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source: branch/logging/exports/G2export_CIF.py @ 2317

Last change on this file since 2317 was 1261, checked in by toby, 11 years ago
reorg exports to implement directory selection
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1	#!/usr/bin/env python
2	# -- coding: utf-8 --
3	########### SVN repository information ###################
4	# $Date: 2014-03-24 22:22:41 +0000 (Mon, 24 Mar 2014) $
5	# $Author: vondreele $
6	# $Revision: 1261 $
7	# $URL: branch/logging/exports/G2export_CIF.py $
8	# $Id: G2export_CIF.py 1261 2014-03-24 22:22:41Z 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: 1261 $")
40	import GSASIIIO as G2IO
41	import GSASIIgrid as G2gd
42	import GSASIIstrIO as G2stIO
43	import GSASIImath as G2mth
44	import GSASIIlattice as G2lat
45	import GSASIIspc as G2spc
46	import GSASIIphsGUI as G2pg
47	import GSASIIstrMain as G2stMn
48
49	DEBUG = False #True to skip printing of reflection/powder profile lists
50
51	CIFdic = None
52
53	class ExportCIF(G2IO.ExportBaseclass):
54	'''Used to create a CIF of an entire project
55
56	:param wx.Frame G2frame: reference to main GSAS-II frame
57	'''
58	def __init__(self,G2frame):
59	super(self.__class__,self).__init__( # fancy way to say <parentclass>.__init__
60	G2frame=G2frame,
61	formatName = 'Full CIF',
62	extension='.cif',
63	longFormatName = 'Export project as CIF'
64	)
65	self.exporttype = ['project']
66	self.author = ''
67	self.mode = 'full'
68
69	def Exporter(self,event=None):
70	'''Export a CIF. Export can be full or simple (as set by self.mode).
71	"simple" skips data, distances & angles, etc. and can only include
72	a single phase while "full" is intended for for publication submission.
73	'''
74
75	#***** define functions for export method =======================================
76	def WriteCIFitem(name,value=''):
77	'''Write CIF data items to the file. Formats values as needed.
78	Also used without a value for loops, comments, loop headers, etc.
79	'''
80	if value:
81	if "\n" in value or len(value)> 70:
82	if name.strip(): self.fp.write(name+'\n')
83	self.fp.write('; '+value+'\n')
84	self.fp.write('; '+'\n')
85	elif " " in value:
86	if len(name)+len(value) > 65:
87	self.fp.write(name + '\n ' + '"' + str(value) + '"'+'\n')
88	else:
89	self.fp.write(name + ' ' + '"' + str(value) + '"'+'\n')
90	else:
91	if len(name)+len(value) > 65:
92	self.fp.write(name+'\n ' + value+'\n')
93	else:
94	self.fp.write(name+' ' + value+'\n')
95	else:
96	self.fp.write(name+'\n')
97
98	def WriteAudit():
99	'Write the CIF audit values. Perhaps should be in a single element loop.'
100	WriteCIFitem('_audit_creation_method',
101	'created in GSAS-II')
102	WriteCIFitem('_audit_creation_date',self.CIFdate)
103	if self.author:
104	WriteCIFitem('_audit_author_name',self.author)
105	WriteCIFitem('_audit_update_record',
106	self.CIFdate+' Initial software-generated CIF')
107
108	def WriteOverall():
109	'''Write out overall refinement information.
110
111	More could be done here, but this is a good start.
112	'''
113	WriteCIFitem('_pd_proc_info_datetime', self.CIFdate)
114	WriteCIFitem('_pd_calc_method', 'Rietveld Refinement')
115	#WriteCIFitem('_refine_ls_shift/su_max',DAT1)
116	#WriteCIFitem('_refine_ls_shift/su_mean',DAT2)
117	#WriteCIFitem('_refine_diff_density_max',rhomax) #these need to be defined for each phase!
118	#WriteCIFitem('_refine_diff_density_min',rhomin)
119	WriteCIFitem('_computing_structure_refinement','GSAS-II (Toby & Von Dreele, J. Appl. Cryst. 46, 544-549, 2013)')
120	try:
121	vars = str(len(self.OverallParms['Covariance']['varyList']))
122	except:
123	vars = '?'
124	WriteCIFitem('_refine_ls_number_parameters',vars)
125	try:
126	GOF = G2mth.ValEsd(self.OverallParms['Covariance']['Rvals']['GOF'],-0.009)
127	except:
128	GOF = '?'
129	WriteCIFitem('_refine_ls_goodness_of_fit_all',GOF)
130
131	# get restraint info
132	# restraintDict = self.OverallParms.get('Restraints',{})
133	# for i in self.OverallParms['Constraints']:
134	# print i
135	# for j in self.OverallParms['Constraints'][i]:
136	# print j
137	#WriteCIFitem('_refine_ls_number_restraints',TEXT)
138	# other things to consider reporting
139	# _refine_ls_number_reflns
140	# _refine_ls_goodness_of_fit_obs
141	# _refine_ls_wR_factor_obs
142	# _refine_ls_restrained_S_all
143	# _refine_ls_restrained_S_obs
144
145	# include an overall profile r-factor, if there is more than one powder histogram
146	R = '%.5f'%(self.OverallParms['Covariance']['Rvals']['Rwp']/100.)
147	WriteCIFitem('\n# OVERALL WEIGHTED R-FACTOR')
148	WriteCIFitem('_refine_ls_wR_factor_obs',R)
149	# _refine_ls_R_factor_all
150	# _refine_ls_R_factor_obs
151	WriteCIFitem('_refine_ls_matrix_type','full')
152	#WriteCIFitem('_refine_ls_matrix_type','userblocks')
153
154	def writeCIFtemplate(G2dict,tmplate,defaultname=''):
155	'''Write out the selected or edited CIF template
156	An unedited CIF template file is copied, comments intact; an edited
157	CIF template is written out from PyCifRW which of course strips comments.
158	In all cases the initial data_ header is stripped (there should only be one!)
159	'''
160	CIFobj = G2dict.get("CIF_template")
161	if defaultname:
162	defaultname = defaultname.encode('ascii','replace').strip().replace(' ','_')
163	defaultname = re.sub(r'[^a-zA-Z0-9_-]','',defaultname)
164	defaultname = tmplate + "_" + defaultname + ".cif"
165	else:
166	defaultname = ''
167	templateDefName = 'template_'+tmplate+'.cif'
168	if not CIFobj: # copying a template
169	for pth in [os.getcwd()]+sys.path:
170	fil = os.path.join(pth,defaultname)
171	if os.path.exists(fil) and defaultname: break
172	else:
173	for pth in sys.path:
174	fil = os.path.join(pth,templateDefName)
175	if os.path.exists(fil): break
176	else:
177	print(CIFobj+' not found in path!')
178	return
179	fp = open(fil,'r')
180	txt = fp.read()
181	fp.close()
182	elif type(CIFobj) is not list and type(CIFobj) is not tuple:
183	if not os.path.exists(CIFobj):
184	print("Error: requested template file has disappeared: "+CIFobj)
185	return
186	fp = open(CIFobj,'r')
187	txt = fp.read()
188	fp.close()
189	else:
190	txt = dict2CIF(CIFobj[0],CIFobj[1]).WriteOut()
191	# remove the PyCifRW header, if present
192	#if txt.find('PyCifRW') > -1 and txt.find('data_') > -1:
193	txt = "# GSAS-II edited template follows "+txt[txt.index("data_")+5:]
194	#txt = txt.replace('data_','#')
195	WriteCIFitem(txt)
196
197	def FormatSH(phasenam):
198	'Format a full spherical harmonics texture description as a string'
199	phasedict = self.Phases[phasenam] # pointer to current phase info
200	pfx = str(phasedict['pId'])+'::'
201	s = ""
202	textureData = phasedict['General']['SH Texture']
203	if textureData.get('Order'):
204	s += "Spherical Harmonics correction. Order = "+str(textureData['Order'])
205	s += " Model: " + str(textureData['Model']) + "\n Orientation angles: "
206	for name in ['omega','chi','phi']:
207	aname = pfx+'SH '+name
208	s += name + " = "
209	sig = self.sigDict.get(aname,-0.09)
210	s += G2mth.ValEsd(self.parmDict[aname],sig)
211	s += "; "
212	s += "\n"
213	s1 = " Coefficients: "
214	for name in textureData['SH Coeff'][1]:
215	aname = pfx+name
216	if len(s1) > 60:
217	s += s1 + "\n"
218	s1 = " "
219	s1 += aname + ' = '
220	sig = self.sigDict.get(aname,-0.0009)
221	s1 += G2mth.ValEsd(self.parmDict[aname],sig)
222	s1 += "; "
223	s += s1
224	return s
225
226	def FormatHAPpo(phasenam):
227	'''return the March-Dollase/SH correction for every
228	histogram in the current phase formatted into a
229	character string
230	'''
231	phasedict = self.Phases[phasenam] # pointer to current phase info
232	s = ''
233	for histogram in sorted(phasedict['Histograms']):
234	if histogram.startswith("HKLF"): continue # powder only
235	Histogram = self.Histograms.get(histogram)
236	if not Histogram: continue
237	hapData = phasedict['Histograms'][histogram]
238	if hapData['Pref.Ori.'][0] == 'MD':
239	aname = str(phasedict['pId'])+':'+str(Histogram['hId'])+':MD'
240	if self.parmDict.get(aname,1.0) != 1.0: continue
241	sig = self.sigDict.get(aname,-0.009)
242	if s != "": s += '\n'
243	s += 'March-Dollase correction'
244	if len(self.powderDict) > 1:
245	s += ', histogram '+str(Histogram['hId']+1)
246	s += ' coef. = ' + G2mth.ValEsd(self.parmDict[aname],sig)
247	s += ' axis = ' + str(hapData['Pref.Ori.'][3])
248	else: # must be SH
249	if s != "": s += '\n'
250	s += 'Simple spherical harmonic correction'
251	if len(self.powderDict) > 1:
252	s += ', histogram '+str(Histogram['hId']+1)
253	s += ' Order = '+str(hapData['Pref.Ori.'][4])+'\n'
254	s1 = " Coefficients: "
255	for item in hapData['Pref.Ori.'][5]:
256	aname = str(phasedict['pId'])+':'+str(Histogram['hId'])+':'+item
257	if len(s1) > 60:
258	s += s1 + "\n"
259	s1 = " "
260	s1 += aname + ' = '
261	sig = self.sigDict.get(aname,-0.0009)
262	s1 += G2mth.ValEsd(self.parmDict[aname],sig)
263	s1 += "; "
264	s += s1
265	return s
266	def FormatBackground(bkg,hId):
267	'''Display the Background information as a descriptive text string.
268
269	TODO: this needs to be expanded to show the diffuse peak and
270	Debye term information as well. (Bob)
271
272	:returns: the text description (str)
273	'''
274	hfx = ':'+str(hId)+':'
275	fxn, bkgdict = bkg
276	terms = fxn[2]
277	txt = 'Background function: "'+fxn[0]+'" function with '+str(terms)+' terms:\n'
278	l = " "
279	for i,v in enumerate(fxn[3:]):
280	name = '%sBack:%d'%(hfx,i)
281	sig = self.sigDict.get(name,-0.009)
282	if len(l) > 60:
283	txt += l + '\n'
284	l = ' '
285	l += G2mth.ValEsd(v,sig)+', '
286	txt += l
287	if bkgdict['nDebye']:
288	txt += '\n Background Debye function parameters: A, R, U:'
289	names = ['A:','R:','U:']
290	for i in range(bkgdict['nDebye']):
291	txt += '\n '
292	for j in range(3):
293	name = hfx+'Debye'+names[j]+str(i)
294	sig = self.sigDict.get(name,-0.009)
295	txt += G2mth.ValEsd(bkgdict['debyeTerms'][i][2*j],sig)+', '
296	if bkgdict['nPeaks']:
297	txt += '\n Background peak parameters: pos, int, sig, gam:'
298	names = ['pos:','int:','sig:','gam:']
299	for i in range(bkgdict['nPeaks']):
300	txt += '\n '
301	for j in range(4):
302	name = hfx+'BkPk'+names[j]+str(i)
303	sig = self.sigDict.get(name,-0.009)
304	txt += G2mth.ValEsd(bkgdict['peaksList'][i][2*j],sig)+', '
305	return txt
306
307	def FormatInstProfile(instparmdict,hId):
308	'''Format the instrumental profile parameters with a
309	string description. Will only be called on PWDR histograms
310	'''
311	s = ''
312	inst = instparmdict[0]
313	hfx = ':'+str(hId)+':'
314	if 'C' in inst['Type'][0]:
315	s = 'Finger-Cox-Jephcoat function parameters U, V, W, X, Y, SH/L:\n'
316	s += ' peak variance(Gauss) = Utan(Th)^2^+Vtan(Th)+W:\n'
317	s += ' peak HW(Lorentz) = X/cos(Th)+Ytan(Th); SH/L = S/L+H/L\n'
318	s += ' U, V, W in (centideg)^2^, X & Y in centideg\n '
319	for item in ['U','V','W','X','Y','SH/L']:
320	name = hfx+item
321	sig = self.sigDict.get(name,-0.009)
322	s += G2mth.ValEsd(inst[item][1],sig)+', '
323	elif 'T' in inst['Type'][0]: #to be tested after TOF Rietveld done
324	s = 'Von Dreele-Jorgenson-Windsor function parameters\n'+ \
325	' alpha, beta-0, beta-1, beta-q, sig-0, sig-1, sig-q, X, Y:\n '
326	for item in ['alpha','bet-0','bet-1','bet-q','sig-0','sig-1','sig-q','X','Y']:
327	name = hfx+item
328	sig = self.sigDict.get(name,-0.009)
329	s += G2mth.ValEsd(inst[item][1],sig)+', '
330	return s
331
332	def FormatPhaseProfile(phasenam):
333	'''Format the phase-related profile parameters (size/strain)
334	with a string description.
335	return an empty string or None if there are no
336	powder histograms for this phase.
337	'''
338	s = ''
339	phasedict = self.Phases[phasenam] # pointer to current phase info
340	SGData = phasedict['General'] ['SGData']
341	for histogram in sorted(phasedict['Histograms']):
342	if histogram.startswith("HKLF"): continue # powder only
343	Histogram = self.Histograms.get(histogram)
344	if not Histogram: continue
345	hapData = phasedict['Histograms'][histogram]
346	pId = phasedict['pId']
347	hId = Histogram['hId']
348	phfx = '%d:%d:'%(pId,hId)
349	size = hapData['Size']
350	mustrain = hapData['Mustrain']
351	hstrain = hapData['HStrain']
352	if len(self.powderDict) > 1:
353	if s:
354	s += '\n'
355	else:
356	s += ' Crystallite size model "%s" for %s (microns)\n '%(size[0],phasenam)
357	s += ' Parameters for histogram #'+str(hId)+' '+str(histogram)+'\n'
358	else:
359	s += ' Crystallite size model "%s" for %s (microns)\n '%(size[0],phasenam)
360
361	names = ['Size;i','Size;mx']
362	if 'uniax' in size[0]:
363	names = ['Size;i','Size;a','Size;mx']
364	s += 'anisotropic axis is %s\n '%(str(size[3]))
365	s += 'parameters: equatorial size, axial size, G/L mix\n '
366	for i,item in enumerate(names):
367	name = phfx+item
368	sig = self.sigDict.get(name,-0.009)
369	s += G2mth.ValEsd(size[1][i],sig)+', '
370	elif 'ellip' in size[0]:
371	s += 'parameters: S11, S22, S33, S12, S13, S23, G/L mix\n '
372	for i in range(6):
373	name = phfx+'Size:'+str(i)
374	sig = self.sigDict.get(name,-0.009)
375	s += G2mth.ValEsd(size[4][i],sig)+', '
376	sig = self.sigDict.get(phfx+'Size;mx',-0.009)
377	s += G2mth.ValEsd(size[1][2],sig)+', '
378	else: #isotropic
379	s += 'parameters: Size, G/L mix\n '
380	i = 0
381	for item in names:
382	name = phfx+item
383	sig = self.sigDict.get(name,-0.009)
384	s += G2mth.ValEsd(size[1][i],sig)+', '
385	i = 2 #skip the aniso value
386	s += '\n Mustrain model "%s" for %s (10^6^)\n '%(mustrain[0],phasenam)
387	names = ['Mustrain;i','Mustrain;mx']
388	if 'uniax' in mustrain[0]:
389	names = ['Mustrain;i','Mustrain;a','Mustrain;mx']
390	s += 'anisotropic axis is %s\n '%(str(size[3]))
391	s += 'parameters: equatorial mustrain, axial mustrain, G/L mix\n '
392	for i,item in enumerate(names):
393	name = phfx+item
394	sig = self.sigDict.get(name,-0.009)
395	s += G2mth.ValEsd(mustrain[1][i],sig)+', '
396	elif 'general' in mustrain[0]:
397	names = 'parameters: '
398	for i,name in enumerate(G2spc.MustrainNames(SGData)):
399	names += name+', '
400	if i == 9:
401	names += '\n '
402	names += 'G/L mix\n '
403	s += names
404	txt = ''
405	for i in range(len(mustrain[4])):
406	name = phfx+'Mustrain:'+str(i)
407	sig = self.sigDict.get(name,-0.009)
408	if len(txt) > 60:
409	s += txt+'\n '
410	txt = ''
411	txt += G2mth.ValEsd(mustrain[4][i],sig)+', '
412	s += txt
413	sig = self.sigDict.get(phfx+'Mustrain;mx',-0.009)
414	s += G2mth.ValEsd(mustrain[1][2],sig)+', '
415
416	else: #isotropic
417	s += ' parameters: Mustrain, G/L mix\n '
418	i = 0
419	for item in names:
420	name = phfx+item
421	sig = self.sigDict.get(name,-0.009)
422	s += G2mth.ValEsd(mustrain[1][i],sig)+', '
423	i = 2 #skip the aniso value
424	s1 = ' \n Macrostrain parameters: '
425	names = G2spc.HStrainNames(SGData)
426	for name in names:
427	s1 += name+', '
428	s1 += '\n '
429	macrostrain = False
430	for i in range(len(names)):
431	name = phfx+name[i]
432	sig = self.sigDict.get(name,-0.009)
433	s1 += G2mth.ValEsd(hstrain[0][i],sig)+', '
434	if hstrain[0][i]: macrostrain = True
435	if macrostrain:
436	s += s1 + '\n'
437	# show revised lattice parameters here someday
438	else:
439	s += '\n'
440	return s
441
442	def FmtAtomType(sym):
443	'Reformat a GSAS-II atom type symbol to match CIF rules'
444	sym = sym.replace('_','') # underscores are not allowed: no isotope designation?
445	# in CIF, oxidation state sign symbols come after, not before
446	if '+' in sym:
447	sym = sym.replace('+','') + '+'
448	elif '-' in sym:
449	sym = sym.replace('-','') + '-'
450	return sym
451
452	def PutInCol(val,wid):
453	'''Pad a value to >=wid+1 columns by adding spaces at the end. Always
454	adds at least one space
455	'''
456	val = str(val).replace(' ','')
457	if not val: val = '?'
458	fmt = '{:' + str(wid) + '} '
459	return fmt.format(val)
460
461	def MakeUniqueLabel(lbl,labellist):
462	'Make sure that every atom label is unique'
463	lbl = lbl.strip()
464	if not lbl: # deal with a blank label
465	lbl = 'A_1'
466	if lbl not in labellist:
467	labellist.append(lbl)
468	return lbl
469	i = 1
470	prefix = lbl
471	if '_' in lbl:
472	prefix = lbl[:lbl.rfind('_')]
473	suffix = lbl[lbl.rfind('_')+1:]
474	try:
475	i = int(suffix)+1
476	except:
477	pass
478	while prefix+'_'+str(i) in labellist:
479	i += 1
480	else:
481	lbl = prefix+'_'+str(i)
482	labellist.append(lbl)
483
484	def WriteAtomsNuclear(phasenam):
485	'Write atom positions to CIF'
486	phasedict = self.Phases[phasenam] # pointer to current phase info
487	General = phasedict['General']
488	cx,ct,cs,cia = General['AtomPtrs']
489	Atoms = phasedict['Atoms']
490	cfrac = cx+3
491	fpfx = str(phasedict['pId'])+'::Afrac:'
492	for i,at in enumerate(Atoms):
493	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
494	if fval != 0.0:
495	break
496	else:
497	WriteCIFitem('\n# PHASE HAS NO ATOMS!')
498	return
499
500	WriteCIFitem('\n# ATOMIC COORDINATES AND DISPLACEMENT PARAMETERS')
501	WriteCIFitem('loop_ '+
502	'\n _atom_site_label'+
503	'\n _atom_site_type_symbol'+
504	'\n _atom_site_fract_x'+
505	'\n _atom_site_fract_y'+
506	'\n _atom_site_fract_z'+
507	'\n _atom_site_occupancy'+
508	'\n _atom_site_adp_type'+
509	'\n _atom_site_U_iso_or_equiv'+
510	'\n _atom_site_symmetry_multiplicity')
511
512	varnames = {cx:'Ax',cx+1:'Ay',cx+2:'Az',cx+3:'Afrac',
513	cia+1:'AUiso',cia+2:'AU11',cia+3:'AU22',cia+4:'AU33',
514	cia+5:'AU12',cia+6:'AU13',cia+7:'AU23'}
515	self.labellist = []
516
517	pfx = str(phasedict['pId'])+'::'
518	# loop over all atoms
519	naniso = 0
520	for i,at in enumerate(Atoms):
521	if phasedict['General']['Type'] == 'macromolecular':
522	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
523	s = PutInCol(MakeUniqueLabel(label,self.labellist),15) # label
524	else:
525	s = PutInCol(MakeUniqueLabel(at[ct-1],self.labellist),6) # label
526	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
527	if fval == 0.0: continue # ignore any atoms that have a occupancy set to 0 (exact)
528	s += PutInCol(FmtAtomType(at[ct]),4) # type
529	if at[cia] == 'I':
530	adp = 'Uiso '
531	else:
532	adp = 'Uani '
533	naniso += 1
534	# compute Uequiv crudely
535	# correct: Defined as "1/3 trace of diagonalized U matrix".
536	# SEE cell2GS & Uij2Ueqv to GSASIIlattice. Former is needed to make the GS matrix used by the latter.
537	t = 0.0
538	for j in (2,3,4):
539	var = pfx+varnames[cia+j]+":"+str(i)
540	t += self.parmDict.get(var,at[cia+j])
541	for j in (cx,cx+1,cx+2,cx+3,cia,cia+1):
542	if j in (cx,cx+1,cx+2):
543	dig = 11
544	sigdig = -0.00009
545	else:
546	dig = 10
547	sigdig = -0.009
548	if j == cia:
549	s += adp
550	else:
551	var = pfx+varnames[j]+":"+str(i)
552	dvar = pfx+"d"+varnames[j]+":"+str(i)
553	if dvar not in self.sigDict:
554	dvar = var
555	if j == cia+1 and adp == 'Uani ':
556	val = t/3.
557	sig = sigdig
558	else:
559	#print var,(var in self.parmDict),(var in self.sigDict)
560	val = self.parmDict.get(var,at[j])
561	sig = self.sigDict.get(dvar,sigdig)
562	s += PutInCol(G2mth.ValEsd(val,sig),dig)
563	s += PutInCol(at[cs+1],3)
564	WriteCIFitem(s)
565	if naniso == 0: return
566	# now loop over aniso atoms
567	WriteCIFitem('\nloop_' + '\n _atom_site_aniso_label' +
568	'\n _atom_site_aniso_U_11' + '\n _atom_site_aniso_U_12' +
569	'\n _atom_site_aniso_U_13' + '\n _atom_site_aniso_U_22' +
570	'\n _atom_site_aniso_U_23' + '\n _atom_site_aniso_U_33')
571	for i,at in enumerate(Atoms):
572	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
573	if fval == 0.0: continue # ignore any atoms that have a occupancy set to 0 (exact)
574	if at[cia] == 'I': continue
575	s = PutInCol(self.labellist[i],6) # label
576	for j in (2,3,4,5,6,7):
577	sigdig = -0.0009
578	var = pfx+varnames[cia+j]+":"+str(i)
579	val = self.parmDict.get(var,at[cia+j])
580	sig = self.sigDict.get(var,sigdig)
581	s += PutInCol(G2mth.ValEsd(val,sig),11)
582	WriteCIFitem(s)
583
584	def HillSortElements(elmlist):
585	'''Sort elements in "Hill" order: C, H, others, (where others
586	are alphabetical).
587
588	:params list elmlist: a list of element strings
589
590	:returns: a sorted list of element strings
591	'''
592	newlist = []
593	oldlist = elmlist[:]
594	for elm in ('C','H'):
595	if elm in elmlist:
596	newlist.append(elm)
597	oldlist.pop(oldlist.index(elm))
598	return newlist+sorted(oldlist)
599
600	def WriteComposition(phasenam):
601	'''determine the composition for the unit cell, crudely determine Z and
602	then compute the composition in formula units
603	'''
604	phasedict = self.Phases[phasenam] # pointer to current phase info
605	General = phasedict['General']
606	Z = General.get('cellZ',0.0)
607	cx,ct,cs,cia = General['AtomPtrs']
608	Atoms = phasedict['Atoms']
609	fpfx = str(phasedict['pId'])+'::Afrac:'
610	cfrac = cx+3
611	cmult = cs+1
612	compDict = {} # combines H,D & T
613	sitemultlist = []
614	massDict = dict(zip(General['AtomTypes'],General['AtomMass']))
615	cellmass = 0
616	for i,at in enumerate(Atoms):
617	atype = at[ct].strip()
618	if atype.find('-') != -1: atype = atype.split('-')[0]
619	if atype.find('+') != -1: atype = atype.split('+')[0]
620	atype = atype[0].upper()+atype[1:2].lower() # force case conversion
621	if atype == "D" or atype == "D": atype = "H"
622	fvar = fpfx+str(i)
623	fval = self.parmDict.get(fvar,at[cfrac])
624	mult = at[cmult]
625	if not massDict.get(at[ct]):
626	print('Error: No mass found for atom type '+at[ct])
627	print('Will not compute cell contents for phase '+phasenam)
628	return
629	cellmass += massDict[at[ct]]multfval
630	compDict[atype] = compDict.get(atype,0.0) + mult*fval
631	if fval == 1: sitemultlist.append(mult)
632	if len(compDict.keys()) == 0: return # no elements!
633	if Z < 1: # Z has not been computed or set by user
634	Z = 1
635	for i in range(2,min(sitemultlist)+1):
636	for m in sitemultlist:
637	if m % i != 0:
638	break
639	else:
640	Z = i
641	General['cellZ'] = Z # save it
642
643	# when scattering factors are included in the CIF, this needs to be
644	# added to the loop here but only in the one-block case.
645	# For multiblock CIFs, scattering factors go in the histogram
646	# blocks (for all atoms in all appropriate phases) - an example?:
647	#loop_
648	# _atom_type_symbol
649	# _atom_type_description
650	# _atom_type_scat_dispersion_real
651	# _atom_type_scat_dispersion_imag
652	# _atom_type_scat_source
653	# 'C' 'C' 0.0033 0.0016
654	# 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
655	# 'H' 'H' 0.0000 0.0000
656	# 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
657	# 'P' 'P' 0.1023 0.0942
658	# 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
659	# 'Cl' 'Cl' 0.1484 0.1585
660	# 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
661	# 'Cu' 'Cu' 0.3201 1.2651
662	# 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
663
664	#if oneblock: # add scattering factors for current phase here
665	WriteCIFitem('\nloop_ _atom_type_symbol _atom_type_number_in_cell')
666	formula = ''
667	reload(G2mth)
668	for elem in HillSortElements(compDict.keys()):
669	WriteCIFitem(' ' + PutInCol(elem,4) +
670	G2mth.ValEsd(compDict[elem],-0.009,True))
671	if formula: formula += " "
672	formula += elem
673	if compDict[elem] == Z: continue
674	formula += G2mth.ValEsd(compDict[elem]/Z,-0.009,True)
675	WriteCIFitem( '\n# Note that Z affects _cell_formula_sum and _weight')
676	WriteCIFitem( '_cell_formula_units_Z',str(Z))
677	WriteCIFitem( '_chemical_formula_sum',formula)
678	WriteCIFitem( '_chemical_formula_weight',
679	G2mth.ValEsd(cellmass/Z,-0.09,True))
680
681	def WriteDistances(phasenam,SymOpList,offsetList,symOpList,G2oprList):
682	'''Report bond distances and angles for the CIF
683
684	Note that _geom__symmetry_ fields are values of form
685	n_klm where n is the symmetry operation in SymOpList (counted
686	starting with 1) and (k-5, l-5, m-5) are translations to add
687	to (x,y,z). See
688	http://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Igeom_angle_site_symmetry_.html
689
690	TODO: need a method to select publication flags for distances/angles
691	'''
692	phasedict = self.Phases[phasenam] # pointer to current phase info
693	Atoms = phasedict['Atoms']
694	generalData = phasedict['General']
695	# create a dict for storing Pub flag for bonds/angles, if needed
696	if phasedict['General'].get("DisAglHideFlag") is None:
697	phasedict['General']["DisAglHideFlag"] = {}
698	DisAngSel = phasedict['General']["DisAglHideFlag"]
699	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
700	cn = ct-1
701	fpfx = str(phasedict['pId'])+'::Afrac:'
702	cfrac = cx+3
703	DisAglData = {}
704	# create a list of atoms, but skip atoms with zero occupancy
705	xyz = []
706	fpfx = str(phasedict['pId'])+'::Afrac:'
707	for i,atom in enumerate(Atoms):
708	if self.parmDict.get(fpfx+str(i),atom[cfrac]) == 0.0: continue
709	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
710	if 'DisAglCtls' not in generalData:
711	# should not happen, since DisAglDialog should be called
712	# for all phases before getting here
713	dlg = G2gd.DisAglDialog(
714	self.G2frame,
715	{},
716	generalData)
717	if dlg.ShowModal() == wx.ID_OK:
718	generalData['DisAglCtls'] = dlg.GetData()
719	else:
720	dlg.Destroy()
721	return
722	dlg.Destroy()
723	DisAglData['OrigAtoms'] = xyz
724	DisAglData['TargAtoms'] = xyz
725	SymOpList,offsetList,symOpList,G2oprList = G2spc.AllOps(
726	generalData['SGData'])
727
728	xpandSGdata = generalData['SGData'].copy()
729	xpandSGdata.update({'SGOps':symOpList,
730	'SGInv':False,
731	'SGLatt':'P',
732	'SGCen':np.array([[0, 0, 0]]),})
733	DisAglData['SGData'] = xpandSGdata
734
735	DisAglData['Cell'] = generalData['Cell'][1:] #+ volume
736	if 'pId' in phasedict:
737	DisAglData['pId'] = phasedict['pId']
738	DisAglData['covData'] = self.OverallParms['Covariance']
739	try:
740	AtomLabels,DistArray,AngArray = G2stMn.RetDistAngle(
741	generalData['DisAglCtls'],
742	DisAglData)
743	except KeyError: # inside DistAngle for missing atom types in DisAglCtls
744	print('** ERROR - try again but do "Reset" to fill in missing atom types **')
745
746	# loop over interatomic distances for this phase
747	WriteCIFitem('\n# MOLECULAR GEOMETRY')
748	WriteCIFitem('loop_' +
749	'\n _geom_bond_atom_site_label_1' +
750	'\n _geom_bond_atom_site_label_2' +
751	'\n _geom_bond_distance' +
752	'\n _geom_bond_site_symmetry_1' +
753	'\n _geom_bond_site_symmetry_2' +
754	'\n _geom_bond_publ_flag')
755
756	for i in sorted(AtomLabels.keys()):
757	Dist = DistArray[i]
758	for D in Dist:
759	line = ' '+PutInCol(AtomLabels[i],6)+PutInCol(AtomLabels[D[0]],6)
760	sig = D[4]
761	if sig == 0: sig = -0.00009
762	line += PutInCol(G2mth.ValEsd(D[3],sig,True),10)
763	line += " 1_555 "
764	line += " {:3d}_".format(D[2])
765	for d in D[1]:
766	line += "{:1d}".format(d+5)
767	if DisAngSel.get((i,tuple(D[0:3]))):
768	line += " no"
769	else:
770	line += " yes"
771	WriteCIFitem(line)
772
773	# loop over interatomic angles for this phase
774	WriteCIFitem('\nloop_' +
775	'\n _geom_angle_atom_site_label_1' +
776	'\n _geom_angle_atom_site_label_2' +
777	'\n _geom_angle_atom_site_label_3' +
778	'\n _geom_angle' +
779	'\n _geom_angle_site_symmetry_1' +
780	'\n _geom_angle_site_symmetry_2' +
781	'\n _geom_angle_site_symmetry_3' +
782	'\n _geom_angle_publ_flag')
783
784	for i in sorted(AtomLabels.keys()):
785	Dist = DistArray[i]
786	for k,j,tup in AngArray[i]:
787	Dj = Dist[j]
788	Dk = Dist[k]
789	line = ' '+PutInCol(AtomLabels[Dj[0]],6)+PutInCol(AtomLabels[i],6)+PutInCol(AtomLabels[Dk[0]],6)
790	sig = tup[1]
791	if sig == 0: sig = -0.009
792	line += PutInCol(G2mth.ValEsd(tup[0],sig,True),10)
793	line += " {:3d}_".format(Dj[2])
794	for d in Dj[1]:
795	line += "{:1d}".format(d+5)
796	line += " 1_555 "
797	line += " {:3d}_".format(Dk[2])
798	for d in Dk[1]:
799	line += "{:1d}".format(d+5)
800	key = (tuple(Dk[0:3]),i,tuple(Dj[0:3]))
801	if DisAngSel.get(key):
802	line += " no"
803	else:
804	line += " yes"
805	WriteCIFitem(line)
806
807	def WritePhaseInfo(phasenam):
808	'Write out the phase information for the selected phase'
809	WriteCIFitem('\n# phase info for '+str(phasenam) + ' follows')
810	phasedict = self.Phases[phasenam] # pointer to current phase info
811	WriteCIFitem('_pd_phase_name', phasenam)
812	cellList,cellSig = self.GetCell(phasenam)
813	defsigL = 3[-0.00001] + 3[-0.001] + [-0.01] # significance to use when no sigma
814	names = ['length_a','length_b','length_c',
815	'angle_alpha','angle_beta ','angle_gamma',
816	'volume']
817	prevsig = 0
818	for lbl,defsig,val,sig in zip(names,defsigL,cellList,cellSig):
819	if sig:
820	txt = G2mth.ValEsd(val,sig)
821	prevsig = -sig # use this as the significance for next value
822	else:
823	txt = G2mth.ValEsd(val,min(defsig,prevsig),True)
824	WriteCIFitem('_cell_'+lbl,txt)
825
826	WriteCIFitem('_symmetry_cell_setting',
827	phasedict['General']['SGData']['SGSys'])
828
829	spacegroup = phasedict['General']['SGData']['SpGrp'].strip()
830	# regularize capitalization and remove trailing H/R
831	spacegroup = spacegroup[0].upper() + spacegroup[1:].lower().rstrip('rh ')
832	WriteCIFitem('_symmetry_space_group_name_H-M',spacegroup)
833
834	# generate symmetry operations including centering and center of symmetry
835	SymOpList,offsetList,symOpList,G2oprList = G2spc.AllOps(
836	phasedict['General']['SGData'])
837	WriteCIFitem('loop_\n _space_group_symop_id\n _space_group_symop_operation_xyz')
838	for i,op in enumerate(SymOpList,start=1):
839	WriteCIFitem(' {:3d} {:}'.format(i,op.lower()))
840
841	# loop over histogram(s) used in this phase
842	if not oneblock and not self.quickmode:
843	# report pointers to the histograms used in this phase
844	histlist = []
845	for hist in self.Phases[phasenam]['Histograms']:
846	if self.Phases[phasenam]['Histograms'][hist]['Use']:
847	if phasebyhistDict.get(hist):
848	phasebyhistDict[hist].append(phasenam)
849	else:
850	phasebyhistDict[hist] = [phasenam,]
851	blockid = datablockidDict.get(hist)
852	if not blockid:
853	print("Internal error: no block for data. Phase "+str(
854	phasenam)+" histogram "+str(hist))
855	histlist = []
856	break
857	histlist.append(blockid)
858
859	if len(histlist) == 0:
860	WriteCIFitem('# Note: phase has no associated data')
861
862	# report atom params
863	if phasedict['General']['Type'] in ['nuclear','macromolecular']: #this needs macromolecular variant, etc!
864	WriteAtomsNuclear(phasenam)
865	else:
866	raise Exception,"no export for "+str(phasedict['General']['Type'])+" coordinates implemented"
867	# report cell contents
868	WriteComposition(phasenam)
869	if not self.quickmode and phasedict['General']['Type'] == 'nuclear': # report distances and angles
870	WriteDistances(phasenam,SymOpList,offsetList,symOpList,G2oprList)
871
872	def Yfmt(ndec,val):
873	'Format intensity values'
874	out = ("{:."+str(ndec)+"f}").format(val)
875	out = out.rstrip('0') # strip zeros to right of decimal
876	return out.rstrip('.') # and decimal place when not needed
877
878	def WriteReflStat(refcount,hklmin,hklmax,dmin,dmax,nRefSets=1):
879	'Write reflection statistics'
880	WriteCIFitem('_reflns_number_total', str(refcount))
881	if hklmin is not None and nRefSets == 1: # hkl range has no meaning with multiple phases
882	WriteCIFitem('_reflns_limit_h_min', str(int(hklmin[0])))
883	WriteCIFitem('_reflns_limit_h_max', str(int(hklmax[0])))
884	WriteCIFitem('_reflns_limit_k_min', str(int(hklmin[1])))
885	WriteCIFitem('_reflns_limit_k_max', str(int(hklmax[1])))
886	WriteCIFitem('_reflns_limit_l_min', str(int(hklmin[2])))
887	WriteCIFitem('_reflns_limit_l_max', str(int(hklmax[2])))
888	if hklmin is not None:
889	WriteCIFitem('_reflns_d_resolution_low ', G2mth.ValEsd(dmax,-0.009))
890	WriteCIFitem('_reflns_d_resolution_high ', G2mth.ValEsd(dmin,-0.009))
891
892	def WritePowderData(histlbl):
893	'Write out the selected powder diffraction histogram info'
894	histblk = self.Histograms[histlbl]
895	inst = histblk['Instrument Parameters'][0]
896	hId = histblk['hId']
897	pfx = ':' + str(hId) + ':'
898
899	if 'Lam1' in inst:
900	ratio = self.parmDict.get('I(L2)/I(L1)',inst['I(L2)/I(L1)'][1])
901	sratio = self.sigDict.get('I(L2)/I(L1)',-0.0009)
902	lam1 = self.parmDict.get('Lam1',inst['Lam1'][1])
903	slam1 = self.sigDict.get('Lam1',-0.00009)
904	lam2 = self.parmDict.get('Lam2',inst['Lam2'][1])
905	slam2 = self.sigDict.get('Lam2',-0.00009)
906	# always assume Ka1 & Ka2 if two wavelengths are present
907	WriteCIFitem('_diffrn_radiation_type','K\\a~1,2~')
908	WriteCIFitem('loop_' +
909	'\n _diffrn_radiation_wavelength' +
910	'\n _diffrn_radiation_wavelength_wt' +
911	'\n _diffrn_radiation_wavelength_id')
912	WriteCIFitem(' ' + PutInCol(G2mth.ValEsd(lam1,slam1),15)+
913	PutInCol('1.0',15) +
914	PutInCol('1',5))
915	WriteCIFitem(' ' + PutInCol(G2mth.ValEsd(lam2,slam2),15)+
916	PutInCol(G2mth.ValEsd(ratio,sratio),15)+
917	PutInCol('2',5))
918	else:
919	lam1 = self.parmDict.get('Lam',inst['Lam'][1])
920	slam1 = self.sigDict.get('Lam',-0.00009)
921	WriteCIFitem('_diffrn_radiation_wavelength',G2mth.ValEsd(lam1,slam1))
922
923	if not oneblock:
924	if not phasebyhistDict.get(histlbl):
925	WriteCIFitem('\n# No phases associated with this data set')
926	else:
927	WriteCIFitem('\n# PHASE TABLE')
928	WriteCIFitem('loop_' +
929	'\n _pd_phase_id' +
930	'\n _pd_phase_block_id' +
931	'\n _pd_phase_mass_%')
932	wtFrSum = 0.
933	for phasenam in phasebyhistDict.get(histlbl):
934	hapData = self.Phases[phasenam]['Histograms'][histlbl]
935	General = self.Phases[phasenam]['General']
936	wtFrSum += hapData['Scale'][0]*General['Mass']
937
938	for phasenam in phasebyhistDict.get(histlbl):
939	hapData = self.Phases[phasenam]['Histograms'][histlbl]
940	General = self.Phases[phasenam]['General']
941	wtFr = hapData['Scale'][0]*General['Mass']/wtFrSum
942	pfx = str(self.Phases[phasenam]['pId'])+':'+str(hId)+':'
943	if pfx+'Scale' in self.sigDict:
944	sig = self.sigDict[pfx+'Scale']*wtFr/hapData['Scale'][0]
945	else:
946	sig = -0.0001
947	WriteCIFitem(
948	' '+
949	str(self.Phases[phasenam]['pId']) +
950	' '+datablockidDict[phasenam]+
951	' '+G2mth.ValEsd(wtFr,sig)
952	)
953	WriteCIFitem('loop_' +
954	'\n _gsas_proc_phase_R_F_factor' +
955	'\n _gsas_proc_phase_R_Fsqd_factor' +
956	'\n _gsas_proc_phase_id' +
957	'\n _gsas_proc_phase_block_id')
958	for phasenam in phasebyhistDict.get(histlbl):
959	pfx = str(self.Phases[phasenam]['pId'])+':'+str(hId)+':'
960	WriteCIFitem(
961	' '+
962	' '+G2mth.ValEsd(histblk[pfx+'Rf']/100.,-.00009) +
963	' '+G2mth.ValEsd(histblk[pfx+'Rf^2']/100.,-.00009)+
964	' '+str(self.Phases[phasenam]['pId'])+
965	' '+datablockidDict[phasenam]
966	)
967	else:
968	# single phase in this histogram
969	pfx = '0:'+str(hId)+':'
970	WriteCIFitem('_refine_ls_R_F_factor ','%.5f'%(histblk[pfx+'Rf']/100.))
971	WriteCIFitem('_refine_ls_R_Fsqd_factor ','%.5f'%(histblk[pfx+'Rf^2']/100.))
972
973	WriteCIFitem('_pd_proc_ls_prof_R_factor ','%.5f'%(histblk['R']/100.))
974	WriteCIFitem('_pd_proc_ls_prof_wR_factor ','%.5f'%(histblk['wR']/100.))
975	WriteCIFitem('_gsas_proc_ls_prof_R_B_factor ','%.5f'%(histblk['Rb']/100.))
976	WriteCIFitem('_gsas_proc_ls_prof_wR_B_factor','%.5f'%(histblk['wRb']/100.))
977	WriteCIFitem('_pd_proc_ls_prof_wR_expected','%.5f'%(histblk['wRmin']/100.))
978
979	if histblk['Instrument Parameters'][0]['Type'][1][1] == 'X':
980	WriteCIFitem('_diffrn_radiation_probe','x-ray')
981	pola = histblk['Instrument Parameters'][0].get('Polariz.')
982	if pola:
983	pfx = ':' + str(hId) + ':'
984	sig = self.sigDict.get(pfx+'Polariz.',-0.0009)
985	txt = G2mth.ValEsd(pola[1],sig)
986	WriteCIFitem('_diffrn_radiation_polarisn_ratio',txt)
987	elif histblk['Instrument Parameters'][0]['Type'][1][1] == 'N':
988	WriteCIFitem('_diffrn_radiation_probe','neutron')
989	# TOF (note that this may not be defined)
990	#if histblk['Instrument Parameters'][0]['Type'][1][2] == 'T':
991	# WriteCIFitem('_pd_meas_2theta_fixed',text)
992
993
994	# TODO: this will need help from Bob
995	#if not oneblock:
996	#WriteCIFitem('\n# SCATTERING FACTOR INFO')
997	#WriteCIFitem('loop_ _atom_type_symbol')
998	#if histblk['Instrument Parameters'][0]['Type'][1][1] == 'X':
999	# WriteCIFitem(' _atom_type_scat_dispersion_real')
1000	# WriteCIFitem(' _atom_type_scat_dispersion_imag')
1001	# for lbl in ('a1','a2','a3', 'a4', 'b1', 'b2', 'b3', 'b4', 'c'):
1002	# WriteCIFitem(' _atom_type_scat_Cromer_Mann_'+lbl)
1003	#elif histblk['Instrument Parameters'][0]['Type'][1][1] == 'N':
1004	# WriteCIFitem(' _atom_type_scat_length_neutron')
1005	#WriteCIFitem(' _atom_type_scat_source')
1006
1007	WriteCIFitem('_pd_proc_ls_background_function',FormatBackground(histblk['Background'],histblk['hId']))
1008
1009	# TODO: this will need help from Bob
1010	#WriteCIFitem('_exptl_absorpt_process_details','?')
1011	#WriteCIFitem('_exptl_absorpt_correction_T_min','?')
1012	#WriteCIFitem('_exptl_absorpt_correction_T_max','?')
1013	#C extinction
1014	#WRITE(IUCIF,'(A)') '# Extinction correction'
1015	#CALL WRVAL(IUCIF,'_gsas_exptl_extinct_corr_T_min',TEXT(1:10))
1016	#CALL WRVAL(IUCIF,'_gsas_exptl_extinct_corr_T_max',TEXT(11:20))
1017
1018	if not oneblock: # instrumental profile terms go here
1019	WriteCIFitem('_pd_proc_ls_profile_function',
1020	FormatInstProfile(histblk["Instrument Parameters"],histblk['hId']))
1021
1022	#refprx = '_refln.' # mm
1023	refprx = '_refln_' # normal
1024	# data collection parameters for the powder dataset
1025
1026	temperature = histblk['Sample Parameters'].get('Temperature') # G2 uses K
1027	if not temperature:
1028	T = '?'
1029	else:
1030	T = G2mth.ValEsd(temperature,-0.009,True) # CIF uses K
1031	WriteCIFitem('_diffrn_ambient_temperature',T)
1032
1033	pressure = histblk['Sample Parameters'].get('Pressure') #G2 uses mega-Pascal
1034	if not pressure:
1035	P = '?'
1036	else:
1037	P = G2mth.ValEsd(pressure*1000,-0.09,True) # CIF uses kilopascal
1038	WriteCIFitem('_diffrn_ambient_pressure',P)
1039
1040	WriteCIFitem('\n# STRUCTURE FACTOR TABLE')
1041	# compute maximum intensity reflection
1042	Imax = 0
1043	for phasenam in histblk['Reflection Lists']:
1044	scale = self.Phases[phasenam]['Histograms'][histlbl]['Scale'][0]
1045	refList = np.asarray(histblk['Reflection Lists'][phasenam]['RefList'])
1046	I100 = scalerefList.T[8]refList.T[11]
1047	#Icorr = np.array([refl[13] for refl in histblk['Reflection Lists'][phasenam]])[0]
1048	#FO2 = np.array([refl[8] for refl in histblk['Reflection Lists'][phasenam]])
1049	#I100 = scaleFO2Icorr
1050	Imax = max(Imax,max(I100))
1051
1052	WriteCIFitem('loop_')
1053	if len(histblk['Reflection Lists'].keys()) > 1:
1054	WriteCIFitem(' _pd_refln_phase_id')
1055	WriteCIFitem(' ' + refprx + 'index_h' +
1056	'\n ' + refprx + 'index_k' +
1057	'\n ' + refprx + 'index_l' +
1058	'\n ' + refprx + 'F_squared_meas' +
1059	'\n ' + refprx + 'F_squared_calc' +
1060	'\n ' + refprx + 'phase_calc' +
1061	'\n _pd_refln_d_spacing')
1062	if Imax > 0:
1063	WriteCIFitem(' _gsas_i100_meas')
1064
1065	refcount = 0
1066	hklmin = None
1067	hklmax = None
1068	dmax = None
1069	dmin = None
1070	for phasenam in histblk['Reflection Lists']:
1071	scale = self.Phases[phasenam]['Histograms'][histlbl]['Scale'][0]
1072	phaseid = self.Phases[phasenam]['pId']
1073	refcount += len(histblk['Reflection Lists'][phasenam]['RefList'])
1074	for j,ref in enumerate(histblk['Reflection Lists'][phasenam]['RefList']):
1075	if DEBUG:
1076	print('DEBUG: skipping reflection list')
1077	break
1078	if hklmin is None:
1079	hklmin = ref[0:3]
1080	hklmax = ref[0:3]
1081	dmax = dmin = ref[4]
1082	if len(histblk['Reflection Lists'].keys()) > 1:
1083	s = PutInCol(phaseid,2)
1084	else:
1085	s = ""
1086	for i,hkl in enumerate(ref[0:3]):
1087	hklmax[i] = max(hkl,hklmax[i])
1088	hklmin[i] = min(hkl,hklmin[i])
1089	s += PutInCol(int(hkl),4)
1090	for I in ref[8:10]:
1091	s += PutInCol(G2mth.ValEsd(I,-0.0009),10)
1092	s += PutInCol(G2mth.ValEsd(ref[10],-0.9),7)
1093	dmax = max(dmax,ref[4])
1094	dmin = min(dmin,ref[4])
1095	s += PutInCol(G2mth.ValEsd(ref[4],-0.009),8)
1096	if Imax > 0:
1097	s += PutInCol(G2mth.ValEsd(100.*I100[j]/Imax,-0.09),6)
1098	WriteCIFitem(" "+s)
1099
1100	WriteReflStat(refcount,hklmin,hklmax,dmin,dmax,len(histblk['Reflection Lists']))
1101	WriteCIFitem('\n# POWDER DATA TABLE')
1102	# is data fixed step? If the step varies by <0.01% treat as fixed step
1103	steps = histblk['Data'][0][1:] - histblk['Data'][0][:-1]
1104	if abs(max(steps)-min(steps)) > abs(max(steps))/10000.:
1105	fixedstep = False
1106	else:
1107	fixedstep = True
1108
1109	if fixedstep: # and not TOF
1110	WriteCIFitem('_pd_meas_2theta_range_min', G2mth.ValEsd(histblk['Data'][0][0],-0.00009))
1111	WriteCIFitem('_pd_meas_2theta_range_max', G2mth.ValEsd(histblk['Data'][0][-1],-0.00009))
1112	WriteCIFitem('_pd_meas_2theta_range_inc', G2mth.ValEsd(steps.sum()/len(steps),-0.00009))
1113	# zero correct, if defined
1114	zero = None
1115	zerolst = histblk['Instrument Parameters'][0].get('Zero')
1116	if zerolst: zero = zerolst[1]
1117	zero = self.parmDict.get('Zero',zero)
1118	if zero:
1119	WriteCIFitem('_pd_proc_2theta_range_min', G2mth.ValEsd(histblk['Data'][0][0]-zero,-0.00009))
1120	WriteCIFitem('_pd_proc_2theta_range_max', G2mth.ValEsd(histblk['Data'][0][-1]-zero,-0.00009))
1121	WriteCIFitem('_pd_proc_2theta_range_inc', G2mth.ValEsd(steps.sum()/len(steps),-0.00009))
1122
1123	if zero:
1124	WriteCIFitem('_pd_proc_number_of_points', str(len(histblk['Data'][0])))
1125	else:
1126	WriteCIFitem('_pd_meas_number_of_points', str(len(histblk['Data'][0])))
1127	WriteCIFitem('\nloop_')
1128	# WriteCIFitem(' _pd_proc_d_spacing') # need easy way to get this
1129	if not fixedstep:
1130	if zero:
1131	WriteCIFitem(' _pd_proc_2theta_corrected')
1132	else:
1133	WriteCIFitem(' _pd_meas_2theta_scan')
1134	# at least for now, always report weights.
1135	#if countsdata:
1136	# WriteCIFitem(' _pd_meas_counts_total')
1137	#else:
1138	WriteCIFitem(' _pd_meas_intensity_total')
1139	WriteCIFitem(' _pd_calc_intensity_total')
1140	WriteCIFitem(' _pd_proc_intensity_bkg_calc')
1141	WriteCIFitem(' _pd_proc_ls_weight')
1142	maxY = max(histblk['Data'][1].max(),histblk['Data'][3].max())
1143	if maxY < 0: maxY *= -10 # this should never happen, but...
1144	ndec = max(0,10-int(np.log10(maxY))-1) # 10 sig figs should be enough
1145	maxSU = histblk['Data'][2].max()
1146	if maxSU < 0: maxSU *= -1 # this should never happen, but...
1147	ndecSU = max(0,8-int(np.log10(maxSU))-1) # 8 sig figs should be enough
1148	lowlim,highlim = histblk['Limits'][1]
1149
1150	if DEBUG:
1151	print('DEBUG: skipping profile list')
1152	else:
1153	for x,yobs,yw,ycalc,ybkg in zip(histblk['Data'][0],
1154	histblk['Data'][1],
1155	histblk['Data'][2],
1156	histblk['Data'][3],
1157	histblk['Data'][4]):
1158	if lowlim <= x <= highlim:
1159	pass
1160	else:
1161	yw = 0.0 # show the point is not in use
1162
1163	if fixedstep:
1164	s = ""
1165	else:
1166	s = PutInCol(G2mth.ValEsd(x-zero,-0.00009),10)
1167	s += PutInCol(Yfmt(ndec,yobs),12)
1168	s += PutInCol(Yfmt(ndec,ycalc),12)
1169	s += PutInCol(Yfmt(ndec,ybkg),11)
1170	s += PutInCol(Yfmt(ndecSU,yw),9)
1171	WriteCIFitem(" "+s)
1172
1173	def WriteSingleXtalData(histlbl):
1174	'Write out the selected single crystal histogram info'
1175	histblk = self.Histograms[histlbl]
1176
1177	#refprx = '_refln.' # mm
1178	refprx = '_refln_' # normal
1179
1180	WriteCIFitem('\n# STRUCTURE FACTOR TABLE')
1181	WriteCIFitem('loop_' +
1182	'\n ' + refprx + 'index_h' +
1183	'\n ' + refprx + 'index_k' +
1184	'\n ' + refprx + 'index_l' +
1185	'\n ' + refprx + 'F_squared_meas' +
1186	'\n ' + refprx + 'F_squared_sigma' +
1187	'\n ' + refprx + 'F_squared_calc' +
1188	'\n ' + refprx + 'phase_calc'
1189	)
1190
1191	hklmin = None
1192	hklmax = None
1193	dmax = None
1194	dmin = None
1195	refcount = len(histblk['Data']['RefList'])
1196	for ref in histblk['Data']['RefList']:
1197	s = " "
1198	if hklmin is None:
1199	hklmin = ref[0:3]
1200	hklmax = ref[0:3]
1201	dmax = dmin = ref[4]
1202	for i,hkl in enumerate(ref[0:3]):
1203	hklmax[i] = max(hkl,hklmax[i])
1204	hklmin[i] = min(hkl,hklmin[i])
1205	s += PutInCol(int(hkl),4)
1206	import sys
1207	if ref[5] == 0.0:
1208	s += PutInCol(G2mth.ValEsd(ref[8],0),12)
1209	s += PutInCol('.',10)
1210	s += PutInCol(G2mth.ValEsd(ref[9],0),12)
1211	s += PutInCol(G2mth.ValEsd(ref[10],-0.9),7)
1212	else:
1213	sig = ref[6] * ref[8] / ref[5]
1214	s += PutInCol(G2mth.ValEsd(ref[8],-abs(sig/10)),12)
1215	s += PutInCol(G2mth.ValEsd(sig,-abs(sig)/10.),10)
1216	s += PutInCol(G2mth.ValEsd(ref[9],-abs(sig/10)),12)
1217	s += PutInCol(G2mth.ValEsd(ref[10],-0.9),7)
1218	dmax = max(dmax,ref[4])
1219	dmin = min(dmin,ref[4])
1220	WriteCIFitem(s)
1221	if not self.quickmode: # statistics only in a full CIF
1222	WriteReflStat(refcount,hklmin,hklmax,dmin,dmax)
1223	hId = histblk[0]['hId']
1224	pfx = '0:'+str(hId)+':'
1225	WriteCIFitem('_reflns_wR_factor_obs ','%.4f'%(histblk[0]['wR']/100.))
1226	WriteCIFitem('_reflns_R_F_factor_obs ','%.4f'%(histblk[0][pfx+'Rf']/100.))
1227	WriteCIFitem('_reflns_R_Fsqd_factor_obs','%.4f'%(histblk[0][pfx+'Rf^2']/100.))
1228	def EditAuthor(event=None):
1229	'dialog to edit the CIF author info'
1230	'Edit the CIF author name'
1231	dlg = G2gd.SingleStringDialog(self.G2frame,
1232	'Get CIF Author',
1233	'Provide CIF Author name (Last, First)',
1234	value=self.author)
1235	if not dlg.Show():
1236	dlg.Destroy()
1237	return False # cancel was pressed
1238	self.author = dlg.GetValue()
1239	dlg.Destroy()
1240	try:
1241	self.OverallParms['Controls']["Author"] = self.author # save for future
1242	except KeyError:
1243	pass
1244	return True
1245	def EditInstNames(event=None):
1246	'Provide a dialog for editing instrument names'
1247	dictlist = []
1248	keylist = []
1249	lbllist = []
1250	for hist in self.Histograms:
1251	if hist.startswith("PWDR"):
1252	key2 = "Sample Parameters"
1253	d = self.Histograms[hist][key2]
1254	elif hist.startswith("HKLF"):
1255	key2 = "Instrument Parameters"
1256	d = self.Histograms[hist][key2][0]
1257
1258	lbllist.append(hist)
1259	dictlist.append(d)
1260	keylist.append('InstrName')
1261	instrname = d.get('InstrName')
1262	if instrname is None:
1263	d['InstrName'] = ''
1264	return G2gd.CallScrolledMultiEditor(
1265	self.G2frame,dictlist,keylist,
1266	prelbl=range(1,len(dictlist)+1),
1267	postlbl=lbllist,
1268	title='Instrument names',
1269	header="Edit instrument names. Note that a non-blank\nname is required for all histograms",
1270	CopyButton=True)
1271
1272	def EditRanges(event):
1273	'''Edit the bond distance/angle search range; phase is determined from
1274	a pointer placed in the button object (.phasedict) that references the
1275	phase dictionary
1276	'''
1277	but = event.GetEventObject()
1278	phasedict = but.phasedict
1279	dlg = G2gd.DisAglDialog(
1280	self.G2frame,
1281	phasedict['General']['DisAglCtls'], # edited
1282	phasedict['General'], # defaults
1283	)
1284	if dlg.ShowModal() == wx.ID_OK:
1285	phasedict['General']['DisAglCtls'] = dlg.GetData()
1286	dlg.Destroy()
1287
1288	def EditCIFDefaults():
1289	'''Fills the CIF Defaults window with controls for editing various CIF export
1290	parameters (mostly related to templates).
1291	'''
1292	self.cifdefs.DestroyChildren()
1293	self.cifdefs.SetTitle('Edit CIF settings')
1294	vbox = wx.BoxSizer(wx.VERTICAL)
1295	vbox.Add(wx.StaticText(self.cifdefs, wx.ID_ANY,'Creating file '+str(self.filename)))
1296	but = wx.Button(self.cifdefs, wx.ID_ANY,'Edit CIF Author')
1297	but.Bind(wx.EVT_BUTTON,EditAuthor)
1298	vbox.Add(but,0,wx.ALIGN_CENTER,3)
1299	but = wx.Button(self.cifdefs, wx.ID_ANY,'Edit Instrument Name(s)')
1300	but.Bind(wx.EVT_BUTTON,EditInstNames)
1301	vbox.Add(but,0,wx.ALIGN_CENTER,3)
1302	cpnl = wxscroll.ScrolledPanel(self.cifdefs,size=(300,300))
1303	cbox = wx.BoxSizer(wx.VERTICAL)
1304	G2gd.HorizontalLine(cbox,cpnl)
1305	cbox.Add(
1306	CIFtemplateSelect(self.cifdefs,
1307	cpnl,'publ',self.OverallParms['Controls'],
1308	EditCIFDefaults,
1309	"Publication (overall) template",
1310	),
1311	0,wx.EXPAND\|wx.ALIGN_LEFT\|wx.ALL)
1312	for phasenam in sorted(self.Phases.keys()):
1313	G2gd.HorizontalLine(cbox,cpnl)
1314	title = 'Phase '+phasenam
1315	phasedict = self.Phases[phasenam] # pointer to current phase info
1316	cbox.Add(
1317	CIFtemplateSelect(self.cifdefs,
1318	cpnl,'phase',phasedict['General'],
1319	EditCIFDefaults,
1320	title,
1321	phasenam),
1322	0,wx.EXPAND\|wx.ALIGN_LEFT\|wx.ALL)
1323	cpnl.SetSizer(cbox)
1324	if phasedict['General']['Type'] == 'nuclear':
1325	but = wx.Button(cpnl, wx.ID_ANY,'Edit distance/angle ranges')
1326	cbox.Add(but,0,wx.ALIGN_LEFT,0)
1327	cbox.Add((-1,2))
1328	but.phasedict = self.Phases[phasenam] # set a pointer to current phase info
1329	but.Bind(wx.EVT_BUTTON,EditRanges) # phase bond/angle ranges
1330	but = wx.Button(cpnl, wx.ID_ANY,'Set distance/angle publication flags')
1331	but.phase = phasenam # set a pointer to current phase info
1332	but.Bind(wx.EVT_BUTTON,SelectDisAglFlags) # phase bond/angle ranges
1333	cbox.Add(but,0,wx.ALIGN_LEFT,0)
1334	cbox.Add((-1,2))
1335	for i in sorted(self.powderDict.keys()):
1336	G2gd.HorizontalLine(cbox,cpnl)
1337	hist = self.powderDict[i]
1338	histblk = self.Histograms[hist]
1339	title = 'Powder dataset '+hist[5:]
1340	cbox.Add(
1341	CIFtemplateSelect(self.cifdefs,
1342	cpnl,'powder',histblk["Sample Parameters"],
1343	EditCIFDefaults,
1344	title,
1345	histblk["Sample Parameters"]['InstrName']),
1346	0,wx.EXPAND\|wx.ALIGN_LEFT\|wx.ALL)
1347	for i in sorted(self.xtalDict.keys()):
1348	G2gd.HorizontalLine(cbox,cpnl)
1349	hist = self.xtalDict[i]
1350	histblk = self.Histograms[hist]
1351	title = 'Single Xtal dataset '+hist[5:]
1352	cbox.Add(
1353	CIFtemplateSelect(self.cifdefs,
1354	cpnl,'single',histblk["Instrument Parameters"][0],
1355	EditCIFDefaults,
1356	title,
1357	histblk["Instrument Parameters"][0]['InstrName']),
1358	0,wx.EXPAND\|wx.ALIGN_LEFT\|wx.ALL)
1359	cpnl.SetSizer(cbox)
1360	cpnl.SetAutoLayout(1)
1361	cpnl.SetupScrolling()
1362	#cpnl.Bind(rw.EVT_RW_LAYOUT_NEEDED, self.OnLayoutNeeded) # needed if sizes change
1363	cpnl.Layout()
1364
1365	vbox.Add(cpnl, 1, wx.ALIGN_LEFT\|wx.ALL\|wx.EXPAND, 0)
1366	btnsizer = wx.StdDialogButtonSizer()
1367	btn = wx.Button(self.cifdefs, wx.ID_OK, "Create CIF")
1368	btn.SetDefault()
1369	btnsizer.AddButton(btn)
1370	btn = wx.Button(self.cifdefs, wx.ID_CANCEL)
1371	btnsizer.AddButton(btn)
1372	btnsizer.Realize()
1373	vbox.Add(btnsizer, 0, wx.ALIGN_CENTER\|wx.ALL, 5)
1374	self.cifdefs.SetSizer(vbox)
1375	vbox.Fit(self.cifdefs)
1376	self.cifdefs.Layout()
1377
1378	def OnToggleButton(event):
1379	'Respond to press of ToggleButton in SelectDisAglFlags'
1380	but = event.GetEventObject()
1381	if but.GetValue():
1382	but.DisAglSel[but.key] = True
1383	else:
1384	try:
1385	del but.DisAglSel[but.key]
1386	except KeyError:
1387	pass
1388	def keepTrue(event):
1389	event.GetEventObject().SetValue(True)
1390	def keepFalse(event):
1391	event.GetEventObject().SetValue(False)
1392
1393	def SelectDisAglFlags(event):
1394	'Select Distance/Angle use flags for the selected phase'
1395	phasenam = event.GetEventObject().phase
1396	phasedict = self.Phases[phasenam]
1397	SymOpList,offsetList,symOpList,G2oprList = G2spc.AllOps(phasedict['General']['SGData'])
1398	generalData = phasedict['General']
1399	# create a dict for storing Pub flag for bonds/angles, if needed
1400	if phasedict['General'].get("DisAglHideFlag") is None:
1401	phasedict['General']["DisAglHideFlag"] = {}
1402	DisAngSel = phasedict['General']["DisAglHideFlag"]
1403
1404	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
1405	cn = ct-1
1406	cfrac = cx+3
1407	DisAglData = {}
1408	# create a list of atoms, but skip atoms with zero occupancy
1409	xyz = []
1410	fpfx = str(phasedict['pId'])+'::Afrac:'
1411	for i,atom in enumerate(phasedict['Atoms']):
1412	if self.parmDict.get(fpfx+str(i),atom[cfrac]) == 0.0: continue
1413	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
1414	if 'DisAglCtls' not in generalData:
1415	# should not be used, since DisAglDialog should be called
1416	# for all phases before getting here
1417	dlg = G2gd.DisAglDialog(
1418	self.cifdefs,
1419	{},
1420	generalData)
1421	if dlg.ShowModal() == wx.ID_OK:
1422	generalData['DisAglCtls'] = dlg.GetData()
1423	else:
1424	dlg.Destroy()
1425	return
1426	dlg.Destroy()
1427	dlg = wx.Dialog(
1428	self.G2frame,
1429	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
1430	vbox = wx.BoxSizer(wx.VERTICAL)
1431	txt = wx.StaticText(dlg,wx.ID_ANY,'Searching distances for phase '+phasenam
1432	+'\nPlease wait...')
1433	vbox.Add(txt,0,wx.ALL\|wx.EXPAND)
1434	dlg.SetSizer(vbox)
1435	dlg.CenterOnParent()
1436	dlg.Show() # post "please wait"
1437	wx.BeginBusyCursor() # and change cursor
1438
1439	DisAglData['OrigAtoms'] = xyz
1440	DisAglData['TargAtoms'] = xyz
1441	SymOpList,offsetList,symOpList,G2oprList = G2spc.AllOps(
1442	generalData['SGData'])
1443
1444	xpandSGdata = generalData['SGData'].copy()
1445	xpandSGdata.update({'SGOps':symOpList,
1446	'SGInv':False,
1447	'SGLatt':'P',
1448	'SGCen':np.array([[0, 0, 0]]),})
1449	DisAglData['SGData'] = xpandSGdata
1450
1451	DisAglData['Cell'] = generalData['Cell'][1:] #+ volume
1452	if 'pId' in phasedict:
1453	DisAglData['pId'] = phasedict['pId']
1454	DisAglData['covData'] = self.OverallParms['Covariance']
1455	try:
1456	AtomLabels,DistArray,AngArray = G2stMn.RetDistAngle(
1457	generalData['DisAglCtls'],
1458	DisAglData)
1459	except KeyError: # inside DistAngle for missing atom types in DisAglCtls
1460	print('** ERROR - try again but do "Reset" to fill in missing atom types **')
1461	wx.EndBusyCursor()
1462	txt.SetLabel('Set publication flags for distances and angles in\nphase '+phasenam)
1463	vbox.Add((5,5))
1464	vbox.Add(wx.StaticText(dlg,wx.ID_ANY,
1465	'The default is to flag all distances and angles as to be'+
1466	'\npublished. Change this by pressing appropriate buttons.'),
1467	0,wx.ALL\|wx.EXPAND)
1468	hbox = wx.BoxSizer(wx.HORIZONTAL)
1469	vbox.Add(hbox)
1470	hbox.Add(wx.StaticText(dlg,wx.ID_ANY,'Button appearance: '))
1471	but = wx.ToggleButton(dlg,wx.ID_ANY,'Publish')
1472	but.Bind(wx.EVT_TOGGLEBUTTON,keepFalse)
1473	hbox.Add(but)
1474	but = wx.ToggleButton(dlg,wx.ID_ANY,"Don't publish")
1475	but.Bind(wx.EVT_TOGGLEBUTTON,keepTrue)
1476	hbox.Add(but)
1477	but.SetValue(True)
1478	G2gd.HorizontalLine(vbox,dlg)
1479
1480	cpnl = wxscroll.ScrolledPanel(dlg,size=(400,300))
1481	cbox = wx.BoxSizer(wx.VERTICAL)
1482	for c in sorted(DistArray):
1483	karr = []
1484	UsedCols = {}
1485	cbox.Add(wx.StaticText(cpnl,wx.ID_ANY,
1486	'distances to/angles around atom '+AtomLabels[c]))
1487	#dbox = wx.GridBagSizer(hgap=5)
1488	dbox = wx.GridBagSizer()
1489	for i,D in enumerate(DistArray[c]):
1490	karr.append(tuple(D[0:3]))
1491	val = "{:.2f}".format(D[3])
1492	sym = " [{:d} {:d} {:d}]".format(*D[1]) + " #{:d}".format(D[2])
1493	dbox.Add(wx.StaticText(cpnl,wx.ID_ANY,AtomLabels[D[0]]),
1494	(i+1,0)
1495	)
1496	dbox.Add(wx.StaticText(cpnl,wx.ID_ANY,sym),
1497	(i+1,1)
1498	)
1499	but = wx.ToggleButton(cpnl,wx.ID_ANY,val)
1500	but.key = (c,karr[-1])
1501	but.DisAglSel = DisAngSel
1502	if DisAngSel.get(but.key): but.SetValue(True)
1503	but.Bind(wx.EVT_TOGGLEBUTTON,OnToggleButton)
1504	dbox.Add(but,(i+1,2),border=1)
1505	for i,D in enumerate(AngArray[c]):
1506	val = "{:.1f}".format(D[2][0])
1507	but = wx.ToggleButton(cpnl,wx.ID_ANY,val)
1508	but.key = (karr[D[0]],c,karr[D[1]])
1509	but.DisAglSel = DisAngSel
1510	if DisAngSel.get(but.key): but.SetValue(True)
1511	but.Bind(wx.EVT_TOGGLEBUTTON,OnToggleButton)
1512	dbox.Add(but,(D[0]+1,D[1]+3),border=1)
1513	UsedCols[D[1]+3] = True
1514	for i,D in enumerate(DistArray[c][:-1]): # label columns that are used
1515	if UsedCols.get(i+3):
1516	dbox.Add(wx.StaticText(cpnl,wx.ID_ANY,AtomLabels[D[0]]),
1517	(0,i+3),
1518	flag=wx.ALIGN_CENTER
1519	)
1520	dbox.Add(wx.StaticText(cpnl,wx.ID_ANY,'distance'),
1521	(0,2),
1522	flag=wx.ALIGN_CENTER
1523	)
1524	cbox.Add(dbox)
1525	G2gd.HorizontalLine(cbox,cpnl)
1526	cpnl.SetSizer(cbox)
1527	cpnl.SetAutoLayout(1)
1528	cpnl.SetupScrolling()
1529	#cpnl.Bind(rw.EVT_RW_LAYOUT_NEEDED, self.OnLayoutNeeded) # needed if sizes change
1530	cpnl.Layout()
1531
1532	vbox.Add(cpnl, 1, wx.ALIGN_LEFT\|wx.ALL\|wx.EXPAND, 0)
1533
1534	btnsizer = wx.StdDialogButtonSizer()
1535	btn = wx.Button(dlg, wx.ID_OK, "Done")
1536	btn.SetDefault()
1537	btnsizer.AddButton(btn)
1538	btnsizer.Realize()
1539	vbox.Add(btnsizer, 0, wx.ALIGN_CENTER\|wx.ALL, 5)
1540	dlg.SetSizer(vbox)
1541	vbox.Fit(dlg)
1542	dlg.Layout()
1543
1544	dlg.CenterOnParent()
1545	dlg.ShowModal()
1546
1547	#***** end of functions for export method =======================================
1548	#=================================================================================
1549
1550	# the export process starts here
1551	self.InitExport(event)
1552	# load all of the tree into a set of dicts
1553	self.loadTree()
1554	# create a dict with refined values and their uncertainties
1555	self.loadParmDict()
1556	if self.mode=='simple':
1557	if self.ExportSelect('ask'): return
1558	else:
1559	if self.ExportSelect('default'): return
1560	# Someday: get restraint & constraint info
1561	#restraintDict = self.OverallParms.get('Restraints',{})
1562	#for i in self.OverallParms['Constraints']:
1563	# print i
1564	# for j in self.OverallParms['Constraints'][i]:
1565	# print j
1566
1567	self.CIFdate = dt.datetime.strftime(dt.datetime.now(),"%Y-%m-%dT%H:%M")
1568	# is there anything to export?
1569	if len(self.Phases) == len(self.powderDict) == len(self.xtalDict) == 0:
1570	self.G2frame.ErrorDialog(
1571	'Empty project',
1572	'Project does not contain any data or phases. Are they interconnected?')
1573	return
1574	# get the project file name
1575	self.CIFname = os.path.splitext(
1576	os.path.split(self.G2frame.GSASprojectfile)[1]
1577	)[0]
1578	self.CIFname = self.CIFname.replace(' ','')
1579	if not self.CIFname: # none defined & needed, save as GPX to get one
1580	self.G2frame.OnFileSaveas(None)
1581	if not self.G2frame.GSASprojectfile: return
1582	self.CIFname = os.path.splitext(
1583	os.path.split(self.G2frame.GSASprojectfile)[1]
1584	)[0]
1585	self.CIFname = self.CIFname.replace(' ','')
1586	# test for quick CIF mode or no data
1587	self.quickmode = False
1588	phasenam = None # include all phases
1589	if self.mode == "simple" and self.currentExportType == 'phase':
1590	if len(self.Phases) == 0: # this check is probably not needed
1591	self.G2frame.ErrorDialog(
1592	'No phase present',
1593	'Cannot create a coordinates CIF with no phases')
1594	return
1595	self.quickmode = True
1596	oneblock = True
1597	if len(self.Phases) > 1: # quick mode: get selected phase
1598	phasenam = self.phasenam[0]
1599	elif self.mode == "simple": # powder/single xtal data export
1600	self.quickmode = True
1601	oneblock = True
1602	# Project export: will this require a multiblock CIF?
1603	elif len(self.Phases) > 1:
1604	oneblock = False
1605	elif len(self.powderDict) + len(self.xtalDict) > 1:
1606	oneblock = False
1607	else: # one phase, one dataset, Full CIF
1608	oneblock = True
1609
1610	# make sure required information is present
1611	# get CIF author name -- required for full CIFs
1612	try:
1613	self.author = self.OverallParms['Controls'].get("Author",'').strip()
1614	except KeyError:
1615	pass
1616	while not (self.author or self.quickmode):
1617	if not EditAuthor(): return
1618	self.shortauthorname = self.author.replace(',','').replace(' ','')[:20]
1619
1620	# check there is an instrument name for every histogram
1621	if not self.quickmode:
1622	invalid = 0
1623	key3 = 'InstrName'
1624	for hist in self.Histograms:
1625	if hist.startswith("PWDR"):
1626	key2 = "Sample Parameters"
1627	d = self.Histograms[hist][key2]
1628	elif hist.startswith("HKLF"):
1629	key2 = "Instrument Parameters"
1630	d = self.Histograms[hist][key2][0]
1631	instrname = d.get(key3)
1632	if instrname is None:
1633	d[key3] = ''
1634	invalid += 1
1635	elif instrname.strip() == '':
1636	invalid += 1
1637	if invalid:
1638	msg = ""
1639	if invalid > 3: msg = (
1640	"\n\nNote: it may be faster to set the name for\n"
1641	"one histogram for each instrument and use the\n"
1642	"File/Copy option to duplicate the name"
1643	)
1644	if not EditInstNames(): return
1645	if not self.quickmode:
1646	# check for a distance-angle range search range for each phase
1647	for phasenam in sorted(self.Phases.keys()):
1648	#i = self.Phases[phasenam]['pId']
1649	phasedict = self.Phases[phasenam] # pointer to current phase info
1650	if 'DisAglCtls' not in phasedict['General']:
1651	dlg = G2gd.DisAglDialog(
1652	self.G2frame,
1653	{},
1654	phasedict['General'])
1655	if dlg.ShowModal() == wx.ID_OK:
1656	phasedict['General']['DisAglCtls'] = dlg.GetData()
1657	else:
1658	dlg.Destroy()
1659	return
1660	dlg.Destroy()
1661	if not self.quickmode:
1662	# check if temperature values & pressure are defaulted
1663	default = 0
1664	for hist in self.Histograms:
1665	if hist.startswith("PWDR"):
1666	key2 = "Sample Parameters"
1667	T = self.Histograms[hist][key2].get('Temperature')
1668	if not T:
1669	default += 1
1670	elif T == 300:
1671	default += 1
1672	P = self.Histograms[hist][key2].get('Pressure')
1673	if not P:
1674	default += 1
1675	elif P == 1:
1676	default += 1
1677	if default > 0:
1678	dlg = wx.MessageDialog(
1679	self.G2frame,
1680	'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?',
1681	'Check T and P values',
1682	wx.OK\|wx.CANCEL)
1683	ret = dlg.ShowModal()
1684	dlg.Destroy()
1685	if ret != wx.ID_OK: return
1686	if oneblock and not self.quickmode:
1687	# select a dataset to use (there should only be one set in one block,
1688	# but take whatever comes 1st)
1689	for hist in self.Histograms:
1690	histblk = self.Histograms[hist]
1691	if hist.startswith("PWDR"):
1692	instnam = histblk["Sample Parameters"]['InstrName']
1693	break # ignore all but 1st data histogram
1694	elif hist.startswith("HKLF"):
1695	instnam = histblk["Instrument Parameters"][0]['InstrName']
1696	break # ignore all but 1st data histogram
1697	if not self.quickmode: # give the user a chance to edit all defaults
1698	self.cifdefs = wx.Dialog(
1699	self.G2frame,
1700	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
1701	EditCIFDefaults()
1702	self.cifdefs.CenterOnParent()
1703	val = self.cifdefs.ShowModal()
1704	self.cifdefs.Destroy()
1705	if val != wx.ID_OK:
1706	return
1707	#======================================================================
1708	# Start writing the CIF - single block
1709	#======================================================================
1710	print('Writing CIF output to file '+str(self.filename)+"...")
1711	self.OpenFile()
1712	if self.currentExportType == 'single' or self.currentExportType == 'powder':
1713	#======Data only CIF (powder/xtal) ====================================
1714	hist = self.histnam[0]
1715	self.CIFname = hist[5:40].replace(' ','')
1716	WriteCIFitem('data_'+self.CIFname)
1717	if hist.startswith("PWDR"):
1718	WritePowderData(hist)
1719	elif hist.startswith("HKLF"):
1720	WriteSingleXtalData(hist)
1721	else:
1722	print "should not happen"
1723	elif self.quickmode:
1724	#====Phase only CIF ====================================================
1725	WriteCIFitem('data_'+self.CIFname)
1726	if phasenam is None: # if not already selected, select the first phase (should be one)
1727	phasenam = self.Phases.keys()[0]
1728	#print 'phasenam',phasenam
1729	phaseblk = self.Phases[phasenam] # pointer to current phase info
1730	# report the phase info
1731	WritePhaseInfo(phasenam)
1732	elif oneblock:
1733	#====Single block, data & phase CIF ===================================
1734	WriteCIFitem('data_'+self.CIFname)
1735	if phasenam is None: # if not already selected, select the first phase (should be one)
1736	phasenam = self.Phases.keys()[0]
1737	#print 'phasenam',phasenam
1738	phaseblk = self.Phases[phasenam] # pointer to current phase info
1739	instnam = instnam.replace(' ','')
1740	WriteCIFitem('_pd_block_id',
1741	str(self.CIFdate) + "\|" + str(self.CIFname) + "\|" +
1742	str(self.shortauthorname) + "\|" + instnam)
1743	WriteAudit()
1744	writeCIFtemplate(self.OverallParms['Controls'],'publ') # overall (publication) template
1745	WriteOverall()
1746	writeCIFtemplate(self.Phases[phasenam]['General'],'phase',phasenam) # write phase template
1747	# report the phase info
1748	WritePhaseInfo(phasenam)
1749	if hist.startswith("PWDR"):
1750	# preferred orientation
1751	SH = FormatSH(phasenam)
1752	MD = FormatHAPpo(phasenam)
1753	if SH and MD:
1754	WriteCIFitem('_pd_proc_ls_pref_orient_corr', SH + '\n' + MD)
1755	elif SH or MD:
1756	WriteCIFitem('_pd_proc_ls_pref_orient_corr', SH + MD)
1757	else:
1758	WriteCIFitem('_pd_proc_ls_pref_orient_corr', 'none')
1759	# report profile, since one-block: include both histogram and phase info
1760	WriteCIFitem('_pd_proc_ls_profile_function',
1761	FormatInstProfile(histblk["Instrument Parameters"],histblk['hId'])
1762	+'\n'+FormatPhaseProfile(phasenam))
1763	histblk = self.Histograms[hist]["Sample Parameters"]
1764	writeCIFtemplate(histblk,'powder',histblk['InstrName']) # write powder template
1765	WritePowderData(hist)
1766	elif hist.startswith("HKLF"):
1767	histprm = self.Histograms[hist]["Instrument Parameters"][0]
1768	writeCIFtemplate(histprm,'single',histprm['InstrName']) # single crystal template
1769	WriteSingleXtalData(hist)
1770	else:
1771	#=== multiblock: multiple phases and/or histograms ====================
1772	nsteps = 1 + len(self.Phases) + len(self.powderDict) + len(self.xtalDict)
1773	try:
1774	dlg = wx.ProgressDialog('CIF progress','starting',nsteps,parent=self.G2frame)
1775	Size = dlg.GetSize()
1776	Size = (int(Size[0]*3),Size[1]) # increase size along x
1777	dlg.SetSize(Size)
1778	dlg.CenterOnParent()
1779
1780	# publication info
1781	step = 1
1782	dlg.Update(step,"Exporting overall section")
1783	WriteCIFitem('\ndata_'+self.CIFname+'_publ')
1784	WriteAudit()
1785	WriteCIFitem('_pd_block_id',
1786	str(self.CIFdate) + "\|" + str(self.CIFname) + "\|" +
1787	str(self.shortauthorname) + "\|Overall")
1788	writeCIFtemplate(self.OverallParms['Controls'],'publ') #insert the publication template
1789	# ``template_publ.cif`` or a modified version
1790	# overall info
1791	WriteCIFitem('data_'+str(self.CIFname)+'_overall')
1792	WriteOverall()
1793	#============================================================
1794	WriteCIFitem('# POINTERS TO PHASE AND HISTOGRAM BLOCKS')
1795	datablockidDict = {} # save block names here -- N.B. check for conflicts between phase & hist names (unlikely!)
1796	# loop over phase blocks
1797	if len(self.Phases) > 1:
1798	loopprefix = ''
1799	WriteCIFitem('loop_ _pd_phase_block_id')
1800	else:
1801	loopprefix = '_pd_phase_block_id'
1802
1803	for phasenam in sorted(self.Phases.keys()):
1804	i = self.Phases[phasenam]['pId']
1805	datablockidDict[phasenam] = (str(self.CIFdate) + "\|" + str(self.CIFname) + "\|" +
1806	'phase_'+ str(i) + '\|' + str(self.shortauthorname))
1807	WriteCIFitem(loopprefix,datablockidDict[phasenam])
1808	# loop over data blocks
1809	if len(self.powderDict) + len(self.xtalDict) > 1:
1810	loopprefix = ''
1811	WriteCIFitem('loop_ _pd_block_diffractogram_id')
1812	else:
1813	loopprefix = '_pd_block_diffractogram_id'
1814	for i in sorted(self.powderDict.keys()):
1815	hist = self.powderDict[i]
1816	histblk = self.Histograms[hist]
1817	instnam = histblk["Sample Parameters"]['InstrName']
1818	instnam = instnam.replace(' ','')
1819	j = histblk['hId']
1820	datablockidDict[hist] = (str(self.CIFdate) + "\|" + str(self.CIFname) + "\|" +
1821	str(self.shortauthorname) + "\|" +
1822	instnam + "_hist_"+str(j))
1823	WriteCIFitem(loopprefix,datablockidDict[hist])
1824	for i in sorted(self.xtalDict.keys()):
1825	hist = self.xtalDict[i]
1826	histblk = self.Histograms[hist]
1827	instnam = histblk["Instrument Parameters"][0]['InstrName']
1828	instnam = instnam.replace(' ','')
1829	i = histblk['hId']
1830	datablockidDict[hist] = (str(self.CIFdate) + "\|" + str(self.CIFname) + "\|" +
1831	str(self.shortauthorname) + "\|" +
1832	instnam + "_hist_"+str(i))
1833	WriteCIFitem(loopprefix,datablockidDict[hist])
1834	#============================================================
1835	# loop over phases, exporting them
1836	phasebyhistDict = {} # create a cross-reference to phases by histogram
1837	for j,phasenam in enumerate(sorted(self.Phases.keys())):
1838	step += 1
1839	dlg.Update(step,"Exporting phase "+phasenam+' (#'+str(j+1)+')')
1840	i = self.Phases[phasenam]['pId']
1841	WriteCIFitem('\ndata_'+self.CIFname+"_phase_"+str(i))
1842	WriteCIFitem('# Information for phase '+str(i))
1843	WriteCIFitem('_pd_block_id',datablockidDict[phasenam])
1844	# report the phase
1845	writeCIFtemplate(self.Phases[phasenam]['General'],'phase',phasenam) # write phase template
1846	WritePhaseInfo(phasenam)
1847	# preferred orientation
1848	SH = FormatSH(phasenam)
1849	MD = FormatHAPpo(phasenam)
1850	if SH and MD:
1851	WriteCIFitem('_pd_proc_ls_pref_orient_corr', SH + '\n' + MD)
1852	elif SH or MD:
1853	WriteCIFitem('_pd_proc_ls_pref_orient_corr', SH + MD)
1854	else:
1855	WriteCIFitem('_pd_proc_ls_pref_orient_corr', 'none')
1856	# report sample profile terms
1857	PP = FormatPhaseProfile(phasenam)
1858	if PP:
1859	WriteCIFitem('_pd_proc_ls_profile_function',PP)
1860
1861	#============================================================
1862	# loop over histograms, exporting them
1863	for i in sorted(self.powderDict.keys()):
1864	hist = self.powderDict[i]
1865	histblk = self.Histograms[hist]
1866	if hist.startswith("PWDR"):
1867	step += 1
1868	dlg.Update(step,"Exporting "+hist.strip())
1869	WriteCIFitem('\ndata_'+self.CIFname+"_pwd_"+str(i))
1870	#instnam = histblk["Sample Parameters"]['InstrName']
1871	# report instrumental profile terms
1872	WriteCIFitem('_pd_proc_ls_profile_function',
1873	FormatInstProfile(histblk["Instrument Parameters"],histblk['hId']))
1874	WriteCIFitem('# Information for histogram '+str(i)+': '+hist)
1875	WriteCIFitem('_pd_block_id',datablockidDict[hist])
1876	histprm = self.Histograms[hist]["Sample Parameters"]
1877	writeCIFtemplate(histprm,'powder',histprm['InstrName']) # powder template
1878	WritePowderData(hist)
1879	for i in sorted(self.xtalDict.keys()):
1880	hist = self.xtalDict[i]
1881	histblk = self.Histograms[hist]
1882	if hist.startswith("HKLF"):
1883	step += 1
1884	dlg.Update(step,"Exporting "+hist.strip())
1885	WriteCIFitem('\ndata_'+self.CIFname+"_sx_"+str(i))
1886	#instnam = histblk["Instrument Parameters"][0]['InstrName']
1887	WriteCIFitem('# Information for histogram '+str(i)+': '+hist)
1888	WriteCIFitem('_pd_block_id',datablockidDict[hist])
1889	histprm = self.Histograms[hist]["Instrument Parameters"][0]
1890	writeCIFtemplate(histprm,'single',histprm['InstrName']) # single crystal template
1891	WriteSingleXtalData(hist)
1892
1893	except Exception:
1894	import traceback
1895	print(traceback.format_exc())
1896	self.G2frame.ErrorDialog('Exception',
1897	'Error occurred in CIF creation. '+
1898	'See full error message in console output ')
1899	finally:
1900	dlg.Destroy()
1901
1902	WriteCIFitem('#--' + 15*'eof--' + '#')
1903	self.CloseFile()
1904	print("...export completed")
1905	print('file '+str(self.fullpath))
1906	# end of CIF export
1907
1908	class ExportPhaseCIF(ExportCIF):
1909	'''Used to create a simple CIF of at most one phase. Uses exact same code as
1910	:class:`ExportCIF` except that `self.mode` is set to "simple" in `self.InitExport`.
1911	Shows up in menu as Quick CIF.
1912
1913	:param wx.Frame G2frame: reference to main GSAS-II frame
1914	'''
1915	def __init__(self,G2frame):
1916	G2IO.ExportBaseclass.__init__(self,
1917	G2frame=G2frame,
1918	formatName = 'Quick CIF',
1919	extension='.cif',
1920	longFormatName = 'Export one phase in CIF'
1921	)
1922	self.exporttype = ['phase']
1923	# CIF-specific items
1924	self.author = ''
1925	self.mode = 'simple'
1926
1927	class ExportDataCIF(ExportCIF):
1928	'''Used to create a simple CIF containing diffraction data only. Uses exact same code as
1929	:class:`ExportCIF` except that `self.mode` is set to "simple" and `self.currentExportType`
1930	is set to "single" or "powder" in `self.InitExport`. Shows up in menus as Data-only CIF.
1931
1932	:param wx.Frame G2frame: reference to main GSAS-II frame
1933	'''
1934	def __init__(self,G2frame):
1935	G2IO.ExportBaseclass.__init__(self,
1936	G2frame=G2frame,
1937	formatName = 'Data-only CIF',
1938	extension='.cif',
1939	longFormatName = 'Export data as CIF'
1940	)
1941	self.exporttype = ['single','powder']
1942	# CIF-specific items
1943	self.author = ''
1944	self.mode = 'simple'
1945
1946	#===============================================================================
1947	# misc CIF utilities
1948	#===============================================================================
1949	def PickleCIFdict(fil):
1950	'''Loads a CIF dictionary, cherry picks out the items needed
1951	by local code and sticks them into a python dict and writes
1952	that dict out as a cPickle file for later reuse.
1953	If the write fails a warning message is printed,
1954	but no exception occurs.
1955
1956	:param str fil: file name of CIF dictionary, will usually end
1957	in .dic
1958	:returns: the dict with the definitions
1959	'''
1960	import CifFile as cif # PyCifRW from James Hester
1961	cifdic = {}
1962	try:
1963	fp = open(fil,'r') # patch: open file to avoid windows bug
1964	dictobj = cif.CifDic(fp)
1965	fp.close()
1966	except IOError:
1967	dictobj = cif.CifDic(fil)
1968	if DEBUG: print('loaded '+str(fil))
1969	for item in dictobj.keys():
1970	cifdic[item] = {}
1971	for j in (
1972	'_definition','_type',
1973	'_enumeration',
1974	'_enumeration_detail',
1975	'_enumeration_range'):
1976	if dictobj[item].get(j):
1977	cifdic[item][j] = dictobj[item][j]
1978	try:
1979	fil = os.path.splitext(fil)[0]+'.cpickle'
1980	fp = open(fil,'w')
1981	cPickle.dump(cifdic,fp)
1982	fp.close()
1983	if DEBUG: print('wrote '+str(fil))
1984	except:
1985	print ('Unable to write '+str(fil))
1986	return cifdic
1987
1988	def LoadCIFdic():
1989	'''Create a composite core+powder CIF lookup dict containing
1990	information about all items in the CIF dictionaries, loading
1991	pickled files if possible. The routine looks for files
1992	named cif_core.cpickle and cif_pd.cpickle in every
1993	directory in the path and if they are not found, files
1994	cif_core.dic and/or cif_pd.dic are read.
1995
1996	:returns: the dict with the definitions
1997	'''
1998	cifdic = {}
1999	for ftyp in "cif_core","cif_pd":
2000	for loc in sys.path:
2001	fil = os.path.join(loc,ftyp+".cpickle")
2002	if not os.path.exists(fil): continue
2003	fp = open(fil,'r')
2004	try:
2005	cifdic.update(cPickle.load(fp))
2006	if DEBUG: print('reloaded '+str(fil))
2007	break
2008	finally:
2009	fp.close()
2010	else:
2011	for loc in sys.path:
2012	fil = os.path.join(loc,ftyp+".dic")
2013	if not os.path.exists(fil): continue
2014	#try:
2015	if True:
2016	cifdic.update(PickleCIFdict(fil))
2017	break
2018	#except:
2019	# pass
2020	else:
2021	print('Could not load '+ftyp+' dictionary')
2022	return cifdic
2023
2024	class CIFdefHelp(wx.Button):
2025	'''Create a help button that displays help information on
2026	the current data item
2027
2028	:param parent: the panel which will be the parent of the button
2029	:param str msg: the help text to be displayed
2030	:param wx.Dialog helpwin: Frame for CIF editing dialog
2031	:param wx.TextCtrl helptxt: TextCtrl where help text is placed
2032	'''
2033	def __init__(self,parent,msg,helpwin,helptxt):
2034	wx.Button.__init__(self,parent,wx.ID_HELP)
2035	self.Bind(wx.EVT_BUTTON,self._onPress)
2036	self.msg=msg
2037	self.parent = parent
2038	#self.helpwin = self.parent.helpwin
2039	self.helpwin = helpwin
2040	self.helptxt = helptxt
2041	def _onPress(self,event):
2042	'Respond to a button press by displaying the requested text'
2043	try:
2044	#helptxt = self.helptxt
2045	ow,oh = self.helptxt.GetSize()
2046	self.helptxt.SetLabel(self.msg)
2047	w,h = self.helptxt.GetSize()
2048	if h > oh:
2049	self.helpwin.GetSizer().Fit(self.helpwin)
2050	except: # error posting help, ignore
2051	return
2052
2053	def CIF2dict(cf):
2054	'''copy the contents of a CIF out from a PyCifRW block object
2055	into a dict
2056
2057	:returns: cifblk, loopstructure where cifblk is a dict with
2058	CIF items and loopstructure is a list of lists that defines
2059	which items are in which loops.
2060	'''
2061	blk = cf.keys()[0] # assume templates are a single CIF block, use the 1st
2062	loopstructure = cf[blk].loopnames()[:] # copy over the list of loop contents
2063	dblk = {}
2064	for item in cf[blk].keys(): # make a copy of all the items in the block
2065	dblk[item] = cf[blk][item]
2066	return dblk,loopstructure
2067
2068	def dict2CIF(dblk,loopstructure,blockname='Template'):
2069	'''Create a PyCifRW CIF object containing a single CIF
2070	block object from a dict and loop structure list.
2071
2072	:param dblk: a dict containing values for each CIF item
2073	:param list loopstructure: a list of lists containing the contents of
2074	each loop, as an example::
2075
2076	[ ["_a","_b"], ["_c"], ["_d_1","_d_2","_d_3"]]
2077
2078	this describes a CIF with this type of structure::
2079
2080	loop_ _a _b <a1> <b1> <a2> ...
2081	loop_ _c <c1> <c2>...
2082	loop _d_1 _d_2 _d_3 ...
2083
2084	Note that the values for each looped CIF item, such as _a,
2085	are contained in a list, for example as cifblk["_a"]
2086
2087	:param str blockname: an optional name for the CIF block.
2088	Defaults to 'Template'
2089
2090	:returns: the newly created PyCifRW CIF object
2091	'''
2092
2093	import CifFile as cif # PyCifRW from James Hester
2094	# compile a 'list' of items in loops
2095	loopnames = set()
2096	for i in loopstructure:
2097	loopnames \|= set(i)
2098	# create a new block
2099	newblk = cif.CifBlock()
2100	# add the looped items
2101	for keys in loopstructure:
2102	vals = []
2103	for key in keys:
2104	vals.append(dblk[key])
2105	newblk.AddCifItem(([keys],[vals]))
2106	# add the non-looped items
2107	for item in dblk:
2108	if item in loopnames: continue
2109	newblk[item] = dblk[item]
2110	# create a CIF and add the block
2111	newcf = cif.CifFile()
2112	newcf[blockname] = newblk
2113	return newcf
2114
2115
2116	class EditCIFtemplate(wx.Dialog):
2117	'''Create a dialog for editing a CIF template. The edited information is
2118	placed in cifblk. If the CIF is saved as a file, the name of that file
2119	is saved as ``self.newfile``.
2120
2121	:param wx.Frame parent: parent frame or None
2122	:param cifblk: dict or PyCifRW block containing values for each CIF item
2123	:param list loopstructure: a list of lists containing the contents of
2124	each loop, as an example::
2125
2126	[ ["_a","_b"], ["_c"], ["_d_1","_d_2","_d_3"]]
2127
2128	this describes a CIF with this type of structure::
2129
2130	loop_ _a _b <a1> <b1> <a2> ...
2131	loop_ _c <c1> <c2>...
2132	loop _d_1 _d_2 _d_3 ...
2133
2134	Note that the values for each looped CIF item, such as _a,
2135	are contained in a list, for example as cifblk["_a"]
2136
2137	:param str defaultname: specifies the default file name to be used for
2138	saving the CIF.
2139	'''
2140	def __init__(self,parent,cifblk,loopstructure,defaultname):
2141	OKbuttons = []
2142	self.cifblk = cifblk
2143	self.loopstructure = loopstructure
2144	self.newfile = None
2145	self.defaultname = defaultname
2146	global CIFdic # once this is loaded, keep it around
2147	if CIFdic is None:
2148	CIFdic = LoadCIFdic()
2149	wx.Dialog.__init__(self,parent,style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
2150
2151	# define widgets that will be needed during panel creation
2152	self.helptxt = wx.StaticText(self,wx.ID_ANY,"")
2153	savebtn = wx.Button(self, wx.ID_CLOSE, "Save as template")
2154	OKbuttons.append(savebtn)
2155	savebtn.Bind(wx.EVT_BUTTON,self._onSave)
2156	OKbtn = wx.Button(self, wx.ID_OK, "Use")
2157	OKbtn.SetDefault()
2158	OKbuttons.append(OKbtn)
2159
2160	self.SetTitle('Edit items in CIF template')
2161	vbox = wx.BoxSizer(wx.VERTICAL)
2162	cpnl = EditCIFpanel(self,cifblk,loopstructure,CIFdic,OKbuttons,size=(300,300))
2163	vbox.Add(cpnl, 1, wx.ALIGN_LEFT\|wx.ALL\|wx.EXPAND, 0)
2164	G2gd.HorizontalLine(vbox,self)
2165	vbox.Add(self.helptxt, 0, wx.EXPAND\|wx.ALL, 5)
2166	G2gd.HorizontalLine(vbox,self)
2167	btnsizer = wx.BoxSizer(wx.HORIZONTAL)
2168	btn = wx.Button(self, wx.ID_CANCEL)
2169	btnsizer.Add(btn,0,wx.ALIGN_CENTER\|wx.ALL)
2170	btnsizer.Add(savebtn,0,wx.ALIGN_CENTER\|wx.ALL)
2171	btnsizer.Add(OKbtn,0,wx.ALIGN_CENTER\|wx.ALL)
2172	vbox.Add(btnsizer, 0, wx.ALIGN_CENTER\|wx.ALL, 5)
2173	self.SetSizer(vbox)
2174	vbox.Fit(self)
2175	def Post(self):
2176	'''Display the dialog
2177
2178	:returns: True unless Cancel has been pressed.
2179	'''
2180	return (self.ShowModal() == wx.ID_OK)
2181	def _onSave(self,event):
2182	'Save CIF entries in a template file'
2183	dlg = wx.FileDialog(
2184	self, message="Save as CIF template",
2185	defaultDir=os.getcwd(),
2186	defaultFile=self.defaultname,
2187	wildcard="CIF (.cif)\|.cif",
2188	style=wx.SAVE \| wx.CHANGE_DIR
2189	)
2190	val = (dlg.ShowModal() == wx.ID_OK)
2191	fil = dlg.GetPath()
2192	dlg.Destroy()
2193	if val: # ignore a Cancel button
2194	fil = os.path.splitext(fil)[0]+'.cif' # force extension
2195	fp = open(fil,'w')
2196	newcf = dict2CIF(self.cifblk,self.loopstructure)
2197	fp.write(newcf.WriteOut())
2198	fp.close()
2199	self.newfile = fil
2200	self.EndModal(wx.ID_OK)
2201
2202	class EditCIFpanel(wxscroll.ScrolledPanel):
2203	'''Creates a scrolled panel for editing CIF template items
2204
2205	:param wx.Frame parent: parent frame where panel will be placed
2206	:param cifblk: dict or PyCifRW block containing values for each CIF item
2207	:param list loopstructure: a list of lists containing the contents of
2208	each loop, as an example::
2209
2210	[ ["_a","_b"], ["_c"], ["_d_1","_d_2","_d_3"]]
2211
2212	this describes a CIF with this type of structure::
2213
2214	loop_ _a _b <a1> <b1> <a2> ...
2215	loop_ _c <c1> <c2>...
2216	loop _d_1 _d_2 _d_3 ...
2217
2218	Note that the values for each looped CIF item, such as _a,
2219	are contained in a list, for example as cifblk["_a"]
2220
2221	:param dict cifdic: optional CIF dictionary definitions
2222	:param list OKbuttons: A list of wx.Button objects that should
2223	be disabled when information in the CIF is invalid
2224	:param (other): optional keyword parameters for wx.ScrolledPanel
2225	'''
2226	def __init__(self, parent, cifblk, loopstructure, cifdic={}, OKbuttons=[], **kw):
2227	self.parent = parent
2228	wxscroll.ScrolledPanel.__init__(self, parent, wx.ID_ANY, **kw)
2229	self.vbox = None
2230	self.AddDict = None
2231	self.cifdic = cifdic
2232	self.cifblk = cifblk
2233	self.loops = loopstructure
2234	self.parent = parent
2235	self.LayoutCalled = False
2236	self.parentOKbuttons = OKbuttons
2237	self.ValidatedControlsList = []
2238	self._fill()
2239	def _fill(self):
2240	'Fill the scrolled panel with widgets for each CIF item'
2241	wx.BeginBusyCursor()
2242	self.AddDict = {}
2243	self.ValidatedControlsList = []
2244	# delete any only contents
2245	if self.vbox:
2246	self.vbox.DeleteWindows()
2247	self.vbox = None
2248	self.Update()
2249	vbox = wx.BoxSizer(wx.VERTICAL)
2250	self.vbox = vbox
2251	# compile a 'list' of items in loops
2252	loopnames = set()
2253	for i in self.loops:
2254	loopnames \|= set(i)
2255	# post the looped CIF items
2256	for lnum,lp in enumerate(self.loops):
2257	hbox = wx.BoxSizer(wx.HORIZONTAL)
2258	hbox.Add(wx.StaticText(self,wx.ID_ANY,'Loop '+str(lnum+1)))
2259	vbox.Add(hbox)
2260	but = wx.Button(self,wx.ID_ANY,"Add row")
2261	self.AddDict[but]=lnum
2262
2263	hbox.Add(but)
2264	but.Bind(wx.EVT_BUTTON,self.OnAddRow)
2265	fbox = wx.GridBagSizer(0, 0)
2266	vbox.Add(fbox)
2267	rows = 0
2268	for i,item in enumerate(lp):
2269	txt = wx.StaticText(self,wx.ID_ANY,item+" ")
2270	fbox.Add(txt,(0,i+1))
2271	# if self.cifdic.get(item):
2272	# df = self.cifdic[item].get('_definition')
2273	# if df:
2274	# txt.SetToolTipString(G2IO.trim(df))
2275	# but = CIFdefHelp(self,
2276	# "Definition for "+item+":\n\n"+G2IO.trim(df),
2277	# self.parent,
2278	# self.parent.helptxt)
2279	# fbox.Add(but,(1,i+1),flag=wx.ALIGN_CENTER)
2280	for j,val in enumerate(self.cifblk[item]):
2281	ent = self.CIFEntryWidget(self.cifblk[item],j,item)
2282	#fbox.Add(ent,(j+2,i+1),flag=wx.EXPAND\|wx.ALL)
2283	fbox.Add(ent,(j+1,i+1),flag=wx.EXPAND\|wx.ALL)
2284	if self.cifdic.get(item):
2285	df = self.cifdic[item].get('_definition')
2286	if df:
2287	txt.SetToolTipString(G2IO.trim(df))
2288	but = CIFdefHelp(self,
2289	"Definition for "+item+":\n\n"+G2IO.trim(df),
2290	self.parent,
2291	self.parent.helptxt)
2292	fbox.Add(but,(j+2,i+1),flag=wx.ALIGN_CENTER)
2293	rows = max(rows,len(self.cifblk[item]))
2294	for i in range(rows):
2295	txt = wx.StaticText(self,wx.ID_ANY,str(i+1))
2296	fbox.Add(txt,(i+2,0))
2297	line = wx.StaticLine(self,wx.ID_ANY, size=(-1,3), style=wx.LI_HORIZONTAL)
2298	vbox.Add(line, 0, wx.EXPAND\|wx.ALIGN_CENTER\|wx.ALL, 10)
2299
2300	# post the non-looped CIF items
2301	for item in sorted(self.cifblk.keys()):
2302	if item not in loopnames:
2303	hbox = wx.BoxSizer(wx.HORIZONTAL)
2304	vbox.Add(hbox)
2305	txt = wx.StaticText(self,wx.ID_ANY,item)
2306	hbox.Add(txt)
2307	ent = self.CIFEntryWidget(self.cifblk,item,item)
2308	hbox.Add(ent)
2309	if self.cifdic.get(item):
2310	df = self.cifdic[item].get('_definition')
2311	if df:
2312	txt.SetToolTipString(G2IO.trim(df))
2313	but = CIFdefHelp(self,
2314	"Definition for "+item+":\n\n"+G2IO.trim(df),
2315	self.parent,
2316	self.parent.helptxt)
2317	hbox.Add(but,0,wx.ALL,2)
2318	self.SetSizer(vbox)
2319	#vbox.Fit(self.parent)
2320	self.SetAutoLayout(1)
2321	self.SetupScrolling()
2322	self.Bind(rw.EVT_RW_LAYOUT_NEEDED, self.OnLayoutNeeded)
2323	self.Layout()
2324	wx.EndBusyCursor()
2325	def OnLayoutNeeded(self,event):
2326	'''Called when an update of the panel layout is needed. Calls
2327	self.DoLayout after the current operations are complete using
2328	CallAfter. This is called only once, according to flag
2329	self.LayoutCalled, which is cleared in self.DoLayout.
2330	'''
2331	if self.LayoutCalled: return # call already queued
2332	wx.CallAfter(self.DoLayout) # queue a call
2333	self.LayoutCalled = True
2334	def DoLayout(self):
2335	'''Update the Layout and scroll bars for the Panel. Clears
2336	self.LayoutCalled so that next change to panel can
2337	request a new update
2338	'''
2339	wx.BeginBusyCursor()
2340	self.Layout()
2341	self.SetupScrolling()
2342	wx.EndBusyCursor()
2343	self.LayoutCalled = False
2344	def OnAddRow(self,event):
2345	'add a row to a loop'
2346	lnum = self.AddDict.get(event.GetEventObject())
2347	if lnum is None: return
2348	for item in self.loops[lnum]:
2349	self.cifblk[item].append('?')
2350	self._fill()
2351
2352	def ControlOKButton(self,setvalue):
2353	'''Enable or Disable the OK button(s) for the dialog. Note that this is
2354	passed into the ValidatedTxtCtrl for use by validators.
2355
2356	:param bool setvalue: if True, all entries in the dialog are
2357	checked for validity. The first invalid control triggers
2358	disabling of buttons.
2359	If False then the OK button(s) are disabled with no checking
2360	of the invalid flag for each control.
2361	'''
2362	if setvalue: # turn button on, do only if all controls show as valid
2363	for ctrl in self.ValidatedControlsList:
2364	if ctrl.invalid:
2365	for btn in self.parentOKbuttons:
2366	btn.Disable()
2367	return
2368	else:
2369	for btn in self.parentOKbuttons:
2370	btn.Enable()
2371	else:
2372	for btn in self.parentOKbuttons:
2373	btn.Disable()
2374
2375	def CIFEntryWidget(self,dct,item,dataname):
2376	'''Create an entry widget for a CIF item. Use a validated entry for numb values
2377	where int is required when limits are integers and floats otherwise.
2378	At present this does not allow entry of the special CIF values of "." and "?" for
2379	numerical values and highlights them as invalid.
2380	Use a selection widget when there are specific enumerated values for a string.
2381	'''
2382	if self.cifdic.get(dataname):
2383	if self.cifdic[dataname].get('_enumeration'):
2384	values = ['?']+self.cifdic[dataname]['_enumeration']
2385	choices = ['undefined']
2386	for i in self.cifdic[dataname].get('_enumeration_detail',values):
2387	choices.append(G2IO.trim(i))
2388	ent = G2gd.EnumSelector(self, dct, item, choices, values, size=(200, -1))
2389	return ent
2390	if self.cifdic[dataname].get('_type') == 'numb':
2391	mn = None
2392	mx = None
2393	hint = int
2394	if self.cifdic[dataname].get('_enumeration_range'):
2395	rng = self.cifdic[dataname]['_enumeration_range'].split(':')
2396	if '.' in rng[0] or '.' in rng[1]: hint = float
2397	if rng[0]: mn = hint(rng[0])
2398	if rng[1]: mx = hint(rng[1])
2399	ent = G2gd.ValidatedTxtCtrl(
2400	self,dct,item,typeHint=hint,min=mn,max=mx,
2401	CIFinput=True,
2402	OKcontrol=self.ControlOKButton)
2403	self.ValidatedControlsList.append(ent)
2404	return ent
2405	rw1 = rw.ResizeWidget(self)
2406	ent = G2gd.ValidatedTxtCtrl(
2407	rw1,dct,item,size=(100, 20),
2408	style=wx.TE_MULTILINE\|wx.TE_PROCESS_ENTER,
2409	CIFinput=True,
2410	OKcontrol=self.ControlOKButton)
2411	self.ValidatedControlsList.append(ent)
2412	return rw1
2413
2414	class CIFtemplateSelect(wx.BoxSizer):
2415	'''Create a set of buttons to show, select and edit a CIF template
2416
2417	:param frame: wx.Frame object of parent
2418	:param panel: wx.Panel object where widgets should be placed
2419	:param str tmplate: one of 'publ', 'phase', or 'instrument' to determine
2420	the type of template
2421	:param dict G2dict: GSAS-II dict where CIF should be placed. The key
2422	"CIF_template" will be used to store either a list or a string.
2423	If a list, it will contain a dict and a list defining loops. If
2424	an str, it will contain a file name.
2425	:param function repaint: reference to a routine to be called to repaint
2426	the frame after a change has been made
2427	:param str title: A line of text to show at the top of the window
2428	:param str defaultname: specifies the default file name to be used for
2429	saving the CIF.
2430	'''
2431	def __init__(self,frame,panel,tmplate,G2dict, repaint, title, defaultname=''):
2432	wx.BoxSizer.__init__(self,wx.VERTICAL)
2433	self.cifdefs = frame
2434	self.dict = G2dict
2435	self.repaint = repaint
2436	templateDefName = 'template_'+tmplate+'.cif'
2437	self.CIF = G2dict.get("CIF_template")
2438	if defaultname:
2439	self.defaultname = defaultname.encode('ascii','replace').strip().replace(' ','_')
2440	self.defaultname = re.sub(r'[^a-zA-Z0-9_-]','',self.defaultname)
2441	self.defaultname = tmplate + "_" + self.defaultname + ".cif"
2442	else:
2443	self.defaultname = ''
2444
2445	txt = wx.StaticText(panel,wx.ID_ANY,title)
2446	self.Add(txt,0,wx.ALIGN_CENTER)
2447	# change font on title
2448	txtfnt = txt.GetFont()
2449	txtfnt.SetWeight(wx.BOLD)
2450	txtfnt.SetPointSize(2+txtfnt.GetPointSize())
2451	txt.SetFont(txtfnt)
2452	self.Add((-1,3))
2453
2454	if not self.CIF: # empty or None
2455	for pth in [os.getcwd()]+sys.path:
2456	fil = os.path.join(pth,self.defaultname)
2457	if os.path.exists(fil) and self.defaultname:
2458	self.CIF = fil
2459	CIFtxt = "Template: "+self.defaultname
2460	break
2461	else:
2462	for pth in sys.path:
2463	fil = os.path.join(pth,templateDefName)
2464	if os.path.exists(fil):
2465	self.CIF = fil
2466	CIFtxt = "Template: "+templateDefName
2467	break
2468	else:
2469	print("Default CIF template "+self.defaultname+' not found in path!')
2470	self.CIF = None
2471	CIFtxt = "none! (No template found)"
2472	elif type(self.CIF) is not list and type(self.CIF) is not tuple:
2473	if not os.path.exists(self.CIF):
2474	print("Error: template file has disappeared: "+self.CIF)
2475	self.CIF = None
2476	CIFtxt = "none! (file not found)"
2477	else:
2478	if len(self.CIF) < 50:
2479	CIFtxt = "File: "+self.CIF
2480	else:
2481	CIFtxt = "File: ..."+self.CIF[-50:]
2482	else:
2483	CIFtxt = "Template is customized"
2484	# show template source
2485	self.Add(wx.StaticText(panel,wx.ID_ANY,CIFtxt))
2486	# show str, button to select file; button to edit (if CIF defined)
2487	but = wx.Button(panel,wx.ID_ANY,"Select Template File")
2488	but.Bind(wx.EVT_BUTTON,self._onGetTemplateFile)
2489	hbox = wx.BoxSizer(wx.HORIZONTAL)
2490	hbox.Add(but,0,0,2)
2491	but = wx.Button(panel,wx.ID_ANY,"Edit Template")
2492	but.Bind(wx.EVT_BUTTON,self._onEditTemplateContents)
2493	if self.CIF is None: but.Disable() # nothing to edit!
2494	hbox.Add(but,0,0,2)
2495	self.Add(hbox)
2496	def _onGetTemplateFile(self,event):
2497	'select a template file'
2498	dlg = wx.FileDialog(
2499	self.cifdefs, message="Read CIF template file",
2500	defaultDir=os.getcwd(),
2501	defaultFile=self.defaultname,
2502	wildcard="CIF (.cif)\|.cif",
2503	style=wx.OPEN \| wx.CHANGE_DIR
2504	)
2505	ret = dlg.ShowModal()
2506	fil = dlg.GetPath()
2507	dlg.Destroy()
2508	if ret == wx.ID_OK:
2509	try:
2510	cf = G2IO.ReadCIF(fil)
2511	if len(cf.keys()) == 0:
2512	raise Exception,"No CIF data_ blocks found"
2513	if len(cf.keys()) != 1:
2514	raise Exception, 'Error, CIF Template has more than one block: '+fil
2515	self.dict["CIF_template"] = fil
2516	except Exception as err:
2517	print('\nError reading CIF: '+fil)
2518	dlg = wx.MessageDialog(self.cifdefs,
2519	'Error reading CIF '+fil,
2520	'Error in CIF file',
2521	wx.OK)
2522	dlg.ShowModal()
2523	dlg.Destroy()
2524	print(err.message)
2525	return
2526	self.repaint() #EditCIFDefaults()
2527
2528	def _onEditTemplateContents(self,event):
2529	'Called to edit the contents of a CIF template'
2530	if type(self.CIF) is list or type(self.CIF) is tuple:
2531	dblk,loopstructure = copy.deepcopy(self.CIF) # don't modify original
2532	else:
2533	cf = G2IO.ReadCIF(self.CIF)
2534	dblk,loopstructure = CIF2dict(cf)
2535	dlg = EditCIFtemplate(self.cifdefs,dblk,loopstructure,self.defaultname)
2536	val = dlg.Post()
2537	if val:
2538	if dlg.newfile: # results saved in file
2539	self.dict["CIF_template"] = dlg.newfile
2540	else:
2541	self.dict["CIF_template"] = [dlg.cifblk,dlg.loopstructure]
2542	self.repaint() #EditCIFDefaults() # note that this does a dlg.Destroy()
2543	else:
2544	dlg.Destroy()
2545
2546	#===============================================================================
2547	# end of misc CIF utilities
2548	#===============================================================================

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