flock 0.1.0 → 0.2.1

data/README.rdoc

@@ -1,6 +1,6 @@
 = Flock
 
-Ruby bindings to Cluster 3.0, http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm
+Ruby bindings to {Cluster 3.0}[http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm]
 
 == Description
 
@@ -8,12 +8,14 @@ Provides bindings to K-Means clustering in Cluster 3.0
 
 == Synopsis
 
+=== Numeric Data
+
+  require 'pp'
   require 'flock'
   
   data     = Array.new(13) {[]}
   mask     = Array.new(13) {[]}
   weights  = Array.new(13) {1.0}
-  clusters = Array.new(13)
 
   data[ 0][ 0]=0.1; data[ 0][ 1]=0.0; data[ 0][ 2]=9.6; data[ 0][ 3] = 5.6;
   data[ 1][ 0]=1.4; data[ 1][ 1]=1.3; data[ 1][ 2]=0.0; data[ 1][ 3] = 3.8;
@@ -43,7 +45,7 @@ Provides bindings to K-Means clustering in Cluster 3.0
   mask[11][ 0]=0; mask[11][ 1]=1; mask[11][ 2]=1; mask[11][ 3] = 1;
   mask[12][ 0]=1; mask[12][ 1]=1; mask[12][ 2]=1; mask[12][ 3] = 1;
   
-  p Flock.kmeans(6, data, mask)
+  pp Flock.kmeans(6, data, mask)
 
   # method: 
   #    - Flock::METHOD_AVERAGE (default)
@@ -57,7 +59,7 @@ Provides bindings to K-Means clustering in Cluster 3.0
   #    - Flock::METRIC_ABSOLUTE_UNCENTERED_CORRELATION
   #    - Flock::METRIC_SPEARMAN
   #    - Flock::METRIC_KENDALL
-  Flock.kmeans(
+  pp Flock.kmeans(
     6,
     data,
     mask,
@@ -67,6 +69,32 @@ Provides bindings to K-Means clustering in Cluster 3.0
     weights:   Array.new(13) {1.0},
   )
 
+
+=== Sparse and Non-Numeric data
+
+  require 'pp'
+  require 'flock'
+  
+  data = []
+  data << { apple:  1, orange: 1 }
+  data << { black:  1, white:  1 }
+  data << { white:  1, cyan:   1 }
+  data << { orange: 1 }
+  data << { apple:  1 }
+  
+  pp Flock.sparse_kmeans(2, data)
+
+  # or even more simply (defaults to 1)
+  
+  data = []
+  data << %w(apple orange)
+  data << %w(black white)
+  data << %w(white cyan)
+  data << %w(orange)
+  data << %w(apple)
+  
+  pp Flock.sparse_kmeans(2, data)
+  
 == TODO
 
 Bindings to,

data/VERSION

@@ -1 +1 @@
-0.1.0
+0.2.1

data/examples/{example.rb → dense.rb}

@@ -1,11 +1,11 @@
 #!/usr/bin/ruby
 
+require 'pp'
 require 'flock'
 
 data     = Array.new(13) {[]}
 mask     = Array.new(13) {[]}
 weights  = Array.new(13) {1.0}
-clusters = Array.new(13)
 
 data[ 0][ 0]=0.1; data[ 0][ 1]=0.0; data[ 0][ 2]=9.6; data[ 0][ 3] = 5.6;
 data[ 1][ 0]=1.4; data[ 1][ 1]=1.3; data[ 1][ 2]=0.0; data[ 1][ 3] = 3.8;
@@ -35,5 +35,4 @@ mask[10][ 0]=1; mask[10][ 1]=1; mask[10][ 2]=1; mask[10][ 3] = 1;
 mask[11][ 0]=0; mask[11][ 1]=1; mask[11][ 2]=1; mask[11][ 3] = 1;
 mask[12][ 0]=1; mask[12][ 1]=1; mask[12][ 2]=1; mask[12][ 3] = 1;
 
-require 'pp'
 pp Flock.kmeans(6, data, mask)

data/examples/sparse.rb

@@ -0,0 +1,22 @@
+#!/usr/bin/ruby
+
+require 'pp'
+require 'flock'
+
+data = []
+data << { apple:  1, orange: 1 }
+data << { black:  1, white:  1 }
+data << { white:  1, cyan:   1 }
+data << { orange: 1 }
+data << { apple:  1 }
+
+pp Flock.sparse_kmeans(2, data)
+
+data = []
+data << %w(apple orange)
+data << %w(black white)
+data << %w(white cyan)
+data << %w(orange)
+data << %w(apple)
+
+pp Flock.sparse_kmeans(2, data)

data/ext/flock.c

@@ -15,11 +15,21 @@ int opt_int_value(VALUE option, char *key, int def) {
 
 VALUE rb_kmeans(int argc, VALUE *argv, VALUE self) {
     VALUE size, data, mask, weights, options;
-    rb_scan_args(argc, argv, "31", &size, &data, &mask, &options);
+    rb_scan_args(argc, argv, "22", &size, &data, &mask, &options);
+
+    if (TYPE(data) != T_ARRAY)
+        rb_raise(rb_eArgError, "data should be an array of arrays");
+
+    if (!NIL_P(mask) && TYPE(mask) != T_ARRAY)
+        rb_raise(rb_eArgError, "mask should be an array of arrays");
+
+    if (NIL_P(size) || NUM2INT(rb_Integer(size)) > RARRAY_LEN(data))
+        rb_raise(rb_eArgError, "size should be > 0 and <= data size");
 
     int i,j;
     int nrows = RARRAY_LEN(data);
     int ncols = RARRAY_LEN(rb_ary_entry(data, 0));
+    int nsets = NUM2INT(rb_Integer(size));
 
     double **cdata          = (double**)malloc(sizeof(double*)*nrows);
     int    **cmask          = (int   **)malloc(sizeof(int   *)*nrows);
@@ -34,14 +44,14 @@ VALUE rb_kmeans(int argc, VALUE *argv, VALUE self) {
         ccentroid[i]      = (double*)malloc(sizeof(double)*ncols);
         ccentroid_mask[i] = (int   *)malloc(sizeof(int   )*ncols);
         for (j = 0; j < ncols; j++) {
-            cdata[i][j] = NUM2DBL(rb_ary_entry(rb_ary_entry(data, i), j));
-            cmask[i][j] = NUM2INT(rb_ary_entry(rb_ary_entry(mask, i), j));
+            cdata[i][j] = NUM2DBL(rb_Float(rb_ary_entry(rb_ary_entry(data, i), j)));
+            cmask[i][j] = NIL_P(mask) ? 1 : NUM2INT(rb_Integer(rb_ary_entry(rb_ary_entry(mask, i), j)));
         }
     }
 
     weights = NIL_P(options) ? Qnil : rb_hash_aref(options, ID2SYM(rb_intern("weights")));
     for (i = 0; i < ncols; i++) {
-        cweights[i] = NIL_P(weights) ? 1.0 : NUM2DBL(rb_ary_entry(weights, i));
+        cweights[i] = NIL_P(weights) ? 1.0 : NUM2DBL(rb_Float(rb_ary_entry(weights, i)));
     }
 
     int transpose = opt_int_value(options, "transpose", 0);
@@ -60,10 +70,10 @@ VALUE rb_kmeans(int argc, VALUE *argv, VALUE self) {
 
     int    ifound;
     double error;
-    kcluster(NUM2INT(size),
+    kcluster(nsets,
         nrows, ncols, cdata, cmask, cweights, transpose, npass, method, dist, ccluster, &error, &ifound);
 
-    getclustercentroids(NUM2INT(size),
+    getclustercentroids(nsets,
         nrows, ncols, cdata, cmask, ccluster, ccentroid, ccentroid_mask, transpose, method);
 
     VALUE result   = rb_hash_new();
@@ -71,7 +81,7 @@ VALUE rb_kmeans(int argc, VALUE *argv, VALUE self) {
     VALUE centroid = rb_ary_new();
 
     for (i = 0; i < nrows; i++) {
-        rb_ary_push(cluster,  INT2NUM(ccluster[i]));
+        rb_ary_push(cluster, INT2NUM(ccluster[i]));
         VALUE point = rb_ary_new();
         for (j = 0; j < ncols; j++)
             rb_ary_push(point, DBL2NUM(ccentroid[i][j]));

data/flock.gemspec

@@ -0,0 +1,50 @@
+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run the gemspec command
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = %q{flock}
+  s.version = "0.2.1"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Bharanee Rathna"]
+  s.date = %q{2011-02-19}
+  s.description = %q{A thin ruby binding to Cluster 3.0}
+  s.email = ["deepfryed@gmail.com"]
+  s.extensions = ["ext/extconf.rb"]
+  s.extra_rdoc_files = [
+    "README.rdoc"
+  ]
+  s.files = [
+    "README.rdoc",
+     "Rakefile",
+     "VERSION",
+     "ext/cluster.c",
+     "ext/cluster.h",
+     "ext/extconf.rb",
+     "ext/flock.c",
+     "flock.gemspec",
+     "lib/flock.rb"
+  ]
+  s.homepage = %q{http://github.com/deepfryed/flock}
+  s.rdoc_options = ["--charset=UTF-8"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = %q{1.3.7}
+  s.summary = %q{Ruby bindings to Cluster 3.0.}
+  s.test_files = [
+    "examples/sparse.rb",
+     "examples/dense.rb"
+  ]
+
+  if s.respond_to? :specification_version then
+    current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+    else
+    end
+  else
+  end
+end
+

data/lib/flock.rb

@@ -0,0 +1,35 @@
+require_relative '../ext/flock'
+module Flock
+
+  def self.sparse_hash_to_data sparse_data
+    dims = Hash[sparse_data.map(&:keys).flatten.uniq.map.with_index{|k,v| [k,v]}]
+    data = sparse_data.map do |sv|
+      vector = Array.new(dims.size) {0}
+      sv.each {|k,v| vector[dims[k]] = v }
+      vector
+    end
+    [dims,data]
+  end
+
+  def self.sparse_array_to_data sparse_data
+    dims = Hash[sparse_data.flatten.uniq.map.with_index{|k,v| [k,v]}]
+    data = sparse_data.map do |sv|
+      vector = Array.new(dims.size) {0}
+      sv.each {|k| vector[dims[k]] = 1 }
+      vector
+    end
+    [dims,data]
+  end
+
+  def self.sparse_kmeans size, sparse_data, options={}
+    dims, data = sparse_data[0].kind_of?(Array) ? sparse_array_to_data(sparse_data) : sparse_hash_to_data(sparse_data)
+
+    if options.key?(:weights)
+      weights = Array.new(dims.size) {1}
+      options[:weights].each {|k,v| weights[dims[k]] = v }
+      options[:weights] = weights
+    end
+
+    kmeans(size, data, nil, options)
+  end
+end

metadata

@@ -4,9 +4,9 @@ version: !ruby/object:Gem::Version
   prerelease: false
   segments: 
   - 0
+  - 2
   - 1
-  - 0
-  version: 0.1.0
+  version: 0.2.1
 platform: ruby
 authors: 
 - Bharanee Rathna
@@ -14,7 +14,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-02-18 00:00:00 +11:00
+date: 2011-02-19 00:00:00 +11:00
 default_executable: 
 dependencies: []
 
@@ -35,7 +35,10 @@ files:
 - ext/cluster.h
 - ext/extconf.rb
 - ext/flock.c
-- examples/example.rb
+- flock.gemspec
+- lib/flock.rb
+- examples/sparse.rb
+- examples/dense.rb
 has_rdoc: true
 homepage: http://github.com/deepfryed/flock
 licenses: []
@@ -69,4 +72,5 @@ signing_key:
 specification_version: 3
 summary: Ruby bindings to Cluster 3.0.
 test_files: 
-- examples/example.rb
+- examples/sparse.rb
+- examples/dense.rb