summaryrefslogtreecommitdiff
path: root/lib/crossvalidation.rb
diff options
context:
space:
mode:
authorChristoph Helma <helma@in-silico.ch>2016-05-13 13:38:24 +0200
committerChristoph Helma <helma@in-silico.ch>2016-05-13 13:38:24 +0200
commitc90644211e214a50f6fdb3a936bf247f45f1f4be (patch)
tree9ae3f0b33feb55f3904c4d7a08e39567223b07aa /lib/crossvalidation.rb
parentb8bb12c8a163c238d7d4387c1914e2100bb660df (diff)
compound tests fixed
Diffstat (limited to 'lib/crossvalidation.rb')
-rw-r--r--lib/crossvalidation.rb26
1 files changed, 4 insertions, 22 deletions
diff --git a/lib/crossvalidation.rb b/lib/crossvalidation.rb
index da4b731..357f0fa 100644
--- a/lib/crossvalidation.rb
+++ b/lib/crossvalidation.rb
@@ -41,6 +41,7 @@ module OpenTox
$logger.debug "Dataset #{training_dataset.name}: Fold #{fold_nr} started"
t = Time.now
validation = Validation.create(model, fold[0], fold[1],cv)
+ #p validation
$logger.debug "Dataset #{training_dataset.name}, Fold #{fold_nr}: #{Time.now-t} seconds"
#end
end
@@ -166,29 +167,10 @@ module OpenTox
end
def correlation_plot
- #unless correlation_plot_id
- tmpfile = "/tmp/#{id.to_s}_correlation.png"
- x = []
- y = []
- predictions.each do |sid,p|
- x << p["value"]
- y << p["measured"].median
- end
- attributes = Model::Lazar.find(self.model_id).attributes
- attributes.delete_if{|key,_| key.match(/_id|_at/) or ["_id","creator","name"].include? key}
- attributes = attributes.values.collect{|v| v.is_a?(String) ? v.sub(/OpenTox::/,'') : v}.join("\n")
- R.assign "measurement", x
- R.assign "prediction", y
- R.eval "all = c(measurement,prediction)"
- R.eval "range = c(min(all), max(all))"
- R.eval "image = qplot(prediction,measurement,main='#{self.name}',asp=1,xlim=range, ylim=range)"
- R.eval "image = image + geom_abline(intercept=0, slope=1)"
- #R.eval "ggsave(file='#{tmpfile}', plot=image)"
- R.eval "ggsave(file='#{tmpfile}')"
- file = Mongo::Grid::File.new(File.read(tmpfile), :filename => "#{self.id.to_s}_correlation_plot.png")
- plot_id = $gridfs.insert_one(file)
+ unless correlation_plot_id
+ plot_id = ValidationStatistics.correlation_plot predictions
update(:correlation_plot_id => plot_id)
- #end
+ end
$gridfs.find_one(_id: correlation_plot_id).data
end
end