def SeqRefine(GPXfile,dlg,refPlotUpdate=None):
'''Perform a sequential refinement -- cycles through all selected histgrams,
one at a time
'''
import GSASIImpsubs as G2mp
G2mp.InitMP()
import pytexture as ptx
ptx.pyqlmninit() #initialize fortran arrays for spherical harmonics
printFile = open(ospath.splitext(GPXfile)[0]+'.lst','w')
G2fil.G2Print ('Starting Sequential Refinement')
G2stIO.ShowBanner(printFile)
Controls = G2stIO.GetControls(GPXfile)
G2stIO.ShowControls(Controls,printFile,SeqRef=True)
restraintDict = G2stIO.GetRestraints(GPXfile)
Histograms,Phases = G2stIO.GetUsedHistogramsAndPhases(GPXfile)
if not Phases:
G2fil.G2Print (' *** ERROR - you have no phases to refine! ***')
G2fil.G2Print (' *** Refine aborted ***')
return False,'No phases'
if not Histograms:
G2fil.G2Print (' *** ERROR - you have no data to refine with! ***')
G2fil.G2Print (' *** Refine aborted ***')
return False,'No data'
rigidbodyDict = G2stIO.GetRigidBodies(GPXfile)
rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,pFile=printFile)
G2mv.InitVars()
(Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,
maxSSwave) = G2stIO.GetPhaseData(Phases,restraintDict,rbIds,
Print=False,pFile=printFile,seqRef=True)
for item in phaseVary:
if '::A0' in item:
G2fil.G2Print ('**** WARNING - lattice parameters should not be refined in a sequential refinement ****')
G2fil.G2Print ('**** instead use the Dij parameters for each powder histogram ****')
return False,'Lattice parameter refinement error - see console message'
if '::C(' in item:
G2fil.G2Print ('**** WARNING - phase texture parameters should not be refined in a sequential refinement ****')
G2fil.G2Print ('**** instead use the C(L,N) parameters for each powder histogram ****')
return False,'Phase texture refinement error - see console message'
if 'Seq Data' in Controls:
histNames = Controls['Seq Data']
else: # patch from before Controls['Seq Data'] was implemented?
histNames = G2stIO.GetHistogramNames(GPXfile,['PWDR',])
if Controls.get('Reverse Seq'):
histNames.reverse()
SeqResult = G2stIO.GetSeqResult(GPXfile)
# SeqResult = {'SeqPseudoVars':{},'SeqParFitEqList':[]}
Histo = {}
NewparmDict = {}
G2stIO.SetupSeqSavePhases(GPXfile)
for ihst,histogram in enumerate(histNames):
if GSASIIpath.GetConfigValue('Show_timing'): t1 = time.time()
G2fil.G2Print('\nRefining with '+str(histogram))
G2mv.InitVars()
(Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,
FFtables,BLtables,MFtables,maxSSwave) = G2stIO.GetPhaseData(
Phases,restraintDict,rbIds,
Print=False,pFile=printFile,seqRef=True)
ifPrint = False
if dlg:
dlg.SetTitle('Residual for histogram '+str(ihst))
calcControls = {}
calcControls['atomIndx'] = atomIndx
calcControls['Natoms'] = Natoms
calcControls['FFtables'] = FFtables
calcControls['BLtables'] = BLtables
calcControls['MFtables'] = MFtables
calcControls['maxSSwave'] = maxSSwave
if histogram not in Histograms:
G2fil.G2Print("Error: not found!")
continue
#TODO - implement "Fix FXU" for seq refinement here - done?
hId = Histograms[histogram]['hId']
redphaseVary = phaseCheck(phaseVary,Phases,histogram)
Histo = {histogram:Histograms[histogram],}
hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(Phases,Histo,Print=False)
calcControls.update(controlDict)
histVary,histDict,controlDict = G2stIO.GetHistogramData(Histo,False)
calcControls.update(controlDict)
varyList = rbVary+redphaseVary+hapVary+histVary
# if not ihst:
# save the initial vary list, but without histogram numbers on parameters
saveVaryList = varyList[:]
for i,item in enumerate(saveVaryList):
items = item.split(':')
if items[1]:
items[1] = ''
item = ':'.join(items)
saveVaryList[i] = item
if not ihst:
SeqResult['varyList'] = saveVaryList
else:
SeqResult['varyList'] = list(set(SeqResult['varyList']+saveVaryList))
parmDict = {}
parmDict.update(rbDict)
parmDict.update(phaseDict)
parmDict.update(hapDict)
parmDict.update(histDict)
if Controls['Copy2Next']: # update with parms from last histogram
#parmDict.update(NewparmDict) # don't use in case extra entries would cause a problem
for parm in NewparmDict:
if parm in parmDict:
parmDict[parm] = NewparmDict[parm]
elif histogram in SeqResult: # update phase from last seq ref
NewparmDict = SeqResult[histogram].get('parmDict',{})
for parm in NewparmDict:
if '::' in parm and parm in parmDict:
parmDict[parm] = NewparmDict[parm]
G2stIO.GetFprime(calcControls,Histo)
# do constraint processing
#reload(G2mv) # debug
constrDict,fixedList = G2stIO.GetConstraints(GPXfile)
varyListStart = tuple(varyList) # save the original varyList before dependent vars are removed
msg = G2mv.EvaluateMultipliers(constrDict,parmDict)
if msg:
return False,'Unable to interpret multiplier(s): '+msg
try:
groups,parmlist = G2mv.GenerateConstraints(varyList,constrDict,fixedList,parmDict,SeqHist=hId)
# if GSASIIpath.GetConfigValue('debug'): print("DBG_"+
# G2mv.VarRemapShow(varyList,True))
# print('DependentVars',G2mv.GetDependentVars())
# print('IndependentVars',G2mv.GetIndependentVars())
constraintInfo = (groups,parmlist,constrDict,fixedList,ihst)
except G2mv.ConstraintException:
G2fil.G2Print (' *** ERROR - your constraints are internally inconsistent ***')
#errmsg, warnmsg = G2mv.CheckConstraints(varyList,constrDict,fixedList)
#print 'Errors',errmsg
#if warnmsg: print 'Warnings',warnmsg
return False,' Constraint error'
#print G2mv.VarRemapShow(varyList)
if not ihst:
# first histogram to refine against
firstVaryList = []
for item in varyList:
items = item.split(':')
if items[1]:
items[1] = ''
item = ':'.join(items)
firstVaryList.append(item)
newVaryList = firstVaryList
else:
newVaryList = []
for item in varyList:
items = item.split(':')
if items[1]:
items[1] = ''
item = ':'.join(items)
newVaryList.append(item)
if newVaryList != firstVaryList and Controls['Copy2Next']:
# variable lists are expected to match between sequential refinements when Copy2Next is on
#print '**** ERROR - variable list for this histogram does not match previous'
#print ' Copy of variables is not possible'
#print '\ncurrent histogram',histogram,'has',len(newVaryList),'variables'
combined = list(set(firstVaryList+newVaryList))
c = [var for var in combined if var not in newVaryList]
p = [var for var in combined if var not in firstVaryList]
G2fil.G2Print('*** Variables change ***')
for typ,vars in [('Removed',c),('Added',p)]:
line = ' '+typ+': '
if vars:
for var in vars:
if len(line) > 70:
G2fil.G2Print(line)
line = ' '
line += var + ', '
else:
line += 'none, '
G2fil.G2Print(line[:-2])
firstVaryList = newVaryList
ifSeq = True
printFile.write('\n Refinement results for histogram: %s\n'%histogram)
printFile.write(135*'-'+'\n')
try:
IfOK,Rvals,result,covMatrix,sig = RefineCore(Controls,Histo,Phases,restraintDict,
rigidbodyDict,parmDict,varyList,calcControls,pawleyLookup,ifSeq,printFile,dlg,
refPlotUpdate=refPlotUpdate)
G2fil.G2Print (' wR = %7.2f%%, chi**2 = %12.6g, reduced chi**2 = %6.2f, last delta chi = %.4f'%(
Rvals['Rwp'],Rvals['chisq'],Rvals['GOF']**2,Rvals['DelChi2']))
# add the uncertainties into the esd dictionary (sigDict)
if not IfOK:
G2fil.G2Print('***** Sequential refinement failed at histogram '+histogram,mode='warn')
break
sigDict = dict(zip(varyList,sig))
# the uncertainties for dependent constrained parms into the esd dict
sigDict.update(G2mv.ComputeDepESD(covMatrix,varyList,parmDict))
# a dict with values & esds for dependent (constrained) parameters - avoid extraneous holds
depParmDict = {i:(parmDict[i],sigDict[i]) for i in varyListStart if i in sigDict and i not in varyList}
newCellDict = copy.deepcopy(G2stMth.GetNewCellParms(parmDict,varyList))
newAtomDict = copy.deepcopy(G2stMth.ApplyXYZshifts(parmDict,varyList))
histRefData = {
'variables':result[0],'varyList':varyList,'sig':sig,'Rvals':Rvals,
'varyListStart':varyListStart,
'covMatrix':covMatrix,'title':histogram,'newAtomDict':newAtomDict,
'newCellDict':newCellDict,'depParmDict':depParmDict,
'constraintInfo':constraintInfo,
'parmDict':parmDict}
SeqResult[histogram] = histRefData
G2stMth.ApplyRBModels(parmDict,Phases,rigidbodyDict,True)
# G2stIO.SetRigidBodyModels(parmDict,sigDict,rigidbodyDict,printFile)
G2stIO.SetHistogramPhaseData(parmDict,sigDict,Phases,Histo,None,ifPrint,printFile)
G2stIO.SetHistogramData(parmDict,sigDict,Histo,None,ifPrint,printFile)
G2stIO.SaveUpdatedHistogramsAndPhases(GPXfile,Histo,Phases,rigidbodyDict,histRefData)
NewparmDict = {}
# make dict of varied parameters in current histogram, renamed to
# next histogram, for use in next refinement.
if Controls['Copy2Next'] and ihst < len(histNames)-1:
hId = Histo[histogram]['hId'] # current histogram
nexthId = Histograms[histNames[ihst+1]]['hId']
for parm in set(list(varyList)+list(varyListStart)):
items = parm.split(':')
if len(items) < 3:
continue
if str(hId) in items[1]:
items[1] = str(nexthId)
newparm = ':'.join(items)
NewparmDict[newparm] = parmDict[parm]
else:
if items[2].startswith('dA'): parm = parm.replace(':dA',':A')
NewparmDict[parm] = parmDict[parm]
except G2obj.G2RefineCancel as Msg:
printFile.close()
G2fil.G2Print (' ***** Refinement stopped *****')
return False,Msg.msg
except G2obj.G2Exception as Msg: # cell metric error, others?
printFile.close()
G2fil.G2Print (' ***** Refinement error *****')
return False,Msg.msg
if GSASIIpath.GetConfigValue('Show_timing'):
t2 = time.time()
G2fil.G2Print("Fit step time {:.2f} sec.".format(t2-t1))
t1 = t2
SeqResult['histNames'] = [itm for itm in G2stIO.GetHistogramNames(GPXfile,['PWDR',]) if itm in SeqResult.keys()]
G2stIO.SetSeqResult(GPXfile,Histograms,SeqResult)
printFile.close()
G2fil.G2Print (' Sequential refinement results are in file: '+ospath.splitext(GPXfile)[0]+'.lst')
G2fil.G2Print (' ***** Sequential refinement successful *****')
return True,'Success'
def SeqRefine(GPXfile,dlg):
'''Perform a sequential refinement -- cycles through all selected histgrams,
one at a time
'''
import pytexture as ptx
ptx.pyqlmninit() #initialize fortran arrays for spherical harmonics
printFile = open(ospath.splitext(GPXfile)[0]+'.lst','w')
print 'Starting Sequential Refinement'
G2stIO.ShowBanner(printFile)
Controls = G2stIO.GetControls(GPXfile)
G2stIO.ShowControls(Controls,printFile,SeqRef=True)
restraintDict = G2stIO.GetRestraints(GPXfile)
Histograms,Phases = G2stIO.GetUsedHistogramsAndPhases(GPXfile)
if not Phases:
print ' *** ERROR - you have no phases to refine! ***'
print ' *** Refine aborted ***'
return False,'No phases'
if not Histograms:
print ' *** ERROR - you have no data to refine with! ***'
print ' *** Refine aborted ***'
return False,'No data'
rigidbodyDict = G2stIO.GetRigidBodies(GPXfile)
rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,pFile=printFile)
Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,maxSSwave = G2stIO.GetPhaseData(Phases,restraintDict,rbIds,False,printFile,seqRef=True)
for item in phaseVary:
if '::A0' in item:
print '**** WARNING - lattice parameters should not be refined in a sequential refinement ****'
print '**** instead use the Dij parameters for each powder histogram ****'
return False,'Lattice parameter refinement error - see console message'
if '::C(' in item:
print '**** WARNING - phase texture parameters should not be refined in a sequential refinement ****'
print '**** instead use the C(L,N) parameters for each powder histogram ****'
return False,'Phase texture refinement error - see console message'
if 'Seq Data' in Controls:
histNames = Controls['Seq Data']
else:
histNames = G2stIO.GetHistogramNames(GPXfile,['PWDR',])
if 'Reverse Seq' in Controls:
if Controls['Reverse Seq']:
histNames.reverse()
SeqResult = {'histNames':histNames}
makeBack = True
Histo = {}
NewparmDict = {}
for ihst,histogram in enumerate(histNames):
print('Refining with '+str(histogram))
ifPrint = False
if dlg:
dlg.SetTitle('Residual for histogram '+str(ihst))
calcControls = {}
calcControls['atomIndx'] = atomIndx
calcControls['Natoms'] = Natoms
calcControls['FFtables'] = FFtables
calcControls['BLtables'] = BLtables
calcControls['maxSSwave'] = maxSSwave
Histo = {histogram:Histograms[histogram],}
hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(Phases,Histo,Print=False)
calcControls.update(controlDict)
histVary,histDict,controlDict = G2stIO.GetHistogramData(Histo,False)
calcControls.update(controlDict)
varyList = rbVary+phaseVary+hapVary+histVary
if not ihst:
# save the initial vary list, but without histogram numbers on parameters
saveVaryList = varyList[:]
for i,item in enumerate(saveVaryList):
items = item.split(':')
if items[1]:
items[1] = ''
item = ':'.join(items)
saveVaryList[i] = item
SeqResult['varyList'] = saveVaryList
origvaryList = varyList[:]
parmDict = {}
parmDict.update(phaseDict)
parmDict.update(hapDict)
parmDict.update(histDict)
if Controls['Copy2Next']:
parmDict.update(NewparmDict)
G2stIO.GetFprime(calcControls,Histo)
# do constraint processing
#reload(G2mv) # debug
G2mv.InitVars()
constrDict,fixedList = G2stIO.GetConstraints(GPXfile)
varyListStart = tuple(varyList) # save the original varyList before dependent vars are removed
try:
groups,parmlist = G2mv.GroupConstraints(constrDict)
G2mv.GenerateConstraints(groups,parmlist,varyList,constrDict,fixedList,parmDict,SeqHist=ihst)
constraintInfo = (groups,parmlist,constrDict,fixedList,ihst)
except:
print ' *** ERROR - your constraints are internally inconsistent ***'
#errmsg, warnmsg = G2mv.CheckConstraints(varyList,constrDict,fixedList)
#print 'Errors',errmsg
#if warnmsg: print 'Warnings',warnmsg
return False,' Constraint error'
#print G2mv.VarRemapShow(varyList)
if not ihst:
# first histogram to refine against
firstVaryList = []
for item in varyList:
items = item.split(':')
if items[1]:
items[1] = ''
item = ':'.join(items)
firstVaryList.append(item)
newVaryList = firstVaryList
else:
newVaryList = []
for item in varyList:
items = item.split(':')
if items[1]:
items[1] = ''
item = ':'.join(items)
newVaryList.append(item)
if newVaryList != firstVaryList and Controls['Copy2Next']:
# variable lists are expected to match between sequential refinements when Copy2Next is on
print '**** ERROR - variable list for this histogram does not match previous'
print ' Copy of variables is not possible'
print '\ncurrent histogram',histogram,'has',len(newVaryList),'variables'
combined = list(set(firstVaryList+newVaryList))
c = [var for var in combined if var not in newVaryList]
p = [var for var in combined if var not in firstVaryList]
line = 'Variables in previous but not in current: '
if c:
for var in c:
if len(line) > 100:
print line
line = ' '
line += var + ', '
else:
line += 'none'
print line
print '\nPrevious refinement has',len(firstVaryList),'variables'
line = 'Variables in current but not in previous: '
if p:
for var in p:
if len(line) > 100:
print line
line = ' '
line += var + ', '
else:
line += 'none'
print line
return False,line
ifPrint = False
print >>printFile,'\n Refinement results for histogram: v'+histogram
print >>printFile,135*'-'
try:
IfOK,Rvals,result,covMatrix,sig = RefineCore(Controls,Histo,Phases,restraintDict,
rigidbodyDict,parmDict,varyList,calcControls,pawleyLookup,ifPrint,printFile,dlg)
print ' wR = %7.2f%%, chi**2 = %12.6g, reduced chi**2 = %6.2f, last delta chi = %.4f'%(
Rvals['Rwp'],Rvals['chisq'],Rvals['GOF']**2,Rvals['DelChi2'])
# add the uncertainties into the esd dictionary (sigDict)
sigDict = dict(zip(varyList,sig))
# the uncertainties for dependent constrained parms into the esd dict
sigDict.update(G2mv.ComputeDepESD(covMatrix,varyList,parmDict))
# a dict with values & esds for dependent (constrained) parameters
depParmDict = {i:(parmDict[i],sigDict[i]) for i in varyListStart
if i not in varyList}
newCellDict = copy.deepcopy(G2stMth.GetNewCellParms(parmDict,varyList))
newAtomDict = copy.deepcopy(G2stMth.ApplyXYZshifts(parmDict,varyList))
histRefData = {
'variables':result[0],'varyList':varyList,'sig':sig,'Rvals':Rvals,
'varyListStart':varyListStart,
'covMatrix':covMatrix,'title':histogram,'newAtomDict':newAtomDict,
'newCellDict':newCellDict,'depParmDict':depParmDict,
'constraintInfo':constraintInfo,
'parmDict':parmDict}
SeqResult[histogram] = histRefData
G2stMth.ApplyRBModels(parmDict,Phases,rigidbodyDict,True)
# G2stIO.SetRigidBodyModels(parmDict,sigDict,rigidbodyDict,printFile)
G2stIO.SetHistogramPhaseData(parmDict,sigDict,Phases,Histo,None,ifPrint,printFile)
G2stIO.SetHistogramData(parmDict,sigDict,Histo,None,ifPrint,printFile)
G2stIO.SetUsedHistogramsAndPhases(GPXfile,Histo,Phases,rigidbodyDict,histRefData,makeBack)
makeBack = False
NewparmDict = {}
# make dict of varied parameters in current histogram, renamed to
# next histogram, for use in next refinement.
if Controls['Copy2Next'] and ihst < len(histNames)-1:
hId = Histo[histogram]['hId'] # current histogram
nexthId = Histograms[histNames[ihst+1]]['hId']
for parm in set(list(varyList)+list(varyListStart)):
items = parm.split(':')
if len(items) < 3: continue
if str(hId) in items[1]:
items[1] = str(nexthId)
newparm = ':'.join(items)
NewparmDict[newparm] = parmDict[parm]
except G2obj.G2Exception,Msg:
printFile.close()
print ' ***** Refinement aborted *****'
return False,Msg.msg
