hierclust 0.1.3 → 0.1.4
Sign up to get free protection for your applications and to get access to all the features.
- data/History.txt +7 -0
- data/lib/hierclust/cluster.rb +4 -2
- data/lib/hierclust/clusterer.rb +13 -2
- data/lib/hierclust/version.rb +1 -1
- data/spec/hierclust/cluster_spec.rb +28 -0
- data/spec/hierclust/clusterer_spec.rb +34 -9
- data/spec/hierclust/point_spec.rb +5 -0
- data/website/index.html +1 -1
- metadata +2 -2
data/History.txt
CHANGED
data/lib/hierclust/cluster.rb
CHANGED
@@ -15,13 +15,15 @@ module Hierclust
|
|
15
15
|
# Returns the average x-coordinates of all items in this Cluster.
|
16
16
|
def x
|
17
17
|
return nil if size == 0
|
18
|
-
|
18
|
+
points = self.points
|
19
|
+
@x ||= points.inject(0.0) {|sum, p| sum + p.x} / points.size
|
19
20
|
end
|
20
21
|
|
21
22
|
# Returns the average y-coordinates of all items in this Cluster.
|
22
23
|
def y
|
23
24
|
return nil if size == 0
|
24
|
-
|
25
|
+
points = self.points
|
26
|
+
@y ||= points.inject(0.0) {|sum, p| sum + p.y} / points.size
|
25
27
|
end
|
26
28
|
|
27
29
|
# Add an +item+ to this Cluster.
|
data/lib/hierclust/clusterer.rb
CHANGED
@@ -10,8 +10,15 @@ module Hierclust
|
|
10
10
|
#
|
11
11
|
# Specify +separation+ to stop the clustering process once all the
|
12
12
|
# items are at least +separation+ units apart.
|
13
|
-
|
13
|
+
#
|
14
|
+
# Specify +resolution+ to give a minimum size for clusters. Points that
|
15
|
+
# are within this distance from each other will not be hierarchically
|
16
|
+
# clustered, but will be put into clusters based strictly on coordinates.
|
17
|
+
# The clusters generated by this "pre-clustering" will then be
|
18
|
+
# hierarchically clustered as normal.
|
19
|
+
def initialize(data, separation = nil, resolution = nil)
|
14
20
|
@separation = separation
|
21
|
+
@resolution = resolution
|
15
22
|
@data = precluster(data)
|
16
23
|
@distances = Distances.new(@data)
|
17
24
|
end
|
@@ -45,6 +52,10 @@ module Hierclust
|
|
45
52
|
end
|
46
53
|
|
47
54
|
def precluster(points)
|
55
|
+
if @resolution.nil?
|
56
|
+
# preclustering is only applicable given lower bound on resolution
|
57
|
+
return points.dup
|
58
|
+
end
|
48
59
|
if @separation.nil?
|
49
60
|
# can't precluster w/ no min separation given
|
50
61
|
return points.dup
|
@@ -53,7 +64,7 @@ module Hierclust
|
|
53
64
|
# if no separation is asked for, it's all one cluster
|
54
65
|
return [Cluster.new(points)]
|
55
66
|
end
|
56
|
-
grid_size = @
|
67
|
+
grid_size = @resolution
|
57
68
|
grid_clusters = Hash.new
|
58
69
|
points.each do |point|
|
59
70
|
grid_x = (point.x / grid_size).floor
|
data/lib/hierclust/version.rb
CHANGED
@@ -58,4 +58,32 @@ module Hierclust
|
|
58
58
|
@points.should include(@p_1, @p_2)
|
59
59
|
end
|
60
60
|
end
|
61
|
+
|
62
|
+
describe Cluster, " with one point and one cluster" do
|
63
|
+
before do
|
64
|
+
@x_1, @x_2, @x_3 = 1, 2, 3
|
65
|
+
@y_1, @y_2, @y_3 = 2, 2, 5
|
66
|
+
@p_1 = Point.new(@x_1, @y_1)
|
67
|
+
@p_2 = Point.new(@x_2, @y_2)
|
68
|
+
@p_3 = Point.new(@x_3, @y_3)
|
69
|
+
@c_1 = Cluster.new([@p_1, @p_2])
|
70
|
+
@c_2 = Cluster.new([@p_3, @c_1])
|
71
|
+
end
|
72
|
+
|
73
|
+
it "should have two items" do
|
74
|
+
@c_2.items.size.should == 2
|
75
|
+
end
|
76
|
+
|
77
|
+
it "should have three points" do
|
78
|
+
@c_2.points.size.should == 3
|
79
|
+
end
|
80
|
+
|
81
|
+
it "should have x-coordinate at average of point's x-coordinates" do
|
82
|
+
@c_2.x.should == 2
|
83
|
+
end
|
84
|
+
|
85
|
+
it "should have y-coordinate at average of point's y-coordinates" do
|
86
|
+
@c_2.y.should == 3
|
87
|
+
end
|
88
|
+
end
|
61
89
|
end
|
@@ -164,18 +164,43 @@ module Hierclust
|
|
164
164
|
end
|
165
165
|
|
166
166
|
describe "and separation 3" do
|
167
|
-
|
168
|
-
|
167
|
+
describe "with no resolution limit" do
|
168
|
+
before do
|
169
|
+
@clusters = Clusterer.new(@points, 3).clusters.sort
|
170
|
+
end
|
171
|
+
|
172
|
+
it "should have three clusters" do
|
173
|
+
@clusters.size.should == 3
|
174
|
+
end
|
175
|
+
|
176
|
+
it "should have clusters size 2, 2, and 4 " do
|
177
|
+
@clusters[0].points.size.should == 2
|
178
|
+
@clusters[1].points.size.should == 2
|
179
|
+
@clusters[2].points.size.should == 4
|
180
|
+
end
|
181
|
+
|
182
|
+
it "should have 2 items in large cluster" do
|
183
|
+
@clusters[2].items.size.should == 2
|
184
|
+
end
|
169
185
|
end
|
170
186
|
|
171
|
-
|
172
|
-
|
173
|
-
|
187
|
+
describe "with coarse resolution" do
|
188
|
+
before do
|
189
|
+
@clusters = Clusterer.new(@points, 3, 5).clusters.sort
|
190
|
+
end
|
191
|
+
|
192
|
+
it "should have three clusters" do
|
193
|
+
@clusters.size.should == 2
|
194
|
+
end
|
195
|
+
|
196
|
+
it "should have clusters size 2, 2, and 4 " do
|
197
|
+
@clusters[0].points.size.should == 4
|
198
|
+
@clusters[1].points.size.should == 4
|
199
|
+
end
|
174
200
|
|
175
|
-
|
176
|
-
|
177
|
-
|
178
|
-
@clusters[2].points.size.should == 4
|
201
|
+
it "should have 4 items in large cluster" do
|
202
|
+
@clusters[1].items.size.should == 4
|
203
|
+
end
|
179
204
|
end
|
180
205
|
end
|
181
206
|
end
|
@@ -4,10 +4,15 @@ module Hierclust
|
|
4
4
|
describe Point do
|
5
5
|
before do
|
6
6
|
@p = Point.new(1, 1)
|
7
|
+
@p2 = Point.new(2, 1)
|
7
8
|
end
|
8
9
|
|
9
10
|
it "should have points that is an array of only self" do
|
10
11
|
@p.points.should == [@p]
|
11
12
|
end
|
13
|
+
|
14
|
+
it "should calculate distance to other" do
|
15
|
+
@p.distance_to(@p2).should == 1.0
|
16
|
+
end
|
12
17
|
end
|
13
18
|
end
|
data/website/index.html
CHANGED
@@ -33,7 +33,7 @@
|
|
33
33
|
<h1>Simple Hierarchical Clustering</h1>
|
34
34
|
<div id="version" class="clickable" onclick='document.location = "http://rubyforge.org/projects/hierclust"; return false'>
|
35
35
|
<p>Get Version</p>
|
36
|
-
<a href="http://rubyforge.org/projects/hierclust" class="numbers">0.1.
|
36
|
+
<a href="http://rubyforge.org/projects/hierclust" class="numbers">0.1.4</a>
|
37
37
|
</div>
|
38
38
|
<h1>→ ‘hierclust’</h1>
|
39
39
|
|
metadata
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: hierclust
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.1.
|
4
|
+
version: 0.1.4
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Brandt Kurowski
|
@@ -9,7 +9,7 @@ autorequire:
|
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
11
|
|
12
|
-
date: 2008-02-
|
12
|
+
date: 2008-02-13 00:00:00 -05:00
|
13
13
|
default_executable:
|
14
14
|
dependencies: []
|
15
15
|
|