buncher 1.0.3 → 1.0.4

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Files changed (4) hide show
  1. data/lib/buncher.rb +4 -4
  2. data/lib/buncher/buncher.bundle +0 -0
  3. data/test/test_buncher.rb +27 -23
  4. metadata +2 -2
data/lib/buncher.rb CHANGED
@@ -1,6 +1,6 @@
1
1
  require 'buncher/buncher'
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2
  module Buncher
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- VERSION = "1.0.3"
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+ VERSION = "1.0.4"
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  # your cluster needs to look like this. Make a bunch of them and pass them in. It's ok to pass in empty elements to start.
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  class Cluster
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  attr_accessor :elements
@@ -58,7 +58,7 @@ module Buncher
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  end
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  end
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- # run the clustering algorithm until have calculated the current number of clusters, taken from this paper:
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+ # run the clustering algorithm until we have calculated the best number of clusters, taken from this paper:
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  # http://papers.nips.cc/paper/2526-learning-the-k-in-k-means.pdf
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  def self.cluster(elements, weights,options={})
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  solutions={}
@@ -76,11 +76,11 @@ module Buncher
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  last_fK, last_sK, last_aK = fK(centers,last_sK, last_aK,weights)
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  puts "summary #{number_clusters}: fK() = #{last_fK}, last_sK=#{last_sK} last_aK=#{last_aK} "
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  solutions[last_fK]=centers if number_clusters >= min_size
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- # break if number_clusters == 2 ## debugging
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+ # break if number_clusters == 3 ## debugging
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  end
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  min_fK =solutions.keys.sort.first || 1.0
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  if min_fK > 0.85
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- nil # ie, not clustered at all
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+ elements.map {|ele| Cluster.new(ele,[ele])} # ie, not clustered at all
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  else
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  solutions[min_fK]
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  end
data/lib/buncher/buncher.bundle CHANGED
Binary file
data/test/test_buncher.rb CHANGED
@@ -1,10 +1,11 @@
1
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  require "buncher"
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  require 'rubystats'
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  require 'gnuplot'
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+ require "minitest/focus"
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5
 
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  def dump(centers)
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- puts "centers are"
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- centers.each {|ccc| puts "center #{ccc.center.inspect} #{ccc.elements[0]}, #{ccc.elements[1]}"}
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+ puts "#{centers.size} centers are"
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+ centers.each {|ccc| puts "center #{ccc.center.inspect} elements #{ccc.elements[0]}, #{ccc.elements[1]}"}
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  end
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  def init_data(number_points, number_clusters)
@@ -64,13 +65,19 @@ def plot(file_name,points,centers, initial_centers=nil)
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  end
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  class TestBuncher < Minitest::Test
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- # WORKING=<<-'EOS'
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+
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  def test_distance
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  element1= [1.0, 0.5, 0.533333333333333, 1.0, 0.0, 0.0, 0.333333333333333, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.333333333333333, 0.333333333333333, 0.666666666666667, 0.0, 0.0, 1.0, 0.333333333333333, 0.333333333333333, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.333333333333333, 0.0, 0.0, 0.0, 0.0, 0.0, 0.333333333333333, 0.0, 0.333333333333333, 0.0, 0.4, 0.0, 0.0, 0.0, 0.0, 0.0, 0.333333333333333, 0.333333333333333, 0.0, 0.333333333333333, 0.4, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.4, 0.333333333333333, 0.0, 0.666666666666667, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
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  element2= [1.0, 1.0, 0.5, 1.0, 0.0, 0.0, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.2, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.5, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.5, 1.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
71
72
  weights= [0.12158054711246201, 0.060790273556231005, 0.060790273556231005, 0.060790273556231005, 0.060790273556231005, 0.060790273556231005, 0.060790273556231005, 0.0121580547112462, 0.0060790273556231, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.0060790273556231, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.0060790273556231, 0.00303951367781155, 0.00303951367781155, 0.0060790273556231, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.0060790273556231, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.0060790273556231, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.0060790273556231, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.0121580547112462, 0.0060790273556231, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.0060790273556231, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.0121580547112462, 0.0060790273556231, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.0060790273556231, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.0121580547112462, 0.0060790273556231, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.0060790273556231, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.0060790273556231, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.0060790273556231, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.0060790273556231, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.0121580547112462, 0.0060790273556231, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.0060790273556231, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.0121580547112462, 0.0060790273556231, 0.0060790273556231, 0.0060790273556231, 0.0121580547112462, 0.0060790273556231, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.0121580547112462, 0.0060790273556231, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.0121580547112462, 0.0060790273556231, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155, 0.00303951367781155]
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  assert_in_delta(Buncher::distance(element1,element2, weights),0.098,0.001)
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  end
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+ def test_distance_nan
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+ element1 = [nil, 1, 1]
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+ element2 = [nil, nil, 1]
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+ weights = [1] * 3
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+ assert_in_delta(Buncher::distance(element1,element2, weights),0.5,0.01)
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+ end
74
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  def test_should_find_the_one_center
75
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  elements = [[1,1]]
76
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  starting_centers = elements.sample(1).map {|aaa| Buncher::Cluster.new(aaa)}
@@ -80,9 +87,13 @@ class TestBuncher < Minitest::Test
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  assert_in_delta(new_centers.first.center[1],1.0,0.01)
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  end
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90
+
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  def test_choose_centers_wrapper
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  elements = [[1,1]]
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+ puts "test_choose_centers_wrapper - start"
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  new_centers = Buncher::choose_centers(elements,[1]*2, 1)
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+ puts "test_choose_centers_wrapper - well well"
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+ puts new_centers.inspect
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  dump(new_centers)
87
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  assert_in_delta(new_centers.first.center[1],1.0,0.01)
88
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  assert_in_delta(new_centers.first.center[1],1.0,0.01)
@@ -91,41 +102,34 @@ class TestBuncher < Minitest::Test
91
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  elements = init_data(100,3)
92
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  new_centers = Buncher::choose_centers(elements, [1]*2, 3)
93
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  dump(new_centers)
94
- assert_equal(new_centers.size,3)
105
+ assert_equal(3, new_centers.size)
95
106
  end
96
- # EOS
107
+
108
+
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  def test_min_size_works
98
- elements = init_data(100,4)
110
+ elements = init_data(100,1)
99
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  new_centers = Buncher::cluster(elements,[1]*2,:min_size=>2)
100
- dump(new_centers)
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- assert_equal(new_centers.size,4)
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- end
103
-
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- # WWW=<<-'EOS'
105
-
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- def test_choose_centers_wrapper2
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- elements = init_data(100,3)
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- new_centers = Buncher::choose_centers(elements, [1]*2, 3)
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- plot("/tmp/kmeans_initial_#{new_centers.size}.png",elements, new_centers)
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- dump(new_centers)
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- `open /tmp/kmeans_initial_#{new_centers.size}.png`
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- assert_equal(new_centers.size,3)
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+ assert(new_centers.size >=2,"at least 2 centers")
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113
  end
114
-
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+ focus
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  def test_gaussian_distribution_of_100_points_in_3_clusters
116
- 12.times do |run|
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+ 1.times do |run|
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  # srand(843284148793854177950180651080082381)
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  elements = init_data(100,3)
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  # elements.each {|eee| puts "#{eee[0]},#{eee[1]}"}
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+ graphfile=nil;
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  # new_centers = Buncher::cluster(elements) {|elements,centers, initial_centers| puts "run #{run} setup";plot("/tmp/#{run}_centers_#{centers.size}.png",elements,initial_centers)}
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  new_centers = Buncher::cluster(elements,[1]*2) {|elements,centers, initial_centers|
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- plot("/tmp/#{run}_centers_#{centers.size}.png",elements,centers, initial_centers)
123
+ graphfile = "/tmp/#{run}_centers_#{centers.size}.png"
124
+ plot(graphfile,elements,centers, initial_centers)
123
125
  }
124
126
  puts "run #{run}: k is #{new_centers.size}, seed was #{srand}"
125
127
  puts "ERROR "*4 if new_centers.size != 3
126
128
  puts
127
129
  assert_equal(3,new_centers.size)
130
+ refute(new_centers.first.elements.empty?)
131
+ graphfile = "/tmp/#{run}_centers_3.png"
132
+ `open #{graphfile}`
128
133
  end
129
134
  end
130
- # EOS
131
135
  end
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: buncher
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3
  version: !ruby/object:Gem::Version
4
- version: 1.0.3
4
+ version: 1.0.4
5
5
  prerelease:
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  platform: ruby
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7
  authors:
@@ -9,7 +9,7 @@ authors:
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9
  autorequire:
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  bindir: bin
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  cert_chain: []
12
- date: 2015-04-25 00:00:00.000000000 Z
12
+ date: 2015-04-27 00:00:00.000000000 Z
13
13
  dependencies:
14
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  - !ruby/object:Gem::Dependency
15
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  name: minitest