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barycenter returns the configuration with lowest crossings
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,56 @@ | ||
| // Wilhelm Barth, Petra Mutzel, Michael Jünger: | ||
| // Simple and Efficient Bilayer Cross Counting. | ||
| // J. Graph Algorithms Appl. 8(2): 179-194 (2004) | ||
| function count_crossings(graph, north, south) { | ||
| var i, j, n, | ||
| firstIndex, treeSize, tree, index, weightSum, | ||
| invert = false, crosscount; | ||
|
|
||
| // Choose the smaller axis | ||
| if (north.length < south.length) { | ||
| var tmp = north; | ||
| north = south; | ||
| south = tmp; | ||
| invert = true; | ||
| } | ||
|
|
||
| var south_inv = inverse_permutation(south), | ||
| southsequence = []; | ||
|
|
||
| for (i = 0; i < north.length; i++) { | ||
| if (invert) { | ||
| n = graph.inEdges(north[i]) | ||
| .map(function(e) { | ||
| return south_inv[e.target.index]; | ||
| }); | ||
| } | ||
| else { | ||
| n = graph.outEdges(north[i]) | ||
| .map(function(e) { | ||
| return south_inv[e.source.index]; | ||
| }); | ||
| } | ||
| n.sort(function(a,b){ return a-b; }); | ||
| southsequence = southsequence.concat(n); | ||
| } | ||
|
|
||
| firstIndex = 1; | ||
| while (firstIndex < south.length) | ||
| firstIndex <<= 1; | ||
| treeSize = 2 * firstIndex - 1; | ||
| firstIndex -= 1; | ||
| tree = science.zeroes(treeSize); | ||
|
|
||
| crosscount = 0; | ||
| for (i = 0; i < southsequence.length; i++) { | ||
| index = southsequence[i] + firstIndex; | ||
| tree[index]++; | ||
| while (index > 0) { | ||
| if (index%2) crosscount += tree[index+1]; | ||
| index = (index - 1) >> 1; | ||
| tree[index]++; | ||
| } | ||
| } | ||
| return crosscount; | ||
| } | ||
| reorder.count_crossings = count_crossings; |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,142 @@ | ||
| require("science"); | ||
| require("../reorder.v1"); | ||
| require("../reorder.v1"); | ||
|
|
||
| var vows = require("vows"), | ||
| assert = require("assert"), | ||
| seedrandom = require('seedrandom'); | ||
| //var jf = require('jsonfile'); | ||
|
|
||
| Math.seedrandom('reorder'); | ||
|
|
||
| var suite = vows.describe("reorder.count_crossings"); | ||
|
|
||
| function naive_count_crossings(graph, north, south) { | ||
| var i, j, e1, e2, v, count = 0, | ||
| inv_north = reorder.inverse_permutation(north), | ||
| inv_south = reorder.inverse_permutation(south), | ||
| links = []; | ||
| for (i = 0; i < north.length; i++) { | ||
| v = north[i]; | ||
| links = links.concat(graph.outEdges(v).map(function(e) { | ||
| return [ inv_north[e.target.index], inv_south[e.source.index] ]; | ||
| })); | ||
| } | ||
| for (i = 0; i < links.length; i++) { | ||
| e1 = links[i]; | ||
| for (j = i+1; j < links.length; j++) { | ||
| e2 = links[j]; | ||
| if ((e1[0] < e2[0] && e1[1] > e2[1]) | ||
| || (e1[0] > e2[0] && e1[1] < e2[1])) | ||
| count++; | ||
| } | ||
| } | ||
| return count; | ||
| } | ||
|
|
||
| function dohard(mat) { | ||
| var graph = reorder.mat2graph(mat, true), | ||
| comps = graph.components(), | ||
| comp = comps.reduce(function(a, b) { | ||
| return (a.length > b.length) ? a : b; | ||
| }); | ||
| comp.sort(function(a,b){return a-b; }); | ||
| var layer1 = comp.filter(function(n) { | ||
| return graph.outEdges(n).length!=0; | ||
| }), | ||
| layer2 = comp.filter(function(n) { | ||
| return graph.inEdges(n).length!=0; | ||
| }); | ||
| //console.time('fast_crossings'); | ||
| var c1 = reorder.count_crossings(graph, layer1, layer2); | ||
| //console.timeEnd('fast_crossings'); | ||
| //console.time('naive_crossings'); | ||
| var c2 = naive_count_crossings(graph, layer1, layer2); | ||
| //console.timeEnd('naive_crossings'); | ||
| // if (c1 != c2) { | ||
| // var file = 'error_count_crossings.json'; | ||
| // jf.writeFile(file, mat, function(err) { | ||
| // console.log(err); | ||
| // }); | ||
| // } | ||
| assert.equal(c1, c2); | ||
| } | ||
|
|
||
| suite.addBatch({ | ||
| "count_crossings": { | ||
| "simple": function() { | ||
| var graph = reorder.graph() | ||
| .nodes([{id: 0}, {id: 1}, {id: 2}, {id: 3}, {id: 4}, {id: 5}]) | ||
| .links([{source: 0, target: 0}, | ||
| {source: 1, target: 1}, | ||
| {source: 1, target: 2}, | ||
| {source: 2, target: 0}, | ||
| {source: 2, target: 3}, | ||
| {source: 2, target: 4}, | ||
| {source: 3, target: 0}, | ||
| {source: 3, target: 2}, | ||
| {source: 4, target: 3}, | ||
| {source: 5, target: 2}, | ||
| {source: 5, target: 4}]) | ||
| .directed(true) | ||
| .init(), | ||
| comp = graph.components()[0], | ||
| layer1 = comp.filter(function(n) { | ||
| return graph.outEdges(n).length!=0; | ||
| }), | ||
| layer2 = comp.filter(function(n) { | ||
| return graph.inEdges(n).length!=0; | ||
| }); | ||
|
|
||
|
|
||
| assert.equal(naive_count_crossings(graph, layer1, layer2), | ||
| 12); | ||
| assert.equal(reorder.count_crossings(graph, layer1, layer2), | ||
| 12); | ||
| }, | ||
| "bug": function() { | ||
| dohard([ | ||
| [0, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0], | ||
| [0, 0, 0, 1, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], | ||
| [0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1], | ||
| [1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1], | ||
| [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0, 0, 1, 0, 0, 0], | ||
| [1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], | ||
| [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], | ||
| [1, 1, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0], | ||
| [0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0], | ||
| [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1], | ||
| [0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1], | ||
| [0, 0, 1, 1, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 1, 1, 1, 0, 0, 0], | ||
| [0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], | ||
| [0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 1], | ||
| [0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0], | ||
| [0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0], | ||
| [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0], | ||
| [0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1], | ||
| [1, 0, 0, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], | ||
| [0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0], | ||
| [0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0], | ||
| [0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], | ||
| [0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0], | ||
| [1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0], | ||
| [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], | ||
| [0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 1, 1, 1], | ||
| [0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0], | ||
| [1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 0, 0], | ||
| [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0], | ||
| [0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 1, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0] | ||
| ]); | ||
| }, | ||
| "hard": function() { | ||
| for (var i = 10; i < 100; i += 20) { | ||
| for (var j = 10; j < 100; j += 20) { | ||
| var mat = reorder.randomMatrix(0.2, i, j, false); | ||
| dohard(mat); | ||
| } | ||
| } | ||
| } | ||
| } | ||
| }); | ||
|
|
||
| suite.export(module); |