def monoCellReduce(ibrav,A):
'needs a doc string'
a,b,c,alp,bet,gam = G2lat.A2cell(A)
G,g = G2lat.A2Gmat(A)
if ibrav in [11]:
u = [0,0,-1]
v = [1,0,2]
anew = math.sqrt(np.dot(np.dot(v,g),v))
if anew < a:
cang = np.dot(np.dot(u,g),v)/(anew*c)
beta = acosd(-abs(cang))
A = G2lat.cell2A([anew,b,c,90,beta,90])
else:
u = [-1,0,0]
v = [1,0,1]
cnew = math.sqrt(np.dot(np.dot(v,g),v))
if cnew < c:
cang = np.dot(np.dot(u,g),v)/(a*cnew)
beta = acosd(-abs(cang))
A = G2lat.cell2A([a,b,cnew,90,beta,90])
return A
def monoCellReduce(ibrav,A):
'needs a doc string'
a,b,c,alp,bet,gam = G2lat.A2cell(A)
G,g = G2lat.A2Gmat(A)
if ibrav in [13]:
u = [0,0,-1]
v = [1,0,2]
anew = math.sqrt(np.dot(np.dot(v,g),v))
if anew < a:
cang = np.dot(np.dot(u,g),v)/(anew*c)
beta = acosd(-abs(cang))
A = G2lat.cell2A([anew,b,c,90,beta,90])
else:
u = [-1,0,0]
v = [1,0,1]
cnew = math.sqrt(np.dot(np.dot(v,g),v))
if cnew < c:
cang = np.dot(np.dot(u,g),v)/(a*cnew)
beta = acosd(-abs(cang))
A = G2lat.cell2A([a,b,cnew,90,beta,90])
return A
def convert_lattice(self, paramList, params):
'''
Convert between A and unit cell parameters. A is defined in GSAS-II
as A = [G11, G22, G33, 2*G12, 2*G13, 2*G23] with G as the
reciprocal metric tensor elements.
'''
latparamList = [
'0::A0', '1::A0', '2::A0', '3::A0', '4::A0', '5::A0', '6::A0',
'7::A0', '8::A0', '9::A0', '10::A0'
]
check = any(item in paramList for item in latparamList)
if check is True:
return G2latt.A2cell(params)
else:
return G2latt.cell2A(params)
def findMV(peaks,controls,ssopt,Inst,dlg):
def Val2Vec(vec,Vref,values):
Vec = []
i = 0
for j,r in enumerate(Vref):
if r:
if values.size > 1:
Vec.append(max(0.0,min(1.0,values[i])))
else:
Vec.append(max(0.0,min(1.0,values)))
i += 1
else:
Vec.append(vec[j])
return np.array(Vec)
def ZSSfunc(values,peaks,dmin,Inst,SGData,SSGData,vec,Vref,maxH,A,wave,Z,dlg=None):
Vec = Val2Vec(vec,Vref,values)
HKL = G2pwd.getHKLMpeak(dmin,Inst,SGData,SSGData,Vec,maxH,A)
Peaks = np.array(IndexSSPeaks(peaks,HKL)[1]).T
Qo = 1./Peaks[-2]**2
Qc = G2lat.calc_rDsqZSS(Peaks[4:8],A,Vec,Z,Peaks[0],wave)
chi = np.sum((Qo-Qc)**2)
if dlg:
dlg.Pulse()
return chi
if 'C' in Inst['Type'][0]:
wave = G2mth.getWave(Inst)
else:
difC = Inst['difC'][1]
SGData = G2spc.SpcGroup(controls[13])[1]
SSGData = G2spc.SSpcGroup(SGData,ssopt['ssSymb'])[1]
A = G2lat.cell2A(controls[6:12])
Z = controls[1]
Vref = [True if x in ssopt['ssSymb'] else False for x in ['a','b','g']]
values = []
ranges = []
for v,r in zip(ssopt['ModVec'],Vref):
if r:
ranges += [slice(.02,.98,.05),]
values += [v,]
dmin = getDmin(peaks)-0.005
Peaks = np.copy(np.array(peaks).T)
result = so.brute(ZSSfunc,ranges,finish=so.fmin_cg,
args=(peaks,dmin,Inst,SGData,SSGData,ssopt['ModVec'],Vref,ssopt['maxH'],A,wave,Z,dlg))
return Val2Vec(ssopt['ModVec'],Vref,result)
def test0():
if NeedTestData: TestData()
ibrav, cell, bestcell, Pwr, peaks = TestData
print('best cell:', bestcell)
print('old cell:', cell)
Peaks = np.array(peaks)
HKL = Peaks[4:7]
print(calc_M20(peaks, HKL))
A = G2lat.cell2A(cell)
OK, smin, A, result = FitHKL(ibrav, peaks, A, Pwr)
print('new cell:', G2lat.A2cell(A))
print('x:', result[0])
print('cov_x:', result[1])
print('infodict:')
for item in result[2]:
print(item, result[2][item])
print('msg:', result[3])
print('ier:', result[4])
result = refinePeaks(peaks, ibrav, A)
N, M20, X20, A = result
print('refinePeaks:', N, M20, X20, G2lat.A2cell(A))
print('compare bestcell:', bestcell)
def SHPenalty(POData):
def OnHKLList(event):
dlg = G2G.G2MultiChoiceDialog(G2frame, 'Select penalty hkls',
'Penalty hkls',hkls,filterBox=False)
try:
if dlg.ShowModal() == wx.ID_OK:
POData[6] = [hkls[i] for i in dlg.GetSelections()]
if not POData[6]:
POData[6] = ['',]
else:
return
finally:
dlg.Destroy()
wx.CallLater(100,RepaintHistogramInfo)
def OnshToler(event):
try:
value = float(shToler.GetValue())
POData[7] = value
except ValueError:
pass
shToler.SetValue('%.2f'%(POData[7]))
A = G2lat.cell2A(generalData['Cell'][1:7])
hkls = G2lat.GenPfHKLs(10,SGData,A)
shPenalty = wx.BoxSizer(wx.HORIZONTAL)
shPenalty.Add(wx.StaticText(DData,wx.ID_ANY,' Negative MRD penalty list: '),0,WACV)
shPenalty.Add(wx.ComboBox(DData,value=POData[6][0],choices=POData[6],
style=wx.CB_DROPDOWN),0,WACV)
hklList = wx.Button(DData,label='Select penalty hkls')
hklList.Bind(wx.EVT_BUTTON,OnHKLList)
shPenalty.Add(hklList,0,WACV)
shPenalty.Add(wx.StaticText(DData,wx.ID_ANY,' Zero MRD tolerance: '),0,WACV)
shToler = wx.TextCtrl(DData,wx.ID_ANY,'%.2f'%(POData[7]),style=wx.TE_PROCESS_ENTER)
shToler.Bind(wx.EVT_TEXT_ENTER,OnshToler)
shToler.Bind(wx.EVT_KILL_FOCUS,OnshToler)
shPenalty.Add(shToler,0,WACV)
return shPenalty
def test0():
if NeedTestData: TestData()
msg = 'test FitHKL'
ibrav, cell, bestcell, Pwr, peaks = TestData
print 'best cell:', bestcell
print 'old cell:', cell
Peaks = np.array(peaks)
HKL = Peaks[4:7]
print calc_M20(peaks, HKL)
A = G2lat.cell2A(cell)
OK, smin, A, result = FitHKL(ibrav, peaks, A, Pwr)
print 'new cell:', G2lat.A2cell(A)
print 'x:', result[0]
print 'cov_x:', result[1]
print 'infodict:'
for item in result[2]:
print item, result[2][item]
print 'msg:', result[3]
print 'ier:', result[4]
result = refinePeaks(peaks, ibrav, A)
N, M20, X20, A = result
print 'refinePeaks:', N, M20, X20, G2lat.A2cell(A)
print 'compare bestcell:', bestcell
def test0():
if NeedTestData: TestData()
msg = 'test FitHKL'
ibrav,cell,bestcell,Pwr,peaks = TestData
print 'best cell:',bestcell
print 'old cell:',cell
Peaks = np.array(peaks)
HKL = Peaks[4:7]
print calc_M20(peaks,HKL)
A = G2lat.cell2A(cell)
OK,smin,A,result = FitHKL(ibrav,peaks,A,Pwr)
print 'new cell:',G2lat.A2cell(A)
print 'x:',result[0]
print 'cov_x:',result[1]
print 'infodict:'
for item in result[2]:
print item,result[2][item]
print 'msg:',result[3]
print 'ier:',result[4]
result = refinePeaks(peaks,ibrav,A)
N,M20,X20,A = result
print 'refinePeaks:',N,M20,X20,G2lat.A2cell(A)
print 'compare bestcell:',bestcell
def ReadPDFPhase(self, G2frame, fp):
'''Read a phase from a ICDD .str file.
'''
EightPiSq = 8. * math.pi**2
self.errors = 'Error opening file'
Phase = {}
Atoms = []
S = fp.readline()
line = 1
SGData = None
cell = []
cellkey = []
while S:
if 'space_group' in S:
break
S = fp.readline()
while S:
self.errors = 'Error reading at line ' + str(line)
if 'phase_name' in S:
Title = S.split('"')[1]
elif 'Space group (HMS)' in S:
SpGrp = S.split()[-1]
SpGrpNorm = G2spc.StandardizeSpcName(SpGrp)
E, SGData = G2spc.SpcGroup(SpGrpNorm)
# space group processing failed, try to look up name in table
while E:
print(G2spc.SGErrors(E))
dlg = wx.TextEntryDialog(
G2frame,
SpGrp[:-1] +
' is invalid \nN.B.: make sure spaces separate axial fields in symbol',
'ERROR in space group symbol',
'',
style=wx.OK)
if dlg.ShowModal() == wx.ID_OK:
SpGrp = dlg.GetValue()
E, SGData = G2spc.SpcGroup(SpGrp)
else:
SGData = G2obj.P1SGData # P 1
self.warnings += '\nThe space group was not interpreted and has been set to "P 1".'
self.warnings += "Change this in phase's General tab."
dlg.Destroy()
G2spc.SGPrint(SGData) #silent check of space group symbol
elif 'a a_' in S[:7]:
data = S.split()
cell.append(float(data[2]))
cellkey.append(data[1])
elif 'b b_' in S[:7]:
data = S.split()
cell.append(float(data[2]))
cellkey.append(data[1])
elif 'b =' in S[:6]:
data = S.split('=')
indx = cellkey.index(data[1].split(';')[0])
cell.append(cell[indx])
elif 'c c_' in S[:7]:
data = S.split()
cell.append(float(data[2]))
elif 'c =' in S[:6]:
data = S.split('=')
indx = cellkey.index(data[1].split(';')[0])
cell.append(cell[indx])
elif 'al' in S[:5]:
cell.append(float(S.split()[1]))
elif 'be' in S[:5]:
cell.append(float(S.split()[1]))
elif 'ga' in S[:5]:
cell.append(float(S.split()[1]))
Volume = G2lat.calc_V(G2lat.cell2A(cell))
break
S = fp.readline()
S = fp.readline()
while S:
if '/*' in S[:5]:
break
if 'site' in S[:7]:
atom = []
xyzkey = []
data = S.split()
atom.append(data[1]) #name
pos = data.index('occ') + 1
atom.append(data[pos]) #type
atom.append('') #refine
for xid in ['x =', 'y =', 'z =']:
if xid in S:
xpos = S.index(xid) + 3
xend = xpos + S[xpos:].index(';')
if S[xpos:xend] in xyzkey:
atom.append(atom[3 + xyzkey.index(S[xpos:xend])])
else:
atom.append(eval(S[xpos:xend] + '.'))
else:
xpos = data.index(xid[0]) + 2
xyzkey.append(data[xpos - 1][1:])
atom.append(float(data[xpos]))
atom.append(float(data[pos + 2]))
SytSym, Mult = G2spc.SytSym(np.array(atom[3:6]), SGData)[:2]
atom.append(SytSym)
atom.append(Mult)
if 'beq' in S:
atom.append('I')
upos = data.index('beq')
atom.append(float(data[upos + 2]) / EightPiSq)
atom += [
0.,
0.,
0.,
0.,
0.,
0.,
]
elif 'ADPs' in S:
upos = data.index('ADPs')
atom.append('A')
atom.append(0.0)
for uid in [
'Bani11', 'Bani22', 'Bani33', 'Bani12', 'Bani13',
'Bani23'
]:
upos = data.index(uid) + 1
atom.append(float(data[upos]) / EightPiSq)
else:
atom.append('I')
atom += [
0.02,
0.,
0.,
0.,
0.,
0.,
0.,
]
atom.append(ran.randint(0, sys.maxsize))
Atoms.append(atom)
S = fp.readline()
fp.close()
self.errors = 'Error after read complete'
if not SGData:
raise self.ImportException("No space group (spcgroup entry) found")
if not cell:
raise self.ImportException("No cell found")
Phase = G2obj.SetNewPhase(Name=Title,
SGData=SGData,
cell=cell + [
Volume,
])
Phase['General']['Type'] = 'nuclear'
Phase['General']['AtomPtrs'] = [3, 1, 7, 9]
Phase['Atoms'] = Atoms
return Phase
def ReadEXPPhase(self, G2frame, filepointer):
'''Read a phase from a GSAS .EXP file.
'''
shModels = ['cylindrical', 'none', 'shear - 2/m', 'rolling - mmm']
textureData = {
'Order': 0,
'Model': 'cylindrical',
'Sample omega': [False, 0.0],
'Sample chi': [False, 0.0],
'Sample phi': [False, 0.0],
'SH Coeff': [False, {}],
'SHShow': False,
'PFhkl': [0, 0, 1],
'PFxyz': [0, 0, 1],
'PlotType': 'Pole figure'
}
shNcof = 0
S = 1
NPhas = []
Expr = [{}, {}, {}, {}, {}, {}, {}, {},
{}] # GSAS can have at most 9 phases
for line, S in enumerate(filepointer):
self.errors = 'Error reading at line ' + str(line + 1)
if 'EXPR NPHAS' in S[:12]:
NPhas = S[12:-1].split()
if 'CRS' in S[:3]:
N = int(S[3:4]) - 1
Expr[N][S[:12]] = S[12:-1]
PNames = []
if not NPhas:
raise self.ImportException("No EXPR NPHAS record found")
self.errors = 'Error interpreting file'
for n, N in enumerate(NPhas):
if N != '0':
result = n
key = 'CRS' + str(n + 1) + ' PNAM'
PNames.append(Expr[n][key])
if len(PNames) == 0:
raise self.ImportException("No phases found")
elif len(PNames) > 1:
dlg = wx.SingleChoiceDialog(G2frame, 'Which phase to read?',
'Read phase data', PNames,
wx.CHOICEDLG_STYLE)
try:
if dlg.ShowModal() == wx.ID_OK:
result = dlg.GetSelection(
) # I think this breaks is there are skipped phases. Cant this happen?
finally:
dlg.Destroy()
EXPphase = Expr[result]
keyList = list(EXPphase.keys())
keyList.sort()
SGData = {}
MPtype = ''
if NPhas[result] == '1':
Ptype = 'nuclear'
elif NPhas[result] == '2':
Ptype = 'nuclear'
MPtype = 'magnetic'
MagDmin = 1.0
elif NPhas[result] == '3':
Ptype = 'magnetic'
MagDmin = 1.0
elif NPhas[result] == '4':
Ptype = 'macromolecular'
elif NPhas[result] == '10':
Ptype = 'Pawley'
else:
raise self.ImportException("Phase type not recognized")
for key in keyList:
if 'PNAM' in key:
PhaseName = EXPphase[key].strip()
elif 'ABC ' in key:
abc = [
float(EXPphase[key][:10]),
float(EXPphase[key][10:20]),
float(EXPphase[key][20:30])
]
elif 'ANGLES' in key:
angles = [
float(EXPphase[key][:10]),
float(EXPphase[key][10:20]),
float(EXPphase[key][20:30])
]
elif 'SG SYM' in key:
SpGrp = EXPphase[key][:15].strip()
E, SGData = G2spc.SpcGroup(SpGrp)
if E:
SGData = G2obj.P1SGData # P 1 -- unlikely to need this!
self.warnings += '\nThe GSAS space group was not interpreted(!) and has been set to "P 1".'
self.warnings += "Change this in phase's General tab."
elif 'SPNFLP' in key:
SpnFlp = np.array(
[int(float(s)) for s in EXPphase[key].split()])
SpnFlp = np.where(SpnFlp == 0, 1, SpnFlp)
SpnFlp = [
1,
] + list(SpnFlp)
if SGData['SpGrp'][0] in ['A', 'B', 'C', 'I', 'R', 'F']:
SpnFlp = list(SpnFlp) + [1, 1, 1, 1]
elif 'MXDSTR' in key:
MagDmin = float(EXPphase[key][:10])
elif 'OD ' in key:
SHdata = EXPphase[key].split() # may not have all 9 values
SHvals = 9 * [0]
for i in range(9):
try:
float(SHdata[i])
SHvals[i] = SHdata[i]
except:
pass
textureData['Order'] = int(SHvals[0])
textureData['Model'] = shModels[int(SHvals[2])]
textureData['Sample omega'] = [False, float(SHvals[6])]
textureData['Sample chi'] = [False, float(SHvals[7])]
textureData['Sample phi'] = [False, float(SHvals[8])]
shNcof = int(SHvals[1])
Volume = G2lat.calc_V(G2lat.cell2A(abc + angles))
Atoms = []
MAtoms = []
Bmat = G2lat.cell2AB(abc + angles)[1]
if Ptype == 'macromolecular':
for key in keyList:
if 'AT' in key[6:8]:
S = EXPphase[key]
Atom = [
S[56:60].strip(), S[50:54].strip().upper(), S[54:56],
S[46:51].strip(), S[:8].strip().capitalize(), '',
float(S[16:24]),
float(S[24:32]),
float(S[32:40]),
float(S[8:16]), '1', 1, 'I',
float(S[40:46]), 0, 0, 0, 0, 0, 0
]
XYZ = Atom[6:9]
Atom[10], Atom[11] = G2spc.SytSym(XYZ, SGData)[:2]
Atom.append(ran.randint(0, sys.maxsize))
Atoms.append(Atom)
else:
for key in keyList:
if 'AT' in key:
if key[11:] == 'A':
S = EXPphase[key]
elif key[11:] == 'B':
S1 = EXPphase[key]
Atom = [
S[50:58].strip(), S[:10].strip().capitalize(), '',
float(S[10:20]),
float(S[20:30]),
float(S[30:40]),
float(S[40:50]), '',
int(S[60:62]), S1[62:63]
]
#float(S[40:50]),'',int(S[60:62]),S1[130:131]]
if Atom[9] == 'I':
Atom += [float(S1[0:10]), 0., 0., 0., 0., 0., 0.]
elif Atom[9] == 'A':
Atom += [
0.0,
float(S1[0:10]),
float(S1[10:20]),
float(S1[20:30]),
float(S1[30:40]),
float(S1[40:50]),
float(S1[50:60])
]
else:
print('Error in line with key: ' + key)
Atom += [0., 0., 0., 0., 0., 0., 0.]
XYZ = Atom[3:6]
Atom[7], Atom[8] = G2spc.SytSym(XYZ, SGData)[:2]
Atom.append(ran.randint(0, sys.maxsize))
Atoms.append(Atom)
elif key[11:] == 'M' and key[6:8] == 'AT':
S = EXPphase[key]
mom = np.array(
[float(S[:10]),
float(S[10:20]),
float(S[20:30])])
mag = np.sqrt(np.sum(mom**2))
mom = np.inner(Bmat, mom) * mag
MAtoms.append(Atom)
MAtoms[-1] = Atom[:7] + list(mom) + Atom[7:]
if shNcof:
shCoef = {}
nRec = [i + 1 for i in range((shNcof - 1) // 6 + 1)]
for irec in nRec:
ODkey = keyList[0][:6] + 'OD' + '%3dA' % (irec)
indx = EXPphase[ODkey].split()
ODkey = ODkey[:-1] + 'B'
vals = EXPphase[ODkey].split()
for i, val in enumerate(vals):
key = 'C(%s,%s,%s)' % (indx[3 * i], indx[3 * i + 1],
indx[3 * i + 2])
shCoef[key] = float(val)
textureData['SH Coeff'] = [False, shCoef]
if not SGData:
raise self.ImportException("No space group found in phase")
if not abc:
raise self.ImportException("No cell lengths found in phase")
if not angles:
raise self.ImportException("No cell angles found in phase")
if not Atoms:
raise self.ImportException("No atoms found in phase")
self.Phase['General'].update({
'Type':
Ptype,
'Name':
PhaseName,
'Cell': [
False,
] + abc + angles + [
Volume,
],
'SGData':
SGData
})
if MPtype == 'magnetic':
self.MPhase['General'].update({
'Type':
'magnetic',
'Name':
PhaseName + ' mag',
'Cell': [
False,
] + abc + angles + [
Volume,
],
'SGData':
SGData
})
else:
self.MPhase = None
if Ptype == 'macromolecular':
self.Phase['General']['AtomPtrs'] = [6, 4, 10, 12]
self.Phase['Atoms'] = Atoms
elif Ptype == 'magnetic':
self.Phase['General']['AtomPtrs'] = [3, 1, 10, 12]
self.Phase['General']['SGData']['SGSpin'] = SpnFlp
self.Phase['General']['MagDmin'] = MagDmin
self.Phase['Atoms'] = MAtoms
else: #nuclear
self.Phase['General']['AtomPtrs'] = [3, 1, 7, 9]
self.Phase['General']['SH Texture'] = textureData
self.Phase['Atoms'] = Atoms
if MPtype == 'magnetic':
self.MPhase['General']['AtomPtrs'] = [3, 1, 10, 12]
self.MPhase['General']['SGData']['SGSpin'] = SpnFlp
self.MPhase['General']['MagDmin'] = MagDmin
self.MPhase['Atoms'] = MAtoms
def ReadPDBPhase(self,filename,parent=None):
'''Read a phase from a PDB file.
'''
EightPiSq = 8.*math.pi**2
self.errors = 'Error opening file'
file = open(filename, 'Ur')
Phase = {}
Title = ''
Compnd = ''
Atoms = []
A = np.zeros(shape=(3,3))
S = file.readline()
line = 1
SGData = None
cell = None
while S:
self.errors = 'Error reading at line '+str(line)
Atom = []
if 'TITLE' in S[:5]:
Title = S[10:72].strip()
elif 'COMPND ' in S[:10]:
Compnd = S[10:72].strip()
elif 'CRYST' in S[:5]:
abc = S[7:34].split()
angles = S[34:55].split()
cell=[float(abc[0]),float(abc[1]),float(abc[2]),
float(angles[0]),float(angles[1]),float(angles[2])]
Volume = G2lat.calc_V(G2lat.cell2A(cell))
AA,AB = G2lat.cell2AB(cell)
SpGrp = S[55:65]
E,SGData = G2spc.SpcGroup(SpGrp)
# space group processing failed, try to look up name in table
if E:
SpGrpNorm = G2spc.StandardizeSpcName(SpGrp)
if SpGrpNorm:
E,SGData = G2spc.SpcGroup(SpGrpNorm)
while E:
print G2spc.SGErrors(E)
dlg = wx.TextEntryDialog(parent,
SpGrp[:-1]+' is invalid \nN.B.: make sure spaces separate axial fields in symbol',
'ERROR in space group symbol','',style=wx.OK)
if dlg.ShowModal() == wx.ID_OK:
SpGrp = dlg.GetValue()
E,SGData = G2spc.SpcGroup(SpGrp)
else:
SGData = G2IO.SGData # P 1
self.warnings += '\nThe space group was not interpreted and has been set to "P 1".'
self.warnings += "Change this in phase's General tab."
dlg.Destroy()
SGlines = G2spc.SGPrint(SGData)
for l in SGlines: print l
elif 'SCALE' in S[:5]:
V = S[10:41].split()
A[int(S[5])-1] = [float(V[0]),float(V[1]),float(V[2])]
elif 'ATOM' in S[:4] or 'HETATM' in S[:6]:
if not SGData:
self.warnings += '\nThe space group was not read before atoms and has been set to "P 1". '
self.warnings += "Change this in phase's General tab."
SGData = G2IO.SGData # P 1
XYZ = [float(S[31:39]),float(S[39:47]),float(S[47:55])]
XYZ = np.inner(AB,XYZ)
XYZ = np.where(abs(XYZ)<0.00001,0,XYZ)
SytSym,Mult = G2spc.SytSym(XYZ,SGData)
Uiso = float(S[61:67])/EightPiSq
Type = S[12:14].lower()
if Type[0] in '123456789':
Type = Type[1:]
Atom = [S[22:27].strip(),S[17:20].upper(),S[20:22],
S[12:17].strip(),Type.strip().capitalize(),'',XYZ[0],XYZ[1],XYZ[2],
float(S[55:61]),SytSym,Mult,'I',Uiso,0,0,0,0,0,0]
S = file.readline()
line += 1
if 'ANISOU' in S[:6]:
Uij = S[30:72].split()
Uij = [float(Uij[0])/10000.,float(Uij[1])/10000.,float(Uij[2])/10000.,
float(Uij[3])/10000.,float(Uij[4])/10000.,float(Uij[5])/10000.]
Atom = Atom[:14]+Uij
Atom[12] = 'A'
Atom.append(ran.randint(0,sys.maxint))
Atoms.append(Atom)
S = file.readline()
line += 1
file.close()
self.errors = 'Error after read complete'
if Title:
PhaseName = Title
elif Compnd:
PhaseName = Compnd
else:
PhaseName = 'None'
if not SGData:
raise self.ImportException("No space group (CRYST entry) found")
if not cell:
raise self.ImportException("No cell (CRYST entry) found")
Phase = G2IO.SetNewPhase(Name=PhaseName,SGData=SGData,cell=cell+[Volume,])
Phase['General']['Type'] = 'macromolecular'
Phase['General']['AtomPtrs'] = [6,4,10,12]
Phase['Atoms'] = Atoms
return Phase
def ReadJANAPhase(self,filename,parent=None):
'''Read a phase from a JANA2006 m50 & m40 files.
'''
self.errors = 'Error opening file'
file = open(filename, 'Ur') #contains only cell & spcgroup
Phase = {}
Title = os.path.basename(filename)
Compnd = ''
Type = 'nuclear'
Atoms = []
Atypes = []
SuperVec = [[0,0,.1],False,4]
S = file.readline()
line = 1
SGData = None
SuperSg = ''
cell = None
nqi = 0
while S:
self.errors = 'Error reading at line '+str(line)
if 'title' in S and S != 'title\n':
Title = S.split()[1]
elif 'cell' in S[:4]:
cell = S[5:].split()
cell=[float(cell[0]),float(cell[1]),float(cell[2]),
float(cell[3]),float(cell[4]),float(cell[5])]
Volume = G2lat.calc_V(G2lat.cell2A(cell))
elif 'spgroup' in S:
if 'X' in S:
raise self.ImportException("Supersymmetry "+S+" too high; GSAS-II limited to (3+1) supersymmetry")
SpGrp = S.split()[1]
SuperSg = ''
if '(' in SpGrp: #supercell symmetry - split in 2
SuperStr = SpGrp.split('(')
SpGrp = SuperStr[0]
SuperSg = '('+SuperStr[1]
SpGrpNorm = G2spc.StandardizeSpcName(SpGrp)
E,SGData = G2spc.SpcGroup(SpGrpNorm)
# space group processing failed, try to look up name in table
while E:
print G2spc.SGErrors(E)
dlg = wx.TextEntryDialog(parent,
SpGrp[:-1]+' is invalid \nN.B.: make sure spaces separate axial fields in symbol',
'ERROR in space group symbol','',style=wx.OK)
if dlg.ShowModal() == wx.ID_OK:
SpGrp = dlg.GetValue()
E,SGData = G2spc.SpcGroup(SpGrp)
else:
SGData = G2IO.SGData # P 1
self.warnings += '\nThe space group was not interpreted and has been set to "P 1".'
self.warnings += "Change this in phase's General tab."
dlg.Destroy()
SGlines = G2spc.SGPrint(SGData)
elif 'qi' in S[:2]:
if nqi:
raise self.ImportException("Supersymmetry too high; GSAS-II limited to (3+1) supersymmetry")
Type = 'modulated'
vec = S.split()[1:]
SuperVec = [[float(vec[i]) for i in range(3)],False,4]
nqi += 1
elif 'atom' in S[:4]:
Atypes.append(S.split()[1])
S = file.readline()
line += 1
file.close()
#read atoms from m40 file
if not SGData:
self.warnings += '\nThe space group was not read before atoms and has been set to "P 1". '
self.warnings += "Change this in phase's General tab."
SGData = G2IO.SGData # P 1
waveTypes = ['Fourier','Sawtooth','ZigZag',]
filename2 = os.path.splitext(filename)[0]+'.m40'
file2 = open(filename2,'Ur')
S = file2.readline()
line = 1
self.errors = 'Error reading at line '+str(line)
nAtoms = int(S.split()[0])
for i in range(4):
S = file2.readline()
for i in range(nAtoms):
S1 = file2.readline()
S1N = S1.split()[-3:] # no. occ, no. pos waves, no. ADP waves
S1N = [int(i) for i in S1N]
S1T = list(S1[60:63])
waveType = waveTypes[int(S1T[1])]
crenelType = ''
Spos = []
Sadp = []
Sfrac = []
Smag = []
XYZ = [float(S1[27:36]),float(S1[36:45]),float(S1[45:54])]
SytSym,Mult = G2spc.SytSym(XYZ,SGData)
aType = Atypes[int(S1[9:11])-1]
Name = S1[:8].strip()
if S1[11:15].strip() == '1':
S2 = file2.readline()
Uiso = float(S2[:9])
Uij = [0,0,0,0,0,0]
IA = 'I'
elif S1[11:15].strip() == '2':
S2 = file2.readline()
IA = 'A'
Uiso = 0.
Uij = [float(S2[:9]),float(S2[9:18]),float(S2[18:27]),
float(S2[27:36]),float(S2[36:45]),float(S2[45:54])]
for i in range(S1N[0]):
if not i:
FS = file2.readline()
Sfrac.append(FS[:9]) #'O' or 'delta' = 'length' for crenel
if int(S1T[0]): #"", "Legendre" or "Xharm" in 18:27 for "crenel"!
waveType = 'Crenel/Fourier' #all waves 'Fourier' no other choice
crenelType = FS[18:27]
Sfrac.append(file2.readline()[:18]) #if not crenel = Osin & Ocos
# else Osin & Ocos except last one is X40 = 'Center'
for i in range(S1N[1]):
Spos.append(file2.readline()[:54])
for i in range(S1N[2]):
Sadp.append(file2.readline()[:54]+file2.readline())
if sum(S1N): #if any waves: skip mystery line?
file2.readline()
for i,it in enumerate(Sfrac):
print i,it
if not i:
if 'Crenel' in waveType:
vals = [float(it),float(Sfrac[-1][:9])]
else:
vals = [float(it),]
else:
vals = [float(it[:9]),float(it[9:18])]
if 'Crenel' in waveType and i == len(Sfrac)-1:
del Sfrac[-1]
break
Sfrac[i] = [vals,False]
print Sfrac[i]
for i,it in enumerate(Spos):
if waveType in ['ZigZag','Sawtooth'] and not i:
vals = [float(it[:9]),float(it[9:18]),float(it[18:27]),float(it[27:36])]
else:
vals = [float(it[:9]),float(it[9:18]),float(it[18:27]),float(it[27:36]),float(it[36:45]),float(it[45:54])]
Spos[i] = [vals,False]
for i,it in enumerate(Sadp):
vals = [float(it[:9]),float(it[9:18]),float(it[18:27]),float(it[27:36]),float(it[36:45]),float(it[45:54]),
float(it[54:63]),float(it[63:72]),float(it[72:81]),float(it[81:90]),float(it[90:99]),float(it[99:108])]
Sadp[i] = [vals,False]
Atom = [Name,aType,'',XYZ[0],XYZ[1],XYZ[2],1.0,SytSym,Mult,IA,Uiso]
Atom += Uij
Atom.append(ran.randint(0,sys.maxint))
Atom.append([])
Atom.append([])
Atom.append({'SS1':{'waveType':waveType,'crenelType':crenelType,'Sfrac':Sfrac,'Spos':Spos,'Sadp':Sadp,'Smag':Smag}}) #SS2 is for (3+2), etc.
Atoms.append(Atom)
file2.close()
self.errors = 'Error after read complete'
if not SGData:
raise self.ImportException("No space group (spcgroup entry) found")
if not cell:
raise self.ImportException("No cell found")
Phase = G2IO.SetNewPhase(Name=Title,SGData=SGData,cell=cell+[Volume,])
Phase['General']['Type'] = Type
Phase['General']['Super'] = nqi
Phase['General']['SuperVec'] = SuperVec
Phase['General']['SuperSg'] = SuperSg
if SuperSg:
Phase['General']['SSGData'] = G2spc.SSpcGroup(SGData,SuperSg)[1]
Phase['General']['AtomPtrs'] = [3,1,7,9]
Phase['Atoms'] = Atoms
return Phase
def PrintDistAngle(DisAglCtls,DisAglData,out=sys.stdout):
'''Print distances and angles
:param dict DisAglCtls: contains distance/angle radii usually defined using
:func:`GSASIIctrlGUI.DisAglDialog`
:param dict DisAglData: contains phase data:
Items 'OrigAtoms' and 'TargAtoms' contain the atoms to be used
for distance/angle origins and atoms to be used as targets.
Item 'SGData' has the space group information (see :ref:`Space Group object<SGData_table>`)
:param file out: file object for output. Defaults to sys.stdout.
'''
def MyPrint(s):
out.write(s+'\n')
# print(s,file=out) # use in Python 3
def ShowBanner(name):
MyPrint(80*'*')
MyPrint(' Interatomic Distances and Angles for phase '+name)
MyPrint((80*'*')+'\n')
ShowBanner(DisAglCtls['Name'])
SGData = DisAglData['SGData']
SGtext,SGtable = G2spc.SGPrint(SGData)
for line in SGtext: MyPrint(line)
if len(SGtable) > 1:
for i,item in enumerate(SGtable[::2]):
if 2*i+1 == len(SGtable):
line = ' %s'%(item.ljust(30))
else:
line = ' %s %s'%(item.ljust(30),SGtable[2*i+1].ljust(30))
MyPrint(line)
else:
MyPrint(' ( 1) %s'%(SGtable[0])) #triclinic case
Cell = DisAglData['Cell']
Amat,Bmat = G2lat.cell2AB(Cell[:6])
covData = {}
if 'covData' in DisAglData:
covData = DisAglData['covData']
pfx = str(DisAglData['pId'])+'::'
A = G2lat.cell2A(Cell[:6])
cellSig = G2stIO.getCellEsd(pfx,SGData,A,covData)
names = [' a = ',' b = ',' c = ',' alpha = ',' beta = ',' gamma = ',' Volume = ']
valEsd = [G2mth.ValEsd(Cell[i],cellSig[i],True) for i in range(7)]
line = '\n Unit cell:'
for name,vals in zip(names,valEsd):
line += name+vals
MyPrint(line)
else:
MyPrint('\n Unit cell: a = '+('%.5f'%Cell[0])+' b = '+('%.5f'%Cell[1])+' c = '+('%.5f'%Cell[2])+
' alpha = '+('%.3f'%Cell[3])+' beta = '+('%.3f'%Cell[4])+' gamma = '+
('%.3f'%Cell[5])+' Volume = '+('%.3f'%Cell[6]))
AtomLabels,DistArray,AngArray = RetDistAngle(DisAglCtls,DisAglData)
origAtoms = DisAglData['OrigAtoms']
for Oatom in origAtoms:
i = Oatom[0]
Dist = DistArray[i]
nDist = len(Dist)
angles = np.zeros((nDist,nDist))
angsig = np.zeros((nDist,nDist))
for k,j,tup in AngArray[i]:
angles[k][j],angsig[k][j] = angles[j][k],angsig[j][k] = tup
line = ''
for i,x in enumerate(Oatom[3:6]):
line += ('%12.5f'%x).rstrip('0')
MyPrint('\n Distances & angles for '+Oatom[1]+' at '+line.rstrip())
MyPrint(80*'*')
line = ''
for dist in Dist[:-1]:
line += '%12s'%(AtomLabels[dist[0]].center(12))
MyPrint(' To cell +(sym. op.) dist. '+line.rstrip())
for i,dist in enumerate(Dist):
line = ''
for j,angle in enumerate(angles[i][0:i]):
sig = angsig[i][j]
if angle:
if sig:
line += '%12s'%(G2mth.ValEsd(angle,sig,True).center(12))
else:
val = '%.3f'%(angle)
line += '%12s'%(val.center(12))
else:
line += 12*' '
if dist[4]: #sig exists!
val = G2mth.ValEsd(dist[3],dist[4])
else:
val = '%8.4f'%(dist[3])
tunit = '[%2d%2d%2d]'% dist[1]
MyPrint((' %8s%10s+(%4d) %12s'%(AtomLabels[dist[0]].ljust(8),tunit.ljust(10),dist[2],val.center(12)))+line.rstrip())
def ReadJANAPhase(self, filename, parent=None):
'''Read a phase from a JANA2006 m50 & m40 files.
'''
self.errors = 'Error opening file'
file = open(filename, 'Ur') #contains only cell & spcgroup
Phase = {}
Title = os.path.basename(filename)
Compnd = ''
Type = 'nuclear'
Atoms = []
Atypes = []
SuperVec = [[0, 0, .1], False, 4]
S = file.readline()
line = 1
SGData = None
SuperSg = ''
cell = None
nqi = 0
while S:
self.errors = 'Error reading at line ' + str(line)
if 'title' in S and S != 'title\n':
Title = S.split()[1]
elif 'cell' in S[:4]:
cell = S[5:].split()
cell = [
float(cell[0]),
float(cell[1]),
float(cell[2]),
float(cell[3]),
float(cell[4]),
float(cell[5])
]
Volume = G2lat.calc_V(G2lat.cell2A(cell))
elif 'spgroup' in S:
if 'X' in S:
raise self.ImportException(
"Supersymmetry " + S +
" too high; GSAS-II limited to (3+1) supersymmetry")
SpGrp = S.split()[1]
SuperSg = ''
if '(' in SpGrp: #supercell symmetry - split in 2
SuperStr = SpGrp.split('(')
SpGrp = SuperStr[0]
SuperSg = '(' + SuperStr[1]
SpGrpNorm = G2spc.StandardizeSpcName(SpGrp)
E, SGData = G2spc.SpcGroup(SpGrpNorm)
# space group processing failed, try to look up name in table
while E:
print G2spc.SGErrors(E)
dlg = wx.TextEntryDialog(
parent,
SpGrp[:-1] +
' is invalid \nN.B.: make sure spaces separate axial fields in symbol',
'ERROR in space group symbol',
'',
style=wx.OK)
if dlg.ShowModal() == wx.ID_OK:
SpGrp = dlg.GetValue()
E, SGData = G2spc.SpcGroup(SpGrp)
else:
SGData = G2IO.SGData # P 1
self.warnings += '\nThe space group was not interpreted and has been set to "P 1".'
self.warnings += "Change this in phase's General tab."
dlg.Destroy()
SGlines = G2spc.SGPrint(SGData)
elif 'qi' in S[:2]:
if nqi:
raise self.ImportException(
"Supersymmetry too high; GSAS-II limited to (3+1) supersymmetry"
)
Type = 'modulated'
vec = S.split()[1:]
SuperVec = [[float(vec[i]) for i in range(3)], False, 4]
nqi += 1
elif 'atom' in S[:4]:
Atypes.append(S.split()[1])
S = file.readline()
line += 1
file.close()
#read atoms from m40 file
if not SGData:
self.warnings += '\nThe space group was not read before atoms and has been set to "P 1". '
self.warnings += "Change this in phase's General tab."
SGData = G2IO.SGData # P 1
waveTypes = [
'Fourier',
'Sawtooth',
'ZigZag',
]
filename2 = os.path.splitext(filename)[0] + '.m40'
file2 = open(filename2, 'Ur')
S = file2.readline()
line = 1
self.errors = 'Error reading at line ' + str(line)
nAtoms = int(S.split()[0])
for i in range(4):
S = file2.readline()
for i in range(nAtoms):
S1 = file2.readline()
S1N = S1.split()[-3:] # no. occ, no. pos waves, no. ADP waves
S1N = [int(i) for i in S1N]
S1T = list(S1[60:63])
waveType = waveTypes[int(S1T[1])]
crenelType = ''
Spos = []
Sadp = []
Sfrac = []
Smag = []
XYZ = [float(S1[27:36]), float(S1[36:45]), float(S1[45:54])]
SytSym, Mult = G2spc.SytSym(XYZ, SGData)
aType = Atypes[int(S1[9:11]) - 1]
Name = S1[:8].strip()
if S1[11:15].strip() == '1':
S2 = file2.readline()
Uiso = float(S2[:9])
Uij = [0, 0, 0, 0, 0, 0]
IA = 'I'
elif S1[11:15].strip() == '2':
S2 = file2.readline()
IA = 'A'
Uiso = 0.
Uij = [
float(S2[:9]),
float(S2[9:18]),
float(S2[18:27]),
float(S2[27:36]),
float(S2[36:45]),
float(S2[45:54])
]
for i in range(S1N[0]):
if not i:
FS = file2.readline()
Sfrac.append(FS[:9]) #'O' or 'delta' = 'length' for crenel
if int(
S1T[0]
): #"", "Legendre" or "Xharm" in 18:27 for "crenel"!
waveType = 'Crenel/Fourier' #all waves 'Fourier' no other choice
crenelType = FS[18:27]
Sfrac.append(
file2.readline()[:18]) #if not crenel = Osin & Ocos
# else Osin & Ocos except last one is X40 = 'Center'
for i in range(S1N[1]):
Spos.append(file2.readline()[:54])
for i in range(S1N[2]):
Sadp.append(file2.readline()[:54] + file2.readline())
if sum(S1N): #if any waves: skip mystery line?
file2.readline()
for i, it in enumerate(Sfrac):
print i, it
if not i:
if 'Crenel' in waveType:
vals = [float(it), float(Sfrac[-1][:9])]
else:
vals = [
float(it),
]
else:
vals = [float(it[:9]), float(it[9:18])]
if 'Crenel' in waveType and i == len(Sfrac) - 1:
del Sfrac[-1]
break
Sfrac[i] = [vals, False]
print Sfrac[i]
for i, it in enumerate(Spos):
if waveType in ['ZigZag', 'Sawtooth'] and not i:
vals = [
float(it[:9]),
float(it[9:18]),
float(it[18:27]),
float(it[27:36])
]
else:
vals = [
float(it[:9]),
float(it[9:18]),
float(it[18:27]),
float(it[27:36]),
float(it[36:45]),
float(it[45:54])
]
Spos[i] = [vals, False]
for i, it in enumerate(Sadp):
vals = [
float(it[:9]),
float(it[9:18]),
float(it[18:27]),
float(it[27:36]),
float(it[36:45]),
float(it[45:54]),
float(it[54:63]),
float(it[63:72]),
float(it[72:81]),
float(it[81:90]),
float(it[90:99]),
float(it[99:108])
]
Sadp[i] = [vals, False]
Atom = [
Name, aType, '', XYZ[0], XYZ[1], XYZ[2], 1.0, SytSym, Mult, IA,
Uiso
]
Atom += Uij
Atom.append(ran.randint(0, sys.maxint))
Atom.append([])
Atom.append([])
Atom.append({
'SS1': {
'waveType': waveType,
'crenelType': crenelType,
'Sfrac': Sfrac,
'Spos': Spos,
'Sadp': Sadp,
'Smag': Smag
}
}) #SS2 is for (3+2), etc.
Atoms.append(Atom)
file2.close()
self.errors = 'Error after read complete'
if not SGData:
raise self.ImportException("No space group (spcgroup entry) found")
if not cell:
raise self.ImportException("No cell found")
Phase = G2IO.SetNewPhase(Name=Title,
SGData=SGData,
cell=cell + [
Volume,
])
Phase['General']['Type'] = Type
Phase['General']['Super'] = nqi
Phase['General']['SuperVec'] = SuperVec
Phase['General']['SuperSg'] = SuperSg
if SuperSg:
Phase['General']['SSGData'] = G2spc.SSpcGroup(SGData, SuperSg)[1]
Phase['General']['AtomPtrs'] = [3, 1, 7, 9]
Phase['Atoms'] = Atoms
return Phase
def ReadINSPhase(self, filename, parent=None):
'''Read a phase from a INS file.
'''
Shelx = [
'TITL', 'CELL', 'ZERR', 'LATT', 'SYMM', 'SFAC', 'DISP', 'UNIT',
'LAUE', 'EADP', 'MORE', 'TIME', 'HKLF', 'OMIT', 'SHEL', 'BASF',
'TWIN', 'EXTI', 'SWAT', 'HOPE', 'MERG', 'SPEC', 'RESI', 'RTAB',
'MPLA', 'HFIX', 'MOVE', 'ANIS', 'AFIX', 'FRAG', 'FEND', 'EXYZ',
'EDAP', 'EQIV', 'CONN', 'PART', 'BIND', 'FREE', 'DFIX', 'DANG',
'BUMP', 'SAME', 'SADI', 'CHIV', 'FLAT', 'DELU', 'SIMU', 'DEFS',
'ISOR', 'NCSY', 'SUMP', 'L.S.', 'CGLS', 'BLOC', 'DAMP', 'STIR',
'WGHT', 'FVAR', 'BOND', 'CONF', 'MPLA', 'HTAB', 'LIST', 'ACTA',
'SIZE', 'TEMP', 'WPDB', 'FMAP', 'GRID', 'PLAN', 'MOLE'
]
self.errors = 'Error opening file'
fp = open(filename, 'Ur')
Phase = {}
Title = ''
Atoms = []
aTypes = []
S = fp.readline()
line = 1
SGData = None
cell = None
while S:
if '!' in S:
S = S.split('!')[0]
self.errors = 'Error reading at line ' + str(line)
Atom = []
if 'TITL' in S[:4].upper():
Title = S[4:72].strip()
elif not S.strip():
pass
elif 'CELL' in S[:4].upper():
cellRec = S.split()
abc = cellRec[2:5]
angles = cellRec[5:8]
cell = [
float(abc[0]),
float(abc[1]),
float(abc[2]),
float(angles[0]),
float(angles[1]),
float(angles[2])
]
Volume = G2lat.calc_V(G2lat.cell2A(cell))
AA, AB = G2lat.cell2AB(cell)
SGData = G2obj.P1SGData # P 1
self.warnings += '\nThe space group is not given in an ins file and has been set to "P 1".'
self.warnings += "\nChange this in phase's General tab; NB: it might be in the Phase name."
elif S[:4].upper() in 'SFAC':
aTypes = S[4:].split()
if 'H' in aTypes:
self.warnings += '\n\nHydrogen atoms found; consider replacing them with stereochemically tied ones'
self.warnings += '\nas Shelx constraints & HFIX commands are ignored.'
self.warnings += "\nDo 'Edit/Insert H atoms' in this phase's Atoms tab after deleting the old ones."
elif S[0] == 'Q':
pass
elif '\x1a' in S[:4]:
pass
elif S[:3].upper() == 'REM':
pass
elif S[:3].upper() == 'END':
pass
elif S[:4].strip().upper(
) not in Shelx: #this will find an atom record!
AtRec = S.split()
Atype = aTypes[int(AtRec[1]) - 1]
Aname = AtRec[0]
Afrac = abs(float(AtRec[5])) % 10.
x, y, z = AtRec[2:5]
XYZ = np.array([float(x), float(y), float(z)])
XYZ = np.where(np.abs(XYZ) < 0.00001, 0, XYZ)
SytSym, Mult = G2spc.SytSym(XYZ, SGData)[:2]
if '=' not in S:
IA = 'I'
Uiso = float(AtRec[6])
if Uiso < 0. or Uiso > 1.0:
Uiso = 0.025
Uij = [0. for i in range(6)]
else:
IA = 'A'
Uiso = 0.
Ustr = AtRec[6:8]
S = fp.readline()
if '!' in S:
S = S.split('!')[0]
AtRec = S.split()
line += 1
Ustr += AtRec
Uij = [float(Ustr[i]) for i in range(6)]
Uij = Uij[0:3] + [Uij[5], Uij[4], Uij[3]]
Atom = [
Aname, Atype, '', XYZ[0], XYZ[1], XYZ[2], Afrac, SytSym,
Mult, IA, Uiso
]
Atom += Uij
Atom.append(ran.randint(0, sys.maxsize))
Atoms.append(Atom)
S = fp.readline()
line += 1
fp.close()
self.errors = 'Error after read complete'
Phase = G2obj.SetNewPhase(Name='ShelX phase',
SGData=SGData,
cell=cell + [
Volume,
])
Phase['General']['Name'] = Title
Phase['General']['Type'] = 'nuclear'
Phase['General']['AtomPtrs'] = [3, 1, 7, 9]
Phase['Atoms'] = Atoms
return Phase
def findMV(peaks, controls, ssopt, Inst, dlg):
def Val2Vec(vec, Vref, values):
Vec = []
i = 0
for j, r in enumerate(Vref):
if r:
if values.size > 1:
Vec.append(max(-1., min(1.0, values[i])))
else:
Vec.append(max(0.0, min(1.0, values)))
i += 1
else:
Vec.append(vec[j])
return np.array(Vec)
def ZSSfunc(values,
peaks,
dmin,
Inst,
SGData,
SSGData,
vec,
Vref,
maxH,
A,
wave,
Z,
dlg=None):
Vec = Val2Vec(vec, Vref, values)
HKL = G2pwd.getHKLMpeak(dmin, Inst, SGData, SSGData, Vec, maxH, A)
Peaks = np.array(IndexSSPeaks(peaks, HKL)[1]).T
Qo = 1. / Peaks[-2]**2
Qc = G2lat.calc_rDsqZSS(Peaks[4:8], A, Vec, Z, Peaks[0], wave)
chi = np.sum((Qo - Qc)**2)
if dlg:
dlg.Pulse()
return chi
def TSSfunc(values,
peaks,
dmin,
Inst,
SGData,
SSGData,
vec,
Vref,
maxH,
A,
difC,
Z,
dlg=None):
Vec = Val2Vec(vec, Vref, values)
HKL = G2pwd.getHKLMpeak(dmin, Inst, SGData, SSGData, Vec, maxH, A)
Peaks = np.array(IndexSSPeaks(peaks, HKL)[1]).T
Qo = 1. / Peaks[-2]**2
Qc = G2lat.calc_rDsqTSS(Peaks[4:8], A, Vec, Z, Peaks[0], difC)
chi = np.sum((Qo - Qc)**2)
if dlg:
dlg.Pulse()
return chi
if 'T' in Inst['Type'][0]:
difC = Inst['difC'][1]
else:
wave = G2mth.getWave(Inst)
SGData = G2spc.SpcGroup(controls[13])[1]
SSGData = G2spc.SSpcGroup(SGData, ssopt['ssSymb'])[1]
A = G2lat.cell2A(controls[6:12])
Z = controls[1]
Vref = [True if x in ssopt['ssSymb'] else False for x in ['a', 'b', 'g']]
values = []
ranges = []
dT = 0.01 #seems to be a good choice
for v, r in zip(ssopt['ModVec'], Vref):
if r:
ranges += [
slice(dT, 1. - dT, dT),
] #NB: unique part for (00g) & (a0g); (abg)?
values += [
v,
]
dmin = getDmin(peaks) - 0.005
if 'T' in Inst['Type'][0]:
result = so.brute(TSSfunc,
ranges,
finish=so.fmin_cg,
full_output=True,
args=(peaks, dmin, Inst, SGData, SSGData,
ssopt['ModVec'], Vref, 1, A, difC, Z, dlg))
else:
result = so.brute(ZSSfunc,
ranges,
finish=so.fmin_cg,
full_output=True,
args=(peaks, dmin, Inst, SGData, SSGData,
ssopt['ModVec'], Vref, 1, A, wave, Z, dlg))
return Val2Vec(ssopt['ModVec'], Vref, result[0]), result
def Reader(self,filename,filepointer, ParentFrame=None, usedRanIdList=[], **unused):
self.isodistort_warnings = ''
self.Phase = G2IO.SetNewPhase(Name='new phase',SGData=G2IO.P1SGData) # create a new empty phase dict
# make sure the ranId is really unique!
while self.Phase['ranId'] in usedRanIdList:
self.Phase['ranId'] = ran.randint(0,sys.maxint)
returnstat = False
cellitems = (
'_cell_length_a','_cell_length_b','_cell_length_c',
'_cell_angle_alpha','_cell_angle_beta','_cell_angle_gamma',)
cellwaveitems = (
'_cell_wave_vector_seq_id',
'_cell_wave_vector_x','_cell_wave_vector_y','_cell_wave_vector_z')
reqitems = (
'_atom_site_fract_x',
'_atom_site_fract_y',
'_atom_site_fract_z',
)
phasenamefields = (
'_chemical_name_common',
'_pd_phase_name',
'_chemical_formula_sum'
)
try:
self.ShowBusy() # this can take a while
try:
cf = G2IO.ReadCIF(filename)
except Exception as detail:
self.errors = "Parse or reading of file failed in pyCifRW; check syntax of file in enCIFer or CheckCIF"
return False
finally:
self.DoneBusy()
# scan blocks for structural info
self.errors = 'Error during scan of blocks for datasets'
str_blklist = []
for blk in cf.keys():
for r in reqitems+cellitems:
if r not in cf[blk].keys():
break
else:
str_blklist.append(blk)
if not str_blklist:
selblk = None # no block to choose
elif len(str_blklist) == 1: # only one choice
selblk = 0
else: # choose from options
choice = []
for blknm in str_blklist:
choice.append('')
# accumumlate some info about this phase
choice[-1] += blknm + ': '
for i in phasenamefields: # get a name for the phase
name = cf[blknm].get(i).strip()
if name is None or name == '?' or name == '.':
continue
else:
choice[-1] += name.strip()[:20] + ', '
break
na = len(cf[blknm].get("_atom_site_fract_x"))
if na == 1:
choice[-1] += '1 atom'
else:
choice[-1] += ('%d' % nd) + ' atoms'
choice[-1] += ', cell: '
fmt = "%.2f,"
for i,key in enumerate(cellitems):
if i == 3: fmt = "%.f,"
if i == 5: fmt = "%.f"
choice[-1] += fmt % cif.get_number_with_esd(
cf[blknm].get(key))[0]
sg = cf[blknm].get("_symmetry_space_group_name_H-M",'')
if not sg: sg = cf[blknm].get("_space_group_name_H-M_alt",'')
if sg: choice[-1] += ', (' + sg.strip() + ')'
selblk = self.PhaseSelector(
choice,
ParentFrame=ParentFrame,
title= 'Select a phase from one the CIF data_ blocks below',
size=(600,100)
)
self.errors = 'Error during reading of selected block'
if selblk is None:
returnstat = False # no block selected or available
else:
blknm = str_blklist[selblk]
blk = cf[str_blklist[selblk]]
E = True
Super = False
SpGrp = blk.get("_symmetry_space_group_name_H-M",'')
if not SpGrp:
SpGrp = blk.get("_space_group_name_H-M_alt",'')
if not SpGrp:
sspgrp = blk.get("_space_group_ssg_name",'').split('(')
SpGrp = sspgrp[0]
SuperSg = '('+sspgrp[1].replace('\\','')
Super = True
SuperVec = [[0,0,.1],False,4]
# try normalizing the space group, to see if we can pick the space group out of a table
SpGrpNorm = G2spc.StandardizeSpcName(SpGrp)
if SpGrpNorm:
E,SGData = G2spc.SpcGroup(SpGrpNorm)
# nope, try the space group "out of the Box"
if E and SpGrp:
E,SGData = G2spc.SpcGroup(SpGrp)
if E:
if not SpGrp:
self.warnings += 'No space group name was found in the CIF.'
self.warnings += '\nThe space group has been set to "P 1". '
self.warnings += "Change this in phase's General tab."
else:
self.warnings += 'ERROR in space group symbol '+SpGrp
self.warnings += '\nThe space group has been set to "P 1". '
self.warnings += "Change this in phase's General tab."
self.warnings += '\nAre there spaces separating axial fields?\n\nError msg: '
self.warnings += G2spc.SGErrors(E)
SGData = G2IO.SGData # P 1
self.Phase['General']['SGData'] = SGData
# cell parameters
cell = []
for lbl in cellitems:
cell.append(cif.get_number_with_esd(blk[lbl])[0])
Volume = G2lat.calc_V(G2lat.cell2A(cell))
self.Phase['General']['Cell'] = [False,]+cell+[Volume,]
# read in atoms
self.errors = 'Error during reading of atoms'
atomlbllist = [] # table to look up atom IDs
atomloop = blk.GetLoop('_atom_site_label')
atomkeys = [i.lower() for i in atomloop.keys()]
if not blk.get('_atom_site_type_symbol'):
self.isodistort_warnings += '\nlack of atom types prevents ISODISTORT processing'
if blk.get('_atom_site_aniso_label'):
anisoloop = blk.GetLoop('_atom_site_aniso_label')
anisokeys = [i.lower() for i in anisoloop.keys()]
else:
anisoloop = None
anisokeys = []
self.Phase['Atoms'] = []
G2AtomDict = { '_atom_site_type_symbol' : 1,
'_atom_site_label' : 0,
'_atom_site_fract_x' : 3,
'_atom_site_fract_y' : 4,
'_atom_site_fract_z' : 5,
'_atom_site_occupancy' : 6,
'_atom_site_aniso_u_11' : 11,
'_atom_site_aniso_u_22' : 12,
'_atom_site_aniso_u_33' : 13,
'_atom_site_aniso_u_12' : 14,
'_atom_site_aniso_u_13' : 15,
'_atom_site_aniso_u_23' : 16, }
ranIdlookup = {}
for aitem in atomloop:
atomlist = ['','','',0,0,0,1.0,'',0,'I',0.01,0,0,0,0,0,0,0]
atomlist[-1] = ran.randint(0,sys.maxint) # add a random Id
while atomlist[-1] in ranIdlookup:
atomlist[-1] = ran.randint(0,sys.maxint) # make it unique
for val,key in zip(aitem,atomkeys):
col = G2AtomDict.get(key)
if col >= 3:
atomlist[col] = cif.get_number_with_esd(val)[0]
elif col is not None:
atomlist[col] = val
elif key in ('_atom_site_thermal_displace_type',
'_atom_site_adp_type'): #Iso or Aniso?
if val.lower() == 'uani':
atomlist[9] = 'A'
elif key == '_atom_site_u_iso_or_equiv':
atomlist[10] =cif.get_number_with_esd(val)[0]
if not atomlist[1] and atomlist[0]:
for i in range(2,0,-1):
typ = atomlist[0].strip()[:i]
if G2elem.CheckElement(typ):
atomlist[1] = typ
if not atomlist[1]: atomlist[1] = 'Xe'
ulbl = '_atom_site_aniso_label'
if atomlist[9] == 'A' and atomlist[0] in blk.get(ulbl):
for val,key in zip(anisoloop.GetKeyedPacket(ulbl,atomlist[0]),
anisokeys):
col = G2AtomDict.get(key)
if col:
atomlist[col] = cif.get_number_with_esd(val)[0]
atomlist[7],atomlist[8] = G2spc.SytSym(atomlist[3:6],SGData)
atomlist[1] = G2elem.FixValence(atomlist[1])
self.Phase['Atoms'].append(atomlist)
ranIdlookup[atomlist[0]] = atomlist[-1]
if atomlist[0] in atomlbllist:
self.warnings += ' ERROR: repeated atom label: '+atomlist[0]
else:
atomlbllist.append(atomlist[0])
if len(atomlbllist) != len(self.Phase['Atoms']):
self.isodistort_warnings += '\nRepeated atom labels prevents ISODISTORT decode'
for lbl in phasenamefields: # get a name for the phase
name = blk.get(lbl)
if name is None:
continue
name = name.strip()
if name == '?' or name == '.':
continue
else:
break
else: # no name found, use block name for lack of a better choice
name = blknm
self.Phase['General']['Name'] = name.strip()[:20]
self.Phase['General']['Super'] = Super
if Super:
self.Phase['General']['Type'] = 'modulated'
self.Phase['General']['SuperVec'] = SuperVec
self.Phase['General']['SuperSg'] = SuperSg
self.Phase['General']['SSGData'] = G2spc.SSpcGroup(SGData,SuperSg)[1]
if not self.isodistort_warnings:
if blk.get('_iso_displacivemode_label') or blk.get('_iso_occupancymode_label'):
self.errors = "Error while processing ISODISTORT constraints"
self.ISODISTORT_proc(blk,atomlbllist,ranIdlookup)
else:
self.warnings += self.isodistort_warnings
returnstat = True
except Exception as detail:
self.errors += '\n '+str(detail)
print 'CIF error:',detail # for testing
print sys.exc_info()[0] # for testing
import traceback
print traceback.format_exc()
returnstat = False
return returnstat
def findMV(peaks, controls, ssopt, Inst, dlg):
def Val2Vec(vec, Vref, values):
Vec = []
i = 0
for j, r in enumerate(Vref):
if r:
if values.size > 1:
Vec.append(max(0.0, min(1.0, values[i])))
else:
Vec.append(max(0.0, min(1.0, values)))
i += 1
else:
Vec.append(vec[j])
return np.array(Vec)
def ZSSfunc(values,
peaks,
dmin,
Inst,
SGData,
SSGData,
vec,
Vref,
maxH,
A,
wave,
Z,
dlg=None):
Vec = Val2Vec(vec, Vref, values)
HKL = G2pwd.getHKLMpeak(dmin, Inst, SGData, SSGData, Vec, maxH, A)
Peaks = np.array(IndexSSPeaks(peaks, HKL)[1]).T
Qo = 1. / Peaks[-2]**2
Qc = G2lat.calc_rDsqZSS(Peaks[4:8], A, Vec, Z, Peaks[0], wave)
chi = np.sum((Qo - Qc)**2)
if dlg:
dlg.Pulse()
return chi
if 'C' in Inst['Type'][0]:
wave = G2mth.getWave(Inst)
else:
difC = Inst['difC'][1]
SGData = G2spc.SpcGroup(controls[13])[1]
SSGData = G2spc.SSpcGroup(SGData, ssopt['ssSymb'])[1]
A = G2lat.cell2A(controls[6:12])
Z = controls[1]
Vref = [True if x in ssopt['ssSymb'] else False for x in ['a', 'b', 'g']]
values = []
ranges = []
for v, r in zip(ssopt['ModVec'], Vref):
if r:
ranges += [
slice(.02, .98, .05),
]
values += [
v,
]
dmin = getDmin(peaks) - 0.005
Peaks = np.copy(np.array(peaks).T)
result = so.brute(ZSSfunc,
ranges,
finish=so.fmin_cg,
args=(peaks, dmin, Inst, SGData, SSGData,
ssopt['ModVec'], Vref, ssopt['maxH'], A, wave, Z,
dlg))
return Val2Vec(ssopt['ModVec'], Vref, result)
def ImageRecalibrate(self,data,masks):
'Needs a doc string'
import ImageCalibrants as calFile
print 'Image recalibration:'
time0 = time.time()
pixelSize = data['pixelSize']
scalex = 1000./pixelSize[0]
scaley = 1000./pixelSize[1]
pixLimit = data['pixLimit']
cutoff = data['cutoff']
data['rings'] = []
data['ellipses'] = []
if not data['calibrant']:
print 'no calibration material selected'
return True
skip = data['calibskip']
dmin = data['calibdmin']
Bravais,SGs,Cells = calFile.Calibrants[data['calibrant']][:3]
HKL = []
for bravais,sg,cell in zip(Bravais,SGs,Cells):
A = G2lat.cell2A(cell)
if sg:
SGData = G2spc.SpcGroup(sg)[1]
hkl = G2pwd.getHKLpeak(dmin,SGData,A)
HKL += hkl
else:
hkl = G2lat.GenHBravais(dmin,bravais,A)
HKL += hkl
HKL = G2lat.sortHKLd(HKL,True,False)
varyList = [item for item in data['varyList'] if data['varyList'][item]]
parmDict = {'dist':data['distance'],'det-X':data['center'][0],'det-Y':data['center'][1],
'tilt':data['tilt'],'phi':data['rotation'],'wave':data['wavelength'],'dep':data['DetDepth']}
Found = False
wave = data['wavelength']
frame = masks['Frames']
tam = ma.make_mask_none(self.ImageZ.shape)
if frame:
tam = ma.mask_or(tam,MakeFrameMask(data,frame))
for iH,H in enumerate(HKL):
if debug: print H
dsp = H[3]
tth = 2.0*asind(wave/(2.*dsp))
if tth+abs(data['tilt']) > 90.:
print 'next line is a hyperbola - search stopped'
break
ellipse = GetEllipse(dsp,data)
Ring = makeRing(dsp,ellipse,pixLimit,cutoff,scalex,scaley,ma.array(self.ImageZ,mask=tam))
if Ring:
if iH >= skip:
data['rings'].append(np.array(Ring))
data['ellipses'].append(copy.deepcopy(ellipse+('r',)))
Found = True
elif not Found: #skipping inner rings, keep looking until ring found
continue
else: #no more rings beyond edge of detector
data['ellipses'].append([])
continue
# break
rings = np.concatenate((data['rings']),axis=0)
chisq = FitDetector(rings,varyList,parmDict)
data['wavelength'] = parmDict['wave']
data['distance'] = parmDict['dist']
data['center'] = [parmDict['det-X'],parmDict['det-Y']]
data['rotation'] = np.mod(parmDict['phi'],360.0)
data['tilt'] = parmDict['tilt']
data['DetDepth'] = parmDict['dep']
data['chisq'] = chisq
N = len(data['ellipses'])
data['ellipses'] = [] #clear away individual ellipse fits
for H in HKL[:N]:
ellipse = GetEllipse(H[3],data)
data['ellipses'].append(copy.deepcopy(ellipse+('b',)))
print 'calibration time = ',time.time()-time0
G2plt.PlotImage(self,newImage=True)
return True
def ImageCalibrate(self,data):
'Needs a doc string'
import copy
import ImageCalibrants as calFile
print 'Image calibration:'
time0 = time.time()
ring = data['ring']
pixelSize = data['pixelSize']
scalex = 1000./pixelSize[0]
scaley = 1000./pixelSize[1]
pixLimit = data['pixLimit']
cutoff = data['cutoff']
varyDict = data['varyList']
if varyDict['dist'] and varyDict['wave']:
print 'ERROR - you can not simultaneously calibrate distance and wavelength'
return False
if len(ring) < 5:
print 'ERROR - not enough inner ring points for ellipse'
return False
#fit start points on inner ring
data['ellipses'] = []
data['rings'] = []
outE = FitEllipse(ring)
fmt = '%s X: %.3f, Y: %.3f, phi: %.3f, R1: %.3f, R2: %.3f'
fmt2 = '%s X: %.3f, Y: %.3f, phi: %.3f, R1: %.3f, R2: %.3f, chi**2: %.3f, Np: %d'
if outE:
print fmt%('start ellipse: ',outE[0][0],outE[0][1],outE[1],outE[2][0],outE[2][1])
ellipse = outE
else:
return False
#setup 360 points on that ring for "good" fit
data['ellipses'].append(ellipse[:]+('g',))
Ring = makeRing(1.0,ellipse,pixLimit,cutoff,scalex,scaley,self.ImageZ)
if Ring:
ellipse = FitEllipse(Ring)
Ring = makeRing(1.0,ellipse,pixLimit,cutoff,scalex,scaley,self.ImageZ) #do again
ellipse = FitEllipse(Ring)
else:
print '1st ring not sufficiently complete to proceed'
return False
if debug:
print fmt2%('inner ring: ',ellipse[0][0],ellipse[0][1],ellipse[1],
ellipse[2][0],ellipse[2][1],0.,len(Ring)) #cent,phi,radii
data['ellipses'].append(ellipse[:]+('r',))
data['rings'].append(np.array(Ring))
G2plt.PlotImage(self,newImage=True)
#setup for calibration
data['rings'] = []
if not data['calibrant']:
print 'no calibration material selected'
return True
skip = data['calibskip']
dmin = data['calibdmin']
#generate reflection set
Bravais,SGs,Cells = calFile.Calibrants[data['calibrant']][:3]
HKL = []
for bravais,sg,cell in zip(Bravais,SGs,Cells):
A = G2lat.cell2A(cell)
if sg:
SGData = G2spc.SpcGroup(sg)[1]
hkl = G2pwd.getHKLpeak(dmin,SGData,A)
HKL += hkl
else:
hkl = G2lat.GenHBravais(dmin,bravais,A)
HKL += hkl
HKL = G2lat.sortHKLd(HKL,True,False)[skip:]
#set up 1st ring
elcent,phi,radii = ellipse #from fit of 1st ring
dsp = HKL[0][3]
print '1st ring: try %.4f'%(dsp)
if varyDict['dist']:
wave = data['wavelength']
tth = 2.0*asind(wave/(2.*dsp))
else: #varyDict['wave']!
dist = data['distance']
tth = npatan2d(radii[0],dist)
data['wavelength'] = wave = 2.0*dsp*sind(tth/2.0)
Ring0 = makeRing(dsp,ellipse,3,cutoff,scalex,scaley,self.ImageZ)
ttth = nptand(tth)
stth = npsind(tth)
ctth = npcosd(tth)
#1st estimate of tilt; assume ellipse - don't know sign though
if varyDict['tilt']:
tilt = npasind(np.sqrt(max(0.,1.-(radii[0]/radii[1])**2))*ctth)
if not tilt:
print 'WARNING - selected ring was fitted as a circle'
print ' - if detector was tilted we suggest you skip this ring - WARNING'
else:
tilt = data['tilt']
#1st estimate of dist: sample to detector normal to plane
if varyDict['dist']:
data['distance'] = dist = radii[0]**2/(ttth*radii[1])
else:
dist = data['distance']
if varyDict['tilt']:
#ellipse to cone axis (x-ray beam); 2 choices depending on sign of tilt
zdisp = radii[1]*ttth*tand(tilt)
zdism = radii[1]*ttth*tand(-tilt)
#cone axis position; 2 choices. Which is right?
#NB: zdisp is || to major axis & phi is rotation of minor axis
#thus shift from beam to ellipse center is [Z*sin(phi),-Z*cos(phi)]
centp = [elcent[0]+zdisp*sind(phi),elcent[1]-zdisp*cosd(phi)]
centm = [elcent[0]+zdism*sind(phi),elcent[1]-zdism*cosd(phi)]
#check get same ellipse parms either way
#now do next ring; estimate either way & do a FitDetector each way; best fit is correct one
fail = True
i2 = 1
while fail:
dsp = HKL[i2][3]
print '2nd ring: try %.4f'%(dsp)
tth = 2.0*asind(wave/(2.*dsp))
ellipsep = GetEllipse2(tth,0.,dist,centp,tilt,phi)
print fmt%('plus ellipse :',ellipsep[0][0],ellipsep[0][1],ellipsep[1],ellipsep[2][0],ellipsep[2][1])
Ringp = makeRing(dsp,ellipsep,3,cutoff,scalex,scaley,self.ImageZ)
parmDict = {'dist':dist,'det-X':centp[0],'det-Y':centp[1],
'tilt':tilt,'phi':phi,'wave':wave,'dep':0.0}
varyList = [item for item in varyDict if varyDict[item]]
if len(Ringp) > 10:
chip = FitDetector(np.array(Ring0+Ringp),varyList,parmDict,True)
tiltp = parmDict['tilt']
phip = parmDict['phi']
centp = [parmDict['det-X'],parmDict['det-Y']]
fail = False
else:
chip = 1e6
ellipsem = GetEllipse2(tth,0.,dist,centm,-tilt,phi)
print fmt%('minus ellipse:',ellipsem[0][0],ellipsem[0][1],ellipsem[1],ellipsem[2][0],ellipsem[2][1])
Ringm = makeRing(dsp,ellipsem,3,cutoff,scalex,scaley,self.ImageZ)
if len(Ringm) > 10:
parmDict['tilt'] *= -1
chim = FitDetector(np.array(Ring0+Ringm),varyList,parmDict,True)
tiltm = parmDict['tilt']
phim = parmDict['phi']
centm = [parmDict['det-X'],parmDict['det-Y']]
fail = False
else:
chim = 1e6
if fail:
i2 += 1
if chip < chim:
data['tilt'] = tiltp
data['center'] = centp
data['rotation'] = phip
else:
data['tilt'] = tiltm
data['center'] = centm
data['rotation'] = phim
data['ellipses'].append(ellipsep[:]+('b',))
data['rings'].append(np.array(Ringp))
data['ellipses'].append(ellipsem[:]+('r',))
data['rings'].append(np.array(Ringm))
G2plt.PlotImage(self,newImage=True)
parmDict = {'dist':data['distance'],'det-X':data['center'][0],'det-Y':data['center'][1],
'tilt':data['tilt'],'phi':data['rotation'],'wave':data['wavelength'],'dep':data['DetDepth']}
varyList = [item for item in varyDict if varyDict[item]]
data['rings'] = []
data['ellipses'] = []
for i,H in enumerate(HKL):
dsp = H[3]
tth = 2.0*asind(wave/(2.*dsp))
if tth+abs(data['tilt']) > 90.:
print 'next line is a hyperbola - search stopped'
break
if debug: print 'HKLD:',H[:4],'2-theta: %.4f'%(tth)
elcent,phi,radii = ellipse = GetEllipse(dsp,data)
data['ellipses'].append(copy.deepcopy(ellipse+('g',)))
if debug: print fmt%('predicted ellipse:',elcent[0],elcent[1],phi,radii[0],radii[1])
Ring = makeRing(dsp,ellipse,pixLimit,cutoff,scalex,scaley,self.ImageZ)
if Ring:
data['rings'].append(np.array(Ring))
rings = np.concatenate((data['rings']),axis=0)
if i:
chisq = FitDetector(rings,varyList,parmDict,False)
data['distance'] = parmDict['dist']
data['center'] = [parmDict['det-X'],parmDict['det-Y']]
data['rotation'] = parmDict['phi']
data['tilt'] = parmDict['tilt']
data['DetDepth'] = parmDict['dep']
data['chisq'] = chisq
elcent,phi,radii = ellipse = GetEllipse(dsp,data)
if debug: print fmt2%('fitted ellipse: ',elcent[0],elcent[1],phi,radii[0],radii[1],chisq,len(rings))
data['ellipses'].append(copy.deepcopy(ellipse+('r',)))
# G2plt.PlotImage(self,newImage=True)
else:
if debug: print 'insufficient number of points in this ellipse to fit'
# break
G2plt.PlotImage(self,newImage=True)
fullSize = len(self.ImageZ)/scalex
if 2*radii[1] < .9*fullSize:
print 'Are all usable rings (>25% visible) used? Try reducing Min ring I/Ib'
N = len(data['ellipses'])
if N > 2:
FitDetector(rings,varyList,parmDict)
data['wavelength'] = parmDict['wave']
data['distance'] = parmDict['dist']
data['center'] = [parmDict['det-X'],parmDict['det-Y']]
data['rotation'] = parmDict['phi']
data['tilt'] = parmDict['tilt']
data['DetDepth'] = parmDict['dep']
for H in HKL[:N]:
ellipse = GetEllipse(H[3],data)
data['ellipses'].append(copy.deepcopy(ellipse+('b',)))
print 'calibration time = ',time.time()-time0
G2plt.PlotImage(self,newImage=True)
return True
def UpdateLattice(self, parmVarDict, phase_index):
'''
Update the lattice parameters in the current model for all phases
'''
# Symmetry Options:
# cubic, tetragonal, hexagonal, rhombohedral, trigonal,
# orthorhombic, monoclinic, triclinic
if self._symmetry[self._phase[phase_index]] == 'cubic':
a = parmVarDict[str(phase_index) + '::a']
b = a
c = a
alpha = 90.
beta = 90.
gamma = 90.
elif self._symmetry[self._phase[phase_index]] == 'tetragonal':
a = parmVarDict[str(phase_index) + '::a']
b = a
c = parmVarDict[str(phase_index) + '::c']
alpha = 90.
beta = 90.
gamma = 90.
elif self._symmetry[self._phase[phase_index]] == 'hexagonal':
a = parmVarDict[str(phase_index) + '::a']
b = a
c = parmVarDict[str(phase_index) + '::c']
alpha = 90.
beta = 90.
gamma = 120.
elif self._symmetry[self._phase[phase_index]] == 'trigonal':
a = parmVarDict[str(phase_index) + '::a']
b = a
c = parmVarDict[str(phase_index) + '::c']
alpha = 90.
beta = 90.
gamma = 120.
elif self._symmetry[self._phase[phase_index]] == 'rhombohedral':
a = parmVarDict[str(phase_index) + '::a']
b = a
c = a
alpha = parmVarDict[str(phase_index) + '::alpha']
beta = alpha
gamma = alpha
elif self._symmetry[self._phase[phase_index]] == 'orthorhombic':
a = parmVarDict[str(phase_index) + '::a']
b = parmVarDict[str(phase_index) + '::b']
c = parmVarDict[str(phase_index) + '::c']
alpha = 90.
beta = 90.
gamma = 90.
elif self._symmetry[self._phase[phase_index]] == 'monoclinic':
a = parmVarDict[str(phase_index) + '::a']
b = parmVarDict[str(phase_index) + '::b']
c = parmVarDict[str(phase_index) + '::c']
beta = parmVarDict[str(phase_index) + '::beta']
alpha = 90.
gamma = 90.
elif self._symmetry[self._phase[phase_index]] == 'triclinic':
a = parmVarDict[str(phase_index) + '::a']
b = parmVarDict[str(phase_index) + '::b']
c = parmVarDict[str(phase_index) + '::c']
alpha = parmVarDict[str(phase_index) + '::alpha']
beta = parmVarDict[str(phase_index) + '::beta']
gamma = parmVarDict[str(phase_index) + '::gamma']
A = G2latt.cell2A([a, b, c, alpha, beta, gamma])
LatticeUpdate = {
str(phase_index) + '::A0': A[0],
str(phase_index) + '::A1': A[1],
str(phase_index) + '::A2': A[2],
str(phase_index) + '::A3': A[3],
str(phase_index) + '::A4': A[4],
str(phase_index) + '::A5': A[5]
}
self._parmDict.update(LatticeUpdate)
return parmVarDict
def ReadEXPPhase(self, G2frame, filepointer):
'''Read a phase from a GSAS .EXP file.
'''
shModels = ['cylindrical', 'none', 'shear - 2/m', 'rolling - mmm']
textureData = {
'Order': 0,
'Model': 'cylindrical',
'Sample omega': [False, 0.0],
'Sample chi': [False, 0.0],
'Sample phi': [False, 0.0],
'SH Coeff': [False, {}],
'SHShow': False,
'PFhkl': [0, 0, 1],
'PFxyz': [0, 0, 1],
'PlotType': 'Pole figure'
}
shNcof = 0
S = 1
NPhas = []
Expr = [{}, {}, {}, {}, {}, {}, {}, {},
{}] # GSAS can have at most 9 phases
for line, S in enumerate(filepointer):
self.errors = 'Error reading at line ' + str(line + 1)
if 'EXPR NPHAS' in S[:12]:
Num = S[12:-1].count('0')
NPhas = S[12:-1].split()
if 'CRS' in S[:3]:
N = int(S[3:4]) - 1
Expr[N][S[:12]] = S[12:-1]
PNames = []
if not NPhas:
raise self.ImportException("No EXPR NPHAS record found")
self.errors = 'Error interpreting file'
for n, N in enumerate(NPhas):
if N != '0':
result = n
key = 'CRS' + str(n + 1) + ' PNAM'
PNames.append(Expr[n][key])
if len(PNames) == 0:
raise self.ImportException("No phases found")
elif len(PNames) > 1:
dlg = wx.SingleChoiceDialog(G2frame, 'Which phase to read?',
'Read phase data', PNames,
wx.CHOICEDLG_STYLE)
try:
if dlg.ShowModal() == wx.ID_OK:
result = dlg.GetSelection(
) # I think this breaks is there are skipped phases. Cant this happen?
finally:
dlg.Destroy()
EXPphase = Expr[result]
keyList = EXPphase.keys()
keyList.sort()
SGData = {}
if NPhas[result] == '1':
Ptype = 'nuclear'
elif NPhas[result] in ['2', '3']:
Ptype = 'magnetic'
elif NPhas[result] == '4':
Ptype = 'macromolecular'
elif NPhas[result] == '10':
Ptype = 'Pawley'
else:
raise self.ImportException("Phase type not recognized")
for key in keyList:
if 'PNAM' in key:
PhaseName = EXPphase[key].strip()
elif 'ABC ' in key:
abc = [
float(EXPphase[key][:10]),
float(EXPphase[key][10:20]),
float(EXPphase[key][20:30])
]
elif 'ANGLES' in key:
angles = [
float(EXPphase[key][:10]),
float(EXPphase[key][10:20]),
float(EXPphase[key][20:30])
]
elif 'SG SYM' in key:
SpGrp = EXPphase[key][:15].strip()
E, SGData = G2spc.SpcGroup(SpGrp)
if E:
SGData = G2IO.SGData # P 1 -- unlikely to need this!
self.warnings += '\nThe GSAS space group was not interpreted(!) and has been set to "P 1".'
self.warnings += "Change this in phase's General tab."
elif 'OD ' in key:
SHdata = EXPphase[key].split() # may not have all 9 values
SHvals = 9 * [0]
for i in range(9):
try:
float(SHdata[i])
SHvals[i] = SHdata[i]
except:
pass
textureData['Order'] = int(SHvals[0])
textureData['Model'] = shModels[int(SHvals[2])]
textureData['Sample omega'] = [False, float(SHvals[6])]
textureData['Sample chi'] = [False, float(SHvals[7])]
textureData['Sample phi'] = [False, float(SHvals[8])]
shNcof = int(SHvals[1])
Atoms = []
if Ptype == 'nuclear':
for key in keyList:
if 'AT' in key:
if key[11:] == 'A':
S = EXPphase[key]
elif key[11:] == 'B':
S += EXPphase[key]
Atom = [
S[50:58].strip(), S[:10].strip().capitalize(), '',
float(S[10:20]),
float(S[20:30]),
float(S[30:40]),
float(S[40:50]), '',
int(S[60:62]), S[130:131]
]
if Atom[9] == 'I':
Atom += [float(S[68:78]), 0., 0., 0., 0., 0., 0.]
elif Atom[9] == 'A':
Atom += [
0.0,
float(S[68:78]),
float(S[78:88]),
float(S[88:98]),
float(S[98:108]),
float(S[108:118]),
float(S[118:128])
]
XYZ = Atom[3:6]
Atom[7], Atom[8] = G2spc.SytSym(XYZ, SGData)
Atom.append(ran.randint(0, sys.maxint))
Atoms.append(Atom)
elif Ptype == 'macromolecular':
for key in keyList:
if 'AT' in key[6:8]:
S = EXPphase[key]
Atom = [
S[56:60], S[50:54].strip().upper(), S[54:56],
S[46:51].strip(), S[:8].strip().capitalize(), '',
float(S[16:24]),
float(S[24:32]),
float(S[32:40]),
float(S[8:16]), '1', 1, 'I',
float(S[40:46]), 0, 0, 0, 0, 0, 0
]
XYZ = Atom[6:9]
Atom[10], Atom[11] = G2spc.SytSym(XYZ, SGData)
Atom.append(ran.randint(0, sys.maxint))
Atoms.append(Atom)
Volume = G2lat.calc_V(G2lat.cell2A(abc + angles))
if shNcof:
shCoef = {}
nRec = [i + 1 for i in range((shNcof - 1) / 6 + 1)]
for irec in nRec:
ODkey = keyList[0][:6] + 'OD' + '%3dA' % (irec)
indx = EXPphase[ODkey].split()
ODkey = ODkey[:-1] + 'B'
vals = EXPphase[ODkey].split()
for i, val in enumerate(vals):
key = 'C(%s,%s,%s)' % (indx[3 * i], indx[3 * i + 1],
indx[3 * i + 2])
shCoef[key] = float(val)
textureData['SH Coeff'] = [False, shCoef]
if not SGData:
raise self.ImportException("No space group found in phase")
if not abc:
raise self.ImportException("No cell lengths found in phase")
if not angles:
raise self.ImportException("No cell angles found in phase")
if not Atoms:
raise self.ImportException("No atoms found in phase")
Phase = G2IO.SetNewPhase(Name=PhaseName,
SGData=SGData,
cell=abc + angles + [
Volume,
])
general = Phase['General']
general['Type'] = Ptype
if general['Type'] == 'macromolecular':
general['AtomPtrs'] = [6, 4, 10, 12]
else:
general['AtomPtrs'] = [3, 1, 7, 9]
general['SH Texture'] = textureData
Phase['Atoms'] = Atoms
return Phase
def ImageRecalibrate(self, data, masks):
'Needs a doc string'
import ImageCalibrants as calFile
print 'Image recalibration:'
time0 = time.time()
pixelSize = data['pixelSize']
scalex = 1000. / pixelSize[0]
scaley = 1000. / pixelSize[1]
pixLimit = data['pixLimit']
cutoff = data['cutoff']
data['rings'] = []
data['ellipses'] = []
if not data['calibrant']:
print 'no calibration material selected'
return True
skip = data['calibskip']
dmin = data['calibdmin']
Bravais, SGs, Cells = calFile.Calibrants[data['calibrant']][:3]
HKL = []
for bravais, sg, cell in zip(Bravais, SGs, Cells):
A = G2lat.cell2A(cell)
if sg:
SGData = G2spc.SpcGroup(sg)[1]
hkl = G2pwd.getHKLpeak(dmin, SGData, A)
HKL += hkl
else:
hkl = G2lat.GenHBravais(dmin, bravais, A)
HKL += hkl
HKL = G2lat.sortHKLd(HKL, True, False)
varyList = [item for item in data['varyList'] if data['varyList'][item]]
parmDict = {
'dist': data['distance'],
'det-X': data['center'][0],
'det-Y': data['center'][1],
'tilt': data['tilt'],
'phi': data['rotation'],
'wave': data['wavelength'],
'dep': data['DetDepth']
}
Found = False
wave = data['wavelength']
frame = masks['Frames']
tam = ma.make_mask_none(self.ImageZ.shape)
if frame:
tam = ma.mask_or(tam, MakeFrameMask(data, frame))
for iH, H in enumerate(HKL):
if debug: print H
dsp = H[3]
tth = 2.0 * asind(wave / (2. * dsp))
if tth + abs(data['tilt']) > 90.:
print 'next line is a hyperbola - search stopped'
break
ellipse = GetEllipse(dsp, data)
Ring = makeRing(dsp, ellipse, pixLimit, cutoff, scalex, scaley,
ma.array(self.ImageZ, mask=tam))
if Ring:
if iH >= skip:
data['rings'].append(np.array(Ring))
data['ellipses'].append(copy.deepcopy(ellipse + ('r', )))
Found = True
elif not Found: #skipping inner rings, keep looking until ring found
continue
else: #no more rings beyond edge of detector
data['ellipses'].append([])
continue
# break
rings = np.concatenate((data['rings']), axis=0)
chisq = FitDetector(rings, varyList, parmDict)
data['wavelength'] = parmDict['wave']
data['distance'] = parmDict['dist']
data['center'] = [parmDict['det-X'], parmDict['det-Y']]
data['rotation'] = np.mod(parmDict['phi'], 360.0)
data['tilt'] = parmDict['tilt']
data['DetDepth'] = parmDict['dep']
data['chisq'] = chisq
N = len(data['ellipses'])
data['ellipses'] = [] #clear away individual ellipse fits
for H in HKL[:N]:
ellipse = GetEllipse(H[3], data)
data['ellipses'].append(copy.deepcopy(ellipse + ('b', )))
print 'calibration time = ', time.time() - time0
G2plt.PlotImage(self, newImage=True)
return True
def ReadPDBPhase(self, filename, parent=None):
'''Read a phase from a PDB file.
'''
EightPiSq = 8. * math.pi**2
self.errors = 'Error opening file'
file = open(filename, 'Ur')
Phase = {}
Title = ''
Compnd = ''
Atoms = []
A = np.zeros(shape=(3, 3))
S = file.readline()
line = 1
SGData = None
cell = None
while S:
self.errors = 'Error reading at line ' + str(line)
Atom = []
if 'TITLE' in S[:5]:
Title = S[10:72].strip()
elif 'COMPND ' in S[:10]:
Compnd = S[10:72].strip()
elif 'CRYST' in S[:5]:
abc = S[7:34].split()
angles = S[34:55].split()
cell = [
float(abc[0]),
float(abc[1]),
float(abc[2]),
float(angles[0]),
float(angles[1]),
float(angles[2])
]
Volume = G2lat.calc_V(G2lat.cell2A(cell))
AA, AB = G2lat.cell2AB(cell)
SpGrp = S[55:65]
E, SGData = G2spc.SpcGroup(SpGrp)
# space group processing failed, try to look up name in table
if E:
SpGrpNorm = G2spc.StandardizeSpcName(SpGrp)
if SpGrpNorm:
E, SGData = G2spc.SpcGroup(SpGrpNorm)
while E:
print G2spc.SGErrors(E)
dlg = wx.TextEntryDialog(
parent,
SpGrp[:-1] +
' is invalid \nN.B.: make sure spaces separate axial fields in symbol',
'ERROR in space group symbol',
'',
style=wx.OK)
if dlg.ShowModal() == wx.ID_OK:
SpGrp = dlg.GetValue()
E, SGData = G2spc.SpcGroup(SpGrp)
else:
SGData = G2IO.SGData # P 1
self.warnings += '\nThe space group was not interpreted and has been set to "P 1".'
self.warnings += "Change this in phase's General tab."
dlg.Destroy()
SGlines = G2spc.SGPrint(SGData)
for l in SGlines:
print l
elif 'SCALE' in S[:5]:
V = S[10:41].split()
A[int(S[5]) - 1] = [float(V[0]), float(V[1]), float(V[2])]
elif 'ATOM' in S[:4] or 'HETATM' in S[:6]:
if not SGData:
self.warnings += '\nThe space group was not read before atoms and has been set to "P 1". '
self.warnings += "Change this in phase's General tab."
SGData = G2IO.SGData # P 1
XYZ = [float(S[31:39]), float(S[39:47]), float(S[47:55])]
XYZ = np.inner(AB, XYZ)
XYZ = np.where(abs(XYZ) < 0.00001, 0, XYZ)
SytSym, Mult = G2spc.SytSym(XYZ, SGData)
Uiso = float(S[61:67]) / EightPiSq
Type = S[12:14].lower()
if Type[0] in '123456789':
Type = Type[1:]
Atom = [
S[22:27].strip(), S[17:20].upper(), S[20:22],
S[12:17].strip(),
Type.strip().capitalize(), '', XYZ[0], XYZ[1], XYZ[2],
float(S[55:61]), SytSym, Mult, 'I', Uiso, 0, 0, 0, 0, 0, 0
]
S = file.readline()
line += 1
if 'ANISOU' in S[:6]:
Uij = S[30:72].split()
Uij = [
float(Uij[0]) / 10000.,
float(Uij[1]) / 10000.,
float(Uij[2]) / 10000.,
float(Uij[3]) / 10000.,
float(Uij[4]) / 10000.,
float(Uij[5]) / 10000.
]
Atom = Atom[:14] + Uij
Atom[12] = 'A'
Atom.append(ran.randint(0, sys.maxint))
Atoms.append(Atom)
S = file.readline()
line += 1
file.close()
self.errors = 'Error after read complete'
if Title:
PhaseName = Title
elif Compnd:
PhaseName = Compnd
else:
PhaseName = 'None'
if not SGData:
raise self.ImportException("No space group (CRYST entry) found")
if not cell:
raise self.ImportException("No cell (CRYST entry) found")
Phase = G2IO.SetNewPhase(Name=PhaseName,
SGData=SGData,
cell=cell + [
Volume,
])
Phase['General']['Type'] = 'macromolecular'
Phase['General']['AtomPtrs'] = [6, 4, 10, 12]
Phase['Atoms'] = Atoms
return Phase
def RetDistAngle(DisAglCtls,DisAglData):
'''Compute and return distances and angles
:param dict DisAglCtls: contains distance/angle radii usually defined using
:func:`GSASIIgrid.DisAglDialog`
:param dict DisAglData: contains phase data:
Items 'OrigAtoms' and 'TargAtoms' contain the atoms to be used
for distance/angle origins and atoms to be used as targets.
Item 'SGData' has the space group information (see :ref:`Space Group object<SGData_table>`)
:returns: AtomLabels,DistArray,AngArray where:
**AtomLabels** is a dict of atom labels, keys are the atom number
**DistArray** is a dict keyed by the origin atom number where the value is a list
of distance entries. The value for each distance is a list containing:
0) the target atom number (int);
1) the unit cell offsets added to x,y & z (tuple of int values)
2) the symmetry operator number (which may be modified to indicate centering and center of symmetry)
3) an interatomic distance in A (float)
4) an uncertainty on the distance in A or 0.0 (float)
**AngArray** is a dict keyed by the origin (central) atom number where
the value is a list of
angle entries. The value for each angle entry consists of three values:
0) a distance item reference for one neighbor (int)
1) a distance item reference for a second neighbor (int)
2) a angle, uncertainty pair; the s.u. may be zero (tuple of two floats)
The AngArray distance reference items refer directly to the index of the items in the
DistArray item for the list of distances for the central atom.
'''
import numpy.ma as ma
SGData = DisAglData['SGData']
Cell = DisAglData['Cell']
Amat,Bmat = G2lat.cell2AB(Cell[:6])
covData = {}
if 'covData' in DisAglData:
covData = DisAglData['covData']
covMatrix = covData['covMatrix']
varyList = covData['varyList']
pfx = str(DisAglData['pId'])+'::'
A = G2lat.cell2A(Cell[:6])
cellSig = G2stIO.getCellEsd(pfx,SGData,A,covData)
names = [' a = ',' b = ',' c = ',' alpha = ',' beta = ',' gamma = ',' Volume = ']
valEsd = [G2mth.ValEsd(Cell[i],cellSig[i],True) for i in range(7)]
Factor = DisAglCtls['Factors']
Radii = dict(zip(DisAglCtls['AtomTypes'],zip(DisAglCtls['BondRadii'],DisAglCtls['AngleRadii'])))
indices = (-1,0,1)
Units = np.array([[h,k,l] for h in indices for k in indices for l in indices])
origAtoms = DisAglData['OrigAtoms']
targAtoms = DisAglData['TargAtoms']
AtomLabels = {}
for Oatom in origAtoms:
AtomLabels[Oatom[0]] = Oatom[1]
for Oatom in targAtoms:
AtomLabels[Oatom[0]] = Oatom[1]
DistArray = {}
AngArray = {}
for Oatom in origAtoms:
DistArray[Oatom[0]] = []
AngArray[Oatom[0]] = []
OxyzNames = ''
IndBlist = []
Dist = []
Vect = []
VectA = []
angles = []
for Tatom in targAtoms:
Xvcov = []
TxyzNames = ''
if 'covData' in DisAglData:
OxyzNames = [pfx+'dAx:%d'%(Oatom[0]),pfx+'dAy:%d'%(Oatom[0]),pfx+'dAz:%d'%(Oatom[0])]
TxyzNames = [pfx+'dAx:%d'%(Tatom[0]),pfx+'dAy:%d'%(Tatom[0]),pfx+'dAz:%d'%(Tatom[0])]
Xvcov = G2mth.getVCov(OxyzNames+TxyzNames,varyList,covMatrix)
result = G2spc.GenAtom(Tatom[3:6],SGData,False,Move=False)
BsumR = (Radii[Oatom[2]][0]+Radii[Tatom[2]][0])*Factor[0]
AsumR = (Radii[Oatom[2]][1]+Radii[Tatom[2]][1])*Factor[1]
for Txyz,Top,Tunit in result:
Dx = (Txyz-np.array(Oatom[3:6]))+Units
dx = np.inner(Amat,Dx)
dist = ma.masked_less(np.sqrt(np.sum(dx**2,axis=0)),0.5)
IndB = ma.nonzero(ma.masked_greater(dist-BsumR,0.))
if np.any(IndB):
for indb in IndB:
for i in range(len(indb)):
if str(dx.T[indb][i]) not in IndBlist:
IndBlist.append(str(dx.T[indb][i]))
unit = Units[indb][i]
tunit = (unit[0]+Tunit[0],unit[1]+Tunit[1],unit[2]+Tunit[2])
pdpx = G2mth.getDistDerv(Oatom[3:6],Tatom[3:6],Amat,unit,Top,SGData)
sig = 0.0
if len(Xvcov):
sig = np.sqrt(np.inner(pdpx,np.inner(Xvcov,pdpx)))
Dist.append([Oatom[0],Tatom[0],tunit,Top,ma.getdata(dist[indb])[i],sig])
if (Dist[-1][-2]-AsumR) <= 0.:
Vect.append(dx.T[indb][i]/Dist[-1][-2])
VectA.append([OxyzNames,np.array(Oatom[3:6]),TxyzNames,np.array(Tatom[3:6]),unit,Top])
else:
Vect.append([0.,0.,0.])
VectA.append([])
for D in Dist:
DistArray[Oatom[0]].append(D[1:])
Vect = np.array(Vect)
angles = np.zeros((len(Vect),len(Vect)))
angsig = np.zeros((len(Vect),len(Vect)))
for i,veca in enumerate(Vect):
if np.any(veca):
for j,vecb in enumerate(Vect):
if np.any(vecb):
angles[i][j],angsig[i][j] = G2mth.getAngSig(VectA[i],VectA[j],Amat,SGData,covData)
if i <= j: continue
AngArray[Oatom[0]].append((i,j,
G2mth.getAngSig(VectA[i],VectA[j],Amat,SGData,covData)))
return AtomLabels,DistArray,AngArray
def PrintDistAngle(DisAglCtls,DisAglData,out=sys.stdout):
'''Print distances and angles
:param dict DisAglCtls: contains distance/angle radii usually defined using
:func:`GSASIIgrid.DisAglDialog`
:param dict DisAglData: contains phase data:
Items 'OrigAtoms' and 'TargAtoms' contain the atoms to be used
for distance/angle origins and atoms to be used as targets.
Item 'SGData' has the space group information (see :ref:`Space Group object<SGData_table>`)
:param file out: file object for output. Defaults to sys.stdout.
'''
import numpy.ma as ma
def MyPrint(s):
out.write(s+'\n')
# print(s,file=out) # use in Python 3
def ShowBanner(name):
MyPrint(80*'*')
MyPrint(' Interatomic Distances and Angles for phase '+name)
MyPrint((80*'*')+'\n')
ShowBanner(DisAglCtls['Name'])
SGData = DisAglData['SGData']
SGtext,SGtable = G2spc.SGPrint(SGData)
for line in SGtext: MyPrint(line)
if len(SGtable):
for i,item in enumerate(SGtable[::2]):
line = ' %s %s'%(item.ljust(30),SGtable[2*i+1].ljust(30))
MyPrint(line)
else:
MyPrint(' ( 1) %s'%(SGtable[0]))
Cell = DisAglData['Cell']
Amat,Bmat = G2lat.cell2AB(Cell[:6])
covData = {}
if 'covData' in DisAglData:
covData = DisAglData['covData']
covMatrix = covData['covMatrix']
varyList = covData['varyList']
pfx = str(DisAglData['pId'])+'::'
A = G2lat.cell2A(Cell[:6])
cellSig = G2stIO.getCellEsd(pfx,SGData,A,covData)
names = [' a = ',' b = ',' c = ',' alpha = ',' beta = ',' gamma = ',' Volume = ']
valEsd = [G2mth.ValEsd(Cell[i],cellSig[i],True) for i in range(7)]
line = '\n Unit cell:'
for name,vals in zip(names,valEsd):
line += name+vals
MyPrint(line)
else:
MyPrint('\n Unit cell: a = '+('%.5f'%Cell[0])+' b = '+('%.5f'%Cell[1])+' c = '+('%.5f'%Cell[2])+
' alpha = '+('%.3f'%Cell[3])+' beta = '+('%.3f'%Cell[4])+' gamma = '+
('%.3f'%Cell[5])+' volume = '+('%.3f'%Cell[6]))
AtomLabels,DistArray,AngArray = RetDistAngle(DisAglCtls,DisAglData)
origAtoms = DisAglData['OrigAtoms']
targAtoms = DisAglData['TargAtoms']
for Oatom in origAtoms:
i = Oatom[0]
Dist = DistArray[i]
nDist = len(Dist)
angles = np.zeros((nDist,nDist))
angsig = np.zeros((nDist,nDist))
for k,j,tup in AngArray[i]:
angles[k][j],angsig[k][j] = angles[j][k],angsig[j][k] = tup
line = ''
for i,x in enumerate(Oatom[3:6]):
line += ('%12.5f'%x).rstrip('0')
MyPrint('\n Distances & angles for '+Oatom[1]+' at '+line.rstrip())
MyPrint(80*'*')
line = ''
for dist in Dist[:-1]:
line += '%12s'%(AtomLabels[dist[0]].center(12))
MyPrint(' To cell +(sym. op.) dist. '+line.rstrip())
for i,dist in enumerate(Dist):
line = ''
for j,angle in enumerate(angles[i][0:i]):
sig = angsig[i][j]
if angle:
if sig:
line += '%12s'%(G2mth.ValEsd(angle,sig,True).center(12))
else:
val = '%.3f'%(angle)
line += '%12s'%(val.center(12))
else:
line += 12*' '
if dist[4]: #sig exists!
val = G2mth.ValEsd(dist[3],dist[4])
else:
val = '%8.4f'%(dist[3])
tunit = '[%2d%2d%2d]'% dist[1]
MyPrint((' %8s%10s+(%4d) %12s'%(AtomLabels[dist[0]].ljust(8),tunit.ljust(10),dist[2],val.center(12)))+line.rstrip())
def ReadEXPPhase(self, G2frame,filepointer):
'''Read a phase from a GSAS .EXP file.
'''
shModels = ['cylindrical','none','shear - 2/m','rolling - mmm']
textureData = {'Order':0,'Model':'cylindrical','Sample omega':[False,0.0],
'Sample chi':[False,0.0],'Sample phi':[False,0.0],'SH Coeff':[False,{}],
'SHShow':False,'PFhkl':[0,0,1],'PFxyz':[0,0,1],'PlotType':'Pole figure'}
shNcof = 0
S = 1
NPhas = []
Expr = [{},{},{},{},{},{},{},{},{}] # GSAS can have at most 9 phases
for line,S in enumerate(filepointer):
self.errors = 'Error reading at line '+str(line+1)
if 'EXPR NPHAS' in S[:12]:
Num = S[12:-1].count('0')
NPhas = S[12:-1].split()
if 'CRS' in S[:3]:
N = int(S[3:4])-1
Expr[N][S[:12]] = S[12:-1]
PNames = []
if not NPhas:
raise self.ImportException("No EXPR NPHAS record found")
self.errors = 'Error interpreting file'
for n,N in enumerate(NPhas):
if N != '0':
result = n
key = 'CRS'+str(n+1)+' PNAM'
PNames.append(Expr[n][key])
if len(PNames) == 0:
raise self.ImportException("No phases found")
elif len(PNames) > 1:
dlg = wx.SingleChoiceDialog(G2frame, 'Which phase to read?', 'Read phase data', PNames, wx.CHOICEDLG_STYLE)
try:
if dlg.ShowModal() == wx.ID_OK:
result = dlg.GetSelection() # I think this breaks is there are skipped phases. Cant this happen?
finally:
dlg.Destroy()
EXPphase = Expr[result]
keyList = EXPphase.keys()
keyList.sort()
SGData = {}
if NPhas[result] == '1':
Ptype = 'nuclear'
elif NPhas[result] in ['2','3']:
Ptype = 'magnetic'
elif NPhas[result] == '4':
Ptype = 'macromolecular'
elif NPhas[result] == '10':
Ptype = 'Pawley'
else:
raise self.ImportException("Phase type not recognized")
for key in keyList:
if 'PNAM' in key:
PhaseName = EXPphase[key].strip()
elif 'ABC ' in key:
abc = [float(EXPphase[key][:10]),float(EXPphase[key][10:20]),float(EXPphase[key][20:30])]
elif 'ANGLES' in key:
angles = [float(EXPphase[key][:10]),float(EXPphase[key][10:20]),float(EXPphase[key][20:30])]
elif 'SG SYM' in key:
SpGrp = EXPphase[key][:15].strip()
E,SGData = G2spc.SpcGroup(SpGrp)
if E:
SGData = G2IO.SGData # P 1 -- unlikely to need this!
self.warnings += '\nThe GSAS space group was not interpreted(!) and has been set to "P 1".'
self.warnings += "Change this in phase's General tab."
elif 'OD ' in key:
SHdata = EXPphase[key].split() # may not have all 9 values
SHvals = 9*[0]
for i in range(9):
try:
float(SHdata[i])
SHvals[i] = SHdata[i]
except:
pass
textureData['Order'] = int(SHvals[0])
textureData['Model'] = shModels[int(SHvals[2])]
textureData['Sample omega'] = [False,float(SHvals[6])]
textureData['Sample chi'] = [False,float(SHvals[7])]
textureData['Sample phi'] = [False,float(SHvals[8])]
shNcof = int(SHvals[1])
Atoms = []
if Ptype == 'nuclear':
for key in keyList:
if 'AT' in key:
if key[11:] == 'A':
S = EXPphase[key]
elif key[11:] == 'B':
S += EXPphase[key]
Atom = [S[50:58].strip(),S[:10].strip().capitalize(),'',
float(S[10:20]),float(S[20:30]),float(S[30:40]),
float(S[40:50]),'',int(S[60:62]),S[130:131]]
if Atom[9] == 'I':
Atom += [float(S[68:78]),0.,0.,0.,0.,0.,0.]
elif Atom[9] == 'A':
Atom += [0.0,float(S[68:78]),float(S[78:88]),
float(S[88:98]),float(S[98:108]),
float(S[108:118]),float(S[118:128])]
XYZ = Atom[3:6]
Atom[7],Atom[8] = G2spc.SytSym(XYZ,SGData)
Atom.append(ran.randint(0,sys.maxint))
Atoms.append(Atom)
elif Ptype == 'macromolecular':
for key in keyList:
if 'AT' in key[6:8]:
S = EXPphase[key]
Atom = [S[56:60],S[50:54].strip().upper(),S[54:56],
S[46:51].strip(),S[:8].strip().capitalize(),'',
float(S[16:24]),float(S[24:32]),float(S[32:40]),
float(S[8:16]),'1',1,'I',float(S[40:46]),0,0,0,0,0,0]
XYZ = Atom[6:9]
Atom[10],Atom[11] = G2spc.SytSym(XYZ,SGData)
Atom.append(ran.randint(0,sys.maxint))
Atoms.append(Atom)
Volume = G2lat.calc_V(G2lat.cell2A(abc+angles))
if shNcof:
shCoef = {}
nRec = [i+1 for i in range((shNcof-1)/6+1)]
for irec in nRec:
ODkey = keyList[0][:6]+'OD'+'%3dA'%(irec)
indx = EXPphase[ODkey].split()
ODkey = ODkey[:-1]+'B'
vals = EXPphase[ODkey].split()
for i,val in enumerate(vals):
key = 'C(%s,%s,%s)'%(indx[3*i],indx[3*i+1],indx[3*i+2])
shCoef[key] = float(val)
textureData['SH Coeff'] = [False,shCoef]
if not SGData:
raise self.ImportException("No space group found in phase")
if not abc:
raise self.ImportException("No cell lengths found in phase")
if not angles:
raise self.ImportException("No cell angles found in phase")
if not Atoms:
raise self.ImportException("No atoms found in phase")
Phase = G2IO.SetNewPhase(Name=PhaseName,SGData=SGData,cell=abc+angles+[Volume,])
general = Phase['General']
general['Type'] = Ptype
if general['Type'] =='macromolecular':
general['AtomPtrs'] = [6,4,10,12]
else:
general['AtomPtrs'] = [3,1,7,9]
general['SH Texture'] = textureData
Phase['Atoms'] = Atoms
return Phase
def ImageCalibrate(self, data):
'Needs a doc string'
import copy
import ImageCalibrants as calFile
print 'Image calibration:'
time0 = time.time()
ring = data['ring']
pixelSize = data['pixelSize']
scalex = 1000. / pixelSize[0]
scaley = 1000. / pixelSize[1]
pixLimit = data['pixLimit']
cutoff = data['cutoff']
varyDict = data['varyList']
if varyDict['dist'] and varyDict['wave']:
print 'ERROR - you can not simultaneously calibrate distance and wavelength'
return False
if len(ring) < 5:
print 'ERROR - not enough inner ring points for ellipse'
return False
#fit start points on inner ring
data['ellipses'] = []
data['rings'] = []
outE = FitEllipse(ring)
fmt = '%s X: %.3f, Y: %.3f, phi: %.3f, R1: %.3f, R2: %.3f'
fmt2 = '%s X: %.3f, Y: %.3f, phi: %.3f, R1: %.3f, R2: %.3f, chi**2: %.3f, Np: %d'
if outE:
print fmt % ('start ellipse: ', outE[0][0], outE[0][1], outE[1],
outE[2][0], outE[2][1])
ellipse = outE
else:
return False
#setup 360 points on that ring for "good" fit
data['ellipses'].append(ellipse[:] + ('g', ))
Ring = makeRing(1.0, ellipse, pixLimit, cutoff, scalex, scaley,
self.ImageZ)
if Ring:
ellipse = FitEllipse(Ring)
Ring = makeRing(1.0, ellipse, pixLimit, cutoff, scalex, scaley,
self.ImageZ) #do again
ellipse = FitEllipse(Ring)
else:
print '1st ring not sufficiently complete to proceed'
return False
if debug:
print fmt2 % ('inner ring: ', ellipse[0][0], ellipse[0][1],
ellipse[1], ellipse[2][0], ellipse[2][1], 0., len(Ring)
) #cent,phi,radii
data['ellipses'].append(ellipse[:] + ('r', ))
data['rings'].append(np.array(Ring))
G2plt.PlotImage(self, newImage=True)
#setup for calibration
data['rings'] = []
if not data['calibrant']:
print 'no calibration material selected'
return True
skip = data['calibskip']
dmin = data['calibdmin']
#generate reflection set
Bravais, SGs, Cells = calFile.Calibrants[data['calibrant']][:3]
HKL = []
for bravais, sg, cell in zip(Bravais, SGs, Cells):
A = G2lat.cell2A(cell)
if sg:
SGData = G2spc.SpcGroup(sg)[1]
hkl = G2pwd.getHKLpeak(dmin, SGData, A)
HKL += hkl
else:
hkl = G2lat.GenHBravais(dmin, bravais, A)
HKL += hkl
HKL = G2lat.sortHKLd(HKL, True, False)[skip:]
#set up 1st ring
elcent, phi, radii = ellipse #from fit of 1st ring
dsp = HKL[0][3]
print '1st ring: try %.4f' % (dsp)
if varyDict['dist']:
wave = data['wavelength']
tth = 2.0 * asind(wave / (2. * dsp))
else: #varyDict['wave']!
dist = data['distance']
tth = npatan2d(radii[0], dist)
data['wavelength'] = wave = 2.0 * dsp * sind(tth / 2.0)
Ring0 = makeRing(dsp, ellipse, 3, cutoff, scalex, scaley, self.ImageZ)
ttth = nptand(tth)
stth = npsind(tth)
ctth = npcosd(tth)
#1st estimate of tilt; assume ellipse - don't know sign though
if varyDict['tilt']:
tilt = npasind(np.sqrt(max(0., 1. - (radii[0] / radii[1])**2)) * ctth)
if not tilt:
print 'WARNING - selected ring was fitted as a circle'
print ' - if detector was tilted we suggest you skip this ring - WARNING'
else:
tilt = data['tilt']
#1st estimate of dist: sample to detector normal to plane
if varyDict['dist']:
data['distance'] = dist = radii[0]**2 / (ttth * radii[1])
else:
dist = data['distance']
if varyDict['tilt']:
#ellipse to cone axis (x-ray beam); 2 choices depending on sign of tilt
zdisp = radii[1] * ttth * tand(tilt)
zdism = radii[1] * ttth * tand(-tilt)
#cone axis position; 2 choices. Which is right?
#NB: zdisp is || to major axis & phi is rotation of minor axis
#thus shift from beam to ellipse center is [Z*sin(phi),-Z*cos(phi)]
centp = [elcent[0] + zdisp * sind(phi), elcent[1] - zdisp * cosd(phi)]
centm = [elcent[0] + zdism * sind(phi), elcent[1] - zdism * cosd(phi)]
#check get same ellipse parms either way
#now do next ring; estimate either way & do a FitDetector each way; best fit is correct one
fail = True
i2 = 1
while fail:
dsp = HKL[i2][3]
print '2nd ring: try %.4f' % (dsp)
tth = 2.0 * asind(wave / (2. * dsp))
ellipsep = GetEllipse2(tth, 0., dist, centp, tilt, phi)
print fmt % ('plus ellipse :', ellipsep[0][0], ellipsep[0][1],
ellipsep[1], ellipsep[2][0], ellipsep[2][1])
Ringp = makeRing(dsp, ellipsep, 3, cutoff, scalex, scaley,
self.ImageZ)
parmDict = {
'dist': dist,
'det-X': centp[0],
'det-Y': centp[1],
'tilt': tilt,
'phi': phi,
'wave': wave,
'dep': 0.0
}
varyList = [item for item in varyDict if varyDict[item]]
if len(Ringp) > 10:
chip = FitDetector(np.array(Ring0 + Ringp), varyList, parmDict,
True)
tiltp = parmDict['tilt']
phip = parmDict['phi']
centp = [parmDict['det-X'], parmDict['det-Y']]
fail = False
else:
chip = 1e6
ellipsem = GetEllipse2(tth, 0., dist, centm, -tilt, phi)
print fmt % ('minus ellipse:', ellipsem[0][0], ellipsem[0][1],
ellipsem[1], ellipsem[2][0], ellipsem[2][1])
Ringm = makeRing(dsp, ellipsem, 3, cutoff, scalex, scaley,
self.ImageZ)
if len(Ringm) > 10:
parmDict['tilt'] *= -1
chim = FitDetector(np.array(Ring0 + Ringm), varyList, parmDict,
True)
tiltm = parmDict['tilt']
phim = parmDict['phi']
centm = [parmDict['det-X'], parmDict['det-Y']]
fail = False
else:
chim = 1e6
if fail:
i2 += 1
if chip < chim:
data['tilt'] = tiltp
data['center'] = centp
data['rotation'] = phip
else:
data['tilt'] = tiltm
data['center'] = centm
data['rotation'] = phim
data['ellipses'].append(ellipsep[:] + ('b', ))
data['rings'].append(np.array(Ringp))
data['ellipses'].append(ellipsem[:] + ('r', ))
data['rings'].append(np.array(Ringm))
G2plt.PlotImage(self, newImage=True)
parmDict = {
'dist': data['distance'],
'det-X': data['center'][0],
'det-Y': data['center'][1],
'tilt': data['tilt'],
'phi': data['rotation'],
'wave': data['wavelength'],
'dep': data['DetDepth']
}
varyList = [item for item in varyDict if varyDict[item]]
data['rings'] = []
data['ellipses'] = []
for i, H in enumerate(HKL):
dsp = H[3]
tth = 2.0 * asind(wave / (2. * dsp))
if tth + abs(data['tilt']) > 90.:
print 'next line is a hyperbola - search stopped'
break
if debug: print 'HKLD:', H[:4], '2-theta: %.4f' % (tth)
elcent, phi, radii = ellipse = GetEllipse(dsp, data)
data['ellipses'].append(copy.deepcopy(ellipse + ('g', )))
if debug:
print fmt % ('predicted ellipse:', elcent[0], elcent[1], phi,
radii[0], radii[1])
Ring = makeRing(dsp, ellipse, pixLimit, cutoff, scalex, scaley,
self.ImageZ)
if Ring:
data['rings'].append(np.array(Ring))
rings = np.concatenate((data['rings']), axis=0)
if i:
chisq = FitDetector(rings, varyList, parmDict, False)
data['distance'] = parmDict['dist']
data['center'] = [parmDict['det-X'], parmDict['det-Y']]
data['rotation'] = parmDict['phi']
data['tilt'] = parmDict['tilt']
data['DetDepth'] = parmDict['dep']
data['chisq'] = chisq
elcent, phi, radii = ellipse = GetEllipse(dsp, data)
if debug:
print fmt2 % ('fitted ellipse: ', elcent[0], elcent[1],
phi, radii[0], radii[1], chisq, len(rings))
data['ellipses'].append(copy.deepcopy(ellipse + ('r', )))
# G2plt.PlotImage(self,newImage=True)
else:
if debug:
print 'insufficient number of points in this ellipse to fit'
# break
G2plt.PlotImage(self, newImage=True)
fullSize = len(self.ImageZ) / scalex
if 2 * radii[1] < .9 * fullSize:
print 'Are all usable rings (>25% visible) used? Try reducing Min ring I/Ib'
N = len(data['ellipses'])
if N > 2:
FitDetector(rings, varyList, parmDict)
data['wavelength'] = parmDict['wave']
data['distance'] = parmDict['dist']
data['center'] = [parmDict['det-X'], parmDict['det-Y']]
data['rotation'] = parmDict['phi']
data['tilt'] = parmDict['tilt']
data['DetDepth'] = parmDict['dep']
for H in HKL[:N]:
ellipse = GetEllipse(H[3], data)
data['ellipses'].append(copy.deepcopy(ellipse + ('b', )))
print 'calibration time = ', time.time() - time0
G2plt.PlotImage(self, newImage=True)
return True
def Readrmc6fPhase(self, filename, parent=None):
'''Read a phase from a rmc6f file.
'''
self.errors = 'Error opening file'
fp = open(filename, 'Ur')
Phase = {}
Title = os.path.split(filename)
G2G.SaveGPXdirectory(Title[0])
Title = os.path.splitext(Title[1])[0]
Atoms = []
S = fp.readline()
line = 1
SGData = None
cell = None
IA = 'I'
Uiso = 0.01
Uij = [0. for i in range(6)]
while S:
self.errors = 'Error reading at line ' + str(line)
Atom = []
if 'Cell' in S[:4]:
cellRec = S.split(':')[1].split()
abc = cellRec[:3]
angles = cellRec[3:]
cell = [
float(abc[0]),
float(abc[1]),
float(abc[2]),
float(angles[0]),
float(angles[1]),
float(angles[2])
]
Volume = G2lat.calc_V(G2lat.cell2A(cell))
AA, AB = G2lat.cell2AB(cell)
SGData = G2obj.P1SGData # P 1
elif 'Atoms' in S[:5]:
S = fp.readline()[:-1]
AtRec = S.split()
for ix, s in enumerate(AtRec):
if '.' in s:
break #is points at x
while S:
AtRec = S.split()
Atype = AtRec[1]
Aname = Atype + AtRec[0]
Afrac = 1.0
x, y, z = AtRec[ix:ix + 3]
XYZ = np.array([float(x), float(y), float(z)])
SytSym, Mult = '1', 1
Atom = [
Aname, Atype, '', XYZ[0], XYZ[1], XYZ[2], Afrac,
SytSym, Mult, IA, Uiso
]
Atom += Uij
Atom.append(ran.randint(0, sys.maxsize))
Atoms.append(Atom)
S = fp.readline()[:-1]
S = fp.readline()
line += 1
fp.close()
self.errors = 'Error after read complete'
Phase = G2obj.SetNewPhase(Name='RMCProfile phase',
SGData=SGData,
cell=cell + [
Volume,
])
Phase['General']['Name'] = Title
Phase['General']['Type'] = 'nuclear'
Phase['General']['AtomPtrs'] = [3, 1, 7, 9]
Phase['Atoms'] = Atoms
return Phase