Source code for G2sfact
# -*- coding: utf-8 -*-
########### SVN repository information ###################
# $Date: 2015-07-09 17:00:23 -0500 (Thu, 09 Jul 2015) $
# $Author: vondreele $
# $Revision: 1924 $
# $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/imports/G2sfact.py $
# $Id: G2sfact.py 1924 2015-07-09 22:00:23Z vondreele $
########### SVN repository information ###################
'''
*Module G2sfact: simple HKL import*
-----------------------------------
Read structure factors from a simple hkl file. Two routines are
provided to read from files containing F or F\ :sup:`2` values.
'''
import sys
import numpy as np
import copy
import GSASIIIO as G2IO
import GSASIIpath
GSASIIpath.SetVersionNumber("$Revision: 1924 $")
[docs]def ColumnValidator(parent, filepointer,nCol=5):
'Validate a file to check that it contains columns of numbers'
l = filepointer.readline()
line = 1
while l[0] in ['#','(']: #get past comments & fortran formats, if any
l = filepointer.readline()
line += 1
for i in range(10): # scan a few lines
S = l.split()
if len(S) < nCol:
parent.errors = 'line '+str(line)+': invalid input\n'+l
return False
for v in S[:nCol]:
try:
float(v)
except ValueError:
parent.errors = 'line '+str(line)+': string found where a number is expected\n'+l
return False
l = filepointer.readline()
line += 1
return True
[docs]class HKLF_ReaderClass(G2IO.ImportStructFactor):
'Routines to import F, sig(F) reflections from a HKLF file'
def __init__(self):
super(self.__class__,self).__init__( # fancy way to self-reference
extensionlist=('.hkl','.HKL'),
strictExtension=False,
formatName = 'HKL F',
longFormatName = 'Simple [hkl, Fo, sig(Fo)] Structure factor text file'
)
[docs] def ContentsValidator(self, filepointer):
'Make sure file contains the expected columns on numbers'
return ColumnValidator(self, filepointer)
[docs] def Reader(self,filename,filepointer, ParentFrame=None, **unused):
'Read the file'
try:
for line,S in enumerate(filepointer):
self.errors = ' Error reading line '+str(line+1)
if S[0] == '#': continue #ignore comments, if any
h,k,l,Fo,sigFo = S.split()
h,k,l = [int(h),int(k),int(l)]
if not any([h,k,l]):
break
Fo = float(Fo)
sigFo = float(sigFo)
# h,k,l,m,dsp,Fo2,sig,Fc2,Fot2,Fct2,phase,...
self.RefDict['RefList'].append([h,k,l,1,0,Fo**2,2.*Fo*sigFo,0,Fo**2,0,0,0])
self.errors = 'Error after reading reflections (unexpected!)'
self.RefDict['RefList'] = np.array(self.RefDict['RefList'])
self.RefDict['Type'] = 'SXC'
self.RefDict['Super'] = 0
self.UpdateParameters(Type='SXC',Wave=None) # histogram type
return True
except Exception as detail:
self.errors += '\n '+str(detail)
print '\n\n'+self.formatName+' read error: '+str(detail) # for testing
import traceback
traceback.print_exc(file=sys.stdout)
return False
[docs]class SHELX4_ReaderClass(G2IO.ImportStructFactor):
'Routines to import F**2, sig(F**2) reflections from a Shelx HKLF 4 file'
def __init__(self):
if 'linux' in sys.platform: # wx 3.0.0.0 on gtk does not like Unicode in menus
formatName = 'HKLF 4'
longFormatName = 'Shelx HKLF 4 [hkl, Fo2, sig(Fo2)] Structure factor text file'
else:
formatName = u'Shelx HKLF 4 F\u00b2'
longFormatName = u'Shelx HKLF 4 [hkl, Fo\u00b2, sig(Fo\u00b2)] Structure factor text file'
super(self.__class__,self).__init__( # fancy way to self-reference
extensionlist=('.hkl','.HKL'),
strictExtension=False,
formatName=formatName,
longFormatName=longFormatName)
[docs] def ContentsValidator(self, filepointer):
'Make sure file contains the expected columns on numbers'
return ColumnValidator(self, filepointer)
[docs] def Reader(self,filename,filepointer, ParentFrame=None, **unused):
'Read the file'
try:
for line,S in enumerate(filepointer):
self.errors = ' Error reading line '+str(line+1)
if S[0] == '#': continue #ignore comments, if any
h,k,l,Fo,sigFo = S[:4],S[4:8],S[8:12],S[12:20],S[20:28]
h,k,l = [int(h),int(k),int(l)]
if not any([h,k,l]):
break
Fo = float(Fo)
sigFo = float(sigFo)
# h,k,l,m,dsp,Fo2,sig,Fc2,Fot2,Fct2,phase,...
self.RefDict['RefList'].append([h,k,l,1,0,Fo,sigFo,0,Fo,0,0,0])
#self.RefDict['FF'].append({}) # now done in OnImportSfact
self.errors = 'Error after reading reflections (unexpected!)'
self.RefDict['RefList'] = np.array(self.RefDict['RefList'])
self.RefDict['Type'] = 'SXC'
self.RefDict['Super'] = 0
self.UpdateParameters(Type='SXC',Wave=None) # histogram type
return True
except Exception as detail:
self.errors += '\n '+str(detail)
print '\n\n'+self.formatName+' read error: '+str(detail) # for testing
import traceback
traceback.print_exc(file=sys.stdout)
return False
[docs]class SHELX5_ReaderClass(G2IO.ImportStructFactor):
'Routines to import F**2, sig(F**2) twin/incommensurate reflections from a fixed format SHELX HKLF5 file'
def __init__(self):
if 'linux' in sys.platform: # wx 3.0.0.0 on gtk does not like Unicode in menus
formatName = 'Shelx HKLF 5 F2 Tw/Incom'
longFormatName = 'Shelx HKLF 5 [hklm, Fo2, sig(Fo2), Tind] Twin/incommensurate structure factor text file'
else:
formatName = u'Shelx HKLF 5 F\u00b2 Tw/Incom'
longFormatName = u'Shelx HKLF 5 [hklm, Fo\u00b2, sig(Fo\u00b2), Tind] Twin/incommensurate structure factor text file'
super(self.__class__,self).__init__( # fancy way to self-reference
extensionlist=('.hkl','.HKL'),
strictExtension=False,
formatName=formatName,
longFormatName=longFormatName)
self.Super = 0
[docs] def ContentsValidator(self, filepointer):
'''Discover how many columns before F^2 are in the SHELX HKL5 file
- could be 3-6 depending on satellites'''
numCols = 0
for i,line in enumerate(filepointer):
for j,item in enumerate(line.split()): #find 1st col with '.'; has F^2
if '.' in item:
numCols = max(numCols,j)
break
if i > 20:
break
self.Super = numCols-3 #= 0,1,2,or 3
if self.Super > 1:
raise self.ImportException("Supersymmetry too high; GSAS-II limited to (3+1) supersymmetry")
return True
[docs] def Reader(self,filename,filepointer, ParentFrame=None, **unused):
'Read the file'
TwDict = {}
TwSet = {}
TwMax = [-1,[]]
first = True
try:
for line,S in enumerate(filepointer):
self.errors = ' Error reading line '+str(line+1)
if self.Super == 0:
h,k,l,Fo,sigFo,Tw = S[:4],S[4:8],S[8:12],S[12:20],S[20:28],S[28:32]
h,k,l = [int(h),int(k),int(l)]
elif self.Super == 1:
h,k,l,m1,Fo,sigFo,Tw = S[:4],S[4:8],S[8:12],S[12:16],S[16:24],S[24:32],S[32:36]
h,k,l,m1 = [int(h),int(k),int(l),int(m1)]
Tw = Tw.strip()
if Tw in ['','0']:
Tw = '1'
if not any([h,k,l]):
break
if '-' in Tw:
if Tw == '-1': #fix reversed twin ids
Tw = '-2'
if first:
self.warnings += '\nPrimary twin id changed to 1'
first = False
TwId = -int(Tw)-1
TwSet[TwId] = np.array([h,k,l])
if TwId not in TwMax[1]:
TwMax[1].append(TwId)
else:
if Tw != '1': #fix reversed twin ids
if first:
self.warnings += '\nPrimary twin id changed to 1\nNB: multiple primary twins not working'
first = False
Tw = '1'
TwId = int(Tw)-1
if TwSet:
TwDict[len(self.RefDict['RefList'])] = TwSet
TwSet = {}
Fo = float(Fo)
sigFo = float(sigFo)
# h,k,l,m,dsp,Fo2,sig,Fc2,Fot2,Fct2,phase,...
if self.Super == 0:
self.RefDict['RefList'].append([h,k,l,int(Tw),0,Fo,sigFo,0,Fo,0,0,0])
elif self.Super == 1:
self.RefDict['RefList'].append([h,k,l,m1,int(Tw),0,Fo,sigFo,0,Fo,0,0,0])
TwMax[0] = max(TwMax[0],TwId)
self.errors = 'Error after reading reflections (unexpected!)'
self.RefDict['RefList'] = np.array(self.RefDict['RefList'])
self.RefDict['Type'] = 'SXC'
self.RefDict['Super'] = self.Super
self.RefDict['TwDict'] = TwDict
self.RefDict['TwMax'] = TwMax
self.UpdateParameters(Type='SXC',Wave=None) # histogram type
return True
except Exception as detail:
self.errors += '\n '+str(detail)
print '\n\n'+self.formatName+' read error: '+str(detail) # for testing
import traceback
traceback.print_exc(file=sys.stdout)
return False
[docs]class M90_ReaderClass(G2IO.ImportStructFactor):
'Routines to import F**2, sig(F**2) reflections from a JANA M90 file'
def __init__(self):
if 'linux' in sys.platform: # wx 3.0.0.0 on gtk does not like Unicode in menus
longFormatName = 'JANA [hkl, Fo2, sig(Fo2)] Structure factor text file'
else:
longFormatName = u'JANA [hkl, Fo\u00b2, sig(Fo\u00b2)] Structure factor text file'
super(self.__class__,self).__init__( # fancy way to self-reference
extensionlist=('.m90','.M90'),
strictExtension=False,
formatName = u'JANA M90',
longFormatName = longFormatName
)
self.Super = 0
[docs] def ContentsValidator(self, filepointer):
'Discover how many columns are in the m90 file - could be 9-12 depending on satellites'
numCols = 0
for i,line in enumerate(filepointer):
if 'Data' in line:
startData = i
break
for i,line in enumerate(filepointer):
if i > startData:
numCols = max(numCols,len(line.split()))
if i > startData+20:
break
self.Super = numCols-9 #= 0,1,2,or 3
if self.Super > 1:
raise self.ImportException("Supersymmetry too high; GSAS-II limited to (3+1) supersymmetry")
return True #ColumnValidator(self, filepointer)
[docs] def Reader(self,filename,filepointer, ParentFrame=None, **unused):
'Read the file'
try:
for line,S in enumerate(filepointer):
self.errors = ' Error reading line '+str(line+1)
if S[0] == '#': continue #ignore comments, if any
try:
if self.Super == 0:
h,k,l,Fo,sigFo = S.split()[:5]
h,k,l = [int(h),int(k),int(l)]
elif self.Super == 1:
h,k,l,m1,Fo,sigFo = S.split()[:6]
h,k,l,m1 = [int(h),int(k),int(l),int(m1)]
except ValueError: #skipping text at front
if not S:
break
text = S.split()
if text[0] == 'lambda':
wave = float(text[1])
continue
Fo = float(Fo)
sigFo = float(sigFo)
# h,k,l,m,dsp,Fo2,sig,Fc2,Fot2,Fct2,phase,...
if self.Super == 0:
self.RefDict['RefList'].append([h,k,l,1,0,Fo,sigFo,0,Fo,0,0,0])
elif self.Super == 1:
self.RefDict['RefList'].append([h,k,l,m1,1,0,Fo,sigFo,0,Fo,0,0,0])
self.errors = 'Error after reading reflections (unexpected!)'
self.RefDict['RefList'] = np.array(self.RefDict['RefList'])
self.RefDict['Type'] = 'SXC'
self.RefDict['Super'] = self.Super
self.UpdateParameters(Type='SXC',Wave=wave) # histogram type
return True
except Exception as detail:
self.errors += '\n '+str(detail)
print '\n\n'+self.formatName+' read error: '+str(detail) # for testing
import traceback
traceback.print_exc(file=sys.stdout)
return False
[docs]class NT_HKLF2_ReaderClass(G2IO.ImportStructFactor):
'Routines to import neutron TOF F**2, sig(F**2) reflections from a HKLF file'
def __init__(self):
if 'linux' in sys.platform: # wx 3.0.0.0 on gtk does not like Unicode in menus
formatName = 'Neutron TOF HKL F2'
longFormatName = 'Neutron TOF [hkl, Fo2, sig(Fo2),...] Structure factor text file'
else:
formatName = u'Neutron TOF HKL F\u00b2'
longFormatName = u'Neutron TOF [hkl, Fo\u00b2, sig(Fo\u00b2),...] Structure factor text file'
super(self.__class__,self).__init__( # fancy way to self-reference
extensionlist=('.hkl','.HKL'),
strictExtension=False,
formatName=formatName,
longFormatName=longFormatName)
[docs] def ContentsValidator(self, filepointer):
'Make sure file contains the expected columns on numbers & count number of data blocks - "Banks"'
oldNo = -1
for line,S in enumerate(filepointer):
if not S: #empty line terminates read
break
if S[0] == '#': continue #ignore comments, if any
if S.split()[:3] == ['0','0','0']:
break
bankNo = S.split()[5]
if bankNo != oldNo:
self.Banks.append({'RefDict':{'RefList':[],}})
oldNo = bankNo
filepointer.seek(0)
return ColumnValidator(self, filepointer,nCol=8)
[docs] def Reader(self,filename,filepointer, ParentFrame=None, **unused):
'Read the file'
filepointer.seek(0)
try:
for line,S in enumerate(filepointer):
self.errors = ' Error reading line '+str(line+1)
if S[0] == '#': continue #ignore comments, if any
data = S.split()
h,k,l,Fo,sigFo,bN,wave,tbar = data[:8] #bN = 1..., 6 dir cos next
h,k,l = [int(h),int(k),int(l)]
if not any([h,k,l]):
break
Fo = float(Fo)
sigFo = float(sigFo)
wave = float(wave)
tbar = float(tbar)
if len(self.Banks):
self.Banks[int(bN)-1]['RefDict']['RefList'].append([h,k,l,1,0,Fo,sigFo,0,Fo,0,0,0,wave,tbar])
else:
# h,k,l,m,dsp,Fo2,sig,Fc2,Fot2,Fct2,phase,...
self.RefDict['RefList'].append([h,k,l,1,0,Fo,sigFo,0,Fo,0,0,0,wave,tbar])
if len(self.Banks):
self.UpdateParameters(Type='SNT',Wave=None) # histogram type
for Bank in self.Banks:
Bank['RefDict']['RefList'] = np.array(Bank['RefDict']['RefList'])
Bank['RefDict']['Type'] = 'SNT'
Bank['RefDict']['Super'] = 0
else:
self.RefDict['RefList'] = np.array(self.RefDict['RefList'])
self.RefDict['Type'] = 'SNT'
self.RefDict['Super'] = 0
self.errors = 'Error after reading reflections (unexpected!)'
self.UpdateParameters(Type='SNT',Wave=None) # histogram type
return True
except Exception as detail:
self.errors += '\n '+str(detail)
print '\n\n'+self.formatName+' read error: '+str(detail) # for testing
import traceback
traceback.print_exc(file=sys.stdout)
return False
[docs]class NT_JANA2K_ReaderClass(G2IO.ImportStructFactor):
'Routines to import neutron TOF F**2, sig(F**2) reflections from a JANA2000 file'
def __init__(self):
if 'linux' in sys.platform: # wx 3.0.0.0 on gtk does not like Unicode in menus
formatName = 'Neutron TOF JANA2000 F2'
longFormatName = 'Neutron TOF [hkl, Fo2, sig(Fo2),...] Structure factor text file'
else:
formatName = u'Neutron TOF JANA2000 F\u00b2'
longFormatName = u'Neutron TOF [hkl, Fo\u00b2, sig(Fo\u00b2),...] Structure factor text file'
super(self.__class__,self).__init__( # fancy way to self-reference
extensionlist=('.int','.INT'),
strictExtension=False,
formatName=formatName,
longFormatName=longFormatName)
[docs] def ContentsValidator(self, filepointer):
'Make sure file contains the expected columns on numbers & count number of data blocks - "Banks"'
oldNo = -1
for line,S in enumerate(filepointer):
if not S: #empty line terminates read
break
if S[0] in ['#','(']: continue #ignore comments & fortran format line
bankNo = S.split()[5]
if bankNo != oldNo:
self.Banks.append({'RefDict':{'RefList':[],}})
oldNo = bankNo
filepointer.seek(0)
return ColumnValidator(self, filepointer,nCol=10)
[docs] def Reader(self,filename,filepointer, ParentFrame=None, **unused):
'Read the file'
filepointer.seek(0)
try:
for line,S in enumerate(filepointer):
self.errors = ' Error reading line '+str(line+1)
if S[0] in ['#','(']: continue #ignore comments & fortran format line
data = S.split()
h,k,l,Fo,sigFo,bN,wave,x,x,tbar = data[:10] #bN = 1..., 6 dir cos next
h,k,l = [int(h),int(k),int(l)]
if not any([h,k,l]):
break
Fo = float(Fo)
sigFo = float(sigFo)
wave = float(wave)
tbar = float(tbar)
if len(self.Banks):
self.Banks[int(bN)-1]['RefDict']['RefList'].append([h,k,l,1,0,Fo,sigFo,0,Fo,0,0,0,wave,tbar])
else:
# h,k,l,m,dsp,Fo2,sig,Fc2,Fot2,Fct2,phase,...
self.RefDict['RefList'].append([h,k,l,1,0,Fo,sigFo,0,Fo,0,0,0,wave,tbar])
if len(self.Banks):
self.UpdateParameters(Type='SNT',Wave=None) # histogram type
for Bank in self.Banks:
Bank['RefDict']['RefList'] = np.array(Bank['RefDict']['RefList'])
Bank['RefDict']['Type'] = 'SNT'
Bank['RefDict']['Super'] = 0 #for now
else:
self.RefDict['RefList'] = np.array(self.RefDict['RefList'])
self.RefDict['Type'] = 'SNT'
self.RefDict['Super'] = 0 #for now
self.errors = 'Error after reading reflections (unexpected!)'
self.UpdateParameters(Type='SNT',Wave=None) # histogram type
return True
except Exception as detail:
self.errors += '\n '+str(detail)
print '\n\n'+self.formatName+' read error: '+str(detail) # for testing
import traceback
traceback.print_exc(file=sys.stdout)
return False
[docs]class ISIS_SXD_INT_ReaderClass(G2IO.ImportStructFactor):
'Routines to import neutron TOF F**2, sig(F**2) reflections from a ISIS int file'
def __init__(self):
if 'linux' in sys.platform: # wx 3.0.0.0 on gtk does not like Unicode in menus
formatName = u'Neutron SXD TOF HKL F2'
longFormatName = u'Neutron SXD TOF [hkl, Fo2, sig(Fo2),...] Structure factor text file'
else:
formatName = u'Neutron SXD TOF HKL F\u00b2'
longFormatName = u'Neutron SXD TOF [hkl, Fo\u00b2, sig(Fo\u00b2),...] Structure factor text file'
super(self.__class__,self).__init__( # fancy way to self-reference
extensionlist=('.int','.INT'),
strictExtension=False,
formatName=formatName,
longFormatName=longFormatName)
[docs] def ContentsValidator(self, filepointer):
'Make sure file contains the expected columns on numbers & count number of data blocks - "Banks"'
oldNo = -1
for line,S in enumerate(filepointer):
if not S: #empty line terminates read
break
if S[0] == '#': continue #ignore comments, if any
if S[0] == '(': continue #ignore format line
bankNo = S.split()[5]
if bankNo != oldNo:
self.Banks.append({'RefDict':{'RefList':[],}})
oldNo = bankNo
filepointer.seek(0)
return ColumnValidator(self, filepointer,nCol=8)
[docs] def Reader(self,filename,filepointer, ParentFrame=None, **unused):
'Read the file'
filepointer.seek(0)
try:
for line,S in enumerate(filepointer):
self.errors = ' Error reading line '+str(line+1)
if S[0] == '#': continue #ignore comments, if any
if S[0] == '(': continue #ignore the format line
data = S.split()
h,k,l,Fo,sigFo,bN,wave,x,x,tbar = data[:10]
h,k,l = [int(h),int(k),int(l)]
if not any([h,k,l]):
break
Fo = float(Fo)
sigFo = float(sigFo)
wave = float(wave)
tbar = float(tbar)
if len(self.Banks):
self.Banks[int(bN)-1]['RefDict']['RefList'].append([h,k,l,1,0,Fo,sigFo,0,Fo,0,0,0,wave,tbar])
else:
# h,k,l,m,dsp,Fo2,sig,Fc2,Fot2,Fct2,phase,...
self.RefDict['RefList'].append([h,k,l,1,0,Fo,sigFo,0,Fo,0,0,0,wave,tbar])
if len(self.Banks):
self.UpdateParameters(Type='SNT',Wave=None) # histogram type
for Bank in self.Banks:
Bank['RefDict']['RefList'] = np.array(Bank['RefDict']['RefList'])
Bank['RefDict']['Type'] = 'SNT'
Bank['RefDict']['Super'] = 0
else:
self.RefDict['RefList'] = np.array(self.RefDict['RefList'])
self.RefDict['Type'] = 'SNT'
self.RefDict['Super'] = 0
self.errors = 'Error after reading reflections (unexpected!)'
self.UpdateParameters(Type='SNT',Wave=None) # histogram type
return True
except Exception as detail:
self.errors += '\n '+str(detail)
print '\n\n'+self.formatName+' read error: '+str(detail) # for testing
import traceback
traceback.print_exc(file=sys.stdout)
return False
