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287 lines
9.4 KiB
Python
Executable File
287 lines
9.4 KiB
Python
Executable File
# $Id$
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#
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# Copyright (C) 2003-2006 greg Landrum and Rational Discovery LLC
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#
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# @@ All Rights Reserved @@
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#
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"""unit testing code for the ScreenComposite functionality
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"""
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import RDConfig
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import unittest,os
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from ML import BuildComposite
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from ML import ScreenComposite
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import cPickle as pickle
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def feq(a,b,tol=1e-4):
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if abs(a-b)>tol: return 0
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else: return 1
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class TestCase(unittest.TestCase):
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def setUp(self):
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#print '\n%s: '%self.shortDescription(),
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self.baseDir = os.path.join(RDConfig.RDCodeDir,'ML','test_data')
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self.dbName = RDConfig.RDTestDatabase
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self.details = ScreenComposite.SetDefaults()
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self.details.dbName = self.dbName
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self.details.dbUser = RDConfig.defaultDBUser
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self.details.dbPassword = RDConfig.defaultDBPassword
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def test1(self):
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""" basics """
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self.details.tableName = 'ferro_quant'
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compos = pickle.load(open(os.path.join(self.baseDir,'ferromag_quant_10.pkl'),
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'rb'))
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tgt = 7
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assert len(compos)==tgt,'bad composite loaded: %d != %d'%(len(compos),tgt)
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nGood,misCount,nSkipped,avgGood,avgBad,avgSkip,tbl = ScreenComposite.ScreenFromDetails(compos,self.details)
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assert nGood==93
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assert misCount==2
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assert nSkipped==0
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assert feq(avgGood,.9753)
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assert feq(avgBad,.8000)
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assert tbl[0,0] == 54
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assert tbl[1,1] == 39
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assert tbl[0,1] == 2
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assert tbl[1,0] == 0
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def test2(self):
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""" include holdout data only """
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self.details.tableName = 'ferro_quant'
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self.details.doHoldout=1
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self.details.doTraining=0
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compos = pickle.load(open(os.path.join(self.baseDir,'ferromag_quant_10.pkl'),
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'rb'))
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tgt = 7
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assert len(compos)==tgt,'bad composite loaded: %d != %d'%(len(compos),tgt)
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nGood,misCount,nSkipped,avgGood,avgBad,avgSkip,tbl = ScreenComposite.ScreenFromDetails(compos,self.details)
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assert nGood==28
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assert misCount==1
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assert nSkipped==0
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assert feq(avgGood,.9607)
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assert feq(avgBad,.9000)
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assert tbl[0,0] == 16
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assert tbl[1,1] == 12
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assert tbl[0,1] == 1
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assert tbl[1,0] == 0
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def test3(self):
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""" include training data only """
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self.details.tableName = 'ferro_quant'
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self.details.doHoldout=0
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self.details.doTraining=1
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compos = pickle.load(open(os.path.join(self.baseDir,'ferromag_quant_10.pkl'),
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'rb'))
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tgt = 7
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assert len(compos)==tgt,'bad composite loaded: %d != %d'%(len(compos),tgt)
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nGood,misCount,nSkipped,avgGood,avgBad,avgSkip,tbl = ScreenComposite.ScreenFromDetails(compos,self.details)
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assert nGood==65
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assert misCount==1
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assert nSkipped==0
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assert feq(avgGood,.9815)
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assert feq(avgBad,.7000)
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assert tbl[0,0] == 38
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assert tbl[1,1] == 27
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assert tbl[0,1] == 1
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assert tbl[1,0] == 0
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def test4(self):
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""" include thresholding """
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self.details.tableName = 'ferro_quant'
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self.details.threshold = 0.80
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self.details.doHoldout=0
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self.details.doTraining=0
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compos = pickle.load(open(os.path.join(self.baseDir,'ferromag_quant_10.pkl'),
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'rb'))
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tgt = 7
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assert len(compos)==tgt,'bad composite loaded: %d != %d'%(len(compos),tgt)
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nGood,misCount,nSkipped,avgGood,avgBad,avgSkip,tbl = ScreenComposite.ScreenFromDetails(compos,self.details)
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assert nGood==86,str(nGood)
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assert misCount==1
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assert nSkipped==8
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assert feq(avgGood,.9930)
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assert feq(avgBad,.9000)
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assert feq(avgSkip,.7500)
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assert tbl[0,0] == 50
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assert tbl[1,1] == 36
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assert tbl[0,1] == 1
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assert tbl[1,0] == 0
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def test5(self):
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""" basics """
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self.details.tableName = 'ferro_noquant'
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compos = pickle.load(open(os.path.join(self.baseDir,'ferromag_auto_10_3.pkl'),
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'rb'))
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tgt = 10
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assert len(compos)==tgt,'bad composite loaded: %d != %d'%(len(compos),tgt)
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nGood,misCount,nSkipped,avgGood,avgBad,avgSkip,tbl = ScreenComposite.ScreenFromDetails(compos,self.details)
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assert nGood==93
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assert misCount==10
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assert nSkipped==0
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assert feq(avgGood,.9505)
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assert feq(avgBad,.7600)
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assert tbl[0,0] == 55
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assert tbl[1,1] == 38
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assert tbl[0,1] == 0
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assert tbl[1,0] == 10
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def test6(self):
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""" multiple models """
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self.details.tableName = 'ferro_noquant'
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compos = pickle.load(open(os.path.join(self.baseDir,'ferromag_auto_10_3.pkl'),
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'rb'))
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tgt = 10
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assert len(compos)==tgt,'bad composite loaded: %d != %d'%(len(compos),tgt)
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composites = [compos,compos]
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nGood,misCount,nSkipped,avgGood,avgBad,avgSkip,tbl = \
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ScreenComposite.ScreenFromDetails(composites,self.details)
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assert feq(nGood[0],93)
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assert feq(misCount[0],10)
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assert feq(nSkipped[0],0)
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assert feq(avgGood[0],.9505)
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assert feq(avgBad[0],.7600)
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assert feq(nGood[1],0)
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assert feq(misCount[1],0)
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assert feq(nSkipped[1],0)
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assert feq(avgGood[1],0)
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assert feq(avgBad[1],0)
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assert feq(tbl[0,0],55)
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assert feq(tbl[1,1],38)
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assert feq(tbl[0,1],0)
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assert feq(tbl[1,0],10)
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def test7(self):
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""" shuffle """
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self.details.tableName = 'ferro_noquant'
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compos = pickle.load(open(os.path.join(self.baseDir,'ferromag_shuffle_10_3.pkl'),
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'rb'))
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tgt = 10
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assert len(compos)==tgt,'bad composite loaded: %d != %d'%(len(compos),tgt)
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self.details.shuffleActivities=1
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nGood,misCount,nSkipped,avgGood,avgBad,avgSkip,tbl = ScreenComposite.ScreenFromDetails(compos,self.details)
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assert nGood==62
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assert misCount==41
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assert nSkipped==0
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assert feq(avgGood,.7839)
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assert feq(avgBad,.7049)
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assert tbl[0,0] == 36
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assert tbl[1,1] == 26
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assert tbl[0,1] == 19
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assert tbl[1,0] == 22
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def test8(self):
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""" shuffle with segmentation """
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self.details.tableName = 'ferro_noquant'
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compos = pickle.load(open(os.path.join(self.baseDir,'ferromag_shuffle_10_3.pkl'),
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'rb'))
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tgt = 10
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assert len(compos)==tgt,'bad composite loaded: %d != %d'%(len(compos),tgt)
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self.details.shuffleActivities=1
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self.details.doHoldout=1
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nGood,misCount,nSkipped,avgGood,avgBad,avgSkip,tbl = ScreenComposite.ScreenFromDetails(compos,self.details)
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assert nGood==15
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assert misCount==16
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assert nSkipped==0
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assert feq(avgGood,.6867)
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assert feq(avgBad,.7750)
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assert tbl[0,0] == 13
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assert tbl[1,1] == 2
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assert tbl[0,1] == 6
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assert tbl[1,0] == 10
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def test9(self):
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""" shuffle with segmentation2 """
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self.details.tableName = 'ferro_noquant'
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compos = pickle.load(open(os.path.join(self.baseDir,'ferromag_shuffle_10_3.pkl'),
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'rb'))
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tgt = 10
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assert len(compos)==tgt,'bad composite loaded: %d != %d'%(len(compos),tgt)
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self.details.shuffleActivities=1
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self.details.doTraining=1
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nGood,misCount,nSkipped,avgGood,avgBad,avgSkip,tbl = ScreenComposite.ScreenFromDetails(compos,self.details)
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assert nGood==47
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assert misCount==25
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assert nSkipped==0
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assert feq(avgGood,.8149)
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assert feq(avgBad,.6600)
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assert tbl[0,0] == 23
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assert tbl[1,1] == 24
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assert tbl[0,1] == 13
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assert tbl[1,0] == 12
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def test10(self):
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""" filtering """
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self.details.tableName = 'ferro_noquant'
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compos = pickle.load(open(os.path.join(self.baseDir,'ferromag_filt_10_3.pkl'),
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'rb'))
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tgt = 10
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assert len(compos)==tgt,'bad composite loaded: %d != %d'%(len(compos),tgt)
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self.details.filterVal=1
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self.details.filterFrac=.33
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nGood,misCount,nSkipped,avgGood,avgBad,avgSkip,tbl = ScreenComposite.ScreenFromDetails(compos,self.details)
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assert nGood==90
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assert misCount==13
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assert nSkipped==0
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assert feq(avgGood,.9578)
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assert feq(avgBad,.8538)
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assert tbl[0,0] == 54
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assert tbl[1,1] == 36
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assert tbl[0,1] == 1
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assert tbl[1,0] == 12
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def _test11(self):
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""" filtering with segmentation """
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self.details.tableName = 'ferro_noquant'
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compos = pickle.load(open(os.path.join(self.baseDir,'ferromag_filt_10_3.pkl'),
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'rb'))
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tgt = 10
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assert len(compos)==tgt,'bad composite loaded: %d != %d'%(len(compos),tgt)
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self.details.doHoldout=1
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self.details.filterVal=1
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self.details.filterFrac=.33
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nGood,misCount,nSkipped,avgGood,avgBad,avgSkip,tbl = ScreenComposite.ScreenFromDetails(compos,self.details)
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print nGood,misCount,nSkipped,avgGood,avgBad,avgSkip
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assert nGood==46,nGood
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assert misCount==6
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assert nSkipped==0
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assert feq(avgGood,.9500)
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assert feq(avgBad,.8333)
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assert tbl[0,0] == 37
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assert tbl[1,1] == 9
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assert tbl[0,1] == 1
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assert tbl[1,0] == 5
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def test12(self):
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""" test the naive bayes composite"""
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self.details.tableName = 'ferro_noquant'
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compos = pickle.load(open(os.path.join(self.baseDir,'ferromag_NaiveBayes.pkl'),
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'rb'))
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tgt = 10
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assert len(compos)==tgt,'bad composite loaded: %d != %d'%(len(compos),tgt)
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self.details.doHoldout=1
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nGood,misCount,nSkipped,avgGood,avgBad,avgSkip,tbl = ScreenComposite.ScreenFromDetails(compos,self.details)
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assert nGood == 26
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assert misCount == 5
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assert nSkipped == 0
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assert feq(avgGood, 0.9538)
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assert feq(avgBad, 0.86)
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assert tbl[0,0] == 9
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assert tbl[0,1] == 4
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assert tbl[1,0] == 1
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assert tbl[1,1] == 17
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if __name__ == '__main__':
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unittest.main()
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