def Exporter(self, event=None):
'''Export a set of powder data as a text file
'''
# the export process starts here
self.InitExport(event)
# load all of the tree into a set of dicts
self.loadTree()
if self.ExportSelect( # set export parameters
AskFile='default' # base name on the GPX file name
):
return
self.OpenFile()
hist = self.histnam[
0] # there should only be one histogram, in any case take the 1st
histblk = self.Histograms[hist]
hfmt = 5 * "{:12s} "
digitList = 2 * ((13, 3), ) + ((13, 5), ) + 2 * ((13, 3), )
self.Write(hfmt.format("x", "y_obs", "weight", "y_calc", "y_bkg"))
for vallist in zip(
histblk['Data'][0],
histblk['Data'][1],
histblk['Data'][2],
histblk['Data'][3],
histblk['Data'][4],
#histblk['Data'][5],
):
strg = ''
for val, digits in zip(vallist, digitList):
strg += G2py3.FormatPadValue(val, digits)
self.Write(strg)
self.CloseFile()
print(str(hist) + ' written to file ' + str(self.fullpath))
def Writer(self,TreeName,filename=None,prmname=''):
'''Write a single PWDR entry to a FXYE file
'''
histblk = self.Histograms[TreeName]
self.OpenFile(filename)
self.Write(TreeName[5:])
if prmname: self.Write('Instrument parameter file:'+os.path.split(prmname)[1])
x = np.array(histblk['Data'][0])
if 'T' in histblk['Instrument Parameters'][0]['Type'][0]:
cw = np.diff(x)
x[:-1] += cw
else:
x *= 100.
# convert weights to sigmas; use largest weight as minimum esd
s = np.sqrt(np.maximum(0.,np.array(histblk['Data'][2])))
s[s==0] = np.max(s)
s = 1./s
self.Write('BANK 1 %d %d CONS %.2f %.2f 0 0 FXYE' % (
len(x),len(x),x[0],(x[1]-x[0])
))
# for X,Y,S in zip(x,histblk['Data'][1],s):
# self.Write("{:15.6g} {:15.6g} {:15.6g}".format(X,Y,S))
for XYS in zip(x,histblk['Data'][1],s):
line = ''
for val in XYS:
line += G2py3.FormatPadValue(val,(15,6))
self.Write(line)
self.CloseFile()
def Writer(self, TreeName, filename=None):
self.OpenFile(filename)
histblk = self.Histograms[TreeName]
if len(self.Histograms[TreeName]['Models']['Size']['Distribution']):
self.Write('"Size Distribution"')
Distr = np.array(
self.Histograms[TreeName]['Models']['Size']['Distribution'])
WriteList(self, ("bin_pos", "bin_width", "bin_value"))
digitList = 2 * ((13, 3), ) + ((13, 4, 'g'), )
for bindata in Distr.T:
line = ""
for val, digits in zip(bindata, digitList):
if line: line += ','
line += G2py3.FormatValue(val, digits)
self.Write(line)
self.Write('"Small angle data"')
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',
]:
line = '"Instparm: %s",%10.6f' % (parm, Parms[parm][1])
else:
line = '"Instparm: %s",%10.2f' % (parm, Parms[parm][1])
self.Write(line)
WriteList(self, ("q", "y_obs", "y_sig", "y_calc", "y_bkg"))
digitList = 5 * ((13, 5, 'g'), )
for vallist in zip(
histblk['Data'][0],
histblk['Data'][1],
1. / np.sqrt(histblk['Data'][2]),
histblk['Data'][3],
histblk['Data'][4],
):
line = ""
for val, digits in zip(vallist, digitList):
if line: line += ','
line += G2py3.FormatValue(val, digits)
self.Write(line)
self.CloseFile()
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 Exporter(self, event=None):
'''Export one or more sets of powder data as FXYE file(s)
'''
# the export process starts here
self.InitExport(event)
# load all of the tree into a set of dicts
self.loadTree()
if self.ExportSelect( # set export parameters
AskFile='single' # get a file name/directory to save in
):
return
filenamelist = []
for hist in self.histnam:
if len(self.histnam) > 1:
# multiple files: create a unique name from the histogram
fileroot = G2obj.MakeUniqueLabel(self.MakePWDRfilename(hist),
filenamelist)
# create an instrument parameter file
self.filename = os.path.join(self.dirname,
fileroot + self.extension)
else:
# use the supplied name, but force the extension
self.filename = os.path.splitext(
self.filename)[0] + self.extension
histblk = self.Histograms[hist]
prmname = self.WriteInstFile(hist,
histblk['Instrument Parameters'][0])
self.OpenFile()
self.Write(hist[5:])
self.Write('Instrument parameter file:' +
os.path.split(prmname)[1])
x = 100 * np.array(histblk['Data'][0])
# convert weights to sigmas; use largest weight as minimum esd
s = np.sqrt(np.maximum(0., np.array(histblk['Data'][2])))
s[s == 0] = np.max(s)
s = 1. / s
self.Write('BANK 1 %d %d CONS %.2f %.2f 0 0 FXYE' %
(len(x), len(x), x[0], (x[1] - x[0])))
# for X,Y,S in zip(x,histblk['Data'][1],s):
# self.Write("{:15.6g} {:15.6g} {:15.6g}".format(X,Y,S))
for XYS in zip(x, histblk['Data'][1], s):
line = ''
for val in XYS:
line += G2py3.FormatPadValue(val, (15, 6))
self.Write(line)
self.CloseFile()
print('Histogram ' + str(hist) + ' written to file ' +
str(self.fullpath))
def Writer(self,TreeName,filename=None):
self.OpenFile(filename)
histblk = self.Histograms[TreeName]
self.Write('/*') #The ugly c comment delimiter used in topas!
self.Write('# '+TreeName[5:]) #evidently this by itself fails in topas
self.Write('*/')
x = np.array(histblk['Data'][0])
# convert weights to sigmas; use largest weight as minimum esd
s = np.sqrt(np.maximum(0.,np.array(histblk['Data'][2])))
s[s==0] = np.max(s)
s = 1./s
for XYS in zip(x,histblk['Data'][1],s):
line = ''
for val in XYS:
line += G2py3.FormatPadValue(val,(15,6))
self.Write(line)
self.CloseFile()
def Exporter(self, event=None):
'''Export one or more sets of powder data as XYE file(s)
'''
# the export process starts here
self.InitExport(event)
# load all of the tree into a set of dicts
self.loadTree()
if self.ExportSelect( # set export parameters
AskFile='single' # get a file name/directory to save in
):
return
filenamelist = []
for hist in self.histnam:
if len(self.histnam) > 1:
# multiple files: create a unique name from the histogram
fileroot = G2obj.MakeUniqueLabel(self.MakePWDRfilename(hist),
filenamelist)
# create an instrument parameter file
self.filename = os.path.join(self.dirname,
fileroot + self.extension)
else:
# use the supplied name, but force the extension
self.filename = os.path.splitext(
self.filename)[0] + self.extension
self.OpenFile()
histblk = self.Histograms[hist]
self.Write('/*') #The ugly c comment delimiter used in topas!
self.Write('# ' +
hist[5:]) #evidently this by itself fails in topas
self.Write('*/')
x = np.array(histblk['Data'][0])
# convert weights to sigmas; use largest weight as minimum esd
s = np.sqrt(np.maximum(0., np.array(histblk['Data'][2])))
s[s == 0] = np.max(s)
s = 1. / s
for XYS in zip(x, histblk['Data'][1], s):
line = ''
for val in XYS:
line += G2py3.FormatPadValue(val, (15, 6))
self.Write(line)
self.CloseFile()
print('Histogram ' + str(hist) + ' written to file ' +
str(self.fullpath))
def Writer(self,TreeName,filename=None):
self.OpenFile(filename)
histblk = self.Histograms[TreeName]
hfmt = 5*"{:12s} "
digitList = 2*((13,3),) + ((13,5),) + 2*((13,3),)
self.Write(hfmt.format("x","y_obs","weight","y_calc","y_bkg"))
for vallist in zip(histblk['Data'][0],
histblk['Data'][1],
histblk['Data'][2],
histblk['Data'][3],
histblk['Data'][4],
#histblk['Data'][5],
):
strg = ''
for val,digits in zip(vallist,digitList):
strg += G2py3.FormatPadValue(val,digits)
self.Write(strg)
self.CloseFile()
def Exporter(self, event=None):
'''Export a set of powder data as a single csv file
'''
# the export process starts here
self.InitExport(event)
# load all of the tree into a set of dicts
self.loadTree()
if self.ExportSelect( # set export parameters
AskFile='ask' # only one file is ever written
):
return
csvData = []
headList = [
"x",
]
digitList = []
self.filename = os.path.join(
self.dirname,
os.path.splitext(self.filename)[0] + self.extension)
for ihst, hist in enumerate(self.histnam):
histblk = self.Histograms[hist]
headList.append('y_obs_' +
G2obj.StripUnicode(hist[5:].replace(' ', '_')))
if not ihst:
digitList = [
(13, 3),
]
csvData.append(histblk['Data'][0])
digitList += [
(13, 3),
]
csvData.append(histblk['Data'][1])
print('Histogram ' + hist + ' added to file...')
self.OpenFile()
WriteList(self, headList)
for vallist in np.array(csvData).T:
line = ""
for val, digits in zip(vallist, digitList):
if line: line += ','
line += G2py3.FormatValue(val, digits)
self.Write(line)
self.CloseFile()
print('...file ' + self.fullpath + ' written')
def Repaint(self,exprObj):
'Redisplay the variables and continue the validation'
self.ShowVars() # show widgets to set vars
msg = self.CheckVars()
if msg:
self.setEvalResult(msg)
return
exprObj.LoadExpression(
self.expr,
self.exprVarLst,
self.varSelect,
self.varName,
self.varValue,
self.varRefflag,
)
try:
calcobj = G2obj.ExpressionCalcObj(exprObj)
calcobj.SetupCalc(self.parmDict)
val = calcobj.EvalExpression()
except Exception as msg:
self.setEvalResult("Error in evaluation: "+str(msg))
return
if not np.isfinite(val):
self.setEvalResult("Expression value is infinite or out-of-bounds")
return
s = G2py3.FormatSigFigs(val).rstrip('0')
depVal = ""
if self.depVarDict:
if not self.dependentVar:
self.setEvalResult("A dependent variable must be selected.")
return
depVal = '; Variable "' + self.dependentVar + '" = ' + str(
self.depVarDict.get(self.dependentVar,'?')
)
self.setEvalResult("Expression evaluates to: "+str(s)+depVal)
self.OKbtn.Enable()
if self.ExtraBtn: self.ExtraBtn.Enable()
def Repaint(self, exprObj):
'Redisplay the variables and continue the validation'
# create widgets to associate vars with labels and/or show messages
self.varSizer.Clear(True)
self.errbox = wxscroll.ScrolledPanel(self, style=wx.HSCROLL)
self.errbox.SetMinSize((100, 130))
self.varSizer.Add(self.errbox, 0, wx.ALL | wx.EXPAND, 1)
self.varbox = wxscroll.ScrolledPanel(self, style=wx.HSCROLL)
self.varSizer.Add(self.varbox, 1, wx.ALL | wx.EXPAND, 1)
Siz = wx.BoxSizer(wx.VERTICAL)
Siz.Add(
wx.StaticText(self.varbox, wx.ID_ANY,
'Assignment of variables to labels:'), 0,
wx.EXPAND | wx.ALIGN_CENTER, 0)
GridSiz = wx.FlexGridSizer(0, 5, 2, 2)
GridSiz.Add(
wx.StaticText(self.varbox, wx.ID_ANY, 'label', style=wx.CENTER), 0,
wx.ALIGN_CENTER)
lbls = ('varib. type\nselection', 'variable\nname', 'value')
choices = ['Free', 'Phase', 'Hist./Phase', 'Hist.', 'Global']
if self.fit:
lbls += ('refine\nflag', )
else:
lbls += ('', )
choices[0] = ''
for i in range(1, len(choices)): # remove empty menus from choice list
if not len(self.parmLists[i]): choices[i] = ''
self.AllowedChoices = [i for i in range(len(choices)) if choices[i]]
for lbl in lbls:
w = wx.StaticText(self.varbox, wx.ID_ANY, lbl, style=wx.CENTER)
w.SetMinSize((80, -1))
GridSiz.Add(w, 0, wx.ALIGN_CENTER)
# show input for each var in expression.
for v in self.exprVarLst:
# label
GridSiz.Add(wx.StaticText(self.varbox, wx.ID_ANY, v), 0,
wx.ALIGN_CENTER, 0)
# assignment type
ch = wx.Choice(self.varbox,
wx.ID_ANY,
choices=[choices[i] for i in self.AllowedChoices])
GridSiz.Add(ch, 0, wx.ALIGN_LEFT, 0)
if v in self.varSelect and self.varSelect.get(
v) in self.AllowedChoices:
i = self.AllowedChoices.index(self.varSelect[v])
ch.SetSelection(i)
else:
ch.SetSelection(wx.NOT_FOUND)
ch.label = v
ch.Bind(wx.EVT_CHOICE, self.OnChoice)
# var name/var assignment
if self.varSelect.get(v) is None:
GridSiz.Add((-1, -1), 0, wx.ALIGN_LEFT | wx.EXPAND, 0)
elif self.varSelect.get(v) == 0:
wid = G2G.ValidatedTxtCtrl(self.varbox,
self.varName,
v,
size=(50, -1))
GridSiz.Add(wid, 0, wx.ALIGN_LEFT | wx.EXPAND, 0)
else:
wid = wx.StaticText(self.varbox, wx.ID_ANY, self.varName[v])
GridSiz.Add(wid, 0, wx.ALIGN_LEFT, 0)
# value
if self.varSelect.get(v) is None:
GridSiz.Add((-1, -1), 0, wx.ALIGN_RIGHT | wx.EXPAND, 0)
elif self.varSelect.get(v) == 0:
wid = G2G.ValidatedTxtCtrl(self.varbox,
self.varValue,
v,
size=(75, -1))
GridSiz.Add(wid, 0, wx.ALIGN_LEFT | wx.EXPAND, 0)
wid.Bind(wx.EVT_CHAR, self.OnChar)
else:
var = self.varName[v]
if var in self.parmDict:
val = self.parmDict[var]
s = G2py3.FormatSigFigs(val).rstrip('0')
elif '*' in var:
vs = G2obj.LookupWildCard(var, self.parmDict.keys())
s = '(' + str(len(vs)) + ' values)'
else:
s = '?'
wid = wx.StaticText(self.varbox, wx.ID_ANY, s)
GridSiz.Add(wid, 0, wx.ALIGN_LEFT, 0)
# show a refine flag for Free Vars only
if self.varSelect.get(v) == 0 and self.fit:
self.varRefflag[v] = self.varRefflag.get(v, True)
wid = G2G.G2CheckBox(self.varbox, '', self.varRefflag, v)
GridSiz.Add(wid, 0, wx.ALIGN_LEFT | wx.EXPAND, 0)
else:
wid = (-1, -1)
GridSiz.Add(wid, 0, wx.ALIGN_LEFT | wx.EXPAND, 0)
Siz.Add(GridSiz)
self.varbox.SetSizer(Siz, True)
# evaluate the expression, displaying errors or the expression value
try:
msg = self.CheckVars()
if msg:
self.setEvalResult(msg)
return
exprObj.LoadExpression(
self.expr,
self.exprVarLst,
self.varSelect,
self.varName,
self.varValue,
self.varRefflag,
)
try:
calcobj = G2obj.ExpressionCalcObj(exprObj)
calcobj.SetupCalc(self.parmDict)
val = calcobj.EvalExpression()
except Exception as msg:
self.setEvalResult("Error in evaluation: " + str(msg))
return
if not np.isfinite(val):
self.setEvalResult(
"Expression value is infinite or out-of-bounds")
return
s = G2py3.FormatSigFigs(val).rstrip('0')
depVal = ""
if self.depVarDict:
if not self.dependentVar:
self.setEvalResult(
"A dependent variable must be selected.")
return
depVal = '; Variable "' + self.dependentVar + '" = ' + str(
self.depVarDict.get(self.dependentVar, '?'))
self.setEvalResult("Expression evaluates to: " + str(s) + depVal)
self.OKbtn.Enable()
if self.ExtraBtn: self.ExtraBtn.Enable()
finally:
xwid, yhgt = Siz.Fit(self.varbox)
self.varbox.SetMinSize((xwid, 130))
self.varbox.SetAutoLayout(1)
self.varbox.SetupScrolling()
self.varbox.Refresh()
self.Layout()
self.SendSizeEvent() # force repaint
def ShowVars(self):
# create widgets to associate vars with labels and/or show messages
self.varSizer.Clear(True)
self.errbox = wxscroll.ScrolledPanel(self,style=wx.HSCROLL)
self.errbox.SetMinSize((100,130))
self.varSizer.Add(self.errbox,0,wx.ALL|wx.EXPAND,1)
self.varbox = wxscroll.ScrolledPanel(self,style=wx.HSCROLL)
self.varSizer.Add(self.varbox,1,wx.ALL|wx.EXPAND,1)
Siz = wx.BoxSizer(wx.VERTICAL)
Siz.Add(
wx.StaticText(self.varbox,wx.ID_ANY,
'Assignment of variables to labels:'),
0,wx.EXPAND|wx.ALIGN_CENTER,0)
GridSiz = wx.FlexGridSizer(0,5,2,2)
GridSiz.Add(
wx.StaticText(self.varbox,wx.ID_ANY,'label',style=wx.CENTER),
0,wx.ALIGN_CENTER)
lbls = ('varib. type\nselection','variable\nname','value')
choices = ['Free','Phase','Hist./Phase','Hist.','Global']
if self.fit:
lbls += ('refine\nflag',)
else:
lbls += ('',)
choices[0] = ''
for i in range(1,len(choices)): # remove empty menus from choice list
if not len(self.parmLists[i]): choices[i] = ''
self.AllowedChoices = [i for i in range(len(choices)) if choices[i]]
for lbl in lbls:
w = wx.StaticText(self.varbox,wx.ID_ANY,lbl,style=wx.CENTER)
w.SetMinSize((80,-1))
GridSiz.Add(w,0,wx.ALIGN_CENTER)
# show input for each var in expression.
for v in self.exprVarLst:
# label
GridSiz.Add(wx.StaticText(self.varbox,wx.ID_ANY,v),0,wx.ALIGN_CENTER,0)
# assignment type
ch = wx.Choice(
self.varbox, wx.ID_ANY,
choices = [choices[i] for i in self.AllowedChoices]
)
GridSiz.Add(ch,0,wx.ALIGN_LEFT,0)
if v in self.varSelect and self.varSelect.get(v) in self.AllowedChoices:
i = self.AllowedChoices.index(self.varSelect[v])
ch.SetSelection(i)
else:
ch.SetSelection(wx.NOT_FOUND)
ch.label = v
ch.Bind(wx.EVT_CHOICE,self.OnChoice)
# var name/var assignment
if self.varSelect.get(v) is None:
GridSiz.Add((-1,-1),0,wx.ALIGN_LEFT|wx.EXPAND,0)
elif self.varSelect.get(v) == 0:
wid = G2G.ValidatedTxtCtrl(self.varbox,self.varName,v,
#OnLeave=self.OnTxtLeave,
size=(50,-1))
GridSiz.Add(wid,0,wx.ALIGN_LEFT|wx.EXPAND,0)
else:
wid = wx.StaticText(self.varbox,wx.ID_ANY,self.varName[v])
GridSiz.Add(wid,0,wx.ALIGN_LEFT,0)
# value
if self.varSelect.get(v) is None:
GridSiz.Add((-1,-1),0,wx.ALIGN_RIGHT|wx.EXPAND,0)
elif self.varSelect.get(v) == 0:
wid = G2G.ValidatedTxtCtrl(self.varbox,self.varValue,v,
#OnLeave=self.OnTxtLeave,
size=(75,-1))
GridSiz.Add(wid,0,wx.ALIGN_LEFT|wx.EXPAND,0)
wid.Bind(wx.EVT_CHAR,self.OnChar)
else:
var = self.varName[v]
if '*' in var:
#[self.parmDict[v] for v in LookupWildCard(var,self.parmDict.keys())]
#print self.varValue[v]
vs = G2obj.LookupWildCard(var,self.parmDict.keys())
s = '('+str(len(vs))+' values)'
elif var in self.parmDict:
val = self.parmDict[var]
s = G2py3.FormatSigFigs(val).rstrip('0')
else:
s = '?'
wid = wx.StaticText(self.varbox,wx.ID_ANY,s)
GridSiz.Add(wid,0,wx.ALIGN_LEFT,0)
# show a refine flag for Free Vars only
if self.varSelect.get(v) == 0 and self.fit:
self.varRefflag[v] = self.varRefflag.get(v,True)
wid = G2G.G2CheckBox(self.varbox,'',self.varRefflag,v)
GridSiz.Add(wid,0,wx.ALIGN_LEFT|wx.EXPAND,0)
else:
wid = (-1,-1)
GridSiz.Add(wid,0,wx.ALIGN_LEFT|wx.EXPAND,0)
Siz.Add(GridSiz)
self.varbox.SetSizer(Siz,True)
xwid,yhgt = Siz.Fit(self.varbox)
self.varbox.SetMinSize((xwid,130))
self.varbox.SetAutoLayout(1)
self.varbox.SetupScrolling()
self.varbox.Refresh()
self.Layout()
#self.mainsizer.Fit(self)
self.SendSizeEvent() # force repaint
return
def ISODISTORT_proc(self,blk,atomlbllist,ranIdlookup):
'Process ISODISTORT items to create constraints etc.'
varLookup = {'dx':'dAx','dy':'dAy','dz':'dAz','do':'Afrac'}
'Maps ISODISTORT parm names to GSAS-II names'
#----------------------------------------------------------------------
# read in the ISODISTORT displacement modes
#----------------------------------------------------------------------
self.Constraints = []
explaination = {}
if blk.get('_iso_displacivemode_label'):
modelist = []
shortmodelist = []
for lbl in blk.get('_iso_displacivemode_label'):
modelist.append(lbl)
# assume lbl is of form SSSSS[x,y,z]AAAA(a,b,...)BBBBB
# where SSSSS is the parent spacegroup, [x,y,z] is a location
regexp = re.match(r'.*?\[.*?\](.*?)\(.*?\)(.*)',lbl)
# this extracts the AAAAA and BBBBB parts of the string
if regexp:
lbl = regexp.expand(r'\1\2') # parse succeeded, make a short version
G2obj.MakeUniqueLabel(lbl,shortmodelist) # make unique and add to list
# read in the coordinate offset variables names and map them to G2 names/objects
coordVarLbl = []
G2varLbl = []
G2varObj = []
error = False
for lbl in blk.get('_iso_deltacoordinate_label'):
coordVarLbl.append(lbl)
if '_' in lbl:
albl = lbl[:lbl.rfind('_')]
vlbl = lbl[lbl.rfind('_')+1:]
else:
self.warnings += ' ERROR: _iso_deltacoordinate_label not parsed: '+lbl
error = True
continue
if albl not in atomlbllist:
self.warnings += ' ERROR: _iso_deltacoordinate_label atom not found: '+lbl
error = True
continue
else:
anum = atomlbllist.index(albl)
var = varLookup.get(vlbl)
if not var:
self.warnings += ' ERROR: _iso_deltacoordinate_label variable not found: '+lbl
error = True
continue
G2varLbl.append('::'+var+':'+str(anum)) # variable name, less phase ID
G2varObj.append(G2obj.G2VarObj(
(self.Phase['ranId'],None,var,ranIdlookup[albl])
))
if error:
raise Exception,"Error decoding variable labels"
if len(G2varObj) != len(modelist):
print "non-square input"
raise Exception,"Rank of _iso_displacivemode != _iso_deltacoordinate"
error = False
ParentCoordinates = {}
for lbl,exp in zip(
blk.get('_iso_coordinate_label'),
blk.get('_iso_coordinate_formula'),
):
if '_' in lbl:
albl = lbl[:lbl.rfind('_')]
vlbl = lbl[lbl.rfind('_')+1:]
else:
self.warnings += ' ERROR: _iso_coordinate_label not parsed: '+lbl
error = True
continue
if vlbl not in 'xyz' or len(vlbl) != 1:
self.warnings += ' ERROR: _iso_coordinate_label coordinate not parsed: '+lbl
error = True
continue
i = 'xyz'.index(vlbl)
if not ParentCoordinates.get(albl):
ParentCoordinates[albl] = [None,None,None]
if '+' in exp:
val = exp.split('+')[0].strip()
val = G2p3.FormulaEval(val)
if val is None:
self.warnings += ' ERROR: _iso_coordinate_formula coordinate not interpreted: '+lbl
error = True
continue
ParentCoordinates[albl][i] = val
else:
ParentCoordinates[albl][i] = G2p3.FormulaEval(exp)
if error:
print self.warnings
raise Exception,"Error decoding variable labels"
# get mapping of modes to atomic coordinate displacements
displacivemodematrix = np.zeros((len(G2varObj),len(G2varObj)))
for row,col,val in zip(
blk.get('_iso_displacivemodematrix_row'),
blk.get('_iso_displacivemodematrix_col'),
blk.get('_iso_displacivemodematrix_value'),):
displacivemodematrix[int(row)-1,int(col)-1] = float(val)
# Invert to get mapping of atom displacements to modes
displacivemodeInvmatrix = np.linalg.inv(displacivemodematrix)
# create the constraints
for i,row in enumerate(displacivemodeInvmatrix):
constraint = []
for j,(lbl,k) in enumerate(zip(coordVarLbl,row)):
if k == 0: continue
constraint.append([k,G2varObj[j]])
constraint += [shortmodelist[i],False,'f']
self.Constraints.append(constraint)
#----------------------------------------------------------------------
# save the ISODISTORT info for "mode analysis"
if 'ISODISTORT' not in self.Phase: self.Phase['ISODISTORT'] = {}
self.Phase['ISODISTORT'].update({
'IsoModeList' : modelist,
'G2ModeList' : shortmodelist,
'IsoVarList' : coordVarLbl,
'G2VarList' : G2varObj,
'ParentStructure' : ParentCoordinates,
'Var2ModeMatrix' : displacivemodeInvmatrix,
'Mode2VarMatrix' : displacivemodematrix,
})
# make explaination dictionary
for mode,shortmode in zip(modelist,shortmodelist):
explaination[shortmode] = "ISODISTORT full name "+str(mode)
#----------------------------------------------------------------------
# now read in the ISODISTORT occupancy modes
#----------------------------------------------------------------------
if blk.get('_iso_occupancymode_label'):
modelist = []
shortmodelist = []
for lbl in blk.get('_iso_occupancymode_label'):
modelist.append(lbl)
# assume lbl is of form SSSSS[x,y,z]AAAA(a,b,...)BBBBB
# where SSSSS is the parent spacegroup, [x,y,z] is a location
regexp = re.match(r'.*?\[.*?\](.*?)\(.*?\)(.*)',lbl)
# this extracts the AAAAA and BBBBB parts of the string
if regexp:
lbl = regexp.expand(r'\1\2') # parse succeeded, make a short version
lbl = lbl.replace('order','o')
G2obj.MakeUniqueLabel(lbl,shortmodelist) # make unique and add to list
# read in the coordinate offset variables names and map them to G2 names/objects
occVarLbl = []
G2varLbl = []
G2varObj = []
error = False
for lbl in blk.get('_iso_deltaoccupancy_label'):
occVarLbl.append(lbl)
if '_' in lbl:
albl = lbl[:lbl.rfind('_')]
vlbl = lbl[lbl.rfind('_')+1:]
else:
self.warnings += ' ERROR: _iso_deltaoccupancy_label not parsed: '+lbl
error = True
continue
if albl not in atomlbllist:
self.warnings += ' ERROR: _iso_deltaoccupancy_label atom not found: '+lbl
error = True
continue
else:
anum = atomlbllist.index(albl)
var = varLookup.get(vlbl)
if not var:
self.warnings += ' ERROR: _iso_deltaoccupancy_label variable not found: '+lbl
error = True
continue
G2varLbl.append('::'+var+':'+str(anum)) # variable name, less phase ID
G2varObj.append(G2obj.G2VarObj(
(self.Phase['ranId'],None,var,ranIdlookup[albl])
))
if error:
raise Exception,"Error decoding variable labels"
if len(G2varObj) != len(modelist):
print "non-square input"
raise Exception,"Rank of _iso_occupancymode != _iso_deltaoccupancy"
error = False
ParentCoordinates = {}
for lbl,exp in zip(
blk.get('_iso_occupancy_label'),
blk.get('_iso_occupancy_formula'),
):
if '_' in lbl:
albl = lbl[:lbl.rfind('_')]
vlbl = lbl[lbl.rfind('_')+1:]
else:
self.warnings += ' ERROR: _iso_occupancy_label not parsed: '+lbl
error = True
continue
if vlbl != 'occ':
self.warnings += ' ERROR: _iso_occupancy_label coordinate not parsed: '+lbl
error = True
continue
if '+' in exp:
val = exp.split('+')[0].strip()
val = G2p3.FormulaEval(val)
if val is None:
self.warnings += ' ERROR: _iso_occupancy_formula coordinate not interpreted: '+lbl
error = True
continue
ParentCoordinates[albl] = val
if error:
raise Exception,"Error decoding occupancy labels"
# get mapping of modes to atomic coordinate displacements
occupancymodematrix = np.zeros((len(G2varObj),len(G2varObj)))
for row,col,val in zip(
blk.get('_iso_occupancymodematrix_row'),
blk.get('_iso_occupancymodematrix_col'),
blk.get('_iso_occupancymodematrix_value'),):
occupancymodematrix[int(row)-1,int(col)-1] = float(val)
# Invert to get mapping of atom displacements to modes
occupancymodeInvmatrix = np.linalg.inv(occupancymodematrix)
# create the constraints
for i,row in enumerate(occupancymodeInvmatrix):
constraint = []
for j,(lbl,k) in enumerate(zip(occVarLbl,row)):
if k == 0: continue
constraint.append([k,G2varObj[j]])
constraint += [shortmodelist[i],False,'f']
self.Constraints.append(constraint)
#----------------------------------------------------------------------
# save the ISODISTORT info for "mode analysis"
if 'ISODISTORT' not in self.Phase: self.Phase['ISODISTORT'] = {}
self.Phase['ISODISTORT'].update({
'OccModeList' : modelist,
'G2OccModeList' : shortmodelist,
'OccVarList' : occVarLbl,
'G2OccVarList' : G2varObj,
'BaseOcc' : ParentCoordinates,
'Var2OccMatrix' : occupancymodeInvmatrix,
'Occ2VarMatrix' : occupancymodematrix,
})
# make explaination dictionary
for mode,shortmode in zip(modelist,shortmodelist):
explaination[shortmode] = "ISODISTORT full name "+str(mode)
#----------------------------------------------------------------------
# done with read
#----------------------------------------------------------------------
if explaination: self.Constraints.append(explaination)