def getBDFromOde(self, A=None):
'''
Returns a list of:class:`Transition` from this object by unrolling
the odes. All the elements are of TransitionType.B or
TransitionType.D
'''
if A is None:
if not ode_utils._noneOrEmptyList(self._odeList):
eqnList = [t.getEquation() for t in self._odeList]
A = sympy.Matrix(checkEquation(eqnList, *self._getListOfVariablesDict(), subsDerived=False))
else:
raise Exception("Object was not initialized using a set of ode")
# A = super(SimulateOdeModel, self).getOde()
bdList, termList = _ode_composition.getUnmatchedExpressionVector(A, True)
if len(bdList) > 0:
M = self._generateTransitionMatrix(A)
# # reduce the original set of ode to only birth and death process remaining
# M1 = M - M.transpose()
# diffA = sympy.zeros(self._numState,1)
# for i in range(self._numState):
# a = sympy.simplify(sum(M1[i,:]))
# diffA[i] = sympy.simplify(a + A[i])
A1 = _ode_composition.pureTransitionToOde(M)
diffA = sympy.simplify(A - A1)
# get our birth and death process
bdListUnroll = list()
states = [str(i) for i in self.getStateList()]
for i, a in enumerate(diffA):
for b in bdList:
if _ode_composition._hasExpression(a, b):
if sympy.Integer(-1) in _ode_composition.getLeafs(b):
bdListUnroll.append(Transition(origState=states[i],
equation=str(b*-1),
transitionType=TransitionType.D))
else:
bdListUnroll.append(Transition(origState=states[i],
equation=str(b),
transitionType=TransitionType.B))
a -= b
return bdListUnroll
else:
return []
def getBDFromOde(self, A=None, transitionExpressionList=None):
'''
Returns a list of:class:`Transition` from this object by unrolling
the odes. All the elements are of TransitionType.B or
TransitionType.D
'''
if A is None:
A = super(SimulateOdeModel, self).getOde()
if transitionExpressionList is None:
transitionList = _ode_composition.getMatchingExpressionVector(A, True)
else:
transitionList = transitionExpressionList
bdList = _ode_composition.getUnmatchedExpressionVector(A, False)
if len(bdList) > 0:
M = self._generateTransitionMatrix(A, transitionList)
# reduce the original set of ode to only birth and death process remaining
M1 = M - M.transpose()
diffA = sympy.zeros(self._numState,1)
for i in range(self._numState):
a = sympy.simplify(sum(M1[i,:]))
diffA[i] = sympy.simplify(a + A[i])
# get our birth and death process
bdListUnroll = list()
states = [str(i) for i in self.getStateList()]
for i, a in enumerate(diffA):
for b in bdList:
if _ode_composition._hasExpression(a, b):
if sympy.Integer(-1) in _ode_composition.getLeafs(b):
bdListUnroll.append(Transition(origState=states[i],
equation=str(b*-1),
transitionType=TransitionType.D))
else:
bdListUnroll.append(Transition(origState=states[i],
equation=str(b),
transitionType=TransitionType.B))
a -= b
return bdListUnroll
else:
return []
def _generateTransitionMatrix(self, A=None): #, transitionExpressionList=None):
'''
Finds the transition matrix from the set of ode. It is
important to note that although some of the functions used
in this method appear to be the same as _getReactantMatrix
and _getStateChangeMatrix, they are different in the sense
that the functions called here is focused on the terms of
the equation rather than the states.
'''
if A is None:
if not ode_utils._noneOrEmptyList(self._odeList):
eqnList = [t.getEquation() for t in self._odeList]
A = sympy.Matrix(checkEquation(eqnList, *self._getListOfVariablesDict(), subsDerived=False))
else:
raise Exception("Object was not initialized using a set of ode")
bdList, termList = _ode_composition.getUnmatchedExpressionVector(A, True)
fx = _ode_composition.stripBDFromOde(A, bdList)
states = [s for s in self._iterStateList()]
M, remainTermList = _ode_composition.odeToPureTransition(fx, states, True)
return M