flock 0.1.0

data/ext/cluster.h

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+/******************************************************************************/
+/* The C Clustering Library.
+ * Copyright (C) 2002 Michiel Jan Laurens de Hoon.
+ *
+ * This library was written at the Laboratory of DNA Information Analysis,
+ * Human Genome Center, Institute of Medical Science, University of Tokyo,
+ * 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
+ * Contact: mdehoon 'AT' gsc.riken.jp
+ * 
+ * Permission to use, copy, modify, and distribute this software and its
+ * documentation with or without modifications and for any purpose and
+ * without fee is hereby granted, provided that any copyright notices
+ * appear in all copies and that both those copyright notices and this
+ * permission notice appear in supporting documentation, and that the
+ * names of the contributors or copyright holders not be used in
+ * advertising or publicity pertaining to distribution of the software
+ * without specific prior permission.
+ * 
+ * THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
+ * WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
+ * CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
+ * OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+ * OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
+ * OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
+ * OR PERFORMANCE OF THIS SOFTWARE.
+ * 
+ */
+
+#ifndef min
+#define min(x, y)	((x) < (y) ? (x) : (y))
+#endif
+#ifndef max
+#define	max(x, y)	((x) > (y) ? (x) : (y))
+#endif
+
+#ifdef WINDOWS
+#  include <windows.h>
+#endif
+
+#define CLUSTERVERSION "1.50"
+
+/* Chapter 2 */
+double clusterdistance (int nrows, int ncolumns, double** data, int** mask,
+  double weight[], int n1, int n2, int index1[], int index2[], char dist,
+  char method, int transpose);
+double** distancematrix (int ngenes, int ndata, double** data,
+  int** mask, double* weight, char dist, int transpose);
+
+/* Chapter 3 */
+int getclustercentroids(int nclusters, int nrows, int ncolumns,
+  double** data, int** mask, int clusterid[], double** cdata, int** cmask,
+  int transpose, char method);
+void getclustermedoids(int nclusters, int nelements, double** distance,
+  int clusterid[], int centroids[], double errors[]);
+void kcluster (int nclusters, int ngenes, int ndata, double** data,
+  int** mask, double weight[], int transpose, int npass, char method, char dist,
+  int clusterid[], double* error, int* ifound);
+void kmedoids (int nclusters, int nelements, double** distance,
+  int npass, int clusterid[], double* error, int* ifound);
+
+/* Chapter 4 */
+typedef struct {int left; int right; double distance;} Node;
+/*
+ * A Node struct describes a single node in a tree created by hierarchical
+ * clustering. The tree can be represented by an array of n Node structs,
+ * where n is the number of elements minus one. The integers left and right
+ * in each Node struct refer to the two elements or subnodes that are joined
+ * in this node. The original elements are numbered 0..nelements-1, and the
+ * nodes -1..-(nelements-1). For each node, distance contains the distance
+ * between the two subnodes that were joined.
+ */
+
+Node* treecluster (int nrows, int ncolumns, double** data, int** mask,
+  double weight[], int transpose, char dist, char method, double** distmatrix);
+void cuttree (int nelements, Node* tree, int nclusters, int clusterid[]);
+
+/* Chapter 5 */
+void somcluster (int nrows, int ncolumns, double** data, int** mask,
+  const double weight[], int transpose, int nxnodes, int nynodes,
+  double inittau, int niter, char dist, double*** celldata,
+  int clusterid[][2]);
+
+/* Chapter 6 */
+int pca(int m, int n, double** u, double** v, double* w);
+
+/* Utility routines, currently undocumented */
+void sort(int n, const double data[], int index[]);
+double mean(int n, double x[]);
+double median (int n, double x[]);
+
+double* calculate_weights(int nrows, int ncolumns, double** data, int** mask,
+  double weights[], int transpose, char dist, double cutoff, double exponent);

data/ext/extconf.rb

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+#!/usr/bin/ruby
+
+require 'mkmf'
+$CFLAGS  = '-fPIC -Os -Wall'
+create_makefile('flock')

data/ext/flock.c

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+#include <ruby/ruby.h>
+#include "cluster.h"
+
+#define ID_CONST_GET rb_intern("const_get")
+#define CONST_GET(scope, constant) (rb_funcall(scope, ID_CONST_GET, 1, rb_str_new2(constant)))
+
+static VALUE mFlock;
+
+int opt_int_value(VALUE option, char *key, int def) {
+  if (NIL_P(option)) return def;
+
+  VALUE value = rb_hash_aref(option, ID2SYM(rb_intern(key)));
+  return NIL_P(value) ? def : NUM2INT(value);
+}
+
+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);
+
+    int i,j;
+    int nrows = RARRAY_LEN(data);
+    int ncols = RARRAY_LEN(rb_ary_entry(data, 0));
+
+    double **cdata          = (double**)malloc(sizeof(double*)*nrows);
+    int    **cmask          = (int   **)malloc(sizeof(int   *)*nrows);
+    double **ccentroid      = (double**)malloc(sizeof(double*)*nrows);
+    int    **ccentroid_mask = (int   **)malloc(sizeof(int   *)*nrows);
+    double *cweights        = (double *)malloc(sizeof(double )*ncols);
+    int    *ccluster        = (int    *)malloc(sizeof(int    )*nrows);
+
+    for (i = 0; i < nrows; i++) {
+        cdata[i]          = (double*)malloc(sizeof(double)*ncols);
+        cmask[i]          = (int   *)malloc(sizeof(int   )*ncols);
+        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));
+        }
+    }
+
+    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));
+    }
+
+    int transpose = opt_int_value(options, "transpose", 0);
+    int npass     = opt_int_value(options, "iterations", 1000);
+    // a = average, m = means
+    int method    = opt_int_value(options, "method", 'a');
+    // e = euclidian,
+    // b = city-block distance
+    // c = correlation
+    // a = absolute value of the correlation
+    // u = uncentered correlation
+    // x = absolute uncentered correlation
+    // s = spearman's rank correlation
+    // k = kendall's tau
+    int dist      = opt_int_value(options, "metric", 'e');
+
+    int    ifound;
+    double error;
+    kcluster(NUM2INT(size),
+        nrows, ncols, cdata, cmask, cweights, transpose, npass, method, dist, ccluster, &error, &ifound);
+
+    getclustercentroids(NUM2INT(size),
+        nrows, ncols, cdata, cmask, ccluster, ccentroid, ccentroid_mask, transpose, method);
+
+    VALUE result   = rb_hash_new();
+    VALUE cluster  = rb_ary_new();
+    VALUE centroid = rb_ary_new();
+
+    for (i = 0; i < nrows; 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]));
+        rb_ary_push(centroid, point);
+    }
+
+    rb_hash_aset(result, ID2SYM(rb_intern("cluster")),   cluster);
+    rb_hash_aset(result, ID2SYM(rb_intern("centroid")),  centroid);
+    rb_hash_aset(result, ID2SYM(rb_intern("error")),     DBL2NUM(error));
+    rb_hash_aset(result, ID2SYM(rb_intern("repeated")),  INT2NUM(ifound));
+
+    for (i = 0; i < nrows; i++) {
+        free(cdata[i]);
+        free(cmask[i]);
+        free(ccentroid[i]);
+        free(ccentroid_mask[i]);
+    }
+
+    free(cdata);
+    free(cmask);
+    free(ccentroid);
+    free(ccentroid_mask);
+    free(cweights);
+    free(ccluster);
+
+    return result;
+}
+
+void Init_flock(void) {
+    mFlock = rb_define_module("Flock");
+    rb_define_module_function(mFlock, "kmeans", RUBY_METHOD_FUNC(rb_kmeans), -1);
+
+    rb_define_const(mFlock, "METHOD_AVERAGE", INT2NUM('a'));
+    rb_define_const(mFlock, "METHOD_MEDIAN",  INT2NUM('m'));
+
+    rb_define_const(mFlock, "METRIC_EUCLIDIAN",                       INT2NUM('e'));
+    rb_define_const(mFlock, "METRIC_CITY_BLOCK",                      INT2NUM('b'));
+    rb_define_const(mFlock, "METRIC_CORRELATION",                     INT2NUM('c'));
+    rb_define_const(mFlock, "METRIC_ABSOLUTE_CORRELATION",            INT2NUM('a'));
+    rb_define_const(mFlock, "METRIC_UNCENTERED_CORRELATION",          INT2NUM('u'));
+    rb_define_const(mFlock, "METRIC_ABSOLUTE_UNCENTERED_CORRELATION", INT2NUM('x'));
+    rb_define_const(mFlock, "METRIC_SPEARMAN",                        INT2NUM('s'));
+    rb_define_const(mFlock, "METRIC_KENDALL",                         INT2NUM('k'));
+}

metadata

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+--- !ruby/object:Gem::Specification 
+name: flock
+version: !ruby/object:Gem::Version 
+  prerelease: false
+  segments: 
+  - 0
+  - 1
+  - 0
+  version: 0.1.0
+platform: ruby
+authors: 
+- Bharanee Rathna
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2011-02-18 00:00:00 +11:00
+default_executable: 
+dependencies: []
+
+description: A thin ruby binding to Cluster 3.0
+email: 
+- deepfryed@gmail.com
+executables: []
+
+extensions: 
+- ext/extconf.rb
+extra_rdoc_files: 
+- README.rdoc
+files: 
+- README.rdoc
+- Rakefile
+- VERSION
+- ext/cluster.c
+- ext/cluster.h
+- ext/extconf.rb
+- ext/flock.c
+- examples/example.rb
+has_rdoc: true
+homepage: http://github.com/deepfryed/flock
+licenses: []
+
+post_install_message: 
+rdoc_options: 
+- --charset=UTF-8
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      segments: 
+      - 0
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.3.7
+signing_key: 
+specification_version: 3
+summary: Ruby bindings to Cluster 3.0.
+test_files: 
+- examples/example.rb