feldtruby 0.4.11 → 0.4.12

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 80276e85ca35677642bd949c9c7c55d5647f040d
+  data.tar.gz: f15ba5e0a5b4d6ff60e2c974a5c6560723a318ab
+SHA512:
+  metadata.gz: 05e6499886ac5c29c2de3848ef24387c138ed14fb4f1a05af9a7a4dfd9e763203b9dc34d8e2705cab6e841bd5501bc2f7eadbc553de932dc8d38c2826938df61
+  data.tar.gz: fff4b90d0b79589ad20839b71692e0c265296989a642d089d4cfa156e4db5f167f4c5b7afb64a39b9da112c00da31fffa341d7e95145c7a0e05e904367e2115d

data/archive.json

@@ -0,0 +1,124 @@
+{
+  "json_class": "FeldtRuby::Optimize::Archive",
+  "data": {
+    "generalists": {
+      "json_class": "FeldtRuby::Optimize::Archive::GlobalTopList",
+      "data": {
+        "max_size": 20,
+        "top_list": [
+          "Vector[495.6220472008826, 426.35485642424766]",
+          "Vector[495.62205148094733, 426.354855256089]",
+          "Vector[495.62206987534034, 426.35501558097434]",
+          "Vector[495.62206987534034, 426.35501558097434]",
+          "Vector[495.6222720656514, 426.3550214881676]",
+          "Vector[495.62243252506755, 426.3551965381708]",
+          "Vector[495.6225366749033, 426.35541061734784]",
+          "Vector[495.62212266198037, 426.35508493132687]",
+          "Vector[495.6221285692303, 426.35482208453755]",
+          "Vector[495.62193937576654, 426.3546416267843]",
+          "Vector[495.6217543885617, 426.3547529062279]",
+          "Vector[495.6218500005808, 426.3545574537555]",
+          "Vector[495.62205148094733, 426.35473354022747]",
+          "Vector[495.6224622727039, 426.35513589259864]",
+          "Vector[495.6219540985794, 426.3549875733886]",
+          "Vector[495.6213699750297, 426.3542789980689]",
+          "Vector[495.6216018228837, 426.3546210939662]",
+          "Vector[495.6213463241329, 426.3542924512532]",
+          "Vector[495.6226218518193, 426.3556277556064]",
+          "Vector[495.6229365324784, 426.3556566577018]"
+        ],
+        "quality_values": [
+          "100.0% (SubQs = [6.14e-09], ver. 43)",
+          "100.0% (SubQs = [7.38e-09], ver. 43)",
+          "100.0% (SubQs = [2.65e-08], ver. 43)",
+          "100.0% (SubQs = [2.65e-08], ver. 43)",
+          "100.0% (SubQs = [2.84e-08], ver. 43)",
+          "100.0% (SubQs = [3.16e-08], ver. 43)",
+          "100.0% (SubQs = [3.63e-08], ver. 43)",
+          "100.0% (SubQs = [3.72e-08], ver. 43)",
+          "100.0% (SubQs = [6.82e-08], ver. 43)",
+          "100.0% (SubQs = [7.38e-08], ver. 43)",
+          "100.0% (SubQs = [7.61e-08], ver. 43)",
+          "100.0% (SubQs = [8.0e-08], ver. 43)",
+          "100.0% (SubQs = [8.29e-08], ver. 43)",
+          "100.0% (SubQs = [9.39e-08], ver. 43)",
+          "100.0% (SubQs = [9.58e-08], ver. 43)",
+          "100.0% (SubQs = [1.04e-07], ver. 43)",
+          "100.0% (SubQs = [1.12e-07], ver. 43)",
+          "100.0% (SubQs = [1.21e-07], ver. 43)",
+          "100.0% (SubQs = [1.37e-07], ver. 43)",
+          "100.0% (SubQs = [1.44e-07], ver. 43)"
+        ],
+        "objective": "#<MinEggHolder:0x007fe62a945878>"
+      }
+    },
+    "specialists": [
+      {
+        "json_class": "FeldtRuby::Optimize::Archive::GoalTopList",
+        "data": {
+          "max_size": 5,
+          "top_list": [
+            "Vector[495.6220472008826, 426.35485642424766]",
+            "Vector[495.62205148094733, 426.354855256089]",
+            "Vector[495.62206987534034, 426.35501558097434]",
+            "Vector[495.62206987534034, 426.35501558097434]",
+            "Vector[495.6222720656514, 426.3550214881676]"
+          ],
+          "quality_values": [
+            "100.0% (SubQs = [6.14e-09], ver. 43)",
+            "100.0% (SubQs = [7.38e-09], ver. 43)",
+            "100.0% (SubQs = [2.65e-08], ver. 43)",
+            "100.0% (SubQs = [2.65e-08], ver. 43)",
+            "100.0% (SubQs = [2.84e-08], ver. 43)"
+          ],
+          "objective": "#<MinEggHolder:0x007fe62a945878>",
+          "objective_index": 0,
+          "objective_name": "objective_min_func"
+        }
+      }
+    ],
+    "weirdos": {
+      "json_class": "FeldtRuby::Optimize::Archive::WeirdoTopList",
+      "data": {
+        "max_size": 10,
+        "top_list": [
+          "Vector[507.3847536905826, -428.24322756547286]",
+          "Vector[508.6757864296741, -425.8072060429839]",
+          "Vector[511.8607587787378, -424.7094976121834]",
+          "Vector[500.3795974754322, -424.47828024297644]",
+          "Vector[511.7927496243458, -423.6663163699823]",
+          "Vector[505.7249524392083, -421.85963040462264]",
+          "Vector[509.5386880993205, -421.0315337832495]",
+          "Vector[507.3309830642148, -418.7568618991539]",
+          "Vector[507.72601159816423, -417.65978621902434]",
+          "Vector[505.48809715871784, -417.65978621902434]"
+        ],
+        "quality_values": [
+          "95.1569% (SubQs = [92.1], ver. 43)",
+          "95.7011% (SubQs = [81.8], ver. 43)",
+          "96.0874% (SubQs = [74.4], ver. 43)",
+          "94.0684% (SubQs = [113.0], ver. 43)",
+          "96.0299% (SubQs = [75.5], ver. 43)",
+          "95.2259% (SubQs = [90.8], ver. 43)",
+          "95.5442% (SubQs = [84.7], ver. 43)",
+          "94.8863% (SubQs = [97.2], ver. 43)",
+          "94.6025% (SubQs = [103.0], ver. 43)",
+          "94.4247% (SubQs = [106.0], ver. 43)"
+        ],
+        "objective": "#<FeldtRuby::Optimize::EuclideanDistanceToBest:0x007fe62b86c900>",
+        "diversity_quality_values": [
+          "95.4506% (SubQs = [855.0], ver. 26)",
+          "95.1807% (SubQs = [852.0], ver. 26)",
+          "95.0642% (SubQs = [851.0], ver. 26)",
+          "95.0226% (SubQs = [851.0], ver. 26)",
+          "94.9476% (SubQs = [850.0], ver. 26)",
+          "94.7354% (SubQs = [848.0], ver. 26)",
+          "94.6489% (SubQs = [848.0], ver. 26)",
+          "94.3912% (SubQs = [845.0], ver. 26)",
+          "94.2693% (SubQs = [844.0], ver. 26)",
+          "94.2661% (SubQs = [844.0], ver. 26)"
+        ]
+      }
+    }
+  }
+}

data/lib/feldtruby/optimize/archive.rb

@@ -1,5 +1,6 @@
 require 'feldtruby/optimize'
 require 'feldtruby/logger'
+require 'json'
 
 module FeldtRuby::Optimize
 
@@ -90,7 +91,7 @@ class Archive
 
     @generalists = GlobalTopList.new(@params[:NumTopAggregate], @objective)
 
-    @weirdos = GlobalTopList.new(@params[:NumTopDiversityAggregate], @diversity_objective)
+    @weirdos = WeirdoTopList.new(@params[:NumTopDiversityAggregate], @diversity_objective, @objective)
   end
 
   # Add a candidate to the top lists if it is good enough to be there. Throws
@@ -113,7 +114,19 @@ class Archive
         "Old best" => prev_best,
         "Old quality" => prev_qv}, "Archive: New best solution found", true
 
-      @weirdos.each {|w| @diversity_objective.invalidate_quality_of(w)}
+      # We must delete weirdos that are no longer good enough to be on the 
+      # weirdos list.
+      to_delete = []
+      @weirdos.each {|w| 
+        # Invalidate quality since it must now be re-calculated (since it will
+        # typically depend on the best and we have a new best...)
+        @diversity_objective.invalidate_quality_of(w)
+
+        to_delete << w unless good_enough_quality_to_be_interesting?(w)
+      }
+      #puts "Deleting #{to_delete.length} out of #{@weirdos.length} weirdos"
+      #@weirdos.delete_candidates(to_delete)
+
     elsif good_enough_quality_to_be_interesting?(candidate)
       # When we add a new one this will lead to re-calc of the diversity quality
       # of the previous ones if there has been a new best since last time.
@@ -124,13 +137,16 @@ class Archive
   # Is quality of candidate good enough (within MaxPercentDistanceToBestForDiversity
   # from quality of best candidate)
   def good_enough_quality_to_be_interesting?(candidate)
-    qv_best = @objective.quality_of(best).value
-    ((qv_best - @objective.quality_of(candidate).value).abs / qv_best) <= @params[:MaxPercentDistanceToBestForDiversity]
+    qv_best = @objective.quality_of(best).display_value
+    qv = @objective.quality_of(candidate).display_value
+    res = ((qv_best - qv).abs / qv_best) <= @params[:MaxPercentDistanceToBestForDiversity]
+    #puts "qvbest = #{qv_best}, qv = #{qv}, res = #{res}"
+    res
   end
 
   # A top list is an array of a fixed size that saves the top candidates
   # based on their (aggregate) quality values.
-  class GlobalTopList
+  class GlobalTopList    
     def initialize(maxSize, objective)
       @max_size =maxSize
       @top_list = Array.new
@@ -159,6 +175,10 @@ class Archive
       @objective.is_better_than?(candidate1, candidate2)
     end
 
+    def delete_candidates(candidates)
+      @top_list = @top_list - candidates
+    end
+
     def sort_top_list
       @top_list.sort_by {|c| @objective.quality_of(c).value}
     end
@@ -166,6 +186,38 @@ class Archive
     def inspect
       self.class.inspect + @top_list.inspect
     end
+
+    def to_json(*a)
+      {
+        'json_class'   => self.class.name,
+        'data'         => data_to_json_hash,
+      }.to_json(*a)
+    end
+
+    def data_to_json_hash
+      {
+        'max_size' => @max_size,
+        'top_list' => @top_list,
+        'quality_values' => @top_list.map {|c| @objective.quality_of(c)},
+        'objective' => @objective
+      }
+    end
+  end
+
+  class WeirdoTopList < GlobalTopList
+    def initialize(maxSize, diversityObjective, qualityObjective)
+      super(maxSize, diversityObjective)
+      @quality_objective = qualityObjective
+    end
+
+    def data_to_json_hash
+      h = super()
+      # Since the diversity objective is used to sort the weirdos their
+      # 'quality_values' are actually the diversity quality values.
+      h['diversity_quality_values'] = h['quality_values']
+      h['quality_values'] = @top_list.map {|c| @quality_objective.quality_of(c)}
+      h
+    end
   end
 
   class GoalTopList < GlobalTopList
@@ -182,6 +234,24 @@ class Archive
         qv.sub_quality(@index, true) # We want the sub quality value posed as a minimization goal regardless of whether it is a min or max goal
       }
     end
+
+    # We add additional data about which goal/objective we are a top list for.
+    def data_to_json_hash
+      h = super()
+      h['objective_index'] = @index
+      h['objective_name'] = @objective.goal_methods[@index]
+      h
+    end
+  end
+
+  def to_json(*a)
+    {
+      'json_class'   => self.class.name,
+      'data'         => {
+        'generalists' => @generalists,
+        'specialists' => @specialists,
+        'weirdos' => @weirdos},
+    }.to_json(*a)
   end
 end
 

data/lib/feldtruby/optimize/objective.rb

@@ -473,8 +473,13 @@ class QualityValue
     -(@sub_qualities[index])
   end
 
+  # The value to display. For this default class we just use the quality value.
+  def display_value
+    value
+  end
+
   def value_to_s
-    "#{value.to_significant_digits(4)}"
+    "#{display_value.to_significant_digits(4)}"
   end
 
   def to_s
@@ -486,9 +491,12 @@ class QualityValue
 end
 
 class PercentageQualityValue < QualityValue
+  def display_value
+    (1.0 - value) * 100.0
+  end
   def value_to_s
     return "N/A" if @sub_qualities.any? {|sq| sq.nil?}
-    "%s%%" % ((1.0 - value) * 100.0).to_significant_digits(6).to_s
+    "%s%%" % display_value.to_significant_digits(6).to_s
   end
 end
 

data/lib/feldtruby/statistics.rb

@@ -110,6 +110,23 @@ class RCommunicator
     end
   end
 
+  # Pull a matrix variable into a hash and name the columns according to
+  # values in columnNames.
+  def pull_matrix_variable_to_hash_with_column_names(variableName, columnNames)
+    var = arg_name(rand(1e5), variableName)
+    RC.eval "#{var} <- toJSON(data.frame(#{variableName}));"
+    hash = pull_json_variable(var).to_h
+
+    # Now convert back to the proper parameter names and delete the ones generated by lhs.
+    index = 0
+    columnNames.each do |p|
+      name_of_column = "X#{index += 1}"
+      hash[p] = hash[name_of_column]
+      hash.delete(name_of_column)
+    end
+    hash
+  end
+
   # Convert a Ruby object of one of the types String, Symbol, Array, Integer 
   # or Float to a String that can be used in R code/scripts to 
   # represent the object.

data/lib/feldtruby/statistics/design_of_experiments.rb

@@ -0,0 +1,48 @@
+module FeldtRuby::Statistics
+
+# Functions for designing parameter exploration experiments using Bayesian
+# Treed Gaussian Process models.
+#
+# Parameters are assumed to be given in a hash, mapping a parameter name to its
+# range of allowed values, like:
+#
+#   IndependenVars = {
+#     :PopulationSize => [5, 500],
+#     :PopulationSamplerRadius => [4, 500], # must actually be smaller than the population size or it makes no difference, how to spec such constraints?
+#     :F => [0.0, 1.0],
+#     :CR => [0.0, 1.0],
+#     :numEvals => [1e3, 1e5] # Or should we vary this for each setting of the others and just measure the outputs at several points of numEvals?
+#   }
+#
+#   DependentVars = {
+#     Y1 = # execution_time for running the algorithm
+#     Y2 = # best model RMS error
+#   }
+module DesignOfExperiments
+  # Do a latin hypercube sampling of the parameter space with bouding box per 
+  # parameter specified in _parameters_.
+  def latin_hypercube_sample_of_parameters(parameters, numSamples)
+    include_library("tgp")
+    param_order = parameters.keys.sort
+    script = <<-EOS
+      params <- #{parameters_to_R_data_frame(parameters, param_order)};
+      x_candidates <- lhs(#{numSamples}, params);
+    EOS
+    subst_eval script, {}
+    pull_matrix_variable_to_hash_with_column_names "x_candidates", param_order
+  end
+
+  def parameters_to_R_data_frame(parameters, param_order = parameter.keys)
+    s = param_order.map do |p|
+      lim = parameters[p]
+      "c(#{lim[0]}, #{lim[1]})"
+    end.join(", ")
+    "rbind(#{s})"
+  end
+end
+
+end
+
+class FeldtRuby::RCommunicator
+  include FeldtRuby::Statistics::DesignOfExperiments
+end

data/lib/feldtruby/version.rb

@@ -1,3 +1,3 @@
 module FeldtRuby
-  VERSION = "0.4.11"
+  VERSION = "0.4.12"
 end

data/spikes/archive.json

@@ -0,0 +1,147 @@
+{
+  "json_class": "FeldtRuby::Optimize::Archive",
+  "data": {
+    "generalists": {
+      "json_class": "FeldtRuby::Optimize::Archive::GlobalTopList",
+      "data": {
+        "max_size": 20,
+        "top_list": [
+          "Vector[3.92978592984352e-34, 3.177186083763661e-35, -6.705768207338718e-34, -1.6854383035496224e-34]",
+          "Vector[1.5144596966432141e-34, 3.2854085523776127e-34, -4.919007599874781e-34, -5.254279363766363e-34]",
+          "Vector[5.690616393750528e-34, -2.3355528642494594e-34, 4.643573191513474e-34, -1.917310422255142e-34]",
+          "Vector[5.841696796512456e-34, 5.961044199327782e-34, 1.493847002166183e-35, -1.0898686439738699e-33]",
+          "Vector[-1.430133126940755e-34, -9.3610480250286e-34, 2.1346746119941773e-34, -1.5536563098293578e-34]",
+          "Vector[-7.985448841993761e-34, -4.650702542519649e-34, 1.0333041708593775e-34, -1.715732599374026e-34]",
+          "Vector[-3.2974922751978836e-34, -1.1378942343472195e-33, 1.2433783562274253e-34, 1.2911154676479549e-33]",
+          "Vector[-4.316734242818529e-34, -1.1378942343472195e-33, 1.2433783562274253e-34, 1.2911154676479549e-33]",
+          "Vector[7.714498498702072e-34, 1.4732439530231907e-34, 4.776830230246573e-34, 1.319508569506661e-34]",
+          "Vector[6.123633511609725e-34, -2.62755936793382e-34, -1.3377160149401275e-33, 3.895644744559003e-34]",
+          "Vector[-4.176201753482501e-34, 7.954221933754592e-34, -1.5160566450653443e-33, 3.7883757691656654e-34]",
+          "Vector[-7.723590455216934e-34, -2.3355528642494594e-34, 4.643573191513474e-34, 1.4410131568651712e-33]",
+          "Vector[1.436165919956631e-33, 2.9867170288833136e-34, -1.5906202273547187e-33, -3.6632624990326594e-34]",
+          "Vector[1.5144596966432141e-34, 1.626004974771429e-33, -4.919007599874781e-34, -3.23180762074661e-34]",
+          "Vector[-1.430133126940755e-34, -9.3610480250286e-34, 2.1346746119941773e-34, -9.510504303572618e-34]",
+          "Vector[-1.5350491811590863e-33, -5.341963141796802e-34, 1.5575490243063648e-33, -1.1393839558555175e-35]",
+          "Vector[-1.5350491811590863e-33, -5.341963141796802e-34, 8.732015868384436e-34, -1.1393839558555175e-35]",
+          "Vector[2.1481152051158145e-34, -1.1561136621745396e-33, 1.1802401093042232e-33, -1.1926088222499382e-33]",
+          "Vector[5.4468703973847035e-34, 1.3947548738235502e-33, 4.244444951915549e-34, -1.5154918934744699e-33]",
+          "Vector[4.407040152206215e-34, -2.6755349121192108e-34, -7.009651291770463e-34, -1.374288578447605e-33]"
+        ],
+        "quality_values": [
+          "100.0% (SubQs = [4.14e-34, 3.98e-34], ver. 420)",
+          "100.0% (SubQs = [5.37e-34, 4.03e-34], ver. 420)",
+          "100.0% (SubQs = [6.08e-34, 3.97e-34], ver. 420)",
+          "100.0% (SubQs = [1.05e-34, 6.86e-34], ver. 420)",
+          "100.0% (SubQs = [1.02e-33, 4.92e-34], ver. 420)",
+          "100.0% (SubQs = [1.33e-33, 4.73e-34], ver. 420)",
+          "100.0% (SubQs = [5.22e-35, 8.78e-34], ver. 420)",
+          "100.0% (SubQs = [1.54e-34, 8.89e-34], ver. 420)",
+          "100.0% (SubQs = [1.53e-33, 4.64e-34], ver. 420)",
+          "100.0% (SubQs = [5.99e-34, 7.72e-34], ver. 420)",
+          "100.0% (SubQs = [7.59e-34, 9.01e-34], ver. 420)",
+          "100.0% (SubQs = [8.99e-34, 8.58e-34], ver. 420)",
+          "100.0% (SubQs = [2.22e-34, 1.1e-33], ver. 420)",
+          "100.0% (SubQs = [9.62e-34, 8.68e-34], ver. 420)",
+          "100.0% (SubQs = [1.82e-33, 6.79e-34], ver. 420)",
+          "100.0% (SubQs = [5.23e-34, 1.13e-33], ver. 420)",
+          "100.0% (SubQs = [1.21e-33, 9.23e-34], ver. 420)",
+          "100.0% (SubQs = [9.54e-34, 1.02e-33], ver. 420)",
+          "100.0% (SubQs = [8.48e-34, 1.09e-33], ver. 420)",
+          "100.0% (SubQs = [1.9e-33, 8.13e-34], ver. 420)"
+        ],
+        "objective": "#<MinimizeRMSAndSum:0x007fe9a184be70>"
+      }
+    },
+    "specialists": [
+      {
+        "json_class": "FeldtRuby::Optimize::Archive::GoalTopList",
+        "data": {
+          "max_size": 5,
+          "top_list": [
+            "Vector[-9.615930905072786e-33, 4.59127418428953e-33, 1.5234591770668713e-32, -1.0213910705788213e-32]",
+            "Vector[2.9703517549037285e-33, -1.248167005887202e-32, 1.1288694472406572e-32, -1.7718788688711247e-33]",
+            "Vector[1.1474528493196208e-32, -2.7528425396866883e-33, 2.6715836582877643e-33, -1.1400340625482263e-32]",
+            "Vector[4.449719771038471e-33, 1.850578404606684e-32, -1.372599097841034e-32, -9.215288004790806e-33]",
+            "Vector[-3.571926477368521e-32, 3.244495926808932e-32, -5.418334544872519e-33, 8.713179387296223e-33]"
+          ],
+          "quality_values": [
+            "100.0% (SubQs = [3.98e-36, 1.06e-32], ver. 420)",
+            "100.0% (SubQs = [5.5e-36, 8.59e-33], ver. 420)",
+            "100.0% (SubQs = [7.07e-36, 8.31e-33], ver. 420)",
+            "100.0% (SubQs = [1.42e-35, 1.26e-32], ver. 420)",
+            "100.0% (SubQs = [2.05e-35, 2.47e-32], ver. 420)"
+          ],
+          "objective": "#<MinimizeRMSAndSum:0x007fe9a184be70>",
+          "objective_index": 0,
+          "objective_name": "objective_min_sum"
+        }
+      },
+      {
+        "json_class": "FeldtRuby::Optimize::Archive::GoalTopList",
+        "data": {
+          "max_size": 5,
+          "top_list": [
+            "Vector[5.690616393750528e-34, -2.3355528642494594e-34, 4.643573191513474e-34, -1.917310422255142e-34]",
+            "Vector[3.92978592984352e-34, 3.177186083763661e-35, -6.705768207338718e-34, -1.6854383035496224e-34]",
+            "Vector[1.5144596966432141e-34, 3.2854085523776127e-34, -4.919007599874781e-34, -5.254279363766363e-34]",
+            "Vector[7.714498498702072e-34, 1.4732439530231907e-34, 4.776830230246573e-34, 1.319508569506661e-34]",
+            "Vector[-7.985448841993761e-34, -4.650702542519649e-34, 1.0333041708593775e-34, -1.715732599374026e-34]"
+          ],
+          "quality_values": [
+            "100.0% (SubQs = [6.08e-34, 3.97e-34], ver. 420)",
+            "100.0% (SubQs = [4.14e-34, 3.98e-34], ver. 420)",
+            "100.0% (SubQs = [5.37e-34, 4.03e-34], ver. 420)",
+            "100.0% (SubQs = [1.53e-33, 4.64e-34], ver. 420)",
+            "100.0% (SubQs = [1.33e-33, 4.73e-34], ver. 420)"
+          ],
+          "objective": "#<MinimizeRMSAndSum:0x007fe9a184be70>",
+          "objective_index": 1,
+          "objective_name": "objective_min_rms"
+        }
+      }
+    ],
+    "weirdos": {
+      "json_class": "FeldtRuby::Optimize::Archive::WeirdoTopList",
+      "data": {
+        "max_size": 10,
+        "top_list": [
+          "Vector[-0.0019044882512560613, 0.009481335601935582, -0.024299149058169944, 0.01644621882943969]",
+          "Vector[-0.002336002098539184, -0.0011328152153534908, -0.002919457015502706, 0.005384406255801217]",
+          "Vector[-0.000212713252898527, -0.00026116276684590893, -0.00015700863312597923, 0.0006925169327167096]",
+          "Vector[-0.0006292872425139322, 0.00028433348523478833, -3.296307630564648e-05, 0.00025614364670802737]",
+          "Vector[-0.00044589271102821995, 0.0001507180794986237, 0.0005375696283590799, -0.00012391959968973396]",
+          "Vector[0.0002685510741798464, -0.00018255262169129994, 0.00011099055409430846, 0.00033646021393768475]",
+          "Vector[-2.9171529527878796e-05, -6.5003814421593835e-06, -8.256851193381469e-06, 5.0270287068797815e-05]",
+          "Vector[1.1999984048880376e-05, -3.223391818033675e-05, 1.1715098248587656e-05, -1.80284782645308e-06]",
+          "Vector[1.285250921671595e-07, -7.961342736434783e-08, -5.3641724601111016e-08, -1.4897905737316017e-07]",
+          "Vector[3.857240621811628e-08, 9.77694067874942e-08, -1.2780417924260806e-07, 3.661084070782956e-07]"
+        ],
+        "quality_values": [
+          "99.1567% (SubQs = [0.000276, 0.0154], ver. 420)",
+          "99.8024% (SubQs = [0.001, 0.00333], ver. 420)",
+          "99.9776% (SubQs = [6.16e-05, 0.000393], ver. 420)",
+          "99.9779% (SubQs = [0.000122, 0.000369], ver. 420)",
+          "99.9783% (SubQs = [0.000118, 0.000363], ver. 420)",
+          "99.9779% (SubQs = [0.000533, 0.00024], ver. 420)",
+          "99.9983% (SubQs = [6.34e-06, 2.95e-05], ver. 420)",
+          "99.9988% (SubQs = [1.03e-05, 1.82e-05], ver. 420)",
+          "100.0% (SubQs = [1.54e-07, 1.09e-07], ver. 420)",
+          "100.0% (SubQs = [3.75e-07, 2.01e-07], ver. 420)"
+        ],
+        "objective": "#<FeldtRuby::Optimize::EuclideanDistanceToBest:0x007fe9a1853ff8>",
+        "diversity_quality_values": [
+          "90.3578% (SubQs = [0.0309], ver. 39)",
+          "19.4568% (SubQs = [0.00665], ver. 39)",
+          "2.29865% (SubQs = [0.000786], ver. 39)",
+          "2.15629% (SubQs = [0.000737], ver. 39)",
+          "2.12095% (SubQs = [0.000725], ver. 39)",
+          "1.40562% (SubQs = [0.000481], ver. 39)",
+          "0.172746% (SubQs = [5.91e-05], ver. 39)",
+          "0.106403% (SubQs = [3.64e-05], ver. 39)",
+          "0.000640308% (SubQs = [2.19e-07], ver. 39)",
+          "0.00117507% (SubQs = [4.02e-07], ver. 39)"
+        ]
+      }
+    }
+  }
+}

data/spikes/long_running_search.rb

@@ -15,7 +15,9 @@ def best_from_de_on_objective(objective, dimensions, numSteps = 25_000,
   best = de.optimize().to_a
   elapsed = Time.now - start_time
 
-  return best, objective, elapsed
+  return best, objective, elapsed, de
 end
 
-best, obj, time = best_from_de_on_objective MinSphere.new, 30, 220_000
+#best, obj, time, de = best_from_de_on_objective MinSphere.new, 30, 220_000
+best, obj, time, de = best_from_de_on_objective MinEggHolder.new, nil, 15_000
+File.open("archive.json", "w") {|fh| fh.puts(JSON.pretty_generate(de.archive))}

data/spikes/simple_de_run.rb

@@ -24,4 +24,6 @@ o2 = MinimizeRMSAndSum.new
 
 de = DEOptimizer.new(o2, s4, {:verbose => true, :maxNumSteps => $NumSteps})
 
-de.optimize()
+best = de.optimize()
+
+File.open("archive.json", "w") {|fh| fh.puts(JSON.pretty_generate(de.archive))}

data/test/long_running/test_single_objective_optimization.rb

@@ -1,5 +1,5 @@
-require File.join(FeldtRubyLongTestDir, "single_objective_problems")
 require 'feldtruby/optimize/differential_evolution'
+require 'feldtruby/optimize/problems/single_objective_problems'
 include FeldtRuby::Optimize
 
 module MiniTest::Assertions
@@ -79,7 +79,7 @@ end
 
 describe "Easom function" do
   it 'can optimize the Easom function' do
-    best, obj, time = best_from_de_on_objective MinEasom.new, nil, 10_000, false, FeldtRuby::Optimize::DEOptimizer_Best_1_Bin
+    best, obj, time = best_from_de_on_objective MinEasom.new, nil, 15_000, false, FeldtRuby::Optimize::DEOptimizer_Best_1_Bin
     best.must_be_close_to_one_solution_of obj
     time.must_be :<, 1.5
   end

data/test/test_statistics_design_of_experiments.rb

@@ -0,0 +1,35 @@
+require 'feldtruby/statistics/design_of_experiments'
+
+describe 'Latin Hypercube Sampling' do
+  it "can sample in a rectangular multi-dim bounding box" do
+    params = {
+      :a => [0,100],
+      :b => [0,50],
+      :c => [0.0, 1.0]
+    }
+    candidates = RC.latin_hypercube_sample_of_parameters(params, 100)
+    candidates.must_be_instance_of Hash
+    candidates.keys.sort.must_equal params.keys.sort
+
+    candidates[:a].must_be_instance_of Array
+    candidates[:a].length.must_equal 100
+    candidates[:a].each do |a|
+      a.must_be :>=, 0
+      a.must_be :<=, 100
+    end
+
+    candidates[:b].must_be_instance_of Array
+    candidates[:b].length.must_equal 100
+    candidates[:b].each do |b|
+      b.must_be :>=, 0
+      b.must_be :<=, 50
+    end
+
+    candidates[:c].must_be_instance_of Array
+    candidates[:c].length.must_equal 100
+    candidates[:c].each do |b|
+      b.must_be :>=, 0.0
+      b.must_be :<=, 1.0
+    end
+  end
+end

metadata

@@ -1,94 +1,83 @@
 --- !ruby/object:Gem::Specification
 name: feldtruby
 version: !ruby/object:Gem::Version
-  version: 0.4.11
-  prerelease: 
+  version: 0.4.12
 platform: ruby
 authors:
 - Robert Feldt
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-04-18 00:00:00.000000000 Z
+date: 2013-04-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rinruby
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: json
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: nokogiri
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: mongo
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: bson_ext
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 description: Robert Feldt's Common Ruby Code lib
@@ -106,6 +95,7 @@ files:
 - README.md
 - Rakefile
 - TODO
+- archive.json
 - feldtruby.gemspec
 - lib/feldtruby.rb
 - lib/feldtruby/annotations.rb
@@ -128,6 +118,8 @@ files:
 - lib/feldtruby/optimize/max_steps_termination_criterion.rb
 - lib/feldtruby/optimize/objective.rb
 - lib/feldtruby/optimize/optimizer.rb
+- lib/feldtruby/optimize/problems/multi_objective_problems.rb
+- lib/feldtruby/optimize/problems/single_objective_problems.rb
 - lib/feldtruby/optimize/random_search.rb
 - lib/feldtruby/optimize/search_space.rb
 - lib/feldtruby/optimize/stdout_logger.rb
@@ -136,6 +128,7 @@ files:
 - lib/feldtruby/statistics.rb
 - lib/feldtruby/statistics/array_archive.rb
 - lib/feldtruby/statistics/clustering.rb
+- lib/feldtruby/statistics/design_of_experiments.rb
 - lib/feldtruby/statistics/distance.rb
 - lib/feldtruby/statistics/distance/string_distance.rb
 - lib/feldtruby/statistics/euclidean_distance.rb
@@ -149,6 +142,7 @@ files:
 - lib/feldtruby/visualization/circos.rb
 - lib/feldtruby/word_counter.rb
 - old/event_logger.rb
+- spikes/archive.json
 - spikes/comparing_samplers_on_classic_optimization_functions/analyze_sampler_comparison_results.R
 - spikes/comparing_samplers_on_classic_optimization_functions/compare_samplers.rb
 - spikes/comparing_samplers_on_classic_optimization_functions/results_comparing_samplers_130405_175934.csv
@@ -160,8 +154,6 @@ files:
 - spikes/simple_de_run.rb
 - spikes/zlib_for_short_strings.rb
 - test/helper.rb
-- test/long_running/multi_objective_problems.rb
-- test/long_running/single_objective_problems.rb
 - test/long_running/test_single_objective_optimization.rb
 - test/skip_test_array_archive.rb
 - test/test_array.rb
@@ -187,6 +179,7 @@ files:
 - test/test_optimize_stochastic_hill_climber.rb
 - test/test_sax.rb
 - test/test_statistics.rb
+- test/test_statistics_design_of_experiments.rb
 - test/test_string_distance.rb
 - test/test_sub_qualitites_comparator.rb
 - test/test_time.rb
@@ -196,32 +189,29 @@ files:
 - test/tmp_shorter.csv
 homepage: https://github.com/robertfeldt/feldtruby
 licenses: []
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.25
+rubygems_version: 2.0.0
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Robert Feldt's Common Ruby Code lib
 test_files:
 - test/helper.rb
-- test/long_running/multi_objective_problems.rb
-- test/long_running/single_objective_problems.rb
 - test/long_running/test_single_objective_optimization.rb
 - test/skip_test_array_archive.rb
 - test/test_array.rb
@@ -247,6 +237,7 @@ test_files:
 - test/test_optimize_stochastic_hill_climber.rb
 - test/test_sax.rb
 - test/test_statistics.rb
+- test/test_statistics_design_of_experiments.rb
 - test/test_string_distance.rb
 - test/test_sub_qualitites_comparator.rb
 - test/test_time.rb