Fix the obtainKineticsFamilyStatistics

retrieves data involving the family
Now shows the top node names, and also the
number of rules
csv file has headers now.
Does not average the families or add training data.
Assumes any type of manipulation has been done outside the folder.

Also, don't load any kineticsLibraries or thermoLibraries
by default except the primaryThermoLibrary.  But do
load all the depositories

Author: connie

testing/evaluateKinetics.py

@@ -158,23 +158,28 @@ def createParityPlot(parityData):
     plt.axis([minimum/10, maximum*10, minimum/10, maximum*10])
 
 def countNodes(family):
+    """
+    Count the number of groups under each tree in the Family's Groups.
+    Returns a list containing the following information
+    [Family Label, Number of Rules, Top Node Label 1, Number of Children, ..., Top Node Label N, Number of Children]
+    """
     countList=[family.label]
 
     #get top nodes
     forwardTemplate = family.groups.top[:]
 
     temporary = []
-    symmetricTree = False
     for entry in forwardTemplate:
         if entry not in temporary:
             temporary.append(entry)
         else:
-            # duplicate node found at top of tree
+            # Duplicate node found at top of tree
             # eg. R_recombination: ['Y_rad', 'Y_rad']
             assert len(forwardTemplate)==2 , 'Can currently only do symmetric trees with nothing else in them'
-            symmetricTree = True
+            
     forwardTemplate = temporary
 
+    countList.append(len(family.rules.entries))
     for group in forwardTemplate:
         checkList=[group]
         childrenList=[group]
@@ -183,28 +188,35 @@ def countNodes(family):
             checkList.extend(checkList[0].children)
             del checkList[0]
 
-        countList.append(len(childrenList))
+        countList.extend([group.label, len(childrenList)])
+    
     return countList
 
 
 ###########################################################################################################
 # Functions for the full Database
 
-def countNodesAll(FullDatabase, trialDir):
-    for family in FullDatabase.kinetics.families.values():
-        family.addKineticsRulesFromTrainingSet(thermoDatabase=FullDatabase.thermo)
-
+def obtainKineticsFamilyStatistics(FullDatabase, trialDir):
+    """
+    Obtains statistics for the kinetics families by creating
+    a FamilyStatistics.csv file that gives information about each family: the total number of
+    rules, and the top node names and the number of groups under each.
+    Note: does NOT average up the database or create any rate rules from training data.  
+    If that is desired it must be done prior to entering this function.  (averaging may not be desired
+    as it would add non-exact rules to the rule count)
+    """
     allFamilyNames=FullDatabase.kinetics.families.keys()
 
     familyCount={}
 
     for familyName in allFamilyNames: 
         family=FullDatabase.kinetics.families[familyName]
-        print "Processing", familyName + '...', '(' + str(len(family.rules.entries)) + ' nodes)'
+        print "Processing", familyName + '...', '(' + str(len(family.rules.entries)) + ' rules)'
         familyCount[familyName]=countNodes(family)
-    
-    with open(os.path.join(trialDir, 'NodeCount.csv'), 'wb') as csvfile:
+
+    with open(os.path.join(trialDir, 'FamilyStatistics.csv'), 'wb') as csvfile:
         csvwriter=csv.writer(csvfile)
+        csvwriter.writerow(['Family','Number of Rules', 'Top Node 1', 'Number of Groups', 'Top Node 2', 'Number of Groups', 'Top Node 3', 'Number of Groups'])
         for key, value in familyCount.iteritems():
             csvwriter.writerow(value)
 
@@ -324,23 +336,36 @@ def leaveOneOut(FullDatabase, trialDir):
 
 if __name__ == '__main__':
     from rmgpy import settings
+    
+    # Create the data evaluation directory
+    trialDir = os.path.join(settings['database.directory'],'..','testing','eval')
+    if not os.path.exists(trialDir):
+        os.makedirs(trialDir)
+        
     print 'Loading the RMG database...'
     FullDatabase=RMGDatabase()
     FullDatabase.load(settings['database.directory'], 
-                      kineticsFamilies=['Disproportionation'], 
+                      kineticsFamilies=['intra_H_migration'], 
                       kineticsDepositories='all',
-                      thermoLibraries=[],
+                      thermoLibraries=['primaryThermoLibrary'],   # Use just the primary thermo library, which contains necessary small molecular thermo
                       reactionLibraries=[],
                       )
 
-    trialDir = os.path.join(settings['database.directory'],'..','testing','eval')
-    if not os.path.exists(trialDir):
-        os.makedirs(trialDir)
+    # Prepare the database by loading training reactions
+    for family in FullDatabase.kinetics.families.values():
+        family.addKineticsRulesFromTrainingSet(thermoDatabase=FullDatabase.thermo)
+
+    print 'Obtaining statistics for the families...'
+    obtainKineticsFamilyStatistics(FullDatabase, trialDir)
+    
+    # Fill in the rate rules by averaging when we are ready to retrieve kinetics
+    for family in FullDatabase.kinetics.families.values():
+        family.fillKineticsRulesByAveragingUp()
+    
+
     print 'Evaluating the NIST Kinetics against the RMG estimates...'
     compareNIST(FullDatabase, trialDir)
 
-    print 'Counting the rate rules in the families...'
-    countNodesAll(FullDatabase, trialDir)
 
     print 'Performing the leave on out test on the kinetics families...'
     leaveOneOut(FullDatabase, trialDir)