igraph 0.3.2 → 0.3.3

data/ext/cIGraph_motif.c

@@ -0,0 +1,109 @@
+#include "igraph.h"
+#include "ruby.h"
+#include "cIGraph.h"
+
+/* call-seq:
+ *   igraph.motifs_randesu(size,cut)
+ *
+ */
+VALUE cIGraph_motifs_randesu(VALUE self, VALUE size, VALUE cuts){
+
+  igraph_t *graph;
+  igraph_vector_t cutsv;
+  igraph_vector_t res;
+  int i;
+  VALUE hist = rb_ary_new();
+
+  Data_Get_Struct(self, igraph_t, graph);
+
+  igraph_vector_init(&res,0);
+
+  //Convert an array of vertices to a vector of vertex ids
+  igraph_vector_init(&cutsv,0);
+  for(i=0;i<RARRAY(cuts)->len;i++){
+    igraph_vector_push_back(&cutsv,NUM2DBL(RARRAY(cuts)->ptr[i]));
+  }
+
+  igraph_motifs_randesu(graph,&res,NUM2INT(size),&cutsv);
+
+  for(i=0; i<igraph_vector_size(&res); i++){
+    rb_ary_push(hist,INT2NUM(VECTOR(res)[i]));
+  }
+
+  igraph_vector_destroy(&cutsv);
+  igraph_vector_destroy(&res);
+ 
+  return hist;
+
+}
+
+/* call-seq:
+ *   igraph.motifs_randesu_no(size,cut)
+ *
+ */
+VALUE cIGraph_motifs_randesu_no(VALUE self, VALUE size, VALUE cuts){
+
+  igraph_t *graph;
+  igraph_vector_t cutsv;
+  igraph_integer_t res;
+  int i;
+
+  Data_Get_Struct(self, igraph_t, graph);
+
+  //Convert an array of vertices to a vector of vertex ids
+  igraph_vector_init(&cutsv,0);
+  for(i=0;i<RARRAY(cuts)->len;i++){
+    igraph_vector_push_back(&cutsv,NUM2DBL(RARRAY(cuts)->ptr[i]));
+  }
+
+  igraph_motifs_randesu_no(graph,&res,NUM2INT(size),&cutsv);
+
+  igraph_vector_destroy(&cutsv);
+ 
+  return INT2NUM(res);
+
+}
+
+/* call-seq:
+ *   igraph.motifs_randesu_estimate(size,cut,samplen,samplev)
+ *
+ */
+VALUE cIGraph_motifs_randesu_estimate(VALUE self, VALUE size, VALUE cuts, 
+				      VALUE samplen, VALUE samplev){
+
+  igraph_t *graph;
+  igraph_vector_t cutsv;
+  igraph_vector_t vidv;
+  igraph_integer_t res;
+  int i;
+
+  if(samplev != Qnil){
+    igraph_vector_init(&vidv,0);
+    //Convert an array of vertices to a vector of vertex ids
+    igraph_vector_init_int(&vidv,0);
+    cIGraph_vertex_arr_to_id_vec(self,samplev,&vidv);
+   }
+
+  Data_Get_Struct(self, igraph_t, graph);
+
+  igraph_vector_init(&cutsv,0);
+  for(i=0;i<RARRAY(cuts)->len;i++){
+    igraph_vector_push_back(&cutsv,NUM2DBL(RARRAY(cuts)->ptr[i]));
+  }
+
+  if(samplev == Qnil){
+    igraph_motifs_randesu_estimate(graph,&res,NUM2INT(size),
+				   &cutsv,NUM2INT(samplen),NULL);
+  } else {
+    igraph_motifs_randesu_estimate(graph,&res,NUM2INT(size),
+				   &cutsv,NUM2INT(samplen),&vidv);
+  }
+
+  igraph_vector_destroy(&cutsv);
+  if(samplev != Qnil){
+    igraph_vector_destroy(&vidv);
+  }
+  
+  return INT2NUM(res);
+
+}

data/ext/cIGraph_spectral.c

@@ -31,7 +31,7 @@ VALUE cIGraph_laplacian(VALUE self, VALUE mode){
   VALUE val;
   VALUE matrix = rb_ary_new();
 
-  if(mode = Qtrue)
+  if(mode == Qtrue)
     pmode = 1;
 
   Data_Get_Struct(self, igraph_t, graph);

data/test/tc_adj_to_distance.rb

@@ -0,0 +1,24 @@
+require 'igraph'
+
+g = IGraph.new(['A','B','A','C','A','D','C','D'],false)
+
+adj = g.get_adjacency(2)
+g.vcount.times do |k|
+  adj[k][k] = 1
+end
+
+dis = Array.new(4){|i| Array.new(4)}
+
+dis.each_with_index do |row,i|
+  row.each_with_index do |cell,j|
+    cij = 0
+    g.vcount.times do |k|
+      puts "#{i} #{j} #{k}"
+      cij += adj[i][k] * adj[j][k]
+    end
+    dis[i][j] = 10 - cij
+  end
+end
+
+p adj
+p dis

data/test/tc_cliques.rb

@@ -0,0 +1,21 @@
+require 'test/unit'
+require 'igraph'
+
+class TestGraph < Test::Unit::TestCase
+   def test_cliques
+     g = IGraph.new([1,2,3,4],false)
+     assert_equal [[1,2],[3,4]], g.cliques(2,0)
+   end
+   def test_largest_cliques
+     g = IGraph.new(['A','B','C','D','A','E','B','E'],false)
+     assert_equal [['A','B','E','B','E']], g.largest_cliques()
+   end
+   def test_maximal_cliques
+     g = IGraph.new(['A','B','C','D','A','E','B','E'],false)
+     assert_equal [['A','B','E'],['C','D']], g.maximal_cliques()
+   end
+   def test_clique_number
+     g = IGraph.new(['A','B','C','D','A','E','B','E'],false)
+     assert_equal 3, g.clique_number
+   end
+ end

data/test/tc_dijkstra.rb

@@ -0,0 +1,11 @@
+require 'test/unit'
+require 'igraph'
+
+Infinity = 1.0/0
+
+class TestGraph < Test::Unit::TestCase
+   def test_dijkstra
+     g = IGraph.new([1,2,3,4],false)
+     assert_equal [[0,1.5,Infinity,Infinity]], g.dijkstra_shortest_paths([1],[1.5,2.5],IGraph::OUT)
+   end
+ end

data/test/tc_generators_random.rb

@@ -0,0 +1,26 @@
+require 'test/unit'
+require 'igraph'
+
+class TestGraph < Test::Unit::TestCase
+  def test_grg
+    g = IGraph.grg_game(10,0.1,false)
+    assert_equal 10, g.vertices.size
+  end
+  def test_barabasi
+    g = IGraph.barabasi_game(10,3,false,false)
+    assert_equal 10, g.vertices.size
+  end
+  def test_nonlinear_barabasi
+    g = IGraph.nonlinear_barabasi_game(10,1.9,3,false,0.1,false)
+    assert_equal 10, g.vertices.size
+  end 
+  def test_erdos_renyi
+    g = IGraph.erdos_renyi_game(IGraph::ERDOS_RENYI_GNP,10,0.5,false,false)
+    assert_equal 10, g.vertices.size    
+    g = IGraph.erdos_renyi_game(IGraph::ERDOS_RENYI_GNM,10,0.5,false,false)
+    assert_equal 10, g.vertices.size    
+  end
+  def test_watts_strogatz
+    
+  end
+end

data/test/tc_independent_vertex_sets.rb

@@ -0,0 +1,21 @@
+require 'test/unit'
+require 'igraph'
+
+class TestGraph < Test::Unit::TestCase
+  def test_independent_vertex_sets
+    g = IGraph.new([1,2,3,4],true)
+    assert_equal [[1,3],[1,4],[2,3],[2,4]], g.independent_vertex_sets(2,0)
+  end
+  def test_largest_independent_vertex_sets
+    g = IGraph.new([1,2,3,4,1,5],true)
+    assert_equal [[2,3,5],[2,4,5]], g.largest_independent_vertex_sets
+  end
+  def test_maximal_independent_vertex_sets
+    g = IGraph.new([1,2,3,4],true)
+    assert_equal [[1,3],[1,4],[2,3],[2,4]], g.maximal_independent_vertex_sets
+  end
+  def test_independence_number
+    g = IGraph.new([1,2,3,4],true)
+    assert_equal 2, g.independence_number
+  end
+end

data/test/tc_isomorphic.rb

@@ -0,0 +1,33 @@
+require 'test/unit'
+require 'igraph'
+
+class TestGraph < Test::Unit::TestCase
+  def test_isomorphic
+    g = IGraph.new([1,2,3,4],false)
+    h = IGraph.new([5,6,7,8],false)
+    assert_equal true, g.isomorphic(h)
+    assert_equal true, h.isomorphic(g)
+  end
+  def test_isomorphic_vf2
+    g = IGraph.new([1,2,3,4],false)
+    h = IGraph.new([5,6,7,8],false)
+    assert_equal true, g.isomorphic_vf2(h)
+    assert_equal true, h.isomorphic_vf2(g)
+  end
+  def test_isoclass
+    g = IGraph.new([1,2,3,4],false)
+    h = IGraph.new([5,6,7,8],false)
+    assert g.isoclass >= 0 and g.isoclass <= 11
+    assert_equal h.isoclass, g.isoclass
+  end
+  def test_isoclass_subgraph
+    g = IGraph.new([1,2,3,4],false)
+    assert g.isoclass_subgraph([1,2,3]) >= 0 and g.isoclass <= 4
+    assert_equal g.isoclass_subgraph([1,2,3]), g.isoclass_subgraph([2,3,4])
+  end
+  def test_igraph_isoclass_create
+    g = IGraph.new([1,2,3,4],false)
+    h = IGraph.isoclass_create(4,g.isoclass,false)
+    assert_equal g.isoclass, h.isoclass
+  end
+end

data/test/tc_layout.rb

@@ -23,4 +23,39 @@ class TestGraph < Test::Unit::TestCase
     assert_equal g.vcount, l.nrow
     assert_equal 2,        l.ncol
   end
+  def test_kamada_kawai
+    g = IGraph.new([1,2,3,4],true)
+    l = g.layout_kamada_kawai(10,1,1,2,1)
+    assert_instance_of IGraphMatrix, l
+    assert_equal g.vcount, l.nrow
+    assert_equal 2,        l.ncol
+  end  
+  def test_reingold_tilford
+    g = IGraph.new([1,2,3,4],true)
+    l = g.layout_reingold_tilford(1)
+    assert_instance_of IGraphMatrix, l
+    assert_equal g.vcount, l.nrow
+    assert_equal 2,        l.ncol
+  end  
+  def test_reingold_tilford_circular
+    g = IGraph.new([1,2,3,4],true)
+    l = g.layout_reingold_tilford_circular(1)
+    assert_instance_of IGraphMatrix, l
+    assert_equal g.vcount, l.nrow
+    assert_equal 2,        l.ncol
+  end   
+  def test_grid_fruchterman_reingold
+    g = IGraph.new([1,2,3,4],true)
+    l = g.layout_grid_fruchterman_reingold(10,1,1,2,1,1,false)
+    assert_instance_of IGraphMatrix, l
+    assert_equal g.vcount, l.nrow
+    assert_equal 2,        l.ncol
+  end
+  def test_lgl
+    g = IGraph.new([1,2,3,4],true)
+    l = g.layout_lgl(10,1,1,2,1,1,1)
+    assert_instance_of IGraphMatrix, l
+    assert_equal g.vcount, l.nrow
+    assert_equal 2,        l.ncol
+  end
 end

data/test/tc_motif.rb

@@ -0,0 +1,19 @@
+require 'test/unit'
+require 'igraph'
+
+class TestGraph < Test::Unit::TestCase
+  def test_motifs_randesu
+    g = IGraph.new(['A','B','C','D','A','C'],false)
+    hist = g.motifs_randesu(3,[0,0,0])
+    assert_equal [0,0,2,0], hist
+  end
+  def test_motifs_randesu_no
+    g = IGraph.new(['A','B','C','D','A','C'],false)
+    assert_equal 2, g.motifs_randesu_no(3,[0,0,0])    
+  end
+  def test_motifs_randesu_estimate
+    g = IGraph.new(['A','B','C','D','A','C'],false)
+    assert_equal 2, g.motifs_randesu_estimate(3,[0,0,0],4,nil)
+    assert_equal 2, g.motifs_randesu_estimate(3,[0,0,0],0,['A','B','C','D'])
+  end 
+end

data/test/test_all.rb

@@ -3,9 +3,8 @@
 require 'test/unit'
 
 require 'tc_attributes'
+require 'tc_cliques'
 require 'tc_create'
-require 'tc_iterators'
-require 'tc_selectors'
 require 'tc_add_delete'
 require 'tc_basic_query'
 require 'tc_basic_properties'
@@ -13,12 +12,19 @@ require 'tc_centrality'
 require 'tc_components'
 require 'tc_copy'
 require 'tc_cores'
+require 'tc_dijkstra'
 require 'tc_directedness'
 require 'tc_error_handling'
 require 'tc_file_read_write'
+require 'tc_generators_random'
+require 'tc_independent_vertex_sets'
+require 'tc_isomorphic'
+require 'tc_iterators'
 require 'tc_layout'
 require 'tc_matrix'
+require 'tc_motif'
 require 'tc_other_ops'
+require 'tc_selectors'
 require 'tc_shortest_paths'
 require 'tc_spanning'
 require 'tc_spectral'

data/test/test_draw.rb

@@ -0,0 +1,61 @@
+require 'igraph'
+require 'cairo'
+
+g = IGraph.barabasi_game(100,3,false,false)
+
+vertices = g.to_a
+layout   = g.send(ARGV.shift.to_sym,*ARGV.map{|a| eval(a)}).to_a
+
+format = Cairo::FORMAT_ARGB32
+width = 1000
+height = 1000
+
+surface = Cairo::ImageSurface.new(format, width, height)
+cr = Cairo::Context.new(surface)
+
+# fill background with white
+cr.set_source_rgba(1.0, 1.0, 1.0, 0.8)
+cr.paint
+
+max_x = layout.map{|a| a[0]}.max
+min_x = layout.map{|a| a[0]}.min
+max_y = layout.map{|a| a[1]}.max
+min_y = layout.map{|a| a[1]}.min
+
+x_var = max_x - min_x
+y_var = max_y - min_y
+
+max_var = [x_var,y_var].max
+
+layout.each_with_index do |a,i|
+  x,y = *a
+
+  x = (x - min_x)/max_var
+  y = (y - min_y)/max_var
+  x *= (width)
+  y *= (height)
+
+  layout[i] = [x,y]
+
+  puts "#{x} #{y}"
+
+end
+
+layout.each_with_index do |a,i|
+
+  v = vertices[i]
+  x,y = *a
+
+  cr.set_source_rgba(rand,rand,rand,0.5)
+  cr.circle(x,y,1).fill
+
+  g.adjacent_vertices(v,IGraph::OUT).each do |w|
+    cr.move_to(x,y)
+    wx,wy = *layout[vertices.index(w)]
+    cr.line_to(wx,wy)
+    cr.stroke
+  end
+
+end
+
+cr.target.write_to_png("test.png")

metadata

@@ -3,8 +3,8 @@ rubygems_version: 0.9.2
 specification_version: 1
 name: igraph
 version: !ruby/object:Gem::Version 
-  version: 0.3.2
-date: 2007-09-03 00:00:00 +09:00
+  version: 0.3.3
+date: 2007-10-02 00:00:00 +09:00
 summary: IGraph is a Ruby extension for interfacing with the C igraph library (http://cneurocvs.rmki.kfki.hu/igraph/). igraph is a library for creating and manipulating graphs with a particular emphasis on network analysis functions.
 require_paths: 
 - test
@@ -41,14 +41,20 @@ files:
 - ext/cIGraph_basic_properties.c
 - ext/cIGraph_basic_query.c
 - ext/cIGraph_centrality.c
+- ext/cIGraph_cliques.c
 - ext/cIGraph_components.c
+- ext/cIGraph_dijkstra.c
 - ext/cIGraph_direction.c
 - ext/cIGraph_error_handlers.c
 - ext/cIGraph_file.c
+- ext/cIGraph_generators_random.c
+- ext/cIGraph_independent_vertex_sets.c
+- ext/cIGraph_isomorphism.c
 - ext/cIGraph_iterators.c
 - ext/cIGraph_kcores.c
 - ext/cIGraph_layout.c
 - ext/cIGraph_matrix.c
+- ext/cIGraph_motif.c
 - ext/cIGraph_operators.c
 - ext/cIGraph_other_ops.c
 - ext/cIGraph_selectors.c
@@ -61,20 +67,27 @@ files:
 - ext/cIGraph_vertex_neighbourhood.c
 - ext/extconf.rb
 - test/tc_add_delete.rb
+- test/tc_adj_to_distance.rb
 - test/tc_attributes.rb
 - test/tc_basic_properties.rb
 - test/tc_basic_query.rb
 - test/tc_centrality.rb
+- test/tc_cliques.rb
 - test/tc_components.rb
 - test/tc_copy.rb
 - test/tc_cores.rb
 - test/tc_create.rb
+- test/tc_dijkstra.rb
 - test/tc_directedness.rb
 - test/tc_error_handling.rb
 - test/tc_file_read_write.rb
+- test/tc_generators_random.rb
+- test/tc_independent_vertex_sets.rb
+- test/tc_isomorphic.rb
 - test/tc_iterators.rb
 - test/tc_layout.rb
 - test/tc_matrix.rb
+- test/tc_motif.rb
 - test/tc_other_ops.rb
 - test/tc_selectors.rb
 - test/tc_shortest_paths.rb
@@ -85,6 +98,7 @@ files:
 - test/tc_transitivity.rb
 - test/tc_vertex_neighbourhood.rb
 - test/test_all.rb
+- test/test_draw.rb
 test_files: 
 - test/test_all.rb
 rdoc_options: