def __init__(self, name, stru):
"""Initialize
name -- A name for this
stru -- A CCTBX structure instance.
"""
ParameterSet.__init__(self, name)
self.stru = stru
self.addParameterSet(CCTBXUnitCellParSet(self))
self.scatterers = []
self._update = False
cdict = {}
for s in stru.scatterers():
el = s.element_symbol()
i = cdict.get(el, 0)
sname = "%s%i" % (el, i)
cdict[el] = i + 1
scatterer = CCTBXScattererParSet(sname, self, i)
self.addParameterSet(scatterer)
self.scatterers.append(scatterer)
# Constrain the lattice
from diffpy.srfit.structure.sgconstraints import _constrainSpaceGroup
symbol = self.getSpaceGroup()
_constrainSpaceGroup(self, symbol)
return
def __init__(self, name):
"""Initialize the attributes."""
Operator.__init__(self)
ParameterSet.__init__(self, name)
self.profile = None
self.meta = {}
return
def __init__(self, name):
ParameterSet.__init__(self, name)
self.meta = {}
# Initialize Operator attributes
Operator.__init__(self, name, name, self.operation, -1, 1)
return
def __init__(self, name, stru):
"""Initialize
name -- A name for this
stru -- A CCTBX structure instance.
"""
ParameterSet.__init__(self, name)
self.stru = stru
self.addParameterSet(CCTBXUnitCellParSet(self))
self.scatterers = []
self._update = False
cdict = {}
for s in stru.scatterers():
el = s.element_symbol()
i = cdict.get(el, 0)
sname = "%s%i"%(el,i)
cdict[el] = i+1
scatterer = CCTBXScattererParSet(sname, self, i)
self.addParameterSet(scatterer)
self.scatterers.append(scatterer)
# Constrain the lattice
from diffpy.srfit.structure.sgconstraints import _constrainSpaceGroup
symbol = self.getSpaceGroup()
_constrainSpaceGroup(self, symbol)
return
def __init__(self, strups):
"""Initialize
strups -- The CCTBXCrystalParSet that contains the cctbx structure
and the unit cell we're wrapper.
"""
ParameterSet.__init__(self, "unitcell")
self.strups = strups
self._latpars = list(self.strups.stru.unit_cell().parameters())
self.addParameter(ParameterAdapter("a", None, self._latgetter(0),
self._latsetter(0)))
self.addParameter(ParameterAdapter("b", None, self._latgetter(1),
self._latsetter(1)))
self.addParameter(ParameterAdapter("c", None, self._latgetter(2),
self._latsetter(2)))
self.addParameter(ParameterAdapter("alpha", None, self._latgetter(3),
self._latsetter(3)))
self.addParameter(ParameterAdapter("beta", None, self._latgetter(4),
self._latsetter(4)))
self.addParameter(ParameterAdapter("gamma", None, self._latgetter(5),
self._latsetter(5)))
return
def __init__(self, name):
ParameterSet.__init__(self, name)
self.meta = {}
# Initialize Operator attributes
Operator.__init__(self, name)
return
def __init__(self, lattice):
"""Initialize
lattice -- A diffpy.Structure.Lattice instance
"""
ParameterSet.__init__(self, "lattice")
self.angunits = "deg"
self.lattice = lattice
l = lattice
self.addParameter(
ParameterAdapter("a", l, _latgetter("a"), _latsetter("a")))
self.addParameter(
ParameterAdapter("b", l, _latgetter("b"), _latsetter("b")))
self.addParameter(
ParameterAdapter("c", l, _latgetter("c"), _latsetter("c")))
self.addParameter(
ParameterAdapter("alpha", l, _latgetter("alpha"),
_latsetter("alpha")))
self.addParameter(
ParameterAdapter("beta", l, _latgetter("beta"),
_latsetter("beta")))
self.addParameter(
ParameterAdapter("gamma", l, _latgetter("gamma"),
_latsetter("gamma")))
# Other setup
self.__repr__ = l.__repr__
return
def __init__(self, name):
"""Initialize the attributes."""
Operator.__init__(self)
ParameterSet.__init__(self, name)
self.profile = None
self.meta = {}
return
def __init__(self, lattice):
"""Initialize
lattice -- A diffpy.Structure.Lattice instance
"""
ParameterSet.__init__(self, "lattice")
self.angunits = "deg"
self.lattice = lattice
l = lattice
self.addParameter(ParameterAdapter("a", l, _latgetter("a"),
_latsetter("a")))
self.addParameter(ParameterAdapter("b", l, _latgetter("b"),
_latsetter("b")))
self.addParameter(ParameterAdapter("c", l, _latgetter("c"),
_latsetter("c")))
self.addParameter(ParameterAdapter("alpha", l, _latgetter("alpha"),
_latsetter("alpha")))
self.addParameter(ParameterAdapter("beta", l, _latgetter("beta"),
_latsetter("beta")))
self.addParameter(ParameterAdapter("gamma", l, _latgetter("gamma"),
_latsetter("gamma")))
# Other setup
self.__repr__ = l.__repr__
return
def __init__(self, strups):
"""Initialize
strups -- The CCTBXCrystalParSet that contains the cctbx structure
and the unit cell we're wrapper.
"""
ParameterSet.__init__(self, "unitcell")
self.strups = strups
self._latpars = list(self.strups.stru.unit_cell().parameters())
self.addParameter(
ParameterAdapter("a", None, self._latgetter(0),
self._latsetter(0)))
self.addParameter(
ParameterAdapter("b", None, self._latgetter(1),
self._latsetter(1)))
self.addParameter(
ParameterAdapter("c", None, self._latgetter(2),
self._latsetter(2)))
self.addParameter(
ParameterAdapter("alpha", None, self._latgetter(3),
self._latsetter(3)))
self.addParameter(
ParameterAdapter("beta", None, self._latgetter(4),
self._latsetter(4)))
self.addParameter(
ParameterAdapter("gamma", None, self._latgetter(5),
self._latsetter(5)))
return
def __init__(self, name, strups, idx):
"""Initialize
name -- The name of this scatterer.
strups -- The CCTBXCrystalParSet that contains the cctbx structure
idx -- The index of the scatterer in the structure.
"""
ParameterSet.__init__(self, name)
self.strups = strups
self.idx = idx
# x, y, z, occupancy
self.addParameter(
ParameterAdapter("x", None, self._xyzgetter(0),
self._xyzsetter(0)))
self.addParameter(
ParameterAdapter("y", None, self._xyzgetter(1),
self._xyzsetter(1)))
self.addParameter(
ParameterAdapter("z", None, self._xyzgetter(2),
self._xyzsetter(2)))
self.addParameter(
ParameterAdapter("occupancy", None, self._getocc, self._setocc))
self.addParameter(
ParameterAdapter("Uiso", None, self._getuiso, self._setuiso))
return
def __init__(self, name):
"""Initialize the attributes."""
ParameterSet.__init__(self, name)
self.profile = None
self.meta = {}
# Operator attributes
Operator.__init__(self, name, name, self.operation, 0, 1)
return
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 __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 __init__(self, name):
"""Initialize the attributes."""
ParameterSet.__init__(self, name)
self.profile = None
self.meta = {}
# Operator attributes
Operator.__init__(self, name, name, self.operation, 0, 1)
return
def __init__(self, name):
"""Initialization."""
ParameterSet.__init__(self, name)
self._eq = None
self._reseq = None
self.profile = None
self._xname = None
self._yname = None
self._dyname = None
self._generators = {}
self._manage(self._generators)
return
def __init__(self, name):
"""Initialization."""
ParameterSet.__init__(self, name)
self._eq = None
self._reseq = None
self.profile = None
self._xname = None
self._yname = None
self._dyname = None
self._generators = {}
self._manage(self._generators)
return
def _validate(self):
"""Validate my state.
This performs ParameterSet validations.
This does not validate the operation, since this could be costly. The
operation should be validated with a containing equation.
Raises AttributeError if validation fails.
"""
ParameterSet._validate(self)
return
def _validate(self):
"""Validate my state.
This performs ParameterSet validations.
This does not validate the operation, since this could be costly. The
operation should be validated with a containing equation.
Raises AttributeError if validation fails.
"""
ParameterSet._validate(self)
return
def _validate(self):
"""Validate my state.
This performs profile validations.
This performs ParameterSet validations.
This does not validate the operation, since this could be costly. The
operation should be validated with a containing equation.
Raises SrFitError if validation fails.
"""
if self.profile is None:
raise SrFitError("profile is None")
self.profile._validate()
ParameterSet._validate(self)
return
def _validate(self):
"""Validate my state.
This performs profile validations.
This performs ParameterSet validations.
This does not validate the operation, since this could be costly. The
operation should be validated with a containing equation.
Raises SrFitError if validation fails.
"""
if self.profile is None:
raise SrFitError("profile is None")
self.profile._validate()
ParameterSet._validate(self)
return
def testAddParameterSet(self):
"""Test the addParameterSet method."""
parset2 = ParameterSet("parset2")
p1 = Parameter("parset2", 1)
self.parset.addParameterSet(parset2)
self.assertTrue(self.parset.parset2 is parset2)
self.assertRaises(ValueError, self.parset.addParameterSet, p1)
p1.name = "p1"
parset2.addParameter(p1)
self.assertTrue(self.parset.parset2.p1 is p1)
return
def testAddParameterSet(self):
"""Test the addParameterSet method."""
parset2 = ParameterSet("parset2")
p1 = Parameter("parset2", 1)
self.parset.addParameterSet(parset2)
self.assertTrue(self.parset.parset2 is parset2)
self.assertRaises(ValueError, self.parset.addParameterSet, p1)
p1.name = "p1"
parset2.addParameter(p1)
self.assertTrue(self.parset.parset2.p1 is p1)
return
def _validate(self):
"""Validate my state.
This performs profile validations.
This performs ProfileGenerator validations.
This validates _eq.
This validates _reseq and residual.
Raises SrFitError if validation fails.
"""
self.profile._validate()
ParameterSet._validate(self)
# Try to get the value of eq.
from diffpy.srfit.equation.visitors import validate
try:
validate(self._eq)
except ValueError as e:
raise SrFitError(e)
if self._eq is None:
raise SrFitError("_eq is None")
val = None
try:
val = self._eq()
except TypeError as e:
raise SrFitError("_eq cannot be evaluated: %s"%e)
if val is None:
raise SrFitError("_eq evaluates to None")
# Try to get the value for residual
try:
validate(self._reseq)
except ValueError as e:
raise SrFitError(e)
try:
val = self.residual()
except TypeError:
raise SrFitError("residual cannot be evaluated")
if val is None:
raise SrFitError("residual evaluates to None")
return
def _validate(self):
"""Validate my state.
This performs profile validations.
This performs ProfileGenerator validations.
This validates _eq.
This validates _reseq and residual.
Raises AttributeError if validation fails.
"""
self.profile._validate()
ParameterSet._validate(self)
# Try to get the value of eq.
from diffpy.srfit.equation.visitors import validate
try:
validate(self._eq)
except ValueError, e:
raise AttributeError(e)
def _validate(self):
"""Validate my state.
This performs profile validations.
This performs ProfileGenerator validations.
This validates _eq.
This validates _reseq and residual.
Raises SrFitError if validation fails.
"""
self.profile._validate()
ParameterSet._validate(self)
# Try to get the value of eq.
from diffpy.srfit.equation.visitors import validate
try:
validate(self._eq)
except ValueError, e:
raise SrFitError(e)
class TestParameterSet(unittest.TestCase):
def setUp(self):
self.parset = ParameterSet("test")
return
def testAddParameterSet(self):
"""Test the addParameterSet method."""
parset2 = ParameterSet("parset2")
p1 = Parameter("parset2", 1)
self.parset.addParameterSet(parset2)
self.assertTrue(self.parset.parset2 is parset2)
self.assertRaises(ValueError, self.parset.addParameterSet, p1)
p1.name = "p1"
parset2.addParameter(p1)
self.assertTrue(self.parset.parset2.p1 is p1)
return
class TestParameterSet(unittest.TestCase):
def setUp(self):
self.parset = ParameterSet("test")
return
def testAddParameterSet(self):
"""Test the addParameterSet method."""
parset2 = ParameterSet("parset2")
p1 = Parameter("parset2", 1)
self.parset.addParameterSet(parset2)
self.assertTrue(self.parset.parset2 is parset2)
self.assertRaises(ValueError, self.parset.addParameterSet, p1)
p1.name = "p1"
parset2.addParameter(p1)
self.assertTrue(self.parset.parset2.p1 is p1)
return
def __init__(self, name, strups, idx):
"""Initialize
name -- The name of this scatterer.
strups -- The CCTBXCrystalParSet that contains the cctbx structure
idx -- The index of the scatterer in the structure.
"""
ParameterSet.__init__(self, name)
self.strups = strups
self.idx = idx
# x, y, z, occupancy
self.addParameter(ParameterAdapter("x", None, self._xyzgetter(0),
self._xyzsetter(0)))
self.addParameter(ParameterAdapter("y", None, self._xyzgetter(1),
self._xyzsetter(1)))
self.addParameter(ParameterAdapter("z", None, self._xyzgetter(2),
self._xyzsetter(2)))
self.addParameter(ParameterAdapter("occupancy", None, self._getocc,
self._setocc))
self.addParameter(ParameterAdapter("Uiso", None, self._getuiso,
self._setuiso))
return
def setUp(self):
self.parset = ParameterSet("test")
return
def setUp(self):
self.parset = ParameterSet("test")
return