCommunities.dense.slice(0, microCommunities.size);
+};
+
+UndirectedLeidenAddenda.prototype.refinePartition = function () {
+ this.groupByCommunities();
+
+ this.macroCommunities = new Array(this.B);
+
+ var i, start, stop, mapping;
+
+ var bounds = this.communitiesBounds;
+
+ for (i = 0; i < this.B; i++) {
+ start = bounds[i];
+ stop = bounds[i + 1];
+
+ mapping = this.mergeNodesSubset(start, stop);
+ this.macroCommunities[i] = mapping;
+ }
+};
+
+UndirectedLeidenAddenda.prototype.split = function () {
+ var index = this.index;
+ var isolates = this.neighboringCommunities;
+
+ isolates.clear();
+
+ var i, community, isolated;
+
+ for (i = 0; i < index.C; i++) {
+ community = this.belongings[i];
+
+ if (i !== community) continue;
+
+ isolated = index.isolate(i, this.degrees[i]);
+ isolates.set(community, isolated);
+ }
+
+ for (i = 0; i < index.C; i++) {
+ community = this.belongings[i];
+
+ if (i === community) continue;
+
+ isolated = isolates.get(community);
+ index.move(i, this.degrees[i], isolated);
+ }
+
+ var j, macro;
+
+ for (i = 0; i < this.macroCommunities.length; i++) {
+ macro = this.macroCommunities[i];
+
+ for (j = 0; j < macro.length; j++) macro[j] = isolates.get(macro[j]);
+ }
+};
+
+UndirectedLeidenAddenda.prototype.zoomOut = function () {
+ var index = this.index;
+ this.refinePartition();
+ this.split();
+
+ var newLabels = index.zoomOut();
+
+ var macro, leader, follower;
+
+ var i, j;
+
+ for (i = 0; i < this.macroCommunities.length; i++) {
+ macro = this.macroCommunities[i];
+ leader = newLabels[macro[0]];
+
+ for (j = 1; j < macro.length; j++) {
+ follower = newLabels[macro[j]];
+ index.expensiveMove(follower, leader);
+ }
+ }
+};
+
+UndirectedLeidenAddenda.prototype.onlySingletons = function () {
+ var index = this.index;
+
+ var i;
+
+ for (i = 0; i < index.C; i++) {
+ if (index.counts[i] > 1) return false;
+ }
+
+ return true;
+};
+
+exports.addWeightToCommunity = addWeightToCommunity;
+exports.UndirectedLeidenAddenda = UndirectedLeidenAddenda;