def __init__(self, parent):
"""
initialization
"""
RietveldClass.__init__(self, parent)
return
def __init__(self, parent):
"""
initialization
"""
RietveldClass.__init__(self, parent)
return
def __init__(self, parent):
"""
initialization
parent: None of real parent class
"""
RietveldClass.__init__(self, parent)
return
def __init__(self, parent, nbas):
"""
initialization
"""
RietveldClass.__init__(self, parent)
for i in xrange(0, nbas):
param_name = "Ireps"+str(i)
self.ParamDict[param_name] = IntInfo(param_name, "real/pure imaginary BSF coefficient flags"+str(i), 0)
self.__dict__[param_name] = self.ParamDict[param_name].get("Default")
return
def __init__(self, Parent, order=None, value=None):
"""
initialization
order: polynomial order
value: Bkgd
"""
RietveldClass.__init__(self, Parent)
if order is not None:
self.set("order", order)
if value is not None:
self.set("Bkgd", value)
return
def __init__(self, parent):
"""
initialization:
"""
RietveldClass.__init__(self, parent)
# initialize subclass-object
operatorset = OperatorSet(self)
self.set("OperatorSet", operatorset)
# initialize attributes
self._contributionlist = []
return
def __init__(self, parent):
"""
initialization:
"""
RietveldClass.__init__(self, parent)
# initialize subclass-object
operatorset = OperatorSet(self)
self.set("OperatorSet", operatorset)
# initialize attributes
self._contributionlist = []
return
def __init__(self, parent, nbas):
"""
initialization
"""
RietveldClass.__init__(self, parent)
for i in xrange(0, nbas):
param_name = "Ireps" + str(i)
self.ParamDict[param_name] = IntInfo(
param_name,
"real/pure imaginary BSF coefficient flags" + str(i), 0)
self.__dict__[param_name] = self.ParamDict[param_name].get(
"Default")
return
def set(self, param_name, value, index=None):
"""
Phase extending RietveldClass.set() method
Arguments:
param_name -- string, parameter name
value -- instance, value to set
"""
rvalue = RietveldClass.set(self, param_name, value, index=index)
if param_name == "Jvi":
self.set("More", True)
elif param_name == "Jdi":
self.set("More", True)
elif param_name == "Hel":
self.set("More", True)
elif param_name == "Sol":
self.set("More", True)
elif param_name == "Mom":
self.set("More", True)
elif param_name == "Ter":
self.set("More", True)
return rvalue
def __init__(self, Parent):
RietveldClass.__init__(self, Parent)
"""
init subclass
"""
background = Background(None)
self.set("Background", background)
lpfactor = LPFactor(None)
self.set("LPFactor", lpfactor)
# init attributes
self._contributionlist = []
self._reflections = {}
return
def __str__(self):
"""
customerized output
"""
rstring = ""
rstring += RietveldClass.__str__(self)
return rstring
def __str__(self):
"""
customerized output
"""
rstring = ""
rstring += RietveldClass.__str__(self)
return rstring
def __init__(self, parent):
"""
initialization: add a new Fit, and create the refine object belonged to this fit object
"""
RietveldClass.__init__(self, parent)
# init refine
refineobj = Refine(None)
self.set("Refine", refineobj)
# bank information: This is for some specific pattern data such as ".gss" with different bank
self.banklist = []
# internal data
self.key = ''
self._param_indices = {}
self.updateParamIndices(self._param_indices)
return
def __init__(self, parent):
"""
initialization: add a new Fit, and create the refine object belonged to this fit object
"""
RietveldClass.__init__(self, parent)
# init refine
refineobj = Refine(None)
self.set("Refine", refineobj)
# bank information: This is for some specific pattern data such as ".gss" with different bank
self.banklist = []
# internal data
self.key = ''
self._param_indices = {}
self.updateParamIndices(self._param_indices)
return
def validate(self):
"""
validate the parameters, subclass and container to meet the refinement requirement
"""
rvalue = RietveldClass.validate(self)
if self.__class__.__name__ == "FormFactor":
print "base class FormFactor is not allowed"
rvalue = False
return rvalue
def validate(self):
"""
validate the parameters, subclass and container to meet the refinement requirement
"""
rvalue = RietveldClass.validate(self)
name = self.__class__.__name__
if name == "Background":
print "base class of Background is not allowed"
rvalue = False
return rvalue
def validate(self):
"""
validate the parameters, subclass and container to meet the refinement requirement
"""
rvalue = RietveldClass.validate(self)
# type check
name = self.__class__.__name__
if name == "AtomicDisplacementFactor":
print "base class AtomicDisplacementFactor is not allowed"
rvalue = False
return rvalue
def validate(self):
"""
validate the parameters, subclass and container to meet the refinement requirement
"""
rvalue = RietveldClass.validate(self)
# type check
name = self.__class__.__name__
if name == "AtomicDisplacementFactor":
print "base class AtomicDisplacementFactor is not allowed"
rvalue = False
return rvalue
def set(self, param_name, value, index=None):
"""
function: set value to parameter 'param'
param_name: parameter name, can be (1) parameter name (2) subclass name
value : (1) corresponding python build-in type
(2) an object reference
index: for the location in ObjectListDict/ParamListDict
"""
rvalue = RietveldClass.set(self, param_name, value, index)
if param_name == "Nba":
nba = self.get(param_name)
background = None
if nba == 0:
background = BackgroundPolynomial(self)
background.set("Order", 6)
elif nba == 1:
background = BackgroundPolynomial(self)
background.set("Order", 4)
elif nba == -1:
background = BackgroundDebye(self)
elif nba == -2:
background = BackgroundFourierwindow(self)
elif nba == -3:
background = BackgroundPolynomial(self)
background.set("Order", 12)
elif nba == -4:
background = BackgroundPolynomial(self)
background.set("Order", 12)
elif nba == 2:
background = BackgroundUserDefinedLinear(self)
elif nba == -5:
background = BackgroundUserDefinedCubic(self)
else:
errmsg = "Nba = %-10s is not supported" % (nba)
raise RietError, errmsg
if background is not None:
self.set("Background", background)
else:
pass
return rvalue
def validate(self):
"""
validate of class Phase
"""
rvalue = RietveldClass.validate(self)
errmsg = ""
# FullProf parameter synchronization
# atom
nat = len(self.get("Atom"))
self.set("Nat", nat)
# dis
dis = len(self.get("DistanceRestraint"))
self.set("Dis", dis)
# momma
ang = len(self.get("AngleRestraint"))
mom = len(self.get("MomentRestraint"))
if ang != 0 and mom != 0:
raise NotImplementedError, "Angular Restraint and Moment Restraint cannot be used simultaneously"
self.set("MomMA", ang + mom)
# nvk
nvk = len(self.get("PropagationVector"))
self.set("Nvk", nvk)
# Situation validation
# 1. Jbt and Atom Number
jbt = self.get("Jbt")
if abs(jbt) != 2 and nat == 0:
# not Le-Bail (profile match)
rvalue = False
errmsg += "No Atom is defined while Jbt = %-5s (Not Le-Bail)" % (
jbt)
# error message output
if errmsg != "":
prtmsg = "Phase Invalid Setup: %-60s" % (errmsg)
print prtmsg
if rvalue is not True:
print "Invalidity Deteced In %-10s" % (self.__class__.__name__)
return rvalue
def validate(self):
"""
validate of class Phase
"""
rvalue = RietveldClass.validate(self)
errmsg = ""
# FullProf parameter synchronization
# atom
nat = len(self.get("Atom"))
self.set("Nat", nat)
# dis
dis = len(self.get("DistanceRestraint"))
self.set("Dis", dis)
# momma
ang = len(self.get("AngleRestraint"))
mom = len(self.get("MomentRestraint"))
if ang != 0 and mom != 0:
raise NotImplementedError, "Angular Restraint and Moment Restraint cannot be used simultaneously"
self.set("MomMA", ang+mom)
# nvk
nvk = len(self.get("PropagationVector"))
self.set("Nvk", nvk)
# Situation validation
# 1. Jbt and Atom Number
jbt = self.get("Jbt")
if abs(jbt) != 2 and nat == 0:
# not Le-Bail (profile match)
rvalue = False
errmsg += "No Atom is defined while Jbt = %-5s (Not Le-Bail)"% (jbt)
# error message output
if errmsg != "":
prtmsg = "Phase Invalid Setup: %-60s"% (errmsg)
print prtmsg
if rvalue is not True:
print "Invalidity Deteced In %-10s"% (self.__class__.__name__)
return rvalue
def set(self, param_name, value, index=None):
"""
Phase extending RietveldClass.set() method
Arguments:
param_name -- string, parameter name
value -- instance, value to set
"""
rvalue = RietveldClass.set(self, param_name, value, index=index)
if param_name == "Jvi":
self.set("More", True)
elif param_name == "Jdi":
self.set("More", True)
elif param_name == "Hel":
self.set("More", True)
elif param_name == "Sol":
self.set("More", True)
elif param_name == "Mom":
self.set("More", True)
elif param_name == "Ter":
self.set("More", True)
return rvalue
def validate(self):
"""
validate the parameters, subclass and container to meet the refinement requirement of
class Pattern
Return -- bool
"""
from diffpy.pyfullprof.utilfunction import checkFileExistence
rvalue = RietveldClass.validate(self)
errmsg = ""
# type check: virtual base class
name = self.__class__.__name__
if name == "Pattern":
errmsg += "%-30s: %-40s"%("Pattern.validate()", "virtual base Pattern")
print errmsg
rvalue = False
# FullProf Parameter Synchronization
# 1. Excluded Region
nex = len(self.get("ExcludedRegion"))
self.set("Nex", nex)
# 2. Scttering Factor
nsc = len(self.get("ScatterFactor"))
self.set("Nsc", nsc)
# 3. background
background = self.get("Background")
if isinstance(background, BackgroundUserDefinedLinear):
#NOTE: avoid using self.set('Nba', 2)
self.Nba = 2
elif isinstance(background, BackgroundUserDefinedCubic):
#NOTE: avoid using self.set('Nba', -5)
self.Nba = -5
elif isinstance(background, BackgroundFourierwindow):
#NOTE: avoid using self.set('Nba', -2)
self.Nba = -2
elif isinstance(background, BackgroundPolynomial):
if background.get("Order") == 6:
#NOTE: avoid using self.set('Nba', 0)
self.Nba = 0
elif background.get("Order") == 12:
#NOTE: avoid using self.set('Nba', -4)
self.Nba = -4
else:
errmsg = "Polynomial Order = %-4s Is Not Supported"% (background.get("Order"))
raise NotImplementedError(errmsg)
else:
pass
if self.get("Nba") <= -5 or self.get("Nba") >= 2:
self.set('NbaPoint', self.get("Background").size())
if background.ParamDict.has_key("Bkpos"):
self.set('Bkpos', self.get("Background").get("Bkpos"))
# 4. output
self.set("Ipr", 3)
if self.get("Prf") == 0:
self.set("Prf", 3)
# 5. peak profile Npr
for contribution in self._contributionlist:
npr = contribution.get("Npr")
self.set("Npr", npr)
# WZ: this section (item 6) is removed as all wdt from fit should be trustful
# 6. Peak range
# for contribution in self._contributionlist:
# wdt = contribution.get("Profile").get("PeakRange")
# if wdt > 0.0:
# self.set("Wdt", wdt)
wdt = self.get("Wdt")
if wdt <= 0.0:
errmsg = String.Format("Pattern has Wdt (peak range) = %f <= 0") % (wdt)
raise RietError(errmsg)
# Check Valid
# 1. resolution file
if self.get("Res") != 0:
exist = checkFileExistence(self.get("Resofile"))
if not exist:
rvalue = False
errmsg += "Resolution File %-10s Cannot Be Found\n"% (self.get("Resofile"))
# 2. data file.... -> moved to Fit.validate()
if rvalue is not True:
print "Invalidity Detected In %-10s: %-60s"% (self.__class__.__name__, errmsg)
return rvalue
def validate(self, mode="Refine"):
"""
validate the parameters, subclass and container to meet the refinement requirement
Arguments
- mode : string, validate mode, (Refine, Calculate)
Return : Boolean
"""
rvalue = RietveldClass.validate(self)
errmsg = ""
# I. Synchronization of FulProf Parameter & Check Data File Existence
for pattern in self.get("Pattern"):
# 2.1 data file existence
if mode == "Refine":
exist = checkFileExistence(pattern.get("Datafile"))
if not exist:
rvalue = False
errmsg += "Data File %-10s Cannot Be Found\n"% (pattern.get("Datafile"))
# 2. Nre
nre = 0
for variable in self.get("Refine").get("Variable"):
if variable.get("usemin") is True:
nre += 1
# End -- for variable in ...
self.set("Nre", nre)
# Check Validity
# 1. parameter
if self.get("NCY") < 1:
rvalue = False
# 2. .hkl file
# the reason why not put the checking .hkl file in Contribution is that
# there is a sequence number related between pattern sequence
# within contribution, it is hard to get this number
for pattern in self.get("Pattern"):
# scan all Phases
pindex = 1
fnamer = pattern.get("Datafile").split(".")[0]
usehkl = False
for phase in self.get("Phase"):
# get contribution
contribution = self.getContribution(pattern, phase)
if contribution is not None and contribution.get("Irf") == 2:
# using reflection
usehkl = True
# check single phase/contribution hkl file
hklfname = fnamer+str(pindex)+".hkl"
try:
hklfile = open(hklfname, "r")
hklfile.close()
except IOError, err:
# if no such file exits, update Irf to 0
contribution.set("Irf", 0)
# error message output
errmsg += "Fit.validate(): Reflection File %-10s Cannot Be Found: "% (hklfname)
errmsg += "Chaning Contribution.Irf to 0 ... Related to Phase[%-5s]"% (pindex)
print errmsg
# End -- if contribution is not None and Irf == 2:
pindex += 1
# End -- for phase in self.get("Phase"):
if usehkl is True:
# check overall hkl file
hklfname = fnamer+".hkl"
try:
hklfile = open(hklfname, "r")
hklfile.close()
except IOError, err:
# if no such file exists, update all Irf to 0
for contribution in self.get("Contribution"):
contribution.set("Irf", 0)
def __init__(self, Parent):
RietveldClass.__init__(self, Parent)
return
def __init__(self, Parent):
RietveldClass.__init__(self, Parent)
return
def validate(self, mode="Refine"):
"""
validate the parameters, subclass and container to meet the refinement requirement
Arguments
- mode : string, validate mode, (Refine, Calculate)
Return : Boolean
"""
rvalue = RietveldClass.validate(self)
errmsg = ""
# I. Synchronization of FulProf Parameter & Check Data File Existence
for pattern in self.get("Pattern"):
# 2.1 data file existence
if mode == "Refine":
exist = checkFileExistence(pattern.get("Datafile"))
if not exist:
rvalue = False
errmsg += "Data File %-10s Cannot Be Found\n" % (
pattern.get("Datafile"))
# 2. Nre
nre = 0
for variable in self.get("Refine").get("Variable"):
if variable.get("usemin") is True:
nre += 1
# End -- for variable in ...
self.set("Nre", nre)
# Check Validity
# 1. parameter
if self.get("NCY") < 1:
rvalue = False
# 2. .hkl file
# the reason why not put the checking .hkl file in Contribution is that
# there is a sequence number related between pattern sequence
# within contribution, it is hard to get this number
for pattern in self.get("Pattern"):
# scan all Phases
pindex = 1
fnamer = pattern.get("Datafile").split(".")[0]
usehkl = False
for phase in self.get("Phase"):
# get contribution
contribution = self.getContribution(pattern, phase)
if contribution is not None and contribution.get("Irf") == 2:
# using reflection
usehkl = True
# check single phase/contribution hkl file
hklfname = fnamer + str(pindex) + ".hkl"
try:
hklfile = open(hklfname, "r")
hklfile.close()
except IOError, err:
# if no such file exits, update Irf to 0
contribution.set("Irf", 0)
# error message output
errmsg += "Fit.validate(): Reflection File %-10s Cannot Be Found: " % (
hklfname)
errmsg += "Chaning Contribution.Irf to 0 ... Related to Phase[%-5s]" % (
pindex)
print errmsg
# End -- if contribution is not None and Irf == 2:
pindex += 1
# End -- for phase in self.get("Phase"):
if usehkl is True:
# check overall hkl file
hklfname = fnamer + ".hkl"
try:
hklfile = open(hklfname, "r")
hklfile.close()
except IOError, err:
# if no such file exists, update all Irf to 0
for contribution in self.get("Contribution"):
contribution.set("Irf", 0)
