diff options
Diffstat (limited to 'report')
| -rw-r--r-- | report/plot_factory.rb | 5 | ||||
| -rwxr-xr-x | report/report_factory.rb | 5 | ||||
| -rwxr-xr-x | report/validation_access.rb | 39 |
3 files changed, 34 insertions, 15 deletions
diff --git a/report/plot_factory.rb b/report/plot_factory.rb index f114dd3..6e90dbc 100644 --- a/report/plot_factory.rb +++ b/report/plot_factory.rb @@ -4,7 +4,8 @@ ENV['RANK_PLOTTER_JAR'] = "RankPlotter/RankPlotter.jar" unless ENV['RANK_PLOTTER CONF_PLOT_RANGE = { :accuracy => [0.45,1.05], :true_positive_rate => [0.45,1.05],:true_negative_rate => [0.45,1.05], :false_positive_rate => [0.45,1.05], :false_negative_rate => [0.45,1.05], :positive_predictive_value => [0.45,1.05], - :negative_predictive_value => [0.45,1.05], :r_square => [0, 1.05], :sample_correlation_coefficient => [0, 1.05] } + :negative_predictive_value => [0.45,1.05], :r_square => [0, 1.05], :sample_correlation_coefficient => [0, 1.05], + :concordance_correlation_coefficient => [0, 1.05] } class Array def swap!(i,j) @@ -124,7 +125,7 @@ module Reports else Reports::r_util.feature_value_plot(out_files, validation_set.validations[0].training_feature_dataset_uri, validation_set.validations[0].test_feature_dataset_uri, "Training Data", "Test Data", - nil, true, validation_set.validations[0].subjectid, waiting_task ) + nil, validation_set.validations[0].subjectid, waiting_task ) end end diff --git a/report/report_factory.rb b/report/report_factory.rb index 07a5ac5..f51b999 100755 --- a/report/report_factory.rb +++ b/report/report_factory.rb @@ -9,7 +9,7 @@ VAL_ATTR_CLASS = [ :num_instances, :num_unpredicted, :accuracy, :weighted_accura :area_under_roc, :f_measure, :true_positive_rate, :true_negative_rate, :positive_predictive_value, :negative_predictive_value ] VAL_ATTR_REGR = [ :num_instances, :num_unpredicted, :root_mean_squared_error, :weighted_root_mean_squared_error, :mean_absolute_error, :weighted_mean_absolute_error, :r_square, :weighted_r_square, - :sample_correlation_coefficient ] + :sample_correlation_coefficient, :concordance_correlation_coefficient ] #VAL_ATTR_BOX_PLOT_CLASS = [ :accuracy, :average_area_under_roc, # :area_under_roc, :f_measure, :true_positive_rate, :true_negative_rate ] @@ -113,6 +113,9 @@ module Reports::ReportFactory report.add_confidence_plot(validation_set, :root_mean_squared_error, nil) report.add_confidence_plot(validation_set, :r_square, nil) report.align_last_two_images "Confidence Plots" + report.add_confidence_plot(validation_set, :sample_correlation_coefficient, nil) + report.add_confidence_plot(validation_set, :concordance_correlation_coefficient, nil) + report.align_last_two_images "More Confidence Plots" end task.progress(70) if task report.add_train_test_plot( validation_set, false, OpenTox::SubTask.create(task,70,80) ) diff --git a/report/validation_access.rb b/report/validation_access.rb index aaa7bdc..e2a3978 100755 --- a/report/validation_access.rb +++ b/report/validation_access.rb @@ -145,20 +145,35 @@ class Reports::ValidationDB end def test_feature_dataset_uri(validation, subjectid) - m = OpenTox::Model::Generic.find(validation.model_uri, subjectid) - feat_gen = nil - m.metadata[OT.parameters].each do |h| - if h[DC.title] and h[DC.title]=~/feature_generation/ and h[OT.paramValue] - feat_gen = h[OT.paramValue] + training_features = Lib::DatasetCache.find( training_feature_dataset_uri(validation,subjectid), subjectid ) + test_dataset = Lib::DatasetCache.find( validation.test_dataset_uri, subjectid ) + features_found = true + training_features.features.keys.each do |f| + unless test_dataset.features.keys.include?(f) + features_found = false + LOGGER.debug "training-feature are not in test-datset #{f}" break end - end if m and m.metadata[OT.parameters] - raise "no feature creation alg found" unless feat_gen - feat_gen = File.join(feat_gen,"match") if feat_gen=~/fminer/ - uri = OpenTox::RestClientWrapper.post(feat_gen,{:subjectid => subjectid, - :feature_dataset_uri=>training_feature_dataset_uri(validation,subjectid), - :dataset_uri=>validation.test_dataset_uri}) - @@tmp_resources << uri + end + if features_found + LOGGER.debug "all training-features found in test-datset" + uri = test_dataset.uri + else + m = OpenTox::Model::Generic.find(validation.model_uri, subjectid) + feat_gen = nil + m.metadata[OT.parameters].each do |h| + if h[DC.title] and h[DC.title]=~/feature_generation/ and h[OT.paramValue] + feat_gen = h[OT.paramValue] + break + end + end if m and m.metadata[OT.parameters] + raise "no feature creation alg found" unless feat_gen + feat_gen = File.join(feat_gen,"match") if feat_gen=~/fminer/ + uri = OpenTox::RestClientWrapper.post(feat_gen,{:subjectid => subjectid, + :feature_dataset_uri=>training_feature_dataset_uri(validation,subjectid), + :dataset_uri=>validation.test_dataset_uri}) + @@tmp_resources << uri + end uri end |