Exemple #1
0
 def TestRead(self):
     file = open(self.testFile, 'rb')
     self.values = cPickle.load(file, encoding='Latin-1')
     self.HistoPhases = cPickle.load(file, encoding='Latin-1')
     (self.constrDict, self.fixedList,
      self.depVarList) = cPickle.load(file, encoding='Latin-1')
     self.parmDict = cPickle.load(file, encoding='Latin-1')
     self.varylist = cPickle.load(file, encoding='Latin-1')
     self.calcControls = cPickle.load(file, encoding='Latin-1')
     self.pawleyLookup = cPickle.load(file, encoding='Latin-1')
     self.names = self.varylist + self.depVarList
     self.use = [False for i in range(len(self.names))]
     self.delt = [
         max(abs(self.parmDict[name]) * 0.0001, 1e-6) for name in self.names
     ]
     for iname, name in enumerate(self.names):
         if name.split(':')[-1] in [
                 'Shift',
                 'DisplaceX',
                 'DisplaceY',
         ]:
             self.delt[iname] = 0.1
     file.close()
     msg = G2mv.EvaluateMultipliers(self.constrDict, self.parmDict)
     if msg:
         print('Unable to interpret multiplier(s): ' + msg)
         raise Exception
     G2mv.GenerateConstraints(self.varylist, self.constrDict,
                              self.fixedList, self.parmDict)
     print(G2mv.VarRemapShow(self.varylist))
     print('Dependent Vary List:', self.depVarList)
Exemple #2
0
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'
Exemple #3
0
def Refine(GPXfile,dlg=None,makeBack=True,refPlotUpdate=None):
    'Global refinement -- refines to minimize against all histograms'
    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')
    G2stIO.ShowBanner(printFile)
    varyList = []
    parmDict = {}
    G2mv.InitVars()
    Controls = G2stIO.GetControls(GPXfile)
    G2stIO.ShowControls(Controls,printFile)
    calcControls = {}
    calcControls.update(Controls)
    constrDict,fixedList = G2stIO.GetConstraints(GPXfile)
    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)
    (Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,
         maxSSwave) = G2stIO.GetPhaseData(Phases,restraintDict,rbIds,pFile=printFile)
    calcControls['atomIndx'] = atomIndx
    calcControls['Natoms'] = Natoms
    calcControls['FFtables'] = FFtables
    calcControls['BLtables'] = BLtables
    calcControls['MFtables'] = MFtables
    calcControls['maxSSwave'] = maxSSwave
    hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(Phases,Histograms,pFile=printFile)
    TwConstr,TwFixed = G2stIO.makeTwinFrConstr(Phases,Histograms,hapVary)
    constrDict += TwConstr
    fixedList += TwFixed
    calcControls.update(controlDict)
    histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,pFile=printFile)
    calcControls.update(controlDict)
    varyList = rbVary+phaseVary+hapVary+histVary
    parmDict.update(rbDict)
    parmDict.update(phaseDict)
    parmDict.update(hapDict)
    parmDict.update(histDict)
    G2stIO.GetFprime(calcControls,Histograms)
    # do constraint processing
    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:
        G2mv.GenerateConstraints(varyList,constrDict,fixedList,parmDict)
        #print(G2mv.VarRemapShow(varyList))
        #print('DependentVars',G2mv.GetDependentVars())
        #print('IndependentVars',G2mv.GetIndependentVars())
    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)

    ifSeq = False
    printFile.write('\n Refinement results:\n')
    printFile.write(135*'-'+'\n')
    try:
        covData = {}
        IfOK,Rvals,result,covMatrix,sig = RefineCore(Controls,Histograms,Phases,restraintDict,
            rigidbodyDict,parmDict,varyList,calcControls,pawleyLookup,ifSeq,printFile,dlg,
            refPlotUpdate=refPlotUpdate)
        if IfOK:
            sigDict = dict(zip(varyList,sig))
            newCellDict = G2stMth.GetNewCellParms(parmDict,varyList)
            newAtomDict = G2stMth.ApplyXYZshifts(parmDict,varyList)
            covData = {'variables':result[0],'varyList':varyList,'sig':sig,'Rvals':Rvals,
                       'varyListStart':varyListStart,
                       'covMatrix':covMatrix,'title':GPXfile,'newAtomDict':newAtomDict,
                       'newCellDict':newCellDict,'freshCOV':True}
            # add the uncertainties into the esd dictionary (sigDict)
            sigDict.update(G2mv.ComputeDepESD(covMatrix,varyList,parmDict))
            G2mv.PrintIndependentVars(parmDict,varyList,sigDict,pFile=printFile)
            G2stMth.ApplyRBModels(parmDict,Phases,rigidbodyDict,True)
            G2stIO.SetRigidBodyModels(parmDict,sigDict,rigidbodyDict,printFile)
            G2stIO.SetPhaseData(parmDict,sigDict,Phases,rbIds,covData,restraintDict,printFile)
            G2stIO.SetHistogramPhaseData(parmDict,sigDict,Phases,Histograms,calcControls['FFtables'],pFile=printFile)
            G2stIO.SetHistogramData(parmDict,sigDict,Histograms,calcControls['FFtables'],pFile=printFile)
            G2stIO.SetUsedHistogramsAndPhases(GPXfile,Histograms,Phases,rigidbodyDict,covData,makeBack)
            printFile.close()
            G2fil.G2Print (' Refinement results are in file: '+ospath.splitext(GPXfile)[0]+'.lst')
            G2fil.G2Print (' ***** Refinement successful *****')
        else:
            G2fil.G2Print ('****ERROR - Refinement failed')
            raise G2obj.G2Exception('****ERROR - Refinement failed')
    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

#for testing purposes, create a file for testderiv
    if GSASIIpath.GetConfigValue('debug'):   # and IfOK:
#needs: values,HistoPhases,parmDict,varylist,calcControls,pawleyLookup
        fl = open(ospath.splitext(GPXfile)[0]+'.testDeriv','wb')
        cPickle.dump(result[0],fl,1)
        cPickle.dump([Histograms,Phases,restraintDict,rigidbodyDict],fl,1)
        cPickle.dump([constrDict,fixedList,G2mv.GetDependentVars()],fl,1)
        cPickle.dump(parmDict,fl,1)
        cPickle.dump(varyList,fl,1)
        cPickle.dump(calcControls,fl,1)
        cPickle.dump(pawleyLookup,fl,1)
        fl.close()
    if dlg:
        return True,Rvals