def getEpsilonElasticityMatrix2(pathwayProxy):
"""
calculate and return the elasticities (matrix)
pathwayProxy: a PathwayProxy instance
return elasticityMatrix
"""
variableList = pathwayProxy.getVariableList()
processList = pathwayProxy.getProcessList()
elasticityMatrix = numpy.zeros((len(variableList), len(processList)), float)
incidentMatrix = pathwayProxy.getIncidentMatrix()
independentGroupList = createIndependentGroupList(incidentMatrix)
activityBuffer = numpy.zeros(len(processList), float)
aSession = pathwayProxy.theEmlSupport.createSession()
aSession.theSimulator.initialize()
for i in range(len(processList)):
activityBuffer[i] = aSession.theSimulator.getEntityProperty(processList[i] + ":Activity")
for groupList in independentGroupList:
aSession = pathwayProxy.theEmlSupport.createSession()
perturbationList = []
for i in groupList:
fullPN = variableList[i] + ":Value"
value = aSession.theSimulator.getEntityProperty(fullPN)
aPerturbation = RELATIVE_PERTURBATION * value + ABSOLUTE_PERTURBATION
perturbationList.append(aPerturbation)
aSession.theSimulator.setEntityProperty(fullPN, value + aPerturbation)
aSession.theSimulator.initialize()
for c in range(len(groupList)):
i = groupList[c]
aPerturbation = perturbationList[c]
for j in range(len(processList)):
if incidentMatrix[i][j]:
elasticityMatrix[i][j] = (
aSession.theSimulator.getEntityProperty(processList[j] + ":Activity") - activityBuffer[j]
) / aPerturbation
return elasticityMatrix
def getJacobianMatrix2( pathwayProxy ):
'''
calculate and return the Jacobian matrix (array)
pathwayProxy: a PathwayProxy instance
return aJacobian
'''
variableList = pathwayProxy.getVariableList()
size = len( variableList )
aJacobianMatrix = numpy.zeros( ( size, size ), float )
incidentMatrix = numpy.dot( pathwayProxy.getIncidentMatrix(), numpy.transpose( pathwayProxy.getIncidentMatrix( 1 ) ) )
independentGroupList = createIndependentGroupList( incidentMatrix )
velocityBuffer = numpy.zeros( size, float )
aSession = pathwayProxy.theEmlSupport.createSession()
aSession.theSimulator.initialize()
for i in range( size ):
velocityBuffer[ i ] = aSession.theSimulator.getEntityProperty( variableList[ i ] + ':Velocity' )
for groupList in independentGroupList:
aSession = pathwayProxy.theEmlSupport.createSession()
perturbationList = []
for i in groupList:
fullPN = variableList[ i ] + ':Value'
value = aSession.theSimulator.getEntityProperty( fullPN )
aPerturbation = RELATIVE_PERTURBATION * value + ABSOLUTE_PERTURBATION
perturbationList.append( aPerturbation )
aSession.theSimulator.setEntityProperty( fullPN, value + aPerturbation )
aSession.theSimulator.initialize()
for c in range( len( groupList ) ):
i = groupList[ c ]
aPerturbation = perturbationList[ c ]
for j in range( len( variableList ) ):
if incidentMatrix[ i ][ j ] != 0:
aJacobianMatrix[ j ][ i ] = ( aSession.theSimulator.getEntityProperty( variableList[ j ] + ':Velocity' ) - velocityBuffer[ j ] ) / aPerturbation
return aJacobianMatrix
def getJacobianMatrix2( pathwayProxy ):
'''
calculate and return the Jacobian matrix (array)
pathwayProxy: a PathwayProxy instance
return aJacobian
'''
variableList = pathwayProxy.getVariableList()
size = len( variableList )
aJacobianMatrix = numpy.zeros( ( size, size ), float )
incidentMatrix = numpy.dot( pathwayProxy.getIncidentMatrix(), numpy.transpose( pathwayProxy.getIncidentMatrix( 1 ) ) )
independentGroupList = createIndependentGroupList( incidentMatrix )
velocityBuffer = numpy.zeros( size, float )
aSession = pathwayProxy.theEmlSupport.createSession()
aSession.theSimulator.initialize()
for i in range( size ):
velocityBuffer[ i ] = aSession.theSimulator.getEntityProperty( variableList[ i ] + ':Velocity' )
for groupList in independentGroupList:
aSession = pathwayProxy.theEmlSupport.createSession()
perturbationList = []
for i in groupList:
fullPN = variableList[ i ] + ':Value'
value = aSession.theSimulator.getEntityProperty( fullPN )
aPerturbation = RELATIVE_PERTURBATION * value + ABSOLUTE_PERTURBATION
perturbationList.append( aPerturbation )
aSession.theSimulator.setEntityProperty( fullPN, value + aPerturbation )
aSession.theSimulator.initialize()
for c in range( len( groupList ) ):
i = groupList[ c ]
aPerturbation = perturbationList[ c ]
for j in range( len( variableList ) ):
if incidentMatrix[ i ][ j ] != 0:
aJacobianMatrix[ j ][ i ] = ( aSession.theSimulator.getEntityProperty( variableList[ j ] + ':Velocity' ) - velocityBuffer[ j ] ) / aPerturbation
return aJacobianMatrix
def getEpsilonElasticityMatrix2( pathwayProxy ):
'''
calculate and return the elasticities (matrix)
pathwayProxy: a PathwayProxy instance
return elasticityMatrix
'''
variableList = pathwayProxy.getVariableList()
processList = pathwayProxy.getProcessList()
elasticityMatrix = numpy.zeros( ( len( variableList ), len( processList ) ), float )
incidentMatrix = pathwayProxy.getIncidentMatrix()
independentGroupList = createIndependentGroupList( incidentMatrix )
activityBuffer = numpy.zeros( len( processList ), float )
aSession = pathwayProxy.theEmlSupport.createSession()
aSession.theSimulator.initialize()
for i in range( len( processList ) ):
activityBuffer[ i ] = aSession.theSimulator.getEntityProperty( processList[ i ] + ':Activity' )
for groupList in independentGroupList:
aSession = pathwayProxy.theEmlSupport.createSession()
perturbationList = []
for i in groupList:
fullPN = variableList[ i ] + ':Value'
value = aSession.theSimulator.getEntityProperty( fullPN )
aPerturbation = RELATIVE_PERTURBATION * value + ABSOLUTE_PERTURBATION
perturbationList.append( aPerturbation )
aSession.theSimulator.setEntityProperty( fullPN, value + aPerturbation )
aSession.theSimulator.initialize()
for c in range( len( groupList ) ):
i = groupList[ c ]
aPerturbation = perturbationList[ c ]
for j in range( len( processList ) ):
if incidentMatrix[ i ][ j ]:
elasticityMatrix[ i ][ j ] = ( aSession.theSimulator.getEntityProperty( processList[ j ] + ':Activity' ) - activityBuffer[ j ] ) / aPerturbation
return elasticityMatrix