louvian_ruby 0.0.4 → 0.0.5

data/lib/louvian.rb

@@ -9,13 +9,21 @@ module Louvian
     @@graph
   end
 
+  def self.graph= value
+    @@graph = value
+  end
+
   def self.levels
     @@levels
   end
+
+  def self.levels= value
+    @@levels = value
+  end
   # This method sets up the whole environemnt for calculations
   #
   # @param string [String] in the form of src dest (one edge per line)
-  def self.init_env string, directed=false
+  def self.init_env string, directed
     list = string.split("\n").map {|line| line.split.map{|n| n.to_i}}
     @@graph = Graph.new list, directed, 0
     @@levels = [] # List of Graphs
@@ -25,12 +33,28 @@ module Louvian
   def self.run
     l = 0
     mod = @@graph.modularity
-    begin
+    puts "Level #{l}: Comms #{@@graph.communities.size}"
+    l +=1
+
+    while self.one_level
       puts "Level #{l}: Comms #{@@graph.communities.size}"
       @@levels << @@graph
       @@graph = @@graph.build_graph_from_comms
       l+=1
-    end while self.one_level
+    end
+  end
+
+  def self.unfold_levels!
+    @@levels[(1..-1)].each_with_index do |graph, i|
+      graph.expand! @@levels[i]
+    end
+  end
+
+  def self.display_hierarchy
+    @@levels.each do |graph|
+      puts "level #{graph.level}: Nodes #{graph.communities.count}"
+    end
+
   end
 
   # This method iterates over the graph to optimze the modularity. Iterations
@@ -54,7 +78,7 @@ module Louvian
 
         neighbour_communities = @@graph.get_neighbour_comms node
 
-        #puts "\tneihbours#{neighbour_communities.map {|i| i.id}}"
+        #puts "\tneihbours#{neighbour_communities.map {|i| i.id}} origin #{orig_community.id}"
         @@graph.remove_node node, orig_community
 
 
@@ -72,6 +96,7 @@ module Louvian
         if best_community != orig_community
           nb_moves += 1
           improvement = true
+          #puts "\t\tbest comm #{best_community.id}"
         end
 
         @@graph.insert_node node, best_community
@@ -79,7 +104,6 @@ module Louvian
         @@graph.garbage_collect orig_community
 
       end
-      #display_communities
       new_mod = @@graph.modularity
       #puts "modularity was #{cur_mod} and now #{new_mod}, moves #{nb_moves}"
     end while  nb_moves > 0 and new_mod - cur_mod >= MIN_INCREASE
@@ -88,20 +112,26 @@ module Louvian
 
 
   def self.example
-    s='0 1
-    0 8
-    1 3
-    1 4
-    1 8
-    2 3
-    2 5
-    2 7
-    3 8
-    5 6
-    5 7'
+    s='0 1 1
+    0 8 1
+    1 3 1
+    1 4 1
+    1 8 1
+    2 3 1
+    2 5 1
+    2 7 1
+    3 8 1
+    4 7 1
+    5 6 1
+    5 7 1'
 
     Louvian.init_env s, false
-    Louvian.run
+    Louvian.one_level
+    ng = Louvian.graph.build_graph_from_comms
+    Louvian.levels << Louvian.graph
+    Louvian.graph = ng
+    #L = Louvian
+    #Louvian.run
     nil
   end
 end

data/lib/louvian/community.rb

@@ -15,43 +15,40 @@ class Louvian::Community
 
     @in = 0
     adj_list.each do |node, neighbors|
-      @in += neighbors.select {|node| @nodes_ids.include? node}.count
+      @in += neighbors.select {|node| @nodes_ids.include? node}.values.inject(0,:+)
+    end
+
+    # sum of links weights inside the community
+    @tot = 0
+    adj_list.each do |node, links|
+      @tot += links.values.inject(0, :+)
     end
 
-    # sum of links weights incident to the community
-    @tot = adj_list.inject(0) {|r,(k,v)| r+v.count}
   end
 
   def self.reset
     @@count = 0
   end
 
-  def insert node, node_adj
-    #puts "\t\tinsert node #{node} to comm #{@id}"
-    @nodes_ids << node
-
-    # what makes sense
-    #@in += links_to_comm
-    #@tot += (Louvian.get_adj(node).count - links_to_comm)
+  def insert node, node_adj, links_from_community
+    links_to_comm = node_adj.select {|n| @nodes_ids.include? n}.values.inject(0,:+)
 
-    links_to_comm = node_adj.select {|n| nodes_ids.include? n}.count
+    @nodes_ids << node
     # Copied from the cpp code
-    @in += 2*links_to_comm
-    @tot += node_adj.count
+    @in += links_to_comm + links_from_community + (node_adj[node] || 0)
+    @tot += node_adj.values.inject(0,:+)
+
   end
 
-  def remove node, node_adj
-    #puts "\t\tremove node #{node} to comm #{@id}"
+  def remove node, node_adj, links_from_community
     @nodes_ids.delete node
+    links_to_comm = node_adj.select {|n| @nodes_ids.include? n}.values.inject(0,:+)
 
-    # what makes sense
-    #@in -= links_to_comm
-    #@tot -= (Louvian.get_adj(node).count - links_to_comm)
-
-    links_to_comm = node_adj.select {|n| nodes_ids.include? n}.count
+    #puts "linksto t-com  #{links_to_comm}"
     # Copied from the cpp code
-    @in -= 2*links_to_comm
-    @tot -= node_adj.count
+    @in -= (links_to_comm + links_from_community + (node_adj[node] || 0))
+    @tot -= node_adj.values.inject(0,:+)
+
   end
 
 end

data/lib/louvian/graph.rb

@@ -1,6 +1,6 @@
 class Louvian::Graph
 
-  attr_accessor :adj_list, :nodes, :communities, :directed, :n2c, :total_weight
+  attr_accessor :adj_list, :nodes, :communities, :directed, :n2c, :total_weight, :level
   def initialize edges_list, directed, level
     # Adjacency list
     @adj_list = Louvian::Graph.make_adj edges_list, directed
@@ -26,21 +26,27 @@ class Louvian::Graph
     end
 
     # Sum of all links half edges (double the number of edges)
-    @total_weight = @adj_list.inject(0) {|r,(k,v)| r+v.count}
+    #@total_weight = @adj_list.inject(0) {|r,(k,v)| r+v.count}
+    @total_weight = 0
+    @adj_list.each do |node, links|
+      @total_weight += links.values.inject(0, :+)
+    end
   end
 
   # This method builds the adjacency list from list of edges
   # @param list [Array] in the form of [src dest] (edge per cell)
   # @param directed, whether the edge list is directed or not
+  # @return hash of hashes {src => {dest1 => weight1, dest1 => weight1}}
   def self.make_adj edges_list, directed
     adj = {}
     edges_list.each do |edge|
-      adj[edge[0]] ||= []
-      adj[edge[1]] ||= []
+      adj[edge[0]] ||= {}
+
+      adj[edge[1]] ||= {}
 
-      adj[edge[0]] << edge[1]
+      adj[edge[0]][edge[1]] = (adj[edge[0]][edge[1]] || 0 ) + (edge[2] || 1)
       if not directed
-        adj[edge[1]] << edge[0]
+        adj[edge[1]][edge[0]]  = (adj[edge[1]][edge[0]] || 0 ) + (edge[2] || 1)
       end
     end
     adj
@@ -68,8 +74,8 @@ class Louvian::Graph
   def get_node_to_comms_links node
     neighbour_nodes = get_neighbour_nodes node
     node_to_comms_links = {}
-    neighbour_nodes.each do |n|
-      node_to_comms_links[@n2c[n]] = (node_to_comms_links[@n2c[n]] || 0) + 1
+    neighbour_nodes.each do |n, weight|
+      node_to_comms_links[@n2c[n]] = (node_to_comms_links[@n2c[n]] || 0) + weight
     end
     node_to_comms_links[@n2c[node]] ||= 0
     return node_to_comms_links
@@ -82,12 +88,13 @@ class Louvian::Graph
 
   # This method calcualtes the current modularity of the communities
   # @returns q [Float] which is the modularity
-  def modularity
+  def modularity verbose=false
     q = 0.0
     m2 = @total_weight
-
-    @communities.each do |m_node|
-      q += m_node.in.to_f/m2 - (m_node.tot.to_f/m2 * m_node.tot.to_f/m2)
+    puts "m2 #{m2},  comms #{@communities.count}" if verbose
+    @communities.each do |comm|
+      puts " in #{comm.in}, tot #{comm.tot}"  if verbose
+      q += comm.in.to_f/m2 - (comm.tot.to_f/m2 * comm.tot.to_f/m2)
     end
     q
   end
@@ -98,9 +105,12 @@ class Louvian::Graph
   # @param nb_links_to_comm is the number of links from +node+ to community
   # @returns delta_q (the gain of modularity)
   def modularity_gain node, community
-    nb_links_to_comm = get_number_of_links node, community
+    nb_links_to_comm = (get_number_of_links node, community) || 0
+    #puts "node #{node}, comm #{community.id}"
+    #puts "####################{nb_links_to_comm}"
+
     tot = community.tot
-    deg = @adj_list[node].count
+    deg = @adj_list[node].values.inject(0,:+)
     m2 = @total_weight
 
     #puts "\t\t\tcomm #{community.id} #{[tot, deg, m2, nb_links_to_comm]}"
@@ -119,13 +129,22 @@ class Louvian::Graph
     nil
   end
 
+  def get_links_from_comm_to_node community, node
+    links = 0
+    nodes = community.nodes_ids - [node]
+    nodes.each do |n|
+      links+=@adj_list[n].select {|adj| adj == node}.values.inject(0,:+)
+    end
+    links
+  end
+
   def insert_node node, comm
-    comm.insert node, @adj_list[node]
+    comm.insert node, @adj_list[node], (get_links_from_comm_to_node comm, node)
     @n2c[node] = comm.id
   end
 
   def remove_node node, comm
-    comm.remove node, @adj_list[node]
+    comm.remove node, @adj_list[node], (get_links_from_comm_to_node comm, node)
     @n2c[node] = -1
   end
 
@@ -136,24 +155,36 @@ class Louvian::Graph
   end
 
   def build_graph_from_comms
-
     comm_edges = []
 
-    count = @communities.count
-    if not directed # iterate only on one half of communities
-      count % 2 == 0 ?  count : count + 1
-      count /=2
-    end
-
-    @communities[0,count].each do |comm|
+    @communities.each do |comm|
       comm.nodes_ids.each do |node|
-        @adj_list[node].each do |linked_node|
+        @adj_list[node].each do |linked_node, weight|
           if not comm.nodes_ids.include? linked_node
-            comm_edges << [comm.id, @n2c[linked_node]]
+            #comm_edges << [comm.id, @n2c[linked_node]] * weight
+            comm_edges << [comm.id, @n2c[linked_node], weight]
           end
         end
       end
+      comm_edges << [comm.id, comm.id, comm.in]
+    end
+    return Louvian::Graph.new comm_edges, true, @level+1
+  end
+
+  def expand! lower_graph
+    comm_2_nodes = lower_graph.communities.inject({}) {|r,comm| r[comm.id]= comm.nodes_ids;r}
+    new_graph_nodes = []
+    @communities.each do |comm|
+      new_comm_nodes = []
+      comm.nodes_ids.each do |node|
+        new_comm_nodes += comm_2_nodes[node]
+        comm_2_nodes[node].each do |low_node|
+          @n2c[low_node] = comm.id
+        end
+      end
+      comm.nodes_ids = new_comm_nodes
+      new_graph_nodes += new_comm_nodes
     end
-    return Louvian::Graph.new comm_edges, directed, @level+1
+    @nodes = new_graph_nodes
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: louvian_ruby
 version: !ruby/object:Gem::Version
-  version: 0.0.4
+  version: 0.0.5
   prerelease: 
 platform: ruby
 authors: