replacing r bar plot with ruby-plot gem

7 files changed, 48 insertions, 145 deletions

diff --git a/example.rb b/example.rb
index 985233c..d9a1657 100644
--- a/example.rb
+++ b/example.rb
@@ -156,7 +156,7 @@ class Example
   
   # logs string and and adds to summary
   def self.log(log_string)
-    LOGGER.info log_string
+    LOGGER.info "EXAMPLE: "+log_string
     @@summary += log_string+"\n"
   end
   
diff --git a/lib/predictions.rb b/lib/predictions.rb
index 5a43d24..f673f8c 100644
--- a/lib/predictions.rb
+++ b/lib/predictions.rb
@@ -1,11 +1,4 @@
 
-if ENV['R_HOME']
-  ENV['PATH'] = ENV['R_HOME']+":"+ENV['PATH'] unless ENV['PATH'].split(":").index(ENV['R_HOME'])
-else
-  LOGGER.warn "Environment variable R_HOME not set"
-end
-require 'rinruby'
-
 module Lib
 
   module Util
diff --git a/report/environment.rb b/report/environment.rb
index a91c226..6d31615 100644
--- a/report/environment.rb
+++ b/report/environment.rb
@@ -9,7 +9,7 @@ require 'yaml'
 require 'opentox-ruby-api-wrapper'
 require 'fileutils'
 require 'mime/types'
-require 'svg_roc_plot'
+require 'ruby-plot'
 
 module Reports
 end
@@ -19,7 +19,6 @@ end
   #LOGGER.datetime_format = "%Y-%m-%d %H:%M:%S "
 #end
 
-require "report/r_plot_factory.rb"
 require "report/plot_factory.rb"
 require "report/xml_report.rb"
 require "report/xml_report_util.rb"
diff --git a/report/plot_factory.rb b/report/plot_factory.rb
index 3973989..d2884e3 100644
--- a/report/plot_factory.rb
+++ b/report/plot_factory.rb
@@ -39,13 +39,40 @@ module Reports
           fp_rates << data[:fp_rate][0]
           tp_rates << data[:tp_rate][0]
         end
-        Svg_Roc_Plot::plot(out_file, "ROC-Plot", "False positive rate", "True Positive Rate", names, fp_rates, tp_rates )
+        RubyPlot::plot_lines(out_file, "ROC-Plot", "False positive rate", "True Positive Rate", names, fp_rates, tp_rates )
       else
         data = transform_predictions(validation_set, class_value, show_single_curves)
-        Svg_Roc_Plot::plot(out_file, "ROC-Plot", "False positive rate", "True Positive Rate", data[:names], data[:fp_rate], data[:tp_rate], data[:faint] )
+        RubyPlot::plot_lines(out_file, "ROC-Plot", "False positive rate", "True Positive Rate", data[:names], data[:fp_rate], data[:tp_rate], data[:faint] )
       end  
     end
     
+    def self.create_bar_plot( out_file, validation_set, class_value, title_attribute, value_attributes )
+  
+      LOGGER.debug "creating bar plot, out-file:"+out_file.to_s
+      
+      data = []
+      validation_set.validations.each do |v|
+        values = []
+        value_attributes.collect do |a|
+          value = v.send(a)
+          if value.is_a?(Hash)
+            raise "bar plot value is hash, but no entry for class-value ("+class_value.to_s+")" unless value.key?(class_value)
+            value = value[class_value]
+          end
+          values.push(value)
+        end
+        data << [v.send(title_attribute).to_s] + values
+      end
+      
+      labels = value_attributes.collect{|a| a.to_s.gsub("_","-")}
+      
+      LOGGER.debug "bar plot labels: "+labels.inspect 
+      LOGGER.debug "bar plot data: "+data.inspect
+      
+      RubyPlot::plot_bars('Bar plot', labels, data, out_file)
+      
+    end
+    
     
     def self.create_ranking_plot( svg_out_file, validation_set, compare_attribute, equal_attribute, rank_attribute )
 
diff --git a/report/r_plot_factory.rb b/report/r_plot_factory.rb
deleted file mode 100644
index 0c3a492..0000000
--- a/report/r_plot_factory.rb
+++ /dev/null
@@ -1,115 +0,0 @@
-
-# the r-path has to be added for the rinruby plugin
-if ENV['R_HOME']
-  ENV['PATH'] = ENV['R_HOME']+":"+ENV['PATH'] unless ENV['PATH'].split(":").index(ENV['R_HOME'])
-else
-  LOGGER.warn "Environment variable R_HOME not set"
-end
-require "rinruby"
-
-# colors for r-plots
-R_PLOT_COLORS = ["red", "blue", "green", "yellow"]
-
-# = Reports::RPlotFactory 
-#
-# creates plots from validation-sets using rinruby
-#
-module Reports::RPlotFactory 
-
-  # creates a bar plot (result is plotted into out_file), 
-  # one category for each attribute in value_attributes, title_attribute is used for the legend
-  #
-  def self.create_bar_plot( out_file, validation_set, class_value, title_attribute, value_attributes )
-  
-    LOGGER.debug "creating bar plot, out-file:"+out_file.to_s
-    b = Reports::BarPlot.new( out_file )
-    validation_set.validations.each do |v|
-      values = []
-      value_attributes.collect do |a|
-        value = v.send(a)
-        if value.is_a?(Hash)
-          raise "bar plat value is hash, but no entry for class-value ("+class_value.to_s+")" unless value.key?(class_value)
-          value = value[class_value]
-        end
-        values.push(value)
-      end
-      b.add_data(v.send(title_attribute), values)
-    end
-    b.build_plot(value_attributes.collect{|a| a.to_s})
-  end
-  
-  def self.demo_bar_plot(file = nil)
-    r = Reports::BarPlot.new(file)
-    r.add_data("Alg1",[0.9, 0.3, 0.2, 0.75, 0.5])
-    r.add_data("Alg2",[0.8, 0.4, 0.2, 0.77, 0.6])
-    r.add_data("Alg3",[0.4, 0.2, 0.1, 0.9, 0.55])
-    r.add_data("Alg4",[0.9, 0.3, 0.2, 0.75, 0.5])
-    r.build_plot(["val1", "val2", "val3", "val4", "high-val"])
-    unless(file)
-      puts "press ENTER to end program"
-      gets
-      puts "program ended"
-    end
-  end
-  
-  private
-  def self.transform_predictions(validation_set, class_value)
-
-    predict_array = Array.new
-    actual_array = Array.new
-    if (validation_set.size > 1)
-      (0..validation_set.size-1).each do |i|
-        predict_array.push(validation_set.get(i).get_predictions.roc_confidence_values(class_value))
-        actual_array.push(validation_set.get(i).get_predictions.roc_actual_values(class_value))
-      end
-    else
-      predict_array = validation_set.first.get_predictions.roc_confidence_values(class_value)
-      actual_array = validation_set.first.get_predictions.roc_actual_values(class_value)
-    end
-    return [ predict_array, actual_array ]
-  end
-
-end
-
-
-class Reports::RPlot
-  
-  def initialize( out_file = nil )
-    if out_file
-      raise "non-svg files not supported yet" unless out_file.to_s.upcase =~ /.*\.SVG.*/
-      R.eval 'library("RSVGTipsDevice")'
-      R.eval 'devSVGTips(file = "'+out_file+'")'
-    end
-  end
-  
-end
-
-class Reports::BarPlot < Reports::RPlot
-  
-  def initialize( out_file = nil )
-    super(out_file)
-    @titles = Array.new
-    @rows = Array.new
-  end
-  
-  def add_data(title, values)
-    
-    row = "row"+(@rows.size+1).to_s 
-    R.assign row, values
-    @rows.push(row)
-    @titles.push(title)
-  end
-
-  def build_plot(value_names, y_axis_scale=[0,1])
-    
-    raise "not enough colors defined" if @titles.size >  R_PLOT_COLORS.size
-    @cols = R_PLOT_COLORS[0, @titles.size]
-    R.assign "titles", @titles
-    R.assign "cols", @cols
-    R.eval "m <-rbind("+@rows.join(",")+")"
-    R.assign "my_names", value_names
-    R.assign "my_ylim", y_axis_scale
-    R.eval 'barplot(m, beside = TRUE, col = cols, names=my_names, legend=titles, ylim = my_ylim)'
-  end
-end
-
diff --git a/report/report_factory.rb b/report/report_factory.rb
index 4331660..e577d70 100644
--- a/report/report_factory.rb
+++ b/report/report_factory.rb
@@ -244,7 +244,6 @@ class Reports::ReportContent
         @xml_report.add_imagefigure(section_roc, image_title, plot_file_name, "SVG", image_caption)
       rescue RuntimeError => ex
         LOGGER.error("could not create roc plot: "+ex.message)
-        LOGGER.debug("if R cannot find your libs, try adding R_LIBS='<lib>' to your ~/.Renviron file")
         rm_tmp_file(plot_file_name)
         @xml_report.add_paragraph(section_roc, "could not create roc plot: "+ex.message)
       end  
@@ -297,7 +296,7 @@ class Reports::ReportContent
     @xml_report.add_paragraph(section_bar, section_text) if section_text
     
     plot_file_path = add_tmp_file(plot_file_name)
-    Reports::RPlotFactory.create_bar_plot(plot_file_path, validation_set, class_value, title_attribute, value_attributes )
+    Reports::PlotFactory.create_bar_plot(plot_file_path, validation_set, class_value, title_attribute, value_attributes )
     @xml_report.add_imagefigure(section_bar, image_title, plot_file_name, "SVG", image_caption)
   end  
   
diff --git a/validation/validation_test.rb b/validation/validation_test.rb
index 3fe1832..5cfd319 100644
--- a/validation/validation_test.rb
+++ b/validation/validation_test.rb
@@ -166,22 +166,22 @@ class ValidationTest < Test::Unit::TestCase
 #    end
 #  end
   
-  def test_split
-    begin
-      data_uri = upload_data(WS_DATA, FILE)
-      #data_uri =  "http://ot.dataset.de/199" #bbrc
-      #data_uri = "http://ot.dataset.de/67" #hamster
-      #puts data_uri
-      
-      #data_uri=WS_DATA+"/"+DATA
-      post '/training_test_split', { :dataset_uri => data_uri, :algorithm_uri => WS_CLASS_ALG, :prediction_feature => FEATURE_URI,
-        :algorithm_params => "feature_generation_uri="+WS_FEATURE_ALG, :split_ratio=>0.75, :random_seed=>6}
-      puts last_response.body
-      #verify_validation
-    ensure
-      #delete_resources
-    end
-  end
+#  def test_split
+#    begin
+#      data_uri = upload_data(WS_DATA, FILE)
+#      #data_uri =  "http://ot.dataset.de/199" #bbrc
+#      #data_uri = "http://ot.dataset.de/67" #hamster
+#      #puts data_uri
+#      
+#      #data_uri=WS_DATA+"/"+DATA
+#      post '/training_test_split', { :dataset_uri => data_uri, :algorithm_uri => WS_CLASS_ALG, :prediction_feature => FEATURE_URI,
+#        :algorithm_params => "feature_generation_uri="+WS_FEATURE_ALG, :split_ratio=>0.75, :random_seed=>6}
+#      puts last_response.body
+#      #verify_validation
+#    ensure
+#      #delete_resources
+#    end
+#  end
   
   def test_nothing