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import unittest
import numpy
import os
import io
from rdkit.six.moves import cPickle
from rdkit import RDConfig, RDRandom
from rdkit.ML.InfoTheory import rdInfoTheory as rdit
from rdkit import DataStructs
def feq(a, b, tol=1e-4):
return abs(a - b) < tol
class TestCase(unittest.TestCase):
def setUp(self):
pass
def test0GainFuns(self):
arr = numpy.array([9, 5])
self.assertTrue(feq(rdit.InfoEntropy(arr), 0.9403))
arr = numpy.array([9, 9])
self.assertTrue(feq(rdit.InfoEntropy(arr), 1.0000))
arr = numpy.array([5, 5])
self.assertTrue(feq(rdit.InfoEntropy(arr), 1.0000))
arr = numpy.array([5, 0])
self.assertTrue(feq(rdit.InfoEntropy(arr), 0.0000))
arr = numpy.array([5, 5, 5])
self.assertTrue(feq(rdit.InfoEntropy(arr), 1.5850))
arr = numpy.array([2, 5, 5])
self.assertTrue(feq(rdit.InfoEntropy(arr), 1.4834))
mat2 = numpy.array([[6, 2], [3, 3]])
self.assertTrue(feq(rdit.InfoGain(mat2), 0.0481))
self.assertTrue(feq(rdit.ChiSquare(mat2), 0.9333))
mat3 = numpy.array([[1, 1], [2, 1]])
self.assertTrue(feq(rdit.InfoGain(mat3), 0.0200))
mat4 = numpy.array([[2, 0], [1, 2]])
self.assertTrue(feq(rdit.InfoGain(mat4), 0.4200))
mat5 = numpy.array([[0, 0], [0, 0]])
self.assertTrue(feq(rdit.InfoGain(mat5), 0.0000))
mat6 = numpy.array([[1, 0], [1, 0]])
self.assertTrue(feq(rdit.InfoGain(mat6), 0.0000))
def test1ranker(self):
nbits = 100
ninst = 100
dm = 50
nact = 10
nc = 2
rn = rdit.InfoBitRanker(nbits, nc, rdit.InfoType.ENTROPY)
fps = []
na = 0
ni = 0
for i in range(ninst):
v = DataStructs.SparseBitVect(nbits)
for j in range(dm):
v.SetBit(RDRandom.randrange(0, nbits))
if (RDRandom.randrange(0, ninst) < nact):
na += 1
rn.AccumulateVotes(v, 1)
fps.append((v, 1))
else:
ni += 1
rn.AccumulateVotes(v, 0)
fps.append((v, 0))
res = rn.GetTopN(50)
rn2 = rdit.InfoBitRanker(nbits, nc)
for fp in fps:
rn2.AccumulateVotes(fp[0], fp[1])
res2 = rn2.GetTopN(50)
self.assertTrue((res == res2).all())
rn3 = rdit.InfoBitRanker(nbits, nc, rdit.InfoType.BIASENTROPY)
#rn3.SetBiasList([0])
for fp in fps:
rn3.AccumulateVotes(fp[0], fp[1])
res3 = rn3.GetTopN(50)
for i in range(50):
fan = res3[i, 2] / na
fin = res3[i, 3] / ni
self.assertTrue(fan > fin)
def test2ranker(self):
nbits = 100
ninst = 100
dm = 50
nact = 10
nc = 2
RDRandom.seed(23)
rn = rdit.InfoBitRanker(nbits, nc, rdit.InfoType.ENTROPY)
rn.SetMaskBits([63, 70, 15, 25, 10])
fps = []
na = 0
ni = 0
for i in range(ninst):
v = DataStructs.SparseBitVect(nbits)
for j in range(dm):
v.SetBit(RDRandom.randrange(0, nbits))
if (RDRandom.randrange(0, ninst) < nact):
na += 1
rn.AccumulateVotes(v, 1)
fps.append((v, 1))
else:
ni += 1
rn.AccumulateVotes(v, 0)
fps.append((v, 0))
res = rn.GetTopN(5)
ids = [int(x[0]) for x in res]
ids.sort()
self.assertTrue(ids == [10, 15, 25, 63, 70])
with self.assertRaisesRegexp(Exception, ""):
res = rn.GetTopN(10)
def test3Issue140(self):
nbits = 2
examples = [[0, 0, 0], [1, 1, 0], [0, 0, 1], [1, 1, 1]]
rn = rdit.InfoBitRanker(2, 2, rdit.InfoType.ENTROPY)
for example in examples:
act = example.pop(-1)
bv = DataStructs.ExplicitBitVect(2)
for i in range(2):
bv[i] = example[i]
rn.AccumulateVotes(bv, act)
try:
res = rn.GetTopN(1)
except Exception:
res = None
self.assertTrue(res is not None)
def test4Issue237(self):
with open(
os.path.join(RDConfig.RDBaseDir, 'Code', 'ML', 'InfoTheory', 'Wrap', 'testData',
'Issue237.pkl'), 'r') as inTF:
buf = inTF.read().replace('\r\n', '\n').encode('utf-8')
inTF.close()
with io.BytesIO(buf) as inF:
examples, avail, bias, nB, nPoss = cPickle.load(inF, encoding='bytes')
ranker = rdit.InfoBitRanker(nB, nPoss, rdit.InfoType.BIASENTROPY)
ranker.SetMaskBits(avail)
for ex in examples:
ranker.AccumulateVotes(ex[1], ex[-1])
# this dumps core on linux if the bug isn't fixed:
v = ranker.GetTopN(1)
self.assertTrue(int(v[0][0]) == 12)
if __name__ == '__main__':
unittest.main()
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