Source Code for Module writepop

  1  """ 
  2  writepop 
  3  ======== 
  4  Contains all classes used to write and extract individuals and populations  
  5  on the SQLite database. 
  6   
  7  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 
  8  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
  9  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 
 10  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
 11  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 
 12  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN 
 13  THE SOFTWARE. 
 14   
 15  @author: by Mehdi Khoury 
 16  @version: 1.20 
 17  @copyright: (c) 2009 Mehdi Khoury under the mit license 
 18  http://www.opensource.org/licenses/mit-license.html 
 19  @contact: mehdi.khoury at gmail.com 
 20   
 21   
 22   
 23   
 24   
 25  """ 
 26   
 27  import settings 
 28  import buildtree 
 29  import cPickle 
 30  import marshal 
 31  import pprint 
 32  import psyco 
 33  import timeit 
 34  import evalfitness 
 35  from pysqlite2 import dbapi2 as sqlite 
 36  import crossutil 
 37   
 38   
 39  psyco.profile() 
 40   
 41   
 42   
 43 -def ClearDBTable(dbname,table): 
 44      """ 
 45      Function:  ClearDBTable 
 46      ======================= 
 47      clear the table of the database 
 48       
 49      @param dbname: path to database e.g. r'D:\3d_work\pythongp\pySTGP_0.51\src\pop_db' 
 50      @param table: name of the database table 
 51       
 52      """  
 53   
 54      con = sqlite.connect(dbname) 
 55      con.execute("drop table %s"%table) 
 56      con.commit() 
 57      con.close() 
 58   
 59   
 60   
 61 -def WriteInitialPopulation2DB(popsize,root_node,mintreesize,maxtreesize,buildmethod,dbname,tablename): 
 62      """ 
 63      Function:  WriteInitialPopulation2DB 
 64      ==================================== 
 65      create a new population of randomly generated trees and write them to a database 
 66    
 67      @param popsize: size of the population 
 68      @param root_node: specify the root node and its arity (nb of children). e.g. (0,2,'root') 
 69      @param mintreesize: min tree depth (at the moment only 2 working) 
 70      @param maxtreesize: max tree depth (At least 2) 
 71      @param buildmethod: which Koza method is used to build the trees (either  
 72      'AddHalfNode' or 'AddFullNode' or 'AddGrowNodeMin' respectively for  
 73      Half, Full, or Ramped Half-n-Half) 
 74      @param dbname: path to database e.g. r'D:\3d_work\pythongp\pySTGP_0.51\src\pop_db' 
 75      @param tablename: name of the database table 
 76    
 77      """  
 78   
 79      con = sqlite.connect(dbname) 
 80      con.execute("create table %s(o_id INTEGER PRIMARY KEY,tree TEXT,\ 
 81       tree_mapping TEXT, treedepth INTEGER, evaluated INTEGER, fitness FLOAT)"%tablename) 
 82      trees=[] 
 83      i=0 
 84      while i <popsize: 
 85          # create a tree individual 
 86          method = getattr(buildtree.buildTree(),buildmethod) 
 87          my_tree = method(root_node,0,mintreesize,maxtreesize) 
 88          if my_tree not in trees: 
 89          #    my_tree = method(root_node,0,mintreesize,maxtreesize) 
 90              trees.append(my_tree) 
 91          # create its tree mapping 
 92              my_tree_indices=crossutil.GetIndicesMappingFromTree(my_tree) 
 93          # get depth of the tree 
 94              depth=crossutil.GetDepthFromIndicesMapping(my_tree_indices) 
 95          # get fitness of the tree 
 96              resultfitness=settings.FitnessFunction(my_tree) 
 97              #myfitness=evalfitness.EvalTreeForAllInputSets(my_tree,xrange(settings.nb_eval)) 
 98              #myfitness=evalfitness.EvalTreeForOneListInputSet(my_tree) 
 99          #print myfitness 
100              #resultfitness=evalfitness.FinalFitness(myfitness) 
101              #resultfitness=evalfitness.FinalFitness2(myfitness) 
102              #resultfitness=evalfitness.FinalFitness4(myfitness) 
103          #print resultfitness 
104              con.execute("insert into %s(o_id,tree,tree_mapping,treedepth,evaluated,fitness) values (NULL,?,?,?,?,?)"%tablename,(buffer(marshal.dumps(my_tree,-1)),buffer(marshal.dumps(my_tree_indices,-1)),depth,1,resultfitness)) 
105              i=i+1 
106      con.commit() 
107      con.close() 
108   
109       
110   
111 -def PrintPopFromDB(dbname,tablename,filename): 
112      """ 
113      Function:  PrintPopFromDB 
114      ========================= 
115      print the population of trees with id references, tree depth and fitness scores 
116       
117      @param dbname: path to database e.g. r'D:\3d_work\pythongp\pySTGP_0.51\src\pop_db' 
118      @param tablename: name of the database table 
119    
120      """  
121   
122      con = sqlite.connect(dbname) 
123      SELECT = "select o_id,tree,treedepth,fitness from %s order by fitness" % tablename 
124      cur = con.cursor() 
125      cur.execute(SELECT) 
126      con.commit() 
127      myresult= cur.fetchall() 
128      con.close() 
129       
130      output = open(filename,'w') 
131      for elem in myresult: 
132          output.write(''.join([`elem[0]`,`marshal.loads(elem[1])`,`elem[2]`,`elem[3]`,'\n'])) 
133      output.close() 
134   
135   
136   
137 -def GetPopStatFromDB(dbname,tablename): 
138      """ 
139      Function:  GetPopStatFromDB 
140      =========================== 
141      get statistical data about the population 
142       
143      @param dbname: path to database e.g. r'D:\3d_work\pythongp\pySTGP_0.51\src\pop_db' 
144      @param tablename: name of the database table 
145    
146      """  
147   
148      con = sqlite.connect(dbname) 
149      SELECT = "select o_id,tree,treedepth,fitness from %s order by fitness" % tablename 
150      cur = con.cursor() 
151      cur.execute(SELECT) 
152      con.commit() 
153      myresult= cur.fetchall() 
154      con.close() 
155       
156       
157      depths=[] 
158      fit=[] 
159      trees=[] 
160      for elem in myresult: 
161          ntree=marshal.loads(elem[1]) 
162          if ntree not in trees: 
163              trees.append(ntree) 
164          depths.append(elem[2]) 
165          #fit.append(elem[3]) 
166      lengt=len(depths) 
167      uniques_trees=len(trees) 
168      av_depth=sum(depths)/len(myresult) 
169      av_fit=sum(fit)/len(myresult) 
170      print ''.join(['average depth: ',`av_depth`,' nb of unique trees: ',`uniques_trees`, ' over ', `lengt`]) 
171       
172       
173   
174   
175   
176  if __name__ == '__main__': 
177      #dbname=r'D:\3d_work\pythongp\pySTGP_0.51\src\pop_db' 
178      dbname=r'D:\mehdi\python projects\pySTGP_0.52\src\pop_db' 
179      tablename='tab1' 
180      #ClearDBTable(dbname,tablename) 
181      #WriteInitialPopulation2DB(100,(0,2,'root'),2,10,'AddHalfNode',dbname,tablename) 
182      #WriteInitialPopulation2File(100,2,2,10,'AddHalfNode','pop') 
183      #WriteInitialPopulation2DB2(100,(0,2,'root'),2,10,'AddHalfNode',dbname,tablename) 
184   
185      #t1 = timeit.Timer("writepop.WriteInitialPopulation2DB2(100,(0,2,'root'),2,10,'AddHalfNode',dbname,tablename)",  'from __main__ import dbname, tablename ;import writepop') 
186      t2 = timeit.Timer("writepop.WriteInitialPopulation2DB(10000,(0,2,'root'),2,10,'AddHalfNode',dbname,tablename)",  'from __main__ import dbname, tablename ;import writepop') 
187      print t2.repeat(1,1) 
188