def Reader(self, filename, ParentFrame=None, **unused):
'''Read a phase from a .GPX file. Does not (yet?) support selecting and reading
more than one phase at a time.'''
try:
phasenames = G2stIO.GetPhaseNames(filename)
except:
self.errors = 'Reading of phase names failed'
return False
if not phasenames:
self.errors = 'No phases found in ' + str(filename)
return False # no blocks with coordinates
elif len(phasenames) == 1: # one block, no choices
selblk = 0
else: # choose from options
selblk = G2IO.PhaseSelector(
phasenames,
ParentFrame=ParentFrame,
title='Select a phase from the list below',
)
if selblk is None:
self.errors = 'No phase selected'
return False # User pressed cancel
self.Phase = G2stIO.GetAllPhaseData(filename, phasenames[selblk])
self.Phase['Histograms'] = {} #remove any histograms
self.Phase['Pawley ref'] = [] # & any Pawley refl.
self.Phase['RBModels'] = {}
if 'MCSA' in self.Phase:
del self.Phase['MCSA']
if 'Map Peaks' in self.Phase:
del self.Phase['Map Peaks']
if 'Map' in self.Phase['General']:
del self.Phase['General']['Map']
self.Phase['ranId'] = ran.randint(0, sys.maxsize)
return True
def Reader(self, filename, filepointer, ParentFrame=None, **unused):
'''Read a phase from a .GPX file. Does not (yet?) support selecting and reading
more than one phase at a time.'''
try:
phasenames = G2stIO.GetPhaseNames(filename)
except:
self.errors = 'Reading of phase names failed'
return False
if not phasenames:
self.errors = 'No phases found in ' + str(filename)
return False # no blocks with coordinates
elif len(phasenames) == 1: # one block, no choices
selblk = 0
else: # choose from options
selblk = self.PhaseSelector(
phasenames,
ParentFrame=ParentFrame,
title='Select a phase from the list below',
)
if selblk is None:
self.errors = 'No phase selected'
return False # User pressed cancel
try:
self.Phase = G2stIO.GetAllPhaseData(filename, phasenames[selblk])
self.Phase['Histograms'] = {} #remove any histograms
self.Phase['Pawley ref'] = [] # & any Pawley refl.
self.Phase['ranId'] = ran.randint(0, sys.maxint)
return True
except Exception as detail:
self.errors = 'Error reading selected phase'
self.errors += '\n ' + str(detail)
print self.formatName + ' error:', detail # for testing
print sys.exc_info()[0] # for testing
import traceback
print traceback.format_exc()
def __init__(self, GPXfile=None):
'''
Initialize the setup using an existing GPXfile
'''
if not GPXfile:
# TO DO: Raise name error
raise NameError('Must input some GPX file')
# Initallizing variables from input file GPXfile
G2path.SetBinaryPath()
varyList = []
parmDict = {}
symmetry = {}
Controls = G2stIO.GetControls(GPXfile)
calcControls = {}
calcControls.update(Controls)
constrDict, fixedList = G2stIO.GetConstraints(GPXfile)
restraintDict = G2stIO.GetRestraints(GPXfile)
Histograms, Phases = G2stIO.GetUsedHistogramsAndPhases(GPXfile)
rigidbodyDict = G2stIO.GetRigidBodies(GPXfile)
rbIds = rigidbodyDict.get('RBIds', {'Vector': [], 'Residue': []})
rbVary, rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict, Print=False)
(Natoms, atomIndx, phaseVary, phaseDict, pawleyLookup, FFtables,
BLtables, MFtables, maxSSwave) = G2stIO.GetPhaseData(Phases,
restraintDict,
rbIds,
Print=False)
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, Print=False)
calcControls.update(controlDict)
histVary, histDict, controlDict = G2stIO.GetHistogramData(Histograms,
Print=False)
calcControls.update(controlDict)
varyList = rbVary + phaseVary + hapVary + histVary
parmDict.update(rbDict)
parmDict.update(phaseDict)
parmDict.update(hapDict)
parmDict.update(histDict)
G2stIO.GetFprime(calcControls, Histograms)
# define phase symmetries, currently only works for one phase
phase = G2stIO.GetPhaseNames(GPXfile)
phaseData = {}
for name in phase:
phaseData[name] = G2stIO.GetAllPhaseData(GPXfile, name)
symmetry[name] = phaseData[name]['General']['SGData']['SGSys']
# Save the instance parameters
self._Histograms = Histograms
self._varyList = varyList
self._parmDict = parmDict
self._Phases = Phases
self._calcControls = calcControls
self._pawleyLookup = pawleyLookup
self._restraintDict = restraintDict
self._rigidbodyDict = rigidbodyDict
self._rbIds = rbIds
self._symmetry = symmetry
self._phase = phase
try:
self._lowerLimit = Histograms[list(
Histograms.keys())[0]][u'Limits'][1][0]
self._upperLimit = Histograms[list(
Histograms.keys())[0]][u'Limits'][1][1]
self._tth = Histograms[list(Histograms.keys())[0]]['Data'][0][0:-1]
self._tthsample = self._tth[np.where(
(self._tth > self._lowerLimit)
& (self._tth < self._upperLimit) == True)] # noqa: E712
self._SingleXtal = False
except: # noqa: E722
self._tth = None
self._MaxDiffSig = None
self._Fosq = 0
self._FoSig = 0
self._Fcsq = 0
self._SingleXtal = True