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 writeMethodXml(simulation, out=None):
if out:
writer = XmlWriter(out)
else:
writer = XmlWriter()
writer.beginDocument()
simulation.writeXml(writer)
writer.endDocument()
def writeModelSbml(model, out=None):
if out:
writer = XmlWriter(out)
else:
writer = XmlWriter()
writer.beginDocument()
model.writeSbml(writer, 3)
writer.endDocument()
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 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
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 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 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()
