Context Navigation

source: trunk/exports/G2export_CIF.py @ 1659

Last change on this file since 1659 was 1659, checked in by vondreele, 8 years ago
get fourier density min/max & keep them enter fourier min/max into cif file
Property svn:eol-style set to `native` Property svn:keywords set to `Date Author Revision URL Id`
File size: 119.6 KB

Line
1	#!/usr/bin/env python
2	# -- coding: utf-8 --
3	########### SVN repository information ###################
4	# $Date: 2015-02-17 16:02:58 +0000 (Tue, 17 Feb 2015) $
5	# $Author: vondreele $
6	# $Revision: 1659 $
7	# $URL: trunk/exports/G2export_CIF.py $
8	# $Id: G2export_CIF.py 1659 2015-02-17 16:02:58Z 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: 1659 $")
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
50	DEBUG = False #True to skip printing of reflection/powder profile lists
51
52	CIFdic = None
53
54	class ExportCIF(G2IO.ExportBaseclass):
55	'''Used to create a CIF of an entire project
56
57	:param wx.Frame G2frame: reference to main GSAS-II frame
58	'''
59	def __init__(self,G2frame):
60	super(self.__class__,self).__init__( # fancy way to say <parentclass>.__init__
61	G2frame=G2frame,
62	formatName = 'Full CIF',
63	extension='.cif',
64	longFormatName = 'Export project as CIF'
65	)
66	self.exporttype = ['project']
67	self.author = ''
68	self.mode = 'full'
69
70	def Exporter(self,event=None):
71	'''Export a CIF. Export can be full or simple (as set by self.mode).
72	"simple" skips data, distances & angles, etc. and can only include
73	a single phase while "full" is intended for for publication submission.
74	'''
75
76	#***** define functions for export method =======================================
77	def WriteCIFitem(name,value=''):
78	'''Write CIF data items to the file. Formats values as needed.
79	Also used without a value for loops, comments, loop headers, etc.
80	'''
81	if value:
82	if "\n" in value or len(value)> 70:
83	if name.strip(): self.fp.write(name+'\n')
84	self.fp.write('; '+value+'\n')
85	self.fp.write('; '+'\n')
86	elif " " in value:
87	if len(name)+len(value) > 65:
88	self.fp.write(name + '\n ' + '"' + str(value) + '"'+'\n')
89	else:
90	self.fp.write(name + ' ' + '"' + str(value) + '"'+'\n')
91	else:
92	if len(name)+len(value) > 65:
93	self.fp.write(name+'\n ' + value+'\n')
94	else:
95	self.fp.write(name+' ' + value+'\n')
96	else:
97	self.fp.write(name+'\n')
98
99	def WriteAudit():
100	'Write the CIF audit values. Perhaps should be in a single element loop.'
101	WriteCIFitem('_audit_creation_method',
102	'created in GSAS-II')
103	WriteCIFitem('_audit_creation_date',self.CIFdate)
104	if self.author:
105	WriteCIFitem('_audit_author_name',self.author)
106	WriteCIFitem('_audit_update_record',
107	self.CIFdate+' Initial software-generated CIF')
108
109	def WriteOverall():
110	'''Write out overall refinement information.
111
112	More could be done here, but this is a good start.
113	'''
114	if self.ifPWDR:
115	WriteCIFitem('_pd_proc_info_datetime', self.CIFdate)
116	WriteCIFitem('_pd_calc_method', 'Rietveld Refinement')
117	#WriteCIFitem('_refine_ls_shift/su_max',DAT1)
118	#WriteCIFitem('_refine_ls_shift/su_mean',DAT2)
119	WriteCIFitem('_computing_structure_refinement','GSAS-II (Toby & Von Dreele, J. Appl. Cryst. 46, 544-549, 2013)')
120	if self.ifHKLF:
121	controls = self.OverallParms['Controls']
122	if controls['F**2']:
123	thresh = 'F2>%.1fu(F2)'%(controls['minF/sig'])
124	else:
125	thresh = 'F>%.1fu(F)'%(controls['minF/sig'])
126	WriteCIFitem('_reflns_threshold_expression', thresh)
127	try:
128	vars = str(len(self.OverallParms['Covariance']['varyList']))
129	except:
130	vars = '?'
131	WriteCIFitem('_refine_ls_number_parameters',vars)
132	try:
133	GOF = G2mth.ValEsd(self.OverallParms['Covariance']['Rvals']['GOF'],-0.009)
134	except:
135	GOF = '?'
136	WriteCIFitem('_refine_ls_goodness_of_fit_all',GOF)
137
138	# get restraint info
139	# restraintDict = self.OverallParms.get('Restraints',{})
140	# for i in self.OverallParms['Constraints']:
141	# print i
142	# for j in self.OverallParms['Constraints'][i]:
143	# print j
144	#WriteCIFitem('_refine_ls_number_restraints',TEXT)
145	# other things to consider reporting
146	# _refine_ls_number_reflns
147	# _refine_ls_goodness_of_fit_obs
148	# _refine_ls_wR_factor_obs
149	# _refine_ls_restrained_S_all
150	# _refine_ls_restrained_S_obs
151
152	# include an overall profile r-factor, if there is more than one powder histogram
153	R = '%.5f'%(self.OverallParms['Covariance']['Rvals']['Rwp']/100.)
154	WriteCIFitem('\n# OVERALL WEIGHTED R-FACTOR')
155	WriteCIFitem('_refine_ls_wR_factor_obs',R)
156	# _refine_ls_R_factor_all
157	# _refine_ls_R_factor_obs
158	WriteCIFitem('_refine_ls_matrix_type','full')
159	#WriteCIFitem('_refine_ls_matrix_type','userblocks')
160
161	def writeCIFtemplate(G2dict,tmplate,defaultname=''):
162	'''Write out the selected or edited CIF template
163	An unedited CIF template file is copied, comments intact; an edited
164	CIF template is written out from PyCifRW which of course strips comments.
165	In all cases the initial data_ header is stripped (there should only be one!)
166	'''
167	CIFobj = G2dict.get("CIF_template")
168	if defaultname:
169	defaultname = defaultname.encode('ascii','replace').strip().replace(' ','_')
170	defaultname = re.sub(r'[^a-zA-Z0-9_-]','',defaultname)
171	defaultname = tmplate + "_" + defaultname + ".cif"
172	else:
173	defaultname = ''
174	templateDefName = 'template_'+tmplate+'.cif'
175	if not CIFobj: # copying a template
176	for pth in [os.getcwd()]+sys.path:
177	fil = os.path.join(pth,defaultname)
178	if os.path.exists(fil) and defaultname: break
179	else:
180	for pth in sys.path:
181	fil = os.path.join(pth,templateDefName)
182	if os.path.exists(fil): break
183	else:
184	print(CIFobj+' not found in path!')
185	return
186	fp = open(fil,'r')
187	txt = fp.read()
188	fp.close()
189	elif type(CIFobj) is not list and type(CIFobj) is not tuple:
190	if not os.path.exists(CIFobj):
191	print("Error: requested template file has disappeared: "+CIFobj)
192	return
193	fp = open(CIFobj,'r')
194	txt = fp.read()
195	fp.close()
196	else:
197	txt = dict2CIF(CIFobj[0],CIFobj[1]).WriteOut()
198	# remove the PyCifRW header, if present
199	#if txt.find('PyCifRW') > -1 and txt.find('data_') > -1:
200	txt = "# GSAS-II edited template follows "+txt[txt.index("data_")+5:]
201	#txt = txt.replace('data_','#')
202	WriteCIFitem(txt)
203
204	def FormatSH(phasenam):
205	'Format a full spherical harmonics texture description as a string'
206	phasedict = self.Phases[phasenam] # pointer to current phase info
207	pfx = str(phasedict['pId'])+'::'
208	s = ""
209	textureData = phasedict['General']['SH Texture']
210	if textureData.get('Order'):
211	s += "Spherical Harmonics correction. Order = "+str(textureData['Order'])
212	s += " Model: " + str(textureData['Model']) + "\n Orientation angles: "
213	for name in ['omega','chi','phi']:
214	aname = pfx+'SH '+name
215	s += name + " = "
216	sig = self.sigDict.get(aname,-0.09)
217	s += G2mth.ValEsd(self.parmDict[aname],sig)
218	s += "; "
219	s += "\n"
220	s1 = " Coefficients: "
221	for name in textureData['SH Coeff'][1]:
222	aname = pfx+name
223	if len(s1) > 60:
224	s += s1 + "\n"
225	s1 = " "
226	s1 += aname + ' = '
227	sig = self.sigDict.get(aname,-0.0009)
228	s1 += G2mth.ValEsd(self.parmDict[aname],sig)
229	s1 += "; "
230	s += s1
231	return s
232
233	def FormatHAPpo(phasenam):
234	'''return the March-Dollase/SH correction for every
235	histogram in the current phase formatted into a
236	character string
237	'''
238	phasedict = self.Phases[phasenam] # pointer to current phase info
239	s = ''
240	for histogram in sorted(phasedict['Histograms']):
241	if histogram.startswith("HKLF"): continue # powder only
242	Histogram = self.Histograms.get(histogram)
243	if not Histogram: continue
244	hapData = phasedict['Histograms'][histogram]
245	if hapData['Pref.Ori.'][0] == 'MD':
246	aname = str(phasedict['pId'])+':'+str(Histogram['hId'])+':MD'
247	if self.parmDict.get(aname,1.0) != 1.0: continue
248	sig = self.sigDict.get(aname,-0.009)
249	if s != "": s += '\n'
250	s += 'March-Dollase correction'
251	if len(self.powderDict) > 1:
252	s += ', histogram '+str(Histogram['hId']+1)
253	s += ' coef. = ' + G2mth.ValEsd(self.parmDict[aname],sig)
254	s += ' axis = ' + str(hapData['Pref.Ori.'][3])
255	else: # must be SH
256	if s != "": s += '\n'
257	s += 'Simple spherical harmonic correction'
258	if len(self.powderDict) > 1:
259	s += ', histogram '+str(Histogram['hId']+1)
260	s += ' Order = '+str(hapData['Pref.Ori.'][4])+'\n'
261	s1 = " Coefficients: "
262	for item in hapData['Pref.Ori.'][5]:
263	aname = str(phasedict['pId'])+':'+str(Histogram['hId'])+':'+item
264	if len(s1) > 60:
265	s += s1 + "\n"
266	s1 = " "
267	s1 += aname + ' = '
268	sig = self.sigDict.get(aname,-0.0009)
269	s1 += G2mth.ValEsd(self.parmDict[aname],sig)
270	s1 += "; "
271	s += s1
272	return s
273	def FormatBackground(bkg,hId):
274	'''Display the Background information as a descriptive text string.
275
276	TODO: this needs to be expanded to show the diffuse peak and
277	Debye term information as well. (Bob)
278
279	:returns: the text description (str)
280	'''
281	hfx = ':'+str(hId)+':'
282	fxn, bkgdict = bkg
283	terms = fxn[2]
284	txt = 'Background function: "'+fxn[0]+'" function with '+str(terms)+' terms:\n'
285	l = " "
286	for i,v in enumerate(fxn[3:]):
287	name = '%sBack;%d'%(hfx,i)
288	sig = self.sigDict.get(name,-0.009)
289	if len(l) > 60:
290	txt += l + '\n'
291	l = ' '
292	l += G2mth.ValEsd(v,sig)+', '
293	txt += l
294	if bkgdict['nDebye']:
295	txt += '\n Background Debye function parameters: A, R, U:'
296	names = ['A;','R;','U;']
297	for i in range(bkgdict['nDebye']):
298	txt += '\n '
299	for j in range(3):
300	name = hfx+'Debye'+names[j]+str(i)
301	sig = self.sigDict.get(name,-0.009)
302	txt += G2mth.ValEsd(bkgdict['debyeTerms'][i][2*j],sig)+', '
303	if bkgdict['nPeaks']:
304	txt += '\n Background peak parameters: pos, int, sig, gam:'
305	names = ['pos;','int;','sig;','gam;']
306	for i in range(bkgdict['nPeaks']):
307	txt += '\n '
308	for j in range(4):
309	name = hfx+'BkPk'+names[j]+str(i)
310	sig = self.sigDict.get(name,-0.009)
311	txt += G2mth.ValEsd(bkgdict['peaksList'][i][2*j],sig)+', '
312	return txt
313
314	def FormatInstProfile(instparmdict,hId):
315	'''Format the instrumental profile parameters with a
316	string description. Will only be called on PWDR histograms
317	'''
318	s = ''
319	inst = instparmdict[0]
320	hfx = ':'+str(hId)+':'
321	if 'C' in inst['Type'][0]:
322	s = 'Finger-Cox-Jephcoat function parameters U, V, W, X, Y, SH/L:\n'
323	s += ' peak variance(Gauss) = Utan(Th)^2^+Vtan(Th)+W:\n'
324	s += ' peak HW(Lorentz) = X/cos(Th)+Ytan(Th); SH/L = S/L+H/L\n'
325	s += ' U, V, W in (centideg)^2^, X & Y in centideg\n '
326	for item in ['U','V','W','X','Y','SH/L']:
327	name = hfx+item
328	sig = self.sigDict.get(name,-0.009)
329	s += G2mth.ValEsd(inst[item][1],sig)+', '
330	elif 'T' in inst['Type'][0]: #to be tested after TOF Rietveld done
331	s = 'Von Dreele-Jorgenson-Windsor function parameters\n'+ \
332	' alpha, beta-0, beta-1, beta-q, sig-0, sig-1, sig-q, X, Y:\n '
333	for item in ['alpha','bet-0','bet-1','bet-q','sig-0','sig-1','sig-q','X','Y']:
334	name = hfx+item
335	sig = self.sigDict.get(name,-0.009)
336	s += G2mth.ValEsd(inst[item][1],sig)+', '
337	return s
338
339	def FormatPhaseProfile(phasenam):
340	'''Format the phase-related profile parameters (size/strain)
341	with a string description.
342	return an empty string or None if there are no
343	powder histograms for this phase.
344	'''
345	s = ''
346	phasedict = self.Phases[phasenam] # pointer to current phase info
347	SGData = phasedict['General'] ['SGData']
348	for histogram in sorted(phasedict['Histograms']):
349	if histogram.startswith("HKLF"): continue # powder only
350	Histogram = self.Histograms.get(histogram)
351	if not Histogram: continue
352	hapData = phasedict['Histograms'][histogram]
353	pId = phasedict['pId']
354	hId = Histogram['hId']
355	phfx = '%d:%d:'%(pId,hId)
356	size = hapData['Size']
357	mustrain = hapData['Mustrain']
358	hstrain = hapData['HStrain']
359	if len(self.powderDict) > 1:
360	if s:
361	s += '\n'
362	else:
363	s += ' Crystallite size model "%s" for %s (microns)\n '%(size[0],phasenam)
364	s += ' Parameters for histogram #'+str(hId)+' '+str(histogram)+'\n'
365	else:
366	s += ' Crystallite size model "%s" for %s (microns)\n '%(size[0],phasenam)
367
368	names = ['Size;i','Size;mx']
369	if 'uniax' in size[0]:
370	names = ['Size;i','Size;a','Size;mx']
371	s += 'anisotropic axis is %s\n '%(str(size[3]))
372	s += 'parameters: equatorial size, axial size, G/L mix\n '
373	for i,item in enumerate(names):
374	name = phfx+item
375	sig = self.sigDict.get(name,-0.009)
376	s += G2mth.ValEsd(size[1][i],sig)+', '
377	elif 'ellip' in size[0]:
378	s += 'parameters: S11, S22, S33, S12, S13, S23, G/L mix\n '
379	for i in range(6):
380	name = phfx+'Size:'+str(i)
381	sig = self.sigDict.get(name,-0.009)
382	s += G2mth.ValEsd(size[4][i],sig)+', '
383	sig = self.sigDict.get(phfx+'Size;mx',-0.009)
384	s += G2mth.ValEsd(size[1][2],sig)+', '
385	else: #isotropic
386	s += 'parameters: Size, G/L mix\n '
387	i = 0
388	for item in names:
389	name = phfx+item
390	sig = self.sigDict.get(name,-0.009)
391	s += G2mth.ValEsd(size[1][i],sig)+', '
392	i = 2 #skip the aniso value
393	s += '\n Mustrain model "%s" for %s (10^6^)\n '%(mustrain[0],phasenam)
394	names = ['Mustrain;i','Mustrain;mx']
395	if 'uniax' in mustrain[0]:
396	names = ['Mustrain;i','Mustrain;a','Mustrain;mx']
397	s += 'anisotropic axis is %s\n '%(str(size[3]))
398	s += 'parameters: equatorial mustrain, axial mustrain, G/L mix\n '
399	for i,item in enumerate(names):
400	name = phfx+item
401	sig = self.sigDict.get(name,-0.009)
402	s += G2mth.ValEsd(mustrain[1][i],sig)+', '
403	elif 'general' in mustrain[0]:
404	names = 'parameters: '
405	for i,name in enumerate(G2spc.MustrainNames(SGData)):
406	names += name+', '
407	if i == 9:
408	names += '\n '
409	names += 'G/L mix\n '
410	s += names
411	txt = ''
412	for i in range(len(mustrain[4])):
413	name = phfx+'Mustrain:'+str(i)
414	sig = self.sigDict.get(name,-0.009)
415	if len(txt) > 60:
416	s += txt+'\n '
417	txt = ''
418	txt += G2mth.ValEsd(mustrain[4][i],sig)+', '
419	s += txt
420	sig = self.sigDict.get(phfx+'Mustrain;mx',-0.009)
421	s += G2mth.ValEsd(mustrain[1][2],sig)+', '
422
423	else: #isotropic
424	s += ' parameters: Mustrain, G/L mix\n '
425	i = 0
426	for item in names:
427	name = phfx+item
428	sig = self.sigDict.get(name,-0.009)
429	s += G2mth.ValEsd(mustrain[1][i],sig)+', '
430	i = 2 #skip the aniso value
431	s1 = ' \n Macrostrain parameters: '
432	names = G2spc.HStrainNames(SGData)
433	for name in names:
434	s1 += name+', '
435	s1 += '\n '
436	macrostrain = False
437	for i in range(len(names)):
438	name = phfx+name[i]
439	sig = self.sigDict.get(name,-0.009)
440	s1 += G2mth.ValEsd(hstrain[0][i],sig)+', '
441	if hstrain[0][i]: macrostrain = True
442	if macrostrain:
443	s += s1 + '\n'
444	# show revised lattice parameters here someday
445	else:
446	s += '\n'
447	return s
448
449	def FmtAtomType(sym):
450	'Reformat a GSAS-II atom type symbol to match CIF rules'
451	sym = sym.replace('_','') # underscores are not allowed: no isotope designation?
452	# in CIF, oxidation state sign symbols come after, not before
453	if '+' in sym:
454	sym = sym.replace('+','') + '+'
455	elif '-' in sym:
456	sym = sym.replace('-','') + '-'
457	return sym
458
459	def PutInCol(val,wid):
460	'''Pad a value to >=wid+1 columns by adding spaces at the end. Always
461	adds at least one space
462	'''
463	val = str(val).replace(' ','')
464	if not val: val = '?'
465	fmt = '{:' + str(wid) + '} '
466	return fmt.format(val)
467
468	def MakeUniqueLabel(lbl,labellist):
469	'Make sure that every atom label is unique'
470	lbl = lbl.strip()
471	if not lbl: # deal with a blank label
472	lbl = 'A_1'
473	if lbl not in labellist:
474	labellist.append(lbl)
475	return lbl
476	i = 1
477	prefix = lbl
478	if '_' in lbl:
479	prefix = lbl[:lbl.rfind('_')]
480	suffix = lbl[lbl.rfind('_')+1:]
481	try:
482	i = int(suffix)+1
483	except:
484	pass
485	while prefix+'_'+str(i) in labellist:
486	i += 1
487	else:
488	lbl = prefix+'_'+str(i)
489	labellist.append(lbl)
490
491	def WriteAtomsNuclear(phasenam):
492	'Write atom positions to CIF'
493	phasedict = self.Phases[phasenam] # pointer to current phase info
494	General = phasedict['General']
495	cx,ct,cs,cia = General['AtomPtrs']
496	Atoms = phasedict['Atoms']
497	cfrac = cx+3
498	fpfx = str(phasedict['pId'])+'::Afrac:'
499	for i,at in enumerate(Atoms):
500	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
501	if fval != 0.0:
502	break
503	else:
504	WriteCIFitem('\n# PHASE HAS NO ATOMS!')
505	return
506
507	WriteCIFitem('\n# ATOMIC COORDINATES AND DISPLACEMENT PARAMETERS')
508	WriteCIFitem('loop_ '+
509	'\n _atom_site_label'+
510	'\n _atom_site_type_symbol'+
511	'\n _atom_site_fract_x'+
512	'\n _atom_site_fract_y'+
513	'\n _atom_site_fract_z'+
514	'\n _atom_site_occupancy'+
515	'\n _atom_site_adp_type'+
516	'\n _atom_site_U_iso_or_equiv'+
517	'\n _atom_site_symmetry_multiplicity')
518
519	varnames = {cx:'Ax',cx+1:'Ay',cx+2:'Az',cx+3:'Afrac',
520	cia+1:'AUiso',cia+2:'AU11',cia+3:'AU22',cia+4:'AU33',
521	cia+5:'AU12',cia+6:'AU13',cia+7:'AU23'}
522	self.labellist = []
523
524	pfx = str(phasedict['pId'])+'::'
525	# loop over all atoms
526	naniso = 0
527	for i,at in enumerate(Atoms):
528	if phasedict['General']['Type'] == 'macromolecular':
529	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
530	s = PutInCol(MakeUniqueLabel(label,self.labellist),15) # label
531	else:
532	s = PutInCol(MakeUniqueLabel(at[ct-1],self.labellist),6) # label
533	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
534	if fval == 0.0: continue # ignore any atoms that have a occupancy set to 0 (exact)
535	s += PutInCol(FmtAtomType(at[ct]),4) # type
536	if at[cia] == 'I':
537	adp = 'Uiso '
538	else:
539	adp = 'Uani '
540	naniso += 1
541	# compute Uequiv crudely
542	# correct: Defined as "1/3 trace of diagonalized U matrix".
543	# SEE cell2GS & Uij2Ueqv to GSASIIlattice. Former is needed to make the GS matrix used by the latter.
544	t = 0.0
545	for j in (2,3,4):
546	var = pfx+varnames[cia+j]+":"+str(i)
547	t += self.parmDict.get(var,at[cia+j])
548	for j in (cx,cx+1,cx+2,cx+3,cia,cia+1):
549	if j in (cx,cx+1,cx+2):
550	dig = 11
551	sigdig = -0.00009
552	else:
553	dig = 10
554	sigdig = -0.009
555	if j == cia:
556	s += adp
557	else:
558	var = pfx+varnames[j]+":"+str(i)
559	dvar = pfx+"d"+varnames[j]+":"+str(i)
560	if dvar not in self.sigDict:
561	dvar = var
562	if j == cia+1 and adp == 'Uani ':
563	val = t/3.
564	sig = sigdig
565	else:
566	#print var,(var in self.parmDict),(var in self.sigDict)
567	val = self.parmDict.get(var,at[j])
568	sig = self.sigDict.get(dvar,sigdig)
569	s += PutInCol(G2mth.ValEsd(val,sig),dig)
570	s += PutInCol(at[cs+1],3)
571	WriteCIFitem(s)
572	if naniso == 0: return
573	# now loop over aniso atoms
574	WriteCIFitem('\nloop_' + '\n _atom_site_aniso_label' +
575	'\n _atom_site_aniso_U_11' + '\n _atom_site_aniso_U_12' +
576	'\n _atom_site_aniso_U_13' + '\n _atom_site_aniso_U_22' +
577	'\n _atom_site_aniso_U_23' + '\n _atom_site_aniso_U_33')
578	for i,at in enumerate(Atoms):
579	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
580	if fval == 0.0: continue # ignore any atoms that have a occupancy set to 0 (exact)
581	if at[cia] == 'I': continue
582	s = PutInCol(self.labellist[i],6) # label
583	for j in (2,3,4,5,6,7):
584	sigdig = -0.0009
585	var = pfx+varnames[cia+j]+":"+str(i)
586	val = self.parmDict.get(var,at[cia+j])
587	sig = self.sigDict.get(var,sigdig)
588	s += PutInCol(G2mth.ValEsd(val,sig),11)
589	WriteCIFitem(s)
590
591	def HillSortElements(elmlist):
592	'''Sort elements in "Hill" order: C, H, others, (where others
593	are alphabetical).
594
595	:params list elmlist: a list of element strings
596
597	:returns: a sorted list of element strings
598	'''
599	newlist = []
600	oldlist = elmlist[:]
601	for elm in ('C','H'):
602	if elm in elmlist:
603	newlist.append(elm)
604	oldlist.pop(oldlist.index(elm))
605	return newlist+sorted(oldlist)
606
607	def WriteComposition(phasenam):
608	'''determine the composition for the unit cell, crudely determine Z and
609	then compute the composition in formula units
610	'''
611	phasedict = self.Phases[phasenam] # pointer to current phase info
612	General = phasedict['General']
613	Z = General.get('cellZ',0.0)
614	cx,ct,cs,cia = General['AtomPtrs']
615	Atoms = phasedict['Atoms']
616	fpfx = str(phasedict['pId'])+'::Afrac:'
617	cfrac = cx+3
618	cmult = cs+1
619	compDict = {} # combines H,D & T
620	sitemultlist = []
621	massDict = dict(zip(General['AtomTypes'],General['AtomMass']))
622	cellmass = 0
623	for i,at in enumerate(Atoms):
624	atype = at[ct].strip()
625	if atype.find('-') != -1: atype = atype.split('-')[0]
626	if atype.find('+') != -1: atype = atype.split('+')[0]
627	atype = atype[0].upper()+atype[1:2].lower() # force case conversion
628	if atype == "D" or atype == "D": atype = "H"
629	fvar = fpfx+str(i)
630	fval = self.parmDict.get(fvar,at[cfrac])
631	mult = at[cmult]
632	if not massDict.get(at[ct]):
633	print('Error: No mass found for atom type '+at[ct])
634	print('Will not compute cell contents for phase '+phasenam)
635	return
636	cellmass += massDict[at[ct]]multfval
637	compDict[atype] = compDict.get(atype,0.0) + mult*fval
638	if fval == 1: sitemultlist.append(mult)
639	if len(compDict.keys()) == 0: return # no elements!
640	if Z < 1: # Z has not been computed or set by user
641	Z = 1
642	for i in range(2,min(sitemultlist)+1):
643	for m in sitemultlist:
644	if m % i != 0:
645	break
646	else:
647	Z = i
648	General['cellZ'] = Z # save it
649
650	# when scattering factors are included in the CIF, this needs to be
651	# added to the loop here but only in the one-block case.
652	# For multiblock CIFs, scattering factors go in the histogram
653	# blocks (for all atoms in all appropriate phases) - an example?:
654	#loop_
655	# _atom_type_symbol
656	# _atom_type_description
657	# _atom_type_scat_dispersion_real
658	# _atom_type_scat_dispersion_imag
659	# _atom_type_scat_source
660	# 'C' 'C' 0.0033 0.0016
661	# 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
662	# 'H' 'H' 0.0000 0.0000
663	# 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
664	# 'P' 'P' 0.1023 0.0942
665	# 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
666	# 'Cl' 'Cl' 0.1484 0.1585
667	# 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
668	# 'Cu' 'Cu' 0.3201 1.2651
669	# 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
670
671	#if oneblock: # add scattering factors for current phase here
672	WriteCIFitem('\nloop_ _atom_type_symbol _atom_type_number_in_cell')
673	formula = ''
674	reload(G2mth)
675	for elem in HillSortElements(compDict.keys()):
676	WriteCIFitem(' ' + PutInCol(elem,4) +
677	G2mth.ValEsd(compDict[elem],-0.009,True))
678	if formula: formula += " "
679	formula += elem
680	if compDict[elem] == Z: continue
681	formula += G2mth.ValEsd(compDict[elem]/Z,-0.009,True)
682	WriteCIFitem( '\n# Note that Z affects _cell_formula_sum and _weight')
683	WriteCIFitem( '_cell_formula_units_Z',str(Z))
684	WriteCIFitem( '_chemical_formula_sum',formula)
685	WriteCIFitem( '_chemical_formula_weight',
686	G2mth.ValEsd(cellmass/Z,-0.09,True))
687
688	def WriteDistances(phasenam,SymOpList,offsetList,symOpList,G2oprList):
689	'''Report bond distances and angles for the CIF
690
691	Note that _geom__symmetry_ fields are values of form
692	n_klm where n is the symmetry operation in SymOpList (counted
693	starting with 1) and (k-5, l-5, m-5) are translations to add
694	to (x,y,z). See
695	http://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Igeom_angle_site_symmetry_.html
696
697	TODO: need a method to select publication flags for distances/angles
698	'''
699	phasedict = self.Phases[phasenam] # pointer to current phase info
700	Atoms = phasedict['Atoms']
701	generalData = phasedict['General']
702	# create a dict for storing Pub flag for bonds/angles, if needed
703	if phasedict['General'].get("DisAglHideFlag") is None:
704	phasedict['General']["DisAglHideFlag"] = {}
705	DisAngSel = phasedict['General']["DisAglHideFlag"]
706	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
707	cn = ct-1
708	fpfx = str(phasedict['pId'])+'::Afrac:'
709	cfrac = cx+3
710	DisAglData = {}
711	# create a list of atoms, but skip atoms with zero occupancy
712	xyz = []
713	fpfx = str(phasedict['pId'])+'::Afrac:'
714	for i,atom in enumerate(Atoms):
715	if self.parmDict.get(fpfx+str(i),atom[cfrac]) == 0.0: continue
716	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
717	if 'DisAglCtls' not in generalData:
718	# should not happen, since DisAglDialog should be called
719	# for all phases before getting here
720	dlg = G2gd.DisAglDialog(
721	self.G2frame,
722	{},
723	generalData)
724	if dlg.ShowModal() == wx.ID_OK:
725	generalData['DisAglCtls'] = dlg.GetData()
726	else:
727	dlg.Destroy()
728	return
729	dlg.Destroy()
730	DisAglData['OrigAtoms'] = xyz
731	DisAglData['TargAtoms'] = xyz
732	SymOpList,offsetList,symOpList,G2oprList = G2spc.AllOps(
733	generalData['SGData'])
734
735	xpandSGdata = generalData['SGData'].copy()
736	xpandSGdata.update({'SGOps':symOpList,
737	'SGInv':False,
738	'SGLatt':'P',
739	'SGCen':np.array([[0, 0, 0]]),})
740	DisAglData['SGData'] = xpandSGdata
741
742	DisAglData['Cell'] = generalData['Cell'][1:] #+ volume
743	if 'pId' in phasedict:
744	DisAglData['pId'] = phasedict['pId']
745	DisAglData['covData'] = self.OverallParms['Covariance']
746	try:
747	AtomLabels,DistArray,AngArray = G2stMn.RetDistAngle(
748	generalData['DisAglCtls'],
749	DisAglData)
750	except KeyError: # inside DistAngle for missing atom types in DisAglCtls
751	print('** ERROR - try again but do "Reset" to fill in missing atom types **')
752
753	# loop over interatomic distances for this phase
754	WriteCIFitem('\n# MOLECULAR GEOMETRY')
755	WriteCIFitem('loop_' +
756	'\n _geom_bond_atom_site_label_1' +
757	'\n _geom_bond_atom_site_label_2' +
758	'\n _geom_bond_distance' +
759	'\n _geom_bond_site_symmetry_1' +
760	'\n _geom_bond_site_symmetry_2' +
761	'\n _geom_bond_publ_flag')
762
763	for i in sorted(AtomLabels.keys()):
764	Dist = DistArray[i]
765	for D in Dist:
766	line = ' '+PutInCol(AtomLabels[i],6)+PutInCol(AtomLabels[D[0]],6)
767	sig = D[4]
768	if sig == 0: sig = -0.00009
769	line += PutInCol(G2mth.ValEsd(D[3],sig,True),10)
770	line += " 1_555 "
771	line += " {:3d}_".format(D[2])
772	for d in D[1]:
773	line += "{:1d}".format(d+5)
774	if DisAngSel.get((i,tuple(D[0:3]))):
775	line += " no"
776	else:
777	line += " yes"
778	WriteCIFitem(line)
779
780	# loop over interatomic angles for this phase
781	WriteCIFitem('\nloop_' +
782	'\n _geom_angle_atom_site_label_1' +
783	'\n _geom_angle_atom_site_label_2' +
784	'\n _geom_angle_atom_site_label_3' +
785	'\n _geom_angle' +
786	'\n _geom_angle_site_symmetry_1' +
787	'\n _geom_angle_site_symmetry_2' +
788	'\n _geom_angle_site_symmetry_3' +
789	'\n _geom_angle_publ_flag')
790
791	for i in sorted(AtomLabels.keys()):
792	Dist = DistArray[i]
793	for k,j,tup in AngArray[i]:
794	Dj = Dist[j]
795	Dk = Dist[k]
796	line = ' '+PutInCol(AtomLabels[Dj[0]],6)+PutInCol(AtomLabels[i],6)+PutInCol(AtomLabels[Dk[0]],6)
797	sig = tup[1]
798	if sig == 0: sig = -0.009
799	line += PutInCol(G2mth.ValEsd(tup[0],sig,True),10)
800	line += " {:3d}_".format(Dj[2])
801	for d in Dj[1]:
802	line += "{:1d}".format(d+5)
803	line += " 1_555 "
804	line += " {:3d}_".format(Dk[2])
805	for d in Dk[1]:
806	line += "{:1d}".format(d+5)
807	key = (tuple(Dk[0:3]),i,tuple(Dj[0:3]))
808	if DisAngSel.get(key):
809	line += " no"
810	else:
811	line += " yes"
812	WriteCIFitem(line)
813
814	def WritePhaseInfo(phasenam):
815	'Write out the phase information for the selected phase'
816	WriteCIFitem('\n# phase info for '+str(phasenam) + ' follows')
817	phasedict = self.Phases[phasenam] # pointer to current phase info
818	WriteCIFitem('_pd_phase_name', phasenam)
819	cellList,cellSig = self.GetCell(phasenam)
820	defsigL = 3[-0.00001] + 3[-0.001] + [-0.01] # significance to use when no sigma
821	names = ['length_a','length_b','length_c',
822	'angle_alpha','angle_beta ','angle_gamma',
823	'volume']
824	prevsig = 0
825	for lbl,defsig,val,sig in zip(names,defsigL,cellList,cellSig):
826	if sig:
827	txt = G2mth.ValEsd(val,sig)
828	prevsig = -sig # use this as the significance for next value
829	else:
830	txt = G2mth.ValEsd(val,min(defsig,prevsig),True)
831	WriteCIFitem('_cell_'+lbl,txt)
832
833	WriteCIFitem('_symmetry_cell_setting',
834	phasedict['General']['SGData']['SGSys'])
835
836	spacegroup = phasedict['General']['SGData']['SpGrp'].strip()
837	# regularize capitalization and remove trailing H/R
838	spacegroup = spacegroup[0].upper() + spacegroup[1:].lower().rstrip('rh ')
839	WriteCIFitem('_symmetry_space_group_name_H-M',spacegroup)
840
841	# generate symmetry operations including centering and center of symmetry
842	SymOpList,offsetList,symOpList,G2oprList = G2spc.AllOps(
843	phasedict['General']['SGData'])
844	WriteCIFitem('loop_\n _space_group_symop_id\n _space_group_symop_operation_xyz')
845	for i,op in enumerate(SymOpList,start=1):
846	WriteCIFitem(' {:3d} {:}'.format(i,op.lower()))
847
848	# loop over histogram(s) used in this phase
849	if not oneblock and not self.quickmode:
850	# report pointers to the histograms used in this phase
851	histlist = []
852	for hist in self.Phases[phasenam]['Histograms']:
853	if self.Phases[phasenam]['Histograms'][hist]['Use']:
854	if phasebyhistDict.get(hist):
855	phasebyhistDict[hist].append(phasenam)
856	else:
857	phasebyhistDict[hist] = [phasenam,]
858	blockid = datablockidDict.get(hist)
859	if not blockid:
860	print("Internal error: no block for data. Phase "+str(
861	phasenam)+" histogram "+str(hist))
862	histlist = []
863	break
864	histlist.append(blockid)
865
866	if len(histlist) == 0:
867	WriteCIFitem('# Note: phase has no associated data')
868
869	# report atom params
870	if phasedict['General']['Type'] in ['nuclear','macromolecular']: #this needs macromolecular variant, etc!
871	WriteAtomsNuclear(phasenam)
872	else:
873	raise Exception,"no export for "+str(phasedict['General']['Type'])+" coordinates implemented"
874	# report cell contents
875	WriteComposition(phasenam)
876	if not self.quickmode and phasedict['General']['Type'] == 'nuclear': # report distances and angles
877	WriteDistances(phasenam,SymOpList,offsetList,symOpList,G2oprList)
878	if 'Map' in phasedict['General'] and 'minmax' in phasedict['General']['Map']:
879	WriteCIFitem('\n# Difference density results')
880	MinMax = phasedict['General']['Map']['minmax']
881	WriteCIFitem('_refine_diff_density_max',G2mth.ValEsd(MinMax[1],-0.009))
882	WriteCIFitem('_refine_diff_density_min',G2mth.ValEsd(MinMax[0],-0.009))
883
884	def Yfmt(ndec,val):
885	'Format intensity values'
886	out = ("{:."+str(ndec)+"f}").format(val)
887	out = out.rstrip('0') # strip zeros to right of decimal
888	return out.rstrip('.') # and decimal place when not needed
889
890	def WriteReflStat(refcount,hklmin,hklmax,dmin,dmax,nRefSets=1):
891	'Write reflection statistics'
892	WriteCIFitem('_reflns_number_total', str(refcount))
893	if hklmin is not None and nRefSets == 1: # hkl range has no meaning with multiple phases
894	WriteCIFitem('_reflns_limit_h_min', str(int(hklmin[0])))
895	WriteCIFitem('_reflns_limit_h_max', str(int(hklmax[0])))
896	WriteCIFitem('_reflns_limit_k_min', str(int(hklmin[1])))
897	WriteCIFitem('_reflns_limit_k_max', str(int(hklmax[1])))
898	WriteCIFitem('_reflns_limit_l_min', str(int(hklmin[2])))
899	WriteCIFitem('_reflns_limit_l_max', str(int(hklmax[2])))
900	if hklmin is not None:
901	WriteCIFitem('_reflns_d_resolution_low ', G2mth.ValEsd(dmax,-0.009))
902	WriteCIFitem('_reflns_d_resolution_high ', G2mth.ValEsd(dmin,-0.009))
903
904	def WritePowderData(histlbl):
905	'Write out the selected powder diffraction histogram info'
906	histblk = self.Histograms[histlbl]
907	inst = histblk['Instrument Parameters'][0]
908	hId = histblk['hId']
909	pfx = ':' + str(hId) + ':'
910
911	if 'Lam1' in inst:
912	ratio = self.parmDict.get('I(L2)/I(L1)',inst['I(L2)/I(L1)'][1])
913	sratio = self.sigDict.get('I(L2)/I(L1)',-0.0009)
914	lam1 = self.parmDict.get('Lam1',inst['Lam1'][1])
915	slam1 = self.sigDict.get('Lam1',-0.00009)
916	lam2 = self.parmDict.get('Lam2',inst['Lam2'][1])
917	slam2 = self.sigDict.get('Lam2',-0.00009)
918	# always assume Ka1 & Ka2 if two wavelengths are present
919	WriteCIFitem('_diffrn_radiation_type','K\\a~1,2~')
920	WriteCIFitem('loop_' +
921	'\n _diffrn_radiation_wavelength' +
922	'\n _diffrn_radiation_wavelength_wt' +
923	'\n _diffrn_radiation_wavelength_id')
924	WriteCIFitem(' ' + PutInCol(G2mth.ValEsd(lam1,slam1),15)+
925	PutInCol('1.0',15) +
926	PutInCol('1',5))
927	WriteCIFitem(' ' + PutInCol(G2mth.ValEsd(lam2,slam2),15)+
928	PutInCol(G2mth.ValEsd(ratio,sratio),15)+
929	PutInCol('2',5))
930	else:
931	lam1 = self.parmDict.get('Lam',inst['Lam'][1])
932	slam1 = self.sigDict.get('Lam',-0.00009)
933	WriteCIFitem('_diffrn_radiation_wavelength',G2mth.ValEsd(lam1,slam1))
934
935	if not oneblock:
936	if not phasebyhistDict.get(histlbl):
937	WriteCIFitem('\n# No phases associated with this data set')
938	else:
939	WriteCIFitem('\n# PHASE TABLE')
940	WriteCIFitem('loop_' +
941	'\n _pd_phase_id' +
942	'\n _pd_phase_block_id' +
943	'\n _pd_phase_mass_%')
944	wtFrSum = 0.
945	for phasenam in phasebyhistDict.get(histlbl):
946	hapData = self.Phases[phasenam]['Histograms'][histlbl]
947	General = self.Phases[phasenam]['General']
948	wtFrSum += hapData['Scale'][0]*General['Mass']
949
950	for phasenam in phasebyhistDict.get(histlbl):
951	hapData = self.Phases[phasenam]['Histograms'][histlbl]
952	General = self.Phases[phasenam]['General']
953	wtFr = hapData['Scale'][0]*General['Mass']/wtFrSum
954	pfx = str(self.Phases[phasenam]['pId'])+':'+str(hId)+':'
955	if pfx+'Scale' in self.sigDict:
956	sig = self.sigDict[pfx+'Scale']*wtFr/hapData['Scale'][0]
957	else:
958	sig = -0.0001
959	WriteCIFitem(
960	' '+
961	str(self.Phases[phasenam]['pId']) +
962	' '+datablockidDict[phasenam]+
963	' '+G2mth.ValEsd(wtFr,sig)
964	)
965	WriteCIFitem('loop_' +
966	'\n _gsas_proc_phase_R_F_factor' +
967	'\n _gsas_proc_phase_R_Fsqd_factor' +
968	'\n _gsas_proc_phase_id' +
969	'\n _gsas_proc_phase_block_id')
970	for phasenam in phasebyhistDict.get(histlbl):
971	pfx = str(self.Phases[phasenam]['pId'])+':'+str(hId)+':'
972	WriteCIFitem(
973	' '+
974	' '+G2mth.ValEsd(histblk[pfx+'Rf']/100.,-.00009) +
975	' '+G2mth.ValEsd(histblk[pfx+'Rf^2']/100.,-.00009)+
976	' '+str(self.Phases[phasenam]['pId'])+
977	' '+datablockidDict[phasenam]
978	)
979	else:
980	# single phase in this histogram
981	pfx = '0:'+str(hId)+':'
982	WriteCIFitem('_refine_ls_R_F_factor ','%.5f'%(histblk[pfx+'Rf']/100.))
983	WriteCIFitem('_refine_ls_R_Fsqd_factor ','%.5f'%(histblk[pfx+'Rf^2']/100.))
984
985	WriteCIFitem('_pd_proc_ls_prof_R_factor ','%.5f'%(histblk['R']/100.))
986	WriteCIFitem('_pd_proc_ls_prof_wR_factor ','%.5f'%(histblk['wR']/100.))
987	WriteCIFitem('_gsas_proc_ls_prof_R_B_factor ','%.5f'%(histblk['Rb']/100.))
988	WriteCIFitem('_gsas_proc_ls_prof_wR_B_factor','%.5f'%(histblk['wRb']/100.))
989	WriteCIFitem('_pd_proc_ls_prof_wR_expected','%.5f'%(histblk['wRmin']/100.))
990
991	if histblk['Instrument Parameters'][0]['Type'][1][1] == 'X':
992	WriteCIFitem('_diffrn_radiation_probe','x-ray')
993	pola = histblk['Instrument Parameters'][0].get('Polariz.')
994	if pola:
995	pfx = ':' + str(hId) + ':'
996	sig = self.sigDict.get(pfx+'Polariz.',-0.0009)
997	txt = G2mth.ValEsd(pola[1],sig)
998	WriteCIFitem('_diffrn_radiation_polarisn_ratio',txt)
999	elif histblk['Instrument Parameters'][0]['Type'][1][1] == 'N':
1000	WriteCIFitem('_diffrn_radiation_probe','neutron')
1001	# TOF (note that this may not be defined)
1002	#if histblk['Instrument Parameters'][0]['Type'][1][2] == 'T':
1003	# WriteCIFitem('_pd_meas_2theta_fixed',text)
1004
1005
1006	# TODO: this will need help from Bob
1007	#if not oneblock:
1008	#WriteCIFitem('\n# SCATTERING FACTOR INFO')
1009	#WriteCIFitem('loop_ _atom_type_symbol')
1010	#if histblk['Instrument Parameters'][0]['Type'][1][1] == 'X':
1011	# WriteCIFitem(' _atom_type_scat_dispersion_real')
1012	# WriteCIFitem(' _atom_type_scat_dispersion_imag')
1013	# for lbl in ('a1','a2','a3', 'a4', 'b1', 'b2', 'b3', 'b4', 'c'):
1014	# WriteCIFitem(' _atom_type_scat_Cromer_Mann_'+lbl)
1015	#elif histblk['Instrument Parameters'][0]['Type'][1][1] == 'N':
1016	# WriteCIFitem(' _atom_type_scat_length_neutron')
1017	#WriteCIFitem(' _atom_type_scat_source')
1018
1019	WriteCIFitem('_pd_proc_ls_background_function',FormatBackground(histblk['Background'],histblk['hId']))
1020
1021	# TODO: this will need help from Bob
1022	#WriteCIFitem('_exptl_absorpt_process_details','?')
1023	#WriteCIFitem('_exptl_absorpt_correction_T_min','?')
1024	#WriteCIFitem('_exptl_absorpt_correction_T_max','?')
1025	#C extinction
1026	#WRITE(IUCIF,'(A)') '# Extinction correction'
1027	#CALL WRVAL(IUCIF,'_gsas_exptl_extinct_corr_T_min',TEXT(1:10))
1028	#CALL WRVAL(IUCIF,'_gsas_exptl_extinct_corr_T_max',TEXT(11:20))
1029
1030	if not oneblock: # instrumental profile terms go here
1031	WriteCIFitem('_pd_proc_ls_profile_function',
1032	FormatInstProfile(histblk["Instrument Parameters"],histblk['hId']))
1033
1034	#refprx = '_refln.' # mm
1035	refprx = '_refln_' # normal
1036	# data collection parameters for the powder dataset
1037
1038	temperature = histblk['Sample Parameters'].get('Temperature') # G2 uses K
1039	if not temperature:
1040	T = '?'
1041	else:
1042	T = G2mth.ValEsd(temperature,-0.009,True) # CIF uses K
1043	WriteCIFitem('_diffrn_ambient_temperature',T)
1044
1045	pressure = histblk['Sample Parameters'].get('Pressure') #G2 uses mega-Pascal
1046	if not pressure:
1047	P = '?'
1048	else:
1049	P = G2mth.ValEsd(pressure*1000,-0.09,True) # CIF uses kilopascal
1050	WriteCIFitem('_diffrn_ambient_pressure',P)
1051
1052	WriteCIFitem('\n# STRUCTURE FACTOR TABLE')
1053	# compute maximum intensity reflection
1054	Imax = 0
1055	for phasenam in histblk['Reflection Lists']:
1056	scale = self.Phases[phasenam]['Histograms'][histlbl]['Scale'][0]
1057	refList = np.asarray(histblk['Reflection Lists'][phasenam]['RefList'])
1058	I100 = scalerefList.T[8]refList.T[11]
1059	#Icorr = np.array([refl[13] for refl in histblk['Reflection Lists'][phasenam]])[0]
1060	#FO2 = np.array([refl[8] for refl in histblk['Reflection Lists'][phasenam]])
1061	#I100 = scaleFO2Icorr
1062	Imax = max(Imax,max(I100))
1063
1064	WriteCIFitem('loop_')
1065	if len(histblk['Reflection Lists'].keys()) > 1:
1066	WriteCIFitem(' _pd_refln_phase_id')
1067	WriteCIFitem(' ' + refprx + 'index_h' +
1068	'\n ' + refprx + 'index_k' +
1069	'\n ' + refprx + 'index_l' +
1070	'\n ' + refprx + 'F_squared_meas' +
1071	'\n ' + refprx + 'F_squared_calc' +
1072	'\n ' + refprx + 'phase_calc' +
1073	'\n _pd_refln_d_spacing')
1074	if Imax > 0:
1075	WriteCIFitem(' _gsas_i100_meas')
1076
1077	refcount = 0
1078	hklmin = None
1079	hklmax = None
1080	dmax = None
1081	dmin = None
1082	for phasenam in histblk['Reflection Lists']:
1083	scale = self.Phases[phasenam]['Histograms'][histlbl]['Scale'][0]
1084	phaseid = self.Phases[phasenam]['pId']
1085	refcount += len(histblk['Reflection Lists'][phasenam]['RefList'])
1086	for j,ref in enumerate(histblk['Reflection Lists'][phasenam]['RefList']):
1087	if DEBUG:
1088	print('DEBUG: skipping reflection list')
1089	break
1090	if hklmin is None:
1091	hklmin = ref[0:3]
1092	hklmax = ref[0:3]
1093	dmax = dmin = ref[4]
1094	if len(histblk['Reflection Lists'].keys()) > 1:
1095	s = PutInCol(phaseid,2)
1096	else:
1097	s = ""
1098	for i,hkl in enumerate(ref[0:3]):
1099	hklmax[i] = max(hkl,hklmax[i])
1100	hklmin[i] = min(hkl,hklmin[i])
1101	s += PutInCol(int(hkl),4)
1102	for I in ref[8:10]:
1103	s += PutInCol(G2mth.ValEsd(I,-0.0009),10)
1104	s += PutInCol(G2mth.ValEsd(ref[10],-0.9),7)
1105	dmax = max(dmax,ref[4])
1106	dmin = min(dmin,ref[4])
1107	s += PutInCol(G2mth.ValEsd(ref[4],-0.009),8)
1108	if Imax > 0:
1109	s += PutInCol(G2mth.ValEsd(100.*I100[j]/Imax,-0.09),6)
1110	WriteCIFitem(" "+s)
1111
1112	WriteReflStat(refcount,hklmin,hklmax,dmin,dmax,len(histblk['Reflection Lists']))
1113	WriteCIFitem('\n# POWDER DATA TABLE')
1114	# is data fixed step? If the step varies by <0.01% treat as fixed step
1115	steps = histblk['Data'][0][1:] - histblk['Data'][0][:-1]
1116	if abs(max(steps)-min(steps)) > abs(max(steps))/10000.:
1117	fixedstep = False
1118	else:
1119	fixedstep = True
1120
1121	if fixedstep: # and not TOF
1122	WriteCIFitem('_pd_meas_2theta_range_min', G2mth.ValEsd(histblk['Data'][0][0],-0.00009))
1123	WriteCIFitem('_pd_meas_2theta_range_max', G2mth.ValEsd(histblk['Data'][0][-1],-0.00009))
1124	WriteCIFitem('_pd_meas_2theta_range_inc', G2mth.ValEsd(steps.sum()/len(steps),-0.00009))
1125	# zero correct, if defined
1126	zero = None
1127	zerolst = histblk['Instrument Parameters'][0].get('Zero')
1128	if zerolst: zero = zerolst[1]
1129	zero = self.parmDict.get('Zero',zero)
1130	if zero:
1131	WriteCIFitem('_pd_proc_2theta_range_min', G2mth.ValEsd(histblk['Data'][0][0]-zero,-0.00009))
1132	WriteCIFitem('_pd_proc_2theta_range_max', G2mth.ValEsd(histblk['Data'][0][-1]-zero,-0.00009))
1133	WriteCIFitem('_pd_proc_2theta_range_inc', G2mth.ValEsd(steps.sum()/len(steps),-0.00009))
1134
1135	if zero:
1136	WriteCIFitem('_pd_proc_number_of_points', str(len(histblk['Data'][0])))
1137	else:
1138	WriteCIFitem('_pd_meas_number_of_points', str(len(histblk['Data'][0])))
1139	WriteCIFitem('\nloop_')
1140	# WriteCIFitem(' _pd_proc_d_spacing') # need easy way to get this
1141	if not fixedstep:
1142	if zero:
1143	WriteCIFitem(' _pd_proc_2theta_corrected')
1144	else:
1145	WriteCIFitem(' _pd_meas_2theta_scan')
1146	# at least for now, always report weights.
1147	#if countsdata:
1148	# WriteCIFitem(' _pd_meas_counts_total')
1149	#else:
1150	WriteCIFitem(' _pd_meas_intensity_total')
1151	WriteCIFitem(' _pd_calc_intensity_total')
1152	WriteCIFitem(' _pd_proc_intensity_bkg_calc')
1153	WriteCIFitem(' _pd_proc_ls_weight')
1154	maxY = max(histblk['Data'][1].max(),histblk['Data'][3].max())
1155	if maxY < 0: maxY *= -10 # this should never happen, but...
1156	ndec = max(0,10-int(np.log10(maxY))-1) # 10 sig figs should be enough
1157	maxSU = histblk['Data'][2].max()
1158	if maxSU < 0: maxSU *= -1 # this should never happen, but...
1159	ndecSU = max(0,8-int(np.log10(maxSU))-1) # 8 sig figs should be enough
1160	lowlim,highlim = histblk['Limits'][1]
1161
1162	if DEBUG:
1163	print('DEBUG: skipping profile list')
1164	else:
1165	for x,yobs,yw,ycalc,ybkg in zip(histblk['Data'][0],
1166	histblk['Data'][1],
1167	histblk['Data'][2],
1168	histblk['Data'][3],
1169	histblk['Data'][4]):
1170	if lowlim <= x <= highlim:
1171	pass
1172	else:
1173	yw = 0.0 # show the point is not in use
1174
1175	if fixedstep:
1176	s = ""
1177	else:
1178	s = PutInCol(G2mth.ValEsd(x-zero,-0.00009),10)
1179	s += PutInCol(Yfmt(ndec,yobs),12)
1180	s += PutInCol(Yfmt(ndec,ycalc),12)
1181	s += PutInCol(Yfmt(ndec,ybkg),11)
1182	s += PutInCol(Yfmt(ndecSU,yw),9)
1183	WriteCIFitem(" "+s)
1184
1185	def WriteSingleXtalData(histlbl):
1186	'Write out the selected single crystal histogram info'
1187	histblk = self.Histograms[histlbl]
1188
1189	#refprx = '_refln.' # mm
1190	refprx = '_refln_' # normal
1191
1192	WriteCIFitem('\n# STRUCTURE FACTOR TABLE')
1193	WriteCIFitem('loop_' +
1194	'\n ' + refprx + 'index_h' +
1195	'\n ' + refprx + 'index_k' +
1196	'\n ' + refprx + 'index_l' +
1197	'\n ' + refprx + 'F_squared_meas' +
1198	'\n ' + refprx + 'F_squared_sigma' +
1199	'\n ' + refprx + 'F_squared_calc' +
1200	'\n ' + refprx + 'phase_calc'
1201	)
1202
1203	hklmin = None
1204	hklmax = None
1205	dmax = None
1206	dmin = None
1207	refcount = len(histblk['Data']['RefList'])
1208	for ref in histblk['Data']['RefList']:
1209	s = " "
1210	if hklmin is None:
1211	hklmin = ref[0:3]
1212	hklmax = ref[0:3]
1213	dmax = dmin = ref[4]
1214	for i,hkl in enumerate(ref[0:3]):
1215	hklmax[i] = max(hkl,hklmax[i])
1216	hklmin[i] = min(hkl,hklmin[i])
1217	s += PutInCol(int(hkl),4)
1218	import sys
1219	if ref[5] == 0.0:
1220	s += PutInCol(G2mth.ValEsd(ref[8],0),12)
1221	s += PutInCol('.',10)
1222	s += PutInCol(G2mth.ValEsd(ref[9],0),12)
1223	s += PutInCol(G2mth.ValEsd(ref[10],-0.9),7)
1224	else:
1225	sig = ref[6] * ref[8] / ref[5]
1226	s += PutInCol(G2mth.ValEsd(ref[8],-abs(sig/10)),12)
1227	s += PutInCol(G2mth.ValEsd(sig,-abs(sig)/10.),10)
1228	s += PutInCol(G2mth.ValEsd(ref[9],-abs(sig/10)),12)
1229	s += PutInCol(G2mth.ValEsd(ref[10],-0.9),7)
1230	dmax = max(dmax,ref[4])
1231	dmin = min(dmin,ref[4])
1232	WriteCIFitem(s)
1233	if not self.quickmode: # statistics only in a full CIF
1234	WriteReflStat(refcount,hklmin,hklmax,dmin,dmax)
1235	hId = histblk['hId']
1236	hfx = '0:'+str(hId)+':'
1237	phfx = '%d:%d:'%(0,hId)
1238	extType,extModel,extParms = self.Phases[phasenam]['Histograms'][histlbl]['Extinction']
1239	if extModel != 'None':
1240	WriteCIFitem('# Extinction scaled by 1.e5')
1241	WriteCIFitem('_refine_ls_extinction_method','Becker-Coppens %s %s'%(extModel,extType))
1242	sig = -1.e-3
1243	if extModel == 'Primary':
1244	parm = extParms['Ep'][0]*1.e5
1245	if extParms['Ep'][1]:
1246	sig = self.sigDict[phfx+'Ep']*1.e5
1247	text = G2mth.ValEsd(parm,sig)
1248	elif extModel == 'Secondary Type I':
1249	parm = extParms['Eg'][0]*1.e5
1250	if extParms['Eg'][1]:
1251	sig = self.sigDict[phfx+'Eg']*1.e5
1252	text = G2mth.ValEsd(parm,sig)
1253	elif extModel == 'Secondary Type II':
1254	parm = extParms['Es'][0]*1.e5
1255	if extParms['Es'][1]:
1256	sig = self.sigDict[phfx+'Es']*1.e5
1257	text = G2mth.ValEsd(parm,sig)
1258	elif extModel == 'Secondary Type I & II':
1259	parm = extParms['Eg'][0]*1.e5
1260	if extParms['Es'][1]:
1261	sig = self.sigDict[phfx+'Es']*1.e5
1262	text = G2mth.ValEsd(parm,sig)
1263	sig = -1.0e-3
1264	parm = extParms['Es'][0]*1.e5
1265	if extParms['Es'][1]:
1266	sig = self.sigDict[phfx+'Es']*1.e5
1267	text += G2mth.ValEsd(parm,sig)
1268	WriteCIFitem('_refine_ls_extinction_coef',text)
1269	WriteCIFitem('_refine_ls_extinction_expression','Becker & Coppens (1974). Acta Cryst. A30, 129-147')
1270
1271	WriteCIFitem('_refine_ls_wR_factor_gt ','%.4f'%(histblk['wR']/100.))
1272	WriteCIFitem('_refine_ls_R_factor_gt ','%.4f'%(histblk[hfx+'Rf']/100.))
1273	WriteCIFitem('_refine_ls_R_Fsqd_factor ','%.4f'%(histblk[hfx+'Rf^2']/100.))
1274	def EditAuthor(event=None):
1275	'dialog to edit the CIF author info'
1276	'Edit the CIF author name'
1277	dlg = G2gd.SingleStringDialog(self.G2frame,
1278	'Get CIF Author',
1279	'Provide CIF Author name (Last, First)',
1280	value=self.author)
1281	if not dlg.Show():
1282	dlg.Destroy()
1283	return False # cancel was pressed
1284	self.author = dlg.GetValue()
1285	dlg.Destroy()
1286	try:
1287	self.OverallParms['Controls']["Author"] = self.author # save for future
1288	except KeyError:
1289	pass
1290	return True
1291	def EditInstNames(event=None):
1292	'Provide a dialog for editing instrument names'
1293	dictlist = []
1294	keylist = []
1295	lbllist = []
1296	for hist in self.Histograms:
1297	if hist.startswith("PWDR"):
1298	key2 = "Sample Parameters"
1299	d = self.Histograms[hist][key2]
1300	elif hist.startswith("HKLF"):
1301	key2 = "Instrument Parameters"
1302	d = self.Histograms[hist][key2][0]
1303
1304	lbllist.append(hist)
1305	dictlist.append(d)
1306	keylist.append('InstrName')
1307	instrname = d.get('InstrName')
1308	if instrname is None:
1309	d['InstrName'] = ''
1310	return G2ctrls.CallScrolledMultiEditor(
1311	self.G2frame,dictlist,keylist,
1312	prelbl=range(1,len(dictlist)+1),
1313	postlbl=lbllist,
1314	title='Instrument names',
1315	header="Edit instrument names. Note that a non-blank\nname is required for all histograms",
1316	CopyButton=True)
1317
1318	def EditRanges(event):
1319	'''Edit the bond distance/angle search range; phase is determined from
1320	a pointer placed in the button object (.phasedict) that references the
1321	phase dictionary
1322	'''
1323	but = event.GetEventObject()
1324	phasedict = but.phasedict
1325	dlg = G2gd.DisAglDialog(
1326	self.G2frame,
1327	phasedict['General']['DisAglCtls'], # edited
1328	phasedict['General'], # defaults
1329	)
1330	if dlg.ShowModal() == wx.ID_OK:
1331	phasedict['General']['DisAglCtls'] = dlg.GetData()
1332	dlg.Destroy()
1333
1334	def EditCIFDefaults():
1335	'''Fills the CIF Defaults window with controls for editing various CIF export
1336	parameters (mostly related to templates).
1337	'''
1338	self.cifdefs.DestroyChildren()
1339	self.cifdefs.SetTitle('Edit CIF settings')
1340	vbox = wx.BoxSizer(wx.VERTICAL)
1341	vbox.Add(wx.StaticText(self.cifdefs, wx.ID_ANY,'Creating file '+str(self.filename)))
1342	but = wx.Button(self.cifdefs, wx.ID_ANY,'Edit CIF Author')
1343	but.Bind(wx.EVT_BUTTON,EditAuthor)
1344	vbox.Add(but,0,wx.ALIGN_CENTER,3)
1345	but = wx.Button(self.cifdefs, wx.ID_ANY,'Edit Instrument Name(s)')
1346	but.Bind(wx.EVT_BUTTON,EditInstNames)
1347	vbox.Add(but,0,wx.ALIGN_CENTER,3)
1348	cpnl = wxscroll.ScrolledPanel(self.cifdefs,size=(300,300))
1349	cbox = wx.BoxSizer(wx.VERTICAL)
1350	G2gd.HorizontalLine(cbox,cpnl)
1351	cbox.Add(
1352	CIFtemplateSelect(self.cifdefs,
1353	cpnl,'publ',self.OverallParms['Controls'],
1354	EditCIFDefaults,
1355	"Publication (overall) template",
1356	),
1357	0,wx.EXPAND\|wx.ALIGN_LEFT\|wx.ALL)
1358	for phasenam in sorted(self.Phases.keys()):
1359	G2gd.HorizontalLine(cbox,cpnl)
1360	title = 'Phase '+phasenam
1361	phasedict = self.Phases[phasenam] # pointer to current phase info
1362	cbox.Add(
1363	CIFtemplateSelect(self.cifdefs,
1364	cpnl,'phase',phasedict['General'],
1365	EditCIFDefaults,
1366	title,
1367	phasenam),
1368	0,wx.EXPAND\|wx.ALIGN_LEFT\|wx.ALL)
1369	cpnl.SetSizer(cbox)
1370	if phasedict['General']['Type'] == 'nuclear':
1371	but = wx.Button(cpnl, wx.ID_ANY,'Edit distance/angle ranges')
1372	cbox.Add(but,0,wx.ALIGN_LEFT,0)
1373	cbox.Add((-1,2))
1374	but.phasedict = self.Phases[phasenam] # set a pointer to current phase info
1375	but.Bind(wx.EVT_BUTTON,EditRanges) # phase bond/angle ranges
1376	but = wx.Button(cpnl, wx.ID_ANY,'Set distance/angle publication flags')
1377	but.phase = phasenam # set a pointer to current phase info
1378	but.Bind(wx.EVT_BUTTON,SelectDisAglFlags) # phase bond/angle ranges
1379	cbox.Add(but,0,wx.ALIGN_LEFT,0)
1380	cbox.Add((-1,2))
1381	for i in sorted(self.powderDict.keys()):
1382	G2gd.HorizontalLine(cbox,cpnl)
1383	hist = self.powderDict[i]
1384	histblk = self.Histograms[hist]
1385	title = 'Powder dataset '+hist[5:]
1386	cbox.Add(
1387	CIFtemplateSelect(self.cifdefs,
1388	cpnl,'powder',histblk["Sample Parameters"],
1389	EditCIFDefaults,
1390	title,
1391	histblk["Sample Parameters"]['InstrName']),
1392	0,wx.EXPAND\|wx.ALIGN_LEFT\|wx.ALL)
1393	for i in sorted(self.xtalDict.keys()):
1394	G2gd.HorizontalLine(cbox,cpnl)
1395	hist = self.xtalDict[i]
1396	histblk = self.Histograms[hist]
1397	title = 'Single Xtal dataset '+hist[5:]
1398	cbox.Add(
1399	CIFtemplateSelect(self.cifdefs,
1400	cpnl,'single',histblk["Instrument Parameters"][0],
1401	EditCIFDefaults,
1402	title,
1403	histblk["Instrument Parameters"][0]['InstrName']),
1404	0,wx.EXPAND\|wx.ALIGN_LEFT\|wx.ALL)
1405	cpnl.SetSizer(cbox)
1406	cpnl.SetAutoLayout(1)
1407	cpnl.SetupScrolling()
1408	#cpnl.Bind(rw.EVT_RW_LAYOUT_NEEDED, self.OnLayoutNeeded) # needed if sizes change
1409	cpnl.Layout()
1410
1411	vbox.Add(cpnl, 1, wx.ALIGN_LEFT\|wx.ALL\|wx.EXPAND, 0)
1412	btnsizer = wx.StdDialogButtonSizer()
1413	btn = wx.Button(self.cifdefs, wx.ID_OK, "Create CIF")
1414	btn.SetDefault()
1415	btnsizer.AddButton(btn)
1416	btn = wx.Button(self.cifdefs, wx.ID_CANCEL)
1417	btnsizer.AddButton(btn)
1418	btnsizer.Realize()
1419	vbox.Add(btnsizer, 0, wx.ALIGN_CENTER\|wx.ALL, 5)
1420	self.cifdefs.SetSizer(vbox)
1421	vbox.Fit(self.cifdefs)
1422	self.cifdefs.Layout()
1423
1424	def OnToggleButton(event):
1425	'Respond to press of ToggleButton in SelectDisAglFlags'
1426	but = event.GetEventObject()
1427	if but.GetValue():
1428	but.DisAglSel[but.key] = True
1429	else:
1430	try:
1431	del but.DisAglSel[but.key]
1432	except KeyError:
1433	pass
1434	def keepTrue(event):
1435	event.GetEventObject().SetValue(True)
1436	def keepFalse(event):
1437	event.GetEventObject().SetValue(False)
1438
1439	def SelectDisAglFlags(event):
1440	'Select Distance/Angle use flags for the selected phase'
1441	phasenam = event.GetEventObject().phase
1442	phasedict = self.Phases[phasenam]
1443	SymOpList,offsetList,symOpList,G2oprList = G2spc.AllOps(phasedict['General']['SGData'])
1444	generalData = phasedict['General']
1445	# create a dict for storing Pub flag for bonds/angles, if needed
1446	if phasedict['General'].get("DisAglHideFlag") is None:
1447	phasedict['General']["DisAglHideFlag"] = {}
1448	DisAngSel = phasedict['General']["DisAglHideFlag"]
1449
1450	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
1451	cn = ct-1
1452	cfrac = cx+3
1453	DisAglData = {}
1454	# create a list of atoms, but skip atoms with zero occupancy
1455	xyz = []
1456	fpfx = str(phasedict['pId'])+'::Afrac:'
1457	for i,atom in enumerate(phasedict['Atoms']):
1458	if self.parmDict.get(fpfx+str(i),atom[cfrac]) == 0.0: continue
1459	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
1460	if 'DisAglCtls' not in generalData:
1461	# should not be used, since DisAglDialog should be called
1462	# for all phases before getting here
1463	dlg = G2gd.DisAglDialog(
1464	self.cifdefs,
1465	{},
1466	generalData)
1467	if dlg.ShowModal() == wx.ID_OK:
1468	generalData['DisAglCtls'] = dlg.GetData()
1469	else:
1470	dlg.Destroy()
1471	return
1472	dlg.Destroy()
1473	dlg = wx.Dialog(
1474	self.G2frame,
1475	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
1476	vbox = wx.BoxSizer(wx.VERTICAL)
1477	txt = wx.StaticText(dlg,wx.ID_ANY,'Searching distances for phase '+phasenam
1478	+'\nPlease wait...')
1479	vbox.Add(txt,0,wx.ALL\|wx.EXPAND)
1480	dlg.SetSizer(vbox)
1481	dlg.CenterOnParent()
1482	dlg.Show() # post "please wait"
1483	wx.BeginBusyCursor() # and change cursor
1484
1485	DisAglData['OrigAtoms'] = xyz
1486	DisAglData['TargAtoms'] = xyz
1487	SymOpList,offsetList,symOpList,G2oprList = G2spc.AllOps(
1488	generalData['SGData'])
1489
1490	xpandSGdata = generalData['SGData'].copy()
1491	xpandSGdata.update({'SGOps':symOpList,
1492	'SGInv':False,
1493	'SGLatt':'P',
1494	'SGCen':np.array([[0, 0, 0]]),})
1495	DisAglData['SGData'] = xpandSGdata
1496
1497	DisAglData['Cell'] = generalData['Cell'][1:] #+ volume
1498	if 'pId' in phasedict:
1499	DisAglData['pId'] = phasedict['pId']
1500	DisAglData['covData'] = self.OverallParms['Covariance']
1501	try:
1502	AtomLabels,DistArray,AngArray = G2stMn.RetDistAngle(
1503	generalData['DisAglCtls'],
1504	DisAglData)
1505	except KeyError: # inside DistAngle for missing atom types in DisAglCtls
1506	print('** ERROR - try again but do "Reset" to fill in missing atom types **')
1507	wx.EndBusyCursor()
1508	txt.SetLabel('Set publication flags for distances and angles in\nphase '+phasenam)
1509	vbox.Add((5,5))
1510	vbox.Add(wx.StaticText(dlg,wx.ID_ANY,
1511	'The default is to flag all distances and angles as to be'+
1512	'\npublished. Change this by pressing appropriate buttons.'),
1513	0,wx.ALL\|wx.EXPAND)
1514	hbox = wx.BoxSizer(wx.HORIZONTAL)
1515	vbox.Add(hbox)
1516	hbox.Add(wx.StaticText(dlg,wx.ID_ANY,'Button appearance: '))
1517	but = wx.ToggleButton(dlg,wx.ID_ANY,'Publish')
1518	but.Bind(wx.EVT_TOGGLEBUTTON,keepFalse)
1519	hbox.Add(but)
1520	but = wx.ToggleButton(dlg,wx.ID_ANY,"Don't publish")
1521	but.Bind(wx.EVT_TOGGLEBUTTON,keepTrue)
1522	hbox.Add(but)
1523	but.SetValue(True)
1524	G2gd.HorizontalLine(vbox,dlg)
1525
1526	cpnl = wxscroll.ScrolledPanel(dlg,size=(400,300))
1527	cbox = wx.BoxSizer(wx.VERTICAL)
1528	for c in sorted(DistArray):
1529	karr = []
1530	UsedCols = {}
1531	cbox.Add(wx.StaticText(cpnl,wx.ID_ANY,
1532	'distances to/angles around atom '+AtomLabels[c]))
1533	#dbox = wx.GridBagSizer(hgap=5)
1534	dbox = wx.GridBagSizer()
1535	for i,D in enumerate(DistArray[c]):
1536	karr.append(tuple(D[0:3]))
1537	val = "{:.2f}".format(D[3])
1538	sym = " [{:d} {:d} {:d}]".format(*D[1]) + " #{:d}".format(D[2])
1539	dbox.Add(wx.StaticText(cpnl,wx.ID_ANY,AtomLabels[D[0]]),
1540	(i+1,0)
1541	)
1542	dbox.Add(wx.StaticText(cpnl,wx.ID_ANY,sym),
1543	(i+1,1)
1544	)
1545	but = wx.ToggleButton(cpnl,wx.ID_ANY,val)
1546	but.key = (c,karr[-1])
1547	but.DisAglSel = DisAngSel
1548	if DisAngSel.get(but.key): but.SetValue(True)
1549	but.Bind(wx.EVT_TOGGLEBUTTON,OnToggleButton)
1550	dbox.Add(but,(i+1,2),border=1)
1551	for i,D in enumerate(AngArray[c]):
1552	val = "{:.1f}".format(D[2][0])
1553	but = wx.ToggleButton(cpnl,wx.ID_ANY,val)
1554	but.key = (karr[D[0]],c,karr[D[1]])
1555	but.DisAglSel = DisAngSel
1556	if DisAngSel.get(but.key): but.SetValue(True)
1557	but.Bind(wx.EVT_TOGGLEBUTTON,OnToggleButton)
1558	dbox.Add(but,(D[0]+1,D[1]+3),border=1)
1559	UsedCols[D[1]+3] = True
1560	for i,D in enumerate(DistArray[c][:-1]): # label columns that are used
1561	if UsedCols.get(i+3):
1562	dbox.Add(wx.StaticText(cpnl,wx.ID_ANY,AtomLabels[D[0]]),
1563	(0,i+3),
1564	flag=wx.ALIGN_CENTER
1565	)
1566	dbox.Add(wx.StaticText(cpnl,wx.ID_ANY,'distance'),
1567	(0,2),
1568	flag=wx.ALIGN_CENTER
1569	)
1570	cbox.Add(dbox)
1571	G2gd.HorizontalLine(cbox,cpnl)
1572	cpnl.SetSizer(cbox)
1573	cpnl.SetAutoLayout(1)
1574	cpnl.SetupScrolling()
1575	#cpnl.Bind(rw.EVT_RW_LAYOUT_NEEDED, self.OnLayoutNeeded) # needed if sizes change
1576	cpnl.Layout()
1577
1578	vbox.Add(cpnl, 1, wx.ALIGN_LEFT\|wx.ALL\|wx.EXPAND, 0)
1579
1580	btnsizer = wx.StdDialogButtonSizer()
1581	btn = wx.Button(dlg, wx.ID_OK, "Done")
1582	btn.SetDefault()
1583	btnsizer.AddButton(btn)
1584	btnsizer.Realize()
1585	vbox.Add(btnsizer, 0, wx.ALIGN_CENTER\|wx.ALL, 5)
1586	dlg.SetSizer(vbox)
1587	vbox.Fit(dlg)
1588	dlg.Layout()
1589
1590	dlg.CenterOnParent()
1591	dlg.ShowModal()
1592
1593	#***** end of functions for export method =======================================
1594	#=================================================================================
1595
1596	# the export process starts here
1597	self.InitExport(event)
1598	# load all of the tree into a set of dicts
1599	self.loadTree()
1600	# create a dict with refined values and their uncertainties
1601	self.loadParmDict()
1602	if self.mode=='simple':
1603	if self.ExportSelect('ask'): return
1604	else:
1605	if self.ExportSelect('default'): return
1606	# Someday: get restraint & constraint info
1607	#restraintDict = self.OverallParms.get('Restraints',{})
1608	#for i in self.OverallParms['Constraints']:
1609	# print i
1610	# for j in self.OverallParms['Constraints'][i]:
1611	# print j
1612
1613	self.CIFdate = dt.datetime.strftime(dt.datetime.now(),"%Y-%m-%dT%H:%M")
1614	# is there anything to export?
1615	if len(self.Phases) == len(self.powderDict) == len(self.xtalDict) == 0:
1616	self.G2frame.ErrorDialog(
1617	'Empty project',
1618	'Project does not contain any data or phases. Are they interconnected?')
1619	return
1620	# get the project file name
1621	self.CIFname = os.path.splitext(
1622	os.path.split(self.G2frame.GSASprojectfile)[1]
1623	)[0]
1624	self.CIFname = self.CIFname.replace(' ','')
1625	if not self.CIFname: # none defined & needed, save as GPX to get one
1626	self.G2frame.OnFileSaveas(None)
1627	if not self.G2frame.GSASprojectfile: return
1628	self.CIFname = os.path.splitext(
1629	os.path.split(self.G2frame.GSASprojectfile)[1]
1630	)[0]
1631	self.CIFname = self.CIFname.replace(' ','')
1632	# test for quick CIF mode or no data
1633	self.quickmode = False
1634	phasenam = None # include all phases
1635	if self.mode == "simple" and self.currentExportType == 'phase':
1636	if len(self.Phases) == 0: # this check is probably not needed
1637	self.G2frame.ErrorDialog(
1638	'No phase present',
1639	'Cannot create a coordinates CIF with no phases')
1640	return
1641	self.quickmode = True
1642	oneblock = True
1643	if len(self.Phases) > 1: # quick mode: get selected phase
1644	phasenam = self.phasenam[0]
1645	elif self.mode == "simple": # powder/single xtal data export
1646	self.quickmode = True
1647	oneblock = True
1648	# Project export: will this require a multiblock CIF?
1649	elif len(self.Phases) > 1:
1650	oneblock = False
1651	elif len(self.powderDict) + len(self.xtalDict) > 1:
1652	oneblock = False
1653	else: # one phase, one dataset, Full CIF
1654	oneblock = True
1655
1656	# make sure required information is present
1657	# get CIF author name -- required for full CIFs
1658	try:
1659	self.author = self.OverallParms['Controls'].get("Author",'').strip()
1660	except KeyError:
1661	pass
1662	while not (self.author or self.quickmode):
1663	if not EditAuthor(): return
1664	self.shortauthorname = self.author.replace(',','').replace(' ','')[:20]
1665
1666	# check there is an instrument name for every histogram
1667	self.ifPWDR = False
1668	self.ifHKLF = False
1669	if not self.quickmode:
1670	invalid = 0
1671	key3 = 'InstrName'
1672	for hist in self.Histograms:
1673	if hist.startswith("PWDR"):
1674	self.ifPWDR = True
1675	key2 = "Sample Parameters"
1676	d = self.Histograms[hist][key2]
1677	elif hist.startswith("HKLF"):
1678	self.ifHKLF = True
1679	key2 = "Instrument Parameters"
1680	d = self.Histograms[hist][key2][0]
1681	instrname = d.get(key3)
1682	if instrname is None:
1683	d[key3] = ''
1684	invalid += 1
1685	elif instrname.strip() == '':
1686	invalid += 1
1687	if invalid:
1688	msg = ""
1689	if invalid > 3: msg = (
1690	"\n\nNote: it may be faster to set the name for\n"
1691	"one histogram for each instrument and use the\n"
1692	"File/Copy option to duplicate the name"
1693	)
1694	if not EditInstNames(): return
1695	if not self.quickmode:
1696	# check for a distance-angle range search range for each phase
1697	for phasenam in sorted(self.Phases.keys()):
1698	#i = self.Phases[phasenam]['pId']
1699	phasedict = self.Phases[phasenam] # pointer to current phase info
1700	if 'DisAglCtls' not in phasedict['General']:
1701	dlg = G2gd.DisAglDialog(
1702	self.G2frame,
1703	{},
1704	phasedict['General'])
1705	if dlg.ShowModal() == wx.ID_OK:
1706	phasedict['General']['DisAglCtls'] = dlg.GetData()
1707	else:
1708	dlg.Destroy()
1709	return
1710	dlg.Destroy()
1711	if not self.quickmode:
1712	# check if temperature values & pressure are defaulted
1713	default = 0
1714	for hist in self.Histograms:
1715	if hist.startswith("PWDR"):
1716	key2 = "Sample Parameters"
1717	T = self.Histograms[hist][key2].get('Temperature')
1718	if not T:
1719	default += 1
1720	elif T == 300:
1721	default += 1
1722	P = self.Histograms[hist][key2].get('Pressure')
1723	if not P:
1724	default += 1
1725	elif P == 1:
1726	default += 1
1727	if default > 0:
1728	dlg = wx.MessageDialog(
1729	self.G2frame,
1730	'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?',
1731	'Check T and P values',
1732	wx.OK\|wx.CANCEL)
1733	ret = dlg.ShowModal()
1734	dlg.Destroy()
1735	if ret != wx.ID_OK: return
1736	if oneblock and not self.quickmode:
1737	# select a dataset to use (there should only be one set in one block,
1738	# but take whatever comes 1st)
1739	for hist in self.Histograms:
1740	histblk = self.Histograms[hist]
1741	if hist.startswith("PWDR"):
1742	instnam = histblk["Sample Parameters"]['InstrName']
1743	break # ignore all but 1st data histogram
1744	elif hist.startswith("HKLF"):
1745	instnam = histblk["Instrument Parameters"][0]['InstrName']
1746	break # ignore all but 1st data histogram
1747	if not self.quickmode: # give the user a chance to edit all defaults
1748	self.cifdefs = wx.Dialog(
1749	self.G2frame,
1750	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
1751	EditCIFDefaults()
1752	self.cifdefs.CenterOnParent()
1753	val = self.cifdefs.ShowModal()
1754	self.cifdefs.Destroy()
1755	if val != wx.ID_OK:
1756	return
1757	#======================================================================
1758	# Start writing the CIF - single block
1759	#======================================================================
1760	print('Writing CIF output to file '+str(self.filename)+"...")
1761	self.OpenFile()
1762	if self.currentExportType == 'single' or self.currentExportType == 'powder':
1763	#======Data only CIF (powder/xtal) ====================================
1764	hist = self.histnam[0]
1765	self.CIFname = hist[5:40].replace(' ','')
1766	WriteCIFitem('data_'+self.CIFname)
1767	if hist.startswith("PWDR"):
1768	WritePowderData(hist)
1769	elif hist.startswith("HKLF"):
1770	WriteSingleXtalData(hist)
1771	else:
1772	print "should not happen"
1773	elif self.quickmode:
1774	#====Phase only CIF ====================================================
1775	WriteCIFitem('data_'+self.CIFname)
1776	if phasenam is None: # if not already selected, select the first phase (should be one)
1777	phasenam = self.Phases.keys()[0]
1778	#print 'phasenam',phasenam
1779	phaseblk = self.Phases[phasenam] # pointer to current phase info
1780	# report the phase info
1781	WritePhaseInfo(phasenam)
1782	elif oneblock:
1783	#====Single block, data & phase CIF ===================================
1784	WriteCIFitem('data_'+self.CIFname)
1785	if phasenam is None: # if not already selected, select the first phase (should be one)
1786	phasenam = self.Phases.keys()[0]
1787	#print 'phasenam',phasenam
1788	phaseblk = self.Phases[phasenam] # pointer to current phase info
1789	instnam = instnam.replace(' ','')
1790	WriteCIFitem('_pd_block_id',
1791	str(self.CIFdate) + "\|" + str(self.CIFname) + "\|" +
1792	str(self.shortauthorname) + "\|" + instnam)
1793	WriteAudit()
1794	writeCIFtemplate(self.OverallParms['Controls'],'publ') # overall (publication) template
1795	WriteOverall()
1796	writeCIFtemplate(self.Phases[phasenam]['General'],'phase',phasenam) # write phase template
1797	# report the phase info
1798	WritePhaseInfo(phasenam)
1799	if hist.startswith("PWDR"):
1800	# preferred orientation
1801	SH = FormatSH(phasenam)
1802	MD = FormatHAPpo(phasenam)
1803	if SH and MD:
1804	WriteCIFitem('_pd_proc_ls_pref_orient_corr', SH + '\n' + MD)
1805	elif SH or MD:
1806	WriteCIFitem('_pd_proc_ls_pref_orient_corr', SH + MD)
1807	else:
1808	WriteCIFitem('_pd_proc_ls_pref_orient_corr', 'none')
1809	# report profile, since one-block: include both histogram and phase info
1810	WriteCIFitem('_pd_proc_ls_profile_function',
1811	FormatInstProfile(histblk["Instrument Parameters"],histblk['hId'])
1812	+'\n'+FormatPhaseProfile(phasenam))
1813	histblk = self.Histograms[hist]["Sample Parameters"]
1814	writeCIFtemplate(histblk,'powder',histblk['InstrName']) # write powder template
1815	WritePowderData(hist)
1816	elif hist.startswith("HKLF"):
1817	histprm = self.Histograms[hist]["Instrument Parameters"][0]
1818	writeCIFtemplate(histprm,'single',histprm['InstrName']) # single crystal template
1819	WriteSingleXtalData(hist)
1820	else:
1821	#=== multiblock: multiple phases and/or histograms ====================
1822	nsteps = 1 + len(self.Phases) + len(self.powderDict) + len(self.xtalDict)
1823	try:
1824	dlg = wx.ProgressDialog('CIF progress','starting',nsteps,parent=self.G2frame)
1825	Size = dlg.GetSize()
1826	Size = (int(Size[0]*3),Size[1]) # increase size along x
1827	dlg.SetSize(Size)
1828	dlg.CenterOnParent()
1829
1830	# publication info
1831	step = 1
1832	dlg.Update(step,"Exporting overall section")
1833	WriteCIFitem('\ndata_'+self.CIFname+'_publ')
1834	WriteAudit()
1835	WriteCIFitem('_pd_block_id',
1836	str(self.CIFdate) + "\|" + str(self.CIFname) + "\|" +
1837	str(self.shortauthorname) + "\|Overall")
1838	writeCIFtemplate(self.OverallParms['Controls'],'publ') #insert the publication template
1839	# ``template_publ.cif`` or a modified version
1840	# overall info
1841	WriteCIFitem('data_'+str(self.CIFname)+'_overall')
1842	WriteOverall()
1843	#============================================================
1844	WriteCIFitem('# POINTERS TO PHASE AND HISTOGRAM BLOCKS')
1845	datablockidDict = {} # save block names here -- N.B. check for conflicts between phase & hist names (unlikely!)
1846	# loop over phase blocks
1847	if len(self.Phases) > 1:
1848	loopprefix = ''
1849	WriteCIFitem('loop_ _pd_phase_block_id')
1850	else:
1851	loopprefix = '_pd_phase_block_id'
1852
1853	for phasenam in sorted(self.Phases.keys()):
1854	i = self.Phases[phasenam]['pId']
1855	datablockidDict[phasenam] = (str(self.CIFdate) + "\|" + str(self.CIFname) + "\|" +
1856	'phase_'+ str(i) + '\|' + str(self.shortauthorname))
1857	WriteCIFitem(loopprefix,datablockidDict[phasenam])
1858	# loop over data blocks
1859	if len(self.powderDict) + len(self.xtalDict) > 1:
1860	loopprefix = ''
1861	WriteCIFitem('loop_ _pd_block_diffractogram_id')
1862	else:
1863	loopprefix = '_pd_block_diffractogram_id'
1864	for i in sorted(self.powderDict.keys()):
1865	hist = self.powderDict[i]
1866	histblk = self.Histograms[hist]
1867	instnam = histblk["Sample Parameters"]['InstrName']
1868	instnam = instnam.replace(' ','')
1869	j = histblk['hId']
1870	datablockidDict[hist] = (str(self.CIFdate) + "\|" + str(self.CIFname) + "\|" +
1871	str(self.shortauthorname) + "\|" +
1872	instnam + "_hist_"+str(j))
1873	WriteCIFitem(loopprefix,datablockidDict[hist])
1874	for i in sorted(self.xtalDict.keys()):
1875	hist = self.xtalDict[i]
1876	histblk = self.Histograms[hist]
1877	instnam = histblk["Instrument Parameters"][0]['InstrName']
1878	instnam = instnam.replace(' ','')
1879	i = histblk['hId']
1880	datablockidDict[hist] = (str(self.CIFdate) + "\|" + str(self.CIFname) + "\|" +
1881	str(self.shortauthorname) + "\|" +
1882	instnam + "_hist_"+str(i))
1883	WriteCIFitem(loopprefix,datablockidDict[hist])
1884	#============================================================
1885	# loop over phases, exporting them
1886	phasebyhistDict = {} # create a cross-reference to phases by histogram
1887	for j,phasenam in enumerate(sorted(self.Phases.keys())):
1888	step += 1
1889	dlg.Update(step,"Exporting phase "+phasenam+' (#'+str(j+1)+')')
1890	i = self.Phases[phasenam]['pId']
1891	WriteCIFitem('\ndata_'+self.CIFname+"_phase_"+str(i))
1892	WriteCIFitem('# Information for phase '+str(i))
1893	WriteCIFitem('_pd_block_id',datablockidDict[phasenam])
1894	# report the phase
1895	writeCIFtemplate(self.Phases[phasenam]['General'],'phase',phasenam) # write phase template
1896	WritePhaseInfo(phasenam)
1897	# preferred orientation
1898	if self.ifPWDR:
1899	SH = FormatSH(phasenam)
1900	MD = FormatHAPpo(phasenam)
1901	if SH and MD:
1902	WriteCIFitem('_pd_proc_ls_pref_orient_corr', SH + '\n' + MD)
1903	elif SH or MD:
1904	WriteCIFitem('_pd_proc_ls_pref_orient_corr', SH + MD)
1905	else:
1906	WriteCIFitem('_pd_proc_ls_pref_orient_corr', 'none')
1907	# report sample profile terms
1908	PP = FormatPhaseProfile(phasenam)
1909	if PP:
1910	WriteCIFitem('_pd_proc_ls_profile_function',PP)
1911
1912	#============================================================
1913	# loop over histograms, exporting them
1914	for i in sorted(self.powderDict.keys()):
1915	hist = self.powderDict[i]
1916	histblk = self.Histograms[hist]
1917	if hist.startswith("PWDR"):
1918	step += 1
1919	dlg.Update(step,"Exporting "+hist.strip())
1920	WriteCIFitem('\ndata_'+self.CIFname+"_pwd_"+str(i))
1921	#instnam = histblk["Sample Parameters"]['InstrName']
1922	# report instrumental profile terms
1923	WriteCIFitem('_pd_proc_ls_profile_function',
1924	FormatInstProfile(histblk["Instrument Parameters"],histblk['hId']))
1925	WriteCIFitem('# Information for histogram '+str(i)+': '+hist)
1926	WriteCIFitem('_pd_block_id',datablockidDict[hist])
1927	histprm = self.Histograms[hist]["Sample Parameters"]
1928	writeCIFtemplate(histprm,'powder',histprm['InstrName']) # powder template
1929	WritePowderData(hist)
1930	for i in sorted(self.xtalDict.keys()):
1931	hist = self.xtalDict[i]
1932	histblk = self.Histograms[hist]
1933	if hist.startswith("HKLF"):
1934	step += 1
1935	dlg.Update(step,"Exporting "+hist.strip())
1936	WriteCIFitem('\ndata_'+self.CIFname+"_sx_"+str(i))
1937	#instnam = histblk["Instrument Parameters"][0]['InstrName']
1938	WriteCIFitem('# Information for histogram '+str(i)+': '+hist)
1939	WriteCIFitem('_pd_block_id',datablockidDict[hist])
1940	histprm = self.Histograms[hist]["Instrument Parameters"][0]
1941	writeCIFtemplate(histprm,'single',histprm['InstrName']) # single crystal template
1942	WriteSingleXtalData(hist)
1943
1944	except Exception:
1945	import traceback
1946	print(traceback.format_exc())
1947	self.G2frame.ErrorDialog('Exception',
1948	'Error occurred in CIF creation. '+
1949	'See full error message in console output ')
1950	finally:
1951	dlg.Destroy()
1952
1953	WriteCIFitem('#--' + 15*'eof--' + '#')
1954	self.CloseFile()
1955	print("...export completed")
1956	print('file '+str(self.fullpath))
1957	# end of CIF export
1958
1959	class ExportPhaseCIF(ExportCIF):
1960	'''Used to create a simple CIF of at most one phase. Uses exact same code as
1961	:class:`ExportCIF` except that `self.mode` is set to "simple" in `self.InitExport`.
1962	Shows up in menu as Quick CIF.
1963
1964	:param wx.Frame G2frame: reference to main GSAS-II frame
1965	'''
1966	def __init__(self,G2frame):
1967	G2IO.ExportBaseclass.__init__(self,
1968	G2frame=G2frame,
1969	formatName = 'Quick CIF',
1970	extension='.cif',
1971	longFormatName = 'Export one phase in CIF'
1972	)
1973	self.exporttype = ['phase']
1974	# CIF-specific items
1975	self.author = ''
1976	self.mode = 'simple'
1977
1978	class ExportDataCIF(ExportCIF):
1979	'''Used to create a simple CIF containing diffraction data only. Uses exact same code as
1980	:class:`ExportCIF` except that `self.mode` is set to "simple" and `self.currentExportType`
1981	is set to "single" or "powder" in `self.InitExport`. Shows up in menus as Data-only CIF.
1982
1983	:param wx.Frame G2frame: reference to main GSAS-II frame
1984	'''
1985	def __init__(self,G2frame):
1986	G2IO.ExportBaseclass.__init__(self,
1987	G2frame=G2frame,
1988	formatName = 'Data-only CIF',
1989	extension='.cif',
1990	longFormatName = 'Export data as CIF'
1991	)
1992	self.exporttype = ['single','powder']
1993	# CIF-specific items
1994	self.author = ''
1995	self.mode = 'simple'
1996
1997	#===============================================================================
1998	# misc CIF utilities
1999	#===============================================================================
2000	def PickleCIFdict(fil):
2001	'''Loads a CIF dictionary, cherry picks out the items needed
2002	by local code and sticks them into a python dict and writes
2003	that dict out as a cPickle file for later reuse.
2004	If the write fails a warning message is printed,
2005	but no exception occurs.
2006
2007	:param str fil: file name of CIF dictionary, will usually end
2008	in .dic
2009	:returns: the dict with the definitions
2010	'''
2011	import CifFile as cif # PyCifRW from James Hester
2012	cifdic = {}
2013	try:
2014	fp = open(fil,'r') # patch: open file to avoid windows bug
2015	dictobj = cif.CifDic(fp)
2016	fp.close()
2017	except IOError:
2018	dictobj = cif.CifDic(fil)
2019	if DEBUG: print('loaded '+str(fil))
2020	for item in dictobj.keys():
2021	cifdic[item] = {}
2022	for j in (
2023	'_definition','_type',
2024	'_enumeration',
2025	'_enumeration_detail',
2026	'_enumeration_range'):
2027	if dictobj[item].get(j):
2028	cifdic[item][j] = dictobj[item][j]
2029	try:
2030	fil = os.path.splitext(fil)[0]+'.cpickle'
2031	fp = open(fil,'w')
2032	cPickle.dump(cifdic,fp)
2033	fp.close()
2034	if DEBUG: print('wrote '+str(fil))
2035	except:
2036	print ('Unable to write '+str(fil))
2037	return cifdic
2038
2039	def LoadCIFdic():
2040	'''Create a composite core+powder CIF lookup dict containing
2041	information about all items in the CIF dictionaries, loading
2042	pickled files if possible. The routine looks for files
2043	named cif_core.cpickle and cif_pd.cpickle in every
2044	directory in the path and if they are not found, files
2045	cif_core.dic and/or cif_pd.dic are read.
2046
2047	:returns: the dict with the definitions
2048	'''
2049	cifdic = {}
2050	for ftyp in "cif_core","cif_pd":
2051	for loc in sys.path:
2052	fil = os.path.join(loc,ftyp+".cpickle")
2053	if not os.path.exists(fil): continue
2054	fp = open(fil,'r')
2055	try:
2056	cifdic.update(cPickle.load(fp))
2057	if DEBUG: print('reloaded '+str(fil))
2058	break
2059	finally:
2060	fp.close()
2061	else:
2062	for loc in sys.path:
2063	fil = os.path.join(loc,ftyp+".dic")
2064	if not os.path.exists(fil): continue
2065	#try:
2066	if True:
2067	cifdic.update(PickleCIFdict(fil))
2068	break
2069	#except:
2070	# pass
2071	else:
2072	print('Could not load '+ftyp+' dictionary')
2073	return cifdic
2074
2075	class CIFdefHelp(wx.Button):
2076	'''Create a help button that displays help information on
2077	the current data item
2078
2079	:param parent: the panel which will be the parent of the button
2080	:param str msg: the help text to be displayed
2081	:param wx.Dialog helpwin: Frame for CIF editing dialog
2082	:param wx.TextCtrl helptxt: TextCtrl where help text is placed
2083	'''
2084	def __init__(self,parent,msg,helpwin,helptxt):
2085	wx.Button.__init__(self,parent,wx.ID_HELP)
2086	self.Bind(wx.EVT_BUTTON,self._onPress)
2087	self.msg=msg
2088	self.parent = parent
2089	#self.helpwin = self.parent.helpwin
2090	self.helpwin = helpwin
2091	self.helptxt = helptxt
2092	def _onPress(self,event):
2093	'Respond to a button press by displaying the requested text'
2094	try:
2095	#helptxt = self.helptxt
2096	ow,oh = self.helptxt.GetSize()
2097	self.helptxt.SetLabel(self.msg)
2098	w,h = self.helptxt.GetSize()
2099	if h > oh:
2100	self.helpwin.GetSizer().Fit(self.helpwin)
2101	except: # error posting help, ignore
2102	return
2103
2104	def CIF2dict(cf):
2105	'''copy the contents of a CIF out from a PyCifRW block object
2106	into a dict
2107
2108	:returns: cifblk, loopstructure where cifblk is a dict with
2109	CIF items and loopstructure is a list of lists that defines
2110	which items are in which loops.
2111	'''
2112	blk = cf.keys()[0] # assume templates are a single CIF block, use the 1st
2113	loopstructure = cf[blk].loopnames()[:] # copy over the list of loop contents
2114	dblk = {}
2115	for item in cf[blk].keys(): # make a copy of all the items in the block
2116	dblk[item] = cf[blk][item]
2117	return dblk,loopstructure
2118
2119	def dict2CIF(dblk,loopstructure,blockname='Template'):
2120	'''Create a PyCifRW CIF object containing a single CIF
2121	block object from a dict and loop structure list.
2122
2123	:param dblk: a dict containing values for each CIF item
2124	:param list loopstructure: a list of lists containing the contents of
2125	each loop, as an example::
2126
2127	[ ["_a","_b"], ["_c"], ["_d_1","_d_2","_d_3"]]
2128
2129	this describes a CIF with this type of structure::
2130
2131	loop_ _a _b <a1> <b1> <a2> ...
2132	loop_ _c <c1> <c2>...
2133	loop _d_1 _d_2 _d_3 ...
2134
2135	Note that the values for each looped CIF item, such as _a,
2136	are contained in a list, for example as cifblk["_a"]
2137
2138	:param str blockname: an optional name for the CIF block.
2139	Defaults to 'Template'
2140
2141	:returns: the newly created PyCifRW CIF object
2142	'''
2143
2144	import CifFile as cif # PyCifRW from James Hester
2145	# compile a 'list' of items in loops
2146	loopnames = set()
2147	for i in loopstructure:
2148	loopnames \|= set(i)
2149	# create a new block
2150	newblk = cif.CifBlock()
2151	# add the looped items
2152	for keys in loopstructure:
2153	vals = []
2154	for key in keys:
2155	vals.append(dblk[key])
2156	newblk.AddCifItem(([keys],[vals]))
2157	# add the non-looped items
2158	for item in dblk:
2159	if item in loopnames: continue
2160	newblk[item] = dblk[item]
2161	# create a CIF and add the block
2162	newcf = cif.CifFile()
2163	newcf[blockname] = newblk
2164	return newcf
2165
2166
2167	class EditCIFtemplate(wx.Dialog):
2168	'''Create a dialog for editing a CIF template. The edited information is
2169	placed in cifblk. If the CIF is saved as a file, the name of that file
2170	is saved as ``self.newfile``.
2171
2172	:param wx.Frame parent: parent frame or None
2173	:param cifblk: dict or PyCifRW block containing values for each CIF item
2174	:param list loopstructure: a list of lists containing the contents of
2175	each loop, as an example::
2176
2177	[ ["_a","_b"], ["_c"], ["_d_1","_d_2","_d_3"]]
2178
2179	this describes a CIF with this type of structure::
2180
2181	loop_ _a _b <a1> <b1> <a2> ...
2182	loop_ _c <c1> <c2>...
2183	loop _d_1 _d_2 _d_3 ...
2184
2185	Note that the values for each looped CIF item, such as _a,
2186	are contained in a list, for example as cifblk["_a"]
2187
2188	:param str defaultname: specifies the default file name to be used for
2189	saving the CIF.
2190	'''
2191	def __init__(self,parent,cifblk,loopstructure,defaultname):
2192	OKbuttons = []
2193	self.cifblk = cifblk
2194	self.loopstructure = loopstructure
2195	self.newfile = None
2196	self.defaultname = defaultname
2197	global CIFdic # once this is loaded, keep it around
2198	if CIFdic is None:
2199	CIFdic = LoadCIFdic()
2200	wx.Dialog.__init__(self,parent,style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
2201
2202	# define widgets that will be needed during panel creation
2203	self.helptxt = wx.StaticText(self,wx.ID_ANY,"")
2204	savebtn = wx.Button(self, wx.ID_CLOSE, "Save as template")
2205	OKbuttons.append(savebtn)
2206	savebtn.Bind(wx.EVT_BUTTON,self._onSave)
2207	OKbtn = wx.Button(self, wx.ID_OK, "Use")
2208	OKbtn.SetDefault()
2209	OKbuttons.append(OKbtn)
2210
2211	self.SetTitle('Edit items in CIF template')
2212	vbox = wx.BoxSizer(wx.VERTICAL)
2213	cpnl = EditCIFpanel(self,cifblk,loopstructure,CIFdic,OKbuttons,size=(300,300))
2214	vbox.Add(cpnl, 1, wx.ALIGN_LEFT\|wx.ALL\|wx.EXPAND, 0)
2215	G2gd.HorizontalLine(vbox,self)
2216	vbox.Add(self.helptxt, 0, wx.EXPAND\|wx.ALL, 5)
2217	G2gd.HorizontalLine(vbox,self)
2218	btnsizer = wx.BoxSizer(wx.HORIZONTAL)
2219	btn = wx.Button(self, wx.ID_CANCEL)
2220	btnsizer.Add(btn,0,wx.ALIGN_CENTER\|wx.ALL)
2221	btnsizer.Add(savebtn,0,wx.ALIGN_CENTER\|wx.ALL)
2222	btnsizer.Add(OKbtn,0,wx.ALIGN_CENTER\|wx.ALL)
2223	vbox.Add(btnsizer, 0, wx.ALIGN_CENTER\|wx.ALL, 5)
2224	self.SetSizer(vbox)
2225	vbox.Fit(self)
2226	def Post(self):
2227	'''Display the dialog
2228
2229	:returns: True unless Cancel has been pressed.
2230	'''
2231	return (self.ShowModal() == wx.ID_OK)
2232	def _onSave(self,event):
2233	'Save CIF entries in a template file'
2234	dlg = wx.FileDialog(
2235	self, message="Save as CIF template",
2236	defaultDir=os.getcwd(),
2237	defaultFile=self.defaultname,
2238	wildcard="CIF (.cif)\|.cif",
2239	style=wx.SAVE \| wx.CHANGE_DIR
2240	)
2241	val = (dlg.ShowModal() == wx.ID_OK)
2242	fil = dlg.GetPath()
2243	dlg.Destroy()
2244	if val: # ignore a Cancel button
2245	fil = os.path.splitext(fil)[0]+'.cif' # force extension
2246	fp = open(fil,'w')
2247	newcf = dict2CIF(self.cifblk,self.loopstructure)
2248	fp.write(newcf.WriteOut())
2249	fp.close()
2250	self.newfile = fil
2251	self.EndModal(wx.ID_OK)
2252
2253	class EditCIFpanel(wxscroll.ScrolledPanel):
2254	'''Creates a scrolled panel for editing CIF template items
2255
2256	:param wx.Frame parent: parent frame where panel will be placed
2257	:param cifblk: dict or PyCifRW block containing values for each CIF item
2258	:param list loopstructure: a list of lists containing the contents of
2259	each loop, as an example::
2260
2261	[ ["_a","_b"], ["_c"], ["_d_1","_d_2","_d_3"]]
2262
2263	this describes a CIF with this type of structure::
2264
2265	loop_ _a _b <a1> <b1> <a2> ...
2266	loop_ _c <c1> <c2>...
2267	loop _d_1 _d_2 _d_3 ...
2268
2269	Note that the values for each looped CIF item, such as _a,
2270	are contained in a list, for example as cifblk["_a"]
2271
2272	:param dict cifdic: optional CIF dictionary definitions
2273	:param list OKbuttons: A list of wx.Button objects that should
2274	be disabled when information in the CIF is invalid
2275	:param (other): optional keyword parameters for wx.ScrolledPanel
2276	'''
2277	def __init__(self, parent, cifblk, loopstructure, cifdic={}, OKbuttons=[], **kw):
2278	self.parent = parent
2279	wxscroll.ScrolledPanel.__init__(self, parent, wx.ID_ANY, **kw)
2280	self.vbox = None
2281	self.AddDict = None
2282	self.cifdic = cifdic
2283	self.cifblk = cifblk
2284	self.loops = loopstructure
2285	self.parent = parent
2286	self.LayoutCalled = False
2287	self.parentOKbuttons = OKbuttons
2288	self.ValidatedControlsList = []
2289	self._fill()
2290	def _fill(self):
2291	'Fill the scrolled panel with widgets for each CIF item'
2292	wx.BeginBusyCursor()
2293	self.AddDict = {}
2294	self.ValidatedControlsList = []
2295	# delete any only contents
2296	if self.vbox:
2297	self.vbox.DeleteWindows()
2298	self.vbox = None
2299	self.Update()
2300	vbox = wx.BoxSizer(wx.VERTICAL)
2301	self.vbox = vbox
2302	# compile a 'list' of items in loops
2303	loopnames = set()
2304	for i in self.loops:
2305	loopnames \|= set(i)
2306	# post the looped CIF items
2307	for lnum,lp in enumerate(self.loops):
2308	hbox = wx.BoxSizer(wx.HORIZONTAL)
2309	hbox.Add(wx.StaticText(self,wx.ID_ANY,'Loop '+str(lnum+1)))
2310	vbox.Add(hbox)
2311	but = wx.Button(self,wx.ID_ANY,"Add row")
2312	self.AddDict[but]=lnum
2313
2314	hbox.Add(but)
2315	but.Bind(wx.EVT_BUTTON,self.OnAddRow)
2316	fbox = wx.GridBagSizer(0, 0)
2317	vbox.Add(fbox)
2318	rows = 0
2319	for i,item in enumerate(lp):
2320	txt = wx.StaticText(self,wx.ID_ANY,item+" ")
2321	fbox.Add(txt,(0,i+1))
2322	# if self.cifdic.get(item):
2323	# df = self.cifdic[item].get('_definition')
2324	# if df:
2325	# txt.SetToolTipString(G2IO.trim(df))
2326	# but = CIFdefHelp(self,
2327	# "Definition for "+item+":\n\n"+G2IO.trim(df),
2328	# self.parent,
2329	# self.parent.helptxt)
2330	# fbox.Add(but,(1,i+1),flag=wx.ALIGN_CENTER)
2331	for j,val in enumerate(self.cifblk[item]):
2332	ent = self.CIFEntryWidget(self.cifblk[item],j,item)
2333	#fbox.Add(ent,(j+2,i+1),flag=wx.EXPAND\|wx.ALL)
2334	fbox.Add(ent,(j+1,i+1),flag=wx.EXPAND\|wx.ALL)
2335	if self.cifdic.get(item):
2336	df = self.cifdic[item].get('_definition')
2337	if df:
2338	txt.SetToolTipString(G2IO.trim(df))
2339	but = CIFdefHelp(self,
2340	"Definition for "+item+":\n\n"+G2IO.trim(df),
2341	self.parent,
2342	self.parent.helptxt)
2343	fbox.Add(but,(j+2,i+1),flag=wx.ALIGN_CENTER)
2344	rows = max(rows,len(self.cifblk[item]))
2345	for i in range(rows):
2346	txt = wx.StaticText(self,wx.ID_ANY,str(i+1))
2347	fbox.Add(txt,(i+2,0))
2348	line = wx.StaticLine(self,wx.ID_ANY, size=(-1,3), style=wx.LI_HORIZONTAL)
2349	vbox.Add(line, 0, wx.EXPAND\|wx.ALIGN_CENTER\|wx.ALL, 10)
2350
2351	# post the non-looped CIF items
2352	for item in sorted(self.cifblk.keys()):
2353	if item not in loopnames:
2354	hbox = wx.BoxSizer(wx.HORIZONTAL)
2355	vbox.Add(hbox)
2356	txt = wx.StaticText(self,wx.ID_ANY,item)
2357	hbox.Add(txt)
2358	ent = self.CIFEntryWidget(self.cifblk,item,item)
2359	hbox.Add(ent)
2360	if self.cifdic.get(item):
2361	df = self.cifdic[item].get('_definition')
2362	if df:
2363	txt.SetToolTipString(G2IO.trim(df))
2364	but = CIFdefHelp(self,
2365	"Definition for "+item+":\n\n"+G2IO.trim(df),
2366	self.parent,
2367	self.parent.helptxt)
2368	hbox.Add(but,0,wx.ALL,2)
2369	self.SetSizer(vbox)
2370	#vbox.Fit(self.parent)
2371	self.SetAutoLayout(1)
2372	self.SetupScrolling()
2373	self.Bind(rw.EVT_RW_LAYOUT_NEEDED, self.OnLayoutNeeded)
2374	self.Layout()
2375	wx.EndBusyCursor()
2376	def OnLayoutNeeded(self,event):
2377	'''Called when an update of the panel layout is needed. Calls
2378	self.DoLayout after the current operations are complete using
2379	CallAfter. This is called only once, according to flag
2380	self.LayoutCalled, which is cleared in self.DoLayout.
2381	'''
2382	if self.LayoutCalled: return # call already queued
2383	wx.CallAfter(self.DoLayout) # queue a call
2384	self.LayoutCalled = True
2385	def DoLayout(self):
2386	'''Update the Layout and scroll bars for the Panel. Clears
2387	self.LayoutCalled so that next change to panel can
2388	request a new update
2389	'''
2390	wx.BeginBusyCursor()
2391	self.Layout()
2392	self.SetupScrolling()
2393	wx.EndBusyCursor()
2394	self.LayoutCalled = False
2395	def OnAddRow(self,event):
2396	'add a row to a loop'
2397	lnum = self.AddDict.get(event.GetEventObject())
2398	if lnum is None: return
2399	for item in self.loops[lnum]:
2400	self.cifblk[item].append('?')
2401	self._fill()
2402
2403	def ControlOKButton(self,setvalue):
2404	'''Enable or Disable the OK button(s) for the dialog. Note that this is
2405	passed into the ValidatedTxtCtrl for use by validators.
2406
2407	:param bool setvalue: if True, all entries in the dialog are
2408	checked for validity. The first invalid control triggers
2409	disabling of buttons.
2410	If False then the OK button(s) are disabled with no checking
2411	of the invalid flag for each control.
2412	'''
2413	if setvalue: # turn button on, do only if all controls show as valid
2414	for ctrl in self.ValidatedControlsList:
2415	if ctrl.invalid:
2416	for btn in self.parentOKbuttons:
2417	btn.Disable()
2418	return
2419	else:
2420	for btn in self.parentOKbuttons:
2421	btn.Enable()
2422	else:
2423	for btn in self.parentOKbuttons:
2424	btn.Disable()
2425
2426	def CIFEntryWidget(self,dct,item,dataname):
2427	'''Create an entry widget for a CIF item. Use a validated entry for numb values
2428	where int is required when limits are integers and floats otherwise.
2429	At present this does not allow entry of the special CIF values of "." and "?" for
2430	numerical values and highlights them as invalid.
2431	Use a selection widget when there are specific enumerated values for a string.
2432	'''
2433	if self.cifdic.get(dataname):
2434	if self.cifdic[dataname].get('_enumeration'):
2435	values = ['?']+self.cifdic[dataname]['_enumeration']
2436	choices = ['undefined']
2437	for i in self.cifdic[dataname].get('_enumeration_detail',values):
2438	choices.append(G2IO.trim(i))
2439	ent = G2gd.EnumSelector(self, dct, item, choices, values, size=(200, -1))
2440	return ent
2441	if self.cifdic[dataname].get('_type') == 'numb':
2442	mn = None
2443	mx = None
2444	hint = int
2445	if self.cifdic[dataname].get('_enumeration_range'):
2446	rng = self.cifdic[dataname]['_enumeration_range'].split(':')
2447	if '.' in rng[0] or '.' in rng[1]: hint = float
2448	if rng[0]: mn = hint(rng[0])
2449	if rng[1]: mx = hint(rng[1])
2450	ent = G2ctrls.ValidatedTxtCtrl(
2451	self,dct,item,typeHint=hint,min=mn,max=mx,
2452	CIFinput=True,
2453	OKcontrol=self.ControlOKButton)
2454	self.ValidatedControlsList.append(ent)
2455	return ent
2456	rw1 = rw.ResizeWidget(self)
2457	ent = G2ctrls.ValidatedTxtCtrl(
2458	rw1,dct,item,size=(100, 20),
2459	style=wx.TE_MULTILINE\|wx.TE_PROCESS_ENTER,
2460	CIFinput=True,
2461	OKcontrol=self.ControlOKButton)
2462	self.ValidatedControlsList.append(ent)
2463	return rw1
2464
2465	class CIFtemplateSelect(wx.BoxSizer):
2466	'''Create a set of buttons to show, select and edit a CIF template
2467
2468	:param frame: wx.Frame object of parent
2469	:param panel: wx.Panel object where widgets should be placed
2470	:param str tmplate: one of 'publ', 'phase', or 'instrument' to determine
2471	the type of template
2472	:param dict G2dict: GSAS-II dict where CIF should be placed. The key
2473	"CIF_template" will be used to store either a list or a string.
2474	If a list, it will contain a dict and a list defining loops. If
2475	an str, it will contain a file name.
2476	:param function repaint: reference to a routine to be called to repaint
2477	the frame after a change has been made
2478	:param str title: A line of text to show at the top of the window
2479	:param str defaultname: specifies the default file name to be used for
2480	saving the CIF.
2481	'''
2482	def __init__(self,frame,panel,tmplate,G2dict, repaint, title, defaultname=''):
2483	wx.BoxSizer.__init__(self,wx.VERTICAL)
2484	self.cifdefs = frame
2485	self.dict = G2dict
2486	self.repaint = repaint
2487	templateDefName = 'template_'+tmplate+'.cif'
2488	self.CIF = G2dict.get("CIF_template")
2489	if defaultname:
2490	self.defaultname = defaultname.encode('ascii','replace').strip().replace(' ','_')
2491	self.defaultname = re.sub(r'[^a-zA-Z0-9_-]','',self.defaultname)
2492	self.defaultname = tmplate + "_" + self.defaultname + ".cif"
2493	else:
2494	self.defaultname = ''
2495
2496	txt = wx.StaticText(panel,wx.ID_ANY,title)
2497	self.Add(txt,0,wx.ALIGN_CENTER)
2498	# change font on title
2499	txtfnt = txt.GetFont()
2500	txtfnt.SetWeight(wx.BOLD)
2501	txtfnt.SetPointSize(2+txtfnt.GetPointSize())
2502	txt.SetFont(txtfnt)
2503	self.Add((-1,3))
2504
2505	if not self.CIF: # empty or None
2506	for pth in [os.getcwd()]+sys.path:
2507	fil = os.path.join(pth,self.defaultname)
2508	if os.path.exists(fil) and self.defaultname:
2509	self.CIF = fil
2510	CIFtxt = "Template: "+self.defaultname
2511	break
2512	else:
2513	for pth in sys.path:
2514	fil = os.path.join(pth,templateDefName)
2515	if os.path.exists(fil):
2516	self.CIF = fil
2517	CIFtxt = "Template: "+templateDefName
2518	break
2519	else:
2520	print("Default CIF template "+self.defaultname+' not found in path!')
2521	self.CIF = None
2522	CIFtxt = "none! (No template found)"
2523	elif type(self.CIF) is not list and type(self.CIF) is not tuple:
2524	if not os.path.exists(self.CIF):
2525	print("Error: template file has disappeared: "+self.CIF)
2526	self.CIF = None
2527	CIFtxt = "none! (file not found)"
2528	else:
2529	if len(self.CIF) < 50:
2530	CIFtxt = "File: "+self.CIF
2531	else:
2532	CIFtxt = "File: ..."+self.CIF[-50:]
2533	else:
2534	CIFtxt = "Template is customized"
2535	# show template source
2536	self.Add(wx.StaticText(panel,wx.ID_ANY,CIFtxt))
2537	# show str, button to select file; button to edit (if CIF defined)
2538	but = wx.Button(panel,wx.ID_ANY,"Select Template File")
2539	but.Bind(wx.EVT_BUTTON,self._onGetTemplateFile)
2540	hbox = wx.BoxSizer(wx.HORIZONTAL)
2541	hbox.Add(but,0,0,2)
2542	but = wx.Button(panel,wx.ID_ANY,"Edit Template")
2543	but.Bind(wx.EVT_BUTTON,self._onEditTemplateContents)
2544	if self.CIF is None: but.Disable() # nothing to edit!
2545	hbox.Add(but,0,0,2)
2546	self.Add(hbox)
2547	def _onGetTemplateFile(self,event):
2548	'select a template file'
2549	dlg = wx.FileDialog(
2550	self.cifdefs, message="Read CIF template file",
2551	defaultDir=os.getcwd(),
2552	defaultFile=self.defaultname,
2553	wildcard="CIF (.cif)\|.cif",
2554	style=wx.OPEN \| wx.CHANGE_DIR
2555	)
2556	ret = dlg.ShowModal()
2557	fil = dlg.GetPath()
2558	dlg.Destroy()
2559	if ret == wx.ID_OK:
2560	try:
2561	cf = G2IO.ReadCIF(fil)
2562	if len(cf.keys()) == 0:
2563	raise Exception,"No CIF data_ blocks found"
2564	if len(cf.keys()) != 1:
2565	raise Exception, 'Error, CIF Template has more than one block: '+fil
2566	self.dict["CIF_template"] = fil
2567	except Exception as err:
2568	print('\nError reading CIF: '+fil)
2569	dlg = wx.MessageDialog(self.cifdefs,
2570	'Error reading CIF '+fil,
2571	'Error in CIF file',
2572	wx.OK)
2573	dlg.ShowModal()
2574	dlg.Destroy()
2575	print(err.message)
2576	return
2577	self.repaint() #EditCIFDefaults()
2578
2579	def _onEditTemplateContents(self,event):
2580	'Called to edit the contents of a CIF template'
2581	if type(self.CIF) is list or type(self.CIF) is tuple:
2582	dblk,loopstructure = copy.deepcopy(self.CIF) # don't modify original
2583	else:
2584	cf = G2IO.ReadCIF(self.CIF)
2585	dblk,loopstructure = CIF2dict(cf)
2586	dlg = EditCIFtemplate(self.cifdefs,dblk,loopstructure,self.defaultname)
2587	val = dlg.Post()
2588	if val:
2589	if dlg.newfile: # results saved in file
2590	self.dict["CIF_template"] = dlg.newfile
2591	else:
2592	self.dict["CIF_template"] = [dlg.cifblk,dlg.loopstructure]
2593	self.repaint() #EditCIFDefaults() # note that this does a dlg.Destroy()
2594	else:
2595	dlg.Destroy()
2596
2597	#===============================================================================
2598	# end of misc CIF utilities
2599	#===============================================================================

Note: See TracBrowser for help on using the repository browser.

Download in other formats: