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source: trunk/exports/G2export_CIF.py @ 2143

Last change on this file since 2143 was 2143, checked in by vondreele, 8 years ago
fix cif UIJ order of keys - values OK work on hkl merge all but 321 & -62m are ok fix issues in G2imgGUI
Property svn:eol-style set to `native` Property svn:keywords set to `Date Author Revision URL Id`
File size: 119.8 KB

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1	#!/usr/bin/env python
2	# -- coding: utf-8 --
3	########### SVN repository information ###################
4	# $Date: 2016-02-10 17:12:20 +0000 (Wed, 10 Feb 2016) $
5	# $Author: vondreele $
6	# $Revision: 2143 $
7	# $URL: trunk/exports/G2export_CIF.py $
8	# $Id: G2export_CIF.py 2143 2016-02-10 17:12:20Z vondreele $
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 two subclasses of :class:`ExportCIF`:
17	:class:`ExportPhaseCIF` and :class:`ExportDataCIF` that
18	export a single phase or data set. Note that ``self.mode`` determines
19	what is written:
20
21	* `self.mode="simple"` creates a simple CIF with only coordinates
22	or data, while
23
24	* `self.mode="full"` creates a complete CIF of project.
25
26	'''
27
28	import datetime as dt
29	import os.path
30	import sys
31	import numpy as np
32	import cPickle
33	import copy
34	import re
35	import wx
36	import wx.lib.scrolledpanel as wxscroll
37	import wx.lib.resizewidget as rw
38	import GSASIIpath
39	GSASIIpath.SetVersionNumber("$Revision: 2143 $")
40	import GSASIIIO as G2IO
41	import GSASIIgrid as G2gd
42	import GSASIIctrls as G2ctrls
43	import GSASIIstrIO as G2stIO
44	import GSASIImath as G2mth
45	import GSASIIlattice as G2lat
46	import GSASIIspc as G2spc
47	import GSASIIphsGUI as G2pg
48	import GSASIIstrMain as G2stMn
49	import GSASIIctrls as G2G
50
51	DEBUG = False #True to skip printing of reflection/powder profile lists
52
53	CIFdic = None
54
55	class ExportCIF(G2IO.ExportBaseclass):
56	'''Used to create a CIF of an entire project
57
58	:param wx.Frame G2frame: reference to main GSAS-II frame
59	'''
60	def __init__(self,G2frame):
61	super(self.__class__,self).__init__( # fancy way to say <parentclass>.__init__
62	G2frame=G2frame,
63	formatName = 'Full CIF',
64	extension='.cif',
65	longFormatName = 'Export project as CIF'
66	)
67	self.exporttype = ['project']
68	self.author = ''
69	self.mode = 'full'
70
71	def Exporter(self,event=None):
72	'''Export a CIF. Export can be full or simple (as set by self.mode).
73	"simple" skips data, distances & angles, etc. and can only include
74	a single phase while "full" is intended for for publication submission.
75	'''
76
77	#***** define functions for export method =======================================
78	def WriteCIFitem(name,value=''):
79	'''Write CIF data items to the file. Formats values as needed.
80	Also used without a value for loops, comments, loop headers, etc.
81	'''
82	if value:
83	if "\n" in value or len(value)> 70:
84	if name.strip(): self.fp.write(name+'\n')
85	self.fp.write('; '+value+'\n')
86	self.fp.write('; '+'\n')
87	elif " " in value:
88	if len(name)+len(value) > 65:
89	self.fp.write(name + '\n ' + '"' + str(value) + '"'+'\n')
90	else:
91	self.fp.write(name + ' ' + '"' + str(value) + '"'+'\n')
92	else:
93	if len(name)+len(value) > 65:
94	self.fp.write(name+'\n ' + value+'\n')
95	else:
96	self.fp.write(name+' ' + value+'\n')
97	else:
98	self.fp.write(name+'\n')
99
100	def WriteAudit():
101	'Write the CIF audit values. Perhaps should be in a single element loop.'
102	WriteCIFitem('_audit_creation_method',
103	'created in GSAS-II')
104	WriteCIFitem('_audit_creation_date',self.CIFdate)
105	if self.author:
106	WriteCIFitem('_audit_author_name',self.author)
107	WriteCIFitem('_audit_update_record',
108	self.CIFdate+' Initial software-generated CIF')
109
110	def WriteOverall():
111	'''Write out overall refinement information.
112
113	More could be done here, but this is a good start.
114	'''
115	if self.ifPWDR:
116	WriteCIFitem('_pd_proc_info_datetime', self.CIFdate)
117	WriteCIFitem('_pd_calc_method', 'Rietveld Refinement')
118	#WriteCIFitem('_refine_ls_shift/su_max',DAT1)
119	#WriteCIFitem('_refine_ls_shift/su_mean',DAT2)
120	WriteCIFitem('_computing_structure_refinement','GSAS-II (Toby & Von Dreele, J. Appl. Cryst. 46, 544-549, 2013)')
121	if self.ifHKLF:
122	controls = self.OverallParms['Controls']
123	if controls['F**2']:
124	thresh = 'F2>%.1fu(F2)'%(controls['minF/sig'])
125	else:
126	thresh = 'F>%.1fu(F)'%(controls['minF/sig'])
127	WriteCIFitem('_reflns_threshold_expression', thresh)
128	try:
129	vars = str(len(self.OverallParms['Covariance']['varyList']))
130	except:
131	vars = '?'
132	WriteCIFitem('_refine_ls_number_parameters',vars)
133	try:
134	GOF = G2mth.ValEsd(self.OverallParms['Covariance']['Rvals']['GOF'],-0.009)
135	except:
136	GOF = '?'
137	WriteCIFitem('_refine_ls_goodness_of_fit_all',GOF)
138
139	# get restraint info
140	# restraintDict = self.OverallParms.get('Restraints',{})
141	# for i in self.OverallParms['Constraints']:
142	# print i
143	# for j in self.OverallParms['Constraints'][i]:
144	# print j
145	#WriteCIFitem('_refine_ls_number_restraints',TEXT)
146	# other things to consider reporting
147	# _refine_ls_number_reflns
148	# _refine_ls_goodness_of_fit_obs
149	# _refine_ls_wR_factor_obs
150	# _refine_ls_restrained_S_all
151	# _refine_ls_restrained_S_obs
152
153	# include an overall profile r-factor, if there is more than one powder histogram
154	R = '%.5f'%(self.OverallParms['Covariance']['Rvals']['Rwp']/100.)
155	WriteCIFitem('\n# OVERALL WEIGHTED R-FACTOR')
156	WriteCIFitem('_refine_ls_wR_factor_obs',R)
157	# _refine_ls_R_factor_all
158	# _refine_ls_R_factor_obs
159	WriteCIFitem('_refine_ls_matrix_type','full')
160	#WriteCIFitem('_refine_ls_matrix_type','userblocks')
161
162	def writeCIFtemplate(G2dict,tmplate,defaultname=''):
163	'''Write out the selected or edited CIF template
164	An unedited CIF template file is copied, comments intact; an edited
165	CIF template is written out from PyCifRW which of course strips comments.
166	In all cases the initial data_ header is stripped (there should only be one!)
167	'''
168	CIFobj = G2dict.get("CIF_template")
169	if defaultname:
170	defaultname = defaultname.encode('ascii','replace').strip().replace(' ','_')
171	defaultname = re.sub(r'[^a-zA-Z0-9_-]','',defaultname)
172	defaultname = tmplate + "_" + defaultname + ".cif"
173	else:
174	defaultname = ''
175	templateDefName = 'template_'+tmplate+'.cif'
176	if not CIFobj: # copying a template
177	for pth in [os.getcwd()]+sys.path:
178	fil = os.path.join(pth,defaultname)
179	if os.path.exists(fil) and defaultname: break
180	else:
181	for pth in sys.path:
182	fil = os.path.join(pth,templateDefName)
183	if os.path.exists(fil): break
184	else:
185	print(CIFobj+' not found in path!')
186	return
187	fp = open(fil,'r')
188	txt = fp.read()
189	fp.close()
190	elif type(CIFobj) is not list and type(CIFobj) is not tuple:
191	if not os.path.exists(CIFobj):
192	print("Error: requested template file has disappeared: "+CIFobj)
193	return
194	fp = open(CIFobj,'r')
195	txt = fp.read()
196	fp.close()
197	else:
198	txt = dict2CIF(CIFobj[0],CIFobj[1]).WriteOut()
199	# remove the PyCifRW header, if present
200	#if txt.find('PyCifRW') > -1 and txt.find('data_') > -1:
201	txt = "# GSAS-II edited template follows "+txt[txt.index("data_")+5:]
202	#txt = txt.replace('data_','#')
203	WriteCIFitem(txt)
204
205	def FormatSH(phasenam):
206	'Format a full spherical harmonics texture description as a string'
207	phasedict = self.Phases[phasenam] # pointer to current phase info
208	pfx = str(phasedict['pId'])+'::'
209	s = ""
210	textureData = phasedict['General']['SH Texture']
211	if textureData.get('Order'):
212	s += "Spherical Harmonics correction. Order = "+str(textureData['Order'])
213	s += " Model: " + str(textureData['Model']) + "\n Orientation angles: "
214	for name in ['omega','chi','phi']:
215	aname = pfx+'SH '+name
216	s += name + " = "
217	sig = self.sigDict.get(aname,-0.09)
218	s += G2mth.ValEsd(self.parmDict[aname],sig)
219	s += "; "
220	s += "\n"
221	s1 = " Coefficients: "
222	for name in textureData['SH Coeff'][1]:
223	aname = pfx+name
224	if len(s1) > 60:
225	s += s1 + "\n"
226	s1 = " "
227	s1 += aname + ' = '
228	sig = self.sigDict.get(aname,-0.0009)
229	s1 += G2mth.ValEsd(self.parmDict[aname],sig)
230	s1 += "; "
231	s += s1
232	return s
233
234	def FormatHAPpo(phasenam):
235	'''return the March-Dollase/SH correction for every
236	histogram in the current phase formatted into a
237	character string
238	'''
239	phasedict = self.Phases[phasenam] # pointer to current phase info
240	s = ''
241	for histogram in sorted(phasedict['Histograms']):
242	if histogram.startswith("HKLF"): continue # powder only
243	Histogram = self.Histograms.get(histogram)
244	if not Histogram: continue
245	hapData = phasedict['Histograms'][histogram]
246	if hapData['Pref.Ori.'][0] == 'MD':
247	aname = str(phasedict['pId'])+':'+str(Histogram['hId'])+':MD'
248	if self.parmDict.get(aname,1.0) != 1.0: continue
249	sig = self.sigDict.get(aname,-0.009)
250	if s != "": s += '\n'
251	s += 'March-Dollase correction'
252	if len(self.powderDict) > 1:
253	s += ', histogram '+str(Histogram['hId']+1)
254	s += ' coef. = ' + G2mth.ValEsd(self.parmDict[aname],sig)
255	s += ' axis = ' + str(hapData['Pref.Ori.'][3])
256	else: # must be SH
257	if s != "": s += '\n'
258	s += 'Simple spherical harmonic correction'
259	if len(self.powderDict) > 1:
260	s += ', histogram '+str(Histogram['hId']+1)
261	s += ' Order = '+str(hapData['Pref.Ori.'][4])+'\n'
262	s1 = " Coefficients: "
263	for item in hapData['Pref.Ori.'][5]:
264	aname = str(phasedict['pId'])+':'+str(Histogram['hId'])+':'+item
265	if len(s1) > 60:
266	s += s1 + "\n"
267	s1 = " "
268	s1 += aname + ' = '
269	sig = self.sigDict.get(aname,-0.0009)
270	s1 += G2mth.ValEsd(self.parmDict[aname],sig)
271	s1 += "; "
272	s += s1
273	return s
274	def FormatBackground(bkg,hId):
275	'''Display the Background information as a descriptive text string.
276
277	TODO: this needs to be expanded to show the diffuse peak and
278	Debye term information as well. (Bob)
279
280	:returns: the text description (str)
281	'''
282	hfx = ':'+str(hId)+':'
283	fxn, bkgdict = bkg
284	terms = fxn[2]
285	txt = 'Background function: "'+fxn[0]+'" function with '+str(terms)+' terms:\n'
286	l = " "
287	for i,v in enumerate(fxn[3:]):
288	name = '%sBack;%d'%(hfx,i)
289	sig = self.sigDict.get(name,-0.009)
290	if len(l) > 60:
291	txt += l + '\n'
292	l = ' '
293	l += G2mth.ValEsd(v,sig)+', '
294	txt += l
295	if bkgdict['nDebye']:
296	txt += '\n Background Debye function parameters: A, R, U:'
297	names = ['A;','R;','U;']
298	for i in range(bkgdict['nDebye']):
299	txt += '\n '
300	for j in range(3):
301	name = hfx+'Debye'+names[j]+str(i)
302	sig = self.sigDict.get(name,-0.009)
303	txt += G2mth.ValEsd(bkgdict['debyeTerms'][i][2*j],sig)+', '
304	if bkgdict['nPeaks']:
305	txt += '\n Background peak parameters: pos, int, sig, gam:'
306	names = ['pos;','int;','sig;','gam;']
307	for i in range(bkgdict['nPeaks']):
308	txt += '\n '
309	for j in range(4):
310	name = hfx+'BkPk'+names[j]+str(i)
311	sig = self.sigDict.get(name,-0.009)
312	txt += G2mth.ValEsd(bkgdict['peaksList'][i][2*j],sig)+', '
313	return txt
314
315	def FormatInstProfile(instparmdict,hId):
316	'''Format the instrumental profile parameters with a
317	string description. Will only be called on PWDR histograms
318	'''
319	s = ''
320	inst = instparmdict[0]
321	hfx = ':'+str(hId)+':'
322	if 'C' in inst['Type'][0]:
323	s = 'Finger-Cox-Jephcoat function parameters U, V, W, X, Y, SH/L:\n'
324	s += ' peak variance(Gauss) = Utan(Th)^2^+Vtan(Th)+W:\n'
325	s += ' peak HW(Lorentz) = X/cos(Th)+Ytan(Th); SH/L = S/L+H/L\n'
326	s += ' U, V, W in (centideg)^2^, X & Y in centideg\n '
327	for item in ['U','V','W','X','Y','SH/L']:
328	name = hfx+item
329	sig = self.sigDict.get(name,-0.009)
330	s += G2mth.ValEsd(inst[item][1],sig)+', '
331	elif 'T' in inst['Type'][0]: #to be tested after TOF Rietveld done
332	s = 'Von Dreele-Jorgenson-Windsor function parameters\n'+ \
333	' alpha, beta-0, beta-1, beta-q, sig-0, sig-1, sig-q, X, Y:\n '
334	for item in ['alpha','bet-0','bet-1','bet-q','sig-0','sig-1','sig-q','X','Y']:
335	name = hfx+item
336	sig = self.sigDict.get(name,-0.009)
337	s += G2mth.ValEsd(inst[item][1],sig)+', '
338	return s
339
340	def FormatPhaseProfile(phasenam):
341	'''Format the phase-related profile parameters (size/strain)
342	with a string description.
343	return an empty string or None if there are no
344	powder histograms for this phase.
345	'''
346	s = ''
347	phasedict = self.Phases[phasenam] # pointer to current phase info
348	SGData = phasedict['General'] ['SGData']
349	for histogram in sorted(phasedict['Histograms']):
350	if histogram.startswith("HKLF"): continue # powder only
351	Histogram = self.Histograms.get(histogram)
352	if not Histogram: continue
353	hapData = phasedict['Histograms'][histogram]
354	pId = phasedict['pId']
355	hId = Histogram['hId']
356	phfx = '%d:%d:'%(pId,hId)
357	size = hapData['Size']
358	mustrain = hapData['Mustrain']
359	hstrain = hapData['HStrain']
360	if len(self.powderDict) > 1:
361	if s:
362	s += '\n'
363	else:
364	s += ' Crystallite size model "%s" for %s (microns)\n '%(size[0],phasenam)
365	s += ' Parameters for histogram #'+str(hId)+' '+str(histogram)+'\n'
366	else:
367	s += ' Crystallite size model "%s" for %s (microns)\n '%(size[0],phasenam)
368
369	names = ['Size;i','Size;mx']
370	if 'uniax' in size[0]:
371	names = ['Size;i','Size;a','Size;mx']
372	s += 'anisotropic axis is %s\n '%(str(size[3]))
373	s += 'parameters: equatorial size, axial size, G/L mix\n '
374	for i,item in enumerate(names):
375	name = phfx+item
376	sig = self.sigDict.get(name,-0.009)
377	s += G2mth.ValEsd(size[1][i],sig)+', '
378	elif 'ellip' in size[0]:
379	s += 'parameters: S11, S22, S33, S12, S13, S23, G/L mix\n '
380	for i in range(6):
381	name = phfx+'Size:'+str(i)
382	sig = self.sigDict.get(name,-0.009)
383	s += G2mth.ValEsd(size[4][i],sig)+', '
384	sig = self.sigDict.get(phfx+'Size;mx',-0.009)
385	s += G2mth.ValEsd(size[1][2],sig)+', '
386	else: #isotropic
387	s += 'parameters: Size, G/L mix\n '
388	i = 0
389	for item in names:
390	name = phfx+item
391	sig = self.sigDict.get(name,-0.009)
392	s += G2mth.ValEsd(size[1][i],sig)+', '
393	i = 2 #skip the aniso value
394	s += '\n Mustrain model "%s" for %s (10^6^)\n '%(mustrain[0],phasenam)
395	names = ['Mustrain;i','Mustrain;mx']
396	if 'uniax' in mustrain[0]:
397	names = ['Mustrain;i','Mustrain;a','Mustrain;mx']
398	s += 'anisotropic axis is %s\n '%(str(size[3]))
399	s += 'parameters: equatorial mustrain, axial mustrain, G/L mix\n '
400	for i,item in enumerate(names):
401	name = phfx+item
402	sig = self.sigDict.get(name,-0.009)
403	s += G2mth.ValEsd(mustrain[1][i],sig)+', '
404	elif 'general' in mustrain[0]:
405	names = 'parameters: '
406	for i,name in enumerate(G2spc.MustrainNames(SGData)):
407	names += name+', '
408	if i == 9:
409	names += '\n '
410	names += 'G/L mix\n '
411	s += names
412	txt = ''
413	for i in range(len(mustrain[4])):
414	name = phfx+'Mustrain:'+str(i)
415	sig = self.sigDict.get(name,-0.009)
416	if len(txt) > 60:
417	s += txt+'\n '
418	txt = ''
419	txt += G2mth.ValEsd(mustrain[4][i],sig)+', '
420	s += txt
421	sig = self.sigDict.get(phfx+'Mustrain;mx',-0.009)
422	s += G2mth.ValEsd(mustrain[1][2],sig)+', '
423
424	else: #isotropic
425	s += ' parameters: Mustrain, G/L mix\n '
426	i = 0
427	for item in names:
428	name = phfx+item
429	sig = self.sigDict.get(name,-0.009)
430	s += G2mth.ValEsd(mustrain[1][i],sig)+', '
431	i = 2 #skip the aniso value
432	s1 = ' \n Macrostrain parameters: '
433	names = G2spc.HStrainNames(SGData)
434	for name in names:
435	s1 += name+', '
436	s1 += '\n '
437	macrostrain = False
438	for i in range(len(names)):
439	name = phfx+name[i]
440	sig = self.sigDict.get(name,-0.009)
441	s1 += G2mth.ValEsd(hstrain[0][i],sig)+', '
442	if hstrain[0][i]: macrostrain = True
443	if macrostrain:
444	s += s1 + '\n'
445	# show revised lattice parameters here someday
446	else:
447	s += '\n'
448	return s
449
450	def FmtAtomType(sym):
451	'Reformat a GSAS-II atom type symbol to match CIF rules'
452	sym = sym.replace('_','') # underscores are not allowed: no isotope designation?
453	# in CIF, oxidation state sign symbols come after, not before
454	if '+' in sym:
455	sym = sym.replace('+','') + '+'
456	elif '-' in sym:
457	sym = sym.replace('-','') + '-'
458	return sym
459
460	def PutInCol(val,wid):
461	'''Pad a value to >=wid+1 columns by adding spaces at the end. Always
462	adds at least one space
463	'''
464	val = str(val).replace(' ','')
465	if not val: val = '?'
466	fmt = '{:' + str(wid) + '} '
467	return fmt.format(val)
468
469	def MakeUniqueLabel(lbl,labellist):
470	'Make sure that every atom label is unique'
471	lbl = lbl.strip()
472	if not lbl: # deal with a blank label
473	lbl = 'A_1'
474	if lbl not in labellist:
475	labellist.append(lbl)
476	return lbl
477	i = 1
478	prefix = lbl
479	if '_' in lbl:
480	prefix = lbl[:lbl.rfind('_')]
481	suffix = lbl[lbl.rfind('_')+1:]
482	try:
483	i = int(suffix)+1
484	except:
485	pass
486	while prefix+'_'+str(i) in labellist:
487	i += 1
488	else:
489	lbl = prefix+'_'+str(i)
490	labellist.append(lbl)
491
492	def WriteAtomsNuclear(phasenam):
493	'Write atom positions to CIF'
494	phasedict = self.Phases[phasenam] # pointer to current phase info
495	General = phasedict['General']
496	cx,ct,cs,cia = General['AtomPtrs']
497	Atoms = phasedict['Atoms']
498	cfrac = cx+3
499	fpfx = str(phasedict['pId'])+'::Afrac:'
500	for i,at in enumerate(Atoms):
501	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
502	if fval != 0.0:
503	break
504	else:
505	WriteCIFitem('\n# PHASE HAS NO ATOMS!')
506	return
507
508	WriteCIFitem('\n# ATOMIC COORDINATES AND DISPLACEMENT PARAMETERS')
509	WriteCIFitem('loop_ '+
510	'\n _atom_site_label'+
511	'\n _atom_site_type_symbol'+
512	'\n _atom_site_fract_x'+
513	'\n _atom_site_fract_y'+
514	'\n _atom_site_fract_z'+
515	'\n _atom_site_occupancy'+
516	'\n _atom_site_adp_type'+
517	'\n _atom_site_U_iso_or_equiv'+
518	'\n _atom_site_symmetry_multiplicity')
519
520	varnames = {cx:'Ax',cx+1:'Ay',cx+2:'Az',cx+3:'Afrac',
521	cia+1:'AUiso',cia+2:'AU11',cia+3:'AU22',cia+4:'AU33',
522	cia+5:'AU12',cia+6:'AU13',cia+7:'AU23'}
523	self.labellist = []
524
525	pfx = str(phasedict['pId'])+'::'
526	# loop over all atoms
527	naniso = 0
528	for i,at in enumerate(Atoms):
529	if phasedict['General']['Type'] == 'macromolecular':
530	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
531	s = PutInCol(MakeUniqueLabel(label,self.labellist),15) # label
532	else:
533	s = PutInCol(MakeUniqueLabel(at[ct-1],self.labellist),6) # label
534	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
535	if fval == 0.0: continue # ignore any atoms that have a occupancy set to 0 (exact)
536	s += PutInCol(FmtAtomType(at[ct]),4) # type
537	if at[cia] == 'I':
538	adp = 'Uiso '
539	else:
540	adp = 'Uani '
541	naniso += 1
542	# compute Uequiv crudely
543	# correct: Defined as "1/3 trace of diagonalized U matrix".
544	# SEE cell2GS & Uij2Ueqv to GSASIIlattice. Former is needed to make the GS matrix used by the latter.
545	t = 0.0
546	for j in (2,3,4):
547	var = pfx+varnames[cia+j]+":"+str(i)
548	t += self.parmDict.get(var,at[cia+j])
549	for j in (cx,cx+1,cx+2,cx+3,cia,cia+1):
550	if j in (cx,cx+1,cx+2):
551	dig = 11
552	sigdig = -0.00009
553	else:
554	dig = 10
555	sigdig = -0.009
556	if j == cia:
557	s += adp
558	else:
559	var = pfx+varnames[j]+":"+str(i)
560	dvar = pfx+"d"+varnames[j]+":"+str(i)
561	if dvar not in self.sigDict:
562	dvar = var
563	if j == cia+1 and adp == 'Uani ':
564	val = t/3.
565	sig = sigdig
566	else:
567	#print var,(var in self.parmDict),(var in self.sigDict)
568	val = self.parmDict.get(var,at[j])
569	sig = self.sigDict.get(dvar,sigdig)
570	s += PutInCol(G2mth.ValEsd(val,sig),dig)
571	s += PutInCol(at[cs+1],3)
572	WriteCIFitem(s)
573	if naniso == 0: return
574	# now loop over aniso atoms
575	WriteCIFitem('\nloop_' + '\n _atom_site_aniso_label' +
576	'\n _atom_site_aniso_U_11' + '\n _atom_site_aniso_U_22' +
577	'\n _atom_site_aniso_U_33' + '\n _atom_site_aniso_U_12' +
578	'\n _atom_site_aniso_U_13' + '\n _atom_site_aniso_U_23')
579	for i,at in enumerate(Atoms):
580	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
581	if fval == 0.0: continue # ignore any atoms that have a occupancy set to 0 (exact)
582	if at[cia] == 'I': continue
583	s = PutInCol(self.labellist[i],6) # label
584	for j in (2,3,4,5,6,7):
585	sigdig = -0.0009
586	var = pfx+varnames[cia+j]+":"+str(i)
587	val = self.parmDict.get(var,at[cia+j])
588	sig = self.sigDict.get(var,sigdig)
589	s += PutInCol(G2mth.ValEsd(val,sig),11)
590	WriteCIFitem(s)
591
592	def HillSortElements(elmlist):
593	'''Sort elements in "Hill" order: C, H, others, (where others
594	are alphabetical).
595
596	:params list elmlist: a list of element strings
597
598	:returns: a sorted list of element strings
599	'''
600	newlist = []
601	oldlist = elmlist[:]
602	for elm in ('C','H'):
603	if elm in elmlist:
604	newlist.append(elm)
605	oldlist.pop(oldlist.index(elm))
606	return newlist+sorted(oldlist)
607
608	def WriteComposition(phasenam):
609	'''determine the composition for the unit cell, crudely determine Z and
610	then compute the composition in formula units
611	'''
612	phasedict = self.Phases[phasenam] # pointer to current phase info
613	General = phasedict['General']
614	Z = General.get('cellZ',0.0)
615	cx,ct,cs,cia = General['AtomPtrs']
616	Atoms = phasedict['Atoms']
617	fpfx = str(phasedict['pId'])+'::Afrac:'
618	cfrac = cx+3
619	cmult = cs+1
620	compDict = {} # combines H,D & T
621	sitemultlist = []
622	massDict = dict(zip(General['AtomTypes'],General['AtomMass']))
623	cellmass = 0
624	for i,at in enumerate(Atoms):
625	atype = at[ct].strip()
626	if atype.find('-') != -1: atype = atype.split('-')[0]
627	if atype.find('+') != -1: atype = atype.split('+')[0]
628	atype = atype[0].upper()+atype[1:2].lower() # force case conversion
629	if atype == "D" or atype == "D": atype = "H"
630	fvar = fpfx+str(i)
631	fval = self.parmDict.get(fvar,at[cfrac])
632	mult = at[cmult]
633	if not massDict.get(at[ct]):
634	print('Error: No mass found for atom type '+at[ct])
635	print('Will not compute cell contents for phase '+phasenam)
636	return
637	cellmass += massDict[at[ct]]multfval
638	compDict[atype] = compDict.get(atype,0.0) + mult*fval
639	if fval == 1: sitemultlist.append(mult)
640	if len(compDict.keys()) == 0: return # no elements!
641	if Z < 1: # Z has not been computed or set by user
642	Z = 1
643	for i in range(2,min(sitemultlist)+1):
644	for m in sitemultlist:
645	if m % i != 0:
646	break
647	else:
648	Z = i
649	General['cellZ'] = Z # save it
650
651	# when scattering factors are included in the CIF, this needs to be
652	# added to the loop here but only in the one-block case.
653	# For multiblock CIFs, scattering factors go in the histogram
654	# blocks (for all atoms in all appropriate phases) - an example?:
655	#loop_
656	# _atom_type_symbol
657	# _atom_type_description
658	# _atom_type_scat_dispersion_real
659	# _atom_type_scat_dispersion_imag
660	# _atom_type_scat_source
661	# 'C' 'C' 0.0033 0.0016
662	# 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
663	# 'H' 'H' 0.0000 0.0000
664	# 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
665	# 'P' 'P' 0.1023 0.0942
666	# 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
667	# 'Cl' 'Cl' 0.1484 0.1585
668	# 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
669	# 'Cu' 'Cu' 0.3201 1.2651
670	# 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
671
672	#if oneblock: # add scattering factors for current phase here
673	WriteCIFitem('\nloop_ _atom_type_symbol _atom_type_number_in_cell')
674	formula = ''
675	reload(G2mth)
676	for elem in HillSortElements(compDict.keys()):
677	WriteCIFitem(' ' + PutInCol(elem,4) +
678	G2mth.ValEsd(compDict[elem],-0.009,True))
679	if formula: formula += " "
680	formula += elem
681	if compDict[elem] == Z: continue
682	formula += G2mth.ValEsd(compDict[elem]/Z,-0.009,True)
683	WriteCIFitem( '\n# Note that Z affects _cell_formula_sum and _weight')
684	WriteCIFitem( '_cell_formula_units_Z',str(Z))
685	WriteCIFitem( '_chemical_formula_sum',formula)
686	WriteCIFitem( '_chemical_formula_weight',
687	G2mth.ValEsd(cellmass/Z,-0.09,True))
688
689	def WriteDistances(phasenam,SymOpList,offsetList,symOpList,G2oprList):
690	'''Report bond distances and angles for the CIF
691
692	Note that _geom__symmetry_ fields are values of form
693	n_klm where n is the symmetry operation in SymOpList (counted
694	starting with 1) and (k-5, l-5, m-5) are translations to add
695	to (x,y,z). See
696	http://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Igeom_angle_site_symmetry_.html
697
698	TODO: need a method to select publication flags for distances/angles
699	'''
700	phasedict = self.Phases[phasenam] # pointer to current phase info
701	Atoms = phasedict['Atoms']
702	generalData = phasedict['General']
703	# create a dict for storing Pub flag for bonds/angles, if needed
704	if phasedict['General'].get("DisAglHideFlag") is None:
705	phasedict['General']["DisAglHideFlag"] = {}
706	DisAngSel = phasedict['General']["DisAglHideFlag"]
707	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
708	cn = ct-1
709	fpfx = str(phasedict['pId'])+'::Afrac:'
710	cfrac = cx+3
711	DisAglData = {}
712	# create a list of atoms, but skip atoms with zero occupancy
713	xyz = []
714	fpfx = str(phasedict['pId'])+'::Afrac:'
715	for i,atom in enumerate(Atoms):
716	if self.parmDict.get(fpfx+str(i),atom[cfrac]) == 0.0: continue
717	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
718	if 'DisAglCtls' not in generalData:
719	# should not happen, since DisAglDialog should be called
720	# for all phases before getting here
721	dlg = G2gd.DisAglDialog(
722	self.G2frame,
723	{},
724	generalData)
725	if dlg.ShowModal() == wx.ID_OK:
726	generalData['DisAglCtls'] = dlg.GetData()
727	else:
728	dlg.Destroy()
729	return
730	dlg.Destroy()
731	DisAglData['OrigAtoms'] = xyz
732	DisAglData['TargAtoms'] = xyz
733	SymOpList,offsetList,symOpList,G2oprList = G2spc.AllOps(
734	generalData['SGData'])
735
736	xpandSGdata = generalData['SGData'].copy()
737	xpandSGdata.update({'SGOps':symOpList,
738	'SGInv':False,
739	'SGLatt':'P',
740	'SGCen':np.array([[0, 0, 0]]),})
741	DisAglData['SGData'] = xpandSGdata
742
743	DisAglData['Cell'] = generalData['Cell'][1:] #+ volume
744	if 'pId' in phasedict:
745	DisAglData['pId'] = phasedict['pId']
746	DisAglData['covData'] = self.OverallParms['Covariance']
747	try:
748	AtomLabels,DistArray,AngArray = G2stMn.RetDistAngle(
749	generalData['DisAglCtls'],
750	DisAglData)
751	except KeyError: # inside DistAngle for missing atom types in DisAglCtls
752	print('** ERROR - try again but do "Reset" to fill in missing atom types **')
753
754	# loop over interatomic distances for this phase
755	WriteCIFitem('\n# MOLECULAR GEOMETRY')
756	WriteCIFitem('loop_' +
757	'\n _geom_bond_atom_site_label_1' +
758	'\n _geom_bond_atom_site_label_2' +
759	'\n _geom_bond_distance' +
760	'\n _geom_bond_site_symmetry_1' +
761	'\n _geom_bond_site_symmetry_2' +
762	'\n _geom_bond_publ_flag')
763
764	for i in sorted(AtomLabels.keys()):
765	Dist = DistArray[i]
766	for D in Dist:
767	line = ' '+PutInCol(AtomLabels[i],6)+PutInCol(AtomLabels[D[0]],6)
768	sig = D[4]
769	if sig == 0: sig = -0.00009
770	line += PutInCol(G2mth.ValEsd(D[3],sig,True),10)
771	line += " 1_555 "
772	line += " {:3d}_".format(D[2])
773	for d in D[1]:
774	line += "{:1d}".format(d+5)
775	if DisAngSel.get((i,tuple(D[0:3]))):
776	line += " no"
777	else:
778	line += " yes"
779	WriteCIFitem(line)
780
781	# loop over interatomic angles for this phase
782	WriteCIFitem('\nloop_' +
783	'\n _geom_angle_atom_site_label_1' +
784	'\n _geom_angle_atom_site_label_2' +
785	'\n _geom_angle_atom_site_label_3' +
786	'\n _geom_angle' +
787	'\n _geom_angle_site_symmetry_1' +
788	'\n _geom_angle_site_symmetry_2' +
789	'\n _geom_angle_site_symmetry_3' +
790	'\n _geom_angle_publ_flag')
791
792	for i in sorted(AtomLabels.keys()):
793	Dist = DistArray[i]
794	for k,j,tup in AngArray[i]:
795	Dj = Dist[j]
796	Dk = Dist[k]
797	line = ' '+PutInCol(AtomLabels[Dj[0]],6)+PutInCol(AtomLabels[i],6)+PutInCol(AtomLabels[Dk[0]],6)
798	sig = tup[1]
799	if sig == 0: sig = -0.009
800	line += PutInCol(G2mth.ValEsd(tup[0],sig,True),10)
801	line += " {:3d}_".format(Dj[2])
802	for d in Dj[1]:
803	line += "{:1d}".format(d+5)
804	line += " 1_555 "
805	line += " {:3d}_".format(Dk[2])
806	for d in Dk[1]:
807	line += "{:1d}".format(d+5)
808	key = (tuple(Dk[0:3]),i,tuple(Dj[0:3]))
809	if DisAngSel.get(key):
810	line += " no"
811	else:
812	line += " yes"
813	WriteCIFitem(line)
814
815	def WritePhaseInfo(phasenam):
816	'Write out the phase information for the selected phase'
817	WriteCIFitem('\n# phase info for '+str(phasenam) + ' follows')
818	phasedict = self.Phases[phasenam] # pointer to current phase info
819	WriteCIFitem('_pd_phase_name', phasenam)
820	cellList,cellSig = self.GetCell(phasenam)
821	defsigL = 3[-0.00001] + 3[-0.001] + [-0.01] # significance to use when no sigma
822	names = ['length_a','length_b','length_c',
823	'angle_alpha','angle_beta ','angle_gamma',
824	'volume']
825	prevsig = 0
826	for lbl,defsig,val,sig in zip(names,defsigL,cellList,cellSig):
827	if sig:
828	txt = G2mth.ValEsd(val,sig)
829	prevsig = -sig # use this as the significance for next value
830	else:
831	txt = G2mth.ValEsd(val,min(defsig,prevsig),True)
832	WriteCIFitem('_cell_'+lbl,txt)
833
834	WriteCIFitem('_symmetry_cell_setting',
835	phasedict['General']['SGData']['SGSys'])
836
837	spacegroup = phasedict['General']['SGData']['SpGrp'].strip()
838	# regularize capitalization and remove trailing H/R
839	spacegroup = spacegroup[0].upper() + spacegroup[1:].lower().rstrip('rh ')
840	WriteCIFitem('_symmetry_space_group_name_H-M',spacegroup)
841
842	# generate symmetry operations including centering and center of symmetry
843	SymOpList,offsetList,symOpList,G2oprList = G2spc.AllOps(
844	phasedict['General']['SGData'])
845	WriteCIFitem('loop_\n _space_group_symop_id\n _space_group_symop_operation_xyz')
846	for i,op in enumerate(SymOpList,start=1):
847	WriteCIFitem(' {:3d} {:}'.format(i,op.lower()))
848
849	# loop over histogram(s) used in this phase
850	if not oneblock and not self.quickmode:
851	# report pointers to the histograms used in this phase
852	histlist = []
853	for hist in self.Phases[phasenam]['Histograms']:
854	if self.Phases[phasenam]['Histograms'][hist]['Use']:
855	if phasebyhistDict.get(hist):
856	phasebyhistDict[hist].append(phasenam)
857	else:
858	phasebyhistDict[hist] = [phasenam,]
859	blockid = datablockidDict.get(hist)
860	if not blockid:
861	print("Internal error: no block for data. Phase "+str(
862	phasenam)+" histogram "+str(hist))
863	histlist = []
864	break
865	histlist.append(blockid)
866
867	if len(histlist) == 0:
868	WriteCIFitem('# Note: phase has no associated data')
869
870	# report atom params
871	if phasedict['General']['Type'] in ['nuclear','macromolecular']: #this needs macromolecular variant, etc!
872	WriteAtomsNuclear(phasenam)
873	else:
874	raise Exception,"no export for "+str(phasedict['General']['Type'])+" coordinates implemented"
875	# report cell contents
876	WriteComposition(phasenam)
877	if not self.quickmode and phasedict['General']['Type'] == 'nuclear': # report distances and angles
878	WriteDistances(phasenam,SymOpList,offsetList,symOpList,G2oprList)
879	if 'Map' in phasedict['General'] and 'minmax' in phasedict['General']['Map']:
880	WriteCIFitem('\n# Difference density results')
881	MinMax = phasedict['General']['Map']['minmax']
882	WriteCIFitem('_refine_diff_density_max',G2mth.ValEsd(MinMax[1],-0.009))
883	WriteCIFitem('_refine_diff_density_min',G2mth.ValEsd(MinMax[0],-0.009))
884
885	def Yfmt(ndec,val):
886	'Format intensity values'
887	out = ("{:."+str(ndec)+"f}").format(val)
888	out = out.rstrip('0') # strip zeros to right of decimal
889	return out.rstrip('.') # and decimal place when not needed
890
891	def WriteReflStat(refcount,hklmin,hklmax,dmin,dmax,nRefSets=1):
892	'Write reflection statistics'
893	WriteCIFitem('_reflns_number_total', str(refcount))
894	if hklmin is not None and nRefSets == 1: # hkl range has no meaning with multiple phases
895	WriteCIFitem('_reflns_limit_h_min', str(int(hklmin[0])))
896	WriteCIFitem('_reflns_limit_h_max', str(int(hklmax[0])))
897	WriteCIFitem('_reflns_limit_k_min', str(int(hklmin[1])))
898	WriteCIFitem('_reflns_limit_k_max', str(int(hklmax[1])))
899	WriteCIFitem('_reflns_limit_l_min', str(int(hklmin[2])))
900	WriteCIFitem('_reflns_limit_l_max', str(int(hklmax[2])))
901	if hklmin is not None:
902	WriteCIFitem('_reflns_d_resolution_low ', G2mth.ValEsd(dmax,-0.009))
903	WriteCIFitem('_reflns_d_resolution_high ', G2mth.ValEsd(dmin,-0.009))
904
905	def WritePowderData(histlbl):
906	'Write out the selected powder diffraction histogram info'
907	histblk = self.Histograms[histlbl]
908	inst = histblk['Instrument Parameters'][0]
909	hId = histblk['hId']
910	pfx = ':' + str(hId) + ':'
911
912	if 'Lam1' in inst:
913	ratio = self.parmDict.get('I(L2)/I(L1)',inst['I(L2)/I(L1)'][1])
914	sratio = self.sigDict.get('I(L2)/I(L1)',-0.0009)
915	lam1 = self.parmDict.get('Lam1',inst['Lam1'][1])
916	slam1 = self.sigDict.get('Lam1',-0.00009)
917	lam2 = self.parmDict.get('Lam2',inst['Lam2'][1])
918	slam2 = self.sigDict.get('Lam2',-0.00009)
919	# always assume Ka1 & Ka2 if two wavelengths are present
920	WriteCIFitem('_diffrn_radiation_type','K\\a~1,2~')
921	WriteCIFitem('loop_' +
922	'\n _diffrn_radiation_wavelength' +
923	'\n _diffrn_radiation_wavelength_wt' +
924	'\n _diffrn_radiation_wavelength_id')
925	WriteCIFitem(' ' + PutInCol(G2mth.ValEsd(lam1,slam1),15)+
926	PutInCol('1.0',15) +
927	PutInCol('1',5))
928	WriteCIFitem(' ' + PutInCol(G2mth.ValEsd(lam2,slam2),15)+
929	PutInCol(G2mth.ValEsd(ratio,sratio),15)+
930	PutInCol('2',5))
931	else:
932	lam1 = self.parmDict.get('Lam',inst['Lam'][1])
933	slam1 = self.sigDict.get('Lam',-0.00009)
934	WriteCIFitem('_diffrn_radiation_wavelength',G2mth.ValEsd(lam1,slam1))
935
936	if not oneblock:
937	if not phasebyhistDict.get(histlbl):
938	WriteCIFitem('\n# No phases associated with this data set')
939	else:
940	WriteCIFitem('\n# PHASE TABLE')
941	WriteCIFitem('loop_' +
942	'\n _pd_phase_id' +
943	'\n _pd_phase_block_id' +
944	'\n _pd_phase_mass_%')
945	wtFrSum = 0.
946	for phasenam in phasebyhistDict.get(histlbl):
947	hapData = self.Phases[phasenam]['Histograms'][histlbl]
948	General = self.Phases[phasenam]['General']
949	wtFrSum += hapData['Scale'][0]*General['Mass']
950
951	for phasenam in phasebyhistDict.get(histlbl):
952	hapData = self.Phases[phasenam]['Histograms'][histlbl]
953	General = self.Phases[phasenam]['General']
954	wtFr = hapData['Scale'][0]*General['Mass']/wtFrSum
955	pfx = str(self.Phases[phasenam]['pId'])+':'+str(hId)+':'
956	if pfx+'Scale' in self.sigDict:
957	sig = self.sigDict[pfx+'Scale']*wtFr/hapData['Scale'][0]
958	else:
959	sig = -0.0001
960	WriteCIFitem(
961	' '+
962	str(self.Phases[phasenam]['pId']) +
963	' '+datablockidDict[phasenam]+
964	' '+G2mth.ValEsd(wtFr,sig)
965	)
966	WriteCIFitem('loop_' +
967	'\n _gsas_proc_phase_R_F_factor' +
968	'\n _gsas_proc_phase_R_Fsqd_factor' +
969	'\n _gsas_proc_phase_id' +
970	'\n _gsas_proc_phase_block_id')
971	for phasenam in phasebyhistDict.get(histlbl):
972	pfx = str(self.Phases[phasenam]['pId'])+':'+str(hId)+':'
973	WriteCIFitem(
974	' '+
975	' '+G2mth.ValEsd(histblk[pfx+'Rf']/100.,-.00009) +
976	' '+G2mth.ValEsd(histblk[pfx+'Rf^2']/100.,-.00009)+
977	' '+str(self.Phases[phasenam]['pId'])+
978	' '+datablockidDict[phasenam]
979	)
980	else:
981	# single phase in this histogram
982	pfx = '0:'+str(hId)+':'
983	WriteCIFitem('_refine_ls_R_F_factor ','%.5f'%(histblk[pfx+'Rf']/100.))
984	WriteCIFitem('_refine_ls_R_Fsqd_factor ','%.5f'%(histblk[pfx+'Rf^2']/100.))
985
986	WriteCIFitem('_pd_proc_ls_prof_R_factor ','%.5f'%(histblk['R']/100.))
987	WriteCIFitem('_pd_proc_ls_prof_wR_factor ','%.5f'%(histblk['wR']/100.))
988	WriteCIFitem('_gsas_proc_ls_prof_R_B_factor ','%.5f'%(histblk['Rb']/100.))
989	WriteCIFitem('_gsas_proc_ls_prof_wR_B_factor','%.5f'%(histblk['wRb']/100.))
990	WriteCIFitem('_pd_proc_ls_prof_wR_expected','%.5f'%(histblk['wRmin']/100.))
991
992	if histblk['Instrument Parameters'][0]['Type'][1][1] == 'X':
993	WriteCIFitem('_diffrn_radiation_probe','x-ray')
994	pola = histblk['Instrument Parameters'][0].get('Polariz.')
995	if pola:
996	pfx = ':' + str(hId) + ':'
997	sig = self.sigDict.get(pfx+'Polariz.',-0.0009)
998	txt = G2mth.ValEsd(pola[1],sig)
999	WriteCIFitem('_diffrn_radiation_polarisn_ratio',txt)
1000	elif histblk['Instrument Parameters'][0]['Type'][1][1] == 'N':
1001	WriteCIFitem('_diffrn_radiation_probe','neutron')
1002	# TOF (note that this may not be defined)
1003	#if histblk['Instrument Parameters'][0]['Type'][1][2] == 'T':
1004	# WriteCIFitem('_pd_meas_2theta_fixed',text)
1005
1006
1007	# TODO: this will need help from Bob
1008	#if not oneblock:
1009	#WriteCIFitem('\n# SCATTERING FACTOR INFO')
1010	#WriteCIFitem('loop_ _atom_type_symbol')
1011	#if histblk['Instrument Parameters'][0]['Type'][1][1] == 'X':
1012	# WriteCIFitem(' _atom_type_scat_dispersion_real')
1013	# WriteCIFitem(' _atom_type_scat_dispersion_imag')
1014	# for lbl in ('a1','a2','a3', 'a4', 'b1', 'b2', 'b3', 'b4', 'c'):
1015	# WriteCIFitem(' _atom_type_scat_Cromer_Mann_'+lbl)
1016	#elif histblk['Instrument Parameters'][0]['Type'][1][1] == 'N':
1017	# WriteCIFitem(' _atom_type_scat_length_neutron')
1018	#WriteCIFitem(' _atom_type_scat_source')
1019
1020	WriteCIFitem('_pd_proc_ls_background_function',FormatBackground(histblk['Background'],histblk['hId']))
1021
1022	# TODO: this will need help from Bob
1023	#WriteCIFitem('_exptl_absorpt_process_details','?')
1024	#WriteCIFitem('_exptl_absorpt_correction_T_min','?')
1025	#WriteCIFitem('_exptl_absorpt_correction_T_max','?')
1026	#C extinction
1027	#WRITE(IUCIF,'(A)') '# Extinction correction'
1028	#CALL WRVAL(IUCIF,'_gsas_exptl_extinct_corr_T_min',TEXT(1:10))
1029	#CALL WRVAL(IUCIF,'_gsas_exptl_extinct_corr_T_max',TEXT(11:20))
1030
1031	if not oneblock: # instrumental profile terms go here
1032	WriteCIFitem('_pd_proc_ls_profile_function',
1033	FormatInstProfile(histblk["Instrument Parameters"],histblk['hId']))
1034
1035	#refprx = '_refln.' # mm
1036	refprx = '_refln_' # normal
1037	# data collection parameters for the powder dataset
1038
1039	temperature = histblk['Sample Parameters'].get('Temperature') # G2 uses K
1040	if not temperature:
1041	T = '?'
1042	else:
1043	T = G2mth.ValEsd(temperature,-0.009,True) # CIF uses K
1044	WriteCIFitem('_diffrn_ambient_temperature',T)
1045
1046	pressure = histblk['Sample Parameters'].get('Pressure') #G2 uses mega-Pascal
1047	if not pressure:
1048	P = '?'
1049	else:
1050	P = G2mth.ValEsd(pressure*1000,-0.09,True) # CIF uses kilopascal
1051	WriteCIFitem('_diffrn_ambient_pressure',P)
1052
1053	WriteCIFitem('\n# STRUCTURE FACTOR TABLE')
1054	# compute maximum intensity reflection
1055	Imax = 0
1056	for phasenam in histblk['Reflection Lists']:
1057	scale = self.Phases[phasenam]['Histograms'][histlbl]['Scale'][0]
1058	refList = np.asarray(histblk['Reflection Lists'][phasenam]['RefList'])
1059	I100 = scalerefList.T[8]refList.T[11]
1060	#Icorr = np.array([refl[13] for refl in histblk['Reflection Lists'][phasenam]])[0]
1061	#FO2 = np.array([refl[8] for refl in histblk['Reflection Lists'][phasenam]])
1062	#I100 = scaleFO2Icorr
1063	Imax = max(Imax,max(I100))
1064
1065	WriteCIFitem('loop_')
1066	if len(histblk['Reflection Lists'].keys()) > 1:
1067	WriteCIFitem(' _pd_refln_phase_id')
1068	WriteCIFitem(' ' + refprx + 'index_h' +
1069	'\n ' + refprx + 'index_k' +
1070	'\n ' + refprx + 'index_l' +
1071	'\n ' + refprx + 'F_squared_meas' +
1072	'\n ' + refprx + 'F_squared_calc' +
1073	'\n ' + refprx + 'phase_calc' +
1074	'\n _pd_refln_d_spacing')
1075	if Imax > 0:
1076	WriteCIFitem(' _gsas_i100_meas')
1077
1078	refcount = 0
1079	hklmin = None
1080	hklmax = None
1081	dmax = None
1082	dmin = None
1083	for phasenam in histblk['Reflection Lists']:
1084	scale = self.Phases[phasenam]['Histograms'][histlbl]['Scale'][0]
1085	phaseid = self.Phases[phasenam]['pId']
1086	refcount += len(histblk['Reflection Lists'][phasenam]['RefList'])
1087	for j,ref in enumerate(histblk['Reflection Lists'][phasenam]['RefList']):
1088	if DEBUG:
1089	print('DEBUG: skipping reflection list')
1090	break
1091	if hklmin is None:
1092	hklmin = ref[0:3]
1093	hklmax = ref[0:3]
1094	dmax = dmin = ref[4]
1095	if len(histblk['Reflection Lists'].keys()) > 1:
1096	s = PutInCol(phaseid,2)
1097	else:
1098	s = ""
1099	for i,hkl in enumerate(ref[0:3]):
1100	hklmax[i] = max(hkl,hklmax[i])
1101	hklmin[i] = min(hkl,hklmin[i])
1102	s += PutInCol(int(hkl),4)
1103	for I in ref[8:10]:
1104	s += PutInCol(G2mth.ValEsd(I,-0.0009),10)
1105	s += PutInCol(G2mth.ValEsd(ref[10],-0.9),7)
1106	dmax = max(dmax,ref[4])
1107	dmin = min(dmin,ref[4])
1108	s += PutInCol(G2mth.ValEsd(ref[4],-0.009),8)
1109	if Imax > 0:
1110	s += PutInCol(G2mth.ValEsd(100.*I100[j]/Imax,-0.09),6)
1111	WriteCIFitem(" "+s)
1112
1113	WriteReflStat(refcount,hklmin,hklmax,dmin,dmax,len(histblk['Reflection Lists']))
1114	WriteCIFitem('\n# POWDER DATA TABLE')
1115	# is data fixed step? If the step varies by <0.01% treat as fixed step
1116	steps = histblk['Data'][0][1:] - histblk['Data'][0][:-1]
1117	if abs(max(steps)-min(steps)) > abs(max(steps))/10000.:
1118	fixedstep = False
1119	else:
1120	fixedstep = True
1121
1122	if fixedstep: # and not TOF
1123	WriteCIFitem('_pd_meas_2theta_range_min', G2mth.ValEsd(histblk['Data'][0][0],-0.00009))
1124	WriteCIFitem('_pd_meas_2theta_range_max', G2mth.ValEsd(histblk['Data'][0][-1],-0.00009))
1125	WriteCIFitem('_pd_meas_2theta_range_inc', G2mth.ValEsd(steps.sum()/len(steps),-0.00009))
1126	# zero correct, if defined
1127	zero = None
1128	zerolst = histblk['Instrument Parameters'][0].get('Zero')
1129	if zerolst: zero = zerolst[1]
1130	zero = self.parmDict.get('Zero',zero)
1131	if zero:
1132	WriteCIFitem('_pd_proc_2theta_range_min', G2mth.ValEsd(histblk['Data'][0][0]-zero,-0.00009))
1133	WriteCIFitem('_pd_proc_2theta_range_max', G2mth.ValEsd(histblk['Data'][0][-1]-zero,-0.00009))
1134	WriteCIFitem('_pd_proc_2theta_range_inc', G2mth.ValEsd(steps.sum()/len(steps),-0.00009))
1135
1136	if zero:
1137	WriteCIFitem('_pd_proc_number_of_points', str(len(histblk['Data'][0])))
1138	else:
1139	WriteCIFitem('_pd_meas_number_of_points', str(len(histblk['Data'][0])))
1140	WriteCIFitem('\nloop_')
1141	# WriteCIFitem(' _pd_proc_d_spacing') # need easy way to get this
1142	if not fixedstep:
1143	if zero:
1144	WriteCIFitem(' _pd_proc_2theta_corrected')
1145	else:
1146	WriteCIFitem(' _pd_meas_2theta_scan')
1147	# at least for now, always report weights.
1148	#if countsdata:
1149	# WriteCIFitem(' _pd_meas_counts_total')
1150	#else:
1151	WriteCIFitem(' _pd_meas_intensity_total')
1152	WriteCIFitem(' _pd_calc_intensity_total')
1153	WriteCIFitem(' _pd_proc_intensity_bkg_calc')
1154	WriteCIFitem(' _pd_proc_ls_weight')
1155	maxY = max(histblk['Data'][1].max(),histblk['Data'][3].max())
1156	if maxY < 0: maxY *= -10 # this should never happen, but...
1157	ndec = max(0,10-int(np.log10(maxY))-1) # 10 sig figs should be enough
1158	maxSU = histblk['Data'][2].max()
1159	if maxSU < 0: maxSU *= -1 # this should never happen, but...
1160	ndecSU = max(0,8-int(np.log10(maxSU))-1) # 8 sig figs should be enough
1161	lowlim,highlim = histblk['Limits'][1]
1162
1163	if DEBUG:
1164	print('DEBUG: skipping profile list')
1165	else:
1166	for x,yobs,yw,ycalc,ybkg in zip(histblk['Data'][0],
1167	histblk['Data'][1],
1168	histblk['Data'][2],
1169	histblk['Data'][3],
1170	histblk['Data'][4]):
1171	if lowlim <= x <= highlim:
1172	pass
1173	else:
1174	yw = 0.0 # show the point is not in use
1175
1176	if fixedstep:
1177	s = ""
1178	else:
1179	s = PutInCol(G2mth.ValEsd(x-zero,-0.00009),10)
1180	s += PutInCol(Yfmt(ndec,yobs),12)
1181	s += PutInCol(Yfmt(ndec,ycalc),12)
1182	s += PutInCol(Yfmt(ndec,ybkg),11)
1183	s += PutInCol(Yfmt(ndecSU,yw),9)
1184	WriteCIFitem(" "+s)
1185
1186	def WriteSingleXtalData(histlbl):
1187	'Write out the selected single crystal histogram info'
1188	histblk = self.Histograms[histlbl]
1189
1190	#refprx = '_refln.' # mm
1191	refprx = '_refln_' # normal
1192
1193	WriteCIFitem('\n# STRUCTURE FACTOR TABLE')
1194	WriteCIFitem('loop_' +
1195	'\n ' + refprx + 'index_h' +
1196	'\n ' + refprx + 'index_k' +
1197	'\n ' + refprx + 'index_l' +
1198	'\n ' + refprx + 'F_squared_meas' +
1199	'\n ' + refprx + 'F_squared_sigma' +
1200	'\n ' + refprx + 'F_squared_calc' +
1201	'\n ' + refprx + 'phase_calc'
1202	)
1203
1204	hklmin = None
1205	hklmax = None
1206	dmax = None
1207	dmin = None
1208	refcount = len(histblk['Data']['RefList'])
1209	for ref in histblk['Data']['RefList']:
1210	if ref[3] <= 0: #skip user rejected reflections (mul <= 0)
1211	continue
1212	s = " "
1213	if hklmin is None:
1214	hklmin = ref[0:3]
1215	hklmax = ref[0:3]
1216	dmax = dmin = ref[4]
1217	for i,hkl in enumerate(ref[0:3]):
1218	hklmax[i] = max(hkl,hklmax[i])
1219	hklmin[i] = min(hkl,hklmin[i])
1220	s += PutInCol(int(hkl),4)
1221	import sys
1222	if ref[5] == 0.0:
1223	s += PutInCol(G2mth.ValEsd(ref[8],0),12)
1224	s += PutInCol('.',10)
1225	s += PutInCol(G2mth.ValEsd(ref[9],0),12)
1226	s += PutInCol(G2mth.ValEsd(ref[10],-0.9),7)
1227	else:
1228	sig = ref[6] * ref[8] / ref[5]
1229	s += PutInCol(G2mth.ValEsd(ref[8],-abs(sig/10)),12)
1230	s += PutInCol(G2mth.ValEsd(sig,-abs(sig)/10.),10)
1231	s += PutInCol(G2mth.ValEsd(ref[9],-abs(sig/10)),12)
1232	s += PutInCol(G2mth.ValEsd(ref[10],-0.9),7)
1233	dmax = max(dmax,ref[4])
1234	dmin = min(dmin,ref[4])
1235	WriteCIFitem(s)
1236	if not self.quickmode: # statistics only in a full CIF
1237	WriteReflStat(refcount,hklmin,hklmax,dmin,dmax)
1238	hId = histblk['hId']
1239	hfx = '0:'+str(hId)+':'
1240	phfx = '%d:%d:'%(0,hId)
1241	extType,extModel,extParms = self.Phases[phasenam]['Histograms'][histlbl]['Extinction']
1242	if extModel != 'None':
1243	WriteCIFitem('# Extinction scaled by 1.e5')
1244	WriteCIFitem('_refine_ls_extinction_method','Becker-Coppens %s %s'%(extModel,extType))
1245	sig = -1.e-3
1246	if extModel == 'Primary':
1247	parm = extParms['Ep'][0]*1.e5
1248	if extParms['Ep'][1]:
1249	sig = self.sigDict[phfx+'Ep']*1.e5
1250	text = G2mth.ValEsd(parm,sig)
1251	elif extModel == 'Secondary Type I':
1252	parm = extParms['Eg'][0]*1.e5
1253	if extParms['Eg'][1]:
1254	sig = self.sigDict[phfx+'Eg']*1.e5
1255	text = G2mth.ValEsd(parm,sig)
1256	elif extModel == 'Secondary Type II':
1257	parm = extParms['Es'][0]*1.e5
1258	if extParms['Es'][1]:
1259	sig = self.sigDict[phfx+'Es']*1.e5
1260	text = G2mth.ValEsd(parm,sig)
1261	elif extModel == 'Secondary Type I & II':
1262	parm = extParms['Eg'][0]*1.e5
1263	if extParms['Es'][1]:
1264	sig = self.sigDict[phfx+'Es']*1.e5
1265	text = G2mth.ValEsd(parm,sig)
1266	sig = -1.0e-3
1267	parm = extParms['Es'][0]*1.e5
1268	if extParms['Es'][1]:
1269	sig = self.sigDict[phfx+'Es']*1.e5
1270	text += G2mth.ValEsd(parm,sig)
1271	WriteCIFitem('_refine_ls_extinction_coef',text)
1272	WriteCIFitem('_refine_ls_extinction_expression','Becker & Coppens (1974). Acta Cryst. A30, 129-147')
1273
1274	WriteCIFitem('_refine_ls_wR_factor_gt ','%.4f'%(histblk['wR']/100.))
1275	WriteCIFitem('_refine_ls_R_factor_gt ','%.4f'%(histblk[hfx+'Rf']/100.))
1276	WriteCIFitem('_refine_ls_R_Fsqd_factor ','%.4f'%(histblk[hfx+'Rf^2']/100.))
1277	def EditAuthor(event=None):
1278	'dialog to edit the CIF author info'
1279	'Edit the CIF author name'
1280	dlg = G2G.SingleStringDialog(self.G2frame,
1281	'Get CIF Author',
1282	'Provide CIF Author name (Last, First)',
1283	value=self.author)
1284	if not dlg.Show():
1285	dlg.Destroy()
1286	return False # cancel was pressed
1287	self.author = dlg.GetValue()
1288	dlg.Destroy()
1289	try:
1290	self.OverallParms['Controls']["Author"] = self.author # save for future
1291	except KeyError:
1292	pass
1293	return True
1294	def EditInstNames(event=None):
1295	'Provide a dialog for editing instrument names'
1296	dictlist = []
1297	keylist = []
1298	lbllist = []
1299	for hist in self.Histograms:
1300	if hist.startswith("PWDR"):
1301	key2 = "Sample Parameters"
1302	d = self.Histograms[hist][key2]
1303	elif hist.startswith("HKLF"):
1304	key2 = "Instrument Parameters"
1305	d = self.Histograms[hist][key2][0]
1306
1307	lbllist.append(hist)
1308	dictlist.append(d)
1309	keylist.append('InstrName')
1310	instrname = d.get('InstrName')
1311	if instrname is None:
1312	d['InstrName'] = ''
1313	return G2ctrls.CallScrolledMultiEditor(
1314	self.G2frame,dictlist,keylist,
1315	prelbl=range(1,len(dictlist)+1),
1316	postlbl=lbllist,
1317	title='Instrument names',
1318	header="Edit instrument names. Note that a non-blank\nname is required for all histograms",
1319	CopyButton=True)
1320
1321	def EditRanges(event):
1322	'''Edit the bond distance/angle search range; phase is determined from
1323	a pointer placed in the button object (.phasedict) that references the
1324	phase dictionary
1325	'''
1326	but = event.GetEventObject()
1327	phasedict = but.phasedict
1328	dlg = G2gd.DisAglDialog(
1329	self.G2frame,
1330	phasedict['General']['DisAglCtls'], # edited
1331	phasedict['General'], # defaults
1332	)
1333	if dlg.ShowModal() == wx.ID_OK:
1334	phasedict['General']['DisAglCtls'] = dlg.GetData()
1335	dlg.Destroy()
1336
1337	def EditCIFDefaults():
1338	'''Fills the CIF Defaults window with controls for editing various CIF export
1339	parameters (mostly related to templates).
1340	'''
1341	self.cifdefs.DestroyChildren()
1342	self.cifdefs.SetTitle('Edit CIF settings')
1343	vbox = wx.BoxSizer(wx.VERTICAL)
1344	vbox.Add(wx.StaticText(self.cifdefs, wx.ID_ANY,'Creating file '+str(self.filename)))
1345	but = wx.Button(self.cifdefs, wx.ID_ANY,'Edit CIF Author')
1346	but.Bind(wx.EVT_BUTTON,EditAuthor)
1347	vbox.Add(but,0,wx.ALIGN_CENTER,3)
1348	but = wx.Button(self.cifdefs, wx.ID_ANY,'Edit Instrument Name(s)')
1349	but.Bind(wx.EVT_BUTTON,EditInstNames)
1350	vbox.Add(but,0,wx.ALIGN_CENTER,3)
1351	cpnl = wxscroll.ScrolledPanel(self.cifdefs,size=(300,300))
1352	cbox = wx.BoxSizer(wx.VERTICAL)
1353	G2G.HorizontalLine(cbox,cpnl)
1354	cbox.Add(
1355	CIFtemplateSelect(self.cifdefs,
1356	cpnl,'publ',self.OverallParms['Controls'],
1357	EditCIFDefaults,
1358	"Publication (overall) template",
1359	),
1360	0,wx.EXPAND\|wx.ALIGN_LEFT\|wx.ALL)
1361	for phasenam in sorted(self.Phases.keys()):
1362	G2G.HorizontalLine(cbox,cpnl)
1363	title = 'Phase '+phasenam
1364	phasedict = self.Phases[phasenam] # pointer to current phase info
1365	cbox.Add(
1366	CIFtemplateSelect(self.cifdefs,
1367	cpnl,'phase',phasedict['General'],
1368	EditCIFDefaults,
1369	title,
1370	phasenam),
1371	0,wx.EXPAND\|wx.ALIGN_LEFT\|wx.ALL)
1372	cpnl.SetSizer(cbox)
1373	if phasedict['General']['Type'] == 'nuclear':
1374	but = wx.Button(cpnl, wx.ID_ANY,'Edit distance/angle ranges')
1375	cbox.Add(but,0,wx.ALIGN_LEFT,0)
1376	cbox.Add((-1,2))
1377	but.phasedict = self.Phases[phasenam] # set a pointer to current phase info
1378	but.Bind(wx.EVT_BUTTON,EditRanges) # phase bond/angle ranges
1379	but = wx.Button(cpnl, wx.ID_ANY,'Set distance/angle publication flags')
1380	but.phase = phasenam # set a pointer to current phase info
1381	but.Bind(wx.EVT_BUTTON,SelectDisAglFlags) # phase bond/angle ranges
1382	cbox.Add(but,0,wx.ALIGN_LEFT,0)
1383	cbox.Add((-1,2))
1384	for i in sorted(self.powderDict.keys()):
1385	G2G.HorizontalLine(cbox,cpnl)
1386	hist = self.powderDict[i]
1387	histblk = self.Histograms[hist]
1388	title = 'Powder dataset '+hist[5:]
1389	cbox.Add(
1390	CIFtemplateSelect(self.cifdefs,
1391	cpnl,'powder',histblk["Sample Parameters"],
1392	EditCIFDefaults,
1393	title,
1394	histblk["Sample Parameters"]['InstrName']),
1395	0,wx.EXPAND\|wx.ALIGN_LEFT\|wx.ALL)
1396	for i in sorted(self.xtalDict.keys()):
1397	G2G.HorizontalLine(cbox,cpnl)
1398	hist = self.xtalDict[i]
1399	histblk = self.Histograms[hist]
1400	title = 'Single Xtal dataset '+hist[5:]
1401	cbox.Add(
1402	CIFtemplateSelect(self.cifdefs,
1403	cpnl,'single',histblk["Instrument Parameters"][0],
1404	EditCIFDefaults,
1405	title,
1406	histblk["Instrument Parameters"][0]['InstrName']),
1407	0,wx.EXPAND\|wx.ALIGN_LEFT\|wx.ALL)
1408	cpnl.SetSizer(cbox)
1409	cpnl.SetAutoLayout(1)
1410	cpnl.SetupScrolling()
1411	#cpnl.Bind(rw.EVT_RW_LAYOUT_NEEDED, self.OnLayoutNeeded) # needed if sizes change
1412	cpnl.Layout()
1413
1414	vbox.Add(cpnl, 1, wx.ALIGN_LEFT\|wx.ALL\|wx.EXPAND, 0)
1415	btnsizer = wx.StdDialogButtonSizer()
1416	btn = wx.Button(self.cifdefs, wx.ID_OK, "Create CIF")
1417	btn.SetDefault()
1418	btnsizer.AddButton(btn)
1419	btn = wx.Button(self.cifdefs, wx.ID_CANCEL)
1420	btnsizer.AddButton(btn)
1421	btnsizer.Realize()
1422	vbox.Add(btnsizer, 0, wx.ALIGN_CENTER\|wx.ALL, 5)
1423	self.cifdefs.SetSizer(vbox)
1424	vbox.Fit(self.cifdefs)
1425	self.cifdefs.Layout()
1426
1427	def OnToggleButton(event):
1428	'Respond to press of ToggleButton in SelectDisAglFlags'
1429	but = event.GetEventObject()
1430	if but.GetValue():
1431	but.DisAglSel[but.key] = True
1432	else:
1433	try:
1434	del but.DisAglSel[but.key]
1435	except KeyError:
1436	pass
1437	def keepTrue(event):
1438	event.GetEventObject().SetValue(True)
1439	def keepFalse(event):
1440	event.GetEventObject().SetValue(False)
1441
1442	def SelectDisAglFlags(event):
1443	'Select Distance/Angle use flags for the selected phase'
1444	phasenam = event.GetEventObject().phase
1445	phasedict = self.Phases[phasenam]
1446	SymOpList,offsetList,symOpList,G2oprList = G2spc.AllOps(phasedict['General']['SGData'])
1447	generalData = phasedict['General']
1448	# create a dict for storing Pub flag for bonds/angles, if needed
1449	if phasedict['General'].get("DisAglHideFlag") is None:
1450	phasedict['General']["DisAglHideFlag"] = {}
1451	DisAngSel = phasedict['General']["DisAglHideFlag"]
1452
1453	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
1454	cn = ct-1
1455	cfrac = cx+3
1456	DisAglData = {}
1457	# create a list of atoms, but skip atoms with zero occupancy
1458	xyz = []
1459	fpfx = str(phasedict['pId'])+'::Afrac:'
1460	for i,atom in enumerate(phasedict['Atoms']):
1461	if self.parmDict.get(fpfx+str(i),atom[cfrac]) == 0.0: continue
1462	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
1463	if 'DisAglCtls' not in generalData:
1464	# should not be used, since DisAglDialog should be called
1465	# for all phases before getting here
1466	dlg = G2gd.DisAglDialog(
1467	self.cifdefs,
1468	{},
1469	generalData)
1470	if dlg.ShowModal() == wx.ID_OK:
1471	generalData['DisAglCtls'] = dlg.GetData()
1472	else:
1473	dlg.Destroy()
1474	return
1475	dlg.Destroy()
1476	dlg = wx.Dialog(
1477	self.G2frame,
1478	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
1479	vbox = wx.BoxSizer(wx.VERTICAL)
1480	txt = wx.StaticText(dlg,wx.ID_ANY,'Searching distances for phase '+phasenam
1481	+'\nPlease wait...')
1482	vbox.Add(txt,0,wx.ALL\|wx.EXPAND)
1483	dlg.SetSizer(vbox)
1484	dlg.CenterOnParent()
1485	dlg.Show() # post "please wait"
1486	wx.BeginBusyCursor() # and change cursor
1487
1488	DisAglData['OrigAtoms'] = xyz
1489	DisAglData['TargAtoms'] = xyz
1490	SymOpList,offsetList,symOpList,G2oprList = G2spc.AllOps(
1491	generalData['SGData'])
1492
1493	xpandSGdata = generalData['SGData'].copy()
1494	xpandSGdata.update({'SGOps':symOpList,
1495	'SGInv':False,
1496	'SGLatt':'P',
1497	'SGCen':np.array([[0, 0, 0]]),})
1498	DisAglData['SGData'] = xpandSGdata
1499
1500	DisAglData['Cell'] = generalData['Cell'][1:] #+ volume
1501	if 'pId' in phasedict:
1502	DisAglData['pId'] = phasedict['pId']
1503	DisAglData['covData'] = self.OverallParms['Covariance']
1504	try:
1505	AtomLabels,DistArray,AngArray = G2stMn.RetDistAngle(
1506	generalData['DisAglCtls'],
1507	DisAglData)
1508	except KeyError: # inside DistAngle for missing atom types in DisAglCtls
1509	print('** ERROR - try again but do "Reset" to fill in missing atom types **')
1510	wx.EndBusyCursor()
1511	txt.SetLabel('Set publication flags for distances and angles in\nphase '+phasenam)
1512	vbox.Add((5,5))
1513	vbox.Add(wx.StaticText(dlg,wx.ID_ANY,
1514	'The default is to flag all distances and angles as to be'+
1515	'\npublished. Change this by pressing appropriate buttons.'),
1516	0,wx.ALL\|wx.EXPAND)
1517	hbox = wx.BoxSizer(wx.HORIZONTAL)
1518	vbox.Add(hbox)
1519	hbox.Add(wx.StaticText(dlg,wx.ID_ANY,'Button appearance: '))
1520	but = wx.ToggleButton(dlg,wx.ID_ANY,'Publish')
1521	but.Bind(wx.EVT_TOGGLEBUTTON,keepFalse)
1522	hbox.Add(but)
1523	but = wx.ToggleButton(dlg,wx.ID_ANY,"Don't publish")
1524	but.Bind(wx.EVT_TOGGLEBUTTON,keepTrue)
1525	hbox.Add(but)
1526	but.SetValue(True)
1527	G2G.HorizontalLine(vbox,dlg)
1528
1529	cpnl = wxscroll.ScrolledPanel(dlg,size=(400,300))
1530	cbox = wx.BoxSizer(wx.VERTICAL)
1531	for c in sorted(DistArray):
1532	karr = []
1533	UsedCols = {}
1534	cbox.Add(wx.StaticText(cpnl,wx.ID_ANY,
1535	'distances to/angles around atom '+AtomLabels[c]))
1536	#dbox = wx.GridBagSizer(hgap=5)
1537	dbox = wx.GridBagSizer()
1538	for i,D in enumerate(DistArray[c]):
1539	karr.append(tuple(D[0:3]))
1540	val = "{:.2f}".format(D[3])
1541	sym = " [{:d} {:d} {:d}]".format(*D[1]) + " #{:d}".format(D[2])
1542	dbox.Add(wx.StaticText(cpnl,wx.ID_ANY,AtomLabels[D[0]]),
1543	(i+1,0)
1544	)
1545	dbox.Add(wx.StaticText(cpnl,wx.ID_ANY,sym),
1546	(i+1,1)
1547	)
1548	but = wx.ToggleButton(cpnl,wx.ID_ANY,val)
1549	but.key = (c,karr[-1])
1550	but.DisAglSel = DisAngSel
1551	if DisAngSel.get(but.key): but.SetValue(True)
1552	but.Bind(wx.EVT_TOGGLEBUTTON,OnToggleButton)
1553	dbox.Add(but,(i+1,2),border=1)
1554	for i,D in enumerate(AngArray[c]):
1555	val = "{:.1f}".format(D[2][0])
1556	but = wx.ToggleButton(cpnl,wx.ID_ANY,val)
1557	but.key = (karr[D[0]],c,karr[D[1]])
1558	but.DisAglSel = DisAngSel
1559	if DisAngSel.get(but.key): but.SetValue(True)
1560	but.Bind(wx.EVT_TOGGLEBUTTON,OnToggleButton)
1561	dbox.Add(but,(D[0]+1,D[1]+3),border=1)
1562	UsedCols[D[1]+3] = True
1563	for i,D in enumerate(DistArray[c][:-1]): # label columns that are used
1564	if UsedCols.get(i+3):
1565	dbox.Add(wx.StaticText(cpnl,wx.ID_ANY,AtomLabels[D[0]]),
1566	(0,i+3),
1567	flag=wx.ALIGN_CENTER
1568	)
1569	dbox.Add(wx.StaticText(cpnl,wx.ID_ANY,'distance'),
1570	(0,2),
1571	flag=wx.ALIGN_CENTER
1572	)
1573	cbox.Add(dbox)
1574	G2G.HorizontalLine(cbox,cpnl)
1575	cpnl.SetSizer(cbox)
1576	cpnl.SetAutoLayout(1)
1577	cpnl.SetupScrolling()
1578	#cpnl.Bind(rw.EVT_RW_LAYOUT_NEEDED, self.OnLayoutNeeded) # needed if sizes change
1579	cpnl.Layout()
1580
1581	vbox.Add(cpnl, 1, wx.ALIGN_LEFT\|wx.ALL\|wx.EXPAND, 0)
1582
1583	btnsizer = wx.StdDialogButtonSizer()
1584	btn = wx.Button(dlg, wx.ID_OK, "Done")
1585	btn.SetDefault()
1586	btnsizer.AddButton(btn)
1587	btnsizer.Realize()
1588	vbox.Add(btnsizer, 0, wx.ALIGN_CENTER\|wx.ALL, 5)
1589	dlg.SetSizer(vbox)
1590	vbox.Fit(dlg)
1591	dlg.Layout()
1592
1593	dlg.CenterOnParent()
1594	dlg.ShowModal()
1595
1596	#***** end of functions for export method =======================================
1597	#=================================================================================
1598
1599	# the export process starts here
1600	self.InitExport(event)
1601	# load all of the tree into a set of dicts
1602	self.loadTree()
1603	# create a dict with refined values and their uncertainties
1604	self.loadParmDict()
1605	if self.mode=='simple':
1606	if self.ExportSelect('ask'): return
1607	else:
1608	if self.ExportSelect('default'): return
1609	# Someday: get restraint & constraint info
1610	#restraintDict = self.OverallParms.get('Restraints',{})
1611	#for i in self.OverallParms['Constraints']:
1612	# print i
1613	# for j in self.OverallParms['Constraints'][i]:
1614	# print j
1615
1616	self.CIFdate = dt.datetime.strftime(dt.datetime.now(),"%Y-%m-%dT%H:%M")
1617	# is there anything to export?
1618	if len(self.Phases) == len(self.powderDict) == len(self.xtalDict) == 0:
1619	self.G2frame.ErrorDialog(
1620	'Empty project',
1621	'Project does not contain any data or phases. Are they interconnected?')
1622	return
1623	# get the project file name
1624	self.CIFname = os.path.splitext(
1625	os.path.split(self.G2frame.GSASprojectfile)[1]
1626	)[0]
1627	self.CIFname = self.CIFname.replace(' ','')
1628	if not self.CIFname: # none defined & needed, save as GPX to get one
1629	self.G2frame.OnFileSaveas(None)
1630	if not self.G2frame.GSASprojectfile: return
1631	self.CIFname = os.path.splitext(
1632	os.path.split(self.G2frame.GSASprojectfile)[1]
1633	)[0]
1634	self.CIFname = self.CIFname.replace(' ','')
1635	# test for quick CIF mode or no data
1636	self.quickmode = False
1637	phasenam = None # include all phases
1638	if self.mode == "simple" and self.currentExportType == 'phase':
1639	if len(self.Phases) == 0: # this check is probably not needed
1640	self.G2frame.ErrorDialog(
1641	'No phase present',
1642	'Cannot create a coordinates CIF with no phases')
1643	return
1644	self.quickmode = True
1645	oneblock = True
1646	if len(self.Phases) > 1: # quick mode: get selected phase
1647	phasenam = self.phasenam[0]
1648	elif self.mode == "simple": # powder/single xtal data export
1649	self.quickmode = True
1650	oneblock = True
1651	# Project export: will this require a multiblock CIF?
1652	elif len(self.Phases) > 1:
1653	oneblock = False
1654	elif len(self.powderDict) + len(self.xtalDict) > 1:
1655	oneblock = False
1656	else: # one phase, one dataset, Full CIF
1657	oneblock = True
1658
1659	# make sure required information is present
1660	# get CIF author name -- required for full CIFs
1661	try:
1662	self.author = self.OverallParms['Controls'].get("Author",'').strip()
1663	except KeyError:
1664	pass
1665	while not (self.author or self.quickmode):
1666	if not EditAuthor(): return
1667	self.shortauthorname = self.author.replace(',','').replace(' ','')[:20]
1668
1669	# check there is an instrument name for every histogram
1670	self.ifPWDR = False
1671	self.ifHKLF = False
1672	if not self.quickmode:
1673	invalid = 0
1674	key3 = 'InstrName'
1675	for hist in self.Histograms:
1676	if hist.startswith("PWDR"):
1677	self.ifPWDR = True
1678	key2 = "Sample Parameters"
1679	d = self.Histograms[hist][key2]
1680	elif hist.startswith("HKLF"):
1681	self.ifHKLF = True
1682	key2 = "Instrument Parameters"
1683	d = self.Histograms[hist][key2][0]
1684	instrname = d.get(key3)
1685	if instrname is None:
1686	d[key3] = ''
1687	invalid += 1
1688	elif instrname.strip() == '':
1689	invalid += 1
1690	if invalid:
1691	msg = ""
1692	if invalid > 3: msg = (
1693	"\n\nNote: it may be faster to set the name for\n"
1694	"one histogram for each instrument and use the\n"
1695	"File/Copy option to duplicate the name"
1696	)
1697	if not EditInstNames(): return
1698	if not self.quickmode:
1699	# check for a distance-angle range search range for each phase
1700	for phasenam in sorted(self.Phases.keys()):
1701	#i = self.Phases[phasenam]['pId']
1702	phasedict = self.Phases[phasenam] # pointer to current phase info
1703	if 'DisAglCtls' not in phasedict['General']:
1704	dlg = G2gd.DisAglDialog(
1705	self.G2frame,
1706	{},
1707	phasedict['General'])
1708	if dlg.ShowModal() == wx.ID_OK:
1709	phasedict['General']['DisAglCtls'] = dlg.GetData()
1710	else:
1711	dlg.Destroy()
1712	return
1713	dlg.Destroy()
1714	if not self.quickmode:
1715	# check if temperature values & pressure are defaulted
1716	default = 0
1717	for hist in self.Histograms:
1718	if hist.startswith("PWDR"):
1719	key2 = "Sample Parameters"
1720	T = self.Histograms[hist][key2].get('Temperature')
1721	if not T:
1722	default += 1
1723	elif T == 300:
1724	default += 1
1725	P = self.Histograms[hist][key2].get('Pressure')
1726	if not P:
1727	default += 1
1728	elif P == 1:
1729	default += 1
1730	if default > 0:
1731	dlg = wx.MessageDialog(
1732	self.G2frame,
1733	'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?',
1734	'Check T and P values',
1735	wx.OK\|wx.CANCEL)
1736	ret = dlg.ShowModal()
1737	dlg.Destroy()
1738	if ret != wx.ID_OK: return
1739	if oneblock and not self.quickmode:
1740	# select a dataset to use (there should only be one set in one block,
1741	# but take whatever comes 1st)
1742	for hist in self.Histograms:
1743	histblk = self.Histograms[hist]
1744	if hist.startswith("PWDR"):
1745	instnam = histblk["Sample Parameters"]['InstrName']
1746	break # ignore all but 1st data histogram
1747	elif hist.startswith("HKLF"):
1748	instnam = histblk["Instrument Parameters"][0]['InstrName']
1749	break # ignore all but 1st data histogram
1750	if not self.quickmode: # give the user a chance to edit all defaults
1751	self.cifdefs = wx.Dialog(
1752	self.G2frame,
1753	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
1754	EditCIFDefaults()
1755	self.cifdefs.CenterOnParent()
1756	val = self.cifdefs.ShowModal()
1757	self.cifdefs.Destroy()
1758	if val != wx.ID_OK:
1759	return
1760	#======================================================================
1761	# Start writing the CIF - single block
1762	#======================================================================
1763	print('Writing CIF output to file '+str(self.filename)+"...")
1764	self.OpenFile()
1765	if self.currentExportType == 'single' or self.currentExportType == 'powder':
1766	#======Data only CIF (powder/xtal) ====================================
1767	hist = self.histnam[0]
1768	self.CIFname = hist[5:40].replace(' ','')
1769	WriteCIFitem('data_'+self.CIFname)
1770	if hist.startswith("PWDR"):
1771	WritePowderData(hist)
1772	elif hist.startswith("HKLF"):
1773	WriteSingleXtalData(hist)
1774	else:
1775	print "should not happen"
1776	elif self.quickmode:
1777	#====Phase only CIF ====================================================
1778	WriteCIFitem('data_'+self.CIFname)
1779	if phasenam is None: # if not already selected, select the first phase (should be one)
1780	phasenam = self.Phases.keys()[0]
1781	#print 'phasenam',phasenam
1782	phaseblk = self.Phases[phasenam] # pointer to current phase info
1783	# report the phase info
1784	WritePhaseInfo(phasenam)
1785	elif oneblock:
1786	#====Single block, data & phase CIF ===================================
1787	WriteCIFitem('data_'+self.CIFname)
1788	if phasenam is None: # if not already selected, select the first phase (should be one)
1789	phasenam = self.Phases.keys()[0]
1790	#print 'phasenam',phasenam
1791	phaseblk = self.Phases[phasenam] # pointer to current phase info
1792	instnam = instnam.replace(' ','')
1793	WriteCIFitem('_pd_block_id',
1794	str(self.CIFdate) + "\|" + str(self.CIFname) + "\|" +
1795	str(self.shortauthorname) + "\|" + instnam)
1796	WriteAudit()
1797	writeCIFtemplate(self.OverallParms['Controls'],'publ') # overall (publication) template
1798	WriteOverall()
1799	writeCIFtemplate(self.Phases[phasenam]['General'],'phase',phasenam) # write phase template
1800	# report the phase info
1801	WritePhaseInfo(phasenam)
1802	if hist.startswith("PWDR"):
1803	# preferred orientation
1804	SH = FormatSH(phasenam)
1805	MD = FormatHAPpo(phasenam)
1806	if SH and MD:
1807	WriteCIFitem('_pd_proc_ls_pref_orient_corr', SH + '\n' + MD)
1808	elif SH or MD:
1809	WriteCIFitem('_pd_proc_ls_pref_orient_corr', SH + MD)
1810	else:
1811	WriteCIFitem('_pd_proc_ls_pref_orient_corr', 'none')
1812	# report profile, since one-block: include both histogram and phase info
1813	WriteCIFitem('_pd_proc_ls_profile_function',
1814	FormatInstProfile(histblk["Instrument Parameters"],histblk['hId'])
1815	+'\n'+FormatPhaseProfile(phasenam))
1816	histblk = self.Histograms[hist]["Sample Parameters"]
1817	writeCIFtemplate(histblk,'powder',histblk['InstrName']) # write powder template
1818	WritePowderData(hist)
1819	elif hist.startswith("HKLF"):
1820	histprm = self.Histograms[hist]["Instrument Parameters"][0]
1821	writeCIFtemplate(histprm,'single',histprm['InstrName']) # single crystal template
1822	WriteSingleXtalData(hist)
1823	else:
1824	#=== multiblock: multiple phases and/or histograms ====================
1825	nsteps = 1 + len(self.Phases) + len(self.powderDict) + len(self.xtalDict)
1826	try:
1827	dlg = wx.ProgressDialog('CIF progress','starting',nsteps,parent=self.G2frame)
1828	Size = dlg.GetSize()
1829	Size = (int(Size[0]*3),Size[1]) # increase size along x
1830	dlg.SetSize(Size)
1831	dlg.CenterOnParent()
1832
1833	# publication info
1834	step = 1
1835	dlg.Update(step,"Exporting overall section")
1836	WriteCIFitem('\ndata_'+self.CIFname+'_publ')
1837	WriteAudit()
1838	WriteCIFitem('_pd_block_id',
1839	str(self.CIFdate) + "\|" + str(self.CIFname) + "\|" +
1840	str(self.shortauthorname) + "\|Overall")
1841	writeCIFtemplate(self.OverallParms['Controls'],'publ') #insert the publication template
1842	# ``template_publ.cif`` or a modified version
1843	# overall info
1844	WriteCIFitem('data_'+str(self.CIFname)+'_overall')
1845	WriteOverall()
1846	#============================================================
1847	WriteCIFitem('# POINTERS TO PHASE AND HISTOGRAM BLOCKS')
1848	datablockidDict = {} # save block names here -- N.B. check for conflicts between phase & hist names (unlikely!)
1849	# loop over phase blocks
1850	if len(self.Phases) > 1:
1851	loopprefix = ''
1852	WriteCIFitem('loop_ _pd_phase_block_id')
1853	else:
1854	loopprefix = '_pd_phase_block_id'
1855
1856	for phasenam in sorted(self.Phases.keys()):
1857	i = self.Phases[phasenam]['pId']
1858	datablockidDict[phasenam] = (str(self.CIFdate) + "\|" + str(self.CIFname) + "\|" +
1859	'phase_'+ str(i) + '\|' + str(self.shortauthorname))
1860	WriteCIFitem(loopprefix,datablockidDict[phasenam])
1861	# loop over data blocks
1862	if len(self.powderDict) + len(self.xtalDict) > 1:
1863	loopprefix = ''
1864	WriteCIFitem('loop_ _pd_block_diffractogram_id')
1865	else:
1866	loopprefix = '_pd_block_diffractogram_id'
1867	for i in sorted(self.powderDict.keys()):
1868	hist = self.powderDict[i]
1869	histblk = self.Histograms[hist]
1870	instnam = histblk["Sample Parameters"]['InstrName']
1871	instnam = instnam.replace(' ','')
1872	j = histblk['hId']
1873	datablockidDict[hist] = (str(self.CIFdate) + "\|" + str(self.CIFname) + "\|" +
1874	str(self.shortauthorname) + "\|" +
1875	instnam + "_hist_"+str(j))
1876	WriteCIFitem(loopprefix,datablockidDict[hist])
1877	for i in sorted(self.xtalDict.keys()):
1878	hist = self.xtalDict[i]
1879	histblk = self.Histograms[hist]
1880	instnam = histblk["Instrument Parameters"][0]['InstrName']
1881	instnam = instnam.replace(' ','')
1882	i = histblk['hId']
1883	datablockidDict[hist] = (str(self.CIFdate) + "\|" + str(self.CIFname) + "\|" +
1884	str(self.shortauthorname) + "\|" +
1885	instnam + "_hist_"+str(i))
1886	WriteCIFitem(loopprefix,datablockidDict[hist])
1887	#============================================================
1888	# loop over phases, exporting them
1889	phasebyhistDict = {} # create a cross-reference to phases by histogram
1890	for j,phasenam in enumerate(sorted(self.Phases.keys())):
1891	step += 1
1892	dlg.Update(step,"Exporting phase "+phasenam+' (#'+str(j+1)+')')
1893	i = self.Phases[phasenam]['pId']
1894	WriteCIFitem('\ndata_'+self.CIFname+"_phase_"+str(i))
1895	WriteCIFitem('# Information for phase '+str(i))
1896	WriteCIFitem('_pd_block_id',datablockidDict[phasenam])
1897	# report the phase
1898	writeCIFtemplate(self.Phases[phasenam]['General'],'phase',phasenam) # write phase template
1899	WritePhaseInfo(phasenam)
1900	# preferred orientation
1901	if self.ifPWDR:
1902	SH = FormatSH(phasenam)
1903	MD = FormatHAPpo(phasenam)
1904	if SH and MD:
1905	WriteCIFitem('_pd_proc_ls_pref_orient_corr', SH + '\n' + MD)
1906	elif SH or MD:
1907	WriteCIFitem('_pd_proc_ls_pref_orient_corr', SH + MD)
1908	else:
1909	WriteCIFitem('_pd_proc_ls_pref_orient_corr', 'none')
1910	# report sample profile terms
1911	PP = FormatPhaseProfile(phasenam)
1912	if PP:
1913	WriteCIFitem('_pd_proc_ls_profile_function',PP)
1914
1915	#============================================================
1916	# loop over histograms, exporting them
1917	for i in sorted(self.powderDict.keys()):
1918	hist = self.powderDict[i]
1919	histblk = self.Histograms[hist]
1920	if hist.startswith("PWDR"):
1921	step += 1
1922	dlg.Update(step,"Exporting "+hist.strip())
1923	WriteCIFitem('\ndata_'+self.CIFname+"_pwd_"+str(i))
1924	#instnam = histblk["Sample Parameters"]['InstrName']
1925	# report instrumental profile terms
1926	WriteCIFitem('_pd_proc_ls_profile_function',
1927	FormatInstProfile(histblk["Instrument Parameters"],histblk['hId']))
1928	WriteCIFitem('# Information for histogram '+str(i)+': '+hist)
1929	WriteCIFitem('_pd_block_id',datablockidDict[hist])
1930	histprm = self.Histograms[hist]["Sample Parameters"]
1931	writeCIFtemplate(histprm,'powder',histprm['InstrName']) # powder template
1932	WritePowderData(hist)
1933	for i in sorted(self.xtalDict.keys()):
1934	hist = self.xtalDict[i]
1935	histblk = self.Histograms[hist]
1936	if hist.startswith("HKLF"):
1937	step += 1
1938	dlg.Update(step,"Exporting "+hist.strip())
1939	WriteCIFitem('\ndata_'+self.CIFname+"_sx_"+str(i))
1940	#instnam = histblk["Instrument Parameters"][0]['InstrName']
1941	WriteCIFitem('# Information for histogram '+str(i)+': '+hist)
1942	WriteCIFitem('_pd_block_id',datablockidDict[hist])
1943	histprm = self.Histograms[hist]["Instrument Parameters"][0]
1944	writeCIFtemplate(histprm,'single',histprm['InstrName']) # single crystal template
1945	WriteSingleXtalData(hist)
1946
1947	except Exception:
1948	import traceback
1949	print(traceback.format_exc())
1950	self.G2frame.ErrorDialog('Exception',
1951	'Error occurred in CIF creation. '+
1952	'See full error message in console output ')
1953	finally:
1954	dlg.Destroy()
1955
1956	WriteCIFitem('#--' + 15*'eof--' + '#')
1957	self.CloseFile()
1958	print("...export completed")
1959	print('file '+str(self.fullpath))
1960	# end of CIF export
1961
1962	class ExportPhaseCIF(ExportCIF):
1963	'''Used to create a simple CIF of at most one phase. Uses exact same code as
1964	:class:`ExportCIF` except that `self.mode` is set to "simple" in `self.InitExport`.
1965	Shows up in menu as Quick CIF.
1966
1967	:param wx.Frame G2frame: reference to main GSAS-II frame
1968	'''
1969	def __init__(self,G2frame):
1970	G2IO.ExportBaseclass.__init__(self,
1971	G2frame=G2frame,
1972	formatName = 'Quick CIF',
1973	extension='.cif',
1974	longFormatName = 'Export one phase in CIF'
1975	)
1976	self.exporttype = ['phase']
1977	# CIF-specific items
1978	self.author = ''
1979	self.mode = 'simple'
1980
1981	class ExportDataCIF(ExportCIF):
1982	'''Used to create a simple CIF containing diffraction data only. Uses exact same code as
1983	:class:`ExportCIF` except that `self.mode` is set to "simple" and `self.currentExportType`
1984	is set to "single" or "powder" in `self.InitExport`. Shows up in menus as Data-only CIF.
1985
1986	:param wx.Frame G2frame: reference to main GSAS-II frame
1987	'''
1988	def __init__(self,G2frame):
1989	G2IO.ExportBaseclass.__init__(self,
1990	G2frame=G2frame,
1991	formatName = 'Data-only CIF',
1992	extension='.cif',
1993	longFormatName = 'Export data as CIF'
1994	)
1995	self.exporttype = ['single','powder']
1996	# CIF-specific items
1997	self.author = ''
1998	self.mode = 'simple'
1999
2000	#===============================================================================
2001	# misc CIF utilities
2002	#===============================================================================
2003	def PickleCIFdict(fil):
2004	'''Loads a CIF dictionary, cherry picks out the items needed
2005	by local code and sticks them into a python dict and writes
2006	that dict out as a cPickle file for later reuse.
2007	If the write fails a warning message is printed,
2008	but no exception occurs.
2009
2010	:param str fil: file name of CIF dictionary, will usually end
2011	in .dic
2012	:returns: the dict with the definitions
2013	'''
2014	import CifFile as cif # PyCifRW from James Hester
2015	cifdic = {}
2016	try:
2017	fp = open(fil,'r') # patch: open file to avoid windows bug
2018	dictobj = cif.CifDic(fp)
2019	fp.close()
2020	except IOError:
2021	dictobj = cif.CifDic(fil)
2022	if DEBUG: print('loaded '+str(fil))
2023	for item in dictobj.keys():
2024	cifdic[item] = {}
2025	for j in (
2026	'_definition','_type',
2027	'_enumeration',
2028	'_enumeration_detail',
2029	'_enumeration_range'):
2030	if dictobj[item].get(j):
2031	cifdic[item][j] = dictobj[item][j]
2032	try:
2033	fil = os.path.splitext(fil)[0]+'.cpickle'
2034	fp = open(fil,'w')
2035	cPickle.dump(cifdic,fp)
2036	fp.close()
2037	if DEBUG: print('wrote '+str(fil))
2038	except:
2039	print ('Unable to write '+str(fil))
2040	return cifdic
2041
2042	def LoadCIFdic():
2043	'''Create a composite core+powder CIF lookup dict containing
2044	information about all items in the CIF dictionaries, loading
2045	pickled files if possible. The routine looks for files
2046	named cif_core.cpickle and cif_pd.cpickle in every
2047	directory in the path and if they are not found, files
2048	cif_core.dic and/or cif_pd.dic are read.
2049
2050	:returns: the dict with the definitions
2051	'''
2052	cifdic = {}
2053	for ftyp in "cif_core","cif_pd":
2054	for loc in sys.path:
2055	fil = os.path.join(loc,ftyp+".cpickle")
2056	if not os.path.exists(fil): continue
2057	fp = open(fil,'r')
2058	try:
2059	cifdic.update(cPickle.load(fp))
2060	if DEBUG: print('reloaded '+str(fil))
2061	break
2062	finally:
2063	fp.close()
2064	else:
2065	for loc in sys.path:
2066	fil = os.path.join(loc,ftyp+".dic")
2067	if not os.path.exists(fil): continue
2068	#try:
2069	if True:
2070	cifdic.update(PickleCIFdict(fil))
2071	break
2072	#except:
2073	# pass
2074	else:
2075	print('Could not load '+ftyp+' dictionary')
2076	return cifdic
2077
2078	class CIFdefHelp(wx.Button):
2079	'''Create a help button that displays help information on
2080	the current data item
2081
2082	:param parent: the panel which will be the parent of the button
2083	:param str msg: the help text to be displayed
2084	:param wx.Dialog helpwin: Frame for CIF editing dialog
2085	:param wx.TextCtrl helptxt: TextCtrl where help text is placed
2086	'''
2087	def __init__(self,parent,msg,helpwin,helptxt):
2088	wx.Button.__init__(self,parent,wx.ID_HELP)
2089	self.Bind(wx.EVT_BUTTON,self._onPress)
2090	self.msg=msg
2091	self.parent = parent
2092	#self.helpwin = self.parent.helpwin
2093	self.helpwin = helpwin
2094	self.helptxt = helptxt
2095	def _onPress(self,event):
2096	'Respond to a button press by displaying the requested text'
2097	try:
2098	#helptxt = self.helptxt
2099	ow,oh = self.helptxt.GetSize()
2100	self.helptxt.SetLabel(self.msg)
2101	w,h = self.helptxt.GetSize()
2102	if h > oh:
2103	self.helpwin.GetSizer().Fit(self.helpwin)
2104	except: # error posting help, ignore
2105	return
2106
2107	def CIF2dict(cf):
2108	'''copy the contents of a CIF out from a PyCifRW block object
2109	into a dict
2110
2111	:returns: cifblk, loopstructure where cifblk is a dict with
2112	CIF items and loopstructure is a list of lists that defines
2113	which items are in which loops.
2114	'''
2115	blk = cf.keys()[0] # assume templates are a single CIF block, use the 1st
2116	loopstructure = cf[blk].loopnames()[:] # copy over the list of loop contents
2117	dblk = {}
2118	for item in cf[blk].keys(): # make a copy of all the items in the block
2119	dblk[item] = cf[blk][item]
2120	return dblk,loopstructure
2121
2122	def dict2CIF(dblk,loopstructure,blockname='Template'):
2123	'''Create a PyCifRW CIF object containing a single CIF
2124	block object from a dict and loop structure list.
2125
2126	:param dblk: a dict containing values for each CIF item
2127	:param list loopstructure: a list of lists containing the contents of
2128	each loop, as an example::
2129
2130	[ ["_a","_b"], ["_c"], ["_d_1","_d_2","_d_3"]]
2131
2132	this describes a CIF with this type of structure::
2133
2134	loop_ _a _b <a1> <b1> <a2> ...
2135	loop_ _c <c1> <c2>...
2136	loop _d_1 _d_2 _d_3 ...
2137
2138	Note that the values for each looped CIF item, such as _a,
2139	are contained in a list, for example as cifblk["_a"]
2140
2141	:param str blockname: an optional name for the CIF block.
2142	Defaults to 'Template'
2143
2144	:returns: the newly created PyCifRW CIF object
2145	'''
2146
2147	import CifFile as cif # PyCifRW from James Hester
2148	# compile a 'list' of items in loops
2149	loopnames = set()
2150	for i in loopstructure:
2151	loopnames \|= set(i)
2152	# create a new block
2153	newblk = cif.CifBlock()
2154	# add the looped items
2155	for keys in loopstructure:
2156	vals = []
2157	for key in keys:
2158	vals.append(dblk[key])
2159	newblk.AddCifItem(([keys],[vals]))
2160	# add the non-looped items
2161	for item in dblk:
2162	if item in loopnames: continue
2163	newblk[item] = dblk[item]
2164	# create a CIF and add the block
2165	newcf = cif.CifFile()
2166	newcf[blockname] = newblk
2167	return newcf
2168
2169
2170	class EditCIFtemplate(wx.Dialog):
2171	'''Create a dialog for editing a CIF template. The edited information is
2172	placed in cifblk. If the CIF is saved as a file, the name of that file
2173	is saved as ``self.newfile``.
2174
2175	:param wx.Frame parent: parent frame or None
2176	:param cifblk: dict or PyCifRW block containing values for each CIF item
2177	:param list loopstructure: a list of lists containing the contents of
2178	each loop, as an example::
2179
2180	[ ["_a","_b"], ["_c"], ["_d_1","_d_2","_d_3"]]
2181
2182	this describes a CIF with this type of structure::
2183
2184	loop_ _a _b <a1> <b1> <a2> ...
2185	loop_ _c <c1> <c2>...
2186	loop _d_1 _d_2 _d_3 ...
2187
2188	Note that the values for each looped CIF item, such as _a,
2189	are contained in a list, for example as cifblk["_a"]
2190
2191	:param str defaultname: specifies the default file name to be used for
2192	saving the CIF.
2193	'''
2194	def __init__(self,parent,cifblk,loopstructure,defaultname):
2195	OKbuttons = []
2196	self.cifblk = cifblk
2197	self.loopstructure = loopstructure
2198	self.newfile = None
2199	self.defaultname = defaultname
2200	global CIFdic # once this is loaded, keep it around
2201	if CIFdic is None:
2202	CIFdic = LoadCIFdic()
2203	wx.Dialog.__init__(self,parent,style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
2204
2205	# define widgets that will be needed during panel creation
2206	self.helptxt = wx.StaticText(self,wx.ID_ANY,"")
2207	savebtn = wx.Button(self, wx.ID_CLOSE, "Save as template")
2208	OKbuttons.append(savebtn)
2209	savebtn.Bind(wx.EVT_BUTTON,self._onSave)
2210	OKbtn = wx.Button(self, wx.ID_OK, "Use")
2211	OKbtn.SetDefault()
2212	OKbuttons.append(OKbtn)
2213
2214	self.SetTitle('Edit items in CIF template')
2215	vbox = wx.BoxSizer(wx.VERTICAL)
2216	cpnl = EditCIFpanel(self,cifblk,loopstructure,CIFdic,OKbuttons,size=(300,300))
2217	vbox.Add(cpnl, 1, wx.ALIGN_LEFT\|wx.ALL\|wx.EXPAND, 0)
2218	G2G.HorizontalLine(vbox,self)
2219	vbox.Add(self.helptxt, 0, wx.EXPAND\|wx.ALL, 5)
2220	G2G.HorizontalLine(vbox,self)
2221	btnsizer = wx.BoxSizer(wx.HORIZONTAL)
2222	btn = wx.Button(self, wx.ID_CANCEL)
2223	btnsizer.Add(btn,0,wx.ALIGN_CENTER\|wx.ALL)
2224	btnsizer.Add(savebtn,0,wx.ALIGN_CENTER\|wx.ALL)
2225	btnsizer.Add(OKbtn,0,wx.ALIGN_CENTER\|wx.ALL)
2226	vbox.Add(btnsizer, 0, wx.ALIGN_CENTER\|wx.ALL, 5)
2227	self.SetSizer(vbox)
2228	vbox.Fit(self)
2229	def Post(self):
2230	'''Display the dialog
2231
2232	:returns: True unless Cancel has been pressed.
2233	'''
2234	return (self.ShowModal() == wx.ID_OK)
2235	def _onSave(self,event):
2236	'Save CIF entries in a template file'
2237	pth = G2G.GetExportPath(self.G2frame)
2238	dlg = wx.FileDialog(
2239	self, message="Save as CIF template",
2240	defaultDir=pth,
2241	defaultFile=self.defaultname,
2242	wildcard="CIF (.cif)\|.cif",
2243	style=wx.SAVE)
2244	val = (dlg.ShowModal() == wx.ID_OK)
2245	fil = dlg.GetPath()
2246	dlg.Destroy()
2247	if val: # ignore a Cancel button
2248	fil = os.path.splitext(fil)[0]+'.cif' # force extension
2249	fp = open(fil,'w')
2250	newcf = dict2CIF(self.cifblk,self.loopstructure)
2251	fp.write(newcf.WriteOut())
2252	fp.close()
2253	self.newfile = fil
2254	self.EndModal(wx.ID_OK)
2255
2256	class EditCIFpanel(wxscroll.ScrolledPanel):
2257	'''Creates a scrolled panel for editing CIF template items
2258
2259	:param wx.Frame parent: parent frame where panel will be placed
2260	:param cifblk: dict or PyCifRW block containing values for each CIF item
2261	:param list loopstructure: a list of lists containing the contents of
2262	each loop, as an example::
2263
2264	[ ["_a","_b"], ["_c"], ["_d_1","_d_2","_d_3"]]
2265
2266	this describes a CIF with this type of structure::
2267
2268	loop_ _a _b <a1> <b1> <a2> ...
2269	loop_ _c <c1> <c2>...
2270	loop _d_1 _d_2 _d_3 ...
2271
2272	Note that the values for each looped CIF item, such as _a,
2273	are contained in a list, for example as cifblk["_a"]
2274
2275	:param dict cifdic: optional CIF dictionary definitions
2276	:param list OKbuttons: A list of wx.Button objects that should
2277	be disabled when information in the CIF is invalid
2278	:param (other): optional keyword parameters for wx.ScrolledPanel
2279	'''
2280	def __init__(self, parent, cifblk, loopstructure, cifdic={}, OKbuttons=[], **kw):
2281	self.parent = parent
2282	wxscroll.ScrolledPanel.__init__(self, parent, wx.ID_ANY, **kw)
2283	self.vbox = None
2284	self.AddDict = None
2285	self.cifdic = cifdic
2286	self.cifblk = cifblk
2287	self.loops = loopstructure
2288	self.parent = parent
2289	self.LayoutCalled = False
2290	self.parentOKbuttons = OKbuttons
2291	self.ValidatedControlsList = []
2292	self._fill()
2293	def _fill(self):
2294	'Fill the scrolled panel with widgets for each CIF item'
2295	wx.BeginBusyCursor()
2296	self.AddDict = {}
2297	self.ValidatedControlsList = []
2298	# delete any only contents
2299	if self.vbox:
2300	self.vbox.DeleteWindows()
2301	self.vbox = None
2302	self.Update()
2303	vbox = wx.BoxSizer(wx.VERTICAL)
2304	self.vbox = vbox
2305	# compile a 'list' of items in loops
2306	loopnames = set()
2307	for i in self.loops:
2308	loopnames \|= set(i)
2309	# post the looped CIF items
2310	for lnum,lp in enumerate(self.loops):
2311	hbox = wx.BoxSizer(wx.HORIZONTAL)
2312	hbox.Add(wx.StaticText(self,wx.ID_ANY,'Loop '+str(lnum+1)))
2313	vbox.Add(hbox)
2314	but = wx.Button(self,wx.ID_ANY,"Add row")
2315	self.AddDict[but]=lnum
2316
2317	hbox.Add(but)
2318	but.Bind(wx.EVT_BUTTON,self.OnAddRow)
2319	fbox = wx.GridBagSizer(0, 0)
2320	vbox.Add(fbox)
2321	rows = 0
2322	for i,item in enumerate(lp):
2323	txt = wx.StaticText(self,wx.ID_ANY,item+" ")
2324	fbox.Add(txt,(0,i+1))
2325	# if self.cifdic.get(item):
2326	# df = self.cifdic[item].get('_definition')
2327	# if df:
2328	# txt.SetToolTipString(G2IO.trim(df))
2329	# but = CIFdefHelp(self,
2330	# "Definition for "+item+":\n\n"+G2IO.trim(df),
2331	# self.parent,
2332	# self.parent.helptxt)
2333	# fbox.Add(but,(1,i+1),flag=wx.ALIGN_CENTER)
2334	for j,val in enumerate(self.cifblk[item]):
2335	ent = self.CIFEntryWidget(self.cifblk[item],j,item)
2336	#fbox.Add(ent,(j+2,i+1),flag=wx.EXPAND\|wx.ALL)
2337	fbox.Add(ent,(j+1,i+1),flag=wx.EXPAND\|wx.ALL)
2338	if self.cifdic.get(item):
2339	df = self.cifdic[item].get('_definition')
2340	if df:
2341	txt.SetToolTipString(G2IO.trim(df))
2342	but = CIFdefHelp(self,
2343	"Definition for "+item+":\n\n"+G2IO.trim(df),
2344	self.parent,
2345	self.parent.helptxt)
2346	fbox.Add(but,(j+2,i+1),flag=wx.ALIGN_CENTER)
2347	rows = max(rows,len(self.cifblk[item]))
2348	for i in range(rows):
2349	txt = wx.StaticText(self,wx.ID_ANY,str(i+1))
2350	fbox.Add(txt,(i+2,0))
2351	line = wx.StaticLine(self,wx.ID_ANY, size=(-1,3), style=wx.LI_HORIZONTAL)
2352	vbox.Add(line, 0, wx.EXPAND\|wx.ALIGN_CENTER\|wx.ALL, 10)
2353
2354	# post the non-looped CIF items
2355	for item in sorted(self.cifblk.keys()):
2356	if item not in loopnames:
2357	hbox = wx.BoxSizer(wx.HORIZONTAL)
2358	vbox.Add(hbox)
2359	txt = wx.StaticText(self,wx.ID_ANY,item)
2360	hbox.Add(txt)
2361	ent = self.CIFEntryWidget(self.cifblk,item,item)
2362	hbox.Add(ent)
2363	if self.cifdic.get(item):
2364	df = self.cifdic[item].get('_definition')
2365	if df:
2366	txt.SetToolTipString(G2IO.trim(df))
2367	but = CIFdefHelp(self,
2368	"Definition for "+item+":\n\n"+G2IO.trim(df),
2369	self.parent,
2370	self.parent.helptxt)
2371	hbox.Add(but,0,wx.ALL,2)
2372	self.SetSizer(vbox)
2373	#vbox.Fit(self.parent)
2374	self.SetAutoLayout(1)
2375	self.SetupScrolling()
2376	self.Bind(rw.EVT_RW_LAYOUT_NEEDED, self.OnLayoutNeeded)
2377	self.Layout()
2378	wx.EndBusyCursor()
2379	def OnLayoutNeeded(self,event):
2380	'''Called when an update of the panel layout is needed. Calls
2381	self.DoLayout after the current operations are complete using
2382	CallAfter. This is called only once, according to flag
2383	self.LayoutCalled, which is cleared in self.DoLayout.
2384	'''
2385	if self.LayoutCalled: return # call already queued
2386	wx.CallAfter(self.DoLayout) # queue a call
2387	self.LayoutCalled = True
2388	def DoLayout(self):
2389	'''Update the Layout and scroll bars for the Panel. Clears
2390	self.LayoutCalled so that next change to panel can
2391	request a new update
2392	'''
2393	wx.BeginBusyCursor()
2394	self.Layout()
2395	self.SetupScrolling()
2396	wx.EndBusyCursor()
2397	self.LayoutCalled = False
2398	def OnAddRow(self,event):
2399	'add a row to a loop'
2400	lnum = self.AddDict.get(event.GetEventObject())
2401	if lnum is None: return
2402	for item in self.loops[lnum]:
2403	self.cifblk[item].append('?')
2404	self._fill()
2405
2406	def ControlOKButton(self,setvalue):
2407	'''Enable or Disable the OK button(s) for the dialog. Note that this is
2408	passed into the ValidatedTxtCtrl for use by validators.
2409
2410	:param bool setvalue: if True, all entries in the dialog are
2411	checked for validity. The first invalid control triggers
2412	disabling of buttons.
2413	If False then the OK button(s) are disabled with no checking
2414	of the invalid flag for each control.
2415	'''
2416	if setvalue: # turn button on, do only if all controls show as valid
2417	for ctrl in self.ValidatedControlsList:
2418	if ctrl.invalid:
2419	for btn in self.parentOKbuttons:
2420	btn.Disable()
2421	return
2422	else:
2423	for btn in self.parentOKbuttons:
2424	btn.Enable()
2425	else:
2426	for btn in self.parentOKbuttons:
2427	btn.Disable()
2428
2429	def CIFEntryWidget(self,dct,item,dataname):
2430	'''Create an entry widget for a CIF item. Use a validated entry for numb values
2431	where int is required when limits are integers and floats otherwise.
2432	At present this does not allow entry of the special CIF values of "." and "?" for
2433	numerical values and highlights them as invalid.
2434	Use a selection widget when there are specific enumerated values for a string.
2435	'''
2436	if self.cifdic.get(dataname):
2437	if self.cifdic[dataname].get('_enumeration'):
2438	values = ['?']+self.cifdic[dataname]['_enumeration']
2439	choices = ['undefined']
2440	for i in self.cifdic[dataname].get('_enumeration_detail',values):
2441	choices.append(G2IO.trim(i))
2442	ent = G2G.EnumSelector(self, dct, item, choices, values, size=(200, -1))
2443	return ent
2444	if self.cifdic[dataname].get('_type') == 'numb':
2445	mn = None
2446	mx = None
2447	hint = int
2448	if self.cifdic[dataname].get('_enumeration_range'):
2449	rng = self.cifdic[dataname]['_enumeration_range'].split(':')
2450	if '.' in rng[0] or '.' in rng[1]: hint = float
2451	if rng[0]: mn = hint(rng[0])
2452	if rng[1]: mx = hint(rng[1])
2453	ent = G2ctrls.ValidatedTxtCtrl(
2454	self,dct,item,typeHint=hint,min=mn,max=mx,
2455	CIFinput=True,
2456	OKcontrol=self.ControlOKButton)
2457	self.ValidatedControlsList.append(ent)
2458	return ent
2459	rw1 = rw.ResizeWidget(self)
2460	ent = G2ctrls.ValidatedTxtCtrl(
2461	rw1,dct,item,size=(100, 20),
2462	style=wx.TE_MULTILINE\|wx.TE_PROCESS_ENTER,
2463	CIFinput=True,
2464	OKcontrol=self.ControlOKButton)
2465	self.ValidatedControlsList.append(ent)
2466	return rw1
2467
2468	class CIFtemplateSelect(wx.BoxSizer):
2469	'''Create a set of buttons to show, select and edit a CIF template
2470
2471	:param frame: wx.Frame object of parent
2472	:param panel: wx.Panel object where widgets should be placed
2473	:param str tmplate: one of 'publ', 'phase', or 'instrument' to determine
2474	the type of template
2475	:param dict G2dict: GSAS-II dict where CIF should be placed. The key
2476	"CIF_template" will be used to store either a list or a string.
2477	If a list, it will contain a dict and a list defining loops. If
2478	an str, it will contain a file name.
2479	:param function repaint: reference to a routine to be called to repaint
2480	the frame after a change has been made
2481	:param str title: A line of text to show at the top of the window
2482	:param str defaultname: specifies the default file name to be used for
2483	saving the CIF.
2484	'''
2485	def __init__(self,frame,panel,tmplate,G2dict, repaint, title, defaultname=''):
2486	wx.BoxSizer.__init__(self,wx.VERTICAL)
2487	self.cifdefs = frame
2488	self.dict = G2dict
2489	self.repaint = repaint
2490	templateDefName = 'template_'+tmplate+'.cif'
2491	self.CIF = G2dict.get("CIF_template")
2492	if defaultname:
2493	self.defaultname = defaultname.encode('ascii','replace').strip().replace(' ','_')
2494	self.defaultname = re.sub(r'[^a-zA-Z0-9_-]','',self.defaultname)
2495	self.defaultname = tmplate + "_" + self.defaultname + ".cif"
2496	else:
2497	self.defaultname = ''
2498
2499	txt = wx.StaticText(panel,wx.ID_ANY,title)
2500	self.Add(txt,0,wx.ALIGN_CENTER)
2501	# change font on title
2502	txtfnt = txt.GetFont()
2503	txtfnt.SetWeight(wx.BOLD)
2504	txtfnt.SetPointSize(2+txtfnt.GetPointSize())
2505	txt.SetFont(txtfnt)
2506	self.Add((-1,3))
2507
2508	if not self.CIF: # empty or None
2509	for pth in [os.getcwd()]+sys.path:
2510	fil = os.path.join(pth,self.defaultname)
2511	if os.path.exists(fil) and self.defaultname:
2512	self.CIF = fil
2513	CIFtxt = "Template: "+self.defaultname
2514	break
2515	else:
2516	for pth in sys.path:
2517	fil = os.path.join(pth,templateDefName)
2518	if os.path.exists(fil):
2519	self.CIF = fil
2520	CIFtxt = "Template: "+templateDefName
2521	break
2522	else:
2523	print("Default CIF template "+self.defaultname+' not found in path!')
2524	self.CIF = None
2525	CIFtxt = "none! (No template found)"
2526	elif type(self.CIF) is not list and type(self.CIF) is not tuple:
2527	if not os.path.exists(self.CIF):
2528	print("Error: template file has disappeared: "+self.CIF)
2529	self.CIF = None
2530	CIFtxt = "none! (file not found)"
2531	else:
2532	if len(self.CIF) < 50:
2533	CIFtxt = "File: "+self.CIF
2534	else:
2535	CIFtxt = "File: ..."+self.CIF[-50:]
2536	else:
2537	CIFtxt = "Template is customized"
2538	# show template source
2539	self.Add(wx.StaticText(panel,wx.ID_ANY,CIFtxt))
2540	# show str, button to select file; button to edit (if CIF defined)
2541	but = wx.Button(panel,wx.ID_ANY,"Select Template File")
2542	but.Bind(wx.EVT_BUTTON,self._onGetTemplateFile)
2543	hbox = wx.BoxSizer(wx.HORIZONTAL)
2544	hbox.Add(but,0,0,2)
2545	but = wx.Button(panel,wx.ID_ANY,"Edit Template")
2546	but.Bind(wx.EVT_BUTTON,self._onEditTemplateContents)
2547	if self.CIF is None: but.Disable() # nothing to edit!
2548	hbox.Add(but,0,0,2)
2549	self.Add(hbox)
2550	def _onGetTemplateFile(self,event):
2551	'select a template file'
2552	pth = G2G.GetImportPath(self.G2frame)
2553	if not pth: pth = '.'
2554	dlg = wx.FileDialog(
2555	self.cifdefs, message="Read CIF template file",
2556	defaultDir=pth,
2557	defaultFile=self.defaultname,
2558	wildcard="CIF (.cif)\|.cif",
2559	style=wx.OPEN)
2560	ret = dlg.ShowModal()
2561	fil = dlg.GetPath()
2562	dlg.Destroy()
2563	if ret == wx.ID_OK:
2564	try:
2565	cf = G2IO.ReadCIF(fil)
2566	if len(cf.keys()) == 0:
2567	raise Exception,"No CIF data_ blocks found"
2568	if len(cf.keys()) != 1:
2569	raise Exception, 'Error, CIF Template has more than one block: '+fil
2570	self.dict["CIF_template"] = fil
2571	except Exception as err:
2572	print('\nError reading CIF: '+fil)
2573	dlg = wx.MessageDialog(self.cifdefs,
2574	'Error reading CIF '+fil,
2575	'Error in CIF file',
2576	wx.OK)
2577	dlg.ShowModal()
2578	dlg.Destroy()
2579	print(err.message)
2580	return
2581	self.repaint() #EditCIFDefaults()
2582
2583	def _onEditTemplateContents(self,event):
2584	'Called to edit the contents of a CIF template'
2585	if type(self.CIF) is list or type(self.CIF) is tuple:
2586	dblk,loopstructure = copy.deepcopy(self.CIF) # don't modify original
2587	else:
2588	cf = G2IO.ReadCIF(self.CIF)
2589	dblk,loopstructure = CIF2dict(cf)
2590	dlg = EditCIFtemplate(self.cifdefs,dblk,loopstructure,self.defaultname)
2591	val = dlg.Post()
2592	if val:
2593	if dlg.newfile: # results saved in file
2594	self.dict["CIF_template"] = dlg.newfile
2595	else:
2596	self.dict["CIF_template"] = [dlg.cifblk,dlg.loopstructure]
2597	self.repaint() #EditCIFDefaults() # note that this does a dlg.Destroy()
2598	else:
2599	dlg.Destroy()
2600
2601	#===============================================================================
2602	# end of misc CIF utilities
2603	#===============================================================================

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