def fit(self, name, free_pars, parest=None):
"""Fit an individual candidate model in its context,
peforming parameter optimization on the given free parameters.
"""
model = self.manager[name]
assert remain(free_pars, model.pars) == [], "Invalid free variables"
model.set(verboselevel=self.verboselevel)
# get initial results of context at default parameters
# if success then done already
if self.context.evaluate(model):
return filteredDict(model.pars, free_pars)
# determine parameter sensitivity of the free parameters
# dict of par -> sensitivity
#sens = param_sensitivity(model, self.context, free_pars)
print("Get pre-defined tols from features somehow")
print("Establish parameter estimation class and run it")
def fit(self, name, free_pars, parest=None):
"""Fit an individual candidate model in its context,
peforming parameter optimization on the given free parameters.
"""
model = self.manager[name]
assert remain(free_pars, model.pars) == [], "Invalid free variables"
model.set(verboselevel=self.verboselevel)
# get initial results of context at default parameters
# if success then done already
if self.context.evaluate(model):
return filteredDict(model.pars, free_pars)
# determine parameter sensitivity of the free parameters
# dict of par -> sensitivity
#sens = param_sensitivity(model, self.context, free_pars)
print("Get pre-defined tols from features somehow")
print("Establish parameter estimation class and run it")
def newCurve(self, initargs):
"""Create new curve with arguments specified in the dictionary initargs."""
curvetype = initargs['type'].upper()
if curvetype not in self.curve_list:
raise PyDSTool_TypeError(str(curvetype) + ' not an allowable curve type')
# Check name
cname = initargs['name']
if 'force' in initargs:
if initargs['force'] and cname in self.curves:
del self.curves[cname]
if cname in self.curves:
raise ValueError('Ambiguous name field: ' + cname \
+ ' already exists (use force=True to override)')
# Check parameters
if (curvetype != 'UD-C' and self.model.pars == {}) or \
(curvetype == 'UD-C' and 'userpars' not in initargs):
raise ValueError('No parameters defined for this system!')
# Process initial point
initargs = initargs.copy() # ensures no side-effects outside
if 'initpoint' not in initargs or initargs['initpoint'] is None:
# Default to initial conditions for model
if self.model.icdict == {}:
raise ValueError('No initial point defined for this system!')
elif 'uservars' in initargs:
if remain(initargs['uservars'], self.model.icdict.keys()) == []:
# uservars just used to select a subset of system's regular state vars
initargs['initpoint'] = filteredDict(self.model.icdict,
initargs['uservars'])
else:
raise ValueError('No initial point defined for this system!')
else:
initargs['initpoint'] = self.model.icdict.copy()
#for p in initargs['freepars']:
# initargs['initpoint'][p] = self.model.pars[p]
else:
if isinstance(initargs['initpoint'], dict):
initargs['initpoint'] = initargs['initpoint'].copy()
#for p in initargs['freepars']:
# if p not in initargs['initpoint'].keys():
# initargs['initpoint'][p] = self.model.pars[p]
elif isinstance(initargs['initpoint'], str):
curvename, pointname = initargs['initpoint'].split(':')
pointtype = pointname.strip('0123456789')
if curvename not in self.curves:
raise KeyError('No curve of name ' + curvename + ' exists.')
else:
point = self.curves[curvename].getSpecialPoint(pointtype, pointname)
if point is None:
raise KeyError('No point of name ' + pointname + ' exists.')
else:
initargs['initpoint'] = point
# Separate from if-else above since 'str' clause returns type Point
if isinstance(initargs['initpoint'], Point):
# Check to see if point contains a cycle. If it does, assume
# we are starting at a cycle and save it in initcycle
for v in initargs['initpoint'].labels.values():
if 'cycle' in v:
initargs['initcycle'] = v # Dictionary w/ cycle, name, and tangent information
# Save initial point information
initPoint = {}
if 'curvename' in locals() and curvename in self.curves:
initPoint = self.curves[curvename].parsdict.copy()
initPoint.update(initargs['initpoint'].copy().todict())
initargs['initpoint'] = initPoint
# initargs['initpoint'] = initargs['initpoint'].copy().todict()
#for p in initargs['freepars']:
# if p not in initargs['initpoint'].keys():
# initargs['initpoint'][p] = self.model.pars[p]
# Process cycle
if 'initcycle' in initargs:
if isinstance(initargs['initcycle'], ndarray):
c0 = {}
c0['data'] = args(V = {'udotps': None, 'rldot': None})
c0['cycle'] = Pointset({'coordnames': self.gensys.funcspec.vars,
'coordarray': initargs['initcycle'][1:,:].copy(),
'indepvarname': 't',
'indepvararray': initargs['initcycle'][0,:].copy()
})
initargs['initcycle'] = c0
elif isinstance(initargs['initcycle'], Pointset):
c0 = {}
c0['data'] = args(V = {'udotps': None, 'rldot': None})
c0['cycle'] = initargs['initcycle']
initargs['initcycle'] = c0
# Load auto module if required
automod = None
if curvetype in auto_list:
if self._autoMod is None:
self.loadAutoMod()
automod = self._autoMod
self.curves[cname] = self.curve_list[curvetype](self.model, self.gensys, automod, self.plot, initargs)
def newCurve(self, initargs):
"""Create new curve with arguments specified in the dictionary initargs."""
curvetype = initargs['type'].upper()
if curvetype not in self.curve_list:
raise PyDSTool_TypeError(
str(curvetype) + ' not an allowable curve type')
# Check name
cname = initargs['name']
if 'force' in initargs:
if initargs['force'] and cname in self.curves:
del self.curves[cname]
if cname in self.curves:
raise ValueError('Ambiguous name field: ' + cname \
+ ' already exists (use force=True to override)')
# Check parameters
if (curvetype != 'UD-C' and self.model.pars == {}) or \
(curvetype == 'UD-C' and 'userpars' not in initargs):
raise ValueError('No parameters defined for this system!')
# Process initial point
initargs = initargs.copy() # ensures no side-effects outside
if 'initpoint' not in initargs or initargs['initpoint'] is None:
# Default to initial conditions for model
if self.model.icdict == {}:
raise ValueError('No initial point defined for this system!')
elif 'uservars' in initargs:
if remain(initargs['uservars'],
self.model.icdict.keys()) == []:
# uservars just used to select a subset of system's regular state vars
initargs['initpoint'] = filteredDict(
self.model.icdict, initargs['uservars'])
else:
raise ValueError(
'No initial point defined for this system!')
else:
initargs['initpoint'] = self.model.icdict.copy()
#for p in initargs['freepars']:
# initargs['initpoint'][p] = self.model.pars[p]
else:
if isinstance(initargs['initpoint'], dict):
initargs['initpoint'] = initargs['initpoint'].copy()
#for p in initargs['freepars']:
# if p not in initargs['initpoint'].keys():
# initargs['initpoint'][p] = self.model.pars[p]
elif isinstance(initargs['initpoint'], str):
curvename, pointname = initargs['initpoint'].split(':')
pointtype = pointname.strip('0123456789')
if curvename not in self.curves:
raise KeyError('No curve of name ' + curvename +
' exists.')
else:
point = self.curves[curvename].getSpecialPoint(
pointtype, pointname)
if point is None:
raise KeyError('No point of name ' + pointname +
' exists.')
else:
initargs['initpoint'] = point
# Separate from if-else above since 'str' clause returns type Point
if isinstance(initargs['initpoint'], Point):
# Check to see if point contains a cycle. If it does, assume
# we are starting at a cycle and save it in initcycle
for v in initargs['initpoint'].labels.values():
if 'cycle' in v:
initargs[
'initcycle'] = v # Dictionary w/ cycle, name, and tangent information
# Save initial point information
initPoint = {}
if 'curvename' in locals() and curvename in self.curves:
initPoint = self.curves[curvename].parsdict.copy()
initPoint.update(initargs['initpoint'].copy().todict())
initargs['initpoint'] = initPoint
# initargs['initpoint'] = initargs['initpoint'].copy().todict()
#for p in initargs['freepars']:
# if p not in initargs['initpoint'].keys():
# initargs['initpoint'][p] = self.model.pars[p]
# Process cycle
if 'initcycle' in initargs:
if isinstance(initargs['initcycle'], ndarray):
c0 = {}
c0['data'] = args(V={'udotps': None, 'rldot': None})
c0['cycle'] = Pointset({
'coordnames':
self.gensys.funcspec.vars,
'coordarray':
initargs['initcycle'][1:, :].copy(),
'indepvarname':
't',
'indepvararray':
initargs['initcycle'][0, :].copy()
})
initargs['initcycle'] = c0
elif isinstance(initargs['initcycle'], Pointset):
c0 = {}
c0['data'] = args(V={'udotps': None, 'rldot': None})
c0['cycle'] = initargs['initcycle']
initargs['initcycle'] = c0
# Load auto module if required
automod = None
if curvetype in auto_list:
if self._autoMod is None:
self.loadAutoMod()
automod = self._autoMod
self.curves[cname] = self.curve_list[curvetype](self.model,
self.gensys, automod,
self.plot, initargs)
