def _checkNameIndex(self, name, index):
"""check the validity of the name and index passed to set/get/remove constraints
name -- the parameter name
index -- the index in the parameter list
raise: RietError if name or index is not right.
"""
if self.ParamDict.has_key(name):
if index is not None:
raise RietError('The parameter "%s" is not a list.' % name)
return
if self.ParamListDict.has_key(name):
if not isinstance(index, int):
raise RietError(
'The parameter list needs an int for index, but "%s"=%s is received.'
% (type(index), str(index)))
return
# otherwise, there is no key.
raise RietError(
"Class %s does not have a parameter or parameter list: %s" %
(self.__class__.__name__, name))
return
def linkConstraint(self):
"""Link all the constraints to the fit object.
called after duplicate() when a new-object is added to the Fit regime
refine: Refine object
"""
from diffpy.pyfullprof.fit import Fit
if isinstance(self, Fit):
_fit = self
else:
_fit = self.getFit()
if _fit:
refine = _fit.get("Refine")
else:
# Should not happen, this is checked in the "set" function
# which is the only one calling this function.
raise RietError("No Fit is created.")
for constraint in self.constraints.values():
constraint.refine = refine
constraint.apply()
for name in self.ObjectDict.keys():
o = self.__dict__[name]
if o: # it may be None
o.linkConstraint()
for name in self.ObjectListDict.keys():
for o in self.__dict__[name]._list:
o.linkConstraint()
return
def adaptPyFullProftoSrRietveld(self,
srtype,
processdir,
weightscheme="standard"):
""" Change some setting to FullProf from SrRietveld """
if srtype == "l":
# Lebail: set Jbt -> Profile Matching Mode, and Auto-calculate
# FIXME In advanced mode, if Fit can capture mult-step refine, Irf=2 in step>1 refine
for phase in self.get("Phase"):
phase.set("Jbt", 2)
self.Jbt = 2
for contr in self.get("Contribution"):
contr.set("Irf", 0)
elif srtype == "r":
# Rietveld
for phase in self.get("Phase"):
phase.set("Jbt", 0)
self.Jbt = 0
# END-IF: if srtype
for pattern in self.get("Pattern"):
if weightscheme[0] == "s":
pattern.set("Iwg", 0)
elif weightscheme[0] == "u":
pattern.set("Iwg", 2)
else:
errmsg = "Weighting Scheme %-10s Is Not Supported" % (
weightscheme)
raise RietError(errmsg)
return
def validate(self):
"""
validating before refinement
"""
rvalue = BackgroundUserDefined.validate(self)
if self.size() < 4:
errmsg = "BackgroundUserDefinedCubic number of background point = %-5s < 4"% \
(self.size())
raise RietError(errmsg)
return rvalue
def importUncertaintyOutFile(self):
"""
parse the .out file and put the data information to a database
Return : None
"""
lineslist = self.readFile(self._outfilename)
# 1. File Flag Line
startlinenum = -1
for lindex in xrange(len(lineslist)):
if lineslist[lindex].count(self._FLAG2) == 1:
startlinenum = lindex
break
if startlinenum < 0:
raise RietError()
# 2. Get Informative Lines:
infolineslist = []
for lindex in xrange(startlinenum + 1, len(lineslist)):
candline = lineslist[lindex]
# 1. Find stop line
if candline[0] == "=" and candline[1] == ">":
break
# 2. Judge
if candline.count(self._FLAG3) > 0:
infolineslist.append(candline)
# LOOP-OVER: for lindex in xrange( startlinenum+1, len(lineslist) )
# 3. Parse to standard database
for line in infolineslist:
terms = line.split(":")[1].split("+/-")
tp1 = terms[0].split()
tp2 = terms[1].split()
name = tp1[0]
valstr = tp1[1].split("(")[0]
val = float(valstr)
sigstr = tp2[0]
sig = float(sigstr)
nameinfotuple = self.parseNameOutFile(name)
self._ParameterList.append((nameinfotuple, val, sig))
# LOOP-OVER: for line in infolineslist
return
def importUncertainty(self):
"""
Parse the input file and put the data information to a database
Return : None
"""
if self._outfilename is not None:
self.importUncertaintyOutFile()
elif self._sumfilename is not None:
self.importUncertaintySumFile()
else:
raise RietError()
return
def getRefineResult(self, fitsummary, srtype, pcrfullname):
""" get out Refinement results
"""
import diffpy.pyfullprof.fpoutputfileparsers as FPP
newfit = fitsummary.getFit()
if isinstance(newfit, Fit):
self.updateFit(newfit)
else:
#FIXME: should change the refine status and let srr to handle the error
raise RietError(self.__class__.__name__ + ".refine(): Fit Error!")
self._readCalculatePattern(pcrfullname)
# if mode=lebail, import reflections from RFL file
if srtype == "l":
patterns = self.get("Pattern")
numpat = len(patterns)
if numpat == 1:
singlepattern = True
else:
singlepattern = False
# b) Phase
numpha = len(self.get("Phase"))
# c) Read all reflections
hklrange = {}
for patid in range(numpat):
tempreflects = []
hklrange["min"] = patterns[patid].get("Thmin")
hklrange["max"] = patterns[patid].get("Thmax")
for phaseid in range(numpha):
# Only work on phase-pattern related case
corecontrib = self.getContribution(
self.get("Phase")[phaseid],
self.get("Pattern")[patid])
if corecontrib is not None:
reflectdict = FPP.parseHKLn(
pcrfullname,
phaseno=phaseid + 1,
singlepattern=singlepattern,
patno=patid + 1,
hklrange=hklrange)
tempreflects.append(reflectdict)
# END-IF
# LOOP-OVER
patterns[patid]._reflections[phaseid] = tempreflects
# LOOP-OVER
# turn all constraint refinement off
#self.fixAll()
return
def setCalculation(self):
"""
set this instance to pattern calculation mode
return -- None
"""
thisjob = self.get("Job")
if thisjob == 0:
self.set("Job", 2)
elif thisjob == 1:
self.set("Job", 3)
elif thisjob == 2 or thisjob == 3:
pass
else:
errmsg = "Job = %-10s Is Not In Class %-20s Object" % \
(self.get("Job"), self.__class__.__name__)
raise RietError(errmsg)
# END-IF-ELSE
return
def duplicate(self):
"""
duplicate self object to a exact copy
(1) parameter...(copy)
(2) subclass... (copy)
(3) container... (copy)
For Constraint object, only the pattern_range, phase_range and parname are copied;
No link to Refine is established!
scenario -- After duplicate() and the corresponding linking work by Rietveld.set()
method 'RietveldClass.linkConstraint()' is always called
return -- the new generated twin object
"""
try:
newobject = self.__class__(None)
except TypeError, err:
errmsg = "RietveldClass.duplicate(): instantiated as %-20s\n" % (
self.__class__.__name__)
errmsg += str(err)
raise RietError(errmsg)
def getConstraintByPath(self, path):
"""Get a constraint by path
path -- a full path, e.g., x.y.z[i].a
return: a constraint object
"""
if path.count('.') > 0:
try:
objpath, paramname = path.rsplit('.', 1)
except:
raise RietError('Invalid format for a parameter name: ' + path)
objects = self.getByPath(objpath)
if isinstance(objects, list):
constraints = []
for object in objects:
_constraints = object.getConstraintByPath(paramname)
if isinstance(_constraints, list):
constraints.extend(_constraints)
else:
constraints.append(_constraints)
return constraints
# else it is a single object
return objects.getConstraintByPath(paramname)
name, index = self._parseIndex(path)
# If index is a slice, we need get constraint one by one
if isinstance(index, slice):
constraints = []
indices = self._rangeParam(name, index)
for i in indices:
constraints.append(self.getConstraint(name, i))
return constraints
# else the index is an int or None
return self.getConstraint(name, index)
def addBackgroundPoints(self, bkgdpointlist):
"""
add Background point (x, intensity) to this InterpolatedBackground instance
Arguments:
bkgdpointlist -- list of 2-tuple(x, intensity) for pre-selected background points
Return -- None
"""
background = self.get("Background")
for bkgdtup in bkgdpointlist:
# 1. verify the input list term
try:
pos = bkgdtup[0]
bck = bkgdtup[1]
except IndexError, err:
errmsg = "%-30s: Input Error! Element in input bkgdpointlist is not 2-tuple\n"% \
(self.__class__.__name__+"addBackgroundPoints()")
errmsg += "Error message: %-40s"% (err)
raise RietError(errmsg)
# 2. make Core objects
background.set("POS", pos)
background.set("BCK", bck)
def locateParameterByPath(rietobj, parfullname, srtype="r"):
"""
according to the parameter's name and path and input Rietveld instance reference,
locate the Rietveld class instance has this parameter and the name of the parameter
return -- 2-tuple (RietveldClass_Instance_Refernece, Parameter_Name)
Arguments:
- rietobj : reference to a RietveldClass object
- parfullname : string of the parameter with full path to locate this parameter from rietobj
- srtype : string, "r" for Rietveld, "l" for Lebail
Exception
(1) If cannot find the next RietveldClass to hold the parameter
"""
# get path-list
pathlist = GetPathListFromString(parfullname)
parName = pathlist[-1]
retObj = rietobj
index = 0
Continue = True
returntuple = None
while Continue:
# progress
name = pathlist[index]
index += 1
if name == parName and retObj.ParamDict.has_key(parName):
# ending case
returntuple = (retObj, parName)
Continue = False
elif index == len(pathlist):
# error case 1: cannot find parName in the final RietveldClass object
estring = "utilfunction.locateParameterByPath() cannot locate parameter " + parfullname
raise RietError(estring)
elif retObj.ObjectDict.has_key(name):
# progress case: subclass
retObj = retObj.get(name)
elif retObj.ObjectListDict.has_key(name):
# progress case: container
try:
seq = int(pathlist[index])
retObj = retObj.get(name)[seq]
index += 1
except IndexError, err:
estring = "utilfunction.locateParameterByPath() Locate parameter " + parfullname + " Error!"
estring += "RietveldClass " + retObj.__class__.__name__ + " has no " + str(
seq) + "-th " + name
estring += str(err)
raise RietError(estring)
else:
print "Parameter with Path and Name: " + str(parfullname)
print retObj.ParamDict.keys()
print "Parameter Name: " + name + " doesn't match input parameter name " + parName
print "Last object: " + retObj.__class__.__name__ + " name = " + str(
name)
#print retObj
raise NotImplementedError, "path_list: " + str(
pathlist) + " incorrect"
def readFPOutput(lines):
""" read the output of FullProf output file
1. Last line contains "=> END"
- check Chi2: is last Chi2 = "NaN"? "Chi2:-NaN,
- refined output
2. otherwise to 1
a) "Error During Opening File" + file_name : terminate the program
b) "NO REFLECTIONS FOUND": as Chi2 = NaN
algorithm:
(1) split Chi2 line with ":"
return 1: good refinement
0 not refined
-1: setup error
-2: excessive peak overlap
-3: singular matrix
"""
result = 0
# 1. Exception!
if len(lines) == 1:
raise RietError("Fullprof fp2k Does Not Work")
lastline = lines[-1]
if lastline.count("=> END") >= 1:
# 1. collect Chi2
chi2lines = []
for line in lines:
if line.count("Chi2") == 1 and line.count("Rp")==1:
chi2lines.append(line)
# 2. process last chi2 line
# lastchi2line = chi2lines[len(chi2lines)-1]
if len(chi2lines) > 1:
# refinement mode
lastchi2line = chi2lines[-1]
if lastchi2line.count("NaN") > 0:
# NaN appears in statistic: refine not done
result = 0
else:
# good refinement
result = 1
else:
# calcuation mode
result = -1
else: # not a normal end
if lastline.count("Error") > 0:
# Error
result = -1
print "Exception! FullProf set up error! " + lastline + "\n"
elif lastline.count("Excessive peak overlap") == 1:
# Excessive peak overlap error
result = -2
elif lastline.count("Singular Matrix") == 1:
# Singular Matrix Error
result = -3
elif lastline.count("NO REFLECTIONS FOUND") == 1:
# Singular Matrix Error
result = -4
else:
# intial value error
result = 0
return result
def runFullProf(fit, pcrfilename, mode="refine", srtype="r", processdir=dir, userinfo=None, exportsub=False):
"""
convert fit to FullProf pcr file
execute Rietveld refinement by FullProf,
Arguments:
- fit : a fit object to convert to a pcr file and run by FullProf
- pcrfilename : the name of the pcr file that is to write on the disk
- mode : string, for mode.. options =
1. "Refine" least square refine
2. "Calculate" just calculate the pattern as the forward calculator
3. "pcr" just print out pcr file
- srtype : string, structure solution type, "r" for "Rietveld", "l" for Lebail
- userinfo: : string, user information to add to pcr file
- exportsub : Boolean (export result in .sub in calculation mode)
Return : 1. Refine Mode FitSummary object
2. Calculate Mode list of list of 2-tuple (or list) for a phase or None
"""
from diffpy.pyfullprof.fit import Fit
from diffpy.pyfullprof.pcrfilewriter import pcrFileWriter
from diffpy.pyfullprof.pcrfilereader import ImportFitFromFullProf
from diffpy.pyfullprof.fpoutputfileparsers import FPOutFileParser
from diffpy.pyfullprof.fpuncertaintyreader import FPUncertainty
# FIXME in 'Calculate' mode, only 1 pattern is allowed NOW!
def ProcessOutput(infile):
"""
processing an file thread
(1) each line in intfile will be stored into a list as string without EOF
(2) all lines are ordered according to the original order in infile
infile: an file object
"""
OutLines = []
InLines = infile.readlines()
for line in InLines:
newline = line.split("\n")[0]
OutLines.append(newline)
return OutLines
# END FUNCTION: def ProcessOutput(infile)
def readFPOutput(lines):
""" read the output of FullProf output file
1. Last line contains "=> END"
- check Chi2: is last Chi2 = "NaN"? "Chi2:-NaN,
- refined output
2. otherwise to 1
a) "Error During Opening File" + file_name : terminate the program
b) "NO REFLECTIONS FOUND": as Chi2 = NaN
algorithm:
(1) split Chi2 line with ":"
return 1: good refinement
0 not refined
-1: setup error
-2: excessive peak overlap
-3: singular matrix
"""
result = 0
# 1. Exception!
if len(lines) == 1:
raise RietError("Fullprof fp2k Does Not Work")
lastline = lines[-1]
if lastline.count("=> END") >= 1:
# 1. collect Chi2
chi2lines = []
for line in lines:
if line.count("Chi2") == 1 and line.count("Rp")==1:
chi2lines.append(line)
# 2. process last chi2 line
# lastchi2line = chi2lines[len(chi2lines)-1]
if len(chi2lines) > 1:
# refinement mode
lastchi2line = chi2lines[-1]
if lastchi2line.count("NaN") > 0:
# NaN appears in statistic: refine not done
result = 0
else:
# good refinement
result = 1
else:
# calcuation mode
result = -1
else: # not a normal end
if lastline.count("Error") > 0:
# Error
result = -1
print "Exception! FullProf set up error! " + lastline + "\n"
elif lastline.count("Excessive peak overlap") == 1:
# Excessive peak overlap error
result = -2
elif lastline.count("Singular Matrix") == 1:
# Singular Matrix Error
result = -3
elif lastline.count("NO REFLECTIONS FOUND") == 1:
# Singular Matrix Error
result = -4
else:
# intial value error
result = 0
return result
# END FUNCTION: def readFPOutput(lines)
# -1: process input argument
if userinfo is None:
userinfo = []
verifyType(userinfo, list)
# 0. mandatory setup
fit.set("Pcr", 1)
fit.set("Aut", True)
# 1. check fit object:
isvalid = fit.validate(mode)
if not isvalid:
dbtag = "1721"
refine = fit.get("Refine")
print "Debug Tag: %-20s" % (dbtag)
print str(refine)
errmsg = "runFullProf() Fit object is not valid. Abort!"
raise RietError(errmsg)
if mode == "calculate":
# in this mode, data file is not used, but FullProf needs it!
from diffpy.pyfullprof.utilfunction import checkFileExistence
pattern = fit.get("Pattern")[0]
datafname = pattern.get("Datafile")
isexist = checkFileExistence(datafname)
if isexist is not True:
fakedatafile = True
fakefilename = datafname
cmd = "touch %-10s"% (fakefilename)
os.system(cmd)
else:
fakedatafile = False
# 2. write out the pcr file and run FullProf
pcrFileWriter(fit, pcrfilename, userinfo, srtype=srtype)
# get the root name and ext name of the pcr file
rootName, extname= os.path.splitext(os.path.basename(pcrfilename))
baseName = os.path.basename(pcrfilename)
if mode=="pcr":
return
shutil.copyfile(pcrfilename, rootName + '.prefit')
cmd = 'fp2k ' + baseName
import subprocess
from diffpy.pyfullprof.environment import FullProfSubprocessArgs
fp2kArgs = FullProfSubprocessArgs(cwd=processdir, stdout=subprocess.PIPE,
stderr=subprocess.PIPE, stdin=open(os.devnull))
output = subprocess.Popen(('fp2k', baseName ), **fp2kArgs)
# 3. process output
CodeOutput = ProcessOutput(output.stdout)
#print '\n'.join(CodeOutput)
CodeError = ProcessOutput(output.stderr)
output.stdout.close()
output.stderr.close()
output.wait()
if mode == "refine":
# 4. process fit result
newfit = Fit(None)
try:
importfile = ImportFitFromFullProf(pcrfilename)
importresult = importfile.ImportFile(newfit)
except RietPCRError, err:
print "Error Message: %-30s"% (err)
importresult = False
# 5. pass the parameter and constraint information
summary = FitSummary()
if importresult is True:
# 6. build output
result = readFPOutput(CodeOutput)
outfname = rootName +".out"
# 6.2 Judge refine result
# Note: result > 0 is a more robust flag than refinesuccess
if result == 0:
refinesuccess = False
errmsg = "NAN"
elif result == -1:
outparser = FPOutFileParser(newfit, outfname)
refinesuccess = outparser.getStatus()
errmsg = outparser.getErrorReason()
elif result == -2:
refinesuccess = False
errmsg = "Excessive Peak Overlap"
elif result == -3:
refinesuccess = False
errmsg = "Singular Matrix"
elif result == -4:
refinesuccess = False
errmsg = "NO REFLECTIONS FOUND"
else:
refinesuccess = True
errmsg = None
if result < 0:
quitmessage = "result = %-5s < 0 means a failure error" % result
raise ValueError, quitmessage
# END-IF-ELSE
# 6.3 read uncertainty and phase fraction if refine is good
if refinesuccess is True:
# a) Uncertainty
fpsigma = FPUncertainty(outfname)
fpsigma.importUncertainty()
fpsigma.exportToFit(newfit)
# b) Phase Fraction
sumfilename = rootName + ".sum"
sumparse = FPSumFileParser(sumfilename)
sumparse.parsePhaseFraction(newfit)
# END-IF
# 6.4 Construct Summary
if result > 0:
outparser = FPOutFileParser(newfit, outfname)
summary.set(newfit, outparser, refinesuccess, srtype, errmsg, CodeOutput, CodeError)
else:
summary.setRefineStatus(False)
else:
# Bad refinement
summary.setRefineStatus(False)
# END-IF-ELSE
# 7. Process fp2k remainder
os.rename(pcrfilename, rootName+".posfit")
# 8. return
return summary
simpatternslist = []
for phaseid in xrange(1, len(phases)+1):
# FIXME This is not good for multiple pattern simulation
if len(patterns) > 1:
raise NotImplementedError("See FIXME")
pat = patterns[0]
thmin = pat.get("Thmin")
thmax = pat.get("Thmax")
step = pat.get("Step")
dataset = subParser(rootname, phaseid, thmin=thmin, thmax=thmax, step=step)
simpatternslist.append(dataset)
# 5. clean
if fakedatafile is True:
cmd = "rm %-10s"% (fakefilename)
os.system(cmd)
# 5. return
return simpatternslist
else:
return
# END-IF-ELSE
else:
errmsg = "run-FullProf: mode = %-10s is NOT supported"% (mode)
raise RietError(errmsg)
return
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 exportToFit(self, myfit):
"""
Export the current information to a Fit object
Argument:
- myfit : diffpy.pyfullprof.Fit instance
Return : None
"""
import diffpy.pyfullprof.pattern as PTN
for nameinfotuple, val, sig in self._ParameterList:
# 1. From the suffix of the name, determine if the parameter
# belongs to pattern, phase, or contribution
ispattern = False
isphase = False
iscontribution = False
if nameinfotuple.count("pat") > 0:
ispattern = True
if nameinfotuple.count("ph") > 0:
isphase = True
if ispattern and isphase:
iscontribution = True
ispattern = False
isphase = False
# 2. Get parameter and its index
parname = None
index = None
if ispattern:
# background
patnum = nameinfotuple[1]
pattern = myfit.get("Pattern")[patnum - 1]
if nameinfotuple[-1] == "Bck":
rietobj = pattern.get("Background")
bcknum = nameinfotuple[-2] + 1
if isinstance(rietobj, PTN.BackgroundPolynomial):
parname = "BACK"
index = bcknum - 1
elif isinstance(rietobj, PTN.BackgroundUserDefined):
parname = "BCK"
index = bcknum - 1
else:
errmsg = "1045-1: Object Instance %-10s Unrecoganizable" % (
rietobj.__class__.__name__)
print errmsg
else:
iname = nameinfotuple[-1]
if FPUncertainty._NAMEMAPDICT.has_key(iname):
iname = FPUncertainty._NAMEMAPDICT[iname]
rietobj, parname = pattern.locateParameter(iname)
elif isphase:
phanum = nameinfotuple[1]
phase = myfit.get("Phase")[phanum - 1]
# a. get all atom's name
atomindexmap = {}
for atom in phase.get("Atom"):
atomname = atom.get("Name")
atomindexmap[atomname] = atom
# b. see whether belonging to Atom's property
atomnameslist = atomindexmap.keys()
if atomnameslist.count(nameinfotuple[-2]) == 1:
atom = atomindexmap[nameinfotuple[-2]]
rietobj, parname = atom.locateParameter(nameinfotuple[-1])
# c. if not atom's
if rietobj is None:
iname = nameinfotuple[-1]
if FPUncertainty._NAMEMAPDICT.has_key(iname):
iname = FPUncertainty._NAMEMAPDICT[iname]
rietobj, parname = phase.locateParameter(iname)
elif iscontribution:
patnum = nameinfotuple[1]
phanum = nameinfotuple[3]
pattern = myfit.get("Pattern")[patnum - 1]
phase = myfit.get("Phase")[phanum - 1]
contrib = myfit.getContribution(pattern, phase)
# a. Lattice
if nameinfotuple[-1] == "Cell":
rietobj, parname = phase.locateParameter(nameinfotuple[-2])
else:
iname = nameinfotuple[-1]
if FPUncertainty._NAMEMAPDICT.has_key(iname):
iname = FPUncertainty._NAMEMAPDICT[iname]
rietobj, parname = contrib.locateParameter(iname)
else:
raise RietError(
"Parameter %s does not belong to a known case." %
str(nameinfotuple))
if parname is None:
rstring = "%-20s ispat = %-10s ispha = %-10s iscon = %-10s"% \
(nameinfotuple, ispat, ispha, iscon)
print "# 1045-Warning: Implement this case! %-50s" % (rstring)
else:
if rietobj is None:
raise RietError(
"Parameter %s can not be found in the fit object." %
parname)
constraint = rietobj.getConstraint(parname, index)
if constraint:
constraint.sigma = sig
else:
raise RietError(
"No constraint is bound to the parameter '%s'" %
parname)
if 0: # 1501
print "1501:Par = %-10s Val = %-15s vs. input Val = %-15s Sig = %-15s"% \
(parname, rietobj.get(parname).value(), val, sig)
# END-DEBUG
# LOOP-OVER: for nameinfotuple, val, sig in self._ParameterList
return
import sys
import subprocess
from diffpy.pyfullprof.which import whichall
from diffpy.pyfullprof.exception import RietError
# copy the system environment
FULLPROF_ENV = dict(os.environ)
_mswindows = sys.platform.startswith("win")
# make sure "gsas" variable exists in FULLPROF_ENV and is not empty
if not FULLPROF_ENV.get('FullProf'):
_gsas_executables = whichall('fp2k')
if not _gsas_executables:
emsg = "Fullprof can not find the excutable, please check the system path"
raise RietError(emsg, errorId="CANNOT_FIND_EXECUTABLE")
_gsas_real_path = os.path.realpath(_gsas_executables[0])
FULLPROF_ENV['FullProf'] = os.path.dirname(_gsas_real_path)
FULLPROF_ENV['FULLPROF'] = FULLPROF_ENV['FullProf']
# make sure its exe directory is first in the path
FULLPROF = FULLPROF_ENV['FullProf']
_path_org = FULLPROF_ENV.get('PATH', '').split(os.pathsep)
_path_new = [FULLPROF] + filter(lambda d: d != FULLPROF, _path_org)
FULLPROF_ENV['PATH'] = os.pathsep.join(_path_new)
FULLPROF_PATH = FULLPROF_ENV['PATH']
if _mswindows:
def extend(self, baseobj):
"""
extend a base-object to 'self', and replace base-object with 'self' in
Rietveld-class hierachy
baseobj = base object
"""
def class_in_list(classname, classnamelist):
"""
identify whether a class_name is one in classnamelist
class_name can be extended class while the name in classnamelist is base class
classname -
classnamelist -
"""
for basename in classnamelist:
if classname.count(basename) == 1:
return True
return False
def getClassName(classname, classnamelist):
"""
if classname is an extended class name, then return the base class name
class_name can be extended class while the name in classnamelist is base class
classname -
classnamelist -
"""
for basename in classnamelist:
if classname.count(basename) == 1:
return basename
raise RietError, "rietveldclass.extend - getClassName"
return
from diffpy.pyfullprof.contribution import Contribution
if isinstance(baseobj, Contribution):
errmsg = "Contribution should extend this function because of its dual parent"
raise RietError(errmsg)
# 1 check
if not isinstance(self, baseobj.__class__):
return False
# 2 copy
for name in baseobj.ParamDict.keys():
self.__dict__[name] = baseobj.__dict__[name]
for name in baseobj.ParamListDict.keys():
for i in range(len(baseobj.__dict__[name])):
self.__dict__[name].set(baseobj.__dict__[name].get(i))
for name in baseobj.ObjectDict.keys():
self.__dict__[name] = baseobj.__dict__[name]
# set parent
self.__dict__[name].parent = self
self.__dict__[name].parent = self
for name in baseobj.ObjectListDict.keys():
self.__dict__[name] = baseobj.__dict__[name]
# set parent
self.__dict__[name].parent = self
for objref in self.get(name):
objref.parent = self
# 3 find and set parent
parentobj = baseobj.parent
self.parent = parentobj
# 4 replace from the parent class view
# if baseobj.__class__.__name__ in parentobj.ObjectDict.keys():
if class_in_list(baseobj.__class__.__name__,
parentobj.ObjectDict.keys()):
classname = getClassName(baseobj.__class__.__name__,
parentobj.ObjectDict.keys())
parentobj.set(classname, self)
# elif baseobj.__class__.__name__ in parentobj.ObjectListDict.keys():
elif class_in_list(baseobj.__class__.__name__,
parentobj.ObjectListDict.keys()):
classname = getClassName(baseobj.__class__.__name__,
parentobj.ObjectListDict.keys())
for i, obj in enumerate(parentobj.get(classname)):
if baseobj == obj:
parentobj.set(classname, self, i)
break
else:
raise RietError("RietveldClass.extend(): Can not find the ")
else:
print "base obj:\t" + baseobj.__class__.__name__
print "parent obj:\t" + str(parentobj.ObjectDict.keys())
raise RietError(
"RietveldClass.extend(): Parent Class Cannot Locate Object")
return True
def setConstraintByPath(self,
path,
formula,
value=None,
damping=None,
varIndex=None):
"""Constrain a parameter by path
path -- a full path, e.g., x.y.z[i].a
formula -- a formula to be applied to the parameter
value -- the initial value of the constrained parameter.
damping -- damping
varIndex -- if it is not None, append it to the formula; if the path
corresponds to multiple parameters, varIndex will increase
by one for each parameter.
return: the newly created constraint object
"""
if path.count('.') > 0:
try:
objpath, paramname = path.rsplit('.', 1)
except:
raise RietError('Invalid format for a parameter name: ' + path)
objects = self.getByPath(objpath)
# There are multiple objects
if isinstance(objects, list):
constraints = []
for i, object in enumerate(objects):
_constraints = object.setConstraintByPath(
paramname, formula, value, damping, varIndex)
# Append results to the result constraint list,
# and increase the varIndex accordingly if it is not None.
if isinstance(_constraints, list):
constraints.extend(_constraints)
if varIndex is not None:
varIndex += len(_constraints)
else:
constraints.append(_constraints)
if varIndex is not None:
varIndex += 1
return constraints
# else it is a single object
return objects.setConstraintByPath(paramname, formula, value,
damping, varIndex)
name, index = self._parseIndex(path)
# If index is a slice, we need set constraint one by one
if isinstance(index, slice):
constraints = []
indices = self._rangeParam(name, index)
for i in indices:
if varIndex is not None:
_formula = formula + '%i' % (varIndex + i)
else:
_formula = formula
constraints.append(
self.setConstraint(name, _formula, value, damping,
index=i))
return constraints
# else the index is an int or None
if varIndex is not None:
formula = formula + '%i' % varIndex
return self.setConstraint(name,
formula,
value=value,
damping=damping,
index=index)