diff --git a/html/admin/js/graphViewer/graph/modularityJoiner.js b/html/admin/js/graphViewer/graph/modularityJoiner.js
index e369a3ed80..383d2c5a8f 100644
--- a/html/admin/js/graphViewer/graph/modularityJoiner.js
+++ b/html/admin/js/graphViewer/graph/modularityJoiner.js
@@ -1,4 +1,5 @@
/*jslint indent: 2, nomen: true, maxlen: 100, white: true plusplus: true */
+/*global _*/
////////////////////////////////////////////////////////////////////////////////
/// @brief Graph functionality
///
@@ -70,9 +71,9 @@ function ModularityJoiner(nodes, edges) {
a = {};
_.each(nodes, function (n) {
a[n._id] = {
- in: n._inboundCounter / m,
- out: n._outboundCounter / m
- }
+ _in: n._inboundCounter / m,
+ _out: n._outboundCounter / m
+ };
});
return a;
},
@@ -83,12 +84,12 @@ function ModularityJoiner(nodes, edges) {
_.each(ts, function(tar) {
if (src < tar) {
dQ[src] = dQ[src] || {};
- dQ[src][tar] = (dQ[src][tar] || 0) + revM - a[src].in * a[tar].out;
+ dQ[src][tar] = (dQ[src][tar] || 0) + revM - a[src]._in * a[tar]._out;
return;
}
if (tar < src) {
dQ[tar] = dQ[tar] || {};
- dQ[tar][src] = (dQ[tar][src] || 0) + revM - a[src].in * a[tar].out;
+ dQ[tar][src] = (dQ[tar][src] || 0) + revM - a[src]._in * a[tar]._out;
return;
}
});
@@ -110,12 +111,12 @@ function ModularityJoiner(nodes, edges) {
}
if (s < t) {
dQ[s] = dQ[s] || {};
- dQ[s][t] = (dQ[s][t] || 0) + ast * revM - a[s].in * a[t].out;
+ dQ[s][t] = (dQ[s][t] || 0) + ast * revM - a[s]._in * a[t]._out;
return;
}
if (t < s) {
dQ[t] = dQ[t] || {};
- dQ[t][s] = (dQ[t][s] || 0) + ast * revM - a[s].in * a[t].out;
+ dQ[t][s] = (dQ[t][s] || 0) + ast * revM - a[s]._in * a[t]._out;
return;
}
});
diff --git a/html/admin/js/graphViewer/graph/nodeReducer.js b/html/admin/js/graphViewer/graph/nodeReducer.js
index 7c687c287a..738a0e6257 100644
--- a/html/admin/js/graphViewer/graph/nodeReducer.js
+++ b/html/admin/js/graphViewer/graph/nodeReducer.js
@@ -1,5 +1,5 @@
/*jslint indent: 2, nomen: true, maxlen: 100, white: true plusplus: true */
-/*global $, d3, _, console, alert*/
+/*global $, d3, _, console, alert, ModularityJoiner*/
////////////////////////////////////////////////////////////////////////////////
/// @brief Graph functionality
///
@@ -38,325 +38,92 @@ function NodeReducer(nodes, edges) {
}
var self = this,
- getDegree = function(id) {
- return $.grep(nodes, function(e){
- return e._id === id;
- })[0];
+ joiner = new ModularityJoiner(nodes, edges),
+
+ neighbors = function(sID) {
+ var neigh = [];
+ _.each(edges, function(e) {
+ if (e.source._id === sID) {
+ neigh.push(e.target._id);
+ return;
+ }
+ if (e.target._id === sID) {
+ neigh.push(e.source._id);
+ return;
+ }
+ });
+ return neigh;
},
-
- populateValues = function(dQ, a, heap) {
- var m = edges.length,
- twoM = 2 * m;
- _.each(nodes, function(n) {
- a[n._id] = {
- in: n._inboundCounter / m,
- out: n._outboundCounter / m
- };
- });
-
- _.each(edges, function(e) {
- var sID, lID;
- if (e.source._id < e.target._id) {
- sID = e.source._id;
- lID = e.target._id;
- } else {
- sID = e.target._id;
- lID = e.source._id;
- }
- if (dQ[sID] === undefined) {
- dQ[sID] = {};
- heap[sID] = {};
- heap[sID].val = Number.NEGATIVE_INFINITY;
- }
- dQ[sID][lID] = (dQ[sID][lID] || 0) + 1 / twoM - a[e.source._id].in * a[e.target._id].out;
- if (heap[sID].val < dQ[sID][lID]) {
- heap[sID].val = dQ[sID][lID];
- heap[sID].sID = sID;
- heap[sID].lID = lID;
- }
- });
- console.log(dQ);
- },
-
- // Will Overwrite dQ, a and heap!
- // Old undirected version
- populateValuesUndirected = function(dQ, a, heap) {
- var m = edges.length,
- twoM = 2 * m;
- _.each(nodes, function(n) {
- a[n._id] = n._outboundCounter / m;
- });
-
- _.each(edges, function(e) {
- var sID, lID;
- if (e.source._id < e.target._id) {
- sID = e.source._id;
- lID = e.target._id;
- } else {
- sID = e.target._id;
- lID = e.source._id;
- }
- if (dQ[sID] === undefined) {
- dQ[sID] = {};
- heap[sID] = {};
- heap[sID].val = Number.NEGATIVE_INFINITY;
- }
- dQ[sID][lID] = (dQ[sID][lID] || 0) + 1 / twoM - a[sID] * a[lID];
- if (heap[sID].val < dQ[sID][lID]) {
- heap[sID].val = dQ[sID][lID];
- heap[sID].sID = sID;
- heap[sID].lID = lID;
- }
- });
- console.log(dQ);
- },
-
- getLargestOnHeap = function(heap) {
- return _.max(heap, function(e) {
- return e.val;
- });
- },
-
- joinCommunities = function(sID, lID, coms, heap, val) {
- coms[sID] = coms[sID] || {com: [sID], q: 0};
- coms[lID] = coms[lID] || {com: [lID], q: 0};
- var old = coms[sID].com,
- newC = coms[lID].com;
- coms[sID].com = old.concat(newC);
- coms[sID].q += coms[sID].q + val;
- delete coms[lID];
- },
-
- getDQValue = function(dQ, a, b) {
- if (a < b) {
- if (dQ[a] !== undefined) {
- return dQ[a][b];
- }
- return undefined;
- }
- if (dQ[b] !== undefined) {
- return dQ[b][a];
- }
- return undefined;
- },
-
- setDQValue = function(dQ, heap, a, b, val) {
- if (a < b) {
- if(dQ[a] === undefined) {
- dQ[a] = {};
- heap[a] = {};
- heap[a].val = -1;
- }
- dQ[a][b] = val;
- if (heap[a].val < val) {
- heap[a].val = val;
- heap[a].sID = a;
- heap[a].lID = b;
+ floatDistStep = function(dist, depth, todo) {
+ if (todo.length === 0) {
+ return true;
}
- } else {
- if(dQ[b] === undefined) {
- dQ[b] = {};
- heap[b] = {};
- heap[b].val = -1;
- }
- dQ[b][a] = val;
- if (heap[b].val < val) {
- heap[b].val = val;
- heap[b].sID = b;
- heap[b].lID = a;
+ var nextTodo = [];
+ _.each(todo, function(t) {
+ if (dist[t] !== Number.POSITIVE_INFINITY) {
+ return;
+ }
+ dist[t] = depth;
+ nextTodo = nextTodo.concat(neighbors(t));
+ });
+ return floatDistStep(dist, depth+1, nextTodo);
+ },
+
+ floatDist = function(sID) {
+ var dist = {};
+ _.each(_.pluck(nodes, "_id"), function(n) {
+ dist[n] = Number.POSITIVE_INFINITY;
+ });
+ dist[sID] = 0;
+ if (floatDistStep(dist, 1, neighbors(sID))) {
+ return dist;
}
- }
- },
-
- delDQValue = function(dQ, a, b) {
- if (a < b) {
- delete dQ[a][b];
- } else {
- delete dQ[b][a];
- }
- },
-
- calcDQValue2 = function(a, i, j, k, vi, vj) {
- if (vi !== undefined || vj !== undefined) {
- if (vi !== undefined) {
- if (vj !== undefined) {
- return vi + vj;
- } else {
- return vi - 2 * a[j] * a[k];
- }
- } else {
- return vj - 2 * a[i] * a[k];
- }
- }
- },
-
- updateHeap = function(dQ, heap) {
- _.each(heap, function (last, k) {
- var l = dQ[k],
- max = Number.NEGATIVE_INFINITY,
- maxId;
- if (l) {
- _.each(l, function (v, id) {
- if (max < v) {
- max = v;
- maxId = id;
- }
- });
- heap[k] = {
- sID: k,
- lID: maxId,
- val: max
- }
- } else {
- delete heap[k];
- }
- });
- },
-
- updateValues = function(largest, dQ, a, heap) {
- var lID = largest.lID,
- sID = largest.sID,
- listS = dQ[sID] || {},
- listL = dQ[lID] || {};
- _.each(dQ, function (l, k) {
- var c1, c2;
- if (k < sID) {
- l[sID] = calcDQValue2(a, sID, lID, k, l[sID], l[lID]);
- delete l[lID];
- return;
- } else if (k === sID) {
- delete l[lID];
- _.each(l, function(val, key) {
- if (key < lID) {
- if (dQ[key] && dQ[key][lID] !== undefined) {
- l[key] = calcDQValue2(a, sID, lID, key, val, dQ[key][lID]);
- delete dQ[key][lID];
- } else {
- l[key] = calcDQValue2(a, sID, lID, key, val, undefined);
- }
- return;
- } else {
- if (dQ[lID] && dQ[lID][key]) {
- l[key] = calcDQValue2(a, sID, lID, key, val, listL[key]);
- delete listL[key];
- } else {
- l[key] = calcDQValue2(a, sID, lID, key, val, undefined);
- }
- return;
- }
- });
- return;
- } else if (k < lID) {
- listS[k] = calcDQValue2(a, sID, lID, k, undefined, l[lID]);
- } else if (lID === k) {
- _.each(listL, function(val, key) {
- listS[key] = calcDQValue2(a, sID, lID, k, undefined, listL[key]);
- });
- }
- });
- delete dQ[lID];
- a[sID] += a[sID];
- delete a[lID];
- updateHeap(dQ, heap);
- },
-
- sortBySize = function(a, b) {
- return b.length - a.length;
- },
-
- neighbors = function(sID) {
- var neigh = [];
- _.each(edges, function(e) {
- if (e.source._id === sID) {
- neigh.push(e.target._id);
- return;
- }
- if (e.target._id === sID) {
- neigh.push(e.source._id);
- return;
- }
- });
- return neigh;
- },
-
- minDist = function(dist) {
- return function(a) {
- return dist[a];
- };
- },
-
+ throw "FAIL!";
+ },
+
+ minDist = function(dist) {
+ return function(a) {
+ return dist[a];
+ };
+ },
+
+
+/*
dijkstra = function(sID) {
var dist = {},
- toDo, next, neigh,
+ leftOvers, next, neigh,
filterNotNext = function(e) {
return e !== next;
},
computeNeighbours = function(v) {
- if (_.contains(toDo, v)) {
+ if (_.contains(leftOvers, v)) {
if (dist[v] > dist[next] + 1) {
dist[v] = dist[next] + 1;
}
}
};
- toDo = _.pluck(nodes, "_id");
- _.each(toDo, function(n) {
+ leftOvers = _.pluck(nodes, "_id");
+ _.each(leftOvers, function(n) {
dist[n] = Number.POSITIVE_INFINITY;
});
dist[sID] = 0;
- while(toDo.length > 0) {
- next = _.min(toDo, minDist(dist));
+ while(leftOvers.length > 0) {
+ next = _.min(leftOvers, minDist(dist));
if (next === Number.POSITIVE_INFINITY) {
break;
}
- toDo = toDo.filter(filterNotNext);
+ leftOvers = leftOvers.filter(filterNotNext);
neigh = neighbors(next);
_.each(neigh, computeNeighbours);
}
return dist;
},
- floatDistStep = function(dist, depth, todo) {
- if (todo.length === 0) {
- return true;
- }
- var nextTodo = [];
- _.each(todo, function(t) {
- if (dist[t] !== Number.POSITIVE_INFINITY) {
- return;
- }
- dist[t] = depth;
- nextTodo = nextTodo.concat(neighbors(t));
- });
- return floatDistStep(dist, depth+1, nextTodo);
- },
-
- floatDist = function(sID) {
- var dist = {};
- _.each(_.pluck(nodes, "_id"), function(n) {
- dist[n] = Number.POSITIVE_INFINITY;
- });
- dist[sID] = 0;
- if (floatDistStep(dist, 1, neighbors(sID))) {
- return dist;
- }
- throw "FAIL!";
- },
-
- communityDetectionStep = function(dQ, a, heap, coms) {
- var l = getLargestOnHeap(heap);
- if (l === Number.NEGATIVE_INFINITY || l.val < 0) {
- return false;
- }
- joinCommunities(l.sID, l.lID, coms, heap, l.val);
- updateValues(l, dQ, a, heap);
- return true;
- },
-
+ */
addNode = function(bucket, node) {
bucket.push(node);
-
},
getSimilarityValue = function(bucket, node) {
@@ -380,23 +147,19 @@ function NodeReducer(nodes, edges) {
countMatch++;
return countMatch / propCount;
};
-
+
self.getCommunity = function(limit, focus) {
- var dQ = {},
- a = {},
- heap = {},
- coms = {},
+ var coms = {},
res = [],
dist = {},
- dist2 = {},
- detectSteps = true,
+ best,
getBest = function (communities) {
var bestQ = Number.NEGATIVE_INFINITY,
bestC;
_.each(communities, function (obj) {
if (obj.q > bestQ) {
bestQ = obj.q;
- bestC = obj.com;
+ bestC = obj.nodes;
}
});
return bestC;
@@ -413,33 +176,26 @@ function NodeReducer(nodes, edges) {
if (nodes.length === 0 || edges.length === 0) {
throw "Load some nodes first.";
}
- populateValues(dQ, a, heap);
- while (detectSteps) {
- detectSteps = communityDetectionStep(dQ, a, heap, coms);
+ joiner.setup();
+ best = joiner.getBest();
+ while (best !== null) {
+ joiner.joinCommunity(best);
+ best = joiner.getBest();
}
- console.log(coms);
-
+ coms = joiner.getCommunities();
+
if (focus !== undefined) {
_.each(coms, function(obj, key) {
- if (obj.com.length === 1) {
- delete coms[key];
- }
- if (_.contains(obj.com, focus._id)) {
+ if (_.contains(obj.nodes, focus._id)) {
delete coms[key];
}
});
- res = _.pluck(_.values(coms), "com");
+ res = _.pluck(_.values(coms), "nodes");
dist = floatDist(focus._id);
res.sort(sortByDistance);
return res[0];
- } else {
- _.each(coms, function(obj, key) {
- if (obj.com.length === 1) {
- delete coms[key];
- }
- });
- return getBest(coms);
}
+ return getBest(coms);
};
self.bucketNodes = function(toSort, numBuckets) {
diff --git a/html/admin/js/graphViewer/jasmine_test/specNodeReducer/modularityJoinerSpec.js b/html/admin/js/graphViewer/jasmine_test/specNodeReducer/modularityJoinerSpec.js
index b56dd5dec6..11d7ea8a8e 100644
--- a/html/admin/js/graphViewer/jasmine_test/specNodeReducer/modularityJoinerSpec.js
+++ b/html/admin/js/graphViewer/jasmine_test/specNodeReducer/modularityJoinerSpec.js
@@ -4,7 +4,7 @@
/*global window, eb, loadFixtures, document */
/*global $, _, d3*/
/*global helper*/
-/*global NodeReducer*/
+/*global ModularityJoiner*/
////////////////////////////////////////////////////////////////////////////////
/// @brief Graph functionality
@@ -111,7 +111,7 @@
return true;
}
});
- })
+ });
it('should offer the adjacency matrix', function() {
expect("getAdjacencyMatrix").toBeGetter();
@@ -209,20 +209,20 @@
three = 3 / m;
initDeg = {
"0": {
- in: one,
- out: two
+ _in: one,
+ _out: two
},
"1": {
- in: three,
- out: one
+ _in: three,
+ _out: one
},
"2": {
- in: two,
- out: two
+ _in: two,
+ _out: two
},
"3": {
- in: two,
- out: three
+ _in: two,
+ _out: three
}
};
});
@@ -261,34 +261,34 @@
beforeEach(function() {
m = edges.length;
zero = {
- in: 1/m,
- out: 2/m
+ _in: 1/m,
+ _out: 2/m
};
one = {
- in: 3/m,
- out: 1/m
+ _in: 3/m,
+ _out: 1/m
};
two = {
- in: 2/m,
- out: 2/m
+ _in: 2/m,
+ _out: 2/m
};
three = {
- in: 2/m,
- out: 3/m
+ _in: 2/m,
+ _out: 3/m
};
initDQ = {
"0": {
- "1": 1/m - zero.in * one.out - zero.out * one.in,
- "2": - zero.in * two.out - zero.out * two.in,
- "3": 2/m - zero.in * three.out - zero.out * three.in
+ "1": 1/m - zero._in * one._out - zero._out * one._in,
+ "2": - zero._in * two._out - zero._out * two._in,
+ "3": 2/m - zero._in * three._out - zero._out * three._in
},
"1": {
- "2": 2/m - one.in * two.out - one.out * two.in,
- "3": 1/m - one.in * three.out - one.out * three.in
+ "2": 2/m - one._in * two._out - one._out * two._in,
+ "3": 1/m - one._in * three._out - one._out * three._in
},
"2": {
- "3": 2/m - two.in * three.out - two.out * three.in
- },
+ "3": 2/m - two._in * three._out - two._out * three._in
+ }
};
});
@@ -382,25 +382,25 @@
*/
describe('the heap', function() {
- var m, zero, one, two, three
+ var m, zero, one, two, three;
beforeEach(function() {
m = edges.length;
zero = {
- in: 1/m,
- out: 2/m
+ _in: 1/m,
+ _out: 2/m
};
one = {
- in: 3/m,
- out: 1/m
+ _in: 3/m,
+ _out: 1/m
};
two = {
- in: 2/m,
- out: 2/m
+ _in: 2/m,
+ _out: 2/m
};
three = {
- in: 2/m,
- out: 3/m
+ _in: 2/m,
+ _out: 3/m
};
});
@@ -416,7 +416,7 @@
expect(joiner.getBest()).toEqual({
sID: "0",
lID: "3",
- val: 2/m - zero.in * three.out - zero.out * three.in
+ val: 2/m - zero._in * three._out - zero._out * three._in
});
});
@@ -447,7 +447,7 @@
expect(joiner.getBest()).toEqual({
sID: "1",
lID: "2",
- val: 2/m - one.in * two.out - one.out * two.in
+ val: 2/m - one._in * two._out - one._out * two._in
});
});
@@ -483,20 +483,20 @@
expected = {},
m = edges.length,
zero = {
- in: 1/m,
- out: 2/m
+ _in: 1/m,
+ _out: 2/m
},
one = {
- in: 3/m,
- out: 1/m
+ _in: 3/m,
+ _out: 1/m
},
two = {
- in: 2/m,
- out: 2/m
+ _in: 2/m,
+ _out: 2/m
},
three = {
- in: 2/m,
- out: 3/m
+ _in: 2/m,
+ _out: 3/m
};
expected[lowId] = {
nodes: [
@@ -508,7 +508,7 @@
expect(toJoin).toEqual({
sID: "0",
lID: "3",
- val: 2/m - zero.in * three.out - zero.out * three.in
+ val: 2/m - zero._in * three._out - zero._out * three._in
});
joiner.joinCommunity(toJoin);
expect(joiner.getCommunities()).toEqual(expected);
@@ -635,11 +635,10 @@
o.nodes = _.filter(o.nodes, function(n) {
return _.contains(duplicate, n);
});
- })
-
+ });
return "Found duplicate nodes [" + duplicate
+ "] in communities: " + JSON.stringify(outComms);
- }
+ };
return !failed;
}
});
@@ -655,7 +654,10 @@
it('should be able to find communities', function() {
this.addMatchers({
toContainKarateClubCommunities: function() {
- var c1 = ["15", "16", "19", "21", "23", "24", "27", "28", "30", "31", "33", "34", "9"].sort().join(),
+ var c1 = [
+ "15", "16", "19", "21", "23", "24", "27",
+ "28", "30", "31", "33", "34", "9"
+ ].sort().join(),
c2 = ["10", "13", "14", "18", "2", "22", "3", "4", "8"].sort().join(),
c3 = ["1", "11", "12", "17", "20" , "5", "6", "7"].sort().join(),
c4 = ["25", "26", "29", "32"].sort().join(),
@@ -702,14 +704,10 @@
return !failed;
}
});
-
-
var best = joiner.getBest();
- var steps = 0;
while (best !== null) {
joiner.joinCommunity(best);
best = joiner.getBest();
- steps++;
}
expect(joiner.getCommunities()).toContainKarateClubCommunities();
});
diff --git a/html/admin/js/graphViewer/jasmine_test/specNodeReducer/nodeReducerSpec.js b/html/admin/js/graphViewer/jasmine_test/specNodeReducer/nodeReducerSpec.js
index f84679cfff..4ea011b159 100644
--- a/html/admin/js/graphViewer/jasmine_test/specNodeReducer/nodeReducerSpec.js
+++ b/html/admin/js/graphViewer/jasmine_test/specNodeReducer/nodeReducerSpec.js
@@ -58,6 +58,14 @@
var s = new NodeReducer([], []);
}).not.toThrow();
});
+
+ it('should create an instance of the modularityJoiner', function() {
+ spyOn(window, "ModularityJoiner");
+ var n = [],
+ e = [],
+ s = new NodeReducer(n, e);
+ expect(window.ModularityJoiner).wasCalledWith(n, e);
+ });
});
describe('setup correctly', function() {
@@ -158,24 +166,8 @@
expect(com).toContainNodes(["0", "1", "2"]);
});
- it('should also take the best community if no focus is given', function() {
- helper.insertSimpleNodes(nodes, ["0", "1", "2", "3", "4", "5", "6", "7"]);
-
- edges.push(helper.createSimpleEdge(nodes, 0, 1));
- edges.push(helper.createSimpleEdge(nodes, 0, 2));
- edges.push(helper.createSimpleEdge(nodes, 1, 2));
- edges.push(helper.createSimpleEdge(nodes, 2, 3));
- edges.push(helper.createSimpleEdge(nodes, 3, 4));
- edges.push(helper.createSimpleEdge(nodes, 4, 5));
- edges.push(helper.createSimpleEdge(nodes, 5, 6));
- edges.push(helper.createSimpleEdge(nodes, 5, 7));
-
- var com = reducer.getCommunity(6);
- expect(com).toContainNodes(["0", "1", "2", "3", "4"]);
- });
-
});
- /*
+
describe('checking bucket sort of nodes', function() {
var allNodes, buckets;
@@ -315,7 +307,7 @@
});
});
- */
+
});
});
}());
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