more timer details

4 files changed, 40 insertions, 30 deletions

diff --git a/lib/bbrc.rb b/lib/bbrc.rb
index 6b0eb26..6e3af3a 100644
--- a/lib/bbrc.rb
+++ b/lib/bbrc.rb
@@ -34,11 +34,6 @@ module OpenTox
           minfreq = minfreq.round
         end
 
-        #@fminer=OpenTox::Algorithm::Fminer.new
-        #@fminer.check_params(dataset,params,5)
-        #p @fminer.instance_variables
-
-
         @bbrc = Bbrc::Bbrc.new
         @bbrc.Reset
         if prediction_feature.numeric 
@@ -47,8 +42,7 @@ module OpenTox
           bad_request_error "No accept values for "\
                             "dataset '#{training_dataset.id}' and "\
                             "feature '#{prediction_feature.id}'" unless prediction_feature.accept_values
-          act2value = prediction_feature.accept_values.each_index.inject({}) { |h,idx| h[idx+1]=prediction_feature.accept_values[idx]; h }
-          value2act = act2value.invert
+          value2act = Hash[[*prediction_feature.accept_values.map.with_index]]
         end
         @bbrc.SetMinfreq(minfreq)
         @bbrc.SetType(1) if params[:feature_type] == "paths"
@@ -70,10 +64,7 @@ module OpenTox
         )
         feature_dataset.compounds = training_dataset.compounds
 
-        $logger.debug "Setup: #{Time.now-time}"
-        time = Time.now
-        # Add data to fminer
-        #@fminer.add_fminer_data(@bbrc, value_map)
+        # add data 
         training_dataset.compounds.each_with_index do |compound,i|
           @bbrc.AddCompound(compound.smiles,i+1)
           act = value2act[training_dataset.data_entries[i].first]
@@ -84,7 +75,7 @@ module OpenTox
         #task.progress 10
         #step_width = 80 / @bbrc.GetNoRootNodes().to_f
 
-        $logger.debug "Setup: #{Time.now-time}"
+        $logger.debug "BBRC setup: #{Time.now-time}"
         time = Time.now
         ftime = 0
         itime = 0
diff --git a/lib/lazar.rb b/lib/lazar.rb
index d9195ad..1e123d7 100644
--- a/lib/lazar.rb
+++ b/lib/lazar.rb
@@ -51,7 +51,8 @@ module OpenTox
 
       def predict object
 
-        time = Time.now
+        t = Time.now
+        at = Time.now
 
         @training_dataset = OpenTox::Dataset.find(training_dataset_id)
         @feature_dataset = OpenTox::Dataset.find(feature_dataset_id)
@@ -68,17 +69,22 @@ module OpenTox
           bad_request_error "Please provide a OpenTox::Compound an Array of OpenTox::Compounds or an OpenTox::Dataset as parameter."
         end
 
-        $logger.debug "Setup: #{Time.now-time}"
-        time = Time.now
+        $logger.debug "Setup: #{Time.now-t}"
+        t = Time.now
 
         @query_fingerprint = Algorithm.run(feature_calculation_algorithm, compounds, @feature_dataset.features.collect{|f| f.name} )
 
-        $logger.debug "Query fingerprint calculation: #{Time.now-time}"
+        $logger.debug "Query fingerprint calculation: #{Time.now-t}"
+        t = Time.now
 
         predictions = []
         prediction_feature = OpenTox::Feature.find prediction_feature_id
         tt = 0
         pt = 0
+        nt = 0
+        st = 0
+        nit = 0
+        @training_fingerprints ||= @feature_dataset.data_entries
         compounds.each_with_index do |compound,c|
           t = Time.new
 
@@ -95,11 +101,11 @@ module OpenTox
             if prediction_algorithm =~ /Regression/
               mtf = OpenTox::Algorithm::Transform::ModelTransformer.new(self)
               mtf.transform
-              training_fingerprints = mtf.n_prop
+              @training_fingerprints = mtf.n_prop
               query_fingerprint = mtf.q_prop
               neighbors = [[nil,nil,nil,query_fingerprint]]
             else
-              training_fingerprints = @feature_dataset.data_entries
+              #training_fingerprints = @feature_dataset.data_entries
               query_fingerprint = @query_fingerprint[c]
               neighbors = []
             end
@@ -108,22 +114,27 @@ module OpenTox
             
 
             # find neighbors
-            training_fingerprints.each_with_index do |fingerprint, i|
+            @training_fingerprints.each_with_index do |fingerprint, i|
+              ts = Time.new
               sim = Algorithm.run(similarity_algorithm,fingerprint, query_fingerprint)
+              st += Time.now-ts
+              ts = Time.new
               if sim > self.min_sim
                 if prediction_algorithm =~ /Regression/
-                  neighbors << [@feature_dataset.compounds[i],sim,training_activities[i], fingerprint]
+                  neighbors << [@feature_dataset.compound_ids[i],sim,training_activities[i], fingerprint]
                 else
-                  neighbors << [@feature_dataset.compounds[i],sim,training_activities[i]] 
+                  neighbors << [@feature_dataset.compound_ids[i],sim,training_activities[i]] # use compound_ids, instantiation of Compounds is too time consuming
                 end
               end
+              nit += Time.now-ts
             end
 
             if neighbors.empty?
               predictions << {:compound => compound, :value => nil, :confidence => nil, :warning => "No neighbors with similarity > #{min_sim} in dataset #{training_dataset.id}"}
-              #$logger.warn "No neighbors found for compound #{compound}."
               next
             end
+            nt += Time.now-t
+            t = Time.new
 
             if prediction_algorithm =~ /Regression/
               prediction = Algorithm.run(prediction_algorithm, neighbors, :min_train_performance => self.min_train_performance)
@@ -145,7 +156,9 @@ module OpenTox
 
         end 
         $logger.debug "Transform time: #{tt}"
+        $logger.debug "Neighbor search time: #{nt} (Similarity calculation: #{st}, Neighbor insert: #{nit})"
         $logger.debug "Prediction time: #{pt}"
+        $logger.debug "Total prediction time: #{Time.now-at}"
 
         # serialize result
         case object.class.to_s
diff --git a/lib/opentox-algorithm.rb b/lib/opentox-algorithm.rb
index 1764b47..790803b 100644
--- a/lib/opentox-algorithm.rb
+++ b/lib/opentox-algorithm.rb
@@ -15,6 +15,7 @@ require_relative '../last-utils/lu.rb'
 #Dir[File.join(File.dirname(__FILE__),"*.rb")].each{ |f| require_relative f}
 require_relative "algorithm.rb"
 require_relative "descriptor.rb"
+require_relative "bbrc.rb"
 #require_relative "fminer.rb"
 require_relative "lazar.rb"
 require_relative "transform.rb"
diff --git a/lib/similarity.rb b/lib/similarity.rb
index 78783d5..934c4b0 100644
--- a/lib/similarity.rb
+++ b/lib/similarity.rb
@@ -10,22 +10,27 @@ module OpenTox
 
     class Similarity
 
+      #TODO weighted tanimoto
+
       # Tanimoto similarity
       # @param [Array] a fingerprints of first compound
       # @param [Array] b fingerprints of second compound
       # @return [Float] Tanimoto similarity
       def self.tanimoto(a,b)
-        #a = fingerprints.first
-        #b = fingerprints.last
+        bad_request_error "fingerprints #{a} and #{b} don't have equal size" unless a.size == b.size
+        #common = 0.0
+        #a.each_with_index do |n,i|
+          #common += 1 if n == b[i]
+        #end
+        #common/a.size
+        # TODO check if calculation is correct
         common_p_sum = 0.0
         all_p_sum = 0.0
-        size = [ a.size, b.size ].min
-        $logger.warn "fingerprints don't have equal size" if a.size != b.size
-        (0...size).each { |idx|
-          common_p_sum += [ a[idx].to_f, b[idx].to_f ].min
-          all_p_sum += [ a[idx].to_f, b[idx].to_f ].max
+        (0...a.size).each { |idx|
+          common_p_sum += [ a[idx], b[idx] ].min
+          all_p_sum += [ a[idx], b[idx] ].max
         }
-        (all_p_sum > 0.0) ? (common_p_sum/all_p_sum) : 0.0
+        common_p_sum/all_p_sum
       end