def AuxVars(self, t, xdict, pdict=None, asarray=True):
"""asarray is an unused, dummy argument for compatibility with
Model.AuxVars"""
# also, ensure xdict doesn't contain elements like array([4.1]) instead of 4
x = [float(val) for val in sortedDictValues(filteredDict(self._FScompatibleNames(xdict),
self.funcspec.vars))]
if pdict is None:
pdict = self.pars
# internal self.pars already is FS-compatible
p = sortedDictValues(pdict)
else:
p = sortedDictValues(self._FScompatibleNames(pdict))
i = _pollInputs(sortedDictValues(self.inputs),
t, self.checklevel)
return apply(getattr(self, self.funcspec.auxspec[1]), [t, x, p+i])
def __del__(self):
ODEsystem.__del__(self)
# Register this Generator with the database
symbolMapDict = {}
# in future, provide appropriate mappings for libraries math,
# random, etc. (for now it's left to FuncSpec)
theGenSpecHelper.add(Vode_ODEsystem, symbolMapDict, 'python')
raise IOError, e
# Write the vfield.m file
# vfdefines = self._prepareVfieldDefines()
# allfilestr = self._prepareVfieldContents(vfdefines)
allfilestr = self.funcspec.spec[0] + self._prepareAuxContents()
vffile = os.path.join(self._target_dir, self._vfield_file)
try:
file = open(vffile, 'w')
file.write(allfilestr)
file.close()
except IOError, e:
print "Error opening file "+self._vfield_file+" for writing"
raise IOError, e
# We have omitted methods: RHS, compute, etc. because this
# class is intended solely to generate code for ADMC++, not do any integrations
# etc.
def __del__(self):
ODEsystem.__del__(self)
# Register this Generator with the database
symbolMapDict = {}
# in future, provide appropriate mappings for libraries math,
# random, etc. (for now it's left to FuncSpec)
theGenSpecHelper.add(ADMC_ODEsystem, symbolMapDict, 'matlab')
i = sortedDictValues(dict([(n, i(t)) for n, i in self.inputs.iteritems()]))
return apply(eval("self." + self.funcspec.auxfns["Jacobian"][1]), [t, x, p + i])
else:
raise PyDSTool_ExistError, "Jacobian not defined"
def JacobianP(self, t, xdict, pdict):
if self.haveJacobian_pars():
x = sortedDictValues(xdict)
p = sortedDictValues(pdict)
i = sortedDictValues(dict([(n, i(t)) for n, i in self.inputs.iteritems()]))
return apply(eval("self." + self.funcspec.auxfns["Jacobian_pars"][1]), [t, x, p + i])
else:
raise PyDSTool_ExistError, "Jacobian w.r.t. parameters not defined"
def AuxVars(self, t, xdict, pdict):
x = sortedDictValues(xdict)
p = sortedDictValues(pdict)
i = sortedDictValues(dict([(n, i(t)) for n, i in self.inputs.iteritems()]))
return apply(eval("self." + self.funcspec.auxspec[1]), [t, x, p + i])
def __del__(self):
discGen.__del__(self)
# Register this Generator with the database
symbolMapDict = {}
# in future, provide appropriate mappings for libraries math,
# random, etc. (for now it's left to FuncSpec)
theGenSpecHelper.add(MapSystem, symbolMapDict, "python")
self.validateSpec()
self.defined = True
def compute(self, trajname):
return Trajectory(trajname, [copy(v) for v in self.variables.values()],
self.globalt0, self.checklevel)
computeTraj = compute
def validateSpec(self):
ctsGen.validateSpec(self)
try:
assert isoutputcts(self.indepvariable)
for v in self.variables.values():
assert isinstance(v, Variable)
assert not self.inputs
except AssertionError:
print 'Invalid system specification'
raise
def __del__(self):
ctsGen.__del__(self)
# Register this Generator with the database
symbolMapDict = {}
# in future, provide appropriate mappings for libraries math,
# random, etc. (for now it's left to FuncSpec)
theGenSpecHelper.add(InterpolateTable, symbolMapDict, 'python')
if self.defined:
self.validateSpec()
self.clearWarnings()
self.clearErrors()
return Trajectory(trajname, [copy(v) for v in self.variables.values()],
self.globalt0, self.checklevel)
computeTraj = compute
def validateSpec(self):
discGen.validateSpec(self)
try:
assert isoutputdiscrete(self.indepvariable)
for v in self.variables.values():
assert isinstance(v, Variable)
assert not self.inputs
except AssertionError:
print 'Invalid system specification'
raise
def __del__(self):
discGen.__del__(self)
# Register this Generator with the database
symbolMapDict = {}
# in future, provide appropriate mappings for libraries math,
# random, etc. (for now it's left to FuncSpec)
theGenSpecHelper.add(LookupTable, symbolMapDict, 'python')
# pass up to generic treatment for this
ctsGen.set(self, checklevel=kw['checklevel'])
if 'globalt0' in kw:
# pass up to generic treatment for this
ctsGen.set(self, globalt0=kw['globalt0'])
def validateSpec(self):
ctsGen.validateSpec(self)
try:
assert isoutputcts(self.indepvariable)
for v in self.variables.values():
assert isinstance(v, Variable)
assert not self.inputs
except AssertionError:
print 'Invalid system specification'
raise
def __del__(self):
ctsGen.__del__(self)
# Register this Generator with the database
symbolMapDict = {}
# in future, provide appropriate mappings for libraries math,
# random, etc. (for now it's left to FuncSpec)
theGenSpecHelper.add(InterpolateTable, symbolMapDict, 'python')
' at bound')
else:
raise PyDSTool_ValueError('Parameter value out of'
' bounds')
else:
raise PyDSTool_AttributeError('Illegal parameter name')
def validateSpec(self):
ctsGen.validateSpec(self)
try:
for v in self.variables.values():
assert isinstance(v, Variable)
assert not self.inputs
except AssertionError:
print 'Invalid system specification'
raise
def __del__(self):
ctsGen.__del__(self)
# Register this Generator with the database
symbolMapDict = {}
# in future, provide appropriate mappings for libraries math,
# random, etc. (for now it's left to FuncSpec)
theGenSpecHelper.add(EmbeddedSysGen, symbolMapDict, 'python', None)
for k, v in kw['algparams'].iteritems():
self.algparams[k] = v
if 'solvemethod' in self.algparams:
if self.algparams['solvemethod'] not in _implicitSolveMethods:
raise PyDSTool_ValueError('Invalid implicit solver type')
def validateSpec(self):
ctsGen.validateSpec(self)
try:
for v in self.variables.values():
assert isinstance(v, Variable)
assert not self.inputs
except AssertionError:
print 'Invalid system specification'
raise
def __del__(self):
ctsGen.__del__(self)
# Register this Generator with the database
symbolMapDict = {}
# in future, provide appropriate mappings for libraries math,
# random, etc. (for now it's left to FuncSpec)
theGenSpecHelper.add(ImplicitFnGen, symbolMapDict, 'python', 'ImpFuncSpec')
# pass up to generic treatment for this
ctsGen.set(self, checklevel=kw['checklevel'])
if 'globalt0' in kw:
# pass up to generic treatment for this
ctsGen.set(self, globalt0=kw['globalt0'])
def validateSpec(self):
ctsGen.validateSpec(self)
try:
assert isoutputcts(self.indepvariable)
for v in self.variables.values():
assert isinstance(v, Variable)
assert not self.inputs
except AssertionError:
print 'Invalid system specification'
raise
def __del__(self):
ctsGen.__del__(self)
# Register this Generator with the database
symbolMapDict = {}
# in future, provide appropriate mappings for libraries math,
# random, etc. (for now it's left to FuncSpec)
theGenSpecHelper.add(ExtrapolateTable, symbolMapDict, 'python')
checklevel=self.checklevel,
FScompatibleNames=self._FScompatibleNames,
FScompatibleNamesInv=self._FScompatibleNamesInv,
modelNames=self.name,
modelEventStructs=self.eventstruct)
def validateSpec(self):
discGen.validateSpec(self)
try:
assert isoutputdiscrete(self.indepvariable)
for v in self.variables.values():
assert isinstance(v, Variable)
assert not self.inputs
except AssertionError:
print 'Invalid system specification'
raise
def __del__(self):
discGen.__del__(self)
# Register this Generator with the database
symbolMapDict = {}
# in future, provide appropriate mappings for libraries math,
# random, etc. (for now it's left to FuncSpec)
theGenSpecHelper.add(LookupTable, symbolMapDict, 'python')
if 'algparams' in kw:
for k, v in kw['algparams'].iteritems():
self._algparams[k] = v
if 'solvemethod' in self._algparams:
if self._algparams['solvemethod'] not in _implicitSolveMethods:
raise PyDSTool_ValueError, 'Invalid implicit solver type'
# for backwards compatibility
setPars = set
def validateSpec(self):
ctsGen.validateSpec(self)
try:
for v in self.variables.values():
assert isinstance(v, Variable)
assert not self.inputs
except AssertionError:
print 'Invalid system specification'
raise
def __del__(self):
ctsGen.__del__(self)
# Register this Generator with the database
symbolMapDict = {}
# in future, provide appropriate mappings for libraries math,
# random, etc. (for now it's left to FuncSpec)
theGenSpecHelper.add(ImplicitFnGen, symbolMapDict, 'python', 'ImpFuncSpec')
def JacobianP(self, t, xdict, pdict):
if self.haveJacobian_pars():
x = sortedDictValues(xdict)
p = sortedDictValues(pdict)
i = sortedDictValues(dict([(n,i(t)) for n,i in self.inputs.iteritems()]))
return apply(eval("self."+self.funcspec.auxfns["Jacobian_pars"][1]), \
[t, x, p+i])
else:
raise PyDSTool_ExistError, "Jacobian w.r.t. parameters not defined"
def AuxVars(self, t, xdict, pdict):
x = sortedDictValues(xdict)
p = sortedDictValues(pdict)
i = sortedDictValues(dict([(n,i(t)) for n,i in self.inputs.iteritems()]))
return apply(eval("self."+self.funcspec.auxspec[1]), [t, x, p+i])
def __del__(self):
discGen.__del__(self)
# Register this Generator with the database
symbolMapDict = {}
# in future, provide appropriate mappings for libraries math,
# random, etc. (for now it's left to FuncSpec)
theGenSpecHelper.add(MapSystem, symbolMapDict, 'python')
def _pollInputs(inputVarList, t, checklevel):
ilist = []
try:
for f in inputVarList:
f.clearWarnings
ilist.append(f(t, checklevel))
except AssertionError:
print 'External input call has t out of range: t = ', t
print 'Maybe checklevel is 3 and initial time is not', \
'completely inside valid time interval'
raise
except ValueError:
print 'External input call has value out of range: t = ', t
print 'Check beginning and end time of integration'
for f in inputVarList:
if len(f.warnings):
print 'External input %s out of range:' % f.name
print ' t = ', repr(f.warnings[-1][0]), ', ', \
f.name, ' = ', repr(f.warnings[-1][1])
raise
return ilist
# Register this Generator with the database
symbolMapDict = {}
# in future, provide appropriate mappings for libraries math,
# random, etc. (for now it's left to FuncSpec)
theGenSpecHelper.add(Vode_ODEsystem, symbolMapDict, 'python')
raise PyDSTool_ExistError("Jacobian w.r.t. parameters not defined")
def AuxVars(self, t, xdict, pdict=None, asarray=True):
"""asarray is an unused, dummy argument for compatibility with
Model.AuxVars"""
x = [float(val) for val in sortedDictValues(filteredDict(self._FScompatibleNames(xdict),
self.funcspec.vars))]
if pdict is None:
pdict = self.pars
# internal self.pars already is FS-compatible
p = sortedDictValues(pdict)
else:
p = sortedDictValues(self._FScompatibleNames(pdict))
i = _pollInputs(sortedDictValues(self.inputs),
t, self.checklevel)
return apply(getattr(self,self.funcspec.auxspec[1]), [t, x, p+i])
def __del__(self):
discGen.__del__(self)
# Register this Generator with the database
symbolMapDict = {}
# in future, provide appropriate mappings for libraries math,
# random, etc. (for now it's left to FuncSpec)
theGenSpecHelper.add(MapSystem, symbolMapDict, 'python')
print "Error opening file " + self._set_file + " for writing"
raise IOError, e
# Write the vfield.m file
# vfdefines = self._prepareVfieldDefines()
# allfilestr = self._prepareVfieldContents(vfdefines)
allfilestr = self.funcspec.spec[0] + self._prepareAuxContents()
vffile = os.path.join(self._target_dir, self._vfield_file)
try:
file = open(vffile, 'w')
file.write(allfilestr)
file.close()
except IOError, e:
print "Error opening file " + self._vfield_file + " for writing"
raise IOError, e
# We have omitted RHS, computeTraj, etc. because this
# class is intended solely to generate code for ADMC++, not do any integrations
# etc.
def __del__(self):
ODEsystem.__del__(self)
# Register this Generator with the database
symbolMapDict = {}
# in future, provide appropriate mappings for libraries math,
# random, etc. (for now it's left to FuncSpec)
theGenSpecHelper.add(ADMC_ODEsystem, symbolMapDict, 'matlab')