def testReplacementSelection(self):
# " use selection with replacement "
RDRandom.seed(self.randomSeed)
examples, attrs, nPossibleVals = randomtest.GenRandomExamples(
nExamples=200, seed=self.randomArraySeed)
tree, frac = CrossValidate.CrossValidationDriver(
examples, attrs, nPossibleVals, silent=1, replacementSelection=1)
self.assertTrue(tree)
self.assertAlmostEqual(frac, 0.01666, 4)
def testRun(self):
" test that the CrossValidationDriver runs "
from rdkit.ML.DecTree import randomtest
examples, attrs, nPossibleVals = randomtest.GenRandomExamples(
nExamples=200)
tree, frac = CrossValidate.CrossValidationDriver(examples,
attrs,
nPossibleVals,
silent=1)
def testReplacementSelection(self):
" use selection with replacement "
from rdkit.ML.DecTree import randomtest
from rdkit import RDRandom
RDRandom.seed(self.randomSeed)
examples, attrs, nPossibleVals = randomtest.GenRandomExamples(
nExamples=200, seed=self.randomArraySeed)
tree, frac = CrossValidate.CrossValidationDriver(
examples, attrs, nPossibleVals, silent=1, replacementSelection=1)
assert tree
assert feq(frac, 0.0833)
def TestRun():
""" testing code """
examples, attrs, nPossibleVals = randomtest.GenRandomExamples(
nExamples=200)
tree, _ = CrossValidationDriver(examples, attrs, nPossibleVals)
tree.Pickle('save.pkl')
import copy
t2 = copy.deepcopy(tree)
print('t1 == t2', tree == t2)
l = [tree]
print('t2 in [tree]', t2 in l, l.index(t2))
def _testRandom():
from rdkit.ML.DecTree import randomtest
# examples, attrs, nPossibleVals = randomtest.GenRandomExamples(nVars=20, randScale=0.25,
# nExamples=200)
examples, attrs, nPossibleVals = randomtest.GenRandomExamples(nVars=10, randScale=0.5,
nExamples=200)
tree, frac = CrossValidate.CrossValidationDriver(examples, attrs, nPossibleVals)
tree.Print()
tree.Pickle('orig.pkl')
print('original error is:', frac)
print('----Pruning')
newTree, frac2 = PruneTree(tree, tree.GetTrainingExamples(), tree.GetTestExamples())
newTree.Print()
print('pruned error is:', frac2)
newTree.Pickle('prune.pkl')
def testResults(self):
# " test the results of CrossValidation "
RDRandom.seed(self.randomSeed)
examples, attrs, nPossibleVals = randomtest.GenRandomExamples(
nExamples=200, seed=self.randomArraySeed)
tree, frac = CrossValidate.CrossValidationDriver(examples,
attrs,
nPossibleVals,
silent=1)
self.assertGreater(frac, 0)
with open(self.origTreeName, 'r') as inTFile:
buf = inTFile.read().replace('\r\n', '\n').encode('utf-8')
inTFile.close()
inFile = BytesIO(buf)
oTree = pickle.load(inFile)
assert oTree == tree, 'Random CrossValidation test failed'
def testResults(self):
" test the results of CrossValidation "
from rdkit.ML.DecTree import randomtest
from rdkit import RDRandom
RDRandom.seed(self.randomSeed)
examples, attrs, nPossibleVals = randomtest.GenRandomExamples(
nExamples=200, seed=self.randomArraySeed)
tree, frac = CrossValidate.CrossValidationDriver(examples,
attrs,
nPossibleVals,
silent=1)
import cPickle
#cPickle.dump(tree,file(self.origTreeName,'w+'))
inFile = open(self.origTreeName, 'r')
oTree = cPickle.load(inFile)
assert oTree == tree, 'Random CrossValidation test failed'
def testResults(self):
" test the results of CrossValidation "
from rdkit.ML.DecTree import randomtest
from rdkit import RDRandom
RDRandom.seed(self.randomSeed)
examples,attrs,nPossibleVals = randomtest.GenRandomExamples(nExamples = 200,
seed=self.randomArraySeed)
tree,frac = CrossValidate.CrossValidationDriver(examples,attrs,
nPossibleVals,silent=1)
from rdkit.six.moves import cPickle
#cPickle.dump(tree,open(self.origTreeName,'w+'))
with open(self.origTreeName,'r') as inTFile:
buf = inTFile.read().replace('\r\n', '\n').encode('utf-8')
inTFile.close()
with io.BytesIO(buf) as inFile:
oTree = cPickle.load(inFile)
assert oTree==tree,'Random CrossValidation test failed'
def testRun(self):
# " test that the CrossValidationDriver runs "
examples, attrs, nPossibleVals = randomtest.GenRandomExamples(
nExamples=200)
f = StringIO()
with redirect_stdout(f):
tree, frac = CrossValidate.CrossValidationDriver(examples,
attrs,
nPossibleVals,
silent=False)
self.assertGreater(frac, 0)
self.assertEqual('Var: 1', tree.GetName())
self.assertIn('Validation error', f.getvalue())
CrossValidate.CrossValidationDriver(examples,
attrs,
nPossibleVals,
lessGreedy=True,
calcTotalError=True,
silent=True)
