def setProfile(self, profile, xname = None, yname = None, dyname = None):
"""Assign the Profile for this FitContribution.
profile -- A Profile that specifies the calculation points and that
will store the calculated signal.
xname -- The name of the independent variable from the Profile. If
this is None (default), then the name specified by the
Profile for this parameter will be used. This variable is
usable within string equations with the specified name.
yname -- The name of the observed Profile. If this is None
(default), then the name specified by the Profile for this
parameter will be used. This variable is usable within
string equations with the specified name.
dyname -- The name of the uncertainty in the observed Profile. If
this is None (default), then the name specified by the
Profile for this parameter will be used. This variable is
usable within string equations with the specified name.
"""
# Enforce type of the profile argument
if not isinstance(profile, Profile):
emsg = "Argument must be an instance of the Profile class."
raise TypeError(emsg)
# Set the Profile and add its parameters to this organizer.
self.profile = profile
if xname is None:
xname = self.profile.xpar.name
if yname is None:
yname = self.profile.ypar.name
if dyname is None:
dyname = self.profile.dypar.name
self._xname = xname
self._yname = yname
self._dyname = dyname
xpar = ParameterProxy(xname, self.profile.xpar)
ypar = ParameterProxy(yname, self.profile.ypar)
dypar = ParameterProxy(dyname, self.profile.dypar)
self.addParameter(xpar, check = False)
self.addParameter(ypar, check = False)
self.addParameter(dypar, check = False)
# If we have ProfileGenerators, set their Profiles.
for gen in self._generators.values():
gen.setProfile(profile)
# If we have _eq, but not _reseq, set the residual
if self._eq is not None and self._reseq is None:
self.setResidualEquation('chiv')
return
def addVar(self,
par,
value=None,
name=None,
fixed=False,
tag=None,
tags=[]):
"""Add a variable to be refined.
par -- A Parameter that will be varied during a fit.
value -- An initial value for the variable. If this is None
(default), then the current value of par will be used.
name -- A name for this variable. If name is None (default), then
the name of the parameter will be used.
fixed -- Fix the variable so that it does not vary (default False).
tag -- A tag for the variable. This can be used to retrieve, fix
or free variables by tag (default None). Note that a
variable is automatically tagged with its name and "all".
tags -- A list of tags (default []). Both tag and tags can be
applied.
Returns the ParameterProxy (variable) for the passed Parameter.
Raises ValueError if the name of the variable is already taken by
another managed object.
Raises ValueError if par is constant.
Raises ValueError if par is constrained.
"""
name = name or par.name
if par.const:
raise ValueError("The parameter '%s' is constant" % par)
if par.constrained:
raise ValueError("The parameter '%s' is constrained" % par)
var = ParameterProxy(name, par)
if value is not None:
var.setValue(value)
self._addParameter(var)
if fixed:
self.fix(var)
# Tag with passed tags and by name
self._tagmanager.tag(var, var.name)
self._tagmanager.tag(var, "all")
self._tagmanager.tag(var, *tags)
if tag is not None:
self._tagmanager.tag(var, tag)
return var
def addVar(self, par, value = None, name = None, fixed = False, tag = None,
tags = []):
"""Add a variable to be refined.
par -- A Parameter that will be varied during a fit.
value -- An initial value for the variable. If this is None
(default), then the current value of par will be used.
name -- A name for this variable. If name is None (default), then
the name of the parameter will be used.
fixed -- Fix the variable so that it does not vary (default False).
tag -- A tag for the variable. This can be used to retrieve, fix
or free variables by tag (default None). Note that a
variable is automatically tagged with its name and "all".
tags -- A list of tags (default []). Both tag and tags can be
applied.
Returns the ParameterProxy (variable) for the passed Parameter.
Raises ValueError if the name of the variable is already taken by
another managed object.
Raises ValueError if par is constant.
Raises ValueError if par is constrained.
"""
name = name or par.name
if par.const:
raise ValueError("The parameter '%s' is constant"%par)
if par.constrained:
raise ValueError("The parameter '%s' is constrained"%par)
var = ParameterProxy(name, par)
if value is not None:
var.setValue(value)
self._addParameter(var)
if fixed:
self.fix(var)
# Tag with passed tags and by name
self._tagmanager.tag(var, var.name)
self._tagmanager.tag(var, "all")
self._tagmanager.tag(var, *tags)
if tag is not None:
self._tagmanager.tag(var, tag)
return var
def __addPar(self, parname, par):
"""Constrain a parameter via proxy with a specified name
par -- Parameter to constrain
idx -- Index to identify scatterer from which par comes
"""
newpar = ParameterProxy(parname, par)
self.addParameter(newpar)
return newpar
def __init__(self, name, atom):
"""Initialize
atom -- A diffpy.Structure.Atom instance
"""
ParameterSet.__init__(self, name)
self.atom = atom
a = atom
# x, y, z, occupancy
self.addParameter(
ParameterAdapter("x", a, _xyzgetter(0), _xyzsetter(0)))
self.addParameter(
ParameterAdapter("y", a, _xyzgetter(1), _xyzsetter(1)))
self.addParameter(
ParameterAdapter("z", a, _xyzgetter(2), _xyzsetter(2)))
occupancy = ParameterAdapter("occupancy", a, attr="occupancy")
self.addParameter(occupancy)
self.addParameter(ParameterProxy("occ", occupancy))
# U
self.addParameter(ParameterAdapter("U11", a, attr="U11"))
self.addParameter(ParameterAdapter("U22", a, attr="U22"))
self.addParameter(ParameterAdapter("U33", a, attr="U33"))
U12 = ParameterAdapter("U12", a, attr="U12")
U21 = ParameterProxy("U21", U12)
U13 = ParameterAdapter("U13", a, attr="U13")
U31 = ParameterProxy("U31", U13)
U23 = ParameterAdapter("U23", a, attr="U23")
U32 = ParameterProxy("U32", U23)
self.addParameter(U12)
self.addParameter(U21)
self.addParameter(U13)
self.addParameter(U31)
self.addParameter(U23)
self.addParameter(U32)
self.addParameter(ParameterAdapter("Uiso", a, attr="Uisoequiv"))
# B
self.addParameter(ParameterAdapter("B11", a, attr="B11"))
self.addParameter(ParameterAdapter("B22", a, attr="B22"))
self.addParameter(ParameterAdapter("B33", a, attr="B33"))
B12 = ParameterAdapter("B12", a, attr="B12")
B21 = ParameterProxy("B21", B12)
B13 = ParameterAdapter("B13", a, attr="B13")
B31 = ParameterProxy("B31", B13)
B23 = ParameterAdapter("B23", a, attr="B23")
B32 = ParameterProxy("B32", B23)
self.addParameter(B12)
self.addParameter(B21)
self.addParameter(B13)
self.addParameter(B31)
self.addParameter(B23)
self.addParameter(B32)
self.addParameter(ParameterAdapter("Biso", a, attr="Bisoequiv"))
# Other setup
self.__repr__ = a.__repr__
return
def testProxy(self):
"""Test the ParameterProxy class."""
l = Parameter("l", 3.14)
# Try Accessor adaptation
la = ParameterProxy("l2", l)
self.assertEqual("l2", la.name)
self.assertEqual(l.getValue(), la.getValue())
# Change the parameter
l.value = 2.3
self.assertEqual(l.getValue(), la.getValue())
self.assertEqual(l.value, la.value)
# Change the proxy
la.value = 3.2
self.assertEqual(l.getValue(), la.getValue())
self.assertEqual(l.value, la.value)
return
def testProxy(self):
"""Test the ParameterProxy class."""
l = Parameter("l", 3.14)
# Try Accessor adaptation
la = ParameterProxy("l2", l)
self.assertEqual("l2", la.name)
self.assertEqual(l.getValue(), la.getValue())
# Change the parameter
l.value = 2.3
self.assertEqual(l.getValue(), la.getValue())
self.assertEqual(l.value, la.value)
# Change the proxy
la.value = 3.2
self.assertEqual(l.getValue(), la.getValue())
self.assertEqual(l.value, la.value)
return