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source: trunk/exports/G2export_CIF.py @ 4361

Last change on this file since 4361 was 4361, checked in by toby, 3 years ago
fix hist CIF export, remove dev. ver of IntPDFtool
Property svn:eol-style set to `native` Property svn:keywords set to `Date Author Revision URL Id`
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1	#!/usr/bin/env python
2	# -- coding: utf-8 --
3	########### SVN repository information ###################
4	# $Date: 2020-03-11 21:43:45 +0000 (Wed, 11 Mar 2020) $
5	# $Author: toby $
6	# $Revision: 4361 $
7	# $URL: trunk/exports/G2export_CIF.py $
8	# $Id: G2export_CIF.py 4361 2020-03-11 21:43:45Z toby $
9	########### SVN repository information ###################
10	'''
11	Module G2export_CIF: CIF Exports
12	------------------------------------------------------
13
14	This implements a complex exporter :class:`ExportCIF` that can implement an
15	entire project in a complete CIF intended for submission as a
16	publication. In addition, there are three subclasses of :class:`ExportCIF`:
17	:class:`ExportProjectCIF`,
18	:class:`ExportPhaseCIF` and :class:`ExportDataCIF` where extra parameters
19	for the _Exporter() determine if a project, single phase or data set are written.
20	'''
21
22	from __future__ import division, print_function
23	import platform
24	import datetime as dt
25	import os.path
26	import sys
27	import numpy as np
28	if '2' in platform.python_version_tuple()[0]:
29	import cPickle as pickle
30	else:
31	import pickle
32	import copy
33	import re
34	try:
35	import wx
36	import wx.lib.scrolledpanel as wxscroll
37	import wx.lib.resizewidget as rw
38	except ImportError:
39	# Avoid wx dependency for CLI
40	class Placeholder(object):
41	def __init__(self):
42	self.BoxSizer = object
43	self.Button = object
44	self.Dialog = object
45	self.ScrolledPanel = object
46	wx = Placeholder()
47	wxscroll = Placeholder()
48	import GSASIIpath
49	GSASIIpath.SetVersionNumber("$Revision: 4361 $")
50	import GSASIIIO as G2IO
51	try:
52	import GSASIIctrlGUI as G2G
53	except ImportError:
54	pass
55	import GSASIIobj as G2obj
56	import GSASIImath as G2mth
57	import GSASIIspc as G2spc
58	import GSASIIstrMain as G2stMn
59	import GSASIImapvars as G2mv
60
61	DEBUG = False #True to skip printing of reflection/powder profile lists
62
63	CIFdic = None
64
65	# Refactored over here to allow access by GSASIIscriptable.py
66	def WriteCIFitem(fp, name, value=''):
67	'''Helper function for writing CIF output. Translated from exports/G2export_CIF.py'''
68	# Ignore unicode issues
69	if value:
70	if "\n" in value or len(value)> 70:
71	if name.strip():
72	fp.write(name+'\n')
73	fp.write(';\n'+value+'\n')
74	fp.write(';'+'\n')
75	elif " " in value:
76	if len(name)+len(value) > 65:
77	fp.write(name + '\n ' + '"' + str(value) + '"'+'\n')
78	else:
79	fp.write(name + ' ' + '"' + str(value) + '"'+'\n')
80	else:
81	if len(name)+len(value) > 65:
82	fp.write(name+'\n ' + value+'\n')
83	else:
84	fp.write(name+' ' + value+'\n')
85	else:
86	fp.write(name+'\n')
87
88
89	# Refactored over here to allow access by GSASIIscriptable.py
90	def WriteAtomsNuclear(fp, phasedict, phasenam, parmDict, sigDict, labellist):
91	'Write atom positions to CIF'
92	# phasedict = self.Phases[phasenam] # pointer to current phase info
93	General = phasedict['General']
94	cx,ct,cs,cia = General['AtomPtrs']
95	Atoms = phasedict['Atoms']
96	cfrac = cx+3
97	fpfx = str(phasedict['pId'])+'::Afrac:'
98	for i,at in enumerate(Atoms):
99	fval = parmDict.get(fpfx+str(i),at[cfrac])
100	if fval != 0.0:
101	break
102	else:
103	WriteCIFitem(fp, '\n# PHASE HAS NO ATOMS!')
104	return
105
106	WriteCIFitem(fp, '\n# ATOMIC COORDINATES AND DISPLACEMENT PARAMETERS')
107	WriteCIFitem(fp, 'loop_ '+
108	'\n _atom_site_label'+
109	'\n _atom_site_type_symbol'+
110	'\n _atom_site_fract_x'+
111	'\n _atom_site_fract_y'+
112	'\n _atom_site_fract_z'+
113	'\n _atom_site_occupancy'+
114	'\n _atom_site_adp_type'+
115	'\n _atom_site_U_iso_or_equiv'+
116	'\n _atom_site_symmetry_multiplicity')
117
118	varnames = {cx:'Ax',cx+1:'Ay',cx+2:'Az',cx+3:'Afrac',
119	cia+1:'AUiso',cia+2:'AU11',cia+3:'AU22',cia+4:'AU33',
120	cia+5:'AU12',cia+6:'AU13',cia+7:'AU23'}
121	# Empty the labellist
122	while labellist:
123	labellist.pop()
124
125	pfx = str(phasedict['pId'])+'::'
126	# loop over all atoms
127	naniso = 0
128	for i,at in enumerate(Atoms):
129	if phasedict['General']['Type'] == 'macromolecular':
130	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
131	s = PutInCol(MakeUniqueLabel(label,labellist),15) # label
132	else:
133	s = PutInCol(MakeUniqueLabel(at[ct-1],labellist),6) # label
134	fval = parmDict.get(fpfx+str(i),at[cfrac])
135	if fval == 0.0: continue # ignore any atoms that have a occupancy set to 0 (exact)
136	s += PutInCol(FmtAtomType(at[ct]),4) # type
137	if at[cia] == 'I':
138	adp = 'Uiso '
139	else:
140	adp = 'Uani '
141	naniso += 1
142	# compute Uequiv crudely
143	# correct: Defined as "1/3 trace of diagonalized U matrix".
144	# SEE cell2GS & Uij2Ueqv to GSASIIlattice. Former is needed to make the GS matrix used by the latter.
145	t = 0.0
146	for j in (2,3,4):
147	var = pfx+varnames[cia+j]+":"+str(i)
148	t += parmDict.get(var,at[cia+j])
149	for j in (cx,cx+1,cx+2,cx+3,cia,cia+1):
150	if j in (cx,cx+1,cx+2):
151	dig = 11
152	sigdig = -0.00009
153	else:
154	dig = 10
155	sigdig = -0.009
156	if j == cia:
157	s += adp
158	else:
159	var = pfx+varnames[j]+":"+str(i)
160	dvar = pfx+"d"+varnames[j]+":"+str(i)
161	if dvar not in sigDict:
162	dvar = var
163	if j == cia+1 and adp == 'Uani ':
164	val = t/3.
165	sig = sigdig
166	else:
167	#print var,(var in parmDict),(var in sigDict)
168	val = parmDict.get(var,at[j])
169	sig = sigDict.get(dvar,sigdig)
170	if dvar in G2mv.GetDependentVars(): # do not include an esd for dependent vars
171	sig = -abs(sig)
172	s += PutInCol(G2mth.ValEsd(val,sig),dig)
173	s += PutInCol(at[cs+1],3)
174	WriteCIFitem(fp, s)
175	if naniso == 0: return
176	# now loop over aniso atoms
177	WriteCIFitem(fp, '\nloop_' + '\n _atom_site_aniso_label' +
178	'\n _atom_site_aniso_U_11' + '\n _atom_site_aniso_U_22' +
179	'\n _atom_site_aniso_U_33' + '\n _atom_site_aniso_U_12' +
180	'\n _atom_site_aniso_U_13' + '\n _atom_site_aniso_U_23')
181	for i,at in enumerate(Atoms):
182	fval = parmDict.get(fpfx+str(i),at[cfrac])
183	if fval == 0.0: continue # ignore any atoms that have a occupancy set to 0 (exact)
184	if at[cia] == 'I': continue
185	s = PutInCol(labellist[i],6) # label
186	for j in (2,3,4,5,6,7):
187	sigdig = -0.0009
188	var = pfx+varnames[cia+j]+":"+str(i)
189	val = parmDict.get(var,at[cia+j])
190	sig = sigDict.get(var,sigdig)
191	s += PutInCol(G2mth.ValEsd(val,sig),11)
192	WriteCIFitem(fp, s)
193
194	def WriteAtomsMagnetic(fp, phasedict, phasenam, parmDict, sigDict, labellist):
195	'Write atom positions to CIF'
196	# phasedict = self.Phases[phasenam] # pointer to current phase info
197	General = phasedict['General']
198	cx,ct,cs,cia = General['AtomPtrs']
199	Atoms = phasedict['Atoms']
200	cfrac = cx+3
201	fpfx = str(phasedict['pId'])+'::Afrac:'
202	for i,at in enumerate(Atoms):
203	fval = parmDict.get(fpfx+str(i),at[cfrac])
204	if fval != 0.0:
205	break
206	else:
207	WriteCIFitem(fp, '\n# PHASE HAS NO ATOMS!')
208	return
209
210	WriteCIFitem(fp, '\n# ATOMIC COORDINATES AND DISPLACEMENT PARAMETERS')
211	WriteCIFitem(fp, 'loop_ '+
212	'\n _atom_site_label'+
213	'\n _atom_site_type_symbol'+
214	'\n _atom_site_fract_x'+
215	'\n _atom_site_fract_y'+
216	'\n _atom_site_fract_z'+
217	'\n _atom_site_occupancy'+
218	'\n _atom_site_adp_type'+
219	'\n _atom_site_U_iso_or_equiv'+
220	'\n _atom_site_symmetry_multiplicity')
221
222	varnames = {cx:'Ax',cx+1:'Ay',cx+2:'Az',cx+3:'Afrac',
223	cx+4:'AMx',cx+5:'AMy',cx+6:'AMz',
224	cia+1:'AUiso',cia+2:'AU11',cia+3:'AU22',cia+4:'AU33',
225	cia+5:'AU12',cia+6:'AU13',cia+7:'AU23'}
226	# Empty the labellist
227	while labellist:
228	labellist.pop()
229
230	pfx = str(phasedict['pId'])+'::'
231	# loop over all atoms
232	naniso = 0
233	for i,at in enumerate(Atoms):
234	if phasedict['General']['Type'] == 'macromolecular':
235	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
236	s = PutInCol(MakeUniqueLabel(label,labellist),15) # label
237	else:
238	s = PutInCol(MakeUniqueLabel(at[ct-1],labellist),6) # label
239	fval = parmDict.get(fpfx+str(i),at[cfrac])
240	if fval == 0.0: continue # ignore any atoms that have a occupancy set to 0 (exact)
241	s += PutInCol(FmtAtomType(at[ct]),4) # type
242	if at[cia] == 'I':
243	adp = 'Uiso '
244	else:
245	adp = 'Uani '
246	naniso += 1
247	# compute Uequiv crudely
248	# correct: Defined as "1/3 trace of diagonalized U matrix".
249	# SEE cell2GS & Uij2Ueqv to GSASIIlattice. Former is needed to make the GS matrix used by the latter.
250	t = 0.0
251	for j in (2,3,4):
252	var = pfx+varnames[cia+j]+":"+str(i)
253	t += parmDict.get(var,at[cia+j])
254	for j in (cx,cx+1,cx+2,cx+3,cia,cia+1):
255	if j in (cx,cx+1,cx+2):
256	dig = 11
257	sigdig = -0.00009
258	else:
259	dig = 10
260	sigdig = -0.009
261	if j == cia:
262	s += adp
263	else:
264	var = pfx+varnames[j]+":"+str(i)
265	dvar = pfx+"d"+varnames[j]+":"+str(i)
266	if dvar not in sigDict:
267	dvar = var
268	if j == cia+1 and adp == 'Uani ':
269	val = t/3.
270	sig = sigdig
271	else:
272	#print var,(var in parmDict),(var in sigDict)
273	val = parmDict.get(var,at[j])
274	sig = sigDict.get(dvar,sigdig)
275	if dvar in G2mv.GetDependentVars(): # do not include an esd for dependent vars
276	sig = -abs(sig)
277	s += PutInCol(G2mth.ValEsd(val,sig),dig)
278	s += PutInCol(at[cs+1],3)
279	WriteCIFitem(fp, s)
280	if naniso:
281	# now loop over aniso atoms
282	WriteCIFitem(fp, '\nloop_' + '\n _atom_site_aniso_label' +
283	'\n _atom_site_aniso_U_11' + '\n _atom_site_aniso_U_22' +
284	'\n _atom_site_aniso_U_33' + '\n _atom_site_aniso_U_12' +
285	'\n _atom_site_aniso_U_13' + '\n _atom_site_aniso_U_23')
286	for i,at in enumerate(Atoms):
287	fval = parmDict.get(fpfx+str(i),at[cfrac])
288	if fval == 0.0: continue # ignore any atoms that have a occupancy set to 0 (exact)
289	if at[cia] == 'I': continue
290	s = PutInCol(labellist[i],6) # label
291	for j in (2,3,4,5,6,7):
292	sigdig = -0.0009
293	var = pfx+varnames[cia+j]+":"+str(i)
294	val = parmDict.get(var,at[cia+j])
295	sig = sigDict.get(var,sigdig)
296	s += PutInCol(G2mth.ValEsd(val,sig),11)
297	WriteCIFitem(fp, s)
298	# now loop over mag atoms (e.g. all of them)
299	WriteCIFitem(fp, '\nloop_' + '\n _atom_site_moment.label' +
300	'\n _atom_site_moment.crystalaxis_x' +
301	'\n _atom_site_moment.crystalaxis_y' +
302	'\n _atom_site_moment.crystalaxis_z')
303	for i,at in enumerate(Atoms):
304	fval = parmDict.get(fpfx+str(i),at[cfrac])
305	if fval == 0.0: continue # ignore any atoms that have a occupancy set to 0 (exact)
306	s = PutInCol(labellist[i],6) # label
307	for j in (cx+4,cx+5,cx+6):
308	sigdig = -0.0009
309	var = pfx+varnames[j]+":"+str(i)
310	val = parmDict.get(var,at[j])
311	sig = sigDict.get(var,sigdig)
312	s += PutInCol(G2mth.ValEsd(val,sig),11)
313	WriteCIFitem(fp, s)
314
315	# Refactored over here to allow access by GSASIIscriptable.py
316	def MakeUniqueLabel(lbl, labellist):
317	lbl = lbl.strip()
318	if not lbl: # deal with a blank label
319	lbl = 'A_1'
320	if lbl not in labellist:
321	labellist.append(lbl)
322	return lbl
323	i = 1
324	prefix = lbl
325	if '_' in lbl:
326	prefix = lbl[:lbl.rfind('_')]
327	suffix = lbl[lbl.rfind('_')+1:]
328	try:
329	i = int(suffix)+1
330	except:
331	pass
332	while prefix+'_'+str(i) in labellist:
333	i += 1
334	else:
335	lbl = prefix+'_'+str(i)
336	labellist.append(lbl)
337
338
339	# Refactored over here to allow access by GSASIIscriptable.py
340	def HillSortElements(elmlist):
341	'''Sort elements in "Hill" order: C, H, others, (where others
342	are alphabetical).
343
344	:params list elmlist: a list of element strings
345
346	:returns: a sorted list of element strings
347	'''
348	newlist = []
349	oldlist = elmlist[:]
350	for elm in ('C','H'):
351	if elm in elmlist:
352	newlist.append(elm)
353	oldlist.pop(oldlist.index(elm))
354	return newlist+sorted(oldlist)
355
356
357	# Refactored over here to allow access by GSASIIscriptable.py
358	def FmtAtomType(sym):
359	'Reformat a GSAS-II atom type symbol to match CIF rules'
360	sym = sym.replace('_','') # underscores are not allowed: no isotope designation?
361	# in CIF, oxidation state sign symbols come after, not before
362	if '+' in sym:
363	sym = sym.replace('+','') + '+'
364	elif '-' in sym:
365	sym = sym.replace('-','') + '-'
366	return sym
367
368
369	# Refactored over here to allow access by GSASIIscriptable.py
370	def PutInCol(val, wid):
371	val = str(val).replace(' ', '')
372	if not val: val = '?'
373	fmt = '{:' + str(wid) + '} '
374	return fmt.format(val)
375
376
377	# Refactored over here to allow access by GSASIIscriptable.py
378	def WriteComposition(fp, phasedict, phasenam, parmDict):
379	'''determine the composition for the unit cell, crudely determine Z and
380	then compute the composition in formula units
381	'''
382	General = phasedict['General']
383	Z = General.get('cellZ',0.0)
384	cx,ct,cs,cia = General['AtomPtrs']
385	Atoms = phasedict['Atoms']
386	fpfx = str(phasedict['pId'])+'::Afrac:'
387	cfrac = cx+3
388	cmult = cs+1
389	compDict = {} # combines H,D & T
390	sitemultlist = []
391	massDict = dict(zip(General['AtomTypes'],General['AtomMass']))
392	cellmass = 0
393	for i,at in enumerate(Atoms):
394	atype = at[ct].strip()
395	if atype.find('-') != -1: atype = atype.split('-')[0]
396	if atype.find('+') != -1: atype = atype.split('+')[0]
397	atype = atype[0].upper()+atype[1:2].lower() # force case conversion
398	if atype == "D" or atype == "D": atype = "H"
399	fvar = fpfx+str(i)
400	fval = parmDict.get(fvar,at[cfrac])
401	mult = at[cmult]
402	if not massDict.get(at[ct]):
403	print('Error: No mass found for atom type '+at[ct])
404	print('Will not compute cell contents for phase '+phasenam)
405	return
406	cellmass += massDict[at[ct]]multfval
407	compDict[atype] = compDict.get(atype,0.0) + mult*fval
408	if fval == 1: sitemultlist.append(mult)
409	if len(compDict.keys()) == 0: return # no elements!
410	if Z < 1: # Z has not been computed or set by user
411	Z = 1
412	if not sitemultlist:
413	General['cellZ'] = 1
414	return
415	for i in range(2,min(sitemultlist)+1):
416	for m in sitemultlist:
417	if m % i != 0:
418	break
419	else:
420	Z = i
421	General['cellZ'] = Z # save it
422
423	# when scattering factors are included in the CIF, this needs to be
424	# added to the loop here but only in the one-block case.
425	# For multiblock CIFs, scattering factors go in the histogram
426	# blocks (for all atoms in all appropriate phases) - an example?:
427	#loop_
428	# _atom_type_symbol
429	# _atom_type_description
430	# _atom_type_scat_dispersion_real
431	# _atom_type_scat_dispersion_imag
432	# _atom_type_scat_source
433	# 'C' 'C' 0.0033 0.0016
434	# 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
435	# 'H' 'H' 0.0000 0.0000
436	# 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
437	# 'P' 'P' 0.1023 0.0942
438	# 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
439	# 'Cl' 'Cl' 0.1484 0.1585
440	# 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
441	# 'Cu' 'Cu' 0.3201 1.2651
442	# 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
443
444	#if oneblock: # add scattering factors for current phase here
445	WriteCIFitem(fp, '\nloop_ _atom_type_symbol _atom_type_number_in_cell')
446	formula = ''
447	for elem in HillSortElements(list(compDict.keys())):
448	WriteCIFitem(fp, ' ' + PutInCol(elem,4) +
449	G2mth.ValEsd(compDict[elem],-0.009,True))
450	if formula: formula += " "
451	formula += elem
452	if compDict[elem] == Z: continue
453	formula += G2mth.ValEsd(compDict[elem]/Z,-0.009,True)
454	WriteCIFitem(fp, '\n# Note that Z affects _cell_formula_sum and _weight')
455	WriteCIFitem(fp, '_cell_formula_units_Z',str(Z))
456	WriteCIFitem(fp, '_chemical_formula_sum',formula)
457	WriteCIFitem(fp, '_chemical_formula_weight',
458	G2mth.ValEsd(cellmass/Z,-0.09,True))
459
460
461	class ExportCIF(G2IO.ExportBaseclass):
462	'''Base class for CIF exports
463	'''
464	def __init__(self,G2frame,formatName,extension,longFormatName=None,):
465	G2IO.ExportBaseclass.__init__(self,G2frame,formatName,extension,longFormatName=None)
466	self.exporttype = []
467	self.author = ''
468	self.CIFname = ''
469
470	def ValidateAscii(self,checklist):
471	'''Validate items as ASCII'''
472	msg = ''
473	for lbl,val in checklist:
474	if not all(ord(c) < 128 for c in val):
475	if msg: msg += '\n'
476	msg += lbl + " contains unicode characters: " + val
477	if msg:
478	G2G.G2MessageBox(self.G2frame,
479	'Error: CIFs can contain only ASCII characters. Please change item(s) below:\n\n'+msg,
480	'Unicode not valid for CIF')
481	return True
482
483	def _Exporter(self,event=None,phaseOnly=None,histOnly=None,IncludeOnlyHist=None):
484	'''Basic code to export a CIF. Export can be full or simple, as set by
485	phaseOnly and histOnly which skips distances & angles, etc.
486
487	phaseOnly: used to export only one phase
488	histOnly: used to export only one histogram
489	IncludeOnlyHist: used for a full CIF that includes only one of the
490	histograms (from a sequential fit) #TODO: needs lots of work!
491	'''
492
493	#***** define functions for export method =======================================
494	def WriteAudit():
495	'Write the CIF audit values. Perhaps should be in a single element loop.'
496	WriteCIFitem(self.fp, '_audit_creation_method',
497	'created in GSAS-II')
498	WriteCIFitem(self.fp, '_audit_creation_date',self.CIFdate)
499	if self.author:
500	WriteCIFitem(self.fp, '_audit_author_name',self.author)
501	WriteCIFitem(self.fp, '_audit_update_record',
502	self.CIFdate+' Initial software-generated CIF')
503
504	def WriteOverall():
505	'''Write out overall refinement information.
506
507	More could be done here, but this is a good start.
508	'''
509	if self.ifPWDR:
510	WriteCIFitem(self.fp, '_pd_proc_info_datetime', self.CIFdate)
511	WriteCIFitem(self.fp, '_pd_calc_method', 'Rietveld Refinement')
512
513	#WriteCIFitem(self.fp, '_refine_ls_shift/su_mean',DAT2)
514	WriteCIFitem(self.fp, '_computing_structure_refinement','GSAS-II (Toby & Von Dreele, J. Appl. Cryst. 46, 544-549, 2013)')
515	if self.ifHKLF:
516	controls = self.OverallParms['Controls']
517	if controls['F**2']:
518	thresh = 'F2>%.1fu(F2)'%(controls['UsrReject']['minF/sig'])
519	else:
520	thresh = 'F>%.1fu(F)'%(controls['UsrReject']['minF/sig'])
521	WriteCIFitem(self.fp, '_reflns_threshold_expression', thresh)
522	try:
523	vars = str(len(self.OverallParms['Covariance']['varyList']))
524	except:
525	vars = '?'
526	WriteCIFitem(self.fp, '_refine_ls_number_parameters',vars)
527	try:
528	GOF = G2mth.ValEsd(self.OverallParms['Covariance']['Rvals']['GOF'],-0.009)
529	except:
530	GOF = '?'
531	WriteCIFitem(self.fp, '_refine_ls_goodness_of_fit_all',GOF)
532	DAT1 = self.OverallParms['Covariance']['Rvals'].get('Max shft/sig',0.0)
533	if DAT1:
534	WriteCIFitem(self.fp, '_refine_ls_shift/su_max','%.4f'%DAT1)
535
536	# get restraint info
537	# restraintDict = self.OverallParms.get('Restraints',{})
538	# for i in self.OverallParms['Constraints']:
539	# print i
540	# for j in self.OverallParms['Constraints'][i]:
541	# print j
542	#WriteCIFitem(self.fp, '_refine_ls_number_restraints',TEXT)
543	# other things to consider reporting
544	# _refine_ls_number_reflns
545	# _refine_ls_goodness_of_fit_obs
546	# _refine_ls_wR_factor_obs
547	# _refine_ls_restrained_S_all
548	# _refine_ls_restrained_S_obs
549
550	# include an overall profile r-factor, if there is more than one powder histogram
551	R = '%.5f'%(self.OverallParms['Covariance']['Rvals']['Rwp']/100.)
552	WriteCIFitem(self.fp, '\n# OVERALL WEIGHTED R-FACTOR')
553	WriteCIFitem(self.fp, '_refine_ls_wR_factor_obs',R)
554	# _refine_ls_R_factor_all
555	# _refine_ls_R_factor_obs
556	WriteCIFitem(self.fp, '_refine_ls_matrix_type','full')
557	#WriteCIFitem(self.fp, '_refine_ls_matrix_type','userblocks')
558
559	def writeCIFtemplate(G2dict,tmplate,defaultname=''):
560	'''Write out the selected or edited CIF template
561	An unedited CIF template file is copied, comments intact; an edited
562	CIF template is written out from PyCifRW which of course strips comments.
563	In all cases the initial data_ header is stripped (there should only be one!)
564	'''
565	CIFobj = G2dict.get("CIF_template")
566	if defaultname:
567	defaultname = G2obj.StripUnicode(defaultname)
568	defaultname = re.sub(r'[^a-zA-Z0-9_-]','',defaultname)
569	defaultname = tmplate + "_" + defaultname + ".cif"
570	else:
571	defaultname = ''
572	templateDefName = 'template_'+tmplate+'.cif'
573	if not CIFobj: # copying a template
574	for pth in [os.getcwd()]+sys.path:
575	fil = os.path.join(pth,defaultname)
576	if os.path.exists(fil) and defaultname: break
577	else:
578	for pth in sys.path:
579	fil = os.path.join(pth,templateDefName)
580	if os.path.exists(fil): break
581	else:
582	print(CIFobj+' not found in path!')
583	return
584	fp = open(fil,'r')
585	txt = fp.read()
586	fp.close()
587	elif type(CIFobj) is not list and type(CIFobj) is not tuple:
588	if not os.path.exists(CIFobj):
589	print("Error: requested template file has disappeared: "+CIFobj)
590	return
591	fp = open(CIFobj,'r')
592	txt = fp.read()
593	fp.close()
594	else:
595	txt = dict2CIF(CIFobj[0],CIFobj[1]).WriteOut()
596	# remove the PyCifRW header, if present
597	#if txt.find('PyCifRW') > -1 and txt.find('data_') > -1:
598	txt = "# GSAS-II edited template follows "+txt[txt.index("data_")+5:]
599	#txt = txt.replace('data_','#')
600	WriteCIFitem(self.fp, txt)
601
602	def FormatSH(phasenam):
603	'Format a full spherical harmonics texture description as a string'
604	phasedict = self.Phases[phasenam] # pointer to current phase info
605	pfx = str(phasedict['pId'])+'::'
606	s = ""
607	textureData = phasedict['General']['SH Texture']
608	if textureData.get('Order'):
609	s += "Spherical Harmonics correction. Order = "+str(textureData['Order'])
610	s += " Model: " + str(textureData['Model']) + "\n Orientation angles: "
611	for name in ['omega','chi','phi']:
612	aname = pfx+'SH '+name
613	s += name + " = "
614	sig = self.sigDict.get(aname,-0.09)
615	s += G2mth.ValEsd(self.parmDict[aname],sig)
616	s += "; "
617	s += "\n"
618	s1 = " Coefficients: "
619	for name in textureData['SH Coeff'][1]:
620	aname = pfx+name
621	if len(s1) > 60:
622	s += s1 + "\n"
623	s1 = " "
624	s1 += aname + ' = '
625	sig = self.sigDict.get(aname,-0.0009)
626	s1 += G2mth.ValEsd(self.parmDict[aname],sig)
627	s1 += "; "
628	s += s1
629	return s
630
631	def FormatHAPpo(phasenam):
632	'''return the March-Dollase/SH correction for every
633	histogram in the current phase formatted into a
634	character string
635	'''
636	phasedict = self.Phases[phasenam] # pointer to current phase info
637	s = ''
638	for histogram in sorted(phasedict['Histograms']):
639	if histogram.startswith("HKLF"): continue # powder only
640	if not self.Phases[phasenam]['Histograms'][histogram]['Use']: continue
641	Histogram = self.Histograms.get(histogram)
642	if not Histogram: continue
643	hapData = phasedict['Histograms'][histogram]
644	if hapData['Pref.Ori.'][0] == 'MD':
645	aname = str(phasedict['pId'])+':'+str(Histogram['hId'])+':MD'
646	if self.parmDict.get(aname,1.0) != 1.0: continue
647	sig = self.sigDict.get(aname,-0.009)
648	if s != "": s += '\n'
649	s += 'March-Dollase correction'
650	if len(self.powderDict) > 1:
651	s += ', histogram '+str(Histogram['hId']+1)
652	s += ' coef. = ' + G2mth.ValEsd(self.parmDict[aname],sig)
653	s += ' axis = ' + str(hapData['Pref.Ori.'][3])
654	else: # must be SH
655	if s != "": s += '\n'
656	s += 'Simple spherical harmonic correction'
657	if len(self.powderDict) > 1:
658	s += ', histogram '+str(Histogram['hId']+1)
659	s += ' Order = '+str(hapData['Pref.Ori.'][4])+'\n'
660	s1 = " Coefficients: "
661	for item in hapData['Pref.Ori.'][5]:
662	aname = str(phasedict['pId'])+':'+str(Histogram['hId'])+':'+item
663	if len(s1) > 60:
664	s += s1 + "\n"
665	s1 = " "
666	s1 += aname + ' = '
667	sig = self.sigDict.get(aname,-0.0009)
668	s1 += G2mth.ValEsd(self.parmDict[aname],sig)
669	s1 += "; "
670	s += s1
671	return s
672
673	def FormatBackground(bkg,hId):
674	'''Display the Background information as a descriptive text string.
675
676	TODO: this needs to be expanded to show the diffuse peak and
677	Debye term information as well. (Bob)
678
679	:returns: the text description (str)
680	'''
681	hfx = ':'+str(hId)+':'
682	fxn, bkgdict = bkg
683	terms = fxn[2]
684	txt = 'Background function: "'+fxn[0]+'" function with '+str(terms)+' terms:\n'
685	l = " "
686	for i,v in enumerate(fxn[3:]):
687	name = '%sBack;%d'%(hfx,i)
688	sig = self.sigDict.get(name,-0.009)
689	if len(l) > 60:
690	txt += l + '\n'
691	l = ' '
692	l += G2mth.ValEsd(v,sig)+', '
693	txt += l
694	if bkgdict['nDebye']:
695	txt += '\n Background Debye function parameters: A, R, U:'
696	names = ['A;','R;','U;']
697	for i in range(bkgdict['nDebye']):
698	txt += '\n '
699	for j in range(3):
700	name = hfx+'Debye'+names[j]+str(i)
701	sig = self.sigDict.get(name,-0.009)
702	txt += G2mth.ValEsd(bkgdict['debyeTerms'][i][2*j],sig)+', '
703	if bkgdict['nPeaks']:
704	txt += '\n Background peak parameters: pos, int, sig, gam:'
705	names = ['pos;','int;','sig;','gam;']
706	for i in range(bkgdict['nPeaks']):
707	txt += '\n '
708	for j in range(4):
709	name = hfx+'BkPk'+names[j]+str(i)
710	sig = self.sigDict.get(name,-0.009)
711	txt += G2mth.ValEsd(bkgdict['peaksList'][i][2*j],sig)+', '
712	return txt
713
714	def FormatInstProfile(instparmdict,hId):
715	'''Format the instrumental profile parameters with a
716	string description. Will only be called on PWDR histograms
717	'''
718	s = ''
719	inst = instparmdict[0]
720	hfx = ':'+str(hId)+':'
721	if 'C' in inst['Type'][0]:
722	s = 'Finger-Cox-Jephcoat function parameters U, V, W, X, Y, SH/L:\n'
723	s += ' peak variance(Gauss) = Utan(Th)^2^+Vtan(Th)+W:\n'
724	s += ' peak HW(Lorentz) = X/cos(Th)+Ytan(Th); SH/L = S/L+H/L\n'
725	s += ' U, V, W in (centideg)^2^, X & Y in centideg\n '
726	for item in ['U','V','W','X','Y','SH/L']:
727	name = hfx+item
728	sig = self.sigDict.get(name,-0.009)
729	s += G2mth.ValEsd(inst[item][1],sig)+', '
730	elif 'T' in inst['Type'][0]: #to be tested after TOF Rietveld done
731	s = 'Von Dreele-Jorgenson-Windsor function parameters\n'+ \
732	' alpha, beta-0, beta-1, beta-q, sig-0, sig-1, sig-2, sig-q, X, Y:\n '
733	for item in ['alpha','beta-0','beta-1','beta-q','sig-0','sig-1','sig-2','sig-q','X','Y']:
734	name = hfx+item
735	sig = self.sigDict.get(name,-0.009)
736	s += G2mth.ValEsd(inst[item][1],sig)+', '
737	return s
738
739	def FormatPhaseProfile(phasenam):
740	'''Format the phase-related profile parameters (size/strain)
741	with a string description.
742	return an empty string or None if there are no
743	powder histograms for this phase.
744	'''
745	s = ''
746	phasedict = self.Phases[phasenam] # pointer to current phase info
747	SGData = phasedict['General'] ['SGData']
748	for histogram in sorted(phasedict['Histograms']):
749	if histogram.startswith("HKLF"): continue # powder only
750	Histogram = self.Histograms.get(histogram)
751	if not Histogram: continue
752	hapData = phasedict['Histograms'][histogram]
753	pId = phasedict['pId']
754	hId = Histogram['hId']
755	phfx = '%d:%d:'%(pId,hId)
756	size = hapData['Size']
757	mustrain = hapData['Mustrain']
758	hstrain = hapData['HStrain']
759	if s: s += '\n'
760	if len(self.powderDict) > 1: # if one histogram, no ambiguity
761	s += ' Parameters for histogram #{:} {:} & phase {:}\n'.format(
762	str(hId),str(histogram),phasenam)
763	s += ' Crystallite size in microns with "%s" model:\n '%(size[0])
764	names = ['Size;i','Size;mx']
765	if 'uniax' in size[0]:
766	names = ['Size;i','Size;a','Size;mx']
767	s += 'anisotropic axis is %s\n '%(str(size[3]))
768	s += 'parameters: equatorial size, axial size, G/L mix\n '
769	for i,item in enumerate(names):
770	name = phfx+item
771	sig = self.sigDict.get(name,-0.009)
772	s += G2mth.ValEsd(size[1][i],sig)+', '
773	elif 'ellip' in size[0]:
774	s += 'parameters: S11, S22, S33, S12, S13, S23, G/L mix\n '
775	for i in range(6):
776	name = phfx+'Size:'+str(i)
777	sig = self.sigDict.get(name,-0.009)
778	s += G2mth.ValEsd(size[4][i],sig)+', '
779	sig = self.sigDict.get(phfx+'Size;mx',-0.009)
780	s += G2mth.ValEsd(size[1][2],sig)+', '
781	else: #isotropic
782	s += 'parameters: Size, G/L mix\n '
783	i = 0
784	for item in names:
785	name = phfx+item
786	sig = self.sigDict.get(name,-0.009)
787	s += G2mth.ValEsd(size[1][i],sig)+', '
788	i = 2 #skip the aniso value
789	s += '\n Microstrain, "%s" model (10^6^ * delta Q/Q)\n '%(mustrain[0])
790	names = ['Mustrain;i','Mustrain;mx']
791	if 'uniax' in mustrain[0]:
792	names = ['Mustrain;i','Mustrain;a','Mustrain;mx']
793	s += 'anisotropic axis is %s\n '%(str(size[3]))
794	s += 'parameters: equatorial mustrain, axial mustrain, G/L mix\n '
795	for i,item in enumerate(names):
796	name = phfx+item
797	sig = self.sigDict.get(name,-0.009)
798	s += G2mth.ValEsd(mustrain[1][i],sig)+', '
799	elif 'general' in mustrain[0]:
800	names = 'parameters: '
801	for i,name in enumerate(G2spc.MustrainNames(SGData)):
802	names += name+', '
803	if i == 9:
804	names += '\n '
805	names += 'G/L mix\n '
806	s += names
807	txt = ''
808	for i in range(len(mustrain[4])):
809	name = phfx+'Mustrain:'+str(i)
810	sig = self.sigDict.get(name,-0.009)
811	if len(txt) > 60:
812	s += txt+'\n '
813	txt = ''
814	txt += G2mth.ValEsd(mustrain[4][i],sig)+', '
815	s += txt
816	sig = self.sigDict.get(phfx+'Mustrain;mx',-0.009)
817	s += G2mth.ValEsd(mustrain[1][2],sig)+', '
818
819	else: #isotropic
820	s += ' parameters: Mustrain, G/L mix\n '
821	i = 0
822	for item in names:
823	name = phfx+item
824	sig = self.sigDict.get(name,-0.009)
825	s += G2mth.ValEsd(mustrain[1][i],sig)+', '
826	i = 2 #skip the aniso value
827	s1 = ' \n Macrostrain parameters: '
828	names = G2spc.HStrainNames(SGData)
829	for name in names:
830	s1 += name+', '
831	s1 += '\n '
832	macrostrain = False
833	for i in range(len(names)):
834	name = phfx+names[i]
835	sig = self.sigDict.get(name,-0.000009)
836	s1 += G2mth.ValEsd(hstrain[0][i],sig)+', '
837	if hstrain[0][i]: macrostrain = True
838	if macrostrain:
839	s += s1 + '\n'
840	# show revised lattice parameters here someday
841	else:
842	s += '\n'
843	return s
844
845	def MakeUniqueLabel(lbl,labellist):
846	'Make sure that every atom label is unique'
847	lbl = lbl.strip()
848	if not lbl: # deal with a blank label
849	lbl = 'A_1'
850	if lbl not in labellist:
851	labellist.append(lbl)
852	return lbl
853	i = 1
854	prefix = lbl
855	if '_' in lbl:
856	prefix = lbl[:lbl.rfind('_')]
857	suffix = lbl[lbl.rfind('_')+1:]
858	try:
859	i = int(suffix)+1
860	except:
861	pass
862	while prefix+'_'+str(i) in labellist:
863	i += 1
864	else:
865	lbl = prefix+'_'+str(i)
866	labellist.append(lbl)
867
868	# Factored out to above by Jack O'Donnell, so it
869	# could be accessed by GSASIIscriptable.py
870	# def WriteAtomsNuclear(phasenam):
871	# 'Write atom positions to CIF'
872	# phasedict = self.Phases[phasenam] # pointer to current phase info
873	# General = phasedict['General']
874	# cx,ct,cs,cia = General['AtomPtrs']
875	# Atoms = phasedict['Atoms']
876	# cfrac = cx+3
877	# fpfx = str(phasedict['pId'])+'::Afrac:'
878	# for i,at in enumerate(Atoms):
879	# fval = self.parmDict.get(fpfx+str(i),at[cfrac])
880	# if fval != 0.0:
881	# break
882	# else:
883	# WriteCIFitem(self.fp, '\n# PHASE HAS NO ATOMS!')
884	# return
885
886	# WriteCIFitem(self.fp, '\n# ATOMIC COORDINATES AND DISPLACEMENT PARAMETERS')
887	# WriteCIFitem(self.fp, 'loop_ '+
888	# '\n _atom_site_label'+
889	# '\n _atom_site_type_symbol'+
890	# '\n _atom_site_fract_x'+
891	# '\n _atom_site_fract_y'+
892	# '\n _atom_site_fract_z'+
893	# '\n _atom_site_occupancy'+
894	# '\n _atom_site_adp_type'+
895	# '\n _atom_site_U_iso_or_equiv'+
896	# '\n _atom_site_symmetry_multiplicity')
897
898	# varnames = {cx:'Ax',cx+1:'Ay',cx+2:'Az',cx+3:'Afrac',
899	# cia+1:'AUiso',cia+2:'AU11',cia+3:'AU22',cia+4:'AU33',
900	# cia+5:'AU12',cia+6:'AU13',cia+7:'AU23'}
901	# self.labellist = []
902
903	# pfx = str(phasedict['pId'])+'::'
904	# # loop over all atoms
905	# naniso = 0
906	# for i,at in enumerate(Atoms):
907	# if phasedict['General']['Type'] == 'macromolecular':
908	# label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
909	# s = PutInCol(MakeUniqueLabel(label,self.labellist),15) # label
910	# else:
911	# s = PutInCol(MakeUniqueLabel(at[ct-1],self.labellist),6) # label
912	# fval = self.parmDict.get(fpfx+str(i),at[cfrac])
913	# if fval == 0.0: continue # ignore any atoms that have a occupancy set to 0 (exact)
914	# s += PutInCol(FmtAtomType(at[ct]),4) # type
915	# if at[cia] == 'I':
916	# adp = 'Uiso '
917	# else:
918	# adp = 'Uani '
919	# naniso += 1
920	# # compute Uequiv crudely
921	# # correct: Defined as "1/3 trace of diagonalized U matrix".
922	# # SEE cell2GS & Uij2Ueqv to GSASIIlattice. Former is needed to make the GS matrix used by the latter.
923	# t = 0.0
924	# for j in (2,3,4):
925	# var = pfx+varnames[cia+j]+":"+str(i)
926	# t += self.parmDict.get(var,at[cia+j])
927	# for j in (cx,cx+1,cx+2,cx+3,cia,cia+1):
928	# if j in (cx,cx+1,cx+2):
929	# dig = 11
930	# sigdig = -0.00009
931	# else:
932	# dig = 10
933	# sigdig = -0.009
934	# if j == cia:
935	# s += adp
936	# else:
937	# var = pfx+varnames[j]+":"+str(i)
938	# dvar = pfx+"d"+varnames[j]+":"+str(i)
939	# if dvar not in self.sigDict:
940	# dvar = var
941	# if j == cia+1 and adp == 'Uani ':
942	# val = t/3.
943	# sig = sigdig
944	# else:
945	# #print var,(var in self.parmDict),(var in self.sigDict)
946	# val = self.parmDict.get(var,at[j])
947	# sig = self.sigDict.get(dvar,sigdig)
948	# s += PutInCol(G2mth.ValEsd(val,sig),dig)
949	# s += PutInCol(at[cs+1],3)
950	# WriteCIFitem(self.fp, s)
951	# if naniso == 0: return
952	# # now loop over aniso atoms
953	# WriteCIFitem(self.fp, '\nloop_' + '\n _atom_site_aniso_label' +
954	# '\n _atom_site_aniso_U_11' + '\n _atom_site_aniso_U_22' +
955	# '\n _atom_site_aniso_U_33' + '\n _atom_site_aniso_U_12' +
956	# '\n _atom_site_aniso_U_13' + '\n _atom_site_aniso_U_23')
957	# for i,at in enumerate(Atoms):
958	# fval = self.parmDict.get(fpfx+str(i),at[cfrac])
959	# if fval == 0.0: continue # ignore any atoms that have a occupancy set to 0 (exact)
960	# if at[cia] == 'I': continue
961	# s = PutInCol(self.labellist[i],6) # label
962	# for j in (2,3,4,5,6,7):
963	# sigdig = -0.0009
964	# var = pfx+varnames[cia+j]+":"+str(i)
965	# val = self.parmDict.get(var,at[cia+j])
966	# sig = self.sigDict.get(var,sigdig)
967	# s += PutInCol(G2mth.ValEsd(val,sig),11)
968	# WriteCIFitem(self.fp, s)
969
970	# def HillSortElements(elmlist):
971	# '''Sort elements in "Hill" order: C, H, others, (where others
972	# are alphabetical).
973
974	# :params list elmlist: a list of element strings
975
976	# :returns: a sorted list of element strings
977	# '''
978	# newlist = []
979	# oldlist = elmlist[:]
980	# for elm in ('C','H'):
981	# if elm in elmlist:
982	# newlist.append(elm)
983	# oldlist.pop(oldlist.index(elm))
984	# return newlist+sorted(oldlist)
985
986	# Factored out to above by Jackson O'Donnell
987	# so that it can be accessed by GSASIIscriptable
988
989	# def WriteComposition(phasenam):
990	# '''determine the composition for the unit cell, crudely determine Z and
991	# then compute the composition in formula units
992	# '''
993	# phasedict = self.Phases[phasenam] # pointer to current phase info
994	# General = phasedict['General']
995	# Z = General.get('cellZ',0.0)
996	# cx,ct,cs,cia = General['AtomPtrs']
997	# Atoms = phasedict['Atoms']
998	# fpfx = str(phasedict['pId'])+'::Afrac:'
999	# cfrac = cx+3
1000	# cmult = cs+1
1001	# compDict = {} # combines H,D & T
1002	# sitemultlist = []
1003	# massDict = dict(zip(General['AtomTypes'],General['AtomMass']))
1004	# cellmass = 0
1005	# for i,at in enumerate(Atoms):
1006	# atype = at[ct].strip()
1007	# if atype.find('-') != -1: atype = atype.split('-')[0]
1008	# if atype.find('+') != -1: atype = atype.split('+')[0]
1009	# atype = atype[0].upper()+atype[1:2].lower() # force case conversion
1010	# if atype == "D" or atype == "D": atype = "H"
1011	# fvar = fpfx+str(i)
1012	# fval = self.parmDict.get(fvar,at[cfrac])
1013	# mult = at[cmult]
1014	# if not massDict.get(at[ct]):
1015	# print('Error: No mass found for atom type '+at[ct])
1016	# print('Will not compute cell contents for phase '+phasenam)
1017	# return
1018	# cellmass += massDict[at[ct]]multfval
1019	# compDict[atype] = compDict.get(atype,0.0) + mult*fval
1020	# if fval == 1: sitemultlist.append(mult)
1021	# if len(compDict.keys()) == 0: return # no elements!
1022	# if Z < 1: # Z has not been computed or set by user
1023	# Z = 1
1024	# if not sitemultlist:
1025	# General['cellZ'] = 1
1026	# return
1027	# for i in range(2,min(sitemultlist)+1):
1028	# for m in sitemultlist:
1029	# if m % i != 0:
1030	# break
1031	# else:
1032	# Z = i
1033	# General['cellZ'] = Z # save it
1034
1035	# # when scattering factors are included in the CIF, this needs to be
1036	# # added to the loop here but only in the one-block case.
1037	# # For multiblock CIFs, scattering factors go in the histogram
1038	# # blocks (for all atoms in all appropriate phases) - an example?:
1039	#loop_
1040	# _at# om_type_symbol
1041	# _at# om_type_description
1042	# _at# om_type_scat_dispersion_real
1043	# _at# om_type_scat_dispersion_imag
1044	# _at# om_type_scat_source
1045	# 'C'# 'C' 0.0033 0.0016
1046	# # 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
1047	# 'H'# 'H' 0.0000 0.0000
1048	# # 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
1049	# 'P'# 'P' 0.1023 0.0942
1050	# # 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
1051	# 'Cl# ' 'Cl' 0.1484 0.1585
1052	# # 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
1053	# 'Cu# ' 'Cu' 0.3201 1.2651
1054	# # 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
1055
1056	# #if oneblock: # add scattering factors for current phase here
1057	# WriteCIFitem(self.fp, '\nloop_ _atom_type_symbol _atom_type_number_in_cell')
1058	# formula = ''
1059	# for elem in HillSortElements(compDict.keys()):
1060	# WriteCIFitem(self.fp, ' ' + PutInCol(elem,4) +
1061	# G2mth.ValEsd(compDict[elem],-0.009,True))
1062	# if formula: formula += " "
1063	# formula += elem
1064	# if compDict[elem] == Z: continue
1065	# formula += G2mth.ValEsd(compDict[elem]/Z,-0.009,True)
1066	# WriteCIFitem(self.fp, '\n# Note that Z affects _cell_formula_sum and _weight')
1067	# WriteCIFitem(self.fp, '_cell_formula_units_Z',str(Z))
1068	# WriteCIFitem(self.fp, '_chemical_formula_sum',formula)
1069	# WriteCIFitem(self.fp, '_chemical_formula_weight',
1070	# G2mth.ValEsd(cellmass/Z,-0.09,True))
1071
1072	def WriteDistances(phasenam,SymOpList,offsetList,symOpList,G2oprList):
1073	'''Report bond distances and angles for the CIF
1074
1075	Note that _geom__symmetry_ fields are values of form
1076	n_klm where n is the symmetry operation in SymOpList (counted
1077	starting with 1) and (k-5, l-5, m-5) are translations to add
1078	to (x,y,z). See
1079	http://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Igeom_angle_site_symmetry_.html
1080
1081	TODO: need a method to select publication flags for distances/angles
1082	'''
1083	phasedict = self.Phases[phasenam] # pointer to current phase info
1084	Atoms = phasedict['Atoms']
1085	generalData = phasedict['General']
1086	# create a dict for storing Pub flag for bonds/angles, if needed
1087	if phasedict['General'].get("DisAglHideFlag") is None:
1088	phasedict['General']["DisAglHideFlag"] = {}
1089	DisAngSel = phasedict['General']["DisAglHideFlag"]
1090	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
1091	cn = ct-1
1092	fpfx = str(phasedict['pId'])+'::Afrac:'
1093	cfrac = cx+3
1094	DisAglData = {}
1095	# create a list of atoms, but skip atoms with zero occupancy
1096	xyz = []
1097	fpfx = str(phasedict['pId'])+'::Afrac:'
1098	for i,atom in enumerate(Atoms):
1099	if self.parmDict.get(fpfx+str(i),atom[cfrac]) == 0.0: continue
1100	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
1101	if 'DisAglCtls' not in generalData:
1102	# should not happen, since DisAglDialog should be called
1103	# for all phases before getting here
1104	dlg = G2G.DisAglDialog(
1105	self.G2frame,
1106	{},
1107	generalData)
1108	if dlg.ShowModal() == wx.ID_OK:
1109	generalData['DisAglCtls'] = dlg.GetData()
1110	else:
1111	dlg.Destroy()
1112	return
1113	dlg.Destroy()
1114	DisAglData['OrigAtoms'] = xyz
1115	DisAglData['TargAtoms'] = xyz
1116	SymOpList,offsetList,symOpList,G2oprList,G2opcodes = G2spc.AllOps(
1117	generalData['SGData'])
1118
1119	# xpandSGdata = generalData['SGData'].copy()
1120	# xpandSGdata.update({'SGOps':symOpList,
1121	# 'SGInv':False,
1122	# 'SGLatt':'P',
1123	# 'SGCen':np.array([[0, 0, 0]]),})
1124	# DisAglData['SGData'] = xpandSGdata
1125	DisAglData['SGData'] = generalData['SGData'].copy()
1126
1127	DisAglData['Cell'] = generalData['Cell'][1:] #+ volume
1128	if 'pId' in phasedict:
1129	DisAglData['pId'] = phasedict['pId']
1130	DisAglData['covData'] = self.OverallParms['Covariance']
1131	try:
1132	AtomLabels,DistArray,AngArray = G2stMn.RetDistAngle(
1133	generalData['DisAglCtls'],
1134	DisAglData)
1135	except KeyError: # inside DistAngle for missing atom types in DisAglCtls
1136	print(u'** ERROR computing distances & angles for phase {} **\nresetting to default values'.format(phasenam))
1137	data = generalData['DisAglCtls'] = {}
1138	data['Name'] = generalData['Name']
1139	data['Factors'] = [0.85,0.85]
1140	data['AtomTypes'] = generalData['AtomTypes']
1141	data['BondRadii'] = generalData['BondRadii'][:]
1142	data['AngleRadii'] = generalData['AngleRadii'][:]
1143	try:
1144	AtomLabels,DistArray,AngArray = G2stMn.RetDistAngle(
1145	generalData['DisAglCtls'],
1146	DisAglData)
1147	except:
1148	print('Reset failed. To fix this, use the Reset button in the "edit distance/angle menu" for this phase')
1149	return
1150
1151	# loop over interatomic distances for this phase
1152	WriteCIFitem(self.fp, '\n# MOLECULAR GEOMETRY')
1153	First = True
1154	for i in sorted(AtomLabels.keys()):
1155	Dist = DistArray[i]
1156	for D in Dist:
1157	line = ' '+PutInCol(AtomLabels[i],6)+PutInCol(AtomLabels[D[0]],6)
1158	sig = D[4]
1159	if sig == 0: sig = -0.00009
1160	line += PutInCol(G2mth.ValEsd(D[3],sig,True),10)
1161	line += " 1_555 "
1162	line += " {:3d}_".format(G2opcodes.index(D[2])+1)
1163	for d in D[1]:
1164	line += "{:1d}".format(d+5)
1165	if DisAngSel.get((i,tuple(D[0:3]))):
1166	line += " no"
1167	else:
1168	line += " yes"
1169	if First:
1170	First = False
1171	WriteCIFitem(self.fp, 'loop_' +
1172	'\n _geom_bond_atom_site_label_1' +
1173	'\n _geom_bond_atom_site_label_2' +
1174	'\n _geom_bond_distance' +
1175	'\n _geom_bond_site_symmetry_1' +
1176	'\n _geom_bond_site_symmetry_2' +
1177	'\n _geom_bond_publ_flag')
1178	WriteCIFitem(self.fp, line)
1179
1180	# loop over interatomic angles for this phase
1181	First = True
1182	for i in sorted(AtomLabels.keys()):
1183	Dist = DistArray[i]
1184	for k,j,tup in AngArray[i]:
1185	Dj = Dist[j]
1186	Dk = Dist[k]
1187	line = ' '+PutInCol(AtomLabels[Dj[0]],6)+PutInCol(AtomLabels[i],6)+PutInCol(AtomLabels[Dk[0]],6)
1188	sig = tup[1]
1189	if sig == 0: sig = -0.009
1190	line += PutInCol(G2mth.ValEsd(tup[0],sig,True),10)
1191	line += " {:3d}_".format(G2opcodes.index(Dj[2])+1)
1192	for d in Dj[1]:
1193	line += "{:1d}".format(d+5)
1194	line += " 1_555 "
1195	line += " {:3d}_".format(G2opcodes.index(Dk[2])+1)
1196	for d in Dk[1]:
1197	line += "{:1d}".format(d+5)
1198	key = (tuple(Dk[0:3]),i,tuple(Dj[0:3]))
1199	if DisAngSel.get(key):
1200	line += " no"
1201	else:
1202	line += " yes"
1203	if First:
1204	First = False
1205	WriteCIFitem(self.fp, '\nloop_' +
1206	'\n _geom_angle_atom_site_label_1' +
1207	'\n _geom_angle_atom_site_label_2' +
1208	'\n _geom_angle_atom_site_label_3' +
1209	'\n _geom_angle' +
1210	'\n _geom_angle_site_symmetry_1' +
1211	'\n _geom_angle_site_symmetry_2' +
1212	'\n _geom_angle_site_symmetry_3' +
1213	'\n _geom_angle_publ_flag')
1214	WriteCIFitem(self.fp, line)
1215
1216	def WritePhaseInfo(phasenam,hist=None):
1217	'Write out the phase information for the selected phase'
1218	WriteCIFitem(self.fp, '\n# phase info for '+str(phasenam) + ' follows')
1219	phasedict = self.Phases[phasenam] # pointer to current phase info
1220	WriteCIFitem(self.fp, '_pd_phase_name', phasenam)
1221	cellList,cellSig = self.GetCell(phasenam)
1222	defsigL = 3[-0.00001] + 3[-0.001] + [-0.01] # significance to use when no sigma
1223	names = ['length_a','length_b','length_c',
1224	'angle_alpha','angle_beta ','angle_gamma',
1225	'volume']
1226	prevsig = 0
1227	for lbl,defsig,val,sig in zip(names,defsigL,cellList,cellSig):
1228	if sig:
1229	txt = G2mth.ValEsd(val,sig)
1230	prevsig = -sig # use this as the significance for next value
1231	else:
1232	txt = G2mth.ValEsd(val,min(defsig,prevsig),True)
1233	WriteCIFitem(self.fp, '_cell_'+lbl,txt)
1234
1235	density = G2mth.getDensity(phasedict['General'])[0]
1236	WriteCIFitem(self.fp, '_exptl_crystal_density_diffrn',
1237	G2mth.ValEsd(density,-0.001))
1238
1239	WriteCIFitem(self.fp, '_symmetry_cell_setting',
1240	phasedict['General']['SGData']['SGSys'])
1241
1242	if phasedict['General']['Type'] in ['nuclear','macromolecular']:
1243	spacegroup = phasedict['General']['SGData']['SpGrp'].strip()
1244	# regularize capitalization and remove trailing H/R
1245	spacegroup = spacegroup[0].upper() + spacegroup[1:].lower().rstrip('rh ')
1246	WriteCIFitem(self.fp, '_symmetry_space_group_name_H-M',spacegroup)
1247
1248	# generate symmetry operations including centering and center of symmetry
1249	SymOpList,offsetList,symOpList,G2oprList,G2opcodes = G2spc.AllOps(
1250	phasedict['General']['SGData'])
1251	WriteCIFitem(self.fp, 'loop_\n _space_group_symop_id\n _space_group_symop_operation_xyz')
1252	for i,op in enumerate(SymOpList,start=1):
1253	WriteCIFitem(self.fp, ' {:3d} {:}'.format(i,op.lower()))
1254	elif phasedict['General']['Type'] == 'magnetic':
1255	parentSpGrp = phasedict['General']['SGData']['SpGrp'].strip()
1256	parentSpGrp = parentSpGrp[0].upper() + parentSpGrp[1:].lower().rstrip('rh ')
1257	WriteCIFitem(self.fp, '_parent_space_group.name_H-M_alt',parentSpGrp)
1258	# [Trans,Uvec,Vvec] = phasedict['General']['SGData']['fromParent'] #save these
1259	spacegroup = phasedict['General']['SGData']['MagSpGrp'].strip()
1260	spacegroup = spacegroup[0].upper() + spacegroup[1:].lower().rstrip('rh ')
1261	WriteCIFitem(self.fp, '_space_group_magn.name_BNS',spacegroup)
1262	WriteCIFitem(self.fp, '_space_group.magn_point_group',phasedict['General']['SGData']['MagPtGp'])
1263
1264	# generate symmetry operations including centering and center of symmetry
1265	SymOpList,offsetList,symOpList,G2oprList,G2opcodes = G2spc.AllOps(
1266	phasedict['General']['SGData'])
1267	SpnFlp = phasedict['General']['SGData']['SpnFlp']
1268	WriteCIFitem(self.fp, 'loop_\n _space_group_symop_magn_operation.id\n _space_group_symop_magn_operation.xyz')
1269	for i,op in enumerate(SymOpList,start=1):
1270	if SpnFlp[i-1] >0:
1271	opr = op.lower()+',+1'
1272	else:
1273	opr = op.lower()+',-1'
1274	WriteCIFitem(self.fp, ' {:3d} {:}'.format(i,opr))
1275
1276	# loop over histogram(s) used in this phase
1277	if not oneblock and not self.quickmode and not hist:
1278	# report pointers to the histograms used in this phase
1279	histlist = []
1280	for hist in self.Phases[phasenam]['Histograms']:
1281	if self.Phases[phasenam]['Histograms'][hist]['Use']:
1282	if phasebyhistDict.get(hist):
1283	phasebyhistDict[hist].append(phasenam)
1284	else:
1285	phasebyhistDict[hist] = [phasenam,]
1286	blockid = datablockidDict.get(hist)
1287	if not blockid:
1288	print("Internal error: no block for data. Phase "+str(
1289	phasenam)+" histogram "+str(hist))
1290	histlist = []
1291	break
1292	histlist.append(blockid)
1293
1294	if len(histlist) == 0:
1295	WriteCIFitem(self.fp, '# Note: phase has no associated data')
1296
1297	# report atom params
1298	if phasedict['General']['Type'] in ['nuclear','macromolecular']: #this needs macromolecular variant, etc!
1299	try:
1300	self.labellist
1301	except AttributeError:
1302	self.labellist = []
1303	WriteAtomsNuclear(self.fp, self.Phases[phasenam], phasenam,
1304	self.parmDict, self.sigDict, self.labellist)
1305	else:
1306	try:
1307	self.labellist
1308	except AttributeError:
1309	self.labellist = []
1310	WriteAtomsMagnetic(self.fp, self.Phases[phasenam], phasenam,
1311	self.parmDict, self.sigDict, self.labellist)
1312	# self.CloseFile()
1313	# raise Exception("no export for "+str(phasedict['General']['Type'])+" coordinates implemented")
1314	# report cell contents
1315	WriteComposition(self.fp, self.Phases[phasenam], phasenam, self.parmDict)
1316	if not self.quickmode and phasedict['General']['Type'] == 'nuclear': # report distances and angles
1317	WriteDistances(phasenam,SymOpList,offsetList,symOpList,G2oprList)
1318	if 'Map' in phasedict['General'] and 'minmax' in phasedict['General']['Map']:
1319	WriteCIFitem(self.fp, '\n# Difference density results')
1320	MinMax = phasedict['General']['Map']['minmax']
1321	WriteCIFitem(self.fp, '_refine_diff_density_max',G2mth.ValEsd(MinMax[0],-0.009))
1322	WriteCIFitem(self.fp, '_refine_diff_density_min',G2mth.ValEsd(MinMax[1],-0.009))
1323
1324	def Yfmt(ndec,val):
1325	'Format intensity values'
1326	out = ("{:."+str(ndec)+"f}").format(val)
1327	out = out.rstrip('0') # strip zeros to right of decimal
1328	return out.rstrip('.') # and decimal place when not needed
1329
1330	def WriteReflStat(refcount,hklmin,hklmax,dmin,dmax,nRefSets=1):
1331	'Write reflection statistics'
1332	WriteCIFitem(self.fp, '_reflns_number_total', str(refcount))
1333	if hklmin is not None and nRefSets == 1: # hkl range has no meaning with multiple phases
1334	WriteCIFitem(self.fp, '_reflns_limit_h_min', str(int(hklmin[0])))
1335	WriteCIFitem(self.fp, '_reflns_limit_h_max', str(int(hklmax[0])))
1336	WriteCIFitem(self.fp, '_reflns_limit_k_min', str(int(hklmin[1])))
1337	WriteCIFitem(self.fp, '_reflns_limit_k_max', str(int(hklmax[1])))
1338	WriteCIFitem(self.fp, '_reflns_limit_l_min', str(int(hklmin[2])))
1339	WriteCIFitem(self.fp, '_reflns_limit_l_max', str(int(hklmax[2])))
1340	if hklmin is not None:
1341	WriteCIFitem(self.fp, '_reflns_d_resolution_low ', G2mth.ValEsd(dmax,-0.009))
1342	WriteCIFitem(self.fp, '_reflns_d_resolution_high ', G2mth.ValEsd(dmin,-0.009))
1343
1344	def WritePowderData(histlbl):
1345	'Write out the selected powder diffraction histogram info'
1346	histblk = self.Histograms[histlbl]
1347	inst = histblk['Instrument Parameters'][0]
1348	hId = histblk['hId']
1349	pfx = ':' + str(hId) + ':'
1350
1351	if 'Lam1' in inst:
1352	ratio = self.parmDict.get('I(L2)/I(L1)',inst['I(L2)/I(L1)'][1])
1353	sratio = self.sigDict.get('I(L2)/I(L1)',-0.0009)
1354	lam1 = self.parmDict.get('Lam1',inst['Lam1'][1])
1355	slam1 = self.sigDict.get('Lam1',-0.00009)
1356	lam2 = self.parmDict.get('Lam2',inst['Lam2'][1])
1357	slam2 = self.sigDict.get('Lam2',-0.00009)
1358	# always assume Ka1 & Ka2 if two wavelengths are present
1359	WriteCIFitem(self.fp, '_diffrn_radiation_type','K\\a~1,2~')
1360	WriteCIFitem(self.fp, 'loop_' +
1361	'\n _diffrn_radiation_wavelength' +
1362	'\n _diffrn_radiation_wavelength_wt' +
1363	'\n _diffrn_radiation_wavelength_id')
1364	WriteCIFitem(self.fp, ' ' + PutInCol(G2mth.ValEsd(lam1,slam1),15)+
1365	PutInCol('1.0',15) +
1366	PutInCol('1',5))
1367	WriteCIFitem(self.fp, ' ' + PutInCol(G2mth.ValEsd(lam2,slam2),15)+
1368	PutInCol(G2mth.ValEsd(ratio,sratio),15)+
1369	PutInCol('2',5))
1370	elif 'Lam' in inst:
1371	lam1 = self.parmDict.get('Lam',inst['Lam'][1])
1372	slam1 = self.sigDict.get('Lam',-0.00009)
1373	WriteCIFitem(self.fp, '_diffrn_radiation_wavelength',G2mth.ValEsd(lam1,slam1))
1374
1375	if not oneblock:
1376	if not phasebyhistDict.get(histlbl):
1377	WriteCIFitem(self.fp, '\n# No phases associated with this data set')
1378	else:
1379	WriteCIFitem(self.fp, '\n# PHASE TABLE')
1380	WriteCIFitem(self.fp, 'loop_' +
1381	'\n _pd_phase_id' +
1382	'\n _pd_phase_block_id' +
1383	'\n _pd_phase_mass_%')
1384	wtFrSum = 0.
1385	for phasenam in phasebyhistDict.get(histlbl):
1386	hapData = self.Phases[phasenam]['Histograms'][histlbl]
1387	General = self.Phases[phasenam]['General']
1388	wtFrSum += hapData['Scale'][0]*General['Mass']
1389
1390	for phasenam in phasebyhistDict.get(histlbl):
1391	hapData = self.Phases[phasenam]['Histograms'][histlbl]
1392	General = self.Phases[phasenam]['General']
1393	wtFr = hapData['Scale'][0]*General['Mass']/wtFrSum
1394	pfx = str(self.Phases[phasenam]['pId'])+':'+str(hId)+':'
1395	if pfx+'Scale' in self.sigDict:
1396	sig = self.sigDict[pfx+'Scale']*wtFr/hapData['Scale'][0]
1397	else:
1398	sig = -0.0001
1399	WriteCIFitem(self.fp,
1400	' '+
1401	str(self.Phases[phasenam]['pId']) +
1402	' '+datablockidDict[phasenam]+
1403	' '+G2mth.ValEsd(wtFr,sig)
1404	)
1405	WriteCIFitem(self.fp, 'loop_' +
1406	'\n _gsas_proc_phase_R_F_factor' +
1407	'\n _gsas_proc_phase_R_Fsqd_factor' +
1408	'\n _gsas_proc_phase_id' +
1409	'\n _gsas_proc_phase_block_id')
1410	for phasenam in phasebyhistDict.get(histlbl):
1411	pfx = str(self.Phases[phasenam]['pId'])+':'+str(hId)+':'
1412	WriteCIFitem(self.fp,
1413	' '+
1414	' '+G2mth.ValEsd(histblk[pfx+'Rf']/100.,-.00009) +
1415	' '+G2mth.ValEsd(histblk[pfx+'Rf^2']/100.,-.00009)+
1416	' '+str(self.Phases[phasenam]['pId'])+
1417	' '+datablockidDict[phasenam]
1418	)
1419	elif len(self.Phases) == 1:
1420	# single phase in this histogram
1421	# get the phase number here
1422	pId = self.Phases[list(self.Phases.keys())[0]]['pId']
1423	pfx = str(pId)+':'+str(hId)+':'
1424	WriteCIFitem(self.fp, '_refine_ls_R_F_factor ','%.5f'%(histblk[pfx+'Rf']/100.))
1425	WriteCIFitem(self.fp, '_refine_ls_R_Fsqd_factor ','%.5f'%(histblk[pfx+'Rf^2']/100.))
1426
1427	try:
1428	WriteCIFitem(self.fp, '_pd_proc_ls_prof_R_factor ','%.5f'%(histblk['R']/100.))
1429	WriteCIFitem(self.fp, '_pd_proc_ls_prof_wR_factor ','%.5f'%(histblk['wR']/100.))
1430	WriteCIFitem(self.fp, '_gsas_proc_ls_prof_R_B_factor ','%.5f'%(histblk['Rb']/100.))
1431	WriteCIFitem(self.fp, '_gsas_proc_ls_prof_wR_B_factor','%.5f'%(histblk['wRb']/100.))
1432	WriteCIFitem(self.fp, '_pd_proc_ls_prof_wR_expected','%.5f'%(histblk['wRmin']/100.))
1433	except KeyError:
1434	pass
1435
1436	if histblk['Instrument Parameters'][0]['Type'][1][1] == 'X':
1437	WriteCIFitem(self.fp, '_diffrn_radiation_probe','x-ray')
1438	pola = histblk['Instrument Parameters'][0].get('Polariz.')
1439	if pola:
1440	pfx = ':' + str(hId) + ':'
1441	sig = self.sigDict.get(pfx+'Polariz.',-0.0009)
1442	txt = G2mth.ValEsd(pola[1],sig)
1443	WriteCIFitem(self.fp, '_diffrn_radiation_polarisn_ratio',txt)
1444	elif histblk['Instrument Parameters'][0]['Type'][1][1] == 'N':
1445	WriteCIFitem(self.fp, '_diffrn_radiation_probe','neutron')
1446	if 'T' in inst['Type'][0]:
1447	txt = G2mth.ValEsd(inst['2-theta'][0],-0.009)
1448	WriteCIFitem(self.fp, '_pd_meas_2theta_fixed',txt)
1449
1450	# TODO: this will need help from Bob
1451	#if not oneblock:
1452	#WriteCIFitem(self.fp, '\n# SCATTERING FACTOR INFO')
1453	#WriteCIFitem(self.fp, 'loop_ _atom_type_symbol')
1454	#if histblk['Instrument Parameters'][0]['Type'][1][1] == 'X':
1455	# WriteCIFitem(self.fp, ' _atom_type_scat_dispersion_real')
1456	# WriteCIFitem(self.fp, ' _atom_type_scat_dispersion_imag')
1457	# for lbl in ('a1','a2','a3', 'a4', 'b1', 'b2', 'b3', 'b4', 'c'):
1458	# WriteCIFitem(self.fp, ' _atom_type_scat_Cromer_Mann_'+lbl)
1459	#elif histblk['Instrument Parameters'][0]['Type'][1][1] == 'N':
1460	# WriteCIFitem(self.fp, ' _atom_type_scat_length_neutron')
1461	#WriteCIFitem(self.fp, ' _atom_type_scat_source')
1462
1463	WriteCIFitem(self.fp, '_pd_proc_ls_background_function',FormatBackground(histblk['Background'],histblk['hId']))
1464
1465	# TODO: this will need help from Bob
1466	#WriteCIFitem(self.fp, '_exptl_absorpt_process_details','?')
1467	#WriteCIFitem(self.fp, '_exptl_absorpt_correction_T_min','?')
1468	#WriteCIFitem(self.fp, '_exptl_absorpt_correction_T_max','?')
1469	#C extinction
1470	#WRITE(IUCIF,'(A)') '# Extinction correction'
1471	#CALL WRVAL(IUCIF,'_gsas_exptl_extinct_corr_T_min',TEXT(1:10))
1472	#CALL WRVAL(IUCIF,'_gsas_exptl_extinct_corr_T_max',TEXT(11:20))
1473
1474	# code removed because it is causing duplication in histogram block 1/26/19 BHT
1475	#if not oneblock: # instrumental profile terms go here
1476	# WriteCIFitem(self.fp, '_pd_proc_ls_profile_function',
1477	# FormatInstProfile(histblk["Instrument Parameters"],histblk['hId']))
1478
1479	#refprx = '_refln.' # mm
1480	refprx = '_refln_' # normal
1481	# data collection parameters for the powder dataset
1482
1483	temperature = histblk['Sample Parameters'].get('Temperature') # G2 uses K
1484	if not temperature:
1485	T = '?'
1486	else:
1487	T = G2mth.ValEsd(temperature,-0.009,True) # CIF uses K
1488	WriteCIFitem(self.fp, '_diffrn_ambient_temperature',T)
1489
1490	pressure = histblk['Sample Parameters'].get('Pressure') #G2 uses mega-Pascal
1491	if not pressure:
1492	P = '?'
1493	else:
1494	P = G2mth.ValEsd(pressure*1000,-0.09,True) # CIF uses kilopascal
1495	WriteCIFitem(self.fp, '_diffrn_ambient_pressure',P)
1496
1497	WriteCIFitem(self.fp, '\n# STRUCTURE FACTOR TABLE')
1498	# compute maximum intensity reflection
1499	Imax = 0
1500	for phasenam in histblk['Reflection Lists']:
1501	scale = self.Phases[phasenam]['Histograms'][histlbl]['Scale'][0]
1502	refList = np.asarray(histblk['Reflection Lists'][phasenam]['RefList'])
1503	I100 = scalerefList.T[8]refList.T[11]
1504	#Icorr = np.array([refl[13] for refl in histblk['Reflection Lists'][phasenam]])[0]
1505	#FO2 = np.array([refl[8] for refl in histblk['Reflection Lists'][phasenam]])
1506	#I100 = scaleFO2Icorr
1507	Imax = max(Imax,max(I100))
1508
1509	WriteCIFitem(self.fp, 'loop_')
1510	if len(histblk['Reflection Lists'].keys()) > 1:
1511	WriteCIFitem(self.fp, ' _pd_refln_phase_id')
1512	WriteCIFitem(self.fp, ' ' + refprx + 'index_h' +
1513	'\n ' + refprx + 'index_k' +
1514	'\n ' + refprx + 'index_l' +
1515	'\n ' + refprx + 'F_squared_meas' +
1516	'\n ' + refprx + 'F_squared_calc' +
1517	'\n ' + refprx + 'phase_calc' +
1518	'\n _refln_d_spacing')
1519	if Imax > 0:
1520	WriteCIFitem(self.fp, ' _gsas_i100_meas')
1521
1522	refcount = 0
1523	hklmin = None
1524	hklmax = None
1525	dmax = None
1526	dmin = None
1527	for phasenam in histblk['Reflection Lists']:
1528	scale = self.Phases[phasenam]['Histograms'][histlbl]['Scale'][0]
1529	phaseid = self.Phases[phasenam]['pId']
1530	refcount += len(histblk['Reflection Lists'][phasenam]['RefList'])
1531	refList = np.asarray(histblk['Reflection Lists'][phasenam]['RefList'])
1532	I100 = scalerefList.T[8]refList.T[11]
1533	for j,ref in enumerate(histblk['Reflection Lists'][phasenam]['RefList']):
1534	if DEBUG:
1535	print('DEBUG: skipping reflection list')
1536	break
1537	if hklmin is None:
1538	hklmin = ref[0:3]
1539	hklmax = ref[0:3]
1540	dmax = dmin = ref[4]
1541	if len(histblk['Reflection Lists'].keys()) > 1:
1542	s = PutInCol(phaseid,2)
1543	else:
1544	s = ""
1545	for i,hkl in enumerate(ref[0:3]):
1546	hklmax[i] = max(hkl,hklmax[i])
1547	hklmin[i] = min(hkl,hklmin[i])
1548	s += PutInCol(int(hkl),4)
1549	for I in ref[8:10]:
1550	s += PutInCol(G2mth.ValEsd(I,-0.0009),10)
1551	s += PutInCol(G2mth.ValEsd(ref[10],-0.9),7)
1552	dmax = max(dmax,ref[4])
1553	dmin = min(dmin,ref[4])
1554	s += PutInCol(G2mth.ValEsd(ref[4],-0.00009),8)
1555	if Imax > 0:
1556	s += PutInCol(G2mth.ValEsd(100.*I100[j]/Imax,-0.09),6)
1557	WriteCIFitem(self.fp, " "+s)
1558
1559	WriteReflStat(refcount,hklmin,hklmax,dmin,dmax,len(histblk['Reflection Lists']))
1560	WriteCIFitem(self.fp, '\n# POWDER DATA TABLE')
1561	# is data fixed step? If the step varies by <0.01% treat as fixed step
1562	steps = histblk['Data'][0][1:] - histblk['Data'][0][:-1]
1563	if abs(max(steps)-min(steps)) > abs(max(steps))/10000.:
1564	fixedstep = False
1565	else:
1566	fixedstep = True
1567
1568	zero = None
1569	if fixedstep and 'T' not in inst['Type'][0]: # and not TOF
1570	WriteCIFitem(self.fp, '_pd_meas_2theta_range_min', G2mth.ValEsd(histblk['Data'][0][0],-0.00009))
1571	WriteCIFitem(self.fp, '_pd_meas_2theta_range_max', G2mth.ValEsd(histblk['Data'][0][-1],-0.00009))
1572	WriteCIFitem(self.fp, '_pd_meas_2theta_range_inc', G2mth.ValEsd(steps.sum()/len(steps),-0.00009))
1573	# zero correct, if defined
1574	zerolst = histblk['Instrument Parameters'][0].get('Zero')
1575	if zerolst: zero = zerolst[1]
1576	zero = self.parmDict.get('Zero',zero)
1577	if zero:
1578	WriteCIFitem(self.fp, '_pd_proc_2theta_range_min', G2mth.ValEsd(histblk['Data'][0][0]-zero,-0.00009))
1579	WriteCIFitem(self.fp, '_pd_proc_2theta_range_max', G2mth.ValEsd(histblk['Data'][0][-1]-zero,-0.00009))
1580	WriteCIFitem(self.fp, '_pd_proc_2theta_range_inc', G2mth.ValEsd(steps.sum()/len(steps),-0.00009))
1581
1582	if zero:
1583	WriteCIFitem(self.fp, '_pd_proc_number_of_points', str(len(histblk['Data'][0])))
1584	else:
1585	WriteCIFitem(self.fp, '_pd_meas_number_of_points', str(len(histblk['Data'][0])))
1586	WriteCIFitem(self.fp, '\nloop_')
1587	# WriteCIFitem(self.fp, ' _pd_proc_d_spacing') # need easy way to get this
1588	if not fixedstep:
1589	if zero:
1590	WriteCIFitem(self.fp, ' _pd_proc_2theta_corrected')
1591	elif 'T' in inst['Type'][0]: # and not TOF
1592	WriteCIFitem(self.fp, ' _pd_meas_time_of_flight')
1593	else:
1594	WriteCIFitem(self.fp, ' _pd_meas_2theta_scan')
1595	# at least for now, always report weights.
1596	#if countsdata:
1597	# WriteCIFitem(self.fp, ' _pd_meas_counts_total')
1598	#else:
1599	WriteCIFitem(self.fp, ' _pd_meas_intensity_total')
1600	WriteCIFitem(self.fp, ' _pd_calc_intensity_total')
1601	WriteCIFitem(self.fp, ' _pd_proc_intensity_bkg_calc')
1602	WriteCIFitem(self.fp, ' _pd_proc_ls_weight')
1603	maxY = max(histblk['Data'][1].max(),histblk['Data'][3].max())
1604	if maxY < 0: maxY *= -10 # this should never happen, but...
1605	ndec = max(0,10-int(np.log10(maxY))-1) # 10 sig figs should be enough
1606	maxSU = histblk['Data'][2].max()
1607	if maxSU < 0: maxSU *= -1 # this should never happen, but...
1608	ndecSU = max(0,8-int(np.log10(maxSU))-1) # 8 sig figs should be enough
1609	lowlim,highlim = histblk['Limits'][1]
1610
1611	if DEBUG:
1612	print('DEBUG: skipping profile list')
1613	else:
1614	for x,yobs,yw,ycalc,ybkg in zip(histblk['Data'][0],
1615	histblk['Data'][1],
1616	histblk['Data'][2],
1617	histblk['Data'][3],
1618	histblk['Data'][4]):
1619	if lowlim <= x <= highlim:
1620	pass
1621	else:
1622	yw = 0.0 # show the point is not in use
1623
1624	if fixedstep:
1625	s = ""
1626	elif zero:
1627	s = PutInCol(G2mth.ValEsd(x-zero,-0.00009),10)
1628	else:
1629	s = PutInCol(G2mth.ValEsd(x,-0.00009),10)
1630	s += PutInCol(Yfmt(ndec,yobs),12)
1631	s += PutInCol(Yfmt(ndec,ycalc),12)
1632	s += PutInCol(Yfmt(ndec,ybkg),11)
1633	s += PutInCol(Yfmt(ndecSU,yw),9)
1634	WriteCIFitem(self.fp, " "+s)
1635
1636	def WriteSingleXtalData(histlbl):
1637	'Write out the selected single crystal histogram info'
1638	histblk = self.Histograms[histlbl]
1639
1640	#refprx = '_refln.' # mm
1641	refprx = '_refln_' # normal
1642
1643	WriteCIFitem(self.fp, '\n# STRUCTURE FACTOR TABLE')
1644	WriteCIFitem(self.fp, 'loop_' +
1645	'\n ' + refprx + 'index_h' +
1646	'\n ' + refprx + 'index_k' +
1647	'\n ' + refprx + 'index_l' +
1648	'\n ' + refprx + 'F_squared_meas' +
1649	'\n ' + refprx + 'F_squared_sigma' +
1650	'\n ' + refprx + 'F_squared_calc' +
1651	'\n ' + refprx + 'phase_calc'
1652	)
1653
1654	hklmin = None
1655	hklmax = None
1656	dmax = None
1657	dmin = None
1658	refcount = len(histblk['Data']['RefList'])
1659	for ref in histblk['Data']['RefList']:
1660	if ref[3] <= 0: #skip user rejected reflections (mul <= 0)
1661	continue
1662	s = " "
1663	if hklmin is None:
1664	hklmin = ref[0:3]
1665	hklmax = ref[0:3]
1666	dmax = dmin = ref[4]
1667	for i,hkl in enumerate(ref[0:3]):
1668	hklmax[i] = max(hkl,hklmax[i])
1669	hklmin[i] = min(hkl,hklmin[i])
1670	s += PutInCol(int(hkl),4)
1671	if ref[5] == 0.0:
1672	s += PutInCol(G2mth.ValEsd(ref[8],0),12)
1673	s += PutInCol('.',10)
1674	s += PutInCol(G2mth.ValEsd(ref[9],0),12)
1675	s += PutInCol(G2mth.ValEsd(ref[10],-0.9),7)
1676	else:
1677	sig = ref[6] * ref[8] / ref[5]
1678	s += PutInCol(G2mth.ValEsd(ref[8],-abs(sig/10)),12)
1679	s += PutInCol(G2mth.ValEsd(sig,-abs(sig)/10.),10)
1680	s += PutInCol(G2mth.ValEsd(ref[9],-abs(sig/10)),12)
1681	s += PutInCol(G2mth.ValEsd(ref[10],-0.9),7)
1682	dmax = max(dmax,ref[4])
1683	dmin = min(dmin,ref[4])
1684	WriteCIFitem(self.fp, s)
1685	if not self.quickmode: # statistics only in a full CIF
1686	WriteReflStat(refcount,hklmin,hklmax,dmin,dmax)
1687	hId = histblk['hId']
1688	hfx = '0:'+str(hId)+':'
1689	phfx = '%d:%d:'%(0,hId)
1690	extType,extModel,extParms = self.Phases[phasenam]['Histograms'][histlbl]['Extinction']
1691	if extModel != 'None':
1692	WriteCIFitem(self.fp, '# Extinction scaled by 1.e5')
1693	WriteCIFitem(self.fp, '_refine_ls_extinction_method','Becker-Coppens %s %s'%(extModel,extType))
1694	sig = -1.e-3
1695	if extModel == 'Primary':
1696	parm = extParms['Ep'][0]*1.e5
1697	if extParms['Ep'][1]:
1698	sig = self.sigDict[phfx+'Ep']*1.e5
1699	text = G2mth.ValEsd(parm,sig)
1700	elif extModel == 'Secondary Type I':
1701	parm = extParms['Eg'][0]*1.e5
1702	if extParms['Eg'][1]:
1703	sig = self.sigDict[phfx+'Eg']*1.e5
1704	text = G2mth.ValEsd(parm,sig)
1705	elif extModel == 'Secondary Type II':
1706	parm = extParms['Es'][0]*1.e5
1707	if extParms['Es'][1]:
1708	sig = self.sigDict[phfx+'Es']*1.e5
1709	text = G2mth.ValEsd(parm,sig)
1710	elif extModel == 'Secondary Type I & II':
1711	parm = extParms['Eg'][0]*1.e5
1712	if extParms['Es'][1]:
1713	sig = self.sigDict[phfx+'Es']*1.e5
1714	text = G2mth.ValEsd(parm,sig)
1715	sig = -1.0e-3
1716	parm = extParms['Es'][0]*1.e5
1717	if extParms['Es'][1]:
1718	sig = self.sigDict[phfx+'Es']*1.e5
1719	text += G2mth.ValEsd(parm,sig)
1720	WriteCIFitem(self.fp, '_refine_ls_extinction_coef',text)
1721	WriteCIFitem(self.fp, '_refine_ls_extinction_expression','Becker & Coppens (1974). Acta Cryst. A30, 129-147')
1722
1723	WriteCIFitem(self.fp, '_refine_ls_wR_factor_gt ','%.4f'%(histblk['wR']/100.))
1724	WriteCIFitem(self.fp, '_refine_ls_R_factor_gt ','%.4f'%(histblk[hfx+'Rf']/100.))
1725	WriteCIFitem(self.fp, '_refine_ls_R_Fsqd_factor ','%.4f'%(histblk[hfx+'Rf^2']/100.))
1726	def EditAuthor(event=None):
1727	'dialog to edit the CIF author info'
1728	'Edit the CIF author name'
1729	dlg = G2G.SingleStringDialog(self.G2frame,
1730	'Get CIF Author',
1731	'Provide CIF Author name (Last, First)',
1732	value=self.author)
1733	if not dlg.Show():
1734	dlg.Destroy()
1735	return False # cancel was pressed
1736	self.author = dlg.GetValue()
1737	self.shortauthorname = self.author.replace(',','').replace(' ','')[:20]
1738	dlg.Destroy()
1739	try:
1740	self.OverallParms['Controls']["Author"] = self.author # save for future
1741	except KeyError:
1742	pass
1743	return True
1744
1745	def EditInstNames(event=None):
1746	'Provide a dialog for editing instrument names'
1747	dictlist = []
1748	keylist = []
1749	lbllist = []
1750	for hist in self.Histograms:
1751	if hist.startswith("PWDR"):
1752	key2 = "Sample Parameters"
1753	d = self.Histograms[hist][key2]
1754	elif hist.startswith("HKLF"):
1755	key2 = "Instrument Parameters"
1756	d = self.Histograms[hist][key2][0]
1757
1758	lbllist.append(hist)
1759	dictlist.append(d)
1760	keylist.append('InstrName')
1761	instrname = d.get('InstrName')
1762	if instrname is None:
1763	d['InstrName'] = ''
1764	return G2G.CallScrolledMultiEditor(
1765	self.G2frame,dictlist,keylist,
1766	prelbl=range(1,len(dictlist)+1),
1767	postlbl=lbllist,
1768	title='Instrument names',
1769	header="Edit instrument names. Note that a non-blank\nname is required for all histograms",
1770	CopyButton=True,ASCIIonly=True)
1771
1772	def EditRanges(event):
1773	'''Edit the bond distance/angle search range; phase is determined from
1774	a pointer placed in the button object (.phasedict) that references the
1775	phase dictionary
1776	'''
1777	but = event.GetEventObject()
1778	phasedict = but.phasedict
1779	dlg = G2G.DisAglDialog(
1780	self.G2frame,
1781	phasedict['General']['DisAglCtls'], # edited
1782	phasedict['General'], # defaults
1783	)
1784	if dlg.ShowModal() == wx.ID_OK:
1785	phasedict['General']['DisAglCtls'] = dlg.GetData()
1786	dlg.Destroy()
1787
1788	def EditCIFDefaults():
1789	'''Fills the CIF Defaults window with controls for editing various CIF export
1790	parameters (mostly related to templates).
1791	'''
1792	self.cifdefs.DestroyChildren()
1793	self.cifdefs.SetTitle('Edit CIF settings')
1794	vbox = wx.BoxSizer(wx.VERTICAL)
1795	vbox.Add(wx.StaticText(self.cifdefs, wx.ID_ANY,'Creating file '+self.filename))
1796	but = wx.Button(self.cifdefs, wx.ID_ANY,'Edit CIF Author')
1797	but.Bind(wx.EVT_BUTTON,EditAuthor)
1798	vbox.Add(but,0,wx.ALIGN_CENTER,3)
1799	but = wx.Button(self.cifdefs, wx.ID_ANY,'Edit Instrument Name(s)')
1800	but.Bind(wx.EVT_BUTTON,EditInstNames)
1801	vbox.Add(but,0,wx.ALIGN_CENTER,3)
1802	cpnl = wxscroll.ScrolledPanel(self.cifdefs,size=(300,300))
1803	cbox = wx.BoxSizer(wx.VERTICAL)
1804	G2G.HorizontalLine(cbox,cpnl)
1805	cbox.Add(
1806	CIFtemplateSelect(self.cifdefs,
1807	cpnl,'publ',self.OverallParms['Controls'],
1808	EditCIFDefaults,
1809	"Publication (overall) template",
1810	),
1811	0,wx.EXPAND\|wx.ALIGN_LEFT\|wx.ALL)
1812	for phasenam in sorted(self.Phases.keys()):
1813	G2G.HorizontalLine(cbox,cpnl)
1814	title = 'Phase '+phasenam
1815	phasedict = self.Phases[phasenam] # pointer to current phase info
1816	cbox.Add(
1817	CIFtemplateSelect(self.cifdefs,
1818	cpnl,'phase',phasedict['General'],
1819	EditCIFDefaults,
1820	title,
1821	phasenam),
1822	0,wx.EXPAND\|wx.ALIGN_LEFT\|wx.ALL)
1823	cpnl.SetSizer(cbox)
1824	if phasedict['General']['Type'] == 'nuclear':
1825	but = wx.Button(cpnl, wx.ID_ANY,'Edit distance/angle ranges')
1826	cbox.Add(but,0,wx.ALIGN_LEFT,0)
1827	cbox.Add((-1,2))
1828	but.phasedict = self.Phases[phasenam] # set a pointer to current phase info
1829	but.Bind(wx.EVT_BUTTON,EditRanges) # phase bond/angle ranges
1830	but = wx.Button(cpnl, wx.ID_ANY,'Set distance/angle publication flags')
1831	but.phase = phasenam # set a pointer to current phase info
1832	but.Bind(wx.EVT_BUTTON,SelectDisAglFlags) # phase bond/angle ranges
1833	cbox.Add(but,0,wx.ALIGN_LEFT,0)
1834	cbox.Add((-1,2))
1835	for i in sorted(self.powderDict.keys()):
1836	G2G.HorizontalLine(cbox,cpnl)
1837	hist = self.powderDict[i]
1838	histblk = self.Histograms[hist]
1839	title = 'Powder dataset '+hist[5:]
1840	cbox.Add(
1841	CIFtemplateSelect(self.cifdefs,
1842	cpnl,'powder',histblk["Sample Parameters"],
1843	EditCIFDefaults,
1844	title,
1845	histblk["Sample Parameters"]['InstrName']),
1846	0,wx.EXPAND\|wx.ALIGN_LEFT\|wx.ALL)
1847	for i in sorted(self.xtalDict.keys()):
1848	G2G.HorizontalLine(cbox,cpnl)
1849	hist = self.xtalDict[i]
1850	histblk = self.Histograms[hist]
1851	title = 'Single Xtal dataset '+hist[5:]
1852	cbox.Add(
1853	CIFtemplateSelect(self.cifdefs,
1854	cpnl,'single',histblk["Instrument Parameters"][0],
1855	EditCIFDefaults,
1856	title,
1857	histblk["Instrument Parameters"][0]['InstrName']),
1858	0,wx.EXPAND\|wx.ALIGN_LEFT\|wx.ALL)
1859	cpnl.SetSizer(cbox)
1860	cpnl.SetAutoLayout(1)
1861	cpnl.SetupScrolling()
1862	#cpnl.Bind(rw.EVT_RW_LAYOUT_NEEDED, self.OnLayoutNeeded) # needed if sizes change
1863	cpnl.Layout()
1864
1865	vbox.Add(cpnl, 1, wx.ALIGN_LEFT\|wx.ALL\|wx.EXPAND, 0)
1866	btnsizer = wx.StdDialogButtonSizer()
1867	btn = wx.Button(self.cifdefs, wx.ID_OK, "Create CIF")
1868	btn.SetDefault()
1869	btnsizer.AddButton(btn)
1870	btn = wx.Button(self.cifdefs, wx.ID_CANCEL)
1871	btnsizer.AddButton(btn)
1872	btnsizer.Realize()
1873	vbox.Add(btnsizer, 0, wx.ALIGN_CENTER\|wx.ALL, 5)
1874	self.cifdefs.SetSizer(vbox)
1875	vbox.Fit(self.cifdefs)
1876	self.cifdefs.Layout()
1877
1878	def OnToggleButton(event):
1879	'Respond to press of ToggleButton in SelectDisAglFlags'
1880	but = event.GetEventObject()
1881	if but.GetValue():
1882	but.DisAglSel[but.key] = True
1883	else:
1884	try:
1885	del but.DisAglSel[but.key]
1886	except KeyError:
1887	pass
1888	def keepTrue(event):
1889	event.GetEventObject().SetValue(True)
1890	def keepFalse(event):
1891	event.GetEventObject().SetValue(False)
1892
1893	def SelectDisAglFlags(event):
1894	'Select Distance/Angle use flags for the selected phase'
1895	phasenam = event.GetEventObject().phase
1896	phasedict = self.Phases[phasenam]
1897	SymOpList,offsetList,symOpList,G2oprList,G2opcodes = G2spc.AllOps(phasedict['General']['SGData'])
1898	generalData = phasedict['General']
1899	# create a dict for storing Pub flag for bonds/angles, if needed
1900	if phasedict['General'].get("DisAglHideFlag") is None:
1901	phasedict['General']["DisAglHideFlag"] = {}
1902	DisAngSel = phasedict['General']["DisAglHideFlag"]
1903
1904	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
1905	cn = ct-1
1906	cfrac = cx+3
1907	DisAglData = {}
1908	# create a list of atoms, but skip atoms with zero occupancy
1909	xyz = []
1910	fpfx = str(phasedict['pId'])+'::Afrac:'
1911	for i,atom in enumerate(phasedict['Atoms']):
1912	if self.parmDict.get(fpfx+str(i),atom[cfrac]) == 0.0: continue
1913	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
1914	if 'DisAglCtls' not in generalData:
1915	# should not be used, since DisAglDialog should be called
1916	# for all phases before getting here
1917	dlg = G2G.DisAglDialog(
1918	self.cifdefs,
1919	{},
1920	generalData)
1921	if dlg.ShowModal() == wx.ID_OK:
1922	generalData['DisAglCtls'] = dlg.GetData()
1923	else:
1924	dlg.Destroy()
1925	return
1926	dlg.Destroy()
1927	dlg = wx.Dialog(
1928	self.G2frame,
1929	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
1930	vbox = wx.BoxSizer(wx.VERTICAL)
1931	txt = wx.StaticText(dlg,wx.ID_ANY,'Searching distances for phase '+phasenam
1932	+'\nPlease wait...')
1933	vbox.Add(txt,0,wx.ALL\|wx.EXPAND)
1934	dlg.SetSizer(vbox)
1935	dlg.CenterOnParent()
1936	dlg.Show() # post "please wait"
1937	wx.BeginBusyCursor() # and change cursor
1938
1939	DisAglData['OrigAtoms'] = xyz
1940	DisAglData['TargAtoms'] = xyz
1941	SymOpList,offsetList,symOpList,G2oprList,G2opcodes = G2spc.AllOps(
1942	generalData['SGData'])
1943
1944	# xpandSGdata = generalData['SGData'].copy()
1945	# xpandSGdata.update({'SGOps':symOpList,
1946	# 'SGInv':False,
1947	# 'SGLatt':'P',
1948	# 'SGCen':np.array([[0, 0, 0]]),})
1949	# DisAglData['SGData'] = xpandSGdata
1950	DisAglData['SGData'] = generalData['SGData'].copy()
1951
1952	DisAglData['Cell'] = generalData['Cell'][1:] #+ volume
1953	if 'pId' in phasedict:
1954	DisAglData['pId'] = phasedict['pId']
1955	DisAglData['covData'] = self.OverallParms['Covariance']
1956	try:
1957	AtomLabels,DistArray,AngArray = G2stMn.RetDistAngle(
1958	generalData['DisAglCtls'],
1959	DisAglData)
1960	except KeyError: # inside DistAngle for missing atom types in DisAglCtls
1961	print('** ERROR - try again but do "Reset" to fill in missing atom types **')
1962	wx.EndBusyCursor()
1963	txt.SetLabel('Set publication flags for distances and angles in\nphase '+phasenam)
1964	vbox.Add((5,5))
1965	vbox.Add(wx.StaticText(dlg,wx.ID_ANY,
1966	'The default is to flag all distances and angles as to be'+
1967	'\npublished. Change this by pressing appropriate buttons.'),
1968	0,wx.ALL\|wx.EXPAND)
1969	hbox = wx.BoxSizer(wx.HORIZONTAL)
1970	vbox.Add(hbox)
1971	hbox.Add(wx.StaticText(dlg,wx.ID_ANY,'Button appearance: '))
1972	but = wx.ToggleButton(dlg,wx.ID_ANY,'Publish')
1973	but.Bind(wx.EVT_TOGGLEBUTTON,keepFalse)
1974	hbox.Add(but)
1975	but = wx.ToggleButton(dlg,wx.ID_ANY,"Don't publish")
1976	but.Bind(wx.EVT_TOGGLEBUTTON,keepTrue)
1977	hbox.Add(but)
1978	but.SetValue(True)
1979	G2G.HorizontalLine(vbox,dlg)
1980
1981	cpnl = wxscroll.ScrolledPanel(dlg,size=(400,300))
1982	cbox = wx.BoxSizer(wx.VERTICAL)
1983	for c in sorted(DistArray):
1984	karr = []
1985	UsedCols = {}
1986	cbox.Add(wx.StaticText(cpnl,wx.ID_ANY,
1987	'distances to/angles around atom '+AtomLabels[c]))
1988	#dbox = wx.GridBagSizer(hgap=5)
1989	dbox = wx.GridBagSizer()
1990	for i,D in enumerate(DistArray[c]):
1991	karr.append(tuple(D[0:3]))
1992	val = "{:.2f}".format(D[3])
1993	sym = " [{:d} {:d} {:d}]".format(*D[1]) + " #{:d}".format(D[2])
1994	dbox.Add(wx.StaticText(cpnl,wx.ID_ANY,AtomLabels[D[0]]),
1995	(i+1,0)
1996	)
1997	dbox.Add(wx.StaticText(cpnl,wx.ID_ANY,sym),
1998	(i+1,1)
1999	)
2000	but = wx.ToggleButton(cpnl,wx.ID_ANY,val)
2001	but.key = (c,karr[-1])
2002	but.DisAglSel = DisAngSel
2003	if DisAngSel.get(but.key): but.SetValue(True)
2004	but.Bind(wx.EVT_TOGGLEBUTTON,OnToggleButton)
2005	dbox.Add(but,(i+1,2),border=1)
2006	for i,D in enumerate(AngArray[c]):
2007	val = "{:.1f}".format(D[2][0])
2008	but = wx.ToggleButton(cpnl,wx.ID_ANY,val)
2009	but.key = (karr[D[0]],c,karr[D[1]])
2010	but.DisAglSel = DisAngSel
2011	if DisAngSel.get(but.key): but.SetValue(True)
2012	but.Bind(wx.EVT_TOGGLEBUTTON,OnToggleButton)
2013	dbox.Add(but,(D[0]+1,D[1]+3),border=1)
2014	UsedCols[D[1]+3] = True
2015	for i,D in enumerate(DistArray[c][:-1]): # label columns that are used
2016	if UsedCols.get(i+3):
2017	dbox.Add(wx.StaticText(cpnl,wx.ID_ANY,AtomLabels[D[0]]),
2018	(0,i+3),
2019	flag=wx.ALIGN_CENTER
2020	)
2021	dbox.Add(wx.StaticText(cpnl,wx.ID_ANY,'distance'),
2022	(0,2),
2023	flag=wx.ALIGN_CENTER
2024	)
2025	cbox.Add(dbox)
2026	G2G.HorizontalLine(cbox,cpnl)
2027	cpnl.SetSizer(cbox)
2028	cpnl.SetAutoLayout(1)
2029	cpnl.SetupScrolling()
2030	#cpnl.Bind(rw.EVT_RW_LAYOUT_NEEDED, self.OnLayoutNeeded) # needed if sizes change
2031	cpnl.Layout()
2032
2033	vbox.Add(cpnl, 1, wx.ALIGN_LEFT\|wx.ALL\|wx.EXPAND, 0)
2034
2035	btnsizer = wx.StdDialogButtonSizer()
2036	btn = wx.Button(dlg, wx.ID_OK, "Done")
2037	btn.SetDefault()
2038	btnsizer.AddButton(btn)
2039	btnsizer.Realize()
2040	vbox.Add(btnsizer, 0, wx.ALIGN_CENTER\|wx.ALL, 5)
2041	dlg.SetSizer(vbox)
2042	vbox.Fit(dlg)
2043	dlg.Layout()
2044
2045	dlg.CenterOnParent()
2046	dlg.ShowModal()
2047
2048	#=================================================================================
2049	#===== end of function definitions for _Exporter =================================
2050	#=================================================================================
2051	# make sure required information is present
2052	self.CIFdate = dt.datetime.strftime(dt.datetime.now(),"%Y-%m-%dT%H:%M")
2053	if not self.CIFname: # Get a name for the CIF. If not defined, use the GPX name (save, if that is needed).
2054	if not self.G2frame.GSASprojectfile:
2055	self.G2frame.OnFileSaveas(None)
2056	if not self.G2frame.GSASprojectfile: return
2057	self.CIFname = os.path.splitext(
2058	os.path.split(self.G2frame.GSASprojectfile)[1]
2059	)[0]
2060	self.CIFname = self.CIFname.replace(' ','')
2061	# replace non-ASCII characters in CIFname with dots
2062	s = ''
2063	for c in self.CIFname:
2064	if ord(c) < 128:
2065	s += c
2066	else:
2067	s += '.'
2068	self.CIFname = s
2069	# load saved CIF author name
2070	try:
2071	self.author = self.OverallParms['Controls'].get("Author",'').strip()
2072	except KeyError:
2073	pass
2074	#=================================================================
2075	# write quick CIFs
2076	#=================================================================
2077	if phaseOnly: #====Phase only CIF ================================
2078	print('Writing CIF output to file '+self.filename)
2079	#self.OpenFile()
2080	oneblock = True
2081	self.quickmode = True
2082	self.Write(' ')
2083	self.Write(70*'#')
2084	WriteCIFitem(self.fp, 'data_'+phaseOnly.replace(' ','_'))
2085	#phaseblk = self.Phases[phaseOnly] # pointer to current phase info
2086	# report the phase info
2087	WritePhaseInfo(phaseOnly)
2088	#self.CloseFile()
2089	return
2090	elif histOnly: #====Histogram only CIF ================================
2091	print('Writing CIF output to file '+self.filename)
2092	#self.OpenFile()
2093	hist = histOnly
2094	#histname = histOnly.replace(' ','')
2095	oneblock = True
2096	self.quickmode = True
2097	self.ifHKLF = False
2098	self.ifPWDR = True
2099	self.Write(' ')
2100	self.Write(70*'#')
2101	#phasenam = self.Phases.keys()[0]
2102	WriteCIFitem(self.fp, 'data_'+self.CIFname)
2103	#print 'phasenam',phasenam
2104	#phaseblk = self.Phases[phasenam] # pointer to current phase info
2105	#instnam = instnam.replace(' ','')
2106	#WriteCIFitem(self.fp, '_pd_block_id',
2107	# str(self.CIFdate) + "\|" + str(self.CIFname) + "\|" +
2108	# str(self.shortauthorname) + "\|" + instnam + '\|' + histname)
2109	#WriteAudit()
2110	#writeCIFtemplate(self.OverallParms['Controls'],'publ') # overall (publication) template
2111	#WriteOverall()
2112	#writeCIFtemplate(self.Phases[phasenam]['General'],'phase',phasenam) # write phase template
2113	# report the phase info
2114	#WritePhaseInfo(phasenam,hist)
2115	# preferred orientation
2116	#SH = FormatSH(phasenam)
2117	#MD = FormatHAPpo(phasenam)
2118	#if SH and MD:
2119	# WriteCIFitem(self.fp, '_pd_proc_ls_pref_orient_corr', SH + '\n' + MD)
2120	#elif SH or MD:
2121	# WriteCIFitem(self.fp, '_pd_proc_ls_pref_orient_corr', SH + MD)
2122	#else:
2123	# WriteCIFitem(self.fp, '_pd_proc_ls_pref_orient_corr', 'none')
2124	# report profile, since one-block: include both histogram and phase info
2125	#WriteCIFitem(self.fp, '_pd_proc_ls_profile_function',
2126	# FormatInstProfile(histblk["Instrument Parameters"],histblk['hId'])
2127	# +'\n'+FormatPhaseProfile(phasenam))
2128	if hist.startswith("PWDR"):
2129	WritePowderData(hist)
2130	elif hist.startswith("HKLF"):
2131	WriteSingleXtalData(hist)
2132	#writeCIFtemplate(histblk,'powder',histblk['InstrName']) # write powder template
2133	#self.CloseFile()
2134	return
2135	#elif IncludeOnlyHist is not None: # truncate histogram list to only selected (for sequential export)
2136	# self.Histograms = {IncludeOnlyHist:self.Histograms[IncludeOnlyHist]}
2137
2138	#===============================================================================
2139	# the export process for a full CIF starts here
2140	#===============================================================================
2141	self.InitExport(event)
2142	# load all of the tree into a set of dicts
2143	self.loadTree()
2144	# create a dict with refined values and their uncertainties
2145	self.loadParmDict()
2146	if self.ExportSelect('ask'): return
2147	if not self.filename:
2148	print('No name supplied')
2149	return
2150	self.OpenFile()
2151	#if self.ExportSelect('default'): return
2152	# Someday: get restraint & constraint info
2153	#restraintDict = self.OverallParms.get('Restraints',{})
2154	#for i in self.OverallParms['Constraints']:
2155	# print i
2156	# for j in self.OverallParms['Constraints'][i]:
2157	# print j
2158
2159	# is there anything to export?
2160	if len(self.Phases) == len(self.powderDict) == len(self.xtalDict) == 0:
2161	self.G2frame.ErrorDialog(
2162	'Empty project',
2163	'Project does not contain any data or phases. Are they interconnected?')
2164	return
2165	self.quickmode = False # full CIF
2166	phasenam = None # include all phases
2167	# Will this require a multiblock CIF?
2168	if len(self.Phases) > 1:
2169	oneblock = False
2170	elif len(self.powderDict) + len(self.xtalDict) > 1:
2171	oneblock = False
2172	else: # one phase, one dataset, Full CIF
2173	oneblock = True
2174
2175	# check there is an instrument name for every histogram
2176	self.ifPWDR = False
2177	self.ifHKLF = False
2178	invalid = 0
2179	key3 = 'InstrName'
2180	for hist in self.Histograms:
2181	if hist.startswith("PWDR"):
2182	self.ifPWDR = True
2183	key2 = "Sample Parameters"
2184	d = self.Histograms[hist][key2]
2185	elif hist.startswith("HKLF"):
2186	self.ifHKLF = True
2187	key2 = "Instrument Parameters"
2188	d = self.Histograms[hist][key2][0]
2189	instrname = d.get(key3)
2190	if instrname is None:
2191	d[key3] = ''
2192	invalid += 1
2193	elif instrname.strip() == '':
2194	invalid += 1
2195	if invalid:
2196	#msg = ""
2197	#if invalid > 3: msg = (
2198	# "\n\nNote: it may be faster to set the name for\n"
2199	# "one histogram for each instrument and use the\n"
2200	# "File/Copy option to duplicate the name"
2201	# )
2202	if not EditInstNames(): return
2203
2204	# check for a distance-angle range search range for each phase
2205	for phasenam in sorted(self.Phases.keys()):
2206	#i = self.Phases[phasenam]['pId']
2207	phasedict = self.Phases[phasenam] # pointer to current phase info
2208	if 'DisAglCtls' not in phasedict['General']:
2209	dlg = G2G.DisAglDialog(
2210	self.G2frame,
2211	{},
2212	phasedict['General'])
2213	if dlg.ShowModal() == wx.ID_OK:
2214	phasedict['General']['DisAglCtls'] = dlg.GetData()
2215	else:
2216	dlg.Destroy()
2217	return
2218	dlg.Destroy()
2219
2220	# check if temperature values & pressure are defaulted
2221	default = 0
2222	for hist in self.Histograms:
2223	if hist.startswith("PWDR"):
2224	key2 = "Sample Parameters"
2225	T = self.Histograms[hist][key2].get('Temperature')
2226	if not T:
2227	default += 1
2228	elif T == 300:
2229	default += 1
2230	P = self.Histograms[hist][key2].get('Pressure')
2231	if not P:
2232	default += 1
2233	elif P == 1:
2234	default += 1
2235	if default > 0:
2236	dlg = wx.MessageDialog(
2237	self.G2frame,
2238	'Temperature/Pressure values appear to be defaulted for some powder histograms (See Sample Parameters for each PWDR tree entry). Do you want to use those values?',
2239	'Check T and P values',
2240	wx.OK\|wx.CANCEL)
2241	ret = dlg.ShowModal()
2242	dlg.Destroy()
2243	if ret != wx.ID_OK: return
2244	if oneblock:
2245	# select a dataset to use (there should only be one set in one block,
2246	# but take whatever comes 1st)
2247	for hist in self.Histograms:
2248	histblk = self.Histograms[hist]
2249	if hist.startswith("PWDR"):
2250	instnam = histblk["Sample Parameters"]['InstrName']
2251	break # ignore all but 1st data histogram
2252	elif hist.startswith("HKLF"):
2253	instnam = histblk["Instrument Parameters"][0]['InstrName']
2254	break # ignore all but 1st data histogram
2255	# give the user a window to edit CIF contents
2256	if not self.author:
2257	if not EditAuthor(): return
2258	self.ValidateAscii([('Author name',self.author),]) # check for ASCII strings where needed, warn on problems
2259	self.cifdefs = wx.Dialog(
2260	self.G2frame,
2261	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
2262	EditCIFDefaults()
2263	self.cifdefs.CenterOnParent()
2264	if self.cifdefs.ShowModal() != wx.ID_OK:
2265	self.cifdefs.Destroy()
2266	return
2267	while self.ValidateAscii([('Author name',self.author),
2268	]): # validate a few things as ASCII
2269	if self.cifdefs.ShowModal() != wx.ID_OK:
2270	self.cifdefs.Destroy()
2271	return
2272	self.cifdefs.Destroy()
2273	#======================================================================
2274	# Start writing the CIF - single block
2275	#======================================================================
2276	print('Writing CIF output to file '+self.filename+"...")
2277	#self.OpenFile()
2278	if self.currentExportType == 'single' or self.currentExportType == 'powder':
2279	#======Data only CIF (powder/xtal) ====================================
2280	hist = self.histnam[0]
2281	self.CIFname = hist[5:40].replace(' ','')
2282	WriteCIFitem(self.fp, 'data_'+self.CIFname)
2283	if hist.startswith("PWDR"):
2284	WritePowderData(hist)
2285	elif hist.startswith("HKLF"):
2286	WriteSingleXtalData(hist)
2287	else:
2288	print ("should not happen")
2289	elif oneblock:
2290	#====Single block, data & phase CIF ===================================
2291	WriteCIFitem(self.fp, 'data_'+self.CIFname)
2292	if phasenam is None: # if not already selected, select the first phase (should be one)
2293	phasenam = self.Phases.keys()[0]
2294	#print 'phasenam',phasenam
2295	#phaseblk = self.Phases[phasenam] # pointer to current phase info
2296	instnam = instnam.replace(' ','')
2297	WriteCIFitem(self.fp, '_pd_block_id',
2298	str(self.CIFdate) + "\|" + str(self.CIFname) + "\|" +
2299	str(self.shortauthorname) + "\|" + instnam)
2300	WriteAudit()
2301	writeCIFtemplate(self.OverallParms['Controls'],'publ') # overall (publication) template
2302	WriteOverall()
2303	writeCIFtemplate(self.Phases[phasenam]['General'],'phase',phasenam) # write phase template
2304	# report the phase info
2305	WritePhaseInfo(phasenam)
2306	if hist.startswith("PWDR"): # this is invoked for single-block CIFs
2307	# preferred orientation
2308	SH = FormatSH(phasenam)
2309	MD = FormatHAPpo(phasenam)
2310	if SH and MD:
2311	WriteCIFitem(self.fp, '_pd_proc_ls_pref_orient_corr', SH + '\n' + MD)
2312	elif SH or MD:
2313	WriteCIFitem(self.fp, '_pd_proc_ls_pref_orient_corr', SH + MD)
2314	else:
2315	WriteCIFitem(self.fp, '_pd_proc_ls_pref_orient_corr', 'none')
2316	# report profile, since one-block: include both histogram and phase info (N.B. there is only 1 of each)
2317	WriteCIFitem(self.fp, '_pd_proc_ls_profile_function',
2318	FormatInstProfile(histblk["Instrument Parameters"],histblk['hId'])
2319	+'\n'+FormatPhaseProfile(phasenam))
2320
2321	histblk = self.Histograms[hist]["Sample Parameters"]
2322	writeCIFtemplate(histblk,'powder',histblk['InstrName']) # write powder template
2323	WritePowderData(hist)
2324	elif hist.startswith("HKLF"):
2325	histprm = self.Histograms[hist]["Instrument Parameters"][0]
2326	writeCIFtemplate(histprm,'single',histprm['InstrName']) # single crystal template
2327	WriteSingleXtalData(hist)
2328	else:
2329	#=== multiblock: multiple phases and/or histograms ====================
2330	nsteps = 1 + len(self.Phases) + len(self.powderDict) + len(self.xtalDict)
2331	dlg = wx.ProgressDialog('CIF progress','starting',nsteps,parent=self.G2frame)
2332	# Size = dlg.GetSize()
2333	# Size = (int(Size[0]*3),Size[1]) # increase size along x
2334	# dlg.SetSize(Size)
2335	dlg.CenterOnParent()
2336
2337	# publication info
2338	step = 1
2339	dlg.Update(step,"Exporting overall section")
2340	WriteCIFitem(self.fp, '\ndata_'+self.CIFname+'_publ')
2341	WriteAudit()
2342	WriteCIFitem(self.fp, '_pd_block_id',
2343	str(self.CIFdate) + "\|" + str(self.CIFname) + "\|" +
2344	str(self.shortauthorname) + "\|Overall")
2345	writeCIFtemplate(self.OverallParms['Controls'],'publ') #insert the publication template
2346	# ``template_publ.cif`` or a modified version
2347	# overall info
2348	WriteCIFitem(self.fp, 'data_'+str(self.CIFname)+'_overall')
2349	WriteOverall()
2350	#============================================================
2351	WriteCIFitem(self.fp, '# POINTERS TO PHASE AND HISTOGRAM BLOCKS')
2352	datablockidDict = {} # save block names here -- N.B. check for conflicts between phase & hist names (unlikely!)
2353	# loop over phase blocks
2354	if len(self.Phases) > 1:
2355	loopprefix = ''
2356	WriteCIFitem(self.fp, 'loop_ _pd_phase_block_id')
2357	else:
2358	loopprefix = '_pd_phase_block_id'
2359
2360	for phasenam in sorted(self.Phases.keys()):
2361	i = self.Phases[phasenam]['pId']
2362	datablockidDict[phasenam] = (str(self.CIFdate) + "\|" + str(self.CIFname) + "\|" +
2363	'phase_'+ str(i) + '\|' + str(self.shortauthorname))
2364	WriteCIFitem(self.fp, loopprefix,datablockidDict[phasenam])
2365	# loop over data blocks
2366	if len(self.powderDict) + len(self.xtalDict) > 1:
2367	loopprefix = ''
2368	WriteCIFitem(self.fp, 'loop_ _pd_block_diffractogram_id')
2369	else:
2370	loopprefix = '_pd_block_diffractogram_id'
2371	for i in sorted(self.powderDict.keys()):
2372	hist = self.powderDict[i]
2373	histblk = self.Histograms[hist]
2374	instnam = histblk["Sample Parameters"]['InstrName']
2375	instnam = instnam.replace(' ','')
2376	j = histblk['hId']
2377	datablockidDict[hist] = (str(self.CIFdate) + "\|" + str(self.CIFname) + "\|" +
2378	str(self.shortauthorname) + "\|" +
2379	instnam + "_hist_"+str(j))
2380	WriteCIFitem(self.fp, loopprefix,datablockidDict[hist])
2381	for i in sorted(self.xtalDict.keys()):
2382	hist = self.xtalDict[i]
2383	histblk = self.Histograms[hist]
2384	instnam = histblk["Instrument Parameters"][0]['InstrName']
2385	instnam = instnam.replace(' ','')
2386	i = histblk['hId']
2387	datablockidDict[hist] = (str(self.CIFdate) + "\|" + str(self.CIFname) + "\|" +
2388	str(self.shortauthorname) + "\|" +
2389	instnam + "_hist_"+str(i))
2390	WriteCIFitem(self.fp, loopprefix,datablockidDict[hist])
2391	#============================================================
2392	# loop over phases, exporting them
2393	phasebyhistDict = {} # create a cross-reference to phases by histogram
2394	for j,phasenam in enumerate(sorted(self.Phases.keys())):
2395	step += 1
2396	dlg.Update(step,"Exporting phase "+phasenam+' (#'+str(j+1)+')')
2397	i = self.Phases[phasenam]['pId']
2398	WriteCIFitem(self.fp, '\ndata_'+self.CIFname+"_phase_"+str(i))
2399	WriteCIFitem(self.fp, '# Information for phase '+str(i))
2400	WriteCIFitem(self.fp, '_pd_block_id',datablockidDict[phasenam])
2401	# report the phase
2402	writeCIFtemplate(self.Phases[phasenam]['General'],'phase',phasenam) # write phase template
2403	WritePhaseInfo(phasenam)
2404	# preferred orientation
2405	if self.ifPWDR:
2406	SH = FormatSH(phasenam)
2407	MD = FormatHAPpo(phasenam)
2408	if SH and MD:
2409	WriteCIFitem(self.fp, '_pd_proc_ls_pref_orient_corr', SH + '\n' + MD)
2410	elif SH or MD:
2411	WriteCIFitem(self.fp, '_pd_proc_ls_pref_orient_corr', SH + MD)
2412	else:
2413	WriteCIFitem(self.fp, '_pd_proc_ls_pref_orient_corr', 'none')
2414	# report sample profile terms for all histograms with current phase
2415	PP = FormatPhaseProfile(phasenam)
2416	if PP:
2417	WriteCIFitem(self.fp, '_pd_proc_ls_profile_function',PP)
2418
2419	#============================================================
2420	# loop over histograms, exporting them
2421	for i in sorted(self.powderDict.keys()):
2422	hist = self.powderDict[i]
2423	histblk = self.Histograms[hist]
2424	if hist.startswith("PWDR"):
2425	step += 1
2426	dlg.Update(step,"Exporting "+hist.strip())
2427	WriteCIFitem(self.fp, '\ndata_'+self.CIFname+"_pwd_"+str(i))
2428	#instnam = histblk["Sample Parameters"]['InstrName']
2429	# report instrumental profile terms
2430	WriteCIFitem(self.fp, '_pd_proc_ls_profile_function',
2431	FormatInstProfile(histblk["Instrument Parameters"],histblk['hId']))
2432	WriteCIFitem(self.fp, '# Information for histogram '+str(i)+': '+hist)
2433	WriteCIFitem(self.fp, '_pd_block_id',datablockidDict[hist])
2434	histprm = self.Histograms[hist]["Sample Parameters"]
2435	writeCIFtemplate(histprm,'powder',histprm['InstrName']) # powder template
2436	WritePowderData(hist)
2437	for i in sorted(self.xtalDict.keys()):
2438	hist = self.xtalDict[i]
2439	histblk = self.Histograms[hist]
2440	if hist.startswith("HKLF"):
2441	step += 1
2442	dlg.Update(step,"Exporting "+hist.strip())
2443	WriteCIFitem(self.fp, '\ndata_'+self.CIFname+"_sx_"+str(i))
2444	#instnam = histblk["Instrument Parameters"][0]['InstrName']
2445	WriteCIFitem(self.fp, '# Information for histogram '+str(i)+': '+hist)
2446	WriteCIFitem(self.fp, '_pd_block_id',datablockidDict[hist])
2447	histprm = self.Histograms[hist]["Instrument Parameters"][0]
2448	writeCIFtemplate(histprm,'single',histprm['InstrName']) # single crystal template
2449	WriteSingleXtalData(hist)
2450
2451	dlg.Destroy()
2452
2453	WriteCIFitem(self.fp, '#--' + 15*'eof--' + '#')
2454	#self.CloseFile()
2455	print("...export completed")
2456	print('file '+self.fullpath)
2457	# end of CIF export
2458
2459	class ExportProjectCIF(ExportCIF):
2460	'''Used to create a CIF of an entire project
2461
2462	:param wx.Frame G2frame: reference to main GSAS-II frame
2463	'''
2464	def __init__(self,G2frame):
2465	ExportCIF.__init__(self,
2466	G2frame=G2frame,
2467	formatName = 'Full CIF',
2468	extension='.cif',
2469	longFormatName = 'Export project as CIF'
2470	)
2471	self.exporttype = ['project']
2472
2473	def Exporter(self,event=None):
2474	self._Exporter(event=event)
2475	self.CloseFile()
2476
2477	# def Writer(self,hist,mode='w'):
2478	# '''Used for full project CIF export of a sequential fit.
2479	# TODO: Needs extensive work
2480	# '''
2481	# # set the project file name
2482	# self.CIFname = os.path.splitext(
2483	# os.path.split(self.G2frame.GSASprojectfile)[1]
2484	# )[0]+'_'+hist
2485	# self.CIFname = self.CIFname.replace(' ','')
2486	# self.OpenFile(mode=mode)
2487	# self._Exporter(IncludeOnlyHist=hist)
2488	# if mode == 'w':
2489	# print('CIF written to file '+self.fullpath)
2490	# self.CloseFile()
2491
2492	class ExportPhaseCIF(ExportCIF):
2493	'''Used to create a simple CIF with one phase. Uses exact same code as
2494	:class:`ExportCIF` except that `phaseOnly` is set for the Exporter
2495	Shows up in menu as Quick CIF.
2496
2497	:param wx.Frame G2frame: reference to main GSAS-II frame
2498	'''
2499	def __init__(self,G2frame):
2500	ExportCIF.__init__(self,
2501	G2frame=G2frame,
2502	formatName = 'Quick CIF',
2503	extension='.cif',
2504	longFormatName = 'Export one phase in CIF'
2505	)
2506	self.exporttype = ['phase']
2507	# CIF-specific items
2508	self.author = ''
2509
2510	def Exporter(self,event=None):
2511	# get a phase and file name
2512	# the export process starts here
2513	self.InitExport(event)
2514	# load all of the tree into a set of dicts
2515	self.loadTree()
2516	# create a dict with refined values and their uncertainties
2517	self.loadParmDict()
2518	self.multiple = True
2519	self.currentExportType = 'phase'
2520	if self.ExportSelect('ask'): return
2521	self.OpenFile()
2522	for name in self.phasenam:
2523	self._Exporter(event=event,phaseOnly=name) #TODO: repeat for magnetic phase
2524	self.CloseFile()
2525
2526	def Writer(self,hist,phasenam,mode='w'):
2527	# set the project file name
2528	self.CIFname = os.path.splitext(
2529	os.path.split(self.G2frame.GSASprojectfile)[1]
2530	)[0]+'_'+phasenam+'_'+hist
2531	self.CIFname = self.CIFname.replace(' ','')
2532	self.OpenFile(mode=mode)
2533	self._Exporter(phaseOnly=phasenam)
2534	self.CloseFile()
2535
2536	class ExportPwdrCIF(ExportCIF):
2537	'''Used to create a simple CIF containing diffraction data only. Uses exact same code as
2538	:class:`ExportCIF` except that `histOnly` is set for the Exporter
2539	Shows up in menu as Quick CIF.
2540
2541	:param wx.Frame G2frame: reference to main GSAS-II frame
2542	'''
2543	def __init__(self,G2frame):
2544	ExportCIF.__init__(self,
2545	G2frame=G2frame,
2546	formatName = 'Data-only CIF',
2547	extension='.cif',
2548	longFormatName = 'Export data as CIF'
2549	)
2550	if G2frame is None: raise AttributeError('CIF export requires data tree') # prevent use from Scriptable
2551	self.exporttype = ['powder']
2552	# CIF-specific items
2553	self.author = ''
2554
2555	def Exporter(self,event=None):
2556	self.InitExport(event)
2557	# load all of the tree into a set of dicts
2558	self.currentExportType = None
2559	self.loadTree()
2560	self.currentExportType = 'powder'
2561	# create a dict with refined values and their uncertainties
2562	self.loadParmDict()
2563	self.multiple = False
2564	if self.ExportSelect( # set export parameters
2565	AskFile='ask' # get a file name/directory to save in
2566	): return
2567	self.OpenFile()
2568	self._Exporter(event=event,histOnly=self.histnam[0])
2569
2570	def Writer(self,hist,mode='w'):
2571	'''Used for histogram CIF export of a sequential fit.
2572	'''
2573	# set the project file name
2574	self.CIFname = os.path.splitext(
2575	os.path.split(self.G2frame.GSASprojectfile)[1]
2576	)[0]+'_'+hist
2577	self.CIFname = self.CIFname.replace(' ','')
2578	self.OpenFile(mode=mode)
2579	self._Exporter(histOnly=hist)
2580	if mode == 'w':
2581	print('CIF written to file '+self.fullpath)
2582	self.CloseFile()
2583
2584	class ExportHKLCIF(ExportCIF):
2585	'''Used to create a simple CIF containing diffraction data only. Uses exact same code as
2586	:class:`ExportCIF` except that `histOnly` is set for the Exporter
2587	Shows up in menu as Quick CIF.
2588
2589	:param wx.Frame G2frame: reference to main GSAS-II frame
2590	'''
2591	def __init__(self,G2frame):
2592	ExportCIF.__init__(self,
2593	G2frame=G2frame,
2594	formatName = 'Data-only CIF',
2595	extension='.cif',
2596	longFormatName = 'Export data as CIF'
2597	)
2598	self.exporttype = ['single']
2599	# CIF-specific items
2600	self.author = ''
2601
2602	def Exporter(self,event=None):
2603	self.InitExport(event)
2604	# load all of the tree into a set of dicts
2605	self.currentExportType = None
2606	self.loadTree()
2607	self.currentExportType = 'single'
2608	# create a dict with refined values and their uncertainties
2609	self.loadParmDict()
2610	self.multiple = False
2611	if self.ExportSelect( # set export parameters
2612	AskFile='ask' # get a file name/directory to save in
2613	): return
2614	self.OpenFile()
2615	self._Exporter(event=event,histOnly=self.histnam[0])
2616
2617	#===============================================================================
2618	# misc CIF utilities
2619	#===============================================================================
2620	def PickleCIFdict(fil):
2621	'''Loads a CIF dictionary, cherry picks out the items needed
2622	by local code and sticks them into a python dict and writes
2623	that dict out as a pickle file for later reuse.
2624	If the write fails a warning message is printed,
2625	but no exception occurs.
2626
2627	:param str fil: file name of CIF dictionary, will usually end
2628	in .dic
2629	:returns: the dict with the definitions
2630	'''
2631	import CifFile as cif # PyCifRW from James Hester
2632	cifdic = {}
2633	try:
2634	fp = open(fil,'r') # patch: open file to avoid windows bug
2635	dictobj = cif.CifDic(fp)
2636	fp.close()
2637	except IOError:
2638	dictobj = cif.CifDic(fil)
2639	if DEBUG: print('loaded '+fil)
2640	for item in dictobj.keys():
2641	cifdic[item] = {}
2642	for j in (
2643	'_definition','_type',
2644	'_enumeration',
2645	'_enumeration_detail',
2646	'_enumeration_range'):
2647	if dictobj[item].get(j):
2648	cifdic[item][j] = dictobj[item][j]
2649	try:
2650	fil = os.path.splitext(fil)[0]+'.cpickle'
2651	fp = open(fil,'w')
2652	pickle.dump(cifdic,fp)
2653	fp.close()
2654	if DEBUG: print('wrote '+fil)
2655	except:
2656	print ('Unable to write '+fil)
2657	return cifdic
2658
2659	def LoadCIFdic():
2660	'''Create a composite core+powder CIF lookup dict containing
2661	information about all items in the CIF dictionaries, loading
2662	pickled files if possible. The routine looks for files
2663	named cif_core.cpickle and cif_pd.cpickle in every
2664	directory in the path and if they are not found, files
2665	cif_core.dic and/or cif_pd.dic are read.
2666
2667	:returns: the dict with the definitions
2668	'''
2669	cifdic = {}
2670	for ftyp in "cif_core","cif_pd":
2671	for loc in sys.path:
2672	fil = os.path.join(loc,ftyp+".cpickle")
2673	if not os.path.exists(fil): continue
2674	fp = open(fil,'r')
2675	try:
2676	cifdic.update(pickle.load(fp))
2677	if DEBUG: print('reloaded '+fil)
2678	break
2679	finally:
2680	fp.close()
2681	else:
2682	for loc in sys.path:
2683	fil = os.path.join(loc,ftyp+".dic")
2684	if not os.path.exists(fil): continue
2685	#try:
2686	if True:
2687	cifdic.update(PickleCIFdict(fil))
2688	break
2689	#except:
2690	# pass
2691	else:
2692	print('Could not load '+ftyp+' dictionary')
2693	return cifdic
2694
2695	class CIFdefHelp(wx.Button):
2696	'''Create a help button that displays help information on
2697	the current data item
2698
2699	:param parent: the panel which will be the parent of the button
2700	:param str msg: the help text to be displayed
2701	:param wx.Dialog helpwin: Frame for CIF editing dialog
2702	:param wx.TextCtrl helptxt: TextCtrl where help text is placed
2703	'''
2704	def __init__(self,parent,msg,helpwin,helptxt):
2705	wx.Button.__init__(self,parent,wx.ID_HELP)
2706	self.Bind(wx.EVT_BUTTON,self._onPress)
2707	self.msg=msg
2708	self.parent = parent
2709	#self.helpwin = self.parent.helpwin
2710	self.helpwin = helpwin
2711	self.helptxt = helptxt
2712	def _onPress(self,event):
2713	'Respond to a button press by displaying the requested text'
2714	try:
2715	#helptxt = self.helptxt
2716	ow,oh = self.helptxt.GetSize()
2717	self.helptxt.SetLabel(self.msg)
2718	w,h = self.helptxt.GetSize()
2719	if h > oh:
2720	self.helpwin.GetSizer().Fit(self.helpwin)
2721	except: # error posting help, ignore
2722	return
2723
2724	def CIF2dict(cf):
2725	'''copy the contents of a CIF out from a PyCifRW block object
2726	into a dict
2727
2728	:returns: cifblk, loopstructure where cifblk is a dict with
2729	CIF items and loopstructure is a list of lists that defines
2730	which items are in which loops.
2731	'''
2732	blk = cf.keys()[0] # assume templates are a single CIF block, use the 1st
2733	loopstructure = cf[blk].loopnames()[:] # copy over the list of loop contents
2734	dblk = {}
2735	for item in cf[blk].keys(): # make a copy of all the items in the block
2736	dblk[item] = cf[blk][item]
2737	return dblk,loopstructure
2738
2739	def dict2CIF(dblk,loopstructure,blockname='Template'):
2740	'''Create a PyCifRW CIF object containing a single CIF
2741	block object from a dict and loop structure list.
2742
2743	:param dblk: a dict containing values for each CIF item
2744	:param list loopstructure: a list of lists containing the contents of
2745	each loop, as an example::
2746
2747	[ ["_a","_b"], ["_c"], ["_d_1","_d_2","_d_3"]]
2748
2749	this describes a CIF with this type of structure::
2750
2751	loop_ _a _b <a1> <b1> <a2> ...
2752	loop_ _c <c1> <c2>...
2753	loop _d_1 _d_2 _d_3 ...
2754
2755	Note that the values for each looped CIF item, such as _a,
2756	are contained in a list, for example as cifblk["_a"]
2757
2758	:param str blockname: an optional name for the CIF block.
2759	Defaults to 'Template'
2760
2761	:returns: the newly created PyCifRW CIF object
2762	'''
2763
2764	import CifFile as cif # PyCifRW from James Hester
2765	# compile a 'list' of items in loops
2766	loopnames = set()
2767	for i in loopstructure:
2768	loopnames \|= set(i)
2769	# create a new block
2770	newblk = cif.CifBlock()
2771	# add the looped items
2772	for keys in loopstructure:
2773	vals = []
2774	for key in keys:
2775	vals.append(dblk[key])
2776	newblk.AddCifItem(([keys],[vals]))
2777	# add the non-looped items
2778	for item in dblk:
2779	if item in loopnames: continue
2780	newblk[item] = dblk[item]
2781	# create a CIF and add the block
2782	newcf = cif.CifFile()
2783	newcf[blockname] = newblk
2784	return newcf
2785
2786
2787	class EditCIFtemplate(wx.Dialog):
2788	'''Create a dialog for editing a CIF template. The edited information is
2789	placed in cifblk. If the CIF is saved as a file, the name of that file
2790	is saved as ``self.newfile``.
2791
2792	:param wx.Frame parent: parent frame or None
2793	:param cifblk: dict or PyCifRW block containing values for each CIF item
2794	:param list loopstructure: a list of lists containing the contents of
2795	each loop, as an example::
2796
2797	[ ["_a","_b"], ["_c"], ["_d_1","_d_2","_d_3"]]
2798
2799	this describes a CIF with this type of structure::
2800
2801	loop_ _a _b <a1> <b1> <a2> ...
2802	loop_ _c <c1> <c2>...
2803	loop _d_1 _d_2 _d_3 ...
2804
2805	Note that the values for each looped CIF item, such as _a,
2806	are contained in a list, for example as cifblk["_a"]
2807
2808	:param str defaultname: specifies the default file name to be used for
2809	saving the CIF.
2810	'''
2811	def __init__(self,parent,cifblk,loopstructure,defaultname):
2812	OKbuttons = []
2813	self.cifblk = cifblk
2814	self.loopstructure = loopstructure
2815	self.newfile = None
2816	self.defaultname = defaultname
2817	global CIFdic # once this is loaded, keep it around
2818	if CIFdic is None:
2819	CIFdic = LoadCIFdic()
2820	wx.Dialog.__init__(self,parent,style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
2821
2822	# define widgets that will be needed during panel creation
2823	self.helptxt = wx.StaticText(self,wx.ID_ANY,"")
2824	savebtn = wx.Button(self, wx.ID_CLOSE, "Save as template")
2825	OKbuttons.append(savebtn)
2826	savebtn.Bind(wx.EVT_BUTTON,self._onSave)
2827	OKbtn = wx.Button(self, wx.ID_OK, "Use")
2828	OKbtn.SetDefault()
2829	OKbuttons.append(OKbtn)
2830
2831	self.SetTitle('Edit items in CIF template')
2832	vbox = wx.BoxSizer(wx.VERTICAL)
2833	cpnl = EditCIFpanel(self,cifblk,loopstructure,CIFdic,OKbuttons,size=(300,300))
2834	vbox.Add(cpnl, 1, wx.ALIGN_LEFT\|wx.ALL\|wx.EXPAND, 0)
2835	G2G.HorizontalLine(vbox,self)
2836	vbox.Add(self.helptxt, 0, wx.EXPAND\|wx.ALL, 5)
2837	G2G.HorizontalLine(vbox,self)
2838	btnsizer = wx.BoxSizer(wx.HORIZONTAL)
2839	btn = wx.Button(self, wx.ID_CANCEL)
2840	btnsizer.Add(btn,0,wx.ALIGN_CENTER\|wx.ALL)
2841	btnsizer.Add(savebtn,0,wx.ALIGN_CENTER\|wx.ALL)
2842	btnsizer.Add(OKbtn,0,wx.ALIGN_CENTER\|wx.ALL)
2843	vbox.Add(btnsizer, 0, wx.ALIGN_CENTER\|wx.ALL, 5)
2844	self.SetSizer(vbox)
2845	vbox.Fit(self)
2846	def Post(self):
2847	'''Display the dialog
2848
2849	:returns: True unless Cancel has been pressed.
2850	'''
2851	return (self.ShowModal() == wx.ID_OK)
2852	def _onSave(self,event):
2853	'Save CIF entries in a template file'
2854	pth = G2G.GetExportPath(self.G2frame)
2855	dlg = wx.FileDialog(
2856	self, message="Save as CIF template",
2857	defaultDir=pth,
2858	defaultFile=self.defaultname,
2859	wildcard="CIF (.cif)\|.cif",
2860	style=wx.SAVE)
2861	val = (dlg.ShowModal() == wx.ID_OK)
2862	fil = dlg.GetPath()
2863	dlg.Destroy()
2864	if val: # ignore a Cancel button
2865	fil = os.path.splitext(fil)[0]+'.cif' # force extension
2866	fp = open(fil,'w')
2867	newcf = dict2CIF(self.cifblk,self.loopstructure)
2868	fp.write(newcf.WriteOut())
2869	fp.close()
2870	self.newfile = fil
2871	self.EndModal(wx.ID_OK)
2872
2873	class EditCIFpanel(wxscroll.ScrolledPanel):
2874	'''Creates a scrolled panel for editing CIF template items
2875
2876	:param wx.Frame parent: parent frame where panel will be placed
2877	:param cifblk: dict or PyCifRW block containing values for each CIF item
2878	:param list loopstructure: a list of lists containing the contents of
2879	each loop, as an example::
2880
2881	[ ["_a","_b"], ["_c"], ["_d_1","_d_2","_d_3"]]
2882
2883	this describes a CIF with this type of structure::
2884
2885	loop_ _a _b <a1> <b1> <a2> ...
2886	loop_ _c <c1> <c2>...
2887	loop _d_1 _d_2 _d_3 ...
2888
2889	Note that the values for each looped CIF item, such as _a,
2890	are contained in a list, for example as cifblk["_a"]
2891
2892	:param dict cifdic: optional CIF dictionary definitions
2893	:param list OKbuttons: A list of wx.Button objects that should
2894	be disabled when information in the CIF is invalid
2895	:param (other): optional keyword parameters for wx.ScrolledPanel
2896	'''
2897	def __init__(self, parent, cifblk, loopstructure, cifdic={}, OKbuttons=[], **kw):
2898	self.parent = parent
2899	wxscroll.ScrolledPanel.__init__(self, parent, wx.ID_ANY, **kw)
2900	self.vbox = None
2901	self.AddDict = None
2902	self.cifdic = cifdic
2903	self.cifblk = cifblk
2904	self.loops = loopstructure
2905	self.parent = parent
2906	self.LayoutCalled = False
2907	self.parentOKbuttons = OKbuttons
2908	self.ValidatedControlsList = []
2909	self._fill()
2910	def _fill(self):
2911	'Fill the scrolled panel with widgets for each CIF item'
2912	wx.BeginBusyCursor()
2913	self.AddDict = {}
2914	self.ValidatedControlsList = []
2915	# delete any only contents
2916	if self.vbox:
2917	if 'phoenix' in wx.version():
2918	self.vbox.Clear(True)
2919	else:
2920	self.vbox.DeleteWindows()
2921	self.vbox = None
2922	self.Update()
2923	vbox = wx.BoxSizer(wx.VERTICAL)
2924	self.vbox = vbox
2925	# compile a 'list' of items in loops
2926	loopnames = set()
2927	for i in self.loops:
2928	loopnames \|= set(i)
2929	# post the looped CIF items
2930	for lnum,lp in enumerate(self.loops):
2931	hbox = wx.BoxSizer(wx.HORIZONTAL)
2932	hbox.Add(wx.StaticText(self,wx.ID_ANY,'Loop '+str(lnum+1)))
2933	vbox.Add(hbox)
2934	but = wx.Button(self,wx.ID_ANY,"Add row")
2935	self.AddDict[but]=lnum
2936
2937	hbox.Add(but)
2938	but.Bind(wx.EVT_BUTTON,self.OnAddRow)
2939	fbox = wx.GridBagSizer(0, 0)
2940	vbox.Add(fbox)
2941	rows = 0
2942	for i,item in enumerate(lp):
2943	txt = wx.StaticText(self,wx.ID_ANY,item+" ")
2944	fbox.Add(txt,(0,i+1))
2945	# if self.cifdic.get(item):
2946	# df = self.cifdic[item].get('_definition')
2947	# if df:
2948	# txt.SetToolTipString(G2IO.trim(df))
2949	# but = CIFdefHelp(self,
2950	# "Definition for "+item+":\n\n"+G2IO.trim(df),
2951	# self.parent,
2952	# self.parent.helptxt)
2953	# fbox.Add(but,(1,i+1),flag=wx.ALIGN_CENTER)
2954	for j,val in enumerate(self.cifblk[item]):
2955	ent = self.CIFEntryWidget(self.cifblk[item],j,item)
2956	#fbox.Add(ent,(j+2,i+1),flag=wx.EXPAND\|wx.ALL)
2957	fbox.Add(ent,(j+1,i+1),flag=wx.EXPAND\|wx.ALL)
2958	if self.cifdic.get(item):
2959	df = self.cifdic[item].get('_definition')
2960	if df:
2961	txt.SetToolTipString(G2IO.trim(df))
2962	but = CIFdefHelp(self,
2963	"Definition for "+item+":\n\n"+G2IO.trim(df),
2964	self.parent,
2965	self.parent.helptxt)
2966	fbox.Add(but,(j+2,i+1),flag=wx.ALIGN_CENTER)
2967	rows = max(rows,len(self.cifblk[item]))
2968	for i in range(rows):
2969	txt = wx.StaticText(self,wx.ID_ANY,str(i+1))
2970	fbox.Add(txt,(i+2,0))
2971	line = wx.StaticLine(self,wx.ID_ANY, size=(-1,3), style=wx.LI_HORIZONTAL)
2972	vbox.Add(line, 0, wx.EXPAND\|wx.ALIGN_CENTER\|wx.ALL, 10)
2973
2974	# post the non-looped CIF items
2975	for item in sorted(self.cifblk.keys()):
2976	if item not in loopnames:
2977	hbox = wx.BoxSizer(wx.HORIZONTAL)
2978	vbox.Add(hbox)
2979	txt = wx.StaticText(self,wx.ID_ANY,item)
2980	hbox.Add(txt)
2981	ent = self.CIFEntryWidget(self.cifblk,item,item)
2982	hbox.Add(ent)
2983	if self.cifdic.get(item):
2984	df = self.cifdic[item].get('_definition')
2985	if df:
2986	txt.SetToolTipString(G2IO.trim(df))
2987	but = CIFdefHelp(self,
2988	"Definition for "+item+":\n\n"+G2IO.trim(df),
2989	self.parent,
2990	self.parent.helptxt)
2991	hbox.Add(but,0,wx.ALL,2)
2992	self.SetSizer(vbox)
2993	#vbox.Fit(self.parent)
2994	self.SetAutoLayout(1)
2995	self.SetupScrolling()
2996	self.Bind(rw.EVT_RW_LAYOUT_NEEDED, self.OnLayoutNeeded)
2997	self.Layout()
2998	wx.EndBusyCursor()
2999	def OnLayoutNeeded(self,event):
3000	'''Called when an update of the panel layout is needed. Calls
3001	self.DoLayout after the current operations are complete using
3002	CallAfter. This is called only once, according to flag
3003	self.LayoutCalled, which is cleared in self.DoLayout.
3004	'''
3005	if self.LayoutCalled: return # call already queued
3006	wx.CallAfter(self.DoLayout) # queue a call
3007	self.LayoutCalled = True
3008	def DoLayout(self):
3009	'''Update the Layout and scroll bars for the Panel. Clears
3010	self.LayoutCalled so that next change to panel can
3011	request a new update
3012	'''
3013	wx.BeginBusyCursor()
3014	self.Layout()
3015	self.SetupScrolling()
3016	wx.EndBusyCursor()
3017	self.LayoutCalled = False
3018	def OnAddRow(self,event):
3019	'add a row to a loop'
3020	lnum = self.AddDict.get(event.GetEventObject())
3021	if lnum is None: return
3022	for item in self.loops[lnum]:
3023	self.cifblk[item].append('?')
3024	self._fill()
3025
3026	def ControlOKButton(self,setvalue):
3027	'''Enable or Disable the OK button(s) for the dialog. Note that this is
3028	passed into the ValidatedTxtCtrl for use by validators.
3029
3030	:param bool setvalue: if True, all entries in the dialog are
3031	checked for validity. The first invalid control triggers
3032	disabling of buttons.
3033	If False then the OK button(s) are disabled with no checking
3034	of the invalid flag for each control.
3035	'''
3036	if setvalue: # turn button on, do only if all controls show as valid
3037	for ctrl in self.ValidatedControlsList:
3038	if ctrl.invalid:
3039	for btn in self.parentOKbuttons:
3040	btn.Disable()
3041	return
3042	else:
3043	for btn in self.parentOKbuttons:
3044	btn.Enable()
3045	else:
3046	for btn in self.parentOKbuttons:
3047	btn.Disable()
3048
3049	def CIFEntryWidget(self,dct,item,dataname):
3050	'''Create an entry widget for a CIF item. Use a validated entry for numb values
3051	where int is required when limits are integers and floats otherwise.
3052	At present this does not allow entry of the special CIF values of "." and "?" for
3053	numerical values and highlights them as invalid.
3054	Use a selection widget when there are specific enumerated values for a string.
3055	'''
3056	if self.cifdic.get(dataname):
3057	if self.cifdic[dataname].get('_enumeration'):
3058	values = ['?']+self.cifdic[dataname]['_enumeration']
3059	choices = ['undefined']
3060	for i in self.cifdic[dataname].get('_enumeration_detail',values):
3061	choices.append(G2IO.trim(i))
3062	ent = G2G.EnumSelector(self, dct, item, choices, values, size=(200, -1))
3063	return ent
3064	if self.cifdic[dataname].get('_type') == 'numb':
3065	mn = None
3066	mx = None
3067	hint = int
3068	if self.cifdic[dataname].get('_enumeration_range'):
3069	rng = self.cifdic[dataname]['_enumeration_range'].split(':')
3070	if '.' in rng[0] or '.' in rng[1]: hint = float
3071	if rng[0]: mn = hint(rng[0])
3072	if rng[1]: mx = hint(rng[1])
3073	ent = G2G.ValidatedTxtCtrl(
3074	self,dct,item,typeHint=hint,min=mn,max=mx,
3075	CIFinput=True,ASCIIonly=True,
3076	OKcontrol=self.ControlOKButton)
3077	self.ValidatedControlsList.append(ent)
3078	return ent
3079	rw1 = rw.ResizeWidget(self)
3080	ent = G2G.ValidatedTxtCtrl(
3081	rw1,dct,item,size=(100, 20),
3082	style=wx.TE_MULTILINE\|wx.TE_PROCESS_ENTER,
3083	CIFinput=True,ASCIIonly=True,
3084	OKcontrol=self.ControlOKButton)
3085	self.ValidatedControlsList.append(ent)
3086	return rw1
3087
3088	class CIFtemplateSelect(wx.BoxSizer):
3089	'''Create a set of buttons to show, select and edit a CIF template
3090
3091	:param frame: wx.Frame object of parent
3092	:param panel: wx.Panel object where widgets should be placed
3093	:param str tmplate: one of 'publ', 'phase', or 'instrument' to determine
3094	the type of template
3095	:param dict G2dict: GSAS-II dict where CIF should be placed. The key
3096	"CIF_template" will be used to store either a list or a string.
3097	If a list, it will contain a dict and a list defining loops. If
3098	an str, it will contain a file name.
3099	:param function repaint: reference to a routine to be called to repaint
3100	the frame after a change has been made
3101	:param str title: A line of text to show at the top of the window
3102	:param str defaultname: specifies the default file name to be used for
3103	saving the CIF.
3104	'''
3105	def __init__(self,frame,panel,tmplate,G2dict, repaint, title, defaultname=''):
3106	wx.BoxSizer.__init__(self,wx.VERTICAL)
3107	self.cifdefs = frame
3108	self.dict = G2dict
3109	self.repaint = repaint
3110	templateDefName = 'template_'+tmplate+'.cif'
3111	self.CIF = G2dict.get("CIF_template")
3112	if defaultname:
3113	self.defaultname = G2obj.StripUnicode(defaultname)
3114	self.defaultname = re.sub(r'[^a-zA-Z0-9_-]','',self.defaultname)
3115	self.defaultname = tmplate + "_" + self.defaultname + ".cif"
3116	else:
3117	self.defaultname = ''
3118
3119	txt = wx.StaticText(panel,wx.ID_ANY,title)
3120	self.Add(txt,0,wx.ALIGN_CENTER)
3121	# change font on title
3122	txtfnt = txt.GetFont()
3123	txtfnt.SetWeight(wx.BOLD)
3124	txtfnt.SetPointSize(2+txtfnt.GetPointSize())
3125	txt.SetFont(txtfnt)
3126	self.Add((-1,3))
3127
3128	if not self.CIF: # empty or None
3129	for pth in [os.getcwd()]+sys.path:
3130	fil = os.path.join(pth,self.defaultname)
3131	if os.path.exists(fil) and self.defaultname:
3132	self.CIF = fil
3133	CIFtxt = "Template: "+self.defaultname
3134	break
3135	else:
3136	for pth in sys.path:
3137	fil = os.path.join(pth,templateDefName)
3138	if os.path.exists(fil):
3139	self.CIF = fil
3140	CIFtxt = "Template: "+templateDefName
3141	break
3142	else:
3143	print("Default CIF template "+self.defaultname+' not found in path!')
3144	self.CIF = None
3145	CIFtxt = "none! (No template found)"
3146	elif type(self.CIF) is not list and type(self.CIF) is not tuple:
3147	if not os.path.exists(self.CIF):
3148	print("Error: template file has disappeared: "+self.CIF)
3149	self.CIF = None
3150	CIFtxt = "none! (file not found)"
3151	else:
3152	if len(self.CIF) < 50:
3153	CIFtxt = "File: "+self.CIF
3154	else:
3155	CIFtxt = "File: ..."+self.CIF[-50:]
3156	else:
3157	CIFtxt = "Template is customized"
3158	# show template source
3159	self.Add(wx.StaticText(panel,wx.ID_ANY,CIFtxt))
3160	# show str, button to select file; button to edit (if CIF defined)
3161	but = wx.Button(panel,wx.ID_ANY,"Select Template File")
3162	but.Bind(wx.EVT_BUTTON,self._onGetTemplateFile)
3163	hbox = wx.BoxSizer(wx.HORIZONTAL)
3164	hbox.Add(but,0,0,2)
3165	but = wx.Button(panel,wx.ID_ANY,"Edit Template")
3166	but.Bind(wx.EVT_BUTTON,self._onEditTemplateContents)
3167	if self.CIF is None: but.Disable() # nothing to edit!
3168	hbox.Add(but,0,0,2)
3169	self.Add(hbox)
3170	def _onGetTemplateFile(self,event):
3171	'select a template file'
3172	pth = G2G.GetImportPath(self.G2frame)
3173	if not pth: pth = '.'
3174	dlg = wx.FileDialog(
3175	self.cifdefs, message="Read CIF template file",
3176	defaultDir=pth,
3177	defaultFile=self.defaultname,
3178	wildcard="CIF (.cif)\|.cif",
3179	style=wx.OPEN)
3180	ret = dlg.ShowModal()
3181	fil = dlg.GetPath()
3182	dlg.Destroy()
3183	if ret == wx.ID_OK:
3184	cf = G2IO.ReadCIF(fil)
3185	if len(cf.keys()) == 0:
3186	raise Exception("No CIF data_ blocks found")
3187	if len(cf.keys()) != 1:
3188	raise Exception('Error, CIF Template has more than one block: '+fil)
3189	self.dict["CIF_template"] = fil
3190	self.repaint() #EditCIFDefaults()
3191
3192	def _onEditTemplateContents(self,event):
3193	'Called to edit the contents of a CIF template'
3194	if type(self.CIF) is list or type(self.CIF) is tuple:
3195	dblk,loopstructure = copy.deepcopy(self.CIF) # don't modify original
3196	else:
3197	cf = G2IO.ReadCIF(self.CIF)
3198	dblk,loopstructure = CIF2dict(cf)
3199	dlg = EditCIFtemplate(self.cifdefs,dblk,loopstructure,self.defaultname)
3200	val = dlg.Post()
3201	if val:
3202	if dlg.newfile: # results saved in file
3203	self.dict["CIF_template"] = dlg.newfile
3204	else:
3205	self.dict["CIF_template"] = [dlg.cifblk,dlg.loopstructure]
3206	self.repaint() #EditCIFDefaults() # note that this does a dlg.Destroy()
3207	else:
3208	dlg.Destroy()
3209
3210	#===============================================================================
3211	# end of misc CIF utilities
3212	#===============================================================================

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