bribera-rubyvor 0.0.6 → 0.0.7

data/History.txt

@@ -1,3 +1,9 @@
+=== 0.0.7 / 2008-12-12
+
+* Bugfix: there are cases where performing a Delaunay triangulation on a set of points will not yield a complete nearest neighbor graph. This causes computation of the minimum spanning tree and clustering to fail for these nodes (they always appear as disconnected from the main graph).
+
+* To fix this, the nn_graph function now treats any point that is excluded from Delaunay triangulation as having *all* other points as nearest neighbors. This is a naive approach, but is a good fix while a more efficient solution is considered.
+
 === 0.0.6 / 2008-12-11
 
 * Implementation of cluster_by_size to partition points into N clusters.

data/Manifest.txt

@@ -12,12 +12,13 @@ ext/output.c
 ext/rb_cComputation.c
 ext/rb_cPoint.c
 ext/rb_cPriorityQueue.c
-ext/ruby_vor.c
-ext/ruby_vor.h
+ext/ruby_vor_c.c
+ext/ruby_vor_c.h
 ext/vdefs.h
 ext/voronoi.c
 lib/ruby_vor.rb
 lib/ruby_vor/computation.rb
+lib/ruby_vor/geo_ruby_extensions.rb
 lib/ruby_vor/point.rb
 lib/ruby_vor/priority_queue.rb
 lib/ruby_vor/version.rb

data/Rakefile

@@ -19,7 +19,7 @@ desc "Compile extensions"
 task :compile => EXT
 task :test => :compile
 
-file EXT => ['ext/extconf.rb', 'ext/ruby_vor.c'] do
+file EXT => ['ext/extconf.rb', 'ext/ruby_vor_c.c'] do
   Dir.chdir 'ext' do
     ruby 'extconf.rb'
     sh 'make'

data/ext/extconf.rb

@@ -1,3 +1,3 @@
 require 'mkmf'
-dir_config('ruby_vor')
-create_makefile('ruby_vor')
+dir_config('ruby_vor_c')
+create_makefile('ruby_vor_c')

data/ext/rb_cComputation.c

@@ -1,6 +1,6 @@
 #include <ruby.h>
 #include <vdefs.h>
-#include <ruby_vor.h>
+#include <ruby_vor_c.h>
 #include <stdio.h>
 #include <stdlib.h>
 
@@ -189,7 +189,7 @@ RubyVor_minimum_spanning_tree(int argc, VALUE *argv, VALUE self)
 VALUE
 RubyVor_nn_graph(VALUE self)
 {
-    long i;
+    long i, j;
     VALUE dtRaw, graph, points, * dtPtr, * tripletPtr, * graphPtr;
 
     graph = rb_iv_get(self, "@nn_graph");
@@ -222,8 +222,20 @@ RubyVor_nn_graph(VALUE self)
         rb_ary_push(graphPtr[FIX2INT(tripletPtr[2])], tripletPtr[1]);
     }
 
-    for (i = 0; i < RARRAY(graph)->len; i++)
-        rb_funcall(graphPtr[i], rb_intern("uniq!"), 0);
+    for (i = 0; i < RARRAY(graph)->len; i++) {
+        if (RARRAY(graphPtr[i])->len < 1) {
+            // No valid triangles touched this node -- include *all* possible neighbors
+            for(j = 0; j < RARRAY(points)->len; j++) {
+                if (j != i) {
+                    rb_ary_push(graphPtr[i], INT2FIX(j));
+                    if (RARRAY(graphPtr[j])->len > 0 && !rb_ary_includes(graphPtr[j], INT2FIX(i)))
+                        rb_ary_push(graphPtr[j], INT2FIX(i));
+                }
+            }
+        } else {
+            rb_funcall(graphPtr[i], rb_intern("uniq!"), 0);
+        }
+    }
 
     rb_iv_set(self, "@nn_graph", graph);
     

data/ext/rb_cPoint.c

@@ -1,6 +1,6 @@
 #include <ruby.h>
 #include <vdefs.h>
-#include <ruby_vor.h>
+#include <ruby_vor_c.h>
 #include <math.h>
 
 /*

data/ext/rb_cPriorityQueue.c

@@ -1,6 +1,6 @@
 #include <ruby.h>
 #include <vdefs.h>
-#include <ruby_vor.h>
+#include <ruby_vor_c.h>
 
 //
 // Instance methods for RubyVor::VDDT::PriorityQueue

data/ext/{ruby_vor.c → ruby_vor_c.c}

@@ -1,12 +1,12 @@
 #include <ruby.h>
 #include <vdefs.h>
-#include <ruby_vor.h>
+#include <ruby_vor_c.h>
 
 //
 // Extension initialization
 //
 void
-Init_ruby_vor(void)
+Init_ruby_vor_c(void)
 {
     //
     // Set up our Modules and Class.

data/lib/ruby_vor/geo_ruby_extensions.rb

@@ -0,0 +1,15 @@
+if require 'geo_ruby'
+  # Let us call uniq on a set of Points or use one as a Hash key.
+  module GeoRuby
+    module SimpleFeatures
+      class Point < Geometry
+        def eql?(other)
+          self == other
+        end
+        def hash
+          [x,y,z,m].hash
+        end
+      end
+    end
+  end
+end

data/lib/ruby_vor/point.rb

@@ -1,8 +1,17 @@
 module RubyVor
   class Point
-    attr_accessor :x, :y
+    attr_reader :x, :y
     def initialize(x=0.0,y=0.0)
       @x = x; @y = y
     end
+    
+    def ==(p)
+      @x == p.x && @y == p.y
+    end
+    alias :eql? :==
+    def hash
+      [x.to_f, y.to_f].hash
+    end
+
   end
 end

data/lib/ruby_vor/version.rb

@@ -1,3 +1,3 @@
 module RubyVor
-  VERSION = '0.0.6'
+  VERSION = '0.0.7'
 end

data/lib/ruby_vor.rb

@@ -5,9 +5,10 @@ require 'ruby_vor/version'
 require 'ruby_vor/point'
 require 'ruby_vor/priority_queue'
 require 'ruby_vor/computation'
+require 'ruby_vor/geo_ruby_extensions'
 
 # Require ruby_vor.so last to clobber old from_points
-require 'ruby_vor.so'
+require 'ruby_vor_c.so'
 
 # DOC HERE
 module RubyVor

data/rubyvor.gemspec

@@ -2,16 +2,16 @@
 
 Gem::Specification.new do |s|
   s.name = %q{rubyvor}
-  s.version = "0.0.6"
+  s.version = "0.0.7"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Brendan Ribera"]
-  s.date = %q{2008-12-11}
+  s.date = %q{2008-12-12}
   s.description = %q{RubyVor provides efficient computation of Voronoi diagrams and Delaunay triangulation for a set of Ruby points. It is intended to function as a complemenet to GeoRuby. These structures can be used to compute a nearest-neighbor graph for a set of points. This graph can in turn be used for proximity-based clustering of the input points.}
   s.email = ["brendan.ribera+rubyvor@gmail.com"]
   s.extensions = ["ext/extconf.rb"]
   s.extra_rdoc_files = ["History.txt", "Manifest.txt", "README.txt"]
-  s.files = ["History.txt", "Manifest.txt", "README.txt", "Rakefile", "ext/Doc", "ext/edgelist.c", "ext/extconf.rb", "ext/geometry.c", "ext/heap.c", "ext/memory.c", "ext/output.c", "ext/rb_cComputation.c", "ext/rb_cPoint.c", "ext/rb_cPriorityQueue.c", "ext/ruby_vor.c", "ext/ruby_vor.h", "ext/vdefs.h", "ext/voronoi.c", "lib/ruby_vor.rb", "lib/ruby_vor/computation.rb", "lib/ruby_vor/point.rb", "lib/ruby_vor/priority_queue.rb", "lib/ruby_vor/version.rb", "rubyvor.gemspec", "test/test_computation.rb", "test/test_priority_queue.rb", "test/test_voronoi_interface.rb"]
+  s.files = ["History.txt", "Manifest.txt", "README.txt", "Rakefile", "ext/Doc", "ext/edgelist.c", "ext/extconf.rb", "ext/geometry.c", "ext/heap.c", "ext/memory.c", "ext/output.c", "ext/rb_cComputation.c", "ext/rb_cPoint.c", "ext/rb_cPriorityQueue.c", "ext/ruby_vor_c.c", "ext/ruby_vor_c.h", "ext/vdefs.h", "ext/voronoi.c", "lib/ruby_vor.rb", "lib/ruby_vor/computation.rb", "lib/ruby_vor/geo_ruby_extensions.rb", "lib/ruby_vor/point.rb", "lib/ruby_vor/priority_queue.rb", "lib/ruby_vor/version.rb", "rubyvor.gemspec", "test/test_computation.rb", "test/test_priority_queue.rb", "test/test_voronoi_interface.rb"]
   s.has_rdoc = true
   s.homepage = %q{http://github.com/bribera/rubyvor}
   s.rdoc_options = ["--main", "README.txt"]

data/test/test_computation.rb

@@ -34,6 +34,10 @@ class TestComputation < MiniTest::Unit::TestCase
                       [4, 5, 6, 8],       # 7
                       [0, 2, 3, 5, 6, 7], # 8
                      ]
+    
+    comp.nn_graph.each_with_index do |neighbors,i|
+      refute_empty neighbors, "@nn_graph returned empty neighbors for node #{i}"
+    end
 
     assert_equal comp.nn_graph.map{|v| v.sort}.sort, \
                  expected_graph.map{|v| v.sort}.sort
@@ -149,11 +153,36 @@ class TestComputation < MiniTest::Unit::TestCase
 
   
   def test_duplicate_points
-    comp = RubyVor::VDDT::Computation.from_points([RubyVor::Point.new(1,1), RubyVor::Point.new(1,1), RubyVor::Point.new(2,3), RubyVor::Point.new(1,1), RubyVor::Point.new(4,0)])
-    refute_equal comp.nn_graph,               nil
-    refute_equal comp.minimum_spanning_tree,  nil
-    refute_equal comp.cluster_by_distance(3), nil
-    refute_equal comp.cluster_by_size([2]),   nil
+    comp = RubyVor::VDDT::Computation.from_points([
+                                                   RubyVor::Point.new(2,3),      # 0
+                                                   RubyVor::Point.new(1,1),      # 1
+                                                   RubyVor::Point.new(1,1),      # 2
+                                                   RubyVor::Point.new(1,1),      # 3
+                                                   RubyVor::Point.new(1,1),      # 4
+                                                   RubyVor::Point.new(1,1),      # 5
+                                                   RubyVor::Point.new(1,1),      # 6
+                                                   RubyVor::Point.new(1,1),      # 7
+                                                   RubyVor::Point.new(1,1),      # 8
+                                                   RubyVor::Point.new(4,10),     # 9
+                                                   RubyVor::Point.new(4,10.0),   # 10
+                                                   RubyVor::Point.new(4.0,10.0), # 11
+                                                   RubyVor::Point.new(4.0,10.0), # 12
+                                                  ])
+    comp.nn_graph.each_with_index do |neighbors,i|
+      refute_empty neighbors, "@nn_graph returned empty neighbors for node #{i}"
+    end
+    
+    assert_equal [[0], [1,2,3,4,5,6,7,8], [9,10,11,12]], \
+                 comp.cluster_by_distance(1).map{|cl| cl.sort}.sort
+    
+    assert_equal [[0,1,2,3,4,5,6,7,8], [9,10,11,12]], \
+                 comp.cluster_by_distance(5).map{|cl| cl.sort}.sort
+
+    assert_equal [[0,1,2,3,4,5,6,7,8,9,10,11,12]], \
+                 comp.cluster_by_distance(10).map{|cl| cl.sort}.sort
+    
+    assert_equal [[0,1,2,3,4,5,6,7,8], [9,10,11,12]], \
+                 comp.cluster_by_size([2])[2].map{|cl| cl.sort}.sort
   end
 
   

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: bribera-rubyvor
 version: !ruby/object:Gem::Version 
-  version: 0.0.6
+  version: 0.0.7
 platform: ruby
 authors: 
 - Brendan Ribera
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2008-12-11 00:00:00 -08:00
+date: 2008-12-12 00:00:00 -08:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -47,12 +47,13 @@ files:
 - ext/rb_cComputation.c
 - ext/rb_cPoint.c
 - ext/rb_cPriorityQueue.c
-- ext/ruby_vor.c
-- ext/ruby_vor.h
+- ext/ruby_vor_c.c
+- ext/ruby_vor_c.h
 - ext/vdefs.h
 - ext/voronoi.c
 - lib/ruby_vor.rb
 - lib/ruby_vor/computation.rb
+- lib/ruby_vor/geo_ruby_extensions.rb
 - lib/ruby_vor/point.rb
 - lib/ruby_vor/priority_queue.rb
 - lib/ruby_vor/version.rb