def refinePeaksT(peaks, difC, ibrav, A, Zero, ZeroRef):
'needs a doc string'
dmin = getDmin(peaks)
OK, smin, Aref, Z, result = FitHKLT(difC, ibrav, peaks, A, Zero, ZeroRef)
Peaks = np.array(peaks).T
H = Peaks[4:7]
Peaks[8] = 1. / np.sqrt(G2lat.calc_rDsqT(H, Aref, Z, Peaks[0], difC))
peaks = Peaks.T
HKL = G2lat.GenHBravais(dmin, ibrav, A)
M20, X20 = calc_M20(peaks, HKL)
return len(HKL), M20, X20, Aref, Z
def ranAbyV(Bravais,dmin,dmax,V):
'needs a doc string'
cell = [0,0,0,0,0,0]
bad = True
while bad:
bad = False
cell = rancell(Bravais,dmin,dmax)
G,g = G2lat.cell2Gmat(cell)
A = G2lat.Gmat2A(G)
if G2lat.calc_rVsq(A) < 1:
scaleAbyV(A,V)
cell = G2lat.A2cell(A)
for i in range(3):
bad |= cell[i] < dmin
return A
def ranAbyV(Bravais,dmin,dmax,V):
'needs a doc string'
cell = [0,0,0,0,0,0]
bad = True
while bad:
bad = False
cell = rancell(Bravais,dmin,dmax)
G,g = G2lat.cell2Gmat(cell)
A = G2lat.Gmat2A(G)
if G2lat.calc_rVsq(A) < 1:
scaleAbyV(A,V)
cell = G2lat.A2cell(A)
for i in range(3):
bad |= cell[i] < dmin
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 refinePeaksTSS(peaks, difC, Inst, SGData, SSGData, maxH, ibrav, A, vec,
vecRef, Zero, ZeroRef):
'needs a doc string'
dmin = getDmin(peaks)
OK, smin, Aref, Vref, Z, result = FitHKLTSS(difC, ibrav, peaks, A, vec,
vecRef, Zero, ZeroRef)
Peaks = np.array(peaks).T
H = Peaks[4:8]
Peaks[9] = 1. / np.sqrt(
G2lat.calc_rDsqTSS(H, Aref, Vref, Z, Peaks[0], difC))
peaks = Peaks.T
HKL = G2pwd.getHKLMpeak(dmin, Inst, SGData, SSGData, Vref, maxH, Aref)
HKL = G2lat.GenHBravais(dmin, ibrav, A)
M20, X20 = calc_M20SS(peaks, HKL)
return len(HKL), M20, X20, Aref, Vref, Z
def Exporter(self,event=None):
'''Export as a XYZ file
'''
# the export process starts here
self.InitExport(event)
# load all of the tree into a set of dicts
self.loadTree()
# create a dict with refined values and their uncertainties
self.loadParmDict()
if self.ExportSelect(): # set export parameters; ask for file name
return
filename = self.filename
for phasenam in self.phasenam:
phasedict = self.Phases[phasenam] # pointer to current phase info
General = phasedict['General']
i = self.Phases[phasenam]['pId']
Atoms = phasedict['Atoms']
if not len(Atoms):
print('**** ERROR - Phase '+str(phasenam)+' has no atoms! ****')
continue
if len(self.phasenam) > 1: # if more than one filename is included, add a phase #
self.filename = os.path.splitext(filename)[1] + "_" + str(i) + self.extension
fp = self.OpenFile()
cx,ct,cs,cia = General['AtomPtrs']
Cell = General['Cell'][1:7]
A,B = G2lat.cell2AB(Cell)
fmt = '{:4s}'+3*'{:12.4f}'
self.Write('{:6d}'.format(len(Atoms)))
self.Write(' ')
for atom in Atoms:
xyz = np.inner(A,np.array(atom[cx:cx+3]))
self.Write(fmt.format(atom[ct],*xyz))
self.CloseFile()
print('Phase '+str(phasenam)+' written to XYZ file '+str(self.fullpath))
def _run_rietveld_pawley_refinement(self, gsas_proj, do_pawley):
"""
Run a Rietveld or Pawley refinement
:param gsas_proj: The project to work on
:param do_pawley: True if doing a Pawley refinement (the default), False if doing a Rietveld refinement
:return: (R weighted profile, goodness-of-fit coefficient, table containing refined lattice parameters)
"""
phase_paths = self.getPropertyValue(self.PROP_PATHS_TO_PHASE_FILES).split(",")
pawley_tmin = None
if self._refinement_method_is_pawley():
pawley_dmin = float(self.getPropertyValue(self.PROP_PAWLEY_DMIN))
pawley_tmin = GSASIIlattice.Dsp2pos(Inst=gsas_proj.histogram(0).data["Instrument Parameters"][0],
dsp=pawley_dmin)
refinements = self._create_refinement_params_dict(num_phases=len(phase_paths), pawley_tmin=pawley_tmin)
prog = Progress(self, start=0, end=1, nreports=2)
prog.report("Reading phase files")
for phase_path in phase_paths:
phase = gsas_proj.add_phase(phasefile=phase_path, histograms=[gsas_proj.histograms()[0]])
if do_pawley:
self._set_pawley_phase_parameters(phase)
pawley_reflections = self._generate_pawley_reflections(phase)
phase.data["Pawley ref"] = pawley_reflections
prog.report("Running {} refinement steps".format(len(refinements)))
for refinement in refinements:
gsas_proj.do_refinements([refinement])
gsas_proj.save()
rwp = gsas_proj.histogram(0).get_wR()
lattice_params = gsas_proj.phases()[0].get_cell()
lattice_params_table = self._build_output_lattice_table(lattice_params)
return rwp, lattice_params_table
def errFitT(values,ibrav,d,H,tof,difC,Z,Zref):
Zero = Z
if Zref:
Zero = values[-1]
A = Values2A(ibrav,values)
Qo = 1./d**2
Qc = G2lat.calc_rDsqT(H,A,Zero,tof,difC)
return (Qo-Qc)
def errFitZ(values,ibrav,d,H,tth,wave,Z,Zref):
Zero = Z
if Zref:
Zero = values[-1]
A = Values2A(ibrav,values)
Qo = 1./d**2
Qc = G2lat.calc_rDsqZ(H,A,Zero,tth,wave)
return (Qo-Qc)
def errFitZ(values, ibrav, d, H, tth, wave, Z, Zref):
Zero = Z
if Zref:
Zero = values[-1]
A = Values2A(ibrav, values)
Qo = 1. / d**2
Qc = G2lat.calc_rDsqZ(H, A, Zero, tth, wave)
return (Qo - Qc)
def errFitT(values, ibrav, d, H, tof, difC, Z, Zref):
Zero = Z
if Zref:
Zero = values[-1]
A = Values2A(ibrav, values)
Qo = 1. / d**2
Qc = G2lat.calc_rDsqT(H, A, Zero, tof, difC)
return (Qo - Qc)
def SetPOCoef(Order,hist):
cofNames = G2lat.GenSHCoeff(SGData['SGLaue'],'0',Order,False) #cylindrical & no M
newPOCoef = dict(zip(cofNames,np.zeros(len(cofNames))))
POCoeff = UseList[G2frame.hist]['Pref.Ori.'][5]
for cofName in POCoeff:
if cofName in cofNames:
newPOCoef[cofName] = POCoeff[cofName]
return newPOCoef
def errFitZSS(values,ibrav,d,H,tth,wave,vec,Vref,Z,Zref):
Zero = Z
if Zref:
Zero = values[-1]
A = Values2A(ibrav,values)
Vec = Values2Vec(ibrav,vec,Vref,values)
Qo = 1./d**2
Qc = G2lat.calc_rDsqZSS(H,A,Vec,Zero,tth,wave)
return (Qo-Qc)
def errFitTSS(values, ibrav, d, H, tof, difC, vec, Vref, Z, Zref):
Zero = Z
if Zref:
Zero = values[-1]
A = Values2A(ibrav, values)
Vec = Values2Vec(ibrav, vec, Vref, values)
Qo = 1. / d**2
Qc = G2lat.calc_rDsqTSS(H, A, Vec, Zero, tof, difC)
return (Qo - Qc)
def test1():
if NeedTestData: TestData()
ibrav, A, Pwr, peaks = TestData2
print('bad cell:', G2lat.A2cell(A))
print('FitHKL')
OK, smin, A, result = FitHKL(ibrav, peaks, A, Pwr)
result = refinePeaks(peaks, ibrav, A)
N, M20, X20, A = result
print('refinePeaks:', N, M20, X20, A)
def refinePeaks(peaks, ibrav, A, ifX20=True):
'needs a doc string'
dmin = getDmin(peaks)
smin = 1.0e10
pwr = 8
maxTries = 10
OK = False
tries = 0
HKL = G2lat.GenHBravais(dmin, ibrav, A)
while len(HKL) > 2 and IndexPeaks(peaks, HKL)[0]:
Pwr = pwr - (tries % 2)
HKL = []
tries += 1
osmin = smin
oldA = A[:]
Vold = G2lat.calc_V(oldA)
OK, smin, A, result = FitHKL(ibrav, peaks, A, Pwr)
Vnew = G2lat.calc_V(A)
if Vnew > 2.0 * Vold or Vnew < 2.:
A = ranAbyR(ibrav, oldA, tries + 1, maxTries, ran2axis)
OK = False
continue
try:
HKL = G2lat.GenHBravais(dmin, ibrav, A)
except FloatingPointError:
A = oldA
OK = False
break
if len(HKL) == 0: break #absurd cell obtained!
rat = (osmin - smin) / smin
if abs(rat) < 1.0e-5 or not OK: break
if tries > maxTries: break
if OK:
OK, smin, A, result = FitHKL(ibrav, peaks, A, 2)
Peaks = np.array(peaks).T
H = Peaks[4:7]
try:
Peaks[8] = 1. / np.sqrt(G2lat.calc_rDsq(H, A))
peaks = Peaks.T
except FloatingPointError:
A = oldA
M20, X20 = calc_M20(peaks, HKL, ifX20)
return len(HKL), M20, X20, A
def refinePeaks(peaks,ibrav,A,ifX20=True):
'needs a doc string'
dmin = getDmin(peaks)
smin = 1.0e10
pwr = 8
maxTries = 10
OK = False
tries = 0
HKL = G2lat.GenHBravais(dmin,ibrav,A)
while len(HKL) > 2 and IndexPeaks(peaks,HKL)[0]:
Pwr = pwr - (tries % 2)
HKL = []
tries += 1
osmin = smin
oldA = A[:]
Vold = G2lat.calc_V(oldA)
OK,smin,A,result = FitHKL(ibrav,peaks,A,Pwr)
Vnew = G2lat.calc_V(A)
if Vnew > 2.0*Vold or Vnew < 2.:
A = ranAbyR(ibrav,oldA,tries+1,maxTries,ran2axis)
OK = False
continue
try:
HKL = G2lat.GenHBravais(dmin,ibrav,A)
except FloatingPointError:
A = oldA
OK = False
break
if len(HKL) == 0: break #absurd cell obtained!
rat = (osmin-smin)/smin
if abs(rat) < 1.0e-5 or not OK: break
if tries > maxTries: break
if OK:
OK,smin,A,result = FitHKL(ibrav,peaks,A,2)
Peaks = np.array(peaks).T
H = Peaks[4:7]
try:
Peaks[8] = 1./np.sqrt(G2lat.calc_rDsq(H,A))
peaks = Peaks.T
except FloatingPointError:
A = oldA
M20,X20 = calc_M20(peaks,HKL,ifX20)
return len(HKL),M20,X20,A
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 refinePeaksZSS(peaks,wave,Inst,SGData,SSGData,maxH,ibrav,A,vec,vecRef,Zero,ZeroRef):
'needs a doc string'
dmin = getDmin(peaks)
OK,smin,Aref,Vref,Z,result = FitHKLZSS(wave,ibrav,peaks,A,vec,vecRef,Zero,ZeroRef)
Peaks = np.array(peaks).T
H = Peaks[4:8]
Peaks[9] = 1./np.sqrt(G2lat.calc_rDsqZSS(H,Aref,Vref,Z,Peaks[0],wave)) #H,A,vec,Z,tth,lam
peaks = Peaks.T
HKL = G2pwd.getHKLMpeak(dmin,Inst,SGData,SSGData,Vref,maxH,Aref)
M20,X20 = calc_M20SS(peaks,HKL)
return len(HKL),M20,X20,Aref,Vref,Z
def refinePeaksT(peaks,difC,ibrav,A,Zero,ZeroRef):
'needs a doc string'
dmin = getDmin(peaks)
OK,smin,Aref,Z,result = FitHKLT(difC,ibrav,peaks,A,Zero,ZeroRef)
Peaks = np.array(peaks).T
H = Peaks[4:7]
Peaks[8] = 1./np.sqrt(G2lat.calc_rDsqT(H,Aref,Z,Peaks[0],difC))
peaks = Peaks.T
HKL = G2lat.GenHBravais(dmin,ibrav,A)
M20,X20 = calc_M20(peaks,HKL)
return len(HKL),M20,X20,Aref,Z
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 Writer(self, TreeName, filename=None):
#print filename
self.OpenFile(filename)
histblk = self.Histograms[TreeName]
Parms = self.Histograms[TreeName]['Instrument Parameters'][0]
for parm in Parms:
if parm in [
'Type',
'Source',
]:
line = '"Instparm: %s","%s"' % (parm, Parms[parm][0])
elif parm in [
'Lam',
'Zero',
]:
line = '"Instparm: %s",%10.6f' % (parm, Parms[parm][1])
else:
line = '"Instparm: %s",%10.2f' % (parm, Parms[parm][1])
self.Write(line)
Samp = self.Histograms[TreeName]['Sample Parameters']
for samp in Samp:
if samp in ['InstrName', 'Type']:
line = '"Samparm: %s",%s' % (samp, Samp[samp])
elif samp in [
'Azimuth', 'Chi', 'Gonio. radius', 'Omega', 'Phi',
'Pressure', 'Temperature', 'Time'
]:
line = '"Samparm: %s",%10.2f' % (samp, Samp[samp])
elif samp in [
'DisplaceX', 'DisplaceY', 'Scale', 'Shift', 'SurfRoughA',
'SurfRoughB', 'Transparency'
]:
line = '"Samparm: %s",%10.2f' % (samp, Samp[samp][0])
else:
continue
self.Write(line)
WriteList(self, ("x", "y_obs", "weight", "y_calc", "y_bkg", "Q"))
digitList = 2 * ((13, 3), ) + ((13, 5), ) + 3 * ((13, 3), )
for vallist in zip(
histblk['Data'][0],
histblk['Data'][1],
histblk['Data'][2],
histblk['Data'][3],
histblk['Data'][4],
#histblk['Data'][5],
2 * np.pi / G2lat.Pos2dsp(Parms, histblk['Data'][0])):
line = ""
for val, digits in zip(vallist, digitList):
if line: line += ','
line += G2py3.FormatValue(val, digits)
self.Write(line)
self.CloseFile()
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()
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 DisAglTor(DATData):
'Needs a doc string'
SGData = DATData['SGData']
Cell = DATData['Cell']
Amat, Bmat = G2lat.cell2AB(Cell[:6])
covData = {}
pfx = ''
if 'covData' in DATData:
covData = DATData['covData']
pfx = str(DATData['pId']) + '::'
Datoms = []
Oatoms = []
for i, atom in enumerate(DATData['Datoms']):
symop = atom[-1].split('+')
if len(symop) == 1:
symop.append('0,0,0')
symop[0] = int(symop[0])
symop[1] = eval(symop[1])
atom.append(symop)
Datoms.append(atom)
oatom = DATData['Oatoms'][i]
names = ['', '', '']
if pfx:
names = [
pfx + 'dAx:' + str(oatom[0]), pfx + 'dAy:' + str(oatom[0]),
pfx + 'dAz:' + str(oatom[0])
]
oatom += [
names,
]
Oatoms.append(oatom)
atmSeq = [atom[1] + '(' + atom[-2] + ')' for atom in Datoms]
if DATData['Natoms'] == 4: #torsion
Tors, sig = G2mth.GetDATSig(Oatoms, Datoms, Amat, SGData, covData)
print(' Torsion angle for %s atom sequence: %s = %s' %
(DATData['Name'], str(atmSeq).replace(
"'", "")[1:-1], G2mth.ValEsd(Tors, sig)))
print(' NB: Atom sequence determined by selection order')
return # done with torsion
elif DATData['Natoms'] == 3: #angle
Ang, sig = G2mth.GetDATSig(Oatoms, Datoms, Amat, SGData, covData)
print(' Angle in %s for atom sequence: %s = %s' %
(DATData['Name'], str(atmSeq).replace(
"'", "")[1:-1], G2mth.ValEsd(Ang, sig)))
print(' NB: Atom sequence determined by selection order')
else: #2 atoms - distance
Dist, sig = G2mth.GetDATSig(Oatoms, Datoms, Amat, SGData, covData)
print(' Distance in %s for atom sequence: %s = %s' %
(DATData['Name'], str(atmSeq).replace(
"'", "")[1:-1], G2mth.ValEsd(Dist, sig)))
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 refinePeaksZSS(peaks, wave, Inst, SGData, SSGData, maxH, ibrav, A, vec,
vecRef, Zero, ZeroRef):
'needs a doc string'
dmin = getDmin(peaks)
OK, smin, Aref, Vref, Z, result = FitHKLZSS(wave, ibrav, peaks, A, vec,
vecRef, Zero, ZeroRef)
Peaks = np.array(peaks).T
H = Peaks[4:8]
Peaks[9] = 1. / np.sqrt(
G2lat.calc_rDsqZSS(H, Aref, Vref, Z, Peaks[0],
wave)) #H,A,vec,Z,tth,lam
peaks = Peaks.T
HKL = G2pwd.getHKLMpeak(dmin, Inst, SGData, SSGData, Vref, maxH, Aref)
M20, X20 = calc_M20SS(peaks, HKL)
return len(HKL), M20, X20, Aref, Vref, Z
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 DisAglTor(DATData):
'Needs a doc string'
SGData = DATData['SGData']
Cell = DATData['Cell']
Amat,Bmat = G2lat.cell2AB(Cell[:6])
covData = {}
pfx = ''
if 'covData' in DATData:
covData = DATData['covData']
covMatrix = covData['covMatrix']
varyList = covData['varyList']
pfx = str(DATData['pId'])+'::'
Datoms = []
Oatoms = []
for i,atom in enumerate(DATData['Datoms']):
symop = atom[-1].split('+')
if len(symop) == 1:
symop.append('0,0,0')
symop[0] = int(symop[0])
symop[1] = eval(symop[1])
atom.append(symop)
Datoms.append(atom)
oatom = DATData['Oatoms'][i]
names = ['','','']
if pfx:
names = [pfx+'dAx:'+str(oatom[0]),pfx+'dAy:'+str(oatom[0]),pfx+'dAz:'+str(oatom[0])]
oatom += [names,]
Oatoms.append(oatom)
atmSeq = [atom[1]+'('+atom[-2]+')' for atom in Datoms]
if DATData['Natoms'] == 4: #torsion
Tors,sig = G2mth.GetDATSig(Oatoms,Datoms,Amat,SGData,covData)
print ' Torsion angle for '+DATData['Name']+' atom sequence: ',atmSeq,'=',G2mth.ValEsd(Tors,sig)
print ' NB: Atom sequence determined by selection order'
return # done with torsion
elif DATData['Natoms'] == 3: #angle
Ang,sig = G2mth.GetDATSig(Oatoms,Datoms,Amat,SGData,covData)
print ' Angle in '+DATData['Name']+' for atom sequence: ',atmSeq,'=',G2mth.ValEsd(Ang,sig)
print ' NB: Atom sequence determined by selection order'
else: #2 atoms - distance
Dist,sig = G2mth.GetDATSig(Oatoms,Datoms,Amat,SGData,covData)
print ' Distance in '+DATData['Name']+' for atom sequence: ',atmSeq,'=',G2mth.ValEsd(Dist,sig)
def Writer(self, TreeName, filename=None):
import GSASIIlattice as G2lat
self.OpenFile(filename)
histblk = self.Histograms[TreeName]
inst = histblk['Instrument Parameters'][0]
self.Write(str(TreeName)[5:]) # drop 'PWDR '
if 'Lam1' in inst:
print(
'Do you really want to write a multi-wavelength pattern in Q?')
lam = 0.
else:
lam = inst['Lam'][1]
self.Write("Q{:>20.6f}".format(lam))
self.Write("Intensity")
self.Write(" " + str(len(histblk['Data'][0])))
for X, Y in zip(histblk['Data'][0], histblk['Data'][1]):
line = " %5.7e" % (2. * np.pi / G2lat.Pos2dsp(inst, X))
line += " %5.7e" % Y
self.Write(line)
self.CloseFile()
def BestPlane(PlaneData):
'Needs a doc string'
def ShowBanner(name):
print(80 * '*')
print(' Best plane result for phase ' + name)
print(80 * '*', '\n')
ShowBanner(PlaneData['Name'])
Cell = PlaneData['Cell']
Amat, Bmat = G2lat.cell2AB(Cell[:6])
Atoms = PlaneData['Atoms']
sumXYZ = np.zeros(3)
XYZ = []
Natoms = len(Atoms)
for atom in Atoms:
xyz = np.array(atom[3:6])
XYZ.append(xyz)
sumXYZ += xyz
sumXYZ /= Natoms
XYZ = np.array(XYZ) - sumXYZ
XYZ = np.inner(Amat, XYZ).T
Zmat = np.zeros((3, 3))
for i, xyz in enumerate(XYZ):
Zmat += np.outer(xyz.T, xyz)
print(' Selected atoms centered at %10.5f %10.5f %10.5f' %
(sumXYZ[0], sumXYZ[1], sumXYZ[2]))
Evec, Emat = nl.eig(Zmat)
Evec = np.sqrt(Evec) / (Natoms - 3)
Order = np.argsort(Evec)
XYZ = np.inner(XYZ, Emat.T).T
XYZ = np.array([XYZ[Order[2]], XYZ[Order[1]], XYZ[Order[0]]]).T
print(' Atoms in Cartesian best plane coordinates:')
print(' Name X Y Z')
for i, xyz in enumerate(XYZ):
print(' %6s%10.3f%10.3f%10.3f' %
(Atoms[i][1].ljust(6), xyz[0], xyz[1], xyz[2]))
print('\n Best plane RMS X =%8.3f, Y =%8.3f, Z =%8.3f' %
(Evec[Order[2]], Evec[Order[1]], Evec[Order[0]]))
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
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 BestPlane(PlaneData):
'Needs a doc string'
def ShowBanner(name):
print 80*'*'
print ' Best plane result for phase '+name
print 80*'*','\n'
ShowBanner(PlaneData['Name'])
Cell = PlaneData['Cell']
Amat,Bmat = G2lat.cell2AB(Cell[:6])
Atoms = PlaneData['Atoms']
sumXYZ = np.zeros(3)
XYZ = []
Natoms = len(Atoms)
for atom in Atoms:
xyz = np.array(atom[3:6])
XYZ.append(xyz)
sumXYZ += xyz
sumXYZ /= Natoms
XYZ = np.array(XYZ)-sumXYZ
XYZ = np.inner(Amat,XYZ).T
Zmat = np.zeros((3,3))
for i,xyz in enumerate(XYZ):
Zmat += np.outer(xyz.T,xyz)
print ' Selected atoms centered at %10.5f %10.5f %10.5f'%(sumXYZ[0],sumXYZ[1],sumXYZ[2])
Evec,Emat = nl.eig(Zmat)
Evec = np.sqrt(Evec)/(Natoms-3)
Order = np.argsort(Evec)
XYZ = np.inner(XYZ,Emat.T).T
XYZ = np.array([XYZ[Order[2]],XYZ[Order[1]],XYZ[Order[0]]]).T
print ' Atoms in Cartesian best plane coordinates:'
print ' Name X Y Z'
for i,xyz in enumerate(XYZ):
print ' %6s%10.3f%10.3f%10.3f'%(Atoms[i][1].ljust(6),xyz[0],xyz[1],xyz[2])
print '\n Best plane RMS X =%8.3f, Y =%8.3f, Z =%8.3f'%(Evec[Order[2]],Evec[Order[1]],Evec[Order[0]])
def scaleAbyV(A,V):
'needs a doc string'
v = G2lat.calc_V(A)
scale = math.exp(math.log(v/V)/3.)**2
for i in range(6):
A[i] *= scale
def RetDistAngle(DisAglCtls,DisAglData):
'''Compute and return 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>`)
: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'])+'::'
Factor = DisAglCtls['Factors']
Radii = dict(zip(DisAglCtls['AtomTypes'],zip(DisAglCtls['BondRadii'],DisAglCtls['AngleRadii'])))
indices = (-2,-1,0,1,2)
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,Spn] 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(pdpx,Xvcov)))
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 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 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 DoIndexPeaks(peaks,controls,bravais,ifX20=True):
'needs a doc string'
delt = 0.005 #lowest d-spacing cushion - can be fixed?
amin = 2.5
amax = 5.0*getDmax(peaks)
dmin = getDmin(peaks)-delt
bravaisNames = ['Cubic-F','Cubic-I','Cubic-P','Trigonal-R','Trigonal/Hexagonal-P',
'Tetragonal-I','Tetragonal-P','Orthorhombic-F','Orthorhombic-I','Orthorhombic-C',
'Orthorhombic-P','Monoclinic-C','Monoclinic-P','Triclinic']
tries = ['1st','2nd','3rd','4th','5th','6th','7th','8th','9th','10th']
N1s = [1,1,1, 5,5, 5,5, 50,50,50,50, 50,50, 200]
N2s = [1,1,1, 2,2, 2,2, 2,2,2,2, 2,2, 4]
Nm = [1,1,1, 1,1, 1,1, 1,1,1,1, 2,2, 4]
Nobs = len(peaks)
zero,ncno = controls[1:3]
ncMax = Nobs*ncno
print "%s %8.3f %8.3f" % ('lattice parameter range = ',amin,amax)
print "%s %.4f %s %d %s %d" % ('Zero =',zero,'Nc/No max =',ncno,' Max Nc =',ncno*Nobs)
cells = []
for ibrav in range(14):
begin = time.time()
if bravais[ibrav]:
print 'cell search for ',bravaisNames[ibrav]
print ' M20 X20 Nc a b c alpha beta gamma volume V-test'
V1 = controls[3]
bestM20 = 0
topM20 = 0
cycle = 0
while cycle < 5:
dlg = wx.ProgressDialog("Generated reflections",tries[cycle]+" cell search for "+bravaisNames[ibrav],ncMax,
style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_REMAINING_TIME|wx.PD_CAN_ABORT)
screenSize = wx.ClientDisplayRect()
Size = dlg.GetSize()
dlg.SetPosition(wx.Point(screenSize[2]-Size[0]-305,screenSize[1]+5))
try:
GoOn = True
while GoOn: #Loop over increment of volume
N2 = 0
while N2 < N2s[ibrav]: #Table 2 step (iii)
if ibrav > 2:
if not N2:
A = []
GoOn,Nc,M20,X20,A = findBestCell(dlg,ncMax,A,Nm[ibrav]*N1s[ibrav],ibrav,peaks,V1,ifX20)
if A:
GoOn,Nc,M20,X20,A = findBestCell(dlg,ncMax,A[:],N1s[ibrav],ibrav,peaks,0,ifX20)
else:
GoOn,Nc,M20,X20,A = findBestCell(dlg,ncMax,0,Nm[ibrav]*N1s[ibrav],ibrav,peaks,V1,ifX20)
if Nc >= ncMax:
GoOn = False
break
elif 3*Nc < Nobs:
N2 = 10
break
else:
if not GoOn:
break
if M20 > 1.0:
bestM20 = max(bestM20,M20)
A = halfCell(ibrav,A[:],peaks)
if ibrav in [12]:
A = monoCellReduce(ibrav,A[:])
HKL = G2lat.GenHBravais(dmin,ibrav,A)
peaks = IndexPeaks(peaks,HKL)[1]
a,b,c,alp,bet,gam = G2lat.A2cell(A)
V = G2lat.calc_V(A)
if M20 >= 2.0:
print "%10.3f %3d %3d %10.5f %10.5f %10.5f %10.3f %10.3f %10.3f %10.2f %10.2f" % (M20,X20,Nc,a,b,c,alp,bet,gam,V,V1)
cells.append([M20,X20,ibrav,a,b,c,alp,bet,gam,V,False,False])
if not GoOn:
break
N2 += 1
if ibrav < 11:
V1 *= 1.1
elif ibrav in range(11,14):
V1 *= 1.05
if not GoOn:
if bestM20 > topM20:
topM20 = bestM20
if cells:
V1 = cells[0][9]
else:
V1 = 25
ncMax += Nobs
cycle += 1
print 'Restart search, new Max Nc = ',ncMax
else:
cycle = 10
finally:
dlg.Destroy()
print '%s%s%s%s'%('finished cell search for ',bravaisNames[ibrav], \
', elapsed time = ',G2lat.sec2HMS(time.time()-begin))
if cells:
return True,dmin,cells
else:
return False,0,[]
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 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 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 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 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 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 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 errFit(values,ibrav,d,H,Pwr):
A = Values2A(ibrav,values)
Qo = 1./d**2
Qc = G2lat.calc_rDsq(H,A)
return (Qo-Qc)*d**Pwr
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 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 ShowHistogramInfo():
try:
histData = UseList[G2frame.hist]
except KeyError:
G2frame.ErrorDialog('Missing data error',
G2frame.hist+' not in GSAS-II data tree')
return
if 'Use' not in UseList[G2frame.hist]: #patch
UseList[G2frame.hist]['Use'] = True
if 'Babinet' not in UseList[G2frame.hist]:
UseList[G2frame.hist]['Babinet'] = {'BabA':[0.0,False],'BabU':[0.0,False]}
bottomSizer = wx.BoxSizer(wx.VERTICAL)
showSizer = wx.BoxSizer(wx.HORIZONTAL)
useData = wx.CheckBox(DData,wx.ID_ANY,label='Use Histogram: '+G2frame.hist+' ?')
showSizer.Add(useData,0,WACV|wx.TOP|wx.BOTTOM,5)
useData.Bind(wx.EVT_CHECKBOX, OnUseData)
useData.SetValue(UseList[G2frame.hist]['Use'])
bottomSizer.Add(showSizer,0,WACV|wx.TOP|wx.BOTTOM|wx.LEFT,5)
bottomSizer.Add(ScaleSizer(),0,WACV|wx.BOTTOM,5)
if G2frame.hist[:4] == 'PWDR':
if UseList[G2frame.hist]['Size'][0] == 'isotropic':
isoSizer = wx.BoxSizer(wx.HORIZONTAL)
isoSizer.Add(TopSizer(' Domain size model: ',['isotropic','uniaxial','ellipsoidal'],
'Size',OnSizeType),0,WACV)
isoSizer.Add(LGmixSizer('Size',OnLGmixVal,OnLGmixRef))
isoSizer.Add(ResetSizer('isotropic',OnResetSize),0,WACV)
bottomSizer.Add(isoSizer)
bottomSizer.Add(IsoSizer(u'size(\xb5m): ','Size','%.5f',
OnSizeVal,OnSizeRef),0,WACV|wx.BOTTOM,5)
elif UseList[G2frame.hist]['Size'][0] == 'uniaxial':
uniSizer = wx.BoxSizer(wx.HORIZONTAL)
uniSizer.Add(TopSizer(' Domain size model: ',['isotropic','uniaxial','ellipsoidal'],
'Size',OnSizeType),0,WACV)
uniSizer.Add(LGmixSizer('Size',OnLGmixVal,OnLGmixRef))
uniSizer.Add(ResetSizer('uniaxial',OnResetSize),0,WACV)
bottomSizer.Add(UniSizer('Size',OnSizeAxis),0,WACV)
bottomSizer.Add(uniSizer)
bottomSizer.Add(UniDataSizer(u'size(\xb5m): ','Size','%.5f',OnSizeVal,OnSizeRef)
,0,WACV|wx.BOTTOM,5)
elif UseList[G2frame.hist]['Size'][0] == 'ellipsoidal':
ellSizer = wx.BoxSizer(wx.HORIZONTAL)
ellSizer.Add(TopSizer(' Domain size model: ',['isotropic','uniaxial','ellipsoidal'],
'Size',OnSizeType),0,WACV)
ellSizer.Add(LGmixSizer('Size',OnLGmixVal,OnLGmixRef))
ellSizer.Add(ResetSizer('ellipsoidal',OnResetSize),0,WACV)
bottomSizer.Add(ellSizer)
bottomSizer.Add(EllSizeDataSizer(),0,WACV|wx.BOTTOM,5)
if UseList[G2frame.hist]['Mustrain'][0] == 'isotropic':
isoSizer = wx.BoxSizer(wx.HORIZONTAL)
isoSizer.Add(TopSizer(' Mustrain model: ',['isotropic','uniaxial','generalized',],
'Mustrain',OnStrainType),0,WACV)
isoSizer.Add(LGmixSizer('Mustrain',OnLGmixVal,OnLGmixRef))
isoSizer.Add(ResetSizer('isotropic',OnResetStrain),0,WACV)
bottomSizer.Add(isoSizer)
bottomSizer.Add(IsoSizer(' microstrain: ','Mustrain','%.1f',
OnStrainVal,OnStrainRef),0,WACV|wx.BOTTOM,5)
elif UseList[G2frame.hist]['Mustrain'][0] == 'uniaxial':
uniSizer = wx.BoxSizer(wx.HORIZONTAL)
uniSizer.Add(TopSizer(' Mustrain model: ',['isotropic','uniaxial','generalized',],
'Mustrain',OnStrainType),0,WACV)
uniSizer.Add(LGmixSizer('Mustrain',OnLGmixVal,OnLGmixRef))
uniSizer.Add(ResetSizer('uniaxial',OnResetStrain),0,WACV)
bottomSizer.Add(uniSizer)
bottomSizer.Add(UniSizer('Mustrain',OnStrainAxis),0,WACV)
bottomSizer.Add(UniDataSizer('mustrain: ','Mustrain','%.1f',OnStrainVal,OnStrainRef)
,0,WACV|wx.BOTTOM,5)
elif UseList[G2frame.hist]['Mustrain'][0] == 'generalized':
genSizer = wx.BoxSizer(wx.HORIZONTAL)
genSizer.Add(TopSizer(' Mustrain model: ',['isotropic','uniaxial','generalized',],
'Mustrain',OnStrainType),0,WACV)
genSizer.Add(LGmixSizer('Mustrain',OnLGmixVal,OnLGmixRef))
genSizer.Add(ResetSizer('generalized',OnResetStrain),0,WACV)
bottomSizer.Add(genSizer)
bottomSizer.Add(GenStrainDataSizer(),0,WACV|wx.BOTTOM,5)
bottomSizer.Add(wx.StaticText(DData,wx.ID_ANY,' Hydrostatic/elastic strain:'))
bottomSizer.Add(HstrainSizer())
poSizer = wx.BoxSizer(wx.VERTICAL)
POData = UseList[G2frame.hist]['Pref.Ori.']
# patch - add penalty items
if len(POData) < 7:
POData.append(['',])
POData.append(0.1)
if not POData[6]:
POData[6] = ['',]
# end patch
poSizer.Add(PoTopSizer(POData))
if POData[0] == 'MD':
poSizer.Add(MDDataSizer(POData))
else: #'SH'
if POData[4]: #SH order > 0
textJ = G2lat.textureIndex(POData[5])
poSizer.Add(wx.StaticText(DData,wx.ID_ANY,' Spherical harmonic coefficients: '+'Texture index: %.3f'%(textJ))
,0,WACV|wx.TOP|wx.BOTTOM,5)
poSizer.Add(SHDataSizer(POData),0,WACV|wx.TOP|wx.BOTTOM,5)
poSizer.Add(SHPenalty(POData),0,WACV|wx.TOP|wx.BOTTOM,5)
bottomSizer.Add(poSizer,0,WACV|wx.TOP|wx.BOTTOM,5)
bottomSizer.Add(ExtSizer(),0,WACV|wx.TOP|wx.BOTTOM,5)
bottomSizer.Add(BabSizer(),0,WACV|wx.BOTTOM,5)
elif G2frame.hist[:4] == 'HKLF':
bottomSizer.Add(SCExtSizer(),0,WACV|wx.TOP|wx.BOTTOM,5)
bottomSizer.Add(BabSizer(),0,WACV|wx.BOTTOM,5)
return bottomSizer