From 74d7882bf3c7ea30fe005345cef83c2b9017182d Mon Sep 17 00:00:00 2001 From: nvtNgan Date: Mon, 29 Aug 2016 09:51:14 +0700 Subject: [PATCH 1/7] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 3edc3e5..e107f67 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # Algorithms for detecting community structure in networks In this project, we implement algorithms for detecting community structure in networks. -Our web application is available at [online demo](http://hexagon.esy.es/)|[back up link](http://hexagon.pe.hu/). +Our web application is available at [online demo](https://nvtngan.github.io/)|[back up link](http://hexagon.pe.hu/). ### Exploring Topics and Events in Political Blogs The following image shows the top 100 terms in nearly 100,000 political blog posts in last 10 years (from 2006 to 2015). Terms are color-coded by clusters (generated by our algorithm). The red dashed slider on the left controls the cut-off value for cluster formation. Terms appear together in the same political blogs are connected by links. The link thickness indicates the frequency of collocated terms. From c1354f4efdb490c62ae96b38ec27394ce30eddbf Mon Sep 17 00:00:00 2001 From: Alex-Nguyen Date: Mon, 13 Feb 2017 10:44:16 -0600 Subject: [PATCH 2/7] Update with new Virtual Nodes algorithm --- .DS_Store | Bin 6148 -> 10244 bytes .idea/NetworkClustering.iml | 12 + .idea/modules.xml | 8 + .idea/vcs.xml | 6 + .idea/workspace.xml | 312 ++++++++ index.html | 1 + scripts/main.js | 1056 ++++++++++++++----------- scripts/math_script.js | 1444 +++++++++++++++++++++-------------- scripts/underscore-min.js | 6 + 9 files changed, 1833 insertions(+), 1012 deletions(-) create mode 100644 .idea/NetworkClustering.iml create mode 100644 .idea/modules.xml create mode 100644 .idea/vcs.xml create mode 100644 .idea/workspace.xml create mode 100755 scripts/underscore-min.js diff --git a/.DS_Store b/.DS_Store index 8fc2b3f0a2a6e6b2b9a12903604351f32d87abd7..328be502320d7f12a6c8f3dfb5c0162f4b7742aa 100644 GIT binary patch literal 10244 zcmeI1Yitx%6vxlMEp%phO_9e^UK?s{!2(+-P~O{ZDMdjlZRrEB>|>xK+ugb|+d^xx zKB7^9L?Wm}F=`?KjEM*)CQ9^+nwX$bB4A>SM*Tp1B!1BkMm;lkTDIHL5G7#jOfvV} zx%Zx#xo3X&oO|yO5dz6bF_D*uBt9*vj^<>L!>YH=0Y`>YVpW3mDb!)Kg`)8gUw=5D zwOim?z_oyD0oMYq1zZdK7c9Ur+d8CCLb|DI0oMYq1^O&t`3Enbmh?NaM@ZXsaAGe3 zSY~mteQ;j2GAzB0^gFUgNUq@nLY1XZg|ozfQ0H>5)6Vb69wCJ~!C8F3c`}?83hbxz z{k?W`f?r5CbuHjpV4wx8VUtA>3X(~|)b)F)Evg%)&vyYCnOP%7W=pax$z!B#H7)Uu z8Z&4njX*H5#lF%bTFA-Q#^cexd@!_G*E*Wj3FYya8PsE1BBlA(dOa42cLd_eSj4dJ zQyny0Sl50~vpT7(%U9%GQqo=I?J6!Q;e4rYVRyGAP0lY~xo&&wp3biOyZ1gLdIZNS z(73c7KAYOTsL@_7wkI+Yz1_QbrF)}1l{ssxnpHJvXq&WX(A3+tilC_(&FVOVd%Z3k zk5wnMcJ5PsI37*5#<(UY9E^sO+*m7%Mr-s=&1f*S-KLdmGU5rd+-}&Qv#wRvtd6(z zH@2C2JZ5ax5(Z0IJ~?_~?##TxxeJ!8C_6u9>^L=Nyev1dU1O%cL)Q{@9eTuUX$%@+ zEf&#ZJL}tZLk~r@+E}nv%gH<_%eK~}$sSKbGNj*^)XhC=o+R0&Q>S_4tr3314e^L| zw}^U1679XyJf1C9O?g7&G~y`Sn(vWo4SriS=ro)?N0w`M@dr~4=TYRcRGcoOJz?(INsXIT`_V{lFATeV;GwgY{!76(gG+0f!AuFBCSd=NZx|xl`ro zy$q+bUB{SdyCsViHCwdy=FXBB4^^@+<^0?NnHg3gYV&h%mn1bq)XmHF$&9UtY(SYmGWwdNmWOR+JIakTZ2iZL6EyDa4*pbdYfVUj4seu4BBOe z>~{uiBvc!)TujAu+{Td2#vBx35f-DAL9;MhgGyB4Zfrs=>KL}|3|klx>_8lCNWfs| z_Tm9Nh==e9_TvDaa^O2E!0N-TsuwgNaV!!)>cXy30`zF(ovpxB|QcxN_q@X2F3to zuo$3RzZf7pzJC^#&2c>(TyH^5I%_`cpfj{ zD30L`oWh$pjd!of_YdT8hzOvJ;s~G=+*BTKR3uRTc_dJVhy+S{Bv4W#fl{jUj|56; 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- svg_ti.append("rect").attr("width","100%") - .attr("height","30px").attr("background","#000");*/ -//body -var margin = {top: 0, right: 20, bottom: 20, left: 0}; -var width = (window.innerWidth -|| document.documentElement.clientWidth -|| document.body.clientWidth) - margin.left - margin.right; -var height = (window.innerHeight -|| document.documentElement.clientHeight -|| document.body.clientHeight) - margin.top - margin.bottom; - -var wtree_b_g = width*0.25; -var htree_b_g = width*0.125; -var mtree_g = {top: 10, right: 50, bottom: 50, left: 50}; -var wtree_g = wtree_b_g-mtree_g.left-mtree_g.right; -var htree_g = htree_b_g-mtree_g.top-mtree_g.bottom; - -var wtree_b = width*0.25; -var htree_b = height-htree_b_g; -var mtree = {top: 10, right: 50, bottom: 0, left: 50}; -var wtree = wtree_b-mtree.left-mtree.right; -var htree = htree_b-mtree.top-mtree.bottom; - -var wgroup = width-wtree-mtree.left-mtree_g.right; -var hgroup = height; -var bar_pos = [{x1:0, y1:height,x2:0, y2:0}]; - -var wtime = 300; -var htime = 50; -var mtime = {top: (hgroup-htime-10), right: 0, bottom: 0, left: (wgroup-wtime-10)}; -d3.select("#container").append("div").attr("id","group").attr("class","group").style("left",(margin.left+wtree_b)+"px"); -var svg = d3.select("#group").append("svg") - .attr("width", wgroup) - .attr("height", hgroup) -var svg_graph = d3.select("#treemap_graph").append("svg") - // .style("background", "#eed") - - .attr("width", wtree_b_g) - .attr("height", htree_b_g) - .append("g") - .attr("width", wtree_b_g) - .attr("height", htree_b_g); - -d3.select("#treemap_main").append("div").attr("id","treemap_tree").attr("class","treemap_tree").style("top",(margin.top+htree_b_g)+"px"); -var svg4 = d3.select("#treemap_tree") - .append("svg") - .style("position", "absolute") - .attr("width", wtree_b) - .attr("height", htree_b) - .append("g") - .attr("width", wtree_b) - .attr("height", htree_b) - .attr("transform", "translate(" + [mtree.left, mtree.top] + ")"); -var svg_bar = d3.select("#treemap_bar").append("svg") - // .style("background", "#eed") - .attr("width", wtree_b) - .attr("height", height); - //.attr("transform", "translate(" + [mtree_g.left, mtree_g.top] + ")"); -var color = d3.scaleOrdinal(d3.schemeCategory10); - - -var simulation = d3.forceSimulation() - .force("link", d3.forceLink().id(function(d) { return d.id; })) - .force("charge", d3.forceManyBody()) - .force("center", d3.forceCenter((width-wtree_b)/2, height/2)); -var tree = d3.cluster() - .size([htree, wtree]) - .separation(function(a, b) { return 1; }); -var bar = svg_bar.append("g") - .attr("class", "bar") - .attr("transform", "translate(" + [mtree_g.left, mtree_g.top] + ")"); -var bar_l1 = bar - .append("line") - .classed('b',true) - .data(bar_pos) - .style("stroke-dasharray", "4, 2") - .style("stroke-width", "2px") - .attr("x1", function(d) { return d.x1; }) - .attr("y1", function(d) { return d.y1; }) - .attr("x2", function(d) { return d.x2; }) - .attr("y2", function(d) { return d.y2; }); -var bar_l2 = bar.append("line") - .classed('a',true) - .data(bar_pos) - .style("opacity", "0") - .attr("x1", function(d) { return d.x1; }) - .attr("y1", function(d) { return d.y1; }) - .attr("x2", function(d) { return d.x2; }) - .attr("y2", function(d) { return d.y2; }); -var focus; -var tree_dx; -var node2; -var node; -var roots; -var tree_deep_cv; -var radius = 6; -/* -<<<<<<< HEAD - -======= ->>>>>>> f41cb8646193b11f7aab076bf481cc71363c0550*/ -//d3.json("data/karate.json", function(error, graph) { - d3.json("data/dataset4_fix.json", function(error, graph) { -if (error) throw error; -var num_n = graph.nodes.length; -var start_time = performance.now(); -//processing - var step = between_e(graph); -var end_time_b = performance.now(); - var max_lv=step.length+1; -// tree - var tree_hi = tree_mapingv3(step,graph); -var end_time_t = performance.now(); - var tree_deep = d3.scaleLinear().domain([tree_hi[0].depth,0]).range([0,wtree]); - tree_deep_cv = d3.scaleLinear().domain([tree_hi[0].depth,0]).range([0,tree_hi[1].length]); - tree_dx = wtree/tree_hi[1].length; -//end - roots = d3.hierarchy(tree_hi[0]); - tree(roots); - var link2 = svg4.selectAll(".link") - .data(roots.descendants().slice(roots.name=="join all"?(roots.children.length+1):1)) - .enter().append("path") - .attr("class", "link") - .attr("d", function(d) { - return "M" + [tree_deep(d.data.depth), d.x] - + "L" + [tree_deep(d.parent.data.depth), d.x] - + "L" + [tree_deep(d.parent.data.depth), d.parent.x]; - /*+ "C" + [(tree_deep(d.parent.data.depth)+tree_deep(d.data.depth))/2, d.x] - + " " + [tree_deep(d.parent.data.depth), (d.x+d.parent.x)/2] - + " " + [tree_deep(d.parent.data.depth), d.parent.x];*/ - }) - .attr("stroke", function(d) { return color(1); }); - - function size_scale (){ - if (num_n*2*4max_Q.val){max_Q.val = d; max_Q.pos = i} return x_range(tree_hi[1].length-i); }) - .y(function(d) { return y_range(d); }); - - svg_graph.append("g") - .attr("class", "axis axis--x") - .attr("transform", "translate(" + [mtree_g.left, mtree_g.top+htree_g] + ")") - .call(d3.axisBottom(x_range).tickSize(5)); - - svg_graph.append("g") - .attr("class", "axis axis--x") - .attr("transform", "translate(" + [mtree_g.left, mtree_g.top] + ")") - .call(d3.axisLeft(y_range)); - - svg_graph.append("path") - .attr("class", "graph") - .attr("transform", "translate(" + [mtree_g.left, mtree_g.top] + ")") - .data([1]) - .attr("d", line_g(tree_hi[1])); - - svg_graph.append("text") - .attr("class","graph-title") - .attr("text-anchor", "middle") - .attr("transform", "translate("+ [mtree_g.left-35, mtree_g.top+htree_g/2] +")rotate(-90)") // text is drawn off the screen top left, move down and out and rotate - .text("Modularity - Q"); - svg_graph.append("text") - .attr("class","graph-title") - .attr("text-anchor", "middle") - .attr("transform", "translate("+ [mtree_g.left+wtree_g/2, mtree_g.top+htree_g+35]+")") // text is drawn off the screen top left, move down and out and rotate - .text("Number of clusters"); - - focus = svg_graph.append("g") - .attr("transform", "translate(" + [mtree_g.left, mtree_g.top] + ")") - .append("g") - .attr("class", "focus") - - .style("display", "none"); - - focus.append("circle") - .attr("r", 4.5); - - focus.append("text") - .attr("x", 9) - .attr("dy", ".35em"); - - focus.append("line") - .classed("x", true) - .attr("fill", "none") - .attr("stroke", "black") - .attr("stroke-width", "1.5px") - .attr("stroke-dasharray", "3 3"); - - /*svg_bar.append("rect") - .attr("class", "overlay") - .attr("width", wtree_g) - .attr("height", htree_g) - .attr("transform", "translate(" + [mtree_g.right, mtree_g.top] + ")") - .on("mouseover", function(d){ focus.style('display', null)}) - .on("mouseout", function(d){focus.style('display', 'none')}) - .on("mousemove", mousemove); - function mousemove() { - var x0 = Math.round(x_range.invert(d3.mouse(this)[0])); - d = y_range(tree_hi[1][x0]); - focus.attr("transform", "translate(" + x_range(x0)+ "," + (d ) + ")"); - focus.select("text").text(tree_hi[1][x0]); - focus.select("line.y") - .attr("x1",0) - .attr("y1",0) - .attr("x2",0) - .attr("y2",d); - }*/ - - //---------------node - var link = svg.append("g") - .attr("class", "links") - .selectAll("line") - .data(graph.links) - .enter().append("line") - .attr("stroke-width", function(d) { return Math.sqrt(d.value); }); - - node = svg.append("g") - .attr("class", "nodes") - .selectAll("circle") - //.data(graph.nodes) - .data(graph.nodes,function(d) { return d.id; }) - .enter().append("circle") - .attr("r", 5) - .attr("fill", function(d) { return color(d.group); }) - .call(d3.drag() - .on("start", dragstarted) - .on("drag", dragged) - .on("end", dragended)); - - node.append("title") - .text(function(d){return takeaname(d);}); - node.append("text") - .attr("dx", 12) - .attr("dy", ".35em") - .text(function(d){return takeaname(d);}); - - simulation.force("charge", d3.forceManyBody().strength(function(){return -wgroup/graph.nodes.length})); - simulation - .nodes(graph.nodes) - .on("tick", ticked); - - simulation.force("link") - .links(graph.links); - - function ticked() { - node - .attr("cx", function(d) { return d.x = Math.max(radius, Math.min(wgroup - radius, d.x)); }) - .attr("cy", function(d) { return d.y = Math.max(radius, Math.min(hgroup - radius, d.y)); }) - .attr("fill" , function(d){ return color(d.group)}); - link - .attr("x1", function(d) { return d.source.x; }) - .attr("y1", function(d) { return d.source.y; }) - .attr("x2", function(d) { return d.target.x; }) - .attr("y2", function(d) { return d.target.y; }); - } - //---------------------init bar - bar_l2.attr("transform", function(d){ - return "translate(" + [ x_range(tree_hi[1].length-max_Q.pos),0 ] + ")"}); - bar_l1.attr("transform", function(d){ - return "translate(" + [ x_range(tree_hi[1].length-max_Q.pos),0 ] + ")"}); - var x0 = x_range(tree_hi[1].length-max_Q.pos); - y0 = y_range(max_Q.val); - focus.attr("transform", "translate(" + x0 + "," + y0 + ")"); - focus.select("text").text(max_Q.val); - focus.select("line.x") - .attr("x1",0) - .attr("y1",0) - .attr("x2",-x0) - .attr("y2",0); - bar_l2.attr("x1",function(d){d.x1 = x0; return bar_pos.x1}); - var numofg=1; - update_group(tree_hi[1].length-max_Q.pos-1); - //--------------- - bar_l2.call(d3.drag() - .on("start", dragstarted_bar) - .on("drag", dragged_bar) - .on("end", dragended_bar)) - .on("mousemove",dragstarted_bar) - .on("mouseout",mouseout); - - function mouseout(d){ - bar_l2.style("opacity", "0"); - focus.style('display', "none"); - clusterbox.style("display","none"); - } - function dragstarted_bar(d) { - bar_l2.style("opacity", "0.5"); - focus.style('display', null); - clusterbox.style("display",null); - var x0 = Math.round(x_range.invert(d.x1)); - d = y_range(tree_hi[1][tree_hi[1].length-x0]); - focus.attr("transform", "translate(" + x_range(x0)+ "," + (d ) + ")"); - focus.select("text").text(tree_hi[1][tree_hi[1].length-x0]); - focus.select("line.x") - .attr("x1",0) - .attr("y1",0) - .attr("x2",-x_range(x0)) - .attr("y2",0); - } - - function dragged_bar(d) { - bar_l2.on("mouseout",null) - d.x1 += d3.event.dx; - if (d.x1<=0) - d.x1 = 0; - else{ - if (d.x1>= wtree) - d.x1 = wtree; - - else - { - bar_l2.attr("transform", function(d){ - return "translate(" + [ d.x1,0 ] + ")"}); - bar_l1.attr("transform", function(d){ - return "translate(" + [ d.x1,0 ] + ")"}); - } - - } - var x0 = Math.round(x_range.invert(d.x1)); - d = y_range(tree_hi[1][tree_hi[1].length-x0]); - focus.attr("transform", "translate(" + x_range(x0)+ "," + (d ) + ")"); - focus.select("text").text(tree_hi[1][tree_hi[1].length-x0]); - focus.select("line.x") - .attr("x1",0) - .attr("y1",0) - .attr("x2",-x_range(x0)) - .attr("y2",0); - //d.x2 = d.x1; - clusterbox.select("text").text("# of clusters : "+(x0+1)+" | Q : "+Math.round((tree_hi[1][tree_hi[1].length-x0])*1000)/1000); - } - - function dragended_bar(d) { - bar_l2.style("opacity", "0") - .on("mouseout",mouseout);; - focus.style('display', "none"); - var depth = Math.round(x_range.invert(d.x1))-1; - if (depth<0) - depth=0; - //update_group(depth tree_hi[1].length-max_Q.pos-1); - update_group(depth); - } - - function update_group(depth){ - var cg = 0; - var leave=[]; - var node_t=[]; - node_t.push(roots); - while (node_t.length!=0){ - var node_t_t = node_t.pop(); - if (tree_deep_cv(node_t_t.data.depth)>>>>>> f41cb8646193b11f7aab076bf481cc71363c0550*/ +// d3.json("data/karate.json", function(error, graph) { +d3.json("data/imdb171.json", function (error, graph) { + // d3.json("data/dataset4_fix.json", function(error, graph) { + if (error) throw error; + // for(var i=0;i max_Q.val) { + max_Q.val = d; + max_Q.pos = i + } + return x_range(tree_hi[1].length - i); + }) + .y(function (d) { + return y_range(d); + }); + + svg_graph.append("g") + .attr("class", "axis axis--x") + .attr("transform", "translate(" + [mtree_g.left, mtree_g.top + htree_g] + ")") + .call(d3.axisBottom(x_range).tickSize(5)); + + svg_graph.append("g") + .attr("class", "axis axis--x") + .attr("transform", "translate(" + [mtree_g.left, mtree_g.top] + ")") + .call(d3.axisLeft(y_range)); + + svg_graph.append("path") + .attr("class", "graph") + .attr("transform", "translate(" + [mtree_g.left, mtree_g.top] + ")") + .data([1]) + .attr("d", line_g(tree_hi[1])); + + svg_graph.append("text") + .attr("class", "graph-title") + .attr("text-anchor", "middle") + .attr("transform", "translate(" + [mtree_g.left - 35, mtree_g.top + htree_g / 2] + ")rotate(-90)") // text is drawn off the screen top left, move down and out and rotate + .text("Modularity - Q"); + svg_graph.append("text") + .attr("class", "graph-title") + .attr("text-anchor", "middle") + .attr("transform", "translate(" + [mtree_g.left + wtree_g / 2, mtree_g.top + htree_g + 35] + ")") // text is drawn off the screen top left, move down and out and rotate + .text("Number of clusters"); + + focus = svg_graph.append("g") + .attr("transform", "translate(" + [mtree_g.left, mtree_g.top] + ")") + .append("g") + .attr("class", "focus") + + .style("display", "none"); + + focus.append("circle") + .attr("r", 4.5); + + focus.append("text") + .attr("x", 9) + .attr("dy", ".35em"); + + focus.append("line") + .classed("x", true) + .attr("fill", "none") + .attr("stroke", "black") + .attr("stroke-width", "1.5px") + .attr("stroke-dasharray", "3 3"); + + /*svg_bar.append("rect") + .attr("class", "overlay") + .attr("width", wtree_g) + .attr("height", htree_g) + .attr("transform", "translate(" + [mtree_g.right, mtree_g.top] + ")") + .on("mouseover", function(d){ focus.style('display', null)}) + .on("mouseout", function(d){focus.style('display', 'none')}) + .on("mousemove", mousemove); + function mousemove() { + var x0 = Math.round(x_range.invert(d3.mouse(this)[0])); + d = y_range(tree_hi[1][x0]); + focus.attr("transform", "translate(" + x_range(x0)+ "," + (d ) + ")"); + focus.select("text").text(tree_hi[1][x0]); + focus.select("line.y") + .attr("x1",0) + .attr("y1",0) + .attr("x2",0) + .attr("y2",d); + }*/ + + //---------------node + var link = svg.append("g") + .attr("class", "links") + .selectAll("line") + .data(graph.links) + .enter().append("line") + .attr("stroke-width", function (d) { + return Math.sqrt(d.value); + }); + + node = svg.append("g") + .attr("class", "nodes") + .selectAll("circle") + //.data(graph.nodes) + .data(graph.nodes, function (d) { + return d.id; + }) + .enter().append("circle") + .attr("r", 5) + .attr("fill", function (d) { + return color(d.group); + }) + .call(d3.drag() + .on("start", dragstarted) + .on("drag", dragged) + .on("end", dragended)); + + node.append("title") + .text(function (d) { + return takeaname(d); + }); + node.append("text") + .attr("dx", 12) + .attr("dy", ".35em") + .text(function (d) { + return takeaname(d); + }); + + simulation.force("charge", d3.forceManyBody().strength(-10)); + simulation + .nodes(graph.nodes) + .on("tick", ticked) + .velocityDecay(0.2) + .force("x", d3.forceX().strength(.0005)) + .force("y", d3.forceY().strength(.0005)); + + simulation.force("link") + .links(graph.links); + + function ticked() { + node + .attr("cx", function (d) { + return d.x + }) + .attr("cy", function (d) { + return d.y + }) + link + .attr("x1", function (d) { + return d.source.x; + }) + .attr("y1", function (d) { + return d.source.y; + }) + .attr("x2", function (d) { + return d.target.x; + }) + .attr("y2", function (d) { + return d.target.y; + }); + } + + //---------------------init bar + bar_l2.attr("transform", function (d) { + return "translate(" + [x_range(tree_hi[1].length - max_Q.pos), 0] + ")" + }); + bar_l1.attr("transform", function (d) { + return "translate(" + [x_range(tree_hi[1].length - max_Q.pos), 0] + ")" + }); + var x0 = x_range(tree_hi[1].length - max_Q.pos); + y0 = y_range(max_Q.val); + focus.attr("transform", "translate(" + x0 + "," + y0 + ")"); + focus.select("text").text(max_Q.val); + focus.select("line.x") + .attr("x1", 0) + .attr("y1", 0) + .attr("x2", -x0) + .attr("y2", 0); + bar_l2.attr("x1", function (d) { + d.x1 = x0; + return bar_pos.x1 + }); + var numofg = 1; + update_group(tree_hi[1].length - max_Q.pos - 1); + //--------------- + bar_l2.call(d3.drag() + .on("start", dragstarted_bar) + .on("drag", dragged_bar) + .on("end", dragended_bar)) + .on("mousemove", dragstarted_bar) + .on("mouseout", mouseout); + + function mouseout(d) { + bar_l2.style("opacity", "0"); + focus.style('display', "none"); + clusterbox.style("display", "none"); + } + + function dragstarted_bar(d) { + bar_l2.style("opacity", "0.5"); + focus.style('display', null); + clusterbox.style("display", null); + var x0 = Math.round(x_range.invert(d.x1)); + d = y_range(tree_hi[1][tree_hi[1].length - x0]); + focus.attr("transform", "translate(" + x_range(x0) + "," + (d ) + ")"); + focus.select("text").text(tree_hi[1][tree_hi[1].length - x0]); + focus.select("line.x") + .attr("x1", 0) + .attr("y1", 0) + .attr("x2", -x_range(x0)) + .attr("y2", 0); + } + + function dragged_bar(d) { + bar_l2.on("mouseout", null) + d.x1 += d3.event.dx; + if (d.x1 <= 0) + d.x1 = 0; + else { + if (d.x1 >= wtree) + d.x1 = wtree; + + else { + bar_l2.attr("transform", function (d) { + return "translate(" + [d.x1, 0] + ")" + }); + bar_l1.attr("transform", function (d) { + return "translate(" + [d.x1, 0] + ")" + }); + } + + } + var x0 = Math.round(x_range.invert(d.x1)); + d = y_range(tree_hi[1][tree_hi[1].length - x0]); + focus.attr("transform", "translate(" + x_range(x0) + "," + (d ) + ")"); + focus.select("text").text(tree_hi[1][tree_hi[1].length - x0]); + focus.select("line.x") + .attr("x1", 0) + .attr("y1", 0) + .attr("x2", -x_range(x0)) + .attr("y2", 0); + //d.x2 = d.x1; + clusterbox.select("text").text("# of clusters : " + (x0 + 1) + " | Q : " + Math.round((tree_hi[1][tree_hi[1].length - x0]) * 1000) / 1000); + } + + function dragended_bar(d) { + bar_l2.style("opacity", "0") + .on("mouseout", mouseout); + ; + focus.style('display', "none"); + var depth = Math.round(x_range.invert(d.x1)) - 1; + if (depth < 0) + depth = 0; + //update_group(depth tree_hi[1].length-max_Q.pos-1); + update_group(depth); + } + + function update_group(depth) { + console.log("test if here first time: " + depth) + clusters = new Array(depth); + + var cg = 0; + var leave = []; + var node_t = []; + node_t.push(roots); + while (node_t.length != 0) { + var node_t_t = node_t.pop(); + if (tree_deep_cv(node_t_t.data.depth) < depth) { + if (node_t_t.children != null) + node_t = node_t_t.children.concat(node_t); + else + leave.push(node_t_t); + } else { + leave.push(node_t_t); + } + } + numofg = leave.length; + clusterbox.select("text").text("# of clusters : " + leave.length + " | Q : " + Math.round(tree_hi[1][tree_hi[1].length - 1 - depth] * 1000) / 1000); + for (var j = 0; j < leave.length; j++) { + //update for tree windown + node2.data(leave[j].leaves(), function (d) { + return takeaname(d.data); + }) + .selectAll("circle") + .attr("fill", function (d) { + return color(j); + }); + var node_temp = []; + link2.data(leave[j].descendants(), function (d) { + return takeaname(d.data); + }) + .attr("stroke", function (d) { + return color(j); + }); + //update for right group windown + leave[j].leaves().forEach(function (e) { + simulation.nodes().filter(function (n) { + if (takeaname(n) == e.data.name) { + n.group = j; + node_temp.push(n); + } + }) + }); + node.attr("fill", function (d) { + return color(d.group) + }); + } + + graph.nodes.forEach(function (d) { + if (!clusters[d.group]) { + clusters[d.group] = d; + } + }) + + var newlinks = []; + graph.links.forEach(function (d, i) { + if (d.source.group === d.target.group) + newlinks.push(i); + }) + simulation.force("cluster", clustering); + simulation.alphaTarget(0.2).restart(); + link.attr("opacity", function (d, i) { + return newlinks.indexOf(i) > -1 ? 0.1 : 1; + }) + + + function clustering(alpha) { + graph.nodes.forEach(function (d) { + var cluster = clusters[d.group]; + if (cluster === d) return; + var x = d.x - cluster.x, + y = d.y - cluster.y, + l = Math.sqrt(x * x + y * y), + r = 10; + if (l !== r) { + l = (l - r) / l * alpha; + d.x -= x *= l; + d.y -= y *= l; + cluster.x += x; + cluster.y += y; + } + }); + } + } + + +}); + +function dragstarted(d) { + if (!d3.event.active) simulation.alphaTarget(0.3).restart(); + d.fx = d.x; + d.fy = d.y; +} + +function dragged(d) { + d.fx = d3.event.x; + d.fy = d3.event.y; +} + +function dragended(d) { + if (!d3.event.active) simulation.alphaTarget(0); + d.fx = null; + d.fy = null; +} + + + diff --git a/scripts/math_script.js b/scripts/math_script.js index e5aa617..21c6999 100644 --- a/scripts/math_script.js +++ b/scripts/math_script.js @@ -1,555 +1,891 @@ -function findbi(e,key,start,end){ - while (start<=end){ - var p = Math.floor((start+end)/2); - if (e.links[p].sourcekey){ - end=p-1; - }else{ - return p; - } - } - } - return -1; -} - -function findnei(a,key,av){ - var nei=[]; - if (key[1])//virtual node - { - if (a[a[2]][a[0]]>0){//virtual node next - a[a[2]][a[0]] -=av; - a[a[0]][a[2]] -=av; - nei.push(key); - }else{ - nei.push([a[0],false,a[2]]); - } - }else{ - for (var i=0;i0){ - if (a[key[0]][i]>av) - nei.push([i,true,key[0]]);// virtual node - else - nei.push([i,false,key[0]]); - a[key[0]][i]-=av; - a[i][key[0]]-=av; - } - } - } - return nei; -} - -function init(m,n){ - var ar= []; - for (var i = 0; i < m; i++) { - var art=[]; - for (var j = 0; j < n; j++) { - art.push(0); - } - ar.push(art); - } - return ar; - } - -function init_empty(m){ - var ar= []; - for (var i = 0; i < m; i++) { - var art=[]; - ar.push(art); - } - return ar; - } - -function a_array(ee){ - var a = init(ee.nodes.length,ee.nodes.length); - ee.links.forEach(function(e){ - var ii=0; - var jj=0; - ee.nodes.forEach(function(n,i){ - if (e.source==n.id) - ii=i; - else - if (e.target==n.id) - jj=i; - }); - a[ii][jj]=e.value; - a[jj][ii]=e.value; - }); - return a; -} - -function a_array_av(ee){ - var a = init_empty(ee.nodes.length); - var sum = 0; - var m = ee.links.length; - ee.links.forEach(function(e){ - var ii=0; - var jj=0; - ee.nodes.filter(function(n,i){ - if (e.source==n.id) - ii=i; - else - if (e.target==n.id) - jj=i; - }); - sum = sum + (e.value); - a[ii].push({nei: jj,val: e.value}); - a[jj].push({nei: ii,val: e.value}); - - }); - return [a,sum/m]; -} - - - -function calculate_m(ee){ - var sum = 0; - var m = ee.links.length; - ee.links.forEach(function(e){ - var ii=0; - var jj=0; - /*ee.nodes.filter(function(n,i){ - if (e.source==n.id) - ii=i; - else - if (e.target==n.id) - jj=i; - });*/ - sum = sum+e.value; - - }); - return sum; -} - -function a_array_ext(arr,av){ - var l = arr.length; - for (var iii=0;iii1) - { - arr[iii][jjj] = {nei: arr.length, val: av, ori:nei}; - //arr[iii][jjj].nei = arr.length; - //arr[iii][jjj].val = av; - - arr.push([{nei: iii, val: av,ori:nei},{nei: nei,val: av,ori:iii}]); - for (var z = 2; z av: "+av); - while (step.length!=graph.links.length){ - //var alink_oc = copyA(alink_o); - //document.write("
old array size: "+alink_o[3][0].nei); - //var alink_fix = a_array_ext(alink_oc,av); // add virtual nodes - //document.write("
old array size: "+alink_o[3][0].nei); - //var alink = alink_fix[0]; //fixed - // calculate - var ebs=init(num_n,num_n); - var max_ebs=[0,0,0]; - for (var s = 0; s < num_n; s++) { - var S=[]; - var Leaf=[]; - var Pathu=[]; - var Pathd=[]; - var d=[]; - var w=[]; - d[s]=0; - w[s]=1; - var Q=[]; - Q.push(s); - while (Q.length!=0){ - var i = Q.shift(); - if (i"+i+": "); - //console.log(" to: "+i); - alink_fix[i].forEach(function(e,indd){ - var j = e.nei; - if (d[j]==null){ - d[j]=d[i]+1; - w[j]=w[i]; - Q.push(j); - - if (i"+" - "+e.nei+": "+"d :"+d[e.nei]+"w :"+w[e.nei]); - }); - if (Q.length ==l&&(i!=s)&&(i"+" - "+i+" - w:"+w[i]); - - document.write("
"+" --- u"); - if(Pathu[i]!=null) - Pathu[i].forEach(function(e){document.write("- "+e);}); - document.write("
"+" --- d"); - if(Pathd[i]!=null) - Pathd[i].forEach(function(e){document.write("- "+e);}); - };*/ - var eb=init(num_n,num_n); - var gene =[]; - //Leaf - /*while(Leaf.length!=0){ - var t=Leaf.pop(); - console.log("list Leaf: "+t); - //S.filter(function(e,inde){if (e==t){ S.splice(inde,1); return;}}); - //document.write("
"+" -Leaf "+t); - while (Pathu[t].length!=0){ - var i = Pathu[t].pop(); - eb[i][t] += w[i]/w[t]; - eb[t][i] += w[i]/w[t]; - ebs[i][t] += w[i]/w[t]; - ebs[t][i] += w[i]/w[t]; - //console.log(ebs[i][t]); - if (ebs[i][t]>max_ebs[0]){ - max_ebs[0]=ebs[i][t]; - max_ebs[1]=i; - max_ebs[2]=t; - } - if (ebs[t][i]>max_ebs[0]){ - max_ebs[0]=ebs[t][i]; - max_ebs[1]=t; - max_ebs[2]=i; - } - - } - }*/ - //document.write("
"+" ----- "); - //document.write("
"+S); - //cont - S.splice(0,1); - while (S.length!=0){ - var j = S.pop(); - //console.log(j+" -- "+d[j]); - if (Pathd[j]!=null) - { - //document.write("
-- "+j); - var sumb=1; - while (Pathd[j].length!=0){ - var jj = Pathd[j].pop(); - sumb+=eb[j][jj]; - } - if (Pathu[j]!=null) - { - while (Pathu[j].length!=0){ - var i = Pathu[j].pop(); - eb[i][j]=w[i]/w[j]*sumb; - //eb[j][i]+=w[i]/w[j]*sumb; - ebs[i][j]+=w[i]/w[j]*sumb; - //ebs[j][i]+=w[i]/w[j]*sumb; - //console.log("2-10: "+ebs[2][10]+" 10-12: "+ebs[10][12]+"10-9: "+ebs[9][10]); - //console.log(ebs[i][t]); - if (ebs[i][j]>max_ebs[0]){ - max_ebs[0]=ebs[i][j]; - max_ebs[1]=i; - max_ebs[2]=j; - //console.log("i: "+max_ebs[1]+" j: "+max_ebs[2]+" max "+max_ebs[0]); - //document.write("
"+"max "+ max_ebs); - } - else{ - if (ebs[i][j]==max_ebs[0]){ - if (Math.abs(d[i]-d[j])"+"max "+ max_ebs); - } - } - } - - } - } - } - else{ - while (Pathu[j].length!=0){ - var i = Pathu[j].pop(); - eb[i][j] = w[i]/w[j]; - //eb[j][i] += w[i]/w[j]; - ebs[i][j] += w[i]/w[j]; - // ebs[j][i] += w[i]/w[j]; - if (ebs[i][j]>max_ebs[0]){ - max_ebs[0]=ebs[i][j]; - max_ebs[1]=i; - max_ebs[2]=j; - //console.log("i: "+max_ebs[1]+" j: "+max_ebs[2]+" max "+max_ebs[0]); - } else{ - if (ebs[i][j]==max_ebs[0]){ - if (Math.abs(d[i]-d[j])"+"max "+ max_ebs); - } - } - } - - } - } - } - //console.log("----end---- "+s); - } - if (max_ebs[0]!=0){ - step.push([max_ebs[1],max_ebs[2]]); - //av = av*num_l; - //document.write("
"+"max "+ max_ebs[0]); - for (var i =0;i"+"-- "+ alink_o[max_ebs[1]][i].nei); - if (alink_fix[max_ebs[1]][i].nei== max_ebs[2]||alink_fix[max_ebs[1]][i].ori== max_ebs[2]){ - //av = av - alink_o[max_ebs[1]][i].val; - //num_l--; - //av = av/num_l; - alink_fix[max_ebs[1]].splice(i,1); - break; - } - } - - for (var i =0;i"+"--- "+ alink_o[max_ebs[2]][i].nei); - if (alink_fix[max_ebs[2]][i].nei== max_ebs[1]||alink_fix[max_ebs[2]][i].ori== max_ebs[1]){ - alink_fix[max_ebs[2]].splice(i,1); - break; - } - } - } - //console.log("----step: "+ step+" av"+av+"
"); - } - return step; -} - -function Q_init(A,m,a_e){ - var n = A.length; - var Q = 0; - for (var i = 0;i new group - //Q - Q_t += delta_Q(grouping[g1][0],grouping[g2][0],m,A,a_e); - Q.push(Q_t); - //move - grouping.splice(g1,1,grouping[g1].concat(grouping[g2])); - grouping.splice(g2,1); - var hi_t=[]; - hi_t.push(hi[g1]); - hi_t.push(hi[g2]); - hi[g1]={name: li,children: hi_t,depth: lv, Q: Q_t}; - hi.splice(g2,1); - //document.write("case 1 "+g1+" "+g2+" "+JSON.stringify(hi)+"
"); - }else{ - // 1 element + 1 group -> new group - var li_t= li; - if (g2==-1){// li[1] is new element - li_t[0]=li_t[1]; - }else{ - g1=g2; - } - //Q - Q_t += delta_Q(grouping[g1][0],li[0],m,A,a_e); - Q.push(Q_t); - //move - grouping[g1].push(li[0]); - hi[g1]={name: li,children: [hi[g1]], depth: lv, Q:Q_t}; - hi[g1].children.push({name: takeaname(graph.nodes[li_t[0]]) , depth: 0}); - //document.write("case 2 "+JSON.stringify(hi)+"
"); - } - }else{ - if (g1==-1) - { - lv++; - //Q - Q_t += delta_Q(li[0],li[1],m,A,a_e); - Q.push(Q_t); - //move - grouping.push(li); - hi.push({name: li,children: [{name: takeaname(graph.nodes[li[0]]), depth: 0},{name: takeaname(graph.nodes[li[1]]), depth: 0}], depth: lv, Q: Q_t}); - //document.write("case 3 "+JSON.stringify(hi)+"
"); - } - } - } - if (hi.length==1){ - return [hi[0],Q]; - } - else{ - hi[0]={name: "join all",children: [hi[0]],depth: lv+1, Q: Q_t}; - while (grouping.length != 1){ - Q_t += delta_Q(grouping[0][0],grouping[1][0],m,A,a_e); - grouping.splice(0,1,grouping[0].concat(grouping[1])); - grouping.splice(1,1); - hi[0].children.push(hi[1]); - hi.splice(1,1); - } - - Q.push(Q_t); - return [hi[0],Q]; - } +function findbi(e, key, start, end) { + while (start <= end) { + var p = Math.floor((start + end) / 2); + if (e.links[p].source < key) { + start = p + 1; + } else { + if (e.links[p].source > key) { + end = p - 1; + } else { + return p; + } + } + } + return -1; +} + +function findnei(a, key, av) { + var nei = []; + if (key[1])//virtual node + { + if (a[a[2]][a[0]] > 0) {//virtual node next + a[a[2]][a[0]] -= av; + a[a[0]][a[2]] -= av; + nei.push(key); + } else { + nei.push([a[0], false, a[2]]); + } + } else { + for (var i = 0; i < a[0].length; i++) { + if (a[key[0]][i] > 0) { + if (a[key[0]][i] > av) + nei.push([i, true, key[0]]);// virtual node + else + nei.push([i, false, key[0]]); + a[key[0]][i] -= av; + a[i][key[0]] -= av; + } + } + } + return nei; +} + +function init(m, n) { + var ar = []; + for (var i = 0; i < m; i++) { + var art = []; + for (var j = 0; j < n; j++) { + art.push(0); + } + ar.push(art); + } + return ar; +} + +function init_empty(m) { + var ar = []; + for (var i = 0; i < m; i++) { + var art = []; + ar.push(art); + } + return ar; +} + +function a_array(ee) { + var a = init(ee.nodes.length, ee.nodes.length); + ee.links.forEach(function (e) { + var ii = 0; + var jj = 0; + ee.nodes.forEach(function (n, i) { + if (e.source == n.id) + ii = i; + else if (e.target == n.id) + jj = i; + }); + a[ii][jj] = e.value; + a[jj][ii] = e.value; + }); + return a; +} + +function a_array_av(ee) { + var a = init_empty(ee.nodes.length); + var sum = 0; + var m = ee.links.length; + ee.links.forEach(function (e) { + var ii = 0; + var jj = 0; + ee.nodes.filter(function (n, i) { + if (e.source == n.id) + ii = i; + else if (e.target == n.id) + jj = i; + }); + sum = sum + (e.value); + a[ii].push({nei: jj, val: e.value}); + a[jj].push({nei: ii, val: e.value}); + + }); + return [a, sum / m]; +} + + +function calculate_m(ee) { + var sum = 0; + var m = ee.links.length; + ee.links.forEach(function (e) { + var ii = 0; + var jj = 0; + /*ee.nodes.filter(function(n,i){ + if (e.source==n.id) + ii=i; + else + if (e.target==n.id) + jj=i; + });*/ + sum = sum + e.value; + + }); + return sum; +} + +function a_array_ext(arr, av) { + var l = arr.length; + for (var iii = 0; iii < l; iii++) { + for (var jjj = 0; jjj < arr[iii].length; jjj++) { + var n = Math.round(arr[iii][jjj].val / av); + var nei = arr[iii][jjj].nei; + if (n > 1) { + arr[iii][jjj] = {nei: arr.length, val: av, ori: nei}; + //arr[iii][jjj].nei = arr.length; + //arr[iii][jjj].val = av; + + arr.push([{nei: iii, val: av, ori: nei}, {nei: nei, val: av, ori: iii}]); + for (var z = 2; z < n; z++) { + var ll = arr.length; + //arr[ll-1][1].nei = ll; + arr[ll - 1][1] = {nei: ll, var: av, ori: iii}; + arr.push([{nei: ll - 1, val: av}, {nei: nei, val: av, ori: nei}]); + } + arr[nei].filter(function (n, i) { + if (n.nei == iii) { + arr[nei].splice(i, 1, {nei: arr.length - 1, val: av, ori: iii}); + //n.val = av; + //n.nei = arr.length-1;//last virtual node + } + }); + } + } + } + return [arr, av]; +} + +function finditem(grouping, li, graph) { + var g1 = -1; + var g2 = -1; + for (var i = 0; (i < grouping.length) && (g1 == -1 || g2 == -1); i++) { + for (var j = 0; (j < grouping[i].length) && (g1 == -1 || g2 == -1); j++) { + if (g1 == -1 && grouping[i][j] == li[0]) + g1 = i; + if (g2 == -1 && grouping[i][j] == li[1]) + g2 = i; + } + } + return [g1, g2]; +} + +function clone(obj) { + if (null == obj || "object" != typeof obj) return obj; + var copy = obj.constructor(); + for (var attr in obj) { + if (obj.hasOwnProperty(attr)) copy[attr] = obj[attr]; + } + return copy; +} + + +function copyA(a) { + var b = []; + a.forEach(function (e) { + var bb = []; + e.forEach(function (e) { + bb.push(clone(e)); + }); + b.push(bb); + }); + return b; +} +//virtual nodes +function between_e(graph) { + var alink_o = a_array_av(graph); // orgiginal + var av = alink_o[1]; + alink_o = alink_o[0]; + var alink_fix = a_array_ext(alink_o, av)[0]; // add virtual nodes + var num_n = graph.nodes.length;// num of node + var step = []; + var num_l = graph.links.length; + //document.write("
av: "+av); + while (step.length != num_l) { + //var alink_oc = copyA(alink_o); + //document.write("
old array size: "+alink_o[3][0].nei); + //var alink_fix = a_array_ext(alink_oc,av); // add virtual nodes + //document.write("
old array size: "+alink_o[3][0].nei); + //var alink = alink_fix[0]; //fixed + // calculate + var ebs = init(num_n, num_n); + var max_ebs = [0, 0, 0]; + var start_time = performance.now(); + for (var s = 0; s < num_n; s++) { + var S = []; + var Leaf = []; + var Pathu = []; + var Pathd = []; + var d = []; + var w = []; + d[s] = 0; + w[s] = 1; + var Q = []; + Q.push(s); + while (Q.length != 0) { + var i = Q.shift(); + if (i < num_n) S.push(i); + var l = Q.length; + //document.write("
"+i+": "); + //console.log(" to: "+i); + alink_fix[i].forEach(function (e, indd) { + var j = e.nei; + if (d[j] == null) { + d[j] = d[i] + 1; + w[j] = w[i]; + Q.push(j); + + if (i < num_n) {//not virtual node + Pathu[j] = [i]; + if (j < num_n) { + if (Pathd[i] == null) + Pathd[i] = [j]; + else + Pathd[i].push(j); + } + //console.log(i+" Pathd "+ Pathd[i]); + } else { + Pathu[j] = Pathu[i]; + if (j < num_n) { + if (Pathd[alink_fix[i][indd].ori] == null) + Pathd[alink_fix[i][indd].ori] = [j]; + else + Pathd[alink_fix[i][indd].ori].push(j); + + } + //console.log(alink_fix[i][indd].ori+" Pathd "+ Pathd[alink_fix[i][indd].ori]); + } + //console.log(j+" Pathu "+ Pathu[j]); + + } else { + if (d[j] == d[i] + 1) { + w[j] = w[j] + w[i]; + if (i < num_n) {//not virtual node + Pathu[j].push(i); + if (j < num_n) { + if (Pathd[i] == null) + Pathd[i] = [j]; + else + Pathd[i].push(j); + }//if j is virtual , j won't be visit second time + } else { + if (j < num_n) { + Pathu[j].concat(Pathu[i]); + if (Pathd[alink_fix[i][indd].ori] == null) + Pathd[alink_fix[i][indd].ori] = [j]; + else + Pathd[alink_fix[i][indd].ori].concat(Pathd[j]); + + } + } + //console.log(i+" Pathd "+ Pathd[i]); + //console.log(j+" Pathu "+ Pathu[j]); + } + }//document.write("
"+" - "+e.nei+": "+"d :"+d[e.nei]+"w :"+w[e.nei]); + }); + if (Q.length == l && (i != s) && (i < num_n)) + Leaf.push(i); + } + /*for (var i=0;i"+" - "+i+" - w:"+w[i]); + + document.write("
"+" --- u"); + if(Pathu[i]!=null) + Pathu[i].forEach(function(e){document.write("- "+e);}); + document.write("
"+" --- d"); + if(Pathd[i]!=null) + Pathd[i].forEach(function(e){document.write("- "+e);}); + };*/ + var eb = init(num_n, num_n); + var gene = []; + //Leaf + /*while(Leaf.length!=0){ + var t=Leaf.pop(); + console.log("list Leaf: "+t); + //S.filter(function(e,inde){if (e==t){ S.splice(inde,1); return;}}); + //document.write("
"+" -Leaf "+t); + while (Pathu[t].length!=0){ + var i = Pathu[t].pop(); + eb[i][t] += w[i]/w[t]; + eb[t][i] += w[i]/w[t]; + ebs[i][t] += w[i]/w[t]; + ebs[t][i] += w[i]/w[t]; + //console.log(ebs[i][t]); + if (ebs[i][t]>max_ebs[0]){ + max_ebs[0]=ebs[i][t]; + max_ebs[1]=i; + max_ebs[2]=t; + } + if (ebs[t][i]>max_ebs[0]){ + max_ebs[0]=ebs[t][i]; + max_ebs[1]=t; + max_ebs[2]=i; + } + + } + }*/ + //document.write("
"+" ----- "); + //document.write("
"+S); + //cont + S.splice(0, 1); + while (S.length != 0) { + var j = S.pop(); + //console.log(j+" -- "+d[j]); + if (Pathd[j] != null) { + //document.write("
-- "+j); + var sumb = 1; + while (Pathd[j].length != 0) { + var jj = Pathd[j].pop(); + sumb += eb[j][jj]; + } + if (Pathu[j] != null) { + while (Pathu[j].length != 0) { + var i = Pathu[j].pop(); + eb[i][j] = w[i] / w[j] * sumb; + //eb[j][i]+=w[i]/w[j]*sumb; + ebs[i][j] += w[i] / w[j] * sumb; + //ebs[j][i]+=w[i]/w[j]*sumb; + //console.log("2-10: "+ebs[2][10]+" 10-12: "+ebs[10][12]+"10-9: "+ebs[9][10]); + //console.log(ebs[i][t]); + if (ebs[i][j] > max_ebs[0]) { + max_ebs[0] = ebs[i][j]; + max_ebs[1] = i; + max_ebs[2] = j; + //console.log("i: "+max_ebs[1]+" j: "+max_ebs[2]+" max "+max_ebs[0]); + //document.write("
"+"max "+ max_ebs); + } + else { + if (ebs[i][j] == max_ebs[0]) { + if (Math.abs(d[i] - d[j]) < Math.abs(d[max_ebs[1]] - d[max_ebs[2]])) { + max_ebs[0] = ebs[i][j]; + max_ebs[1] = i; + max_ebs[2] = j; + //console.log("i: "+max_ebs[1]+" j: "+max_ebs[2]+" max "+max_ebs[0]); + //document.write("
"+"max "+ max_ebs); + } + } + } + + } + } + } + else { + while (Pathu[j].length != 0) { + var i = Pathu[j].pop(); + eb[i][j] = w[i] / w[j]; + //eb[j][i] += w[i]/w[j]; + ebs[i][j] += w[i] / w[j]; + // ebs[j][i] += w[i]/w[j]; + if (ebs[i][j] > max_ebs[0]) { + max_ebs[0] = ebs[i][j]; + max_ebs[1] = i; + max_ebs[2] = j; + //console.log("i: "+max_ebs[1]+" j: "+max_ebs[2]+" max "+max_ebs[0]); + } else { + if (ebs[i][j] == max_ebs[0]) { + if (Math.abs(d[i] - d[j]) < Math.abs(d[max_ebs[1]] - d[max_ebs[2]])) { + max_ebs[0] = ebs[i][j]; + max_ebs[1] = i; + max_ebs[2] = j; + //console.log("i: "+max_ebs[1]+" j: "+max_ebs[2]+" max "+max_ebs[0]); + //document.write("
"+"max "+ max_ebs); + } + } + } + + } + } + } + //console.log("----end---- "+s); + } + var end_time_b = performance.now(); + console.log("Time for old technique"); + console.log(end_time_b-start_time); + if (max_ebs[0] != 0) { + step.push([max_ebs[1], max_ebs[2]]); + //av = av*num_l; + //document.write("
"+"max "+ max_ebs[0]); + for (var i = 0; i < alink_fix[max_ebs[1]].length; i++) { + //document.write("
"+"-- "+ alink_o[max_ebs[1]][i].nei); + if (alink_fix[max_ebs[1]][i].nei == max_ebs[2] || alink_fix[max_ebs[1]][i].ori == max_ebs[2]) { + //av = av - alink_o[max_ebs[1]][i].val; + //num_l--; + //av = av/num_l; + alink_fix[max_ebs[1]].splice(i, 1); + break; + } + } + + for (var i = 0; i < alink_fix[max_ebs[2]].length; i++) { + //document.write("
"+"--- "+ alink_o[max_ebs[2]][i].nei); + if (alink_fix[max_ebs[2]][i].nei == max_ebs[1] || alink_fix[max_ebs[2]][i].ori == max_ebs[1]) { + alink_fix[max_ebs[2]].splice(i, 1); + break; + } + } + } + //console.log("----step: "+ step+" av"+av+"
"); + } + return step; +} + +function Q_init(A, m, a_e) { + var n = A.length; + var Q = 0; + for (var i = 0; i < n; i++) { + var sum = 0; + for (var j = 0; j < n; j++) { + sum += A[i][j]; + } + a_e.push(sum / 2 / m); + Q -= Math.pow(sum / 2 / m, 2); + } + return Q; +} + +function delta_Q(i, j, m, A, a_e) { + var n = A.length; + var delta_Q = 2 * (A[i][j] / 2 / m - a_e[i] * a_e[j]); + //update + A[i][i] += A[j][j] + A[i][j] + A[j][i]; + A[j][j] = 0; + A[j][i] = 0; + A[i][j] = 0; + var sum = 0; + for (var k = 0; k < n; k++) { + if (k != i && k != j) { + A[i][k] = A[i][k] + A[j][k]; + A[k][i] = A [i][k]; + A[j][k] = 0; + A[k][j] = 0; + } + sum += A[i][k]; + } + a_e[i] = sum / 2 / m; + a_e[j] = 0; + return delta_Q; +} +function takeaname(d) { + return d.label != null ? d.label : (d.name != null ? d.name : d.id); +} +function tree_mapingv3(step, graph) { + var grouping = []; + var ed = step.pop(); + var lv = 1; + var m = calculate_m(graph); + var A = a_array(graph); + var a_e = []; + var Q = []; + var Q_t = Q_init(A, m, a_e); + Q.push(Q_t); + grouping.push(ed); + // join 2 nodes together + Q_t += delta_Q(ed[0], ed[1], m, A, a_e); + //---- + Q.push(Q_t); + var hi = [{ + name: ed, + children: [{name: takeaname(graph.nodes[ed[0]]), depth: 0}, {name: takeaname(graph.nodes[ed[1]]), depth: 0}], + depth: lv, + Q: Q_t + }]; + while (step.length != 0) { + var li = step.pop(); + // 4 main case + for (var i = 0; i < grouping.length; i++) { + var g = finditem(grouping, li, graph); + } + + var g1 = g[0]; + var g2 = g[1]; + if (g1 != g2) { + lv++; + if (g1 != -1 && g2 != -1) { + // 2 groups -> new group + //Q + Q_t += delta_Q(grouping[g1][0], grouping[g2][0], m, A, a_e); + Q.push(Q_t); + //move + grouping.splice(g1, 1, grouping[g1].concat(grouping[g2])); + grouping.splice(g2, 1); + var hi_t = []; + hi_t.push(hi[g1]); + hi_t.push(hi[g2]); + hi[g1] = {name: li, children: hi_t, depth: lv, Q: Q_t}; + hi.splice(g2, 1); + //document.write("case 1 "+g1+" "+g2+" "+JSON.stringify(hi)+"
"); + } else { + // 1 element + 1 group -> new group + var li_t = li; + if (g2 == -1) {// li[1] is new element + li_t[0] = li_t[1]; + } else { + g1 = g2; + } + //Q + Q_t += delta_Q(grouping[g1][0], li[0], m, A, a_e); + Q.push(Q_t); + //move + grouping[g1].push(li[0]); + hi[g1] = {name: li, children: [hi[g1]], depth: lv, Q: Q_t}; + hi[g1].children.push({name: takeaname(graph.nodes[li_t[0]]), depth: 0}); + //document.write("case 2 "+JSON.stringify(hi)+"
"); + } + } else { + if (g1 == -1) { + lv++; + //Q + Q_t += delta_Q(li[0], li[1], m, A, a_e); + Q.push(Q_t); + //move + grouping.push(li); + hi.push({ + name: li, + children: [{name: takeaname(graph.nodes[li[0]]), depth: 0}, { + name: takeaname(graph.nodes[li[1]]), + depth: 0 + }], + depth: lv, + Q: Q_t + }); + //document.write("case 3 "+JSON.stringify(hi)+"
"); + } + } + } + if (hi.length == 1) { + return [hi[0], Q]; + } + else { + hi[0] = {name: "join all", children: [hi[0]], depth: lv + 1, Q: Q_t}; + while (grouping.length != 1) { + Q_t += delta_Q(grouping[0][0], grouping[1][0], m, A, a_e); + grouping.splice(0, 1, grouping[0].concat(grouping[1])); + grouping.splice(1, 1); + hi[0].children.push(hi[1]); + hi.splice(1, 1); + } + + Q.push(Q_t); + return [hi[0], Q]; + } +} +//Start Vinh's code + +function make2dArray(len) { + var a = []; + while (a.push([]) < len); + return a; +} +function graph_nodes_random(nodes, size) { + var oldnodes = []; + for (i = 0; i < nodes; i++) { + oldnodes.push(i) + } + var newnodes = []; + for (i = 0; i < size; i++) { + var value = oldnodes[Math.floor(oldnodes.length * Math.random())]; + var index = oldnodes.indexOf(value); + newnodes.push(value); + oldnodes.splice(index, 1); + } + return newnodes.sort(function (a, b) { + return a - b; + }); +} + +function edge_betweenness_centrality(graph, k='none', normalized=true, weight) { + var num_node = graph.nodes.length; + var num_link = graph.links.length; + //var tempgraph = Object.assign({}, graph.nodes); + var betweenness = new Object(); + for (var linkitem = 0; linkitem < graph.links.length; linkitem++) { + for (var nodeItem = 0; nodeItem < num_node; nodeItem++) { + + if (graph.nodes[nodeItem].id == graph.links[linkitem].source) { + graph.links[linkitem].source = nodeItem; + } + if (graph.nodes[nodeItem].id == graph.links[linkitem].target) { + graph.links[linkitem].target = nodeItem; + } + } + } + var step = []; + + var nodes; + + var neighbours = make2dArray(num_node); + for (var i = 0; i < graph.links.length; i++) { + var source = graph.links[i].source; + var target = graph.links[i].target; + var value = graph.links[i].value; + neighbours[source].push([target, value]); + neighbours[target].push([source, value]); + } + if (k !== 'none') { + nodes = graph_nodes_random(num_node, k) + } + else { + nodes = graph_nodes_random(num_node, num_node); + } + while (step.length != 1) { + for (i = 0; i < num_node; i++) { + betweenness[i] = 0.0 + } + for (var i = 0; i < graph.links.length; i++) { + var source = graph.links[i].source; + var target = graph.links[i].target; + betweenness[source + "," + target] = 0.0; + } + var start_time = performance.now(); + for (s = 0; s < nodes.length; s++) { + if (weight == true) { + var SPSigma = _single_source_dijkstra_path_basic(neighbours, nodes[s], weight); + var S = SPSigma[0]; + var P = SPSigma[1]; + var sigma = SPSigma[2]; + betweenness = _accumulate_edges(betweenness, S, P, sigma, nodes[s]); + } else { + var SPSigma = _single_source_shortest_path_basic(neighbours, nodes[s]); + var S = SPSigma[0]; + var P = SPSigma[1]; + var sigma = SPSigma[2]; + betweenness = _accumulate_edges(betweenness, S, P, sigma, nodes[s]); + } + } + var end_time_b = performance.now(); + console.log(end_time_b-start_time); + for (n = 0; n < num_node; n++) { + delete betweenness[n]; + } + var scale = 1.0 / ((num_node) * (num_node - 1)) + for (var key in betweenness) { + if (!betweenness.hasOwnProperty(key)) continue; + betweenness[key] *= scale; + } + + var obkey, obvalue = 0; + for (var key in betweenness) { + if (betweenness[key] > obvalue) { + obvalue = betweenness[key]; + obkey = key.split(",").map(Number); + } + } + step.push([obkey[0], obkey[1]]); + for (i = 0; i < neighbours[obkey[0]].length; i++) { + if (neighbours[obkey[0]][i][0] === obkey[1]) { + neighbours[obkey[0]].splice(i, 1); + } + } + for (i = 0; i < neighbours[obkey[1]].length; i++) { + if (neighbours[obkey[1]][i][0] === obkey[0]) { + neighbours[obkey[1]].splice(i, 1); + } + } + } + + return step; +} +function _single_source_dijkstra_path_basic(G, s, weight='weight') { + var S = [], P = new Object(), sigma = new Object(), D = new Object(); + var Q = []; + for (var v = 0; v < G.length; v++) { + P[v] = []; + sigma[v] = 0; + } + sigma[s] = 1.0 + seen = new Object(); + seen[s] = 0; + var count = 0; + + Q.push([0, count, s, s]); + + while (Q.length > 0) { + Q.sort(function (a, b) { + return a[0] - b[0]; + }) + var getvalue = Q.shift(); + var dist = getvalue[0]; + var _ = getvalue[1]; + var pred = getvalue[2]; + var v = getvalue[3]; + if (D.hasOwnProperty(v)) { + continue; + } + sigma[v] += sigma[pred]; + S.push(v); + D[v] = dist; + + for (var link = 0; link < G[v].length; link++) { + var vw_dist = dist + G[v][link][1]; + var w = G[v][link][0]; + if (!D.hasOwnProperty(w) && (!seen.hasOwnProperty(w) || vw_dist < seen[w])) { + seen[w] = vw_dist; + Q.push([vw_dist, ++count, v, w]); + sigma[w] = 0.0; + P[w] = [v]; + } else if (vw_dist === seen[w]) { + sigma[w] += sigma[v]; + P[w].push(v) + } + } + } + return [S, P, sigma]; + +} +function _single_source_shortest_path_basic(G, s) { + var S = [], P = new Object(), sigma = new Object(), D = new Object(); + for (var item = 0; item < G.length; item++) { + P[item] = []; + sigma[item] = 0; + } + sigma[s] = 1; + D[s] = 0; + var Q = []; + Q.push(s); + while (Q.length > 0) { + v = Q.shift(); + S.push(v); + Dv = D[v]; + sigmav = sigma[v]; + for (var item = 0; item < G[v].length; item++) { + if (!D.hasOwnProperty(G[v][item][0])) { + Q.push(G[v][item][0]); + D[G[v][item][0]] = Dv + 1; + } + if (D[G[v][item][0]] === Dv + 1) { + sigma[G[v][item][0]] += sigmav; + P[G[v][item][0]].push(v); + } + } + + } + return [S, P, sigma]; +} +function _accumulate_edges(betweenness, S, P, sigma, s) { + var delta = new Object(); + for (var i = 0; i < S.length; i++) { + delta[S[i]] = 0; + } + while (S.length > 0) { + var w = S.pop(); + var coeff = (1.0 + delta[w]) / sigma[w]; + for (var v = 0; v < P[w].length; v++) { + var c = sigma[P[w][v]] * coeff; + var p1 = P[w][v] + "," + w; + var p2 = w + "," + P[w][v]; + if (!betweenness.hasOwnProperty(p1)) { + betweenness[(p2)] += c; + } else { + betweenness[(p1)] += c; + } + delta[P[w][v]] += c; + } + if (w !== P[w][v]) { + betweenness[w] += delta[w]; + } + } + return betweenness; +} +function _getV(graph) { + var alink_o = a_array_av(graph); // orgiginal + var av = alink_o[1]; + alink_o = alink_o[0]; + var alink_fix = a_array_ext(alink_o, av)[0]; + var adjList = []; + for (i = 0; i < alink_fix.length; i++) { + adjList[i] = []; + for (j = 0; j < alink_fix[i].length; j++) { + adjList[i].push(alink_fix[i][j].nei) + } + } + + return adjList; +} +function _removeEdge(_graph, _edge) { + _graph.links.forEach(function (d, i) { + if (d.source === _edge[0] && d.target === _edge[1] || d.source === _edge[1] && d.target === _edge[0]) { + _graph.links.splice(i, 1); + } + }); + return _graph; + +} +function _betweennness_virtual(graph) { + var step = []; + var alink_o = a_array_av(graph); // orgiginal + var av = alink_o[1]; + alink_o = alink_o[0]; + var VirtualAdj = a_array_ext(alink_o, av)[0]; + var betweenness = new Object(); + var nodes = []; + var num_node = graph.nodes.length; + graph.nodes.forEach(function (d) { + nodes.push(+d.id); + }); + if (k !== 'none') { + nodes = graph_nodes_random(num_node, k) + } + graph.links.forEach(function (d) { + betweenness[d.source + ',' + d.target] = 0; + }); + // var start_time = performance.now(); + while (step.length != graph.links.length) { + var start_time = performance.now(); + nodes.forEach(function (s) { + var SPSigma = _single_source_shortest_path_basic_virtual_nodes(VirtualAdj, s, nodes); + var S = SPSigma[0]; + var P = SPSigma[1]; + var sigma = SPSigma[2]; + betweenness = _accumulate_edges(betweenness, S, P, sigma, s); + }); + var end_time_b = performance.now(); + nodes.forEach(function (s) { + delete betweenness[s]; + }); + var result = _.first(_.max(_.pairs(betweenness), _.last)).split(','); + step.push(result.map(Number)); + for (var i = 0; i < VirtualAdj[result[0]].length; i++) { + //document.write("
"+"-- "+ alink_o[max_ebs[1]][i].nei); + if (VirtualAdj[result[0]][i].nei == result[1] || VirtualAdj[result[0]][i].ori == result[1]) { + VirtualAdj[result[0]].splice(i, 1); + break; + } + } + for (var i = 0; i < VirtualAdj[result[1]].length; i++) { + if (VirtualAdj[result[1]][i].nei == result[0] || VirtualAdj[result[1]][i].ori == result[0]) { + VirtualAdj[result[1]].splice(i, 1); + break; + } + } + delete betweenness[_.first(_.max(_.pairs(betweenness), _.last))]; + } + + return step; + +} +function _single_source_shortest_path_basic_virtual_nodes(G, s, nodes) { + var S = [], P = new Object(), sigma = new Object(), D = new Object(); + for (i = 0; i < G.length; i++) { + P[i] = []; + sigma[i] = 0; + D[i] = -1; + } + sigma[s] = 1; + D[s] = 0; + var Q = []; + Q.push(s); + while (Q.length > 0) { + v = Q.shift(); + S.push(v); + for (w = 0; w < G[v].length; w++) { + //G[v].forEach(function (w) { + if (D[G[v][w].nei] < 0) { + Q.push(G[v][w].nei); + D[G[v][w].nei] = D[v] + 1; + } + if 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console.log @@ -88,9 +229,39 @@ @@ -101,8 +272,9 @@ DEFINITION_ORDER - @@ -119,7 +291,6 @@ - @@ -146,9 +317,24 @@ + + + + + + + + + @@ -156,7 +342,15 @@ - + + + + + + + + + @@ -190,6 +384,12 @@ + project + + + + + @@ -216,6 +416,10 @@ + + @@ -224,31 +428,44 @@ - - + - + - - + + - - + + - - + + @@ -259,11 +476,182 @@ - + + + + file://$PROJECT_DIR$/scripts/math_script.js + 889 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -273,37 +661,139 @@ - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - + + - + + + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + diff --git a/README.md b/README.md old mode 100644 new mode 100755 diff --git a/convert.html b/convert.html old mode 100644 new mode 100755 diff --git a/data/IMDB_Graph.js b/data/IMDB_Graph.js new file mode 100644 index 0000000..7f265dc --- /dev/null +++ b/data/IMDB_Graph.js @@ -0,0 +1,26 @@ +var chart = c3.generate({ + data: { + x : 'x', + columns: [['x','250','500','750','1000'], + ['Brandes', 4.356, 16.637, 44.490,94.430], + ['Virtual Node', 8.461, 30.195, 75.712, 131.875], + ['Random Sampling', 2.404, 4.326, 7.219, 9.746] + ], + type: 'bar' + }, + + size: { + width: 500 + + }, + bar: { + width: { + ratio: 0.5 // this makes bar width 50% of length between ticks + } + + // or + //width: 100 // this makes bar width 100px + } +});/** + * Created by vinhtngu on 2/22/17. + */ diff --git a/data/IndexCards.json b/data/IndexCards.json deleted file mode 100644 index dfc864b..0000000 --- a/data/IndexCards.json +++ /dev/null @@ -1,839 +0,0 @@ -{ -"nodes": [ - {"id": "0", "name": "Lysyl hydroxylases", 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b/data/Jazz musicians.json old mode 100644 new mode 100755 diff --git a/data/VisGraph.js b/data/VisGraph.js new file mode 100644 index 0000000..eded1bb --- /dev/null +++ b/data/VisGraph.js @@ -0,0 +1,26 @@ +var chart = c3.generate({ + data: { + x : 'x', + columns: [['x','250','500','750','1000'], + ['Brandes', 14, 128, 480,1078], + ['Virtual Node', 21, 154, 532, 121.874], + ['Random Sampling', 24, 82, 189, 291] + ], + type: 'bar' + }, + + size: { + width: 700 + + }, + bar: { + width: { + ratio: 0.5 // this makes bar width 50% of length between ticks + } + + // or + //width: 100 // this makes bar width 100px + } +});/** + * Created by vinhtngu on 2/23/17. + */ diff --git a/data/barchartIMDB1000.js b/data/barchartIMDB1000.js new file mode 100644 index 0000000..b1fe292 --- /dev/null +++ b/data/barchartIMDB1000.js @@ -0,0 +1,27 @@ +var chart = c3.generate({ + data: { + x : 'x', + columns: [['x','250','500','750','1000'], + ['Brandes', 14.550, 130, 120,91.424], + ['Virtual Node', 21.717, 153.058, 535.127, 325.265], + ['Random Sampling', 23.645, 82.322, 189.146, 70.681] + ], + type: 'bar' + }, + axis: { + y: { + max:300, + ticks : 15}}, + size: { + width: 500 + + }, + bar: { + width: { + ratio: 0.5 // this makes bar width 50% of length between ticks + } + + // or + //width: 100 // this makes bar width 100px + } +}); \ No newline at end of file diff --git a/data/data.csv b/data/data.csv new file mode 100644 index 0000000..e30b9bd --- /dev/null +++ b/data/data.csv @@ -0,0 +1,5 @@ +data,brandes,virtual,sampling,Q +indexCard200,0.14,0.2044,0.2623, +indexCard500,15.927,24.734,18.408, +indexCard970,120.49,115.483,40.132, +indexCard1500,235.401,358.591,70.877, \ No newline at end of file diff --git a/data/dataset1.json b/data/dataset1.json old mode 100644 new mode 100755 diff --git a/data/dataset2.json b/data/dataset2.json old mode 100644 new mode 100755 diff --git a/data/dataset4.json b/data/dataset4.json old mode 100644 new mode 100755 index 574d3f5..fc83d5c --- a/data/dataset4.json +++ b/data/dataset4.json @@ -36,10 +36,10 @@ {"source": "8", "target": "11", "value": 1}, {"source": "9", "target": "10", "value": 1}, {"source": "9", "target": "12", "value": 1}, - {"source": "9", "target": "14", "value": 7}, - {"source": "10", "target": "12", "value": 2}, - {"source": "12", "target": "13", "value": 4}, - {"source": "12", "target": "14", "value": 3}, - {"source": "13", "target": "14", "value": 2} + {"source": "9", "target": "14", "value": 1}, + {"source": "10", "target": "12", "value": 1}, + {"source": "12", "target": "13", "value": 1}, + {"source": "12", "target": "14", "value": 1}, + {"source": "13", "target": "14", "value": 1} ] } \ No newline at end of file diff --git a/data/dataset4_fix.json b/data/dataset4_fix.json old mode 100644 new mode 100755 diff --git a/data/football.json b/data/football.json old mode 100644 new mode 100755 diff --git a/data/imdb.json b/data/imdb.json deleted file mode 100644 index 042c432..0000000 --- a/data/imdb.json +++ /dev/null @@ -1,649 +0,0 @@ -{ -"nodes": [ - {"id": "0", "name": "Schmidt, Michael Q.", "group": 1}, - {"id": "1", "name": "Babu, Mohan (I)", "group": 1}, - {"id": "2", "name": "Rosen, Larry (III)", "group": 1}, - {"id": "3", "name": "Sovagovic, Fabijan", "group": 1}, - {"id": "4", "name": "Sen, Sener", "group": 1}, - {"id": "5", "name": "Graf, David Alan", "group": 1}, - {"id": "6", "name": "Haasan, Kamal", "group": 1}, - {"id": "7", "name": "Walker, Doug (VI)", "group": 1}, - {"id": "8", "name": "Tennant, David (I)", "group": 1}, - {"id": "9", "name": "Buzancic, Boris", "group": 1}, - {"id": "10", "name": "Brahmanandam", "group": 1}, - {"id": "11", "name": "Ramalingaiah, Allu", "group": 1}, - {"id": "12", "name": "Marotti, Josip", "group": 1}, - {"id": "13", "name": "Y�ce, Ihsan", "group": 1}, - {"id": "14", "name": "Drach, Vanja", "group": 1}, - {"id": "15", "name": "Nasser (I)", "group": 1}, - {"id": "16", "name": "Nandamuri, Taraka Rama Rao", "group": 1}, - {"id": "17", 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+1,78 @@ -[{"id":30,"values":[{"key":"Betweenness edge","value":[0,46.64999999999998]},{"key":"Modularity Q","value":[46.64999999999998,51.53499999999997]}]},{"id":51,"values":[{"key":"Betweenness edge","value":[0,127.625]},{"key":"Modularity Q","value":[127.625,136.31]}]},{"id":100,"values":[{"key":"Betweenness edge","value":[0,1980.605]},{"key":"Modularity Q","value":[1980.605,2031.8449999999998]}]}] \ No newline at end of file +[ + { + "id": 200, + "values": [ + { + "key": "Betweenness edge", + "value": [ + 0, + 14 + ] + }, + { + "key": "Modularity Q", + "value": [ + 14, + 14.015 + ] + } + ] + }, + { + "id": 500, + "values": [ + { + "key": "Betweenness edge", + "value": [ + 0, + 15 + ] + }, + { + "key": "Modularity Q", + "value": [ + 15, + 15.092 + ] + } + ] + }, + { + "id": 970, + "values": [ + { + "key": "Betweenness edge", + "value": [ + 0, + 120 + ] + }, + { + "key": "Modularity Q", + "value": [ + 120, + 120.789 + ] + } + ] + }, + { + "id": 1500, + "values": [ + { + "key": "Betweenness edge", + "value": [ + 0, + 120 + ] + }, + { + "key": "Modularity Q", + "value": [ + 120, + 120.789 + ] + } + ] + } +] \ No newline at end of file diff --git a/figures/IndexCards.png b/figures/IndexCards.png old mode 100644 new mode 100755 diff --git a/figures/Jazz musician.png b/figures/Jazz musician.png old mode 100644 new mode 100755 diff --git a/figures/football.png b/figures/football.png old mode 100644 new mode 100755 diff --git a/figures/imdb_125.png b/figures/imdb_125.png old mode 100644 new mode 100755 diff --git a/figures/karate.png b/figures/karate.png old mode 100644 new mode 100755 diff --git a/figures/text_100.png b/figures/text_100.png old mode 100644 new mode 100755 diff --git a/figures/vis_100.png b/figures/vis_100.png old mode 100644 new mode 100755 diff --git a/force.html b/force.html new file mode 100644 index 0000000..5b8a318 --- /dev/null +++ b/force.html @@ -0,0 +1,151 @@ + + + + + + \ No newline at end of file diff --git a/groupbarchart.html b/groupbarchart.html new file mode 100644 index 0000000..b2a780d --- /dev/null +++ b/groupbarchart.html @@ -0,0 +1,191 @@ + + + + + + D3 v4 - Group barChart + + + + +
+ + + + + \ No newline at end of file diff --git a/hull.html b/hull.html new file mode 100755 index 0000000..812bb06 --- /dev/null +++ b/hull.html @@ -0,0 +1,88 @@ + + + + Force-Directed Layout with Convex Hull + + + +
+ + + \ No newline at end of file diff --git a/index.html b/index.html old mode 100644 new mode 100755 index dac277c..0535b17 --- a/index.html +++ b/index.html @@ -22,7 +22,7 @@ .graph { fill: none; - stroke: steelblue; + stroke: black; stroke-width: 1.5px; } .graph-title{ @@ -32,7 +32,7 @@ } .links line { stroke: #999; - stroke-opacity: 0.6; + stroke-opacity: 1; } .nodes circle { @@ -45,8 +45,8 @@ stroke-width: 1.5px; } -.node text { - font: 10px sans-serif; +.nodes text { + font: 25px sans-serif; } .node--internal circle { @@ -60,15 +60,15 @@ .link { fill: none; - stroke-opacity: 0.4; + stroke-opacity: 1; stroke-width: 1.5px; } .bar line { - z-index: 5; + z-index: 15; fill: none; - stroke: #f00; - stroke-opacity: 0.4; + stroke: #000000; + stroke-opacity: 0.8; stroke-width: 20px; } .overlay { @@ -181,4 +181,5 @@ + \ No newline at end of file diff --git a/scripts/barchartforvis.js b/scripts/barchartforvis.js new file mode 100644 index 0000000..44c1eba --- /dev/null +++ b/scripts/barchartforvis.js @@ -0,0 +1,27 @@ +var chart = c3.generate({ + data: { + x : 'x', + columns: [['x','250','500','750','1000'], + ['Brandes', 14.550, 130, 120,235], + ['Virtual Node', 21.717, 153.058, 535.127, 325.265], + ['Random Sampling', 23.645, 82.322, 189.146, 70.681] + ], + type: 'bar' + }, + axis: { + y: { + max:300, + ticks : 15}}, + size: { + width: 500 + + }, + bar: { + width: { + ratio: 0.5 // this makes bar width 50% of length between ticks + } + + // or + //width: 100 // this makes bar width 100px + } +}); \ No newline at end of file diff --git a/scripts/d3.v4.min.js b/scripts/d3.v4.min.js old mode 100644 new mode 100755 diff --git a/scripts/iDVLlibrary.js b/scripts/iDVLlibrary.js new file mode 100755 index 0000000..cf1dcd2 --- /dev/null +++ b/scripts/iDVLlibrary.js @@ -0,0 +1,161 @@ +/** + * Created by alexnguyen on 2/16/17. + */ +function Graph() { + this.vertices = []; + this.adjList = []; +} + +Graph.prototype.addEdge = function(vertex1, vertex2) { + this.adjList[vertex1].push(vertex2); + this.adjList[vertex2].push(vertex1); +}; +function prececessor(G, source) { + var level = 0; + var nextlevel = [source]; + var seen = new Object(); + seen[source] = level; + var pred = new Object(); + pred[source] = []; + while (nextlevel.length > 0) { + level +=1; + var currentlevel = nextlevel; + nextlevel=[]; + for(v=0;v 0) { + level +=1; + var currentlevel = nextlevel; + nextlevel=[]; + for(v=0;v 0) { + level +=1; + var currentlevel = nextlevel; + nextlevel=[]; + for(v=0;v 1) { + arr[iii][jjj] = {nei: arr.length, val: av, ori: nei}; + //arr[iii][jjj].nei = arr.length; + //arr[iii][jjj].val = av; + + arr.push([{nei: iii, val: av, ori: nei}, {nei: nei, val: av, ori: iii}]); + for (var z = 2; z < n; z++) { + var ll = arr.length; + //arr[ll-1][1].nei = ll; + arr[ll - 1][1] = {nei: ll, var: av, ori: iii}; + arr.push([{nei: ll - 1, val: av}, {nei: nei, val: av, ori: nei}]); + } + arr[nei].filter(function (n, i) { + if (n.nei == iii) { + arr[nei].splice(i, 1, {nei: arr.length - 1, val: av, ori: iii}); + //n.val = av; + //n.nei = arr.length-1;//last virtual node + } + }); + } + } + } + return [arr, av]; +} +function a_array_av(ee) { + var a = init_empty(ee.nodes.length); + var sum = 0; + var m = ee.links.length; + ee.links.forEach(function (e) { + var ii = 0; + var jj = 0; + ee.nodes.filter(function (n, i) { + if (e.source == n.id) + ii = i; + else if (e.target == n.id) + jj = i; + }); + sum = sum + (e.value); + a[ii].push({nei: jj, val: e.value}); + a[jj].push({nei: ii, val: e.value}); + + }); + return [a, sum / m]; +} +function init_empty(m) { + var ar = []; + for (var i = 0; i < m; i++) { + var art = []; + ar.push(art); + } + return ar; +} \ No newline at end of file diff --git a/scripts/main.js b/scripts/main.js old mode 100644 new mode 100755 index d2e40a9..05ad155 --- a/scripts/main.js +++ b/scripts/main.js @@ -133,24 +133,37 @@ var radius = 6; ======= >>>>>>> f41cb8646193b11f7aab076bf481cc71363c0550*/ // d3.json("data/karate.json", function(error, graph) { -d3.json("data/imdb171.json", function (error, graph) { +d3.json("data/indexCards250.json", function (error, graph) { // d3.json("data/dataset4_fix.json", function(error, graph) { if (error) throw error; // for(var i=0;i1) return d; + // }) + console.log("number of filtered links:" + graph.links.length) + var AV_W = d3.mean(graph.links, function (d) { + return d.value; + }) + console.log("Average weight: "+ AV_W); + var AV_DG = 2*graph.links.length/graph.nodes.length; + console.log("Average node degree: "+ AV_DG); + console.log("Threshold: "+ (Math.log(graph.nodes.length)/AV_DG ) + 1); + var num_n = graph.nodes.length; - var sample_properties = 0.7; + var sample_properties = 1; var alpha = Math.floor(num_n * sample_properties); var start_time = performance.now(); //processing -// var step = edge_betweenness_centrality(graph, k = alpha, normalized = true, weight = true, virtual = false); - var step = _betweennness_virtual(graph,k=10); + var step = edge_betweenness_centrality(graph, k = num_n, normalized = true, weight = true, virtual = false); + // var step = _betweennness_virtual(graph); // var step = between_e(graph); var end_time_b = performance.now(); var max_lv = step.length + 1; // tree + var start_time_t = performance.now(); var tree_hi = tree_mapingv3(step, graph); var end_time_t = performance.now(); var tree_deep = d3.scaleLinear().domain([tree_hi[0].depth, 0]).range([0, wtree]); @@ -230,7 +243,7 @@ d3.json("data/imdb171.json", function (error, graph) { time_box .append("text") .attr("transform", "translate(" + [10, 35] + ")") - .text("Computing time for Modularity Q: " + Math.round(end_time_t - end_time_b + start_time) + " ms"); + .text("Computing time for Modularity Q: " + Math.round(end_time_t - start_time_t) + " ms"); //-------------graph var domain = {x: {min: 0, max: 0}, y: {min: 0, max: 0}}; domain.y.min = d3.min(tree_hi[1]); @@ -337,7 +350,7 @@ d3.json("data/imdb171.json", function (error, graph) { return d.id; }) .enter().append("circle") - .attr("r", 5) + .attr("r", 7) .attr("fill", function (d) { return color(d.group); }) @@ -366,7 +379,7 @@ d3.json("data/imdb171.json", function (error, graph) { .force("y", d3.forceY().strength(.0005)); simulation.force("link") - .links(graph.links); + .links(graph.links).distance(100); function ticked() { node @@ -550,9 +563,9 @@ d3.json("data/imdb171.json", function (error, graph) { }) simulation.force("cluster", clustering); simulation.alphaTarget(0.2).restart(); - link.attr("opacity", function (d, i) { - return newlinks.indexOf(i) > -1 ? 0.1 : 1; - }) + // link.attr("opacity", function (d, i) { + // return newlinks.indexOf(i) > -1 ? 0.1 : 1; + // }) function clustering(alpha) { diff --git a/scripts/mainv1.js b/scripts/mainv1.js old mode 100644 new mode 100755 diff --git a/scripts/math_script.js b/scripts/math_script.js old mode 100644 new mode 100755 index 21c6999..2768aef --- a/scripts/math_script.js +++ b/scripts/math_script.js @@ -195,7 +195,7 @@ function between_e(graph) { var step = []; var num_l = graph.links.length; //document.write("
av: "+av); - while (step.length != num_l) { + while (step.length != graph.links.length) { //var alink_oc = copyA(alink_o); //document.write("
old array size: "+alink_o[3][0].nei); //var alink_fix = a_array_ext(alink_oc,av); // add virtual nodes @@ -393,8 +393,8 @@ function between_e(graph) { //console.log("----end---- "+s); } var end_time_b = performance.now(); - console.log("Time for old technique"); - console.log(end_time_b-start_time); + //console.log("Time for old technique"); + //console.log(end_time_b-start_time); if (max_ebs[0] != 0) { step.push([max_ebs[1], max_ebs[2]]); //av = av*num_l; @@ -621,7 +621,8 @@ function edge_betweenness_centrality(graph, k='none', normalized=true, weight) { else { nodes = graph_nodes_random(num_node, num_node); } - while (step.length != 1) { + var start_time = performance.now(); + while (step.length != graph.links.length) { for (i = 0; i < num_node; i++) { betweenness[i] = 0.0 } @@ -646,8 +647,7 @@ function edge_betweenness_centrality(graph, k='none', normalized=true, weight) { betweenness = _accumulate_edges(betweenness, S, P, sigma, nodes[s]); } } - var end_time_b = performance.now(); - console.log(end_time_b-start_time); + for (n = 0; n < num_node; n++) { delete betweenness[n]; } @@ -676,7 +676,9 @@ function edge_betweenness_centrality(graph, k='none', normalized=true, weight) { } } } - + var end_time_b = performance.now(); + console.log("Time to run betweenness brandes"); + console.log(end_time_b-start_time); return step; } function _single_source_dijkstra_path_basic(G, s, weight='weight') { @@ -809,37 +811,64 @@ function _betweennness_virtual(graph) { var alink_o = a_array_av(graph); // orgiginal var av = alink_o[1]; alink_o = alink_o[0]; + var totaldegree=0; + for(i=0;i1) return d; + }) + console.log(templink) + var random_node = Math.floor(Math.random() * graph.nodes.length) + var pred =prececessorV_length(VirtualAdj,random_node, graph.nodes.length); + var arrayvalue = Object.values(pred).sort(function (a, b) { + return b - a; }); - if (k !== 'none') { - nodes = graph_nodes_random(num_node, k) + var VDG = arrayvalue[0] + arrayvalue[1]; + + var sigma = 0.1, delta = 0.1, c = 0.5; + var d = Math.floor(Math.log2(VDG) - 2) + 1 + Math.log(1 / delta); + var r = c / Math.pow(sigma, 2) * d; + + for(var i=0;i"+"-- "+ alink_o[max_ebs[1]][i].nei); if (VirtualAdj[result[0]][i].nei == result[1] || VirtualAdj[result[0]][i].ori == result[1]) { VirtualAdj[result[0]].splice(i, 1); break; @@ -853,7 +882,8 @@ function _betweennness_virtual(graph) { } delete betweenness[_.first(_.max(_.pairs(betweenness), _.last))]; } - + console.log("Time to run betweenness VS"); + console.log(end_time_b-start_time); return step; } @@ -869,7 +899,7 @@ function _single_source_shortest_path_basic_virtual_nodes(G, s, nodes) { var Q = []; Q.push(s); while (Q.length > 0) { - v = Q.shift(); + var v = Q.shift(); S.push(v); for (w = 0; w < G[v].length; w++) { //G[v].forEach(function (w) { @@ -888,4 +918,4 @@ function _single_source_shortest_path_basic_virtual_nodes(G, s, nodes) { } } return [S, P, sigma]; -} \ No newline at end of file +} diff --git a/scripts/summary.js b/scripts/summary.js old mode 100644 new mode 100755 diff --git a/summary.html b/summary.html old mode 100644 new mode 100755 diff --git a/test.html b/test.html new file mode 100644 index 0000000..8897bcc --- /dev/null +++ b/test.html @@ -0,0 +1,36 @@ + + + + + Title + + + + + + + + + + \ No newline at end of file From c1a09360f73a652da632d6cbf0cb09afd241d669 Mon Sep 17 00:00:00 2001 From: Alex-Nguyen Date: Sat, 25 Feb 2017 20:22:07 -0600 Subject: [PATCH 4/7] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index e107f67..78aaeb6 100755 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # Algorithms for detecting community structure in networks In this project, we implement algorithms for detecting community structure in networks. -Our web application is available at [online demo](https://nvtngan.github.io/)|[back up link](http://hexagon.pe.hu/). +Our web application is available at [online demo](https://alex-nguyen.github.io/VictorHugo/)|[back up link](http://hexagon.pe.hu/). ### Exploring Topics and Events in Political Blogs The following image shows the top 100 terms in nearly 100,000 political blog posts in last 10 years (from 2006 to 2015). Terms are color-coded by clusters (generated by our algorithm). The red dashed slider on the left controls the cut-off value for cluster formation. Terms appear together in the same political blogs are connected by links. The link thickness indicates the frequency of collocated terms. From f3c222608202a63e42231fe5ef514811752b04ea Mon Sep 17 00:00:00 2001 From: "Vinh T. Nguyen" Date: Sat, 25 Feb 2017 21:41:19 -0600 Subject: [PATCH 5/7] First Commit --- .idea/workspace.xml | 187 +++++++++++++++------------------------- data/IMDB_Graph.js | 2 +- data/IndexCardsGraph.js | 7 +- scripts/main.js | 9 +- scripts/math_script.js | 6 +- 5 files changed, 84 insertions(+), 127 deletions(-) diff --git a/.idea/workspace.xml b/.idea/workspace.xml index 710087e..dddee21 100755 --- a/.idea/workspace.xml +++ b/.idea/workspace.xml @@ -2,60 +2,11 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - - @@ -73,11 +24,21 @@ - + - - + + + + + + + + + + + + @@ -86,8 +47,8 @@ - - + + @@ -95,11 +56,11 @@ - + - - + + @@ -110,8 +71,8 @@ - - + + @@ -142,7 +103,7 @@ - + @@ -152,8 +113,8 @@ - - + + @@ -165,22 +126,11 @@ - - - - - - - - - - - @@ -221,6 +171,7 @@ : 3 numNode = console.log + update_group @@ -257,11 +208,11 @@ @@ -441,11 +392,12 @@ + - @@ -455,18 +407,18 @@ - - + + @@ -518,13 +470,6 @@ - - - - - - - @@ -686,7 +631,6 @@ - @@ -718,7 +662,7 @@ - + @@ -740,38 +684,20 @@ - + - - + + - - - - - - - - - - - + - - - - - - - - - - + + @@ -780,23 +706,48 @@ - - + + - + - - + + + + + + + + + + - + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/data/IMDB_Graph.js b/data/IMDB_Graph.js index 7f265dc..d23ab9b 100644 --- a/data/IMDB_Graph.js +++ b/data/IMDB_Graph.js @@ -10,7 +10,7 @@ var chart = c3.generate({ }, size: { - width: 500 + width: 700 }, bar: { diff --git a/data/IndexCardsGraph.js b/data/IndexCardsGraph.js index 8d27bc2..d34ef7d 100644 --- a/data/IndexCardsGraph.js +++ b/data/IndexCardsGraph.js @@ -11,9 +11,14 @@ var chart = c3.generate({ ], type: 'bar' }, + axis: { + y: { + max: 140 + } + }, size: { - width: 500 + width: 700 }, bar: { diff --git a/scripts/main.js b/scripts/main.js index 05ad155..7caed05 100755 --- a/scripts/main.js +++ b/scripts/main.js @@ -133,7 +133,7 @@ var radius = 6; ======= >>>>>>> f41cb8646193b11f7aab076bf481cc71363c0550*/ // d3.json("data/karate.json", function(error, graph) { -d3.json("data/indexCards250.json", function (error, graph) { +d3.json("data/indexCards500.json", function (error, graph) { // d3.json("data/dataset4_fix.json", function(error, graph) { if (error) throw error; // for(var i=0;i Date: Sat, 25 Feb 2017 21:45:45 -0600 Subject: [PATCH 6/7] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 78aaeb6..ed8fc17 100755 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # Algorithms for detecting community structure in networks In this project, we implement algorithms for detecting community structure in networks. -Our web application is available at [online demo](https://alex-nguyen.github.io/VictorHugo/)|[back up link](http://hexagon.pe.hu/). +Our web application is available at [online demo](https://alex-nguyen.github.io/VictorHugo/)|[Biological Pathway Literature](https://alex-nguyen.github.io/ClusteringIndex500/). ### Exploring Topics and Events in Political Blogs The following image shows the top 100 terms in nearly 100,000 political blog posts in last 10 years (from 2006 to 2015). Terms are color-coded by clusters (generated by our algorithm). The red dashed slider on the left controls the cut-off value for cluster formation. Terms appear together in the same political blogs are connected by links. The link thickness indicates the frequency of collocated terms. From 0acf1a063a1f3126a6c44e429071ab90241a65a8 Mon Sep 17 00:00:00 2001 From: Alex-Nguyen Date: Sat, 25 Feb 2017 22:21:54 -0600 Subject: [PATCH 7/7] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index ed8fc17..b347610 100755 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # Algorithms for detecting community structure in networks In this project, we implement algorithms for detecting community structure in networks. -Our web application is available at [online demo](https://alex-nguyen.github.io/VictorHugo/)|[Biological Pathway Literature](https://alex-nguyen.github.io/ClusteringIndex500/). +Our web application is available at [Victor Hugo Dataset](https://alex-nguyen.github.io/VictorHugo/)|[Biological Pathway Literature](https://alex-nguyen.github.io/ClusteringIndex500/). ### Exploring Topics and Events in Political Blogs The following image shows the top 100 terms in nearly 100,000 political blog posts in last 10 years (from 2006 to 2015). Terms are color-coded by clusters (generated by our algorithm). The red dashed slider on the left controls the cut-off value for cluster formation. Terms appear together in the same political blogs are connected by links. The link thickness indicates the frequency of collocated terms.