malife-libsvm-ruby-swig 0.3.3

data/ext/svm.h

@@ -0,0 +1,76 @@
+#ifndef _LIBSVM_H
+#define _LIBSVM_H
+
+#define LIBSVM_VERSION 289
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+extern int libsvm_version;
+
+struct svm_node
+{
+	int index;
+	double value;
+};
+
+struct svm_problem
+{
+	int l;
+	double *y;
+	struct svm_node **x;
+};
+
+enum { C_SVC, NU_SVC, ONE_CLASS, EPSILON_SVR, NU_SVR };	/* svm_type */
+enum { LINEAR, POLY, RBF, SIGMOID, PRECOMPUTED }; /* kernel_type */
+
+struct svm_parameter
+{
+	int svm_type;
+	int kernel_type;
+	int degree;	/* for poly */
+	double gamma;	/* for poly/rbf/sigmoid */
+	double coef0;	/* for poly/sigmoid */
+
+	/* these are for training only */
+	double cache_size; /* in MB */
+	double eps;	/* stopping criteria */
+	double C;	/* for C_SVC, EPSILON_SVR and NU_SVR */
+	int nr_weight;		/* for C_SVC */
+	int *weight_label;	/* for C_SVC */
+	double* weight;		/* for C_SVC */
+	double nu;	/* for NU_SVC, ONE_CLASS, and NU_SVR */
+	double p;	/* for EPSILON_SVR */
+	int shrinking;	/* use the shrinking heuristics */
+	int probability; /* do probability estimates */
+};
+
+struct svm_model *svm_train(const struct svm_problem *prob, const struct svm_parameter *param);
+void svm_cross_validation(const struct svm_problem *prob, const struct svm_parameter *param, int nr_fold, double *target);
+
+int svm_save_model(const char *model_file_name, const struct svm_model *model);
+struct svm_model *svm_load_model(const char *model_file_name);
+
+int svm_get_svm_type(const struct svm_model *model);
+int svm_get_nr_class(const struct svm_model *model);
+void svm_get_labels(const struct svm_model *model, int *label);
+double svm_get_svr_probability(const struct svm_model *model);
+
+void svm_predict_values(const struct svm_model *model, const struct svm_node *x, double* dec_values);
+double svm_predict(const struct svm_model *model, const struct svm_node *x);
+double svm_predict_probability(const struct svm_model *model, const struct svm_node *x, double* prob_estimates);
+
+void svm_destroy_model(struct svm_model *model);
+void svm_destroy_param(struct svm_parameter *param);
+
+const char *svm_check_parameter(const struct svm_problem *prob, const struct svm_parameter *param);
+int svm_check_probability_model(const struct svm_model *model);
+
+extern void (*svm_print_string) (const char *);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _LIBSVM_H */

data/lib/svm.rb

@@ -0,0 +1,356 @@
+require 'libsvm'
+include Libsvm
+
+def _int_array(seq)
+  size = seq.size
+  array = new_int(size)
+  i = 0
+  for item in seq
+    int_setitem(array,i,item)
+    i = i + 1
+  end
+  return array
+end
+
+def _double_array(seq)
+  size = seq.size
+  array = new_double(size)
+  i = 0
+  for item in seq
+    double_setitem(array,i,item)
+    i = i + 1
+  end
+  return array
+end
+
+def _free_int_array(x)
+  if !x.nil? and !x.empty?
+    delete_int(x)
+  end
+end
+
+def _free_double_array(x)
+  if !x.nil? and !x.empty?
+    delete_double(x)
+  end
+end
+
+def _int_array_to_list(x,n)
+  list = []
+   (0..n-1).each {|i| list << int_getitem(x,i) }
+  return list
+end
+
+def _double_array_to_list(x,n)
+  list = []
+   (0..n-1).each {|i| list << double_getitem(x,i) }
+  return list
+end    
+
+class Parameter
+  attr_accessor :param
+  
+  def initialize(*args)
+    @param = Svm_parameter.new
+    @param.svm_type = C_SVC
+    @param.kernel_type = RBF
+    @param.degree = 3
+    @param.gamma = 0    # 1/k
+    @param.coef0 = 0
+    @param.nu = 0.5
+    @param.cache_size = 100
+    @param.C = 1
+    @param.eps = 1e-3
+    @param.p = 0.1
+    @param.shrinking = 1
+    @param.nr_weight = 0
+    #@param.weight_label = _int_array([])
+    #@param.weight = _double_array([])
+    @param.probability = 0
+    
+    args[0].each {|k,v| 
+      self.send("#{k}=",v)
+    } if !args[0].nil?
+  end
+  
+  def method_missing(m, *args)
+    if m.to_s == 'weight_label='
+      @weight_label_len = args[0].size
+      pargs = _int_array(args[0])
+      _free_int_array(@param.weight_label)
+    elsif m.to_s == 'weight='
+      @weight_len = args[0].size
+      pargs = _double_array(args[0])
+      _free_double_array(@param.weight)
+    else
+      pargs = args[0]
+    end
+    
+    if m.to_s.index('=')
+      @param.send("#{m}",pargs)
+    else
+      @param.send("#{m}")
+    end
+    
+  end
+  
+  def destroy
+    _free_int_array(@param.weight_label)
+    _free_double_array(@param.weight)
+    #delete_svm_parameter(@param)
+    @param = nil
+  end
+end
+
+def _convert_to_svm_node_array(x)
+  # convert a hash or array to an svm_node array
+  
+  # Find non zero elements
+  iter_range = []
+  if x.class == Hash
+    x.each {|k, v|
+      # all zeros kept due to the precomputed kernel; no good solution yet     
+      iter_range << k  # if v != 0
+    }
+  elsif x.class == Array
+    x.each_index {|j| 
+      iter_range << j #if x[j] != 0
+    }
+  else
+    raise TypeError,"data must be a hash or an array"
+  end
+  
+  iter_range.sort!
+  data = svm_node_array(iter_range.size+1)
+  svm_node_array_set(data,iter_range.size,-1,0)
+  
+  j = 0
+  for k in iter_range
+    svm_node_array_set(data,j,k,x[k])
+    j = j + 1
+  end
+  return data
+end
+
+class Problem
+  attr_accessor :prob, :maxlen, :size
+  
+  def initialize(y,x)
+    #assert y.size == x.size
+    @prob = prob = Svm_problem.new 
+    @size = size = y.size
+    
+    @y_array = y_array = new_double(size)
+    for i in (0..size-1)
+      double_setitem(@y_array,i,y[i])
+    end
+    
+    @x_matrix = x_matrix = svm_node_matrix(size)
+    @data = []
+    @maxlen = 0
+    for i in (0..size-1)
+      data = _convert_to_svm_node_array(x[i])
+      @data << data
+      svm_node_matrix_set(x_matrix,i,data)
+      if x[i].class == Hash
+        if x[i].size > 0
+          @maxlen = [@maxlen,x[i].keys.max].max
+        end
+      else
+        @maxlen = [@maxlen,x[i].size].max
+      end
+    end
+    
+    prob.l = size
+    prob.y = y_array
+    prob.x = x_matrix
+  end
+  
+  def inspect
+    return "Problem: size = #{size}"
+  end
+  
+  def destroy
+    delete_svm_problem(@prob)
+    delete_double(@y_array)
+    for i in (0..size-1)
+      svm_node_array_destroy(@data[i])
+    end
+    svm_node_matrix_destroy(@x_matrix)
+  end
+end
+
+class Model
+  attr_accessor :model
+  
+  def initialize(arg1,arg2=nil)
+    if arg2 == nil
+      # create model from file
+      filename = arg1
+      @model = svm_load_model(filename)
+    else
+      # create model from problem and parameter
+      prob,param = arg1,arg2
+      @prob = prob
+      if param.gamma == 0
+        param.gamma = 1.0/prob.maxlen
+      end
+      msg = svm_check_parameter(prob.prob,param.param)
+      raise ::ArgumentError, msg if msg
+      @model = svm_train(prob.prob,param.param)
+    end
+    
+    #setup some classwide variables
+    @nr_class = svm_get_nr_class(@model)
+    @svm_type = svm_get_svm_type(@model)
+    #create labels(classes)
+    intarr = new_int(@nr_class)
+    svm_get_labels(@model,intarr)
+    @labels = _int_array_to_list(intarr, @nr_class)
+    delete_int(intarr)
+    #check if valid probability model
+    @probability = svm_check_probability_model(@model)
+
+  end
+  
+  def predict(x)
+    data = _convert_to_svm_node_array(x)
+    ret = svm_predict(@model,data)
+    svm_node_array_destroy(data)
+    return ret
+  end
+  
+  
+  def get_nr_class
+    return @nr_class
+  end
+  
+  def get_labels
+    if @svm_type == NU_SVR or @svm_type == EPSILON_SVR or @svm_type == ONE_CLASS
+      raise TypeError, "Unable to get label from a SVR/ONE_CLASS model"
+    end
+    return @labels
+  end
+  
+  def predict_values_raw(x)
+    #convert x into svm_node, allocate a double array for return
+    n = (@nr_class*(@nr_class-1)/2).floor
+    data = _convert_to_svm_node_array(x)
+    dblarr = new_double(n)
+    svm_predict_values(@model, data, dblarr)
+    ret = _double_array_to_list(dblarr, n)
+    delete_double(dblarr)
+    svm_node_array_destroy(data)
+    return ret
+  end
+  
+  def predict_values(x)
+    v=predict_values_raw(x)
+    #puts v.inspect
+    if @svm_type == NU_SVR or @svm_type == EPSILON_SVR or @svm_type == ONE_CLASS
+      return v[0]
+    else #self.svm_type == C_SVC or self.svm_type == NU_SVC
+      count = 0
+      
+      # create a width x height array
+      width = @labels.size
+      height = @labels.size
+      d = Array.new(width)
+      d.map! { Array.new(height) }
+      
+      for i in (0..@labels.size-1)
+        for j in (i+1..@labels.size-1)
+          d[@labels[i]][@labels[j]] = v[count]
+          d[@labels[j]][@labels[i]] = -v[count]
+          count += 1
+        end
+      end
+      return d
+    end
+  end
+  
+  def predict_probability(x)
+    #c code will do nothing on wrong type, so we have to check ourself
+    if @svm_type == NU_SVR or @svm_type == EPSILON_SVR
+      raise TypeError, "call get_svr_probability or get_svr_pdf for probability output of regression"
+    elsif @svm_type == ONE_CLASS
+      raise TypeError, "probability not supported yet for one-class problem"
+    end
+    #only C_SVC,NU_SVC goes in
+    if not @probability
+      raise TypeError, "model does not support probabiliy estimates"
+    end
+    
+    #convert x into svm_node, alloc a double array to receive probabilities
+    data = _convert_to_svm_node_array(x)
+    dblarr = new_double(@nr_class)
+    pred = svm_predict_probability(@model, data, dblarr)
+    pv = _double_array_to_list(dblarr, @nr_class)
+    delete_double(dblarr)
+    svm_node_array_destroy(data)
+    p = {}
+    for i in (0..@labels.size-1)
+      p[@labels[i]] = pv[i]
+    end
+    return pred, p
+  end
+  
+  def get_svr_probability
+    #leave the Error checking to svm.cpp code
+    ret = svm_get_svr_probability(@model)
+    if ret == 0
+      raise TypeError, "not a regression model or probability information not available"
+    end
+    return ret
+  end
+  
+  def get_svr_pdf
+    #get_svr_probability will handle error checking
+    sigma = get_svr_probability()
+    return Proc.new{|z| exp(-z.abs/sigma)/(2*sigma)}  # TODO: verify this works
+  end
+  
+  def save(filename)
+    svm_save_model(filename,@model)
+  end
+  
+  def destroy
+    svm_destroy_model(@model)
+  end
+end
+
+
+def cross_validation(prob, param, fold)
+  if param.gamma == 0
+    param.gamma = 1.0/prob.maxlen
+  end
+  dblarr = new_double(prob.size)
+  svm_cross_validation(prob.prob, param.param, fold, dblarr)
+  ret = _double_array_to_list(dblarr, prob.size)
+  delete_double(dblarr)
+  return ret
+end
+
+def read_file filename
+  labels = []
+  samples = []
+  max_index = 0
+
+  f = File.open(filename)
+  f.each do |line|
+    elems = line.split
+    sample = {}
+    for e in elems[1..-1]
+       points = e.split(":")
+       sample[points[0].to_i] = points[1].to_f
+       if points[0].to_i < max_index
+          max_index = points[0].to_i
+       end
+    end
+    labels << elems[0].to_i
+    samples << sample
+  end
+  puts "#{filename}: #{samples.size} samples loaded."
+  return labels,samples
+end
+

metadata

@@ -0,0 +1,78 @@
+--- !ruby/object:Gem::Specification 
+name: malife-libsvm-ruby-swig
+version: !ruby/object:Gem::Version 
+  version: 0.3.3
+platform: ruby
+authors: 
+- Tom Zeng
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2009-09-08 00:00:00 -07:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: hoe
+  type: :development
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 2.3.3
+    version: 
+description: Ruby wrapper of LIBSVM using SWIG
+email: 
+- tom.z.zeng@gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- History.txt
+- Manifest.txt
+files: 
+- History.txt
+- COPYING
+- AUTHORS
+- Manifest.txt
+- README.rdoc
+- Rakefile
+- lib/svm.rb
+- ext/libsvm_wrap.cxx
+- ext/svm.cpp
+- ext/svm.h
+- ext/extconf.rb
+- ext/Makefile
+has_rdoc: false
+homepage: http://www.tomzconsulting.com
+licenses: 
+post_install_message: 
+rdoc_options: 
+- --main
+- README.rdoc
+require_paths: 
+- lib
+- ext
+required_ruby_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.3.5
+signing_key: 
+specification_version: 3
+summary: This is the Ruby port of the LIBSVM Python SWIG (Simplified Wrapper and  Interface Generator) interface
+test_files: []
+