svm_toolkit 1.1.7-java → 1.1.8-java

data/lib/svm_toolkit/problem.rb

@@ -1,308 +1,294 @@
-module SvmToolkit
-
-  # Extends the Java Problem class with some additional features.
-  #
-  class Problem
-
-    # Support constructing a problem from arrays of double values.
-    # 
-    # instances:: an array of instances, each instance being an array of doubles.
-    # labels:: an array of doubles, forming the labels for each instance.
-    #
-    # An ArgumentError exception is raised if all the following conditions are not met:
-    # * the number of instances should equal the number of labels,
-    # * there must be at least one instance, and
-    # * every instance must have the same number of features.
-    #
-    def Problem.from_array(instances, labels)
-      unless instances.size == labels.size
-        raise ArgumentError.new "Number of instances must equal number of labels"
-      end
-      unless instances.size > 0
-        raise ArgumentError.new "There must be at least one instance."
-      end
-      unless instances.collect {|i| i.size}.min == instances.collect {|i| i.size}.max
-        raise ArgumentError.new "All instances must have the same size"
-      end
-
-      problem = Problem.new
-      problem.l = labels.size
-      # -- add in the training data
-      problem.x = Node[instances.size, instances[0].size].new
-      instances.each_with_index do |instance, i|
-        instance.each_with_index do |v, j|
-          problem.x[i][j] = Node.new(j, v)
-        end
-      end
-      # -- add in the labels
-      problem.y = Java::double[labels.size].new
-      labels.each_with_index do |v, i| 
-        problem.y[i] = v
-      end
-
-      return problem
-    end
-
-    # To select SvmLight input file format
-    SvmLight = 0
-
-    # To select Csv input file format
-    Csv = 1
-
-    # To select ARFF input file format
-    Arff = 2
-
-    #
-    # Read in a problem definition from a file. 
-    # 
-    # filename:: the name of the file
-    # format:: either Svm::SvmLight (default), Svm::Csv or Svm::Arff
-    #
-    # Raises ArgumentError if there is any error in format.
-    #
-    def Problem.from_file(filename, format = SvmLight)
-      case format 
-      when SvmLight
-        return Problem.from_file_svmlight filename
-      when Csv
-        return Problem.from_file_csv filename
-      when Arff
-        return Problem.from_file_arff filename
-      end
-    end
-
-    #
-    # Read in a problem definition in svmlight format. 
-    # 
-    # filename:: the name of the file
-    #
-    # Raises ArgumentError if there is any error in format.
-    #
-    def Problem.from_file_svmlight filename
-      instances = []
-      labels = []
-      max_index = 0
-      IO.foreach(filename) do |line|
-        tokens = line.split(" ")
-        labels << tokens[0].to_f
-        instance = []
-        tokens[1..-1].each do |feature|
-          index, value = feature.split(":")
-          instance << Node.new(index.to_i, value.to_f)
-          max_index = [index.to_i, max_index].max 
-        end
-        instances << instance
-      end
-      max_index += 1 # to allow for 0 position
-      unless instances.size == labels.size
-        raise ArgumentError.new "Number of labels read differs from number of instances"
-      end
-      # now create a Problem definition
-      problem = Problem.new
-      problem.l = instances.size
-      # -- add in the training data
-      problem.x = Node[instances.size, max_index].new
-      # -- fill with blank nodes
-      instances.size.times do |i|
-        max_index.times do |j|
-          problem.x[i][j] = Node.new(i, 0)
-        end
-      end
-      # -- add known values
-      instances.each_with_index do |instance, i|
-        instance.each do |node|
-          problem.x[i][node.index] = node
-        end
-      end
-      # -- add in the labels
-      problem.y = Java::double[labels.size].new
-      labels.each_with_index do |v, i| 
-        problem.y[i] = v
-      end
-
-      return problem
-    end
-
-    #
-    # Read in a problem definition in csv format. 
-    # 
-    # filename:: the name of the file
-    #
-    # Raises ArgumentError if there is any error in format.
-    #
-    def Problem.from_file_csv filename
-      instances = []
-      labels = []
-      max_index = 0
-      csv_data = CSV.parse(File.read(filename), headers: false)
-      csv_data.each do |tokens|
-        labels << tokens[0].to_f
-        instance = []
-        tokens[1..-1].each_with_index do |value, index|
-          instance << Node.new(index, value.to_f)
-        end
-        max_index = [tokens.size, max_index].max 
-        instances << instance
-      end
-      max_index += 1 # to allow for 0 position
-      unless instances.size == labels.size
-        raise ArgumentError.new "Number of labels read differs from number of instances"
-      end
-      # now create a Problem definition
-      problem = Problem.new
-      problem.l = instances.size
-      # -- add in the training data
-      problem.x = Node[instances.size, max_index].new
-      # -- fill with blank nodes
-      instances.size.times do |i|
-        max_index.times do |j|
-          problem.x[i][j] = Node.new(i, 0)
-        end
-      end
-      # -- add known values
-      instances.each_with_index do |instance, i|
-        instance.each do |node|
-          problem.x[i][node.index] = node
-        end
-      end
-      # -- add in the labels
-      problem.y = Java::double[labels.size].new
-      labels.each_with_index do |v, i| 
-        problem.y[i] = v
-      end
-
-      return problem
-    end
-
-    #
-    # Read in a problem definition in arff format.
-    # Assumes all values are numbers (non-numbers converted to 0.0), 
-    # and that the class is the last field. 
-    # 
-    # filename:: the name of the file
-    #
-    # Raises ArgumentError if there is any error in format.
-    #
-    def Problem.from_file_arff filename
-      instances = []
-      labels = []
-      max_index = 0
-      found_data = false
-      IO.foreach(filename) do |line|
-        unless found_data
-          puts "Ignoring", line
-          found_data = line.downcase.strip == "@data"
-          next # repeat the loop
-        end
-        tokens = line.split(",")
-        labels << tokens.last.to_f
-        instance = []
-        tokens[1...-1].each_with_index do |value, index|
-          instance << Node.new(index, value.to_f)
-        end
-        max_index = [tokens.size, max_index].max 
-        instances << instance
-      end
-      max_index += 1 # to allow for 0 position
-      unless instances.size == labels.size
-        raise ArgumentError.new "Number of labels read differs from number of instances"
-      end
-      # now create a Problem definition
-      problem = Problem.new
-      problem.l = instances.size
-      # -- add in the training data
-      problem.x = Node[instances.size, max_index].new
-      # -- fill with blank nodes
-      instances.size.times do |i|
-        max_index.times do |j|
-          problem.x[i][j] = Node.new(i, 0)
-        end
-      end
-      # -- add known values
-      instances.each_with_index do |instance, i|
-        instance.each do |node|
-          problem.x[i][node.index] = node
-        end
-      end
-      # -- add in the labels
-      problem.y = Java::double[labels.size].new
-      labels.each_with_index do |v, i| 
-        problem.y[i] = v
-      end
-
-      return problem
-    end
-
-    # Returns the number of instances
-    def size
-      self.l
-    end
-
-    # Rescale values within problem to be in range min_value to max_value
-    #
-    # For SVM models, it is recommended all features be in range [0,1] or [-1,1]
-    def rescale(min_value = 0.0, max_value = 1.0)
-      return if self.l.zero?
-      x[0].size.times do |i|
-        rescale_column(i, min_value, max_value)
-      end
-    end
-
-    # Create a new problem by combining the instances in this problem with 
-    # those in the given problem.
-    def merge problem
-      unless self.x[0].size == problem.x[0].size
-        raise ArgumentError.new "Cannot merge two problems with different numbers of features"
-      end
-      num_features = self.x[0].size
-      num_instances = size + problem.size
-
-      new_problem = Problem.new
-      new_problem.l = num_instances
-      new_problem.x = Node[num_instances, num_features].new
-      new_problem.y = Java::double[num_instances].new
-      # fill out the features
-      num_instances.times do |i|
-        num_features.times do |j|
-          if i < size
-            new_problem.x[i][j] = self.x[i][j]
-          else
-            new_problem.x[i][j] = problem.x[i-size][j]
-          end
-        end
-      end
-      # fill out the labels
-      num_instances.times do |i|
-        if i < size
-          new_problem.y[i] = self.y[i]
-        else
-          new_problem.y[i] = problem.y[i-size]
-        end
-      end
-
-      return new_problem
-    end
-
-    # Rescale values within problem for given column index, 
-    # to be in range min_value to max_value
-    private
-    def rescale_column(col, min_value, max_value)
-      # -- first locate the column's range
-      current_min = x[0][col].value
-      current_max = x[0][col].value
-      self.l.times do |index|
-        if x[index][col].value < current_min
-          current_min = x[index][col].value
-        end
-        if x[index][col].value > current_max
-          current_max = x[index][col].value
-        end
-      end
-      # -- then update each value
-      self.l.times do |index|
-        x[index][col].value = ((max_value - min_value) * (x[index][col].value - current_min) / (current_max - current_min)) + min_value
-      end
-    end
-  end
-end
-
+module SvmToolkit
+
+  # Holds a set of labelled data.
+  class Problem
+
+    # Support constructing a problem from arrays of numbers (floating-point values).
+    # 
+    # * instances - an array of instances, each instance being an array of numbers.
+    # * labels - an array of numbers, forming the labels for each instance.
+    #
+    # An ArgumentError exception is raised if all the following conditions are not met:
+    # * the number of instances should equal the number of labels,
+    # * there must be at least one instance, and
+    # * every instance must have the same number of features.
+    #
+    def self.from_array(instances, labels)
+      unless instances.size == labels.size
+        raise ArgumentError.new "Number of instances must equal number of labels"
+      end
+      unless instances.size > 0
+        raise ArgumentError.new "There must be at least one instance."
+      end
+      unless instances.collect {|i| i.size}.min == instances.collect {|i| i.size}.max
+        raise ArgumentError.new "All instances must have the same size"
+      end
+
+      problem = Problem.new
+      problem.l = labels.size
+      # -- add in the training data
+      problem.x = Node[instances.size, instances[0].size].new
+      instances.each_with_index do |instance, i|
+        instance.each_with_index do |v, j|
+          problem.x[i][j] = Node.new(j, v)
+        end
+      end
+      # -- add in the labels
+      problem.y = Java::double[labels.size].new
+      labels.each_with_index do |v, i| 
+        problem.y[i] = v
+      end
+
+      return problem
+    end
+
+    # To select SvmLight input file format
+    SvmLight = 0
+
+    # To select Csv input file format
+    Csv = 1
+
+    # To select ARFF input file format
+    Arff = 2
+
+    #
+    # Read in a problem definition from a given filename,
+    # using format SvmLight (default), Csv or Arff.
+    def self.from_file(filename, format = SvmLight)
+      case format 
+      when SvmLight
+        return Problem.from_file_svmlight filename
+      when Csv
+        return Problem.from_file_csv filename
+      when Arff
+        return Problem.from_file_arff filename
+      end
+    end
+
+    # Read in a problem definition in svmlight format. 
+    def self.from_file_svmlight filename
+      instances = []
+      labels = []
+      max_index = 0
+      IO.foreach(filename) do |line|
+        tokens = line.split(" ")
+        labels << tokens[0].to_f
+        instance = []
+        tokens[1..-1].each do |feature|
+          index, value = feature.split(":")
+          instance << Node.new(index.to_i, value.to_f)
+          max_index = [index.to_i, max_index].max 
+        end
+        instances << instance
+      end
+      max_index += 1 # to allow for 0 position
+      unless instances.size == labels.size
+        raise ArgumentError.new "Number of labels read differs from number of instances"
+      end
+      # now create a Problem definition
+      problem = Problem.new
+      problem.l = instances.size
+      # -- add in the training data
+      problem.x = Node[instances.size, max_index].new
+      # -- fill with blank nodes
+      instances.size.times do |i|
+        max_index.times do |j|
+          problem.x[i][j] = Node.new(i, 0)
+        end
+      end
+      # -- add known values
+      instances.each_with_index do |instance, i|
+        instance.each do |node|
+          problem.x[i][node.index] = node
+        end
+      end
+      # -- add in the labels
+      problem.y = Java::double[labels.size].new
+      labels.each_with_index do |v, i| 
+        problem.y[i] = v
+      end
+
+      return problem
+    end
+
+    # Read in a problem definition in csv format from given filename.
+    def self.from_file_csv filename
+      instances = []
+      labels = []
+      max_index = 0
+      csv_data = CSV.parse(File.read(filename), headers: false)
+      csv_data.each do |tokens|
+        labels << tokens[0].to_f
+        instance = []
+        tokens[1..-1].each_with_index do |value, index|
+          instance << Node.new(index, value.to_f)
+        end
+        max_index = [tokens.size, max_index].max 
+        instances << instance
+      end
+      max_index += 1 # to allow for 0 position
+      unless instances.size == labels.size
+        raise ArgumentError.new "Number of labels read differs from number of instances"
+      end
+      # now create a Problem definition
+      problem = Problem.new
+      problem.l = instances.size
+      # -- add in the training data
+      problem.x = Node[instances.size, max_index].new
+      # -- fill with blank nodes
+      instances.size.times do |i|
+        max_index.times do |j|
+          problem.x[i][j] = Node.new(i, 0)
+        end
+      end
+      # -- add known values
+      instances.each_with_index do |instance, i|
+        instance.each do |node|
+          problem.x[i][node.index] = node
+        end
+      end
+      # -- add in the labels
+      problem.y = Java::double[labels.size].new
+      labels.each_with_index do |v, i| 
+        problem.y[i] = v
+      end
+
+      return problem
+    end
+
+    # Read in a problem definition in arff format, from given filename.
+    # Assumes all values are numbers (non-numbers converted to 0.0), 
+    # and that the class is the last field. 
+    def self.from_file_arff filename
+      instances = []
+      labels = []
+      max_index = 0
+      found_data = false
+      IO.foreach(filename) do |line|
+        unless found_data
+          puts "Ignoring", line
+          found_data = line.downcase.strip == "@data"
+          next # repeat the loop
+        end
+        tokens = line.split(",")
+        labels << tokens.last.to_f
+        instance = []
+        tokens[1...-1].each_with_index do |value, index|
+          instance << Node.new(index, value.to_f)
+        end
+        max_index = [tokens.size, max_index].max 
+        instances << instance
+      end
+      max_index += 1 # to allow for 0 position
+      unless instances.size == labels.size
+        raise ArgumentError.new "Number of labels read differs from number of instances"
+      end
+      # now create a Problem definition
+      problem = Problem.new
+      problem.l = instances.size
+      # -- add in the training data
+      problem.x = Node[instances.size, max_index].new
+      # -- fill with blank nodes
+      instances.size.times do |i|
+        max_index.times do |j|
+          problem.x[i][j] = Node.new(i, 0)
+        end
+      end
+      # -- add known values
+      instances.each_with_index do |instance, i|
+        instance.each do |node|
+          problem.x[i][node.index] = node
+        end
+      end
+      # -- add in the labels
+      problem.y = Java::double[labels.size].new
+      labels.each_with_index do |v, i| 
+        problem.y[i] = v
+      end
+
+      return problem
+    end
+
+    # Returns the number of instances
+    def size
+      self.l
+    end
+
+    # Return label of nth instance
+    def label(n)
+      self.y[n]
+    end
+
+    # Return array of values for nth instance
+    def values(n)
+      self.x[n].collect { it.value }
+    end
+
+    # Rescale values within problem to be in range min_value to max_value
+    #
+    # For SVM models, it is recommended all features be in range [0,1] or [-1,1]
+    def rescale(min_value = 0.0, max_value = 1.0)
+      return if self.l.zero?
+      x[0].size.times do |i|
+        rescale_column(i, min_value, max_value)
+      end
+    end
+
+    # Create a new problem by combining the instances in this problem with 
+    # those in the given problem.
+    def merge problem
+      unless self.x[0].size == problem.x[0].size
+        raise ArgumentError.new "Cannot merge two problems with different numbers of features"
+      end
+      num_features = self.x[0].size
+      num_instances = size + problem.size
+
+      new_problem = Problem.new
+      new_problem.l = num_instances
+      new_problem.x = Node[num_instances, num_features].new
+      new_problem.y = Java::double[num_instances].new
+      # fill out the features
+      num_instances.times do |i|
+        num_features.times do |j|
+          if i < size
+            new_problem.x[i][j] = self.x[i][j]
+          else
+            new_problem.x[i][j] = problem.x[i-size][j]
+          end
+        end
+      end
+      # fill out the labels
+      num_instances.times do |i|
+        if i < size
+          new_problem.y[i] = self.y[i]
+        else
+          new_problem.y[i] = problem.y[i-size]
+        end
+      end
+
+      return new_problem
+    end
+
+    # Rescale values within problem for given column index, 
+    # to be in range min_value to max_value
+    private
+    def rescale_column(col, min_value, max_value)
+      # -- first locate the column's range
+      current_min = x[0][col].value
+      current_max = x[0][col].value
+      self.l.times do |index|
+        if x[index][col].value < current_min
+          current_min = x[index][col].value
+        end
+        if x[index][col].value > current_max
+          current_max = x[index][col].value
+        end
+      end
+      # -- then update each value
+      self.l.times do |index|
+        x[index][col].value = ((max_value - min_value) * (x[index][col].value - current_min) / (current_max - current_min)) + min_value
+      end
+    end
+  end
+end
+