def writeModelSbml(model, out=None):
if out:
writer = XmlWriter(out)
else:
writer = XmlWriter()
writer.beginDocument()
model.writeSbml(writer, 3)
writer.endDocument()
def writeMethodXml(simulation, out=None):
if out:
writer = XmlWriter(out)
else:
writer = XmlWriter()
writer.beginDocument()
simulation.writeXml(writer)
writer.endDocument()
def main():
import math
import sys
sys.path.insert(1, '..')
from Value import Value
from ParameterEvaluation import evaluateInitialAmounts
from io.XmlWriter import XmlWriter
writer = XmlWriter()
x = Species('C1', 'species 1', '0')
x.writeXml(writer, 's1')
x = Species('C1', 'species 1', '')
print evaluateInitialAmounts({'s1': x}, {})
x = Species('C1', 'species 2', '1')
x.writeXml(writer, 's2')
x = Species('C1', 'species 2', '-1')
# I don't check the initial amount expression with hasErrors().
print evaluateInitialAmounts({'s2': x}, {})
x = Species('C1', 'species 2', 'p1')
print evaluateInitialAmounts({'s1': x}, {})
x = Species('C1', 'species 2', 'p2')
p = Value('', '5.0')
p.value = 5.0
print evaluateInitialAmounts({'s1': x}, {'p1': p})
def test(self):
assert TriggerEvent('e1', '', '', '', 0, True).hasErrors()
assert TriggerEvent('e1', '', '', '', '', True).hasErrors()
assert TriggerEvent('e1', '', '', '', 0., 0).hasErrors()
assert not TriggerEvent('e1', '', '', '', 0., True).hasErrors()
# CONTINUE: '>' is converted to '>'. is this OK?
x = TriggerEvent('e1', '', 't>1', 'p1=1; p2=2', 1., True)
assert not x.hasErrors()
writer = XmlWriter(StringIO())
x.writeXml(writer)
def main():
import math
from ParameterEvaluation import evaluateValues
from io.XmlWriter import XmlWriter
writer = XmlWriter()
x = Value('', '')
x.name = 'Parameter 1'
x.expression = '3'
x.value = 3.0
x.writeParameterXml(writer, 'P1')
x.writeParameterSbml(writer, 'P1')
x.writeCompartmentXml(writer, 'C1')
x.writeCompartmentSbml(writer, 'C1')
# Invalid identifers.
print('\nInvalid identifers:')
x = Value('', '')
result = evaluateValues({'': x})
print(result)
result = evaluateValues({' ': x})
print(result)
result = evaluateValues({'2x': x})
print(result)
result = evaluateValues({'a.txt': x})
print(result)
# Invalid expressions.
print('\nInvalid expressions:')
x.expression = ''
result = evaluateValues({'a': x})
print(result)
x.expression = ' '
result = evaluateValues({'a': x})
print(result)
x.expression = 'x'
result = evaluateValues({'a': x})
print(result)
x.expression = '1 2'
result = evaluateValues({'a': x})
print(result)
x.expression = 'a'
result = evaluateValues({'a': x})
print(result)
# Invalid expressions for two parameters.
print('\nInvalid expressions for two parameters:')
y = Value('', '')
x.expression = 'b'
y.expression = 'a'
result = evaluateValues({'a': x, 'b': y})
print(result)
def test(self):
assert TimeEvent('e1', '', '', '').hasErrors()
x = TimeEvent('e1', '', '[0]', 'p1=1; p2=2')
assert not x.hasErrors()
writer = XmlWriter(StringIO())
x.writeXml(writer)
assert TimeEvent('e1', '', '1', '').hasErrors()
assert not TimeEvent('e1', '', 'range(10)', '').hasErrors()
assert not TimeEvent('e1', '', '[0.1 * i for i in range(10)]', '').\
hasErrors()
def test(self):
numberOfBins = 4
multiplicity = 2
h = Histogram(numberOfBins, multiplicity)
h.setCurrentToMinimum()
h.accumulate(0, 1)
h.accumulate(1, 2)
h.accumulate(2, 2)
h.accumulate(3, 1)
frameTimes = [0, 1]
recordedSpecies = [0, 1, 2]
x = HistogramFrames(numberOfBins, multiplicity, recordedSpecies)
x.setFrameTimes(frameTimes)
for i in range(2):
x.setCurrentToMinimum()
for i in range(len(frameTimes)):
for j in range(len(recordedSpecies)):
x.histograms[i][j].merge(h)
assert not x.hasErrors()
stream = StringIO()
writer = XmlWriter(stream)
writer.beginDocument()
x.writeXml(writer, 'model', 'method')
writer.endDocument()
def main():
import sys
sys.path.insert(1, '..')
from io.XmlWriter import XmlWriter
writer = XmlWriter()
identifiers = ['s1', 's2']
x = SpeciesReference('s1')
x.writeXml(writer)
x = SpeciesReference('s1', 1)
x.writeXml(writer)
x = SpeciesReference('s2', 2)
x.writeXml(writer)
def test(self):
trajectory = TimeSeriesFrames([0, 1])
trajectory.recordedSpecies = [0, 1]
trajectory.recordedReactions = [0, 1]
trajectory.appendPopulations([2, 3, 7, 11])
trajectory.appendReactionCounts([13, 17, 19, 23])
assert not trajectory.hasErrors()
writer = XmlWriter(StringIO())
writer.beginDocument()
trajectory.writeXml(writer, 'model', 'method')
writer.endDocument()
def main():
import sys
sys.path.insert(1, '..')
from io.XmlWriter import XmlWriter
recordedSpecies = [0, 1, 2]
x = StatisticsAverage(recordedSpecies)
x.setStatistics([1, 2, 3, 4, 5, 6])
writer = XmlWriter()
writer.beginDocument()
x.writeXml(writer, 'model', 'method')
writer.endDocument()
def test(self):
# One species, two reactions.
trajectory = TimeSeriesAllReactions([0], [0, 1], 1., 5.)
trajectory.appendInitialPopulations([7.])
trajectory.appendIndices([0, 1, 1, 0])
trajectory.appendTimes([1, 2, 3, 4])
assert not trajectory.hasErrors()
writer = XmlWriter(StringIO())
writer.beginDocument()
trajectory.writeXml(writer, 'model', 'method')
writer.endDocument()
def test(self):
recordedSpecies = [0, 1, 2]
x = StatisticsAverage(recordedSpecies)
x.setStatistics([1, 2, 3, 4, 5, 6])
assert x.statistics[0] == (1, 2)
assert x.statistics[1] == (3, 4)
assert x.statistics[2] == (5, 6)
assert not x.hasErrors()
writer = XmlWriter(StringIO())
writer.beginDocument()
x.writeXml(writer, 'model', 'method')
writer.endDocument()
def test(self):
stream = StringIO()
writer = XmlWriter(stream)
identifiers = ['s1', 's2']
x = SpeciesReference('s1')
assert not x.hasErrors(identifiers)
assert x.hasErrors([])
x.writeXml(writer)
x = SpeciesReference('s1', 1)
assert not x.hasErrors(identifiers)
assert x.hasErrors([])
x.writeXml(writer)
x = SpeciesReference('s2', 2)
assert not x.hasErrors(identifiers)
assert x.hasErrors([])
x.writeXml(writer)
def main():
import sys
sys.path.insert(1, '..')
from io.XmlWriter import XmlWriter
trajectory = TimeSeriesFrames([0, 1])
trajectory.recordedSpecies = [0, 1]
trajectory.recordedReactions = [0, 1]
trajectory.appendPopulations([2, 3, 7, 11])
trajectory.appendReactionCounts([13, 17, 19, 23])
writer = XmlWriter()
writer.beginDocument()
trajectory.writeXml(writer, 'model', 'method')
writer.endDocument()
def main():
import sys
sys.path.insert(1, '..')
from io.XmlWriter import XmlWriter
# One species, two reactions.
trajectory = TimeSeriesAllReactions([0], [0, 1], 1., 5.)
trajectory.appendInitialPopulations([7.])
trajectory.appendIndices([0, 1, 1, 0])
trajectory.appendTimes([1, 2, 3, 4])
writer = XmlWriter()
writer.beginDocument()
trajectory.writeXml(writer, 'model', 'method')
writer.endDocument()
def main():
import sys
sys.path.insert(1, '..')
from io.XmlWriter import XmlWriter
frameTimes = [0, 1]
recordedSpecies = [0, 1, 2]
x = StatisticsFrames(recordedSpecies)
x.setFrameTimes(frameTimes)
x.setStatistics([1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12])
writer = XmlWriter()
writer.beginDocument()
x.writeXml(writer, 'model', 'method')
writer.endDocument()
def test(self):
frameTimes = [0, 1]
recordedSpecies = [0, 1, 2]
x = StatisticsFrames(recordedSpecies)
x.setFrameTimes(frameTimes)
x.setStatistics([1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12])
assert x.statistics[0][0] == (1, 2)
assert x.statistics[0][1] == (3, 4)
assert x.statistics[0][2] == (5, 6)
assert x.statistics[1][0] == (7, 8)
assert x.statistics[1][1] == (9, 10)
assert x.statistics[1][2] == (11, 12)
assert not x.hasErrors()
writer = XmlWriter(StringIO())
writer.beginDocument()
x.writeXml(writer, 'model', 'method')
writer.endDocument()
def testPoisson1(self):
# Poisson with mean 4. 20 bins. PMF = e^-lambda lambda^n / n!
# Store in the first array of bins.
lam = 4.
size = 20
poisson = [math.exp(-lam)]
for n in range(1, size):
poisson.append(poisson[-1] * lam / n)
cardinality = size
sumOfWeights = sum(poisson)
mean = 0.
for i in range(size):
mean += poisson[i] * i
mean /= sumOfWeights
summedSecondCenteredMoment = 0.
for i in range(size):
summedSecondCenteredMoment += poisson[i] * (i - mean)**2
stream = StringIO(repr(cardinality) + '\n' +
repr(sumOfWeights) + '\n' +
repr(mean) + '\n' +
repr(summedSecondCenteredMoment) + '\n' +
'0\n1\n' +
''.join([repr(_x) + ' ' for _x in poisson]) + '\n' +
'0 ' * len(poisson) + '\n')
x = Histogram()
x.read(stream, 2)
assert x.cardinality == cardinality
assert x.sumOfWeights == sumOfWeights
assert x.mean == mean
assert x.summedSecondCenteredMoment == summedSecondCenteredMoment
assert x.size() == len(poisson)
self.assertAlmostEqual(sum(x.getProbabilities()), 1)
stream = StringIO()
writer = XmlWriter(stream)
writer.beginDocument()
x.writeXml(writer, 0, 0)
writer.endDocument()
def test(self):
writer = XmlWriter(StringIO())
x = Value('', '')
assert x.hasErrors()
x.name = 'Parameter 1'
x.expression = '3'
x.value = 3.0
assert not x.hasErrors()
x.writeParameterXml(writer, 'P1')
x.writeParameterSbml(writer, 'P1')
x.writeCompartmentXml(writer, 'C1')
x.writeCompartmentSbml(writer, 'C1')
# Invalid identifers.
x = Value('', '')
result = evaluateValues({'':x})
assert result
result = evaluateValues({' ':x})
assert result
result = evaluateValues({'2x':x})
assert result
result = evaluateValues({'a.txt':x})
assert result
# Invalid expressions.
x.expression = ''
result = evaluateValues({'a':x})
assert result
x.expression = ' '
result = evaluateValues({'a':x})
assert result
x.expression = 'x'
result = evaluateValues({'a':x})
assert result
x.expression = '1 2'
result = evaluateValues({'a':x})
assert result
x.expression = 'a'
result = evaluateValues({'a':x})
assert result
# Valid expressions for a single parameter.
for key in math.__dict__.keys():
x.expression = '1'
assert not evaluateValues({key:x})
assert x.value == 1
x.expression = '1.0'
result = evaluateValues({'a':x})
assert not result
assert x.value == 1
x.expression = '1.0'
result = evaluateValues({'lambda':x})
assert not result
assert x.value == 1
x.expression = '1.0'
result = evaluateValues({'e':x})
assert not result
assert x.value == 1
x.expression = '1.0'
result = evaluateValues({'pi':x})
assert not result
assert x.value == 1
x.expression = '1.0'
result = evaluateValues({'sin':x})
assert not result
assert x.value == 1
x.expression = '1'
result = evaluateValues({'a':x})
assert not result
assert x.value == 1
x.expression = '2 * 3'
result = evaluateValues({'a':x})
assert not result
assert x.value == 2 * 3
x.expression = '2 - 3'
result = evaluateValues({'a':x})
assert not result
assert x.value == 2 - 3
x.expression = '2 ** 3'
result = evaluateValues({'a':x})
assert not result
assert x.value == 2**3
x.expression = '2./3'
result = evaluateValues({'a':x})
assert not result
assert x.value == 2./3
x.expression = 'pi'
result = evaluateValues({'a':x})
assert not result
assert x.value == math.pi
x.expression = 'e'
result = evaluateValues({'a':x})
assert not result
assert x.value == math.e
x.expression = 'sqrt(2)'
result = evaluateValues({'a':x})
assert not result
assert x.value == math.sqrt(2)
x.expression = 'log(2)'
result = evaluateValues({'a':x})
assert not result
assert x.value == math.log(2)
# Valid expressions for two parameters.
y = Value('', '')
x.expression = 'pi'
y.expression = 'e'
result = evaluateValues({'a':x, 'b':y})
assert not result
assert x.value == math.pi
assert y.value == math.e
x.expression = '1.0'
y.expression = 'a'
result = evaluateValues({'a':x, 'b':y})
assert not result
assert x.value == 1
assert y.value == 1
x.expression = 'b'
y.expression = '1'
result = evaluateValues({'a':x, 'b':y})
assert not result
assert x.value == 1
assert y.value == 1
x.expression = '2'
y.expression = 'sqrt(a)'
result = evaluateValues({'a':x, 'b':y})
assert not result
assert x.value == 2
assert y.value == math.sqrt(2)
x.expression = '2**3'
y.expression = 'sqrt(a)'
result = evaluateValues({'a':x, 'b':y})
assert not result
assert x.value == 2**3
assert y.value == math.sqrt(2**3)
# Invalid expressions for two parameters.
y = Value('', '')
x.expression = 'b'
y.expression = 'a'
result = evaluateValues({'a':x, 'b':y})
assert result
# Valid expressions for three parameters.
z = Value('', '')
x.expression = 'pi'
y.expression = 'a**2'
z.expression = 'sqrt(a + b)'
result = evaluateValues({'a':x, 'b':y, 'c':z})
assert not result
assert x.value == math.pi
assert y.value == x.value**2
assert z.value == math.sqrt(x.value + y.value)
attributes['name'] = self.name
writer.writeEmptyElement('timeEvent', attributes)
def readXml(self, attributes):
"""Read from an attributes dictionary. Return any errors encountered."""
# The attribute "dictionary" may not work as it should. In particular
# the test "x in attributes" may not work. Thus we need to directly
# use attributes.keys().
keys = attributes.keys()
for x in ['id', 'times', 'assignments']:
if not x in keys:
return 'Missing ' + x + ' attribute in time event.\n'
self.id = attributes['id']
if 'name' in keys:
self.name = attributes['name']
else:
self.name = ''
self.times = attributes['times']
self.assignments = attributes['assignments']
return ''
if __name__ == '__main__':
import sys
sys.path.insert(1, '..')
from io.XmlWriter import XmlWriter
x = TimeEvent('e1', '', '[0]', 'p1=1; p2=2')
writer = XmlWriter()
x.writeXml(writer)
def main():
import sys
sys.path.insert(1, '..')
from io.XmlWriter import XmlWriter
from ParameterEvaluation import evaluatePropensityFactors
writer = XmlWriter()
assert Reaction('r1', '', [], [], False, '').hasErrors([], True)
# Mass action kinetics.
identifiers = ['s1', 's2']
a = SpeciesReference('s1', 1)
x = Reaction('r1', '1', [a], [], True, '0')
evaluatePropensityFactors([x], {})
x.writeXml(writer)
print(x.makeMassActionPropensityFunction('x', identifiers, True))
print(x.makeMassActionPropensityFunction('x', identifiers, False))
print(x.makeMassActionPropensityFunctionMathematica(identifiers))
print('Mass action term:')
print(x.makeMassActionTerm())
print('')
p = SpeciesReference('s2', 1)
x = Reaction('r1', 'reaction', [a], [p], True, '1')
evaluatePropensityFactors([x], {})
x.writeXml(writer)
print(x.makeMassActionPropensityFunction('x', identifiers, True))
print(x.makeMassActionPropensityFunction('x', identifiers, False))
print(x.makeMassActionPropensityFunctionMathematica(identifiers))
print('')
b = SpeciesReference('s2', 2)
x = Reaction('r1', 'name', [a, b], [p], True, '3')
evaluatePropensityFactors([x], {})
x.writeXml(writer)
print(x.makeMassActionPropensityFunction('x', identifiers, True))
print(x.makeMassActionPropensityFunction('x', identifiers, False))
print(x.makeMassActionPropensityFunctionMathematica(identifiers))
print('')
print('Time inhomogeneous')
p = SpeciesReference('s2', 1)
x = Reaction('r1', 'reaction', [a], [p], True, '2+sin(t)')
x.writeXml(writer)
print(x.makeInhomogeneousMassActionPropensityFunction
('x', identifiers, True))
print(x.makeInhomogeneousMassActionPropensityFunction
('x', identifiers, False))
print('')
p = SpeciesReference('s2', 1)
x = Reaction('r1', 'name', [a, b], [p], True, '2+sin(t)')
x.writeXml(writer)
print(x.makeInhomogeneousMassActionPropensityFunction
('x', identifiers, True))
print(x.makeInhomogeneousMassActionPropensityFunction
('x', identifiers, False))
print('')
# Custom kinetics.
x.massAction = False
x.propensity = '5*s1*s2'
x.writeXml(writer)
print('')
x.propensity = '5'
x.writeXml(writer)
print('')
x.propensity = 's10'
x.writeXml(writer)
print('')
identifiers.append('s3')
x.propensity = 's3'
x.writeXml(writer)
print(x.hasErrors(identifiers, True))
print('')