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simplehmmTest.py
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238 lines (191 loc) · 9.69 KB
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# =============================================================================
# simpleTest.py - Test module for simplehmm.py
#
# Freely extensible biomedical record linkage (Febrl) Version 0.2.2
# See http://datamining.anu.edu.au/projects/linkage.html
#
# =============================================================================
# AUSTRALIAN NATIONAL UNIVERSITY OPEN SOURCE LICENSE (ANUOS LICENSE)
# VERSION 1.1
#
# The contents of this file are subject to the ANUOS License Version 1.1 (the
# "License"); you may not use this file except in compliance with the License.
# Software distributed under the License is distributed on an "AS IS" basis,
# WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for
# the specific language governing rights and limitations under the License.
# The Original Software is "simplehmmTest.py".
# The Initial Developers of the Original Software are Dr Peter Christen
# (Department of Computer Science, Australian National University) and Dr Tim
# Churches (Centre for Epidemiology and Research, New South Wales Department
# of Health). Copyright (C) 2002, 2003 the Australian National University and
# others. All Rights Reserved.
# Contributors:
#
# =============================================================================
"""Module simpleTest.py - Test module for simplehmm.py.
"""
# -----------------------------------------------------------------------------
import unittest
import simplehmm
# -----------------------------------------------------------------------------
class TestCase(unittest.TestCase):
# Initialise test case - - - - - - - - - - - - - - - - - - - - - - - - - - -
#
def setUp(self):
self.delta = 0.000001 # Account for floating-point rounding errors
self.states = ['title','givenname','surname']
self.observ = ['TI','GM','GF','SN','UN']
self.train_data = [[('title','TI'),('givenname','GF'),('surname','SN')], \
[('givenname','GM'),('surname','UN')], \
[('title','UN'),('givenname','GM'),('surname','UN')], \
[('title','TI'),('givenname','SN'),('surname','SN')], \
[('givenname','GM'),('surname','SN')], \
[('title','TI'),('givenname','GF'),('surname','SN')], \
[('title','TI'),('surname','SN'),('givenname','GM')], \
[('title','TI'),('givenname','GM'),('givenname','UN'), \
('surname','SN')], \
[('surname','UN'),('givenname','UN')], \
[('givenname','GF'),('givenname','GF'),('surname','SN')]]
self.test_data = [['TI','GM','SN'], \
['UN','SN'], \
['TI','UN','UN'], \
['TI','GF','UN'], \
['UN','UN','UN','UN'], \
['TI','GM','UN','SN'], \
['SN','SN'], \
['UN','UN'], \
['TI','GM'], \
['TI','GF'], \
['TI','SN'], \
['TI','UN']]
# Clean up test case - - - - - - - - - - - - - - - - - - - - - - - - - - - -
#
def tearDown(self):
pass # Nothing to clean up
# ---------------------------------------------------------------------------
#
# Start test cases
def testHMM(self): # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
"""Test basic HMM functionality"""
hmm1 = simplehmm.hmm('Test HMM', self.states, self.observ)
assert (hmm1.N == len(self.states)), \
'Illegal number of states in HMM ('+str(hmm1.N)+'), should be: '+ \
str(len(self.states))
assert (len(hmm1.S_ind) == len(self.states)), \
'Illegal number of states in HMM state dictionary ('+ \
str(len(hmm1.S_ind))+'), should be: '+str(len(self.states))
assert (hmm1.M == len(self.observ)), \
'Illegal number of observations in HMM ('+str(hmm1.M)+ \
'), should be: '+str(len(self.observ))
assert (len(hmm1.O_ind) == len(self.observ)), \
'Illegal number of observations in HMM observation dictionary ('+ \
str(len(hmm1.O_ind))+'), should be: '+ str(len(self.observ))
for i in range(hmm1.N):
assert (hmm1.pi[i] == 0.0), \
'Initial probability in HMM 1 is not 0.0 at location ['+ \
str(i)+']: '+str(hmm1.pi[i])
for j in range(hmm1.N):
assert (hmm1.A[i][j] == 0.0), \
'Transition probability in HMM 1 is not 0.0 at location ['+ \
str(i)+','+str(j)+']: '+str(hmm1.A[i][j])
for j in range(hmm1.M):
assert (hmm1.B[i][j] == 0.0), \
'Observation probability in HMM 1 is not 0.0 at location ['+ \
str(i)+','+str(j)+']: '+str(hmm1.B[i][j])
hmm1.train(self.train_data)
hmm1.check_prob()
hmm1.print_hmm()
for i in range(hmm1.N):
assert ((hmm1.pi[i] >= 0.0) and (hmm1.pi[i] <= 1.0)), \
'Initial probability in HMM 1 is not between 0.0 and 1.0 at '+ \
'location ['+str(i)+']: '+str(hmm1.pi[i])
for j in range(hmm1.N):
assert ((hmm1.A[i][j] >= 0.0) and (hmm1.A[i][j] <= 1.0)), \
'Transition probability in HMM 1 is not between 0.0 and 1.0'+ \
' at location ['+str(i)+','+str(j)+']: '+str(hmm1.A[i][j])
for j in range(hmm1.M):
assert ((hmm1.B[i][j] >= 0.0) and (hmm1.B[i][j] <= 1.0)), \
'Observation probability in HMM 1 is not between 0.0 and '+ \
'1.0 at location ['+str(i)+','+str(j)+']: '+str(hmm1.B[i][j])
for test_rec in self.test_data:
[state_seq, seq_prob] = hmm1.viterbi(test_rec)
for state in state_seq:
assert (state in self.states), \
'Returned state "'+state+'" not in tate list'
assert ((seq_prob >= 0.0) and (seq_prob <= 1.0)), \
'Sequence probability is not between 0.0 and 1.0:'+ str(seq_prob)
hmm1.train(self.train_data,smoothing='laplace')
hmm1.check_prob()
hmm1.print_hmm()
for i in range(hmm1.N):
assert ((hmm1.pi[i] >= 0.0) and (hmm1.pi[i] <= 1.0)), \
'Initial probability in HMM 1 is not between 0.0 and 1.0 at '+ \
'location ['+str(i)+']: '+str(hmm1.pi[i])
for j in range(hmm1.N):
assert ((hmm1.A[i][j] >= 0.0) and (hmm1.A[i][j] <= 1.0)), \
'Transition probability in HMM 1 is not between 0.0 and 1.0'+ \
' at location ['+str(i)+','+str(j)+']: '+str(hmm1.A[i][j])
for j in range(hmm1.M):
assert ((hmm1.B[i][j] >= 0.0) and (hmm1.B[i][j] <= 1.0)), \
'Observation probability in HMM 1 is not between 0.0 and '+ \
'1.0 at location ['+str(i)+','+str(j)+']: '+str(hmm1.B[i][j])
for test_rec in self.test_data:
[state_seq, seq_prob] = hmm1.viterbi(test_rec)
for state in state_seq:
assert (state in self.states), \
'Returned state "'+state+'" not in tate list'
assert ((seq_prob >= 0.0) and (seq_prob <= 1.0)), \
'Sequence probability is not between 0.0 and 1.0:'+ str(seq_prob)
hmm1.train(self.train_data,smoothing='absdiscount')
hmm1.check_prob()
hmm1.print_hmm()
for i in range(hmm1.N):
assert ((hmm1.pi[i] >= 0.0) and (hmm1.pi[i] <= 1.0)), \
'Initial probability in HMM 1 is not between 0.0 and 1.0 at '+ \
'location ['+str(i)+']: '+str(hmm1.pi[i])
for j in range(hmm1.N):
assert ((hmm1.A[i][j] >= 0.0) and (hmm1.A[i][j] <= 1.0)), \
'Transition probability in HMM 1 is not between 0.0 and 1.0'+ \
' at location ['+str(i)+','+str(j)+']: '+str(hmm1.A[i][j])
for j in range(hmm1.M):
assert ((hmm1.B[i][j] >= 0.0) and (hmm1.B[i][j] <= 1.0)), \
'Observation probability in HMM 1 is not between 0.0 and '+ \
'1.0 at location ['+str(i)+','+str(j)+']: '+str(hmm1.B[i][j])
for test_rec in self.test_data:
[state_seq, seq_prob] = hmm1.viterbi(test_rec)
for state in state_seq:
assert (state in self.states), \
'Returned state "'+state+'" not in tate list'
assert ((seq_prob >= 0.0) and (seq_prob <= 1.0)), \
'Sequence probability is not between 0.0 and 1.0:'+ str(seq_prob)
hmm1.save_hmm('testhmm.hmm')
hmm2 = hmm1
hmm2 = simplehmm.hmm('Test2 HMM', ['dummy'], ['dummy'])
hmm2.load_hmm('testhmm.hmm')
assert (hmm1.N == hmm2.N), \
'Loaded HMM has differnt number of states'
assert (hmm1.M == hmm2.M), \
'Loaded HMM has differnt number of observations'
for i in range(hmm1.N):
assert (abs(hmm1.pi[i]- hmm2.pi[i]) < self.delta), \
'Initial probability in HMM 1 is different from HMM 2: '+ \
str(hmm1.pi[i])+' / '+str(hmm2.pi[i])
for j in range(hmm1.N):
assert (abs(hmm1.A[i][j] - hmm2.A[i][j]) < self.delta), \
'Transition probability in HMM 1 is different from HMM 2 '+ \
'at location ['+str(i)+','+str(j)+']: '+str(hmm1.A[i][j])+ \
' / '+str(hmm2.A[i][j])
for j in range(hmm1.M):
assert (abs(hmm1.B[i][j] - hmm1.B[i][j]) < self.delta), \
'Observation probability in HMM 1 is different from HMM 2 '+ \
'at location ['+str(i)+','+str(j)+']: '+str(hmm1.B[i][j])+ \
' / '+str(hmm2.B[i][j])
# -----------------------------------------------------------------------------
# Start tests when called from command line
if (__name__ == "__main__"):
unittest.main() # Run all test
# The following code does the same as 'unittest.main()'
#
# mysuite = unittest.makeSuite(TestCase,'test')
# testrunner = unittest.TextTestRunner(verbosity=1)
# testrunner.run(mysuite)