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source: trunk/exports/G2cif.py @ 1068

Last change on this file since 1068 was 1068, checked in by toby, 10 years ago
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1	#!/usr/bin/env python
2	# -- coding: utf-8 --
3	#G2cif
4	########### SVN repository information ###################
5	# $Date: 2013-07-22 20:57:37 -0500 (Mon, 22 Jul 2013) $
6	# $Author: toby $
7	# $Revision: 1006 $
8	# $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/exports/G2cif.py $
9	# $Id: G2cif.py 1006 2013-07-23 01:57:37Z toby $
10	########### SVN repository information ###################
11	'''Code to export a GSAS-II project as a CIF
12	The heavy lifting is done in method export
13	'''
14
15	# TODO: set bond pub flags?
16
17	import datetime as dt
18	import os.path
19	import sys
20	import numpy as np
21	import cPickle
22	import copy
23	import re
24	import wx
25	import wx.lib.scrolledpanel as wxscroll
26	import wx.lib.resizewidget as rw
27	import GSASIIpath
28	GSASIIpath.SetVersionNumber("$Revision: 1006 $")
29	import GSASIIIO as G2IO
30	#reload(G2IO)
31	import GSASIIgrid as G2gd
32	reload(G2gd)
33	import GSASIIstrIO as G2stIO
34	#reload(G2stIO)
35	#import GSASIImapvars as G2mv
36	import GSASIImath as G2mth
37	#reload(G2mth)
38	import GSASIIlattice as G2lat
39	import GSASIIspc as G2spc
40	#reload(G2spc)
41	import GSASIIphsGUI as G2pg
42	#reload(G2pg)
43	import GSASIIstrMain as G2stMn
44	#reload(G2stMn)
45
46	DEBUG = False #True to skip printing of reflection/powder profile lists
47
48	CIFdic = None
49
50	def getCallerDocString(): # for development
51	"Return the calling function's doc string"
52	import inspect as ins
53	for item in ins.stack()[1][0].f_code.co_consts:
54	if type(item) is str:
55	return item
56	else:
57	return '?'
58
59	#===============================================================================
60	# misc CIF utilities
61	#===============================================================================
62	def PickleCIFdict(fil):
63	'''Loads a CIF dictionary, cherry picks out the items needed
64	by local code and sticks them into a python dict and writes
65	that dict out as a cPickle file for later reuse.
66	If the write fails a warning message is printed,
67	but no exception occurs.
68
69	:param str fil: file name of CIF dictionary, will usually end
70	in .dic
71	:returns: the dict with the definitions
72	'''
73	import CifFile as cif # PyCifRW from James Hester
74	cifdic = {}
75	dictobj = cif.CifDic(fil)
76	if DEBUG: print('loaded '+str(fil))
77	for item in dictobj.keys():
78	cifdic[item] = {}
79	for j in (
80	'_definition','_type',
81	'_enumeration',
82	'_enumeration_detail',
83	'_enumeration_range'):
84	if dictobj[item].get(j):
85	cifdic[item][j] = dictobj[item][j]
86	try:
87	fil = os.path.splitext(fil)[0]+'.cpickle'
88	fp = open(fil,'w')
89	cPickle.dump(cifdic,fp)
90	fp.close()
91	if DEBUG: print('wrote '+str(fil))
92	except:
93	print ('Unable to write '+str(fil))
94	return cifdic
95
96	def LoadCIFdic():
97	'''Create a composite core+powder CIF lookup dict containing
98	information about all items in the CIF dictionaries, loading
99	pickled files if possible. The routine looks for files
100	named cif_core.cpickle and cif_pd.cpickle in every
101	directory in the path and if they are not found, files
102	cif_core.dic and/or cif_pd.dic are read.
103
104	:returns: the dict with the definitions
105	'''
106	cifdic = {}
107	for ftyp in "cif_core","cif_pd":
108	for loc in sys.path:
109	fil = os.path.join(loc,ftyp+".cpickle")
110	if not os.path.exists(fil): continue
111	fp = open(fil,'r')
112	try:
113	cifdic.update(cPickle.load(fp))
114	if DEBUG: print('reloaded '+str(fil))
115	break
116	finally:
117	fp.close()
118	else:
119	for loc in sys.path:
120	fil = os.path.join(loc,ftyp+".dic")
121	if not os.path.exists(fil): continue
122	#try:
123	if True:
124	cifdic.update(PickleCIFdict(fil))
125	break
126	#except:
127	# pass
128	else:
129	print('Could not load '+ftyp+' dictionary')
130	return cifdic
131
132	class CIFdefHelp(wx.Button):
133	'''Create a help button that displays help information on
134	the current data item
135
136	:param parent: the panel which will be the parent of the button
137	:param str msg: the help text to be displayed
138	:param wx.Dialog helpwin: Frame for CIF editing dialog
139	:param wx.TextCtrl helptxt: TextCtrl where help text is placed
140	'''
141	def __init__(self,parent,msg,helpwin,helptxt):
142	wx.Button.__init__(self,parent,wx.ID_HELP)
143	self.Bind(wx.EVT_BUTTON,self._onPress)
144	self.msg=msg
145	self.parent = parent
146	#self.helpwin = self.parent.helpwin
147	self.helpwin = helpwin
148	self.helptxt = helptxt
149	def _onPress(self,event):
150	'Respond to a button press by displaying the requested text'
151	try:
152	#helptxt = self.helptxt
153	ow,oh = self.helptxt.GetSize()
154	self.helptxt.SetLabel(self.msg)
155	w,h = self.helptxt.GetSize()
156	if h > oh:
157	self.helpwin.GetSizer().Fit(self.helpwin)
158	except: # error posting help, ignore
159	return
160
161	def CIF2dict(cf):
162	'''copy the contents of a CIF out from a PyCifRW block object
163	into a dict
164
165	:returns: cifblk, loopstructure where cifblk is a dict with
166	CIF items and loopstructure is a list of lists that defines
167	which items are in which loops.
168	'''
169	blk = cf.keys()[0] # assume templates are a single CIF block, use the 1st
170	loopstructure = cf[blk].loopnames()[:] # copy over the list of loop contents
171	dblk = {}
172	for item in cf[blk].keys(): # make a copy of all the items in the block
173	dblk[item] = cf[blk][item]
174	return dblk,loopstructure
175
176	def dict2CIF(dblk,loopstructure,blockname='Template'):
177	'''Create a PyCifRW CIF object containing a single CIF
178	block object from a dict and loop structure list.
179
180	:param dblk: a dict containing values for each CIF item
181	:param list loopstructure: a list of lists containing the contents of
182	each loop, as an example::
183
184	[ ["_a","_b"], ["_c"], ["_d_1","_d_2","_d_3"]]
185
186	this describes a CIF with this type of structure::
187
188	loop_ _a _b <a1> <b1> <a2> ...
189	loop_ _c <c1> <c2>...
190	loop _d_1 _d_2 _d_3 ...
191
192	Note that the values for each looped CIF item, such as _a,
193	are contained in a list, for example as cifblk["_a"]
194
195	:param str blockname: an optional name for the CIF block.
196	Defaults to 'Template'
197
198	:returns: the newly created PyCifRW CIF object
199	'''
200
201	import CifFile as cif # PyCifRW from James Hester
202	# compile a 'list' of items in loops
203	loopnames = set()
204	for i in loopstructure:
205	loopnames \|= set(i)
206	# create a new block
207	newblk = cif.CifBlock()
208	# add the looped items
209	for keys in loopstructure:
210	vals = []
211	for key in keys:
212	vals.append(dblk[key])
213	newblk.AddCifItem(([keys],[vals]))
214	# add the non-looped items
215	for item in dblk:
216	if item in loopnames: continue
217	newblk[item] = dblk[item]
218	# create a CIF and add the block
219	newcf = cif.CifFile()
220	newcf[blockname] = newblk
221	return newcf
222
223
224	class EditCIFtemplate(wx.Dialog):
225	'''Create a dialog for editing a CIF template. The edited information is
226	placed in cifblk. If the CIF is saved as a file, the name of that file
227	is saved as ``self.newfile``.
228
229	:param wx.Frame parent: parent frame or None
230	:param cifblk: dict or PyCifRW block containing values for each CIF item
231	:param list loopstructure: a list of lists containing the contents of
232	each loop, as an example::
233
234	[ ["_a","_b"], ["_c"], ["_d_1","_d_2","_d_3"]]
235
236	this describes a CIF with this type of structure::
237
238	loop_ _a _b <a1> <b1> <a2> ...
239	loop_ _c <c1> <c2>...
240	loop _d_1 _d_2 _d_3 ...
241
242	Note that the values for each looped CIF item, such as _a,
243	are contained in a list, for example as cifblk["_a"]
244
245	:param str defaultname: specifies the default file name to be used for
246	saving the CIF.
247	'''
248	def __init__(self,parent,cifblk,loopstructure,defaultname):
249	OKbuttons = []
250	self.cifblk = cifblk
251	self.loopstructure = loopstructure
252	self.newfile = None
253	self.defaultname = defaultname
254	global CIFdic # once this is loaded, keep it around
255	if CIFdic is None:
256	CIFdic = LoadCIFdic()
257	wx.Dialog.__init__(self,parent,style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
258
259	# define widgets that will be needed during panel creation
260	self.helptxt = wx.StaticText(self,wx.ID_ANY,"")
261	savebtn = wx.Button(self, wx.ID_CLOSE, "Save as template")
262	OKbuttons.append(savebtn)
263	savebtn.Bind(wx.EVT_BUTTON,self._onSave)
264	OKbtn = wx.Button(self, wx.ID_OK, "Use")
265	OKbtn.SetDefault()
266	OKbuttons.append(OKbtn)
267
268	self.SetTitle('Edit items in CIF template')
269	vbox = wx.BoxSizer(wx.VERTICAL)
270	cpnl = EditCIFpanel(self,cifblk,loopstructure,CIFdic,OKbuttons,size=(300,300))
271	vbox.Add(cpnl, 1, wx.ALIGN_LEFT\|wx.ALL\|wx.EXPAND, 0)
272	G2gd.HorizontalLine(vbox,self)
273	vbox.Add(self.helptxt, 0, wx.EXPAND\|wx.ALL, 5)
274	G2gd.HorizontalLine(vbox,self)
275	btnsizer = wx.BoxSizer(wx.HORIZONTAL)
276	btn = wx.Button(self, wx.ID_CANCEL)
277	btnsizer.Add(btn,0,wx.ALIGN_CENTER\|wx.ALL)
278	btnsizer.Add(savebtn,0,wx.ALIGN_CENTER\|wx.ALL)
279	btnsizer.Add(OKbtn,0,wx.ALIGN_CENTER\|wx.ALL)
280	vbox.Add(btnsizer, 0, wx.ALIGN_CENTER\|wx.ALL, 5)
281	self.SetSizer(vbox)
282	vbox.Fit(self)
283	def Post(self):
284	'''Display the dialog
285
286	:returns: True unless Cancel has been pressed.
287	'''
288	return (self.ShowModal() == wx.ID_OK)
289	def _onSave(self,event):
290	'Save CIF entries in a template file'
291	dlg = wx.FileDialog(
292	self, message="Save as CIF template",
293	defaultDir=os.getcwd(),
294	defaultFile=self.defaultname,
295	wildcard="CIF (.cif)\|.cif",
296	style=wx.SAVE \| wx.CHANGE_DIR
297	)
298	val = (dlg.ShowModal() == wx.ID_OK)
299	fil = dlg.GetPath()
300	dlg.Destroy()
301	if val: # ignore a Cancel button
302	fil = os.path.splitext(fil)[0]+'.cif' # force extension
303	fp = open(fil,'w')
304	newcf = dict2CIF(self.cifblk,self.loopstructure)
305	fp.write(newcf.WriteOut())
306	fp.close()
307	self.newfile = fil
308	self.EndModal(wx.ID_OK)
309
310	class EditCIFpanel(wxscroll.ScrolledPanel):
311	'''Creates a scrolled panel for editing CIF template items
312
313	:param wx.Frame parent: parent frame where panel will be placed
314	:param cifblk: dict or PyCifRW block containing values for each CIF item
315	:param list loopstructure: a list of lists containing the contents of
316	each loop, as an example::
317
318	[ ["_a","_b"], ["_c"], ["_d_1","_d_2","_d_3"]]
319
320	this describes a CIF with this type of structure::
321
322	loop_ _a _b <a1> <b1> <a2> ...
323	loop_ _c <c1> <c2>...
324	loop _d_1 _d_2 _d_3 ...
325
326	Note that the values for each looped CIF item, such as _a,
327	are contained in a list, for example as cifblk["_a"]
328
329	:param dict cifdic: optional CIF dictionary definitions
330	:param list OKbuttons: A list of wx.Button objects that should
331	be disabled when information in the CIF is invalid
332	:param (other): optional keyword parameters for wx.ScrolledPanel
333	'''
334	def __init__(self, parent, cifblk, loopstructure, cifdic={}, OKbuttons=[], **kw):
335	self.parent = parent
336	wxscroll.ScrolledPanel.__init__(self, parent, wx.ID_ANY, **kw)
337	self.vbox = None
338	self.AddDict = None
339	self.cifdic = cifdic
340	self.cifblk = cifblk
341	self.loops = loopstructure
342	self.parent = parent
343	self.LayoutCalled = False
344	self.parentOKbuttons = OKbuttons
345	self.ValidatedControlsList = []
346	self._fill()
347	def _fill(self):
348	'Fill the scrolled panel with widgets for each CIF item'
349	wx.BeginBusyCursor()
350	self.AddDict = {}
351	self.ValidatedControlsList = []
352	# delete any only contents
353	if self.vbox:
354	self.vbox.DeleteWindows()
355	self.vbox = None
356	self.Update()
357	vbox = wx.BoxSizer(wx.VERTICAL)
358	self.vbox = vbox
359	# compile a 'list' of items in loops
360	loopnames = set()
361	for i in self.loops:
362	loopnames \|= set(i)
363	# post the looped CIF items
364	for lnum,lp in enumerate(self.loops):
365	hbox = wx.BoxSizer(wx.HORIZONTAL)
366	hbox.Add(wx.StaticText(self,wx.ID_ANY,'Loop '+str(lnum+1)))
367	vbox.Add(hbox)
368	but = wx.Button(self,wx.ID_ANY,"Add row")
369	self.AddDict[but]=lnum
370
371	hbox.Add(but)
372	but.Bind(wx.EVT_BUTTON,self.OnAddRow)
373	fbox = wx.GridBagSizer(0, 0)
374	vbox.Add(fbox)
375	rows = 0
376	for i,item in enumerate(lp):
377	txt = wx.StaticText(self,wx.ID_ANY,item+" ")
378	fbox.Add(txt,(0,i+1))
379	if self.cifdic.get(item):
380	df = self.cifdic[item].get('_definition')
381	if df:
382	txt.SetToolTipString(G2IO.trim(df))
383	but = CIFdefHelp(self,
384	"Definition for "+item+":\n\n"+G2IO.trim(df),
385	self.parent,
386	self.parent.helptxt)
387	fbox.Add(but,(1,i+1),flag=wx.ALIGN_CENTER)
388	for j,val in enumerate(self.cifblk[item]):
389	ent = self.CIFEntryWidget(self.cifblk[item],j,item)
390	fbox.Add(ent,(j+2,i+1),flag=wx.EXPAND\|wx.ALL)
391	rows = max(rows,len(self.cifblk[item]))
392	for i in range(rows):
393	txt = wx.StaticText(self,wx.ID_ANY,str(i+1))
394	fbox.Add(txt,(i+2,0))
395	line = wx.StaticLine(self,wx.ID_ANY, size=(-1,3), style=wx.LI_HORIZONTAL)
396	vbox.Add(line, 0, wx.EXPAND\|wx.ALIGN_CENTER\|wx.ALL, 10)
397
398	# post the non-looped CIF items
399	for item in sorted(self.cifblk.keys()):
400	if item not in loopnames:
401	hbox = wx.BoxSizer(wx.HORIZONTAL)
402	vbox.Add(hbox)
403	txt = wx.StaticText(self,wx.ID_ANY,item)
404	hbox.Add(txt)
405	if self.cifdic.get(item):
406	df = self.cifdic[item].get('_definition')
407	if df:
408	txt.SetToolTipString(G2IO.trim(df))
409	but = CIFdefHelp(self,
410	"Definition for "+item+":\n\n"+G2IO.trim(df),
411	self.parent,
412	self.parent.helptxt)
413	hbox.Add(but,0,wx.ALL,2)
414	ent = self.CIFEntryWidget(self.cifblk,item,item)
415	hbox.Add(ent)
416	self.SetSizer(vbox)
417	#vbox.Fit(self.parent)
418	self.SetAutoLayout(1)
419	self.SetupScrolling()
420	self.Bind(rw.EVT_RW_LAYOUT_NEEDED, self.OnLayoutNeeded)
421	self.Layout()
422	wx.EndBusyCursor()
423	def OnLayoutNeeded(self,event):
424	'''Called when an update of the panel layout is needed. Calls
425	self.DoLayout after the current operations are complete using
426	CallAfter. This is called only once, according to flag
427	self.LayoutCalled, which is cleared in self.DoLayout.
428	'''
429	if self.LayoutCalled: return # call already queued
430	wx.CallAfter(self.DoLayout) # queue a call
431	self.LayoutCalled = True
432	def DoLayout(self):
433	'''Update the Layout and scroll bars for the Panel. Clears
434	self.LayoutCalled so that next change to panel can
435	request a new update
436	'''
437	wx.BeginBusyCursor()
438	self.Layout()
439	self.SetupScrolling()
440	wx.EndBusyCursor()
441	self.LayoutCalled = False
442	def OnAddRow(self,event):
443	'add a row to a loop'
444	lnum = self.AddDict.get(event.GetEventObject())
445	if lnum is None: return
446	for item in self.loops[lnum]:
447	self.cifblk[item].append('?')
448	self._fill()
449
450	def ControlOKButton(self,setvalue):
451	'''Enable or Disable the OK button(s) for the dialog. Note that this is
452	passed into the ValidatedTxtCtrl for use by validators.
453
454	:param bool setvalue: if True, all entries in the dialog are
455	checked for validity. The first invalid control triggers
456	disabling of buttons.
457	If False then the OK button(s) are disabled with no checking
458	of the invalid flag for each control.
459	'''
460	if setvalue: # turn button on, do only if all controls show as valid
461	for ctrl in self.ValidatedControlsList:
462	if ctrl.invalid:
463	for btn in self.parentOKbuttons:
464	btn.Disable()
465	return
466	else:
467	for btn in self.parentOKbuttons:
468	btn.Enable()
469	else:
470	for btn in self.parentOKbuttons:
471	btn.Disable()
472
473	def CIFEntryWidget(self,dct,item,dataname):
474	'''Create an entry widget for a CIF item. Use a validated entry for numb values
475	where int is required when limits are integers and floats otherwise.
476	At present this does not allow entry of the special CIF values of "." and "?" for
477	numerical values and highlights them as invalid.
478	Use a selection widget when there are specific enumerated values for a string.
479	'''
480	if self.cifdic.get(dataname):
481	if self.cifdic[dataname].get('_enumeration'):
482	values = ['?']+self.cifdic[dataname]['_enumeration']
483	choices = ['undefined']
484	for i in self.cifdic[dataname].get('_enumeration_detail',values):
485	choices.append(G2IO.trim(i))
486	ent = G2gd.EnumSelector(self, dct, item, choices, values, size=(200, -1))
487	return ent
488	if self.cifdic[dataname].get('_type') == 'numb':
489	mn = None
490	mx = None
491	hint = int
492	if self.cifdic[dataname].get('_enumeration_range'):
493	rng = self.cifdic[dataname]['_enumeration_range'].split(':')
494	if '.' in rng[0] or '.' in rng[1]: hint = float
495	if rng[0]: mn = hint(rng[0])
496	if rng[1]: mx = hint(rng[1])
497	ent = G2gd.ValidatedTxtCtrl(
498	self,dct,item,typeHint=hint,min=mn,max=mx,
499	CIFinput=True,
500	OKcontrol=self.ControlOKButton)
501	self.ValidatedControlsList.append(ent)
502	return ent
503	rw1 = rw.ResizeWidget(self)
504	ent = G2gd.ValidatedTxtCtrl(
505	rw1,dct,item,size=(100, 20),
506	style=wx.TE_MULTILINE\|wx.TE_PROCESS_ENTER,
507	CIFinput=True,
508	OKcontrol=self.ControlOKButton)
509	self.ValidatedControlsList.append(ent)
510	return rw1
511
512	class CIFtemplateSelect(wx.BoxSizer):
513	'''Create a set of buttons to show, select and edit a CIF template
514
515	:param frame: wx.Frame object of parent
516	:param panel: wx.Panel object where widgets should be placed
517	:param str tmplate: one of 'publ', 'phase', or 'instrument' to determine
518	the type of template
519	:param dict G2dict: GSAS-II dict where CIF should be placed. The key
520	"CIF_template" will be used to store either a list or a string.
521	If a list, it will contain a dict and a list defining loops. If
522	an str, it will contain a file name.
523	:param function repaint: reference to a routine to be called to repaint
524	the frame after a change has been made
525	:param str title: A line of text to show at the top of the window
526	:param str defaultname: specifies the default file name to be used for
527	saving the CIF.
528	'''
529	def __init__(self,frame,panel,tmplate,G2dict, repaint, title, defaultname=''):
530	wx.BoxSizer.__init__(self,wx.VERTICAL)
531	self.cifdefs = frame
532	self.dict = G2dict
533	self.repaint = repaint
534	templateDefName = 'template_'+tmplate+'.cif'
535	self.CIF = G2dict.get("CIF_template")
536	if defaultname:
537	self.defaultname = defaultname.encode('ascii','replace').strip().replace(' ','_')
538	self.defaultname = re.sub(r'[^a-zA-Z0-9_-]','',self.defaultname)
539	self.defaultname = tmplate + "_" + self.defaultname + ".cif"
540	else:
541	self.defaultname = ''
542
543	txt = wx.StaticText(panel,wx.ID_ANY,title)
544	self.Add(txt,0,wx.ALIGN_CENTER)
545	# change font on title
546	txtfnt = txt.GetFont()
547	txtfnt.SetWeight(wx.BOLD)
548	txtfnt.SetPointSize(2+txtfnt.GetPointSize())
549	txt.SetFont(txtfnt)
550	self.Add((-1,3))
551
552	if not self.CIF: # empty or None
553	for pth in [os.getcwd()]+sys.path:
554	fil = os.path.join(pth,self.defaultname)
555	if os.path.exists(fil) and self.defaultname:
556	self.CIF = fil
557	CIFtxt = "Template: "+self.defaultname
558	break
559	else:
560	for pth in sys.path:
561	fil = os.path.join(pth,templateDefName)
562	if os.path.exists(fil):
563	self.CIF = fil
564	CIFtxt = "Template: "+templateDefName
565	break
566	else:
567	print(self.CIF+' not found in path!')
568	self.CIF = None
569	CIFtxt = "none! (No template found)"
570	elif type(self.CIF) is not list and type(self.CIF) is not tuple:
571	if not os.path.exists(self.CIF):
572	print("Error: template file has disappeared:"+self.CIF)
573	self.CIF = None
574	CIFtxt = "none! (file not found)"
575	else:
576	if len(self.CIF) < 40:
577	CIFtxt = "File: "+self.CIF
578	else:
579	CIFtxt = "File: ..."+self.CIF[-40:]
580	else:
581	CIFtxt = "Template is customized"
582	# show template source
583	self.Add(wx.StaticText(panel,wx.ID_ANY,CIFtxt))
584	# show str, button to select file; button to edit (if CIF defined)
585	but = wx.Button(panel,wx.ID_ANY,"Select Template File")
586	but.Bind(wx.EVT_BUTTON,self._onGetTemplateFile)
587	hbox = wx.BoxSizer(wx.HORIZONTAL)
588	hbox.Add(but,0,0,2)
589	but = wx.Button(panel,wx.ID_ANY,"Edit Template")
590	but.Bind(wx.EVT_BUTTON,self._onEditTemplateContents)
591	hbox.Add(but,0,0,2)
592	#self.Add(hbox,0,wx.ALIGN_CENTER)
593	self.Add(hbox)
594	def _onGetTemplateFile(self,event):
595	dlg = wx.FileDialog(
596	self.cifdefs, message="Read CIF template file",
597	defaultDir=os.getcwd(),
598	defaultFile=self.defaultname,
599	wildcard="CIF (.cif)\|.cif",
600	style=wx.OPEN \| wx.CHANGE_DIR
601	)
602	ret = dlg.ShowModal()
603	fil = dlg.GetPath()
604	dlg.Destroy()
605	if ret == wx.ID_OK:
606	import CifFile as cif # PyCifRW from James Hester
607	try:
608	cf = cif.ReadCif(fil)
609	if len(cf.keys()) == 0: raise Exception,"No CIF data_ blocks found"
610	if len(cf.keys()) != 1:
611	print('\nWarning: CIF has more than one block, '+fil)
612	self.dict["CIF_template"] = fil
613	except Exception as err:
614	print('\nError reading CIF: '+fil)
615	dlg = wx.MessageDialog(self.cifdefs,
616	'Error reading CIF '+fil,
617	'Error in CIF file',
618	wx.OK)
619	dlg.ShowModal()
620	dlg.Destroy()
621	print(err.message)
622	return
623	self.repaint() #EditCIFDefaults()
624
625	def _onEditTemplateContents(self,event):
626	import CifFile as cif # PyCifRW from James Hester
627	if type(self.CIF) is list or type(self.CIF) is tuple:
628	dblk,loopstructure = copy.deepcopy(self.CIF) # don't modify original
629	else:
630	dblk,loopstructure = CIF2dict(cif.ReadCif(self.CIF))
631	dlg = EditCIFtemplate(self.cifdefs,dblk,loopstructure,self.defaultname)
632	val = dlg.Post()
633	if val:
634	if dlg.newfile: # results saved in file
635	self.dict["CIF_template"] = dlg.newfile
636	else:
637	self.dict["CIF_template"] = [dlg.cifblk,dlg.loopstructure]
638	self.repaint() #EditCIFDefaults() # note that this does a dlg.Destroy()
639	else:
640	dlg.Destroy()
641
642	#===============================================================================
643	# end of misc CIF utilities
644	#===============================================================================
645
646	class ExportCIF(G2IO.ExportBaseclass):
647	'''Used to create a CIF of an entire project
648	'''
649	def __init__(self,G2frame):
650	super(self.__class__,self).__init__( # fancy way to say <parentclass>.__init__
651	G2frame=G2frame,
652	formatName = 'full CIF',
653	extension='.cif',
654	longFormatName = 'Export project as CIF'
655	)
656	self.author = ''
657
658	def export(self,mode='full'):
659	'''Export a CIF
660
661	:param str mode: "full" (default) to create a complete CIF of project,
662	"simple" for a simple CIF with only coordinates
663	'''
664
665	# ===== define functions for export method =======================================
666	def openCIF(filnam):
667	if DEBUG:
668	self.fp = sys.stdout
669	else:
670	self.fp = open(filnam,'w')
671
672	def closeCIF():
673	if not DEBUG:
674	self.fp.close()
675
676	def WriteCIFitem(name,value=''):
677	if value:
678	if "\n" in value or len(value)> 70:
679	if name.strip(): self.fp.write(name+'\n')
680	self.fp.write('; '+value+'\n')
681	self.fp.write('; '+'\n')
682	elif " " in value:
683	if len(name)+len(value) > 65:
684	self.fp.write(name + '\n ' + '"' + str(value) + '"'+'\n')
685	else:
686	self.fp.write(name + ' ' + '"' + str(value) + '"'+'\n')
687	else:
688	if len(name)+len(value) > 65:
689	self.fp.write(name+'\n ' + value+'\n')
690	else:
691	self.fp.write(name+' ' + value+'\n')
692	else:
693	self.fp.write(name+'\n')
694
695	def WriteAudit():
696	WriteCIFitem('_audit_creation_method',
697	'created in GSAS-II')
698	WriteCIFitem('_audit_creation_date',self.CIFdate)
699	if self.author:
700	WriteCIFitem('_audit_author_name',self.author)
701	WriteCIFitem('_audit_update_record',
702	self.CIFdate+' Initial software-generated CIF')
703
704	def WriteOverall():
705	'''Write out overall refinement information.
706
707	More could be done here, but this is a good start.
708	'''
709	WriteCIFitem('_pd_proc_info_datetime', self.CIFdate)
710	WriteCIFitem('_pd_calc_method', 'Rietveld Refinement')
711	#WriteCIFitem('_refine_ls_shift/su_max',DAT1)
712	#WriteCIFitem('_refine_ls_shift/su_mean',DAT2)
713	#WriteCIFitem('_refine_diff_density_max',rhomax) #these need to be defined for each phase!
714	#WriteCIFitem('_refine_diff_density_min',rhomin)
715	WriteCIFitem('_computing_structure_refinement','GSAS-II (Toby & Von Dreele, J. Appl. Cryst. 46, 544-549, 2013)')
716	try:
717	vars = str(len(self.OverallParms['Covariance']['varyList']))
718	except:
719	vars = '?'
720	WriteCIFitem('_refine_ls_number_parameters',vars)
721	try:
722	GOF = G2mth.ValEsd(self.OverallParms['Covariance']['Rvals']['GOF'],-0.009)
723	except:
724	GOF = '?'
725	WriteCIFitem('_refine_ls_goodness_of_fit_all',GOF)
726
727	# get restraint info
728	# restraintDict = self.OverallParms.get('Restraints',{})
729	# for i in self.OverallParms['Constraints']:
730	# print i
731	# for j in self.OverallParms['Constraints'][i]:
732	# print j
733	#WriteCIFitem('_refine_ls_number_restraints',TEXT)
734	# other things to consider reporting
735	# _refine_ls_number_reflns
736	# _refine_ls_goodness_of_fit_obs
737	# _refine_ls_wR_factor_obs
738	# _refine_ls_restrained_S_all
739	# _refine_ls_restrained_S_obs
740
741	# include an overall profile r-factor, if there is more than one powder histogram
742	R = '%.5f'%(self.OverallParms['Covariance']['Rvals']['Rwp']/100.)
743	WriteCIFitem('\n# OVERALL WEIGHTED R-FACTOR')
744	WriteCIFitem('_refine_ls_wR_factor_obs',R)
745	# _refine_ls_R_factor_all
746	# _refine_ls_R_factor_obs
747	WriteCIFitem('_refine_ls_matrix_type','full')
748	#WriteCIFitem('_refine_ls_matrix_type','userblocks')
749
750	def GetCIF(G2dict,tmplate,defaultname=''):
751	CIFobj = G2dict.get("CIF_template")
752	if defaultname:
753	defaultname = defaultname.encode('ascii','replace').strip().replace(' ','_')
754	defaultname = re.sub(r'[^a-zA-Z0-9_-]','',defaultname)
755	defaultname = tmplate + "_" + defaultname + ".cif"
756	else:
757	defaultname = ''
758	templateDefName = 'template_'+tmplate+'.cif'
759	if not CIFobj: # copying a template
760	for pth in [os.getcwd()]+sys.path:
761	fil = os.path.join(pth,defaultname)
762	if os.path.exists(fil) and defaultname: break
763	else:
764	for pth in sys.path:
765	fil = os.path.join(pth,templateDefName)
766	if os.path.exists(fil): break
767	else:
768	print(CIFobj+' not found in path!')
769	return
770	fp = open(fil,'r')
771	txt = fp.read()
772	fp.close()
773	elif type(CIFobj) is not list and type(CIFobj) is not tuple:
774	if not os.path.exists(CIFobj):
775	print("Error: template file has disappeared:"+CIFobj)
776	return
777	fp = open(CIFobj,'r')
778	txt = fp.read()
779	fp.close()
780	else:
781	txt = dict2CIF(CIFobj[0],CIFobj[1]).WriteOut()
782	# remove the PyCifRW header, if present
783	#if txt.find('PyCifRW') > -1 and txt.find('data_') > -1:
784	txt = "# GSAS-II edited template follows "+txt[txt.index("data_")+5:]
785	#txt = txt.replace('data_','#')
786	print '*** Template ******'
787	print txt
788	WriteCIFitem(txt)
789
790	def WritePubTemplate():
791	'''insert the publication template ``template_publ.cif`` or a modified
792	version
793	'''
794	GetCIF(self.OverallParms['Controls'],'publ')
795
796	def WritePhaseTemplate(phasenam):
797	'''insert the phase template ``template_phase.cif`` or a modified
798	version for this project
799	'''
800	GetCIF(self.Phases[phasenam]['General'],'phase',phasenam)
801
802	def WritePowderTemplate(hist):
803	'''TODO: insert the phase template ``template_instrument.cif`` or some modified
804	version for this project
805	'''
806	histblk = self.Histograms[hist]["Sample Parameters"]
807	GetCIF(histblk,'powder',histblk['InstrName'])
808
809	def WriteSnglXtalTemplate(hist):
810	'''TODO: insert the single-crystal histogram template
811	for this project
812	'''
813	histblk = self.Histograms[hist]["Instrument Parameters"][0]
814	GetCIF(histblk,'single',histblk['InstrName'])
815
816	def FormatSH(phasenam):
817	'Format a full spherical harmonics texture description as a string'
818	phasedict = self.Phases[phasenam] # pointer to current phase info
819	pfx = str(phasedict['pId'])+'::'
820	s = ""
821	textureData = phasedict['General']['SH Texture']
822	if textureData.get('Order'):
823	s += "Spherical Harmonics correction. Order = "+str(textureData['Order'])
824	s += " Model: " + str(textureData['Model']) + "\n Orientation angles: "
825	for name in ['omega','chi','phi']:
826	aname = pfx+'SH '+name
827	s += name + " = "
828	sig = self.sigDict.get(aname,-0.09)
829	s += G2mth.ValEsd(self.parmDict[aname],sig)
830	s += "; "
831	s += "\n"
832	s1 = " Coefficients: "
833	for name in textureData['SH Coeff'][1]:
834	aname = pfx+name
835	if len(s1) > 60:
836	s += s1 + "\n"
837	s1 = " "
838	s1 += aname + ' = '
839	sig = self.sigDict.get(aname,-0.0009)
840	s1 += G2mth.ValEsd(self.parmDict[aname],sig)
841	s1 += "; "
842	s += s1
843	return s
844
845	def FormatHAPpo(phasenam):
846	'''return the March-Dollase/SH correction for every
847	histogram in the current phase formatted into a
848	character string
849	'''
850	phasedict = self.Phases[phasenam] # pointer to current phase info
851	s = ''
852	for histogram in sorted(phasedict['Histograms']):
853	if histogram.startswith("HKLF"): continue # powder only
854	Histogram = self.Histograms.get(histogram)
855	if not Histogram: continue
856	hapData = phasedict['Histograms'][histogram]
857	if hapData['Pref.Ori.'][0] == 'MD':
858	aname = str(phasedict['pId'])+':'+str(Histogram['hId'])+':MD'
859	if self.parmDict.get(aname,1.0) != 1.0: continue
860	sig = self.sigDict.get(aname,-0.009)
861	if s != "": s += '\n'
862	s += 'March-Dollase correction'
863	if len(self.powderDict) > 1:
864	s += ', histogram '+str(Histogram['hId']+1)
865	s += ' coef. = ' + G2mth.ValEsd(self.parmDict[aname],sig)
866	s += ' axis = ' + str(hapData['Pref.Ori.'][3])
867	else: # must be SH
868	if s != "": s += '\n'
869	s += 'Simple spherical harmonic correction'
870	if len(self.powderDict) > 1:
871	s += ', histogram '+str(Histogram['hId']+1)
872	s += ' Order = '+str(hapData['Pref.Ori.'][4])+'\n'
873	s1 = " Coefficients: "
874	for item in hapData['Pref.Ori.'][5]:
875	aname = str(phasedict['pId'])+':'+str(Histogram['hId'])+':'+item
876	if len(s1) > 60:
877	s += s1 + "\n"
878	s1 = " "
879	s1 += aname + ' = '
880	sig = self.sigDict.get(aname,-0.0009)
881	s1 += G2mth.ValEsd(self.parmDict[aname],sig)
882	s1 += "; "
883	s += s1
884	return s
885	def FormatBackground(bkg,hId):
886	'''Display the Background information as a descriptive text string.
887
888	TODO: this needs to be expanded to show the diffuse peak and
889	Debye term information as well. (Bob)
890
891	:returns: the text description (str)
892	'''
893	hfx = ':'+str(hId)+':'
894	fxn, bkgdict = bkg
895	terms = fxn[2]
896	txt = 'Background function: "'+fxn[0]+'" function with '+str(terms)+' terms:\n'
897	l = " "
898	for i,v in enumerate(fxn[3:]):
899	name = '%sBack:%d'%(hfx,i)
900	sig = self.sigDict.get(name,-0.009)
901	if len(l) > 60:
902	txt += l + '\n'
903	l = ' '
904	l += G2mth.ValEsd(v,sig)+', '
905	txt += l
906	if bkgdict['nDebye']:
907	txt += '\n Background Debye function parameters: A, R, U:'
908	names = ['A:','R:','U:']
909	for i in range(bkgdict['nDebye']):
910	txt += '\n '
911	for j in range(3):
912	name = hfx+'Debye'+names[j]+str(i)
913	sig = self.sigDict.get(name,-0.009)
914	txt += G2mth.ValEsd(bkgdict['debyeTerms'][i][2*j],sig)+', '
915	if bkgdict['nPeaks']:
916	txt += '\n Background peak parameters: pos, int, sig, gam:'
917	names = ['pos:','int:','sig:','gam:']
918	for i in range(bkgdict['nPeaks']):
919	txt += '\n '
920	for j in range(4):
921	name = hfx+'BkPk'+names[j]+str(i)
922	sig = self.sigDict.get(name,-0.009)
923	txt += G2mth.ValEsd(bkgdict['peaksList'][i][2*j],sig)+', '
924	return txt
925
926	def FormatInstProfile(instparmdict,hId):
927	'''Format the instrumental profile parameters with a
928	string description. Will only be called on PWDR histograms
929	'''
930	s = ''
931	inst = instparmdict[0]
932	hfx = ':'+str(hId)+':'
933	if 'C' in inst['Type'][0]:
934	s = 'Finger-Cox-Jephcoat function parameters U, V, W, X, Y, SH/L:\n'
935	s += ' peak variance(Gauss) = Utan(Th)^2^+Vtan(Th)+W:\n'
936	s += ' peak HW(Lorentz) = X/cos(Th)+Ytan(Th); SH/L = S/L+H/L\n'
937	s += ' U, V, W in (centideg)^2^, X & Y in centideg\n '
938	for item in ['U','V','W','X','Y','SH/L']:
939	name = hfx+item
940	sig = self.sigDict.get(name,-0.009)
941	s += G2mth.ValEsd(inst[item][1],sig)+', '
942	elif 'T' in inst['Type'][0]: #to be tested after TOF Rietveld done
943	s = 'Von Dreele-Jorgenson-Windsor function parameters\n'+ \
944	' alpha, beta-0, beta-1, beta-q, sig-0, sig-1, sig-q, X, Y:\n '
945	for item in ['alpha','bet-0','bet-1','bet-q','sig-0','sig-1','sig-q','X','Y']:
946	name = hfx+item
947	sig = self.sigDict.get(name,-0.009)
948	s += G2mth.ValEsd(inst[item][1],sig)+', '
949	return s
950
951	def FormatPhaseProfile(phasenam):
952	'''Format the phase-related profile parameters (size/strain)
953	with a string description.
954	return an empty string or None if there are no
955	powder histograms for this phase.
956	'''
957	s = ''
958	phasedict = self.Phases[phasenam] # pointer to current phase info
959	SGData = phasedict['General'] ['SGData']
960	for histogram in sorted(phasedict['Histograms']):
961	if histogram.startswith("HKLF"): continue # powder only
962	Histogram = self.Histograms.get(histogram)
963	if not Histogram: continue
964	hapData = phasedict['Histograms'][histogram]
965	pId = phasedict['pId']
966	hId = Histogram['hId']
967	phfx = '%d:%d:'%(pId,hId)
968	size = hapData['Size']
969	mustrain = hapData['Mustrain']
970	hstrain = hapData['HStrain']
971	s = ' Crystallite size model "%s" for %s (microns)\n '%(size[0],phasenam)
972	names = ['Size;i','Size;mx']
973	if 'uniax' in size[0]:
974	names = ['Size;i','Size;a','Size;mx']
975	s += 'anisotropic axis is %s\n '%(str(size[3]))
976	s += 'parameters: equatorial size, axial size, G/L mix\n '
977	for i,item in enumerate(names):
978	name = phfx+item
979	sig = self.sigDict.get(name,-0.009)
980	s += G2mth.ValEsd(size[1][i],sig)+', '
981	elif 'ellip' in size[0]:
982	s += 'parameters: S11, S22, S33, S12, S13, S23, G/L mix\n '
983	for i in range(6):
984	name = phfx+'Size:'+str(i)
985	sig = self.sigDict.get(name,-0.009)
986	s += G2mth.ValEsd(size[4][i],sig)+', '
987	sig = self.sigDict.get(phfx+'Size;mx',-0.009)
988	s += G2mth.ValEsd(size[1][2],sig)+', '
989	else: #isotropic
990	s += 'parameters: Size, G/L mix\n '
991	i = 0
992	for item in names:
993	name = phfx+item
994	sig = self.sigDict.get(name,-0.009)
995	s += G2mth.ValEsd(size[1][i],sig)+', '
996	i = 2 #skip the aniso value
997	s += '\n Mustrain model "%s" for %s (10^6^)\n '%(mustrain[0],phasenam)
998	names = ['Mustrain;i','Mustrain;mx']
999	if 'uniax' in mustrain[0]:
1000	names = ['Mustrain;i','Mustrain;a','Mustrain;mx']
1001	s += 'anisotropic axis is %s\n '%(str(size[3]))
1002	s += 'parameters: equatorial mustrain, axial mustrain, G/L mix\n '
1003	for i,item in enumerate(names):
1004	name = phfx+item
1005	sig = self.sigDict.get(name,-0.009)
1006	s += G2mth.ValEsd(mustrain[1][i],sig)+', '
1007	elif 'general' in mustrain[0]:
1008	names = 'parameters: '
1009	for i,name in enumerate(G2spc.MustrainNames(SGData)):
1010	names += name+', '
1011	if i == 9:
1012	names += '\n '
1013	names += 'G/L mix\n '
1014	s += names
1015	txt = ''
1016	for i in range(len(mustrain[4])):
1017	name = phfx+'Mustrain:'+str(i)
1018	sig = self.sigDict.get(name,-0.009)
1019	if len(txt) > 60:
1020	s += txt+'\n '
1021	txt = ''
1022	txt += G2mth.ValEsd(mustrain[4][i],sig)+', '
1023	s += txt
1024	sig = self.sigDict.get(phfx+'Mustrain;mx',-0.009)
1025	s += G2mth.ValEsd(mustrain[1][2],sig)+', '
1026
1027	else: #isotropic
1028	s += ' parameters: Mustrain, G/L mix\n '
1029	i = 0
1030	for item in names:
1031	name = phfx+item
1032	sig = self.sigDict.get(name,-0.009)
1033	s += G2mth.ValEsd(mustrain[1][i],sig)+', '
1034	i = 2 #skip the aniso value
1035	s += '\n Macrostrain for %s\n'%(phasenam)
1036	txt = ' parameters: '
1037	names = G2spc.HStrainNames(SGData)
1038	for name in names:
1039	txt += name+', '
1040	s += txt+'\n '
1041	for i in range(len(names)):
1042	name = phfx+name[i]
1043	sig = self.sigDict.get(name,-0.009)
1044	s += G2mth.ValEsd(hstrain[0][i],sig)+', '
1045	return s
1046
1047	def FmtAtomType(sym):
1048	'Reformat a GSAS-II atom type symbol to match CIF rules'
1049	sym = sym.replace('_','') # underscores are not allowed: no isotope designation?
1050	# in CIF, oxidation state sign symbols come after, not before
1051	if '+' in sym:
1052	sym = sym.replace('+','') + '+'
1053	elif '-' in sym:
1054	sym = sym.replace('-','') + '-'
1055	return sym
1056
1057	def PutInCol(val,wid):
1058	'''Pad a value to >=wid+1 columns by adding spaces at the end. Always
1059	adds at least one space
1060	'''
1061	val = str(val).replace(' ','')
1062	if not val: val = '?'
1063	fmt = '{:' + str(wid) + '} '
1064	return fmt.format(val)
1065
1066	def MakeUniqueLabel(lbl,labellist):
1067	'Make sure that every atom label is unique'
1068	lbl = lbl.strip()
1069	if not lbl: # deal with a blank label
1070	lbl = 'A_1'
1071	if lbl not in labellist:
1072	labellist.append(lbl)
1073	return lbl
1074	i = 1
1075	prefix = lbl
1076	if '_' in lbl:
1077	prefix = lbl[:lbl.rfind('_')]
1078	suffix = lbl[lbl.rfind('_')+1:]
1079	try:
1080	i = int(suffix)+1
1081	except:
1082	pass
1083	while prefix+'_'+str(i) in labellist:
1084	i += 1
1085	else:
1086	lbl = prefix+'_'+str(i)
1087	labellist.append(lbl)
1088
1089	def WriteAtomsNuclear(phasenam):
1090	'Write atom positions to CIF'
1091	phasedict = self.Phases[phasenam] # pointer to current phase info
1092	General = phasedict['General']
1093	cx,ct,cs,cia = General['AtomPtrs']
1094	Atoms = phasedict['Atoms']
1095	cfrac = cx+3
1096	fpfx = str(phasedict['pId'])+'::Afrac:'
1097	for i,at in enumerate(Atoms):
1098	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
1099	if fval != 0.0:
1100	break
1101	else:
1102	WriteCIFitem('\n# PHASE HAS NO ATOMS!')
1103	return
1104
1105	WriteCIFitem('\n# ATOMIC COORDINATES AND DISPLACEMENT PARAMETERS')
1106	WriteCIFitem('loop_ '+
1107	'\n\t_atom_site_label'+
1108	'\n\t_atom_site_type_symbol'+
1109	'\n\t_atom_site_fract_x'+
1110	'\n\t_atom_site_fract_y'+
1111	'\n\t_atom_site_fract_z'+
1112	'\n\t_atom_site_occupancy'+
1113	'\n\t_atom_site_adp_type'+
1114	'\n\t_atom_site_U_iso_or_equiv'+
1115	'\n\t_atom_site_symmetry_multiplicity')
1116
1117	varnames = {cx:'Ax',cx+1:'Ay',cx+2:'Az',cx+3:'Afrac',
1118	cia+1:'AUiso',cia+2:'AU11',cia+3:'AU22',cia+4:'AU33',
1119	cia+5:'AU12',cia+6:'AU13',cia+7:'AU23'}
1120	self.labellist = []
1121
1122	pfx = str(phasedict['pId'])+'::'
1123	# loop over all atoms
1124	naniso = 0
1125	for i,at in enumerate(Atoms):
1126	s = PutInCol(MakeUniqueLabel(at[ct-1],self.labellist),6) # label
1127	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
1128	if fval == 0.0: continue # ignore any atoms that have a occupancy set to 0 (exact)
1129	s += PutInCol(FmtAtomType(at[ct]),4) # type
1130	if at[cia] == 'I':
1131	adp = 'Uiso '
1132	else:
1133	adp = 'Uani '
1134	naniso += 1
1135	# compute Uequiv crudely
1136	# correct: Defined as "1/3 trace of diagonalized U matrix".
1137	# SEE cell2GS & Uij2Ueqv to GSASIIlattice. Former is needed to make the GS matrix used by the latter.
1138	t = 0.0
1139	for j in (2,3,4):
1140	var = pfx+varnames[cia+j]+":"+str(i)
1141	t += self.parmDict.get(var,at[cia+j])
1142	for j in (cx,cx+1,cx+2,cx+3,cia,cia+1):
1143	if j in (cx,cx+1,cx+2):
1144	dig = 11
1145	sigdig = -0.00009
1146	else:
1147	dig = 10
1148	sigdig = -0.009
1149	if j == cia:
1150	s += adp
1151	else:
1152	var = pfx+varnames[j]+":"+str(i)
1153	dvar = pfx+"d"+varnames[j]+":"+str(i)
1154	if dvar not in self.sigDict:
1155	dvar = var
1156	if j == cia+1 and adp == 'Uani ':
1157	val = t/3.
1158	sig = sigdig
1159	else:
1160	#print var,(var in self.parmDict),(var in self.sigDict)
1161	val = self.parmDict.get(var,at[j])
1162	sig = self.sigDict.get(dvar,sigdig)
1163	s += PutInCol(G2mth.ValEsd(val,sig),dig)
1164	s += PutInCol(at[cs+1],3)
1165	WriteCIFitem(s)
1166	if naniso == 0: return
1167	# now loop over aniso atoms
1168	WriteCIFitem('\nloop_' + '\n\t_atom_site_aniso_label' +
1169	'\n\t_atom_site_aniso_U_11' + '\n\t_atom_site_aniso_U_12' +
1170	'\n\t_atom_site_aniso_U_13' + '\n\t_atom_site_aniso_U_22' +
1171	'\n\t_atom_site_aniso_U_23' + '\n\t_atom_site_aniso_U_33')
1172	for i,at in enumerate(Atoms):
1173	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
1174	if fval == 0.0: continue # ignore any atoms that have a occupancy set to 0 (exact)
1175	if at[cia] == 'I': continue
1176	s = PutInCol(self.labellist[i],6) # label
1177	for j in (2,3,4,5,6,7):
1178	sigdig = -0.0009
1179	var = pfx+varnames[cia+j]+":"+str(i)
1180	val = self.parmDict.get(var,at[cia+j])
1181	sig = self.sigDict.get(var,sigdig)
1182	s += PutInCol(G2mth.ValEsd(val,sig),11)
1183	WriteCIFitem(s)
1184
1185	def HillSortElements(elmlist):
1186	'''Sort elements in "Hill" order: C, H, others, (where others
1187	are alphabetical).
1188
1189	:params list elmlist: a list of element strings
1190
1191	:returns: a sorted list of element strings
1192	'''
1193	newlist = []
1194	oldlist = elmlist[:]
1195	for elm in ('C','H'):
1196	if elm in elmlist:
1197	newlist.append(elm)
1198	oldlist.pop(oldlist.index(elm))
1199	return newlist+sorted(oldlist)
1200
1201	def WriteComposition(phasenam):
1202	'''determine the composition for the unit cell, crudely determine Z and
1203	then compute the composition in formula units
1204	'''
1205	phasedict = self.Phases[phasenam] # pointer to current phase info
1206	General = phasedict['General']
1207	Z = General.get('cellZ',0.0)
1208	cx,ct,cs,cia = General['AtomPtrs']
1209	Atoms = phasedict['Atoms']
1210	fpfx = str(phasedict['pId'])+'::Afrac:'
1211	cfrac = cx+3
1212	cmult = cs+1
1213	compDict = {} # combines H,D & T
1214	sitemultlist = []
1215	massDict = dict(zip(General['AtomTypes'],General['AtomMass']))
1216	cellmass = 0
1217	for i,at in enumerate(Atoms):
1218	atype = at[ct].strip()
1219	if atype.find('-') != -1: atype = atype.split('-')[0]
1220	if atype.find('+') != -1: atype = atype.split('+')[0]
1221	atype = atype[0].upper()+atype[1:2].lower() # force case conversion
1222	if atype == "D" or atype == "D": atype = "H"
1223	fvar = fpfx+str(i)
1224	fval = self.parmDict.get(fvar,at[cfrac])
1225	mult = at[cmult]
1226	if not massDict.get(at[ct]):
1227	print('Error: No mass found for atom type '+at[ct])
1228	print('Will not compute cell contents for phase '+phasenam)
1229	return
1230	cellmass += massDict[at[ct]]multfval
1231	compDict[atype] = compDict.get(atype,0.0) + mult*fval
1232	if fval == 1: sitemultlist.append(mult)
1233	if len(compDict.keys()) == 0: return # no elements!
1234	if Z < 1: # Z has not been computed or set by user
1235	Z = 1
1236	for i in range(2,min(sitemultlist)+1):
1237	for m in sitemultlist:
1238	if m % i != 0:
1239	break
1240	else:
1241	Z = i
1242	General['cellZ'] = Z # save it
1243
1244	# when scattering factors are included in the CIF, this needs to be
1245	# added to the loop here but only in the one-block case.
1246	# For multiblock CIFs, scattering factors go in the histogram
1247	# blocks (for all atoms in all appropriate phases) - an example?:
1248	#loop_
1249	# _atom_type_symbol
1250	# _atom_type_description
1251	# _atom_type_scat_dispersion_real
1252	# _atom_type_scat_dispersion_imag
1253	# _atom_type_scat_source
1254	# 'C' 'C' 0.0033 0.0016
1255	# 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
1256	# 'H' 'H' 0.0000 0.0000
1257	# 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
1258	# 'P' 'P' 0.1023 0.0942
1259	# 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
1260	# 'Cl' 'Cl' 0.1484 0.1585
1261	# 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
1262	# 'Cu' 'Cu' 0.3201 1.2651
1263	# 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
1264
1265	#if oneblock: # add scattering factors for current phase here
1266	WriteCIFitem('\nloop_ _atom_type_symbol _atom_type_number_in_cell')
1267	formula = ''
1268	reload(G2mth)
1269	for elem in HillSortElements(compDict.keys()):
1270	WriteCIFitem(' ' + PutInCol(elem,4) +
1271	G2mth.ValEsd(compDict[elem],-0.009,True))
1272	if formula: formula += " "
1273	formula += elem
1274	if compDict[elem] == Z: continue
1275	formula += G2mth.ValEsd(compDict[elem]/Z,-0.009,True)
1276	WriteCIFitem( '\n# Note that Z affects _cell_formula_sum and _weight')
1277	WriteCIFitem( '_cell_formula_units_Z',str(Z))
1278	WriteCIFitem( '_chemical_formula_sum',formula)
1279	WriteCIFitem( '_chemical_formula_weight',
1280	G2mth.ValEsd(cellmass/Z,-0.09,True))
1281
1282	def WriteDistances(phasenam,SymOpList,offsetList,symOpList,G2oprList):
1283	'''Report bond distances and angles for the CIF
1284
1285	Note that _geom__symmetry_ fields are values of form
1286	n_klm where n is the symmetry operation in SymOpList (counted
1287	starting with 1) and (k-5, l-5, m-5) are translations to add
1288	to (x,y,z). See
1289	http://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Igeom_angle_site_symmetry_.html
1290
1291	TODO: need a method to select publication flags for distances/angles
1292	'''
1293	phasedict = self.Phases[phasenam] # pointer to current phase info
1294	Atoms = phasedict['Atoms']
1295	generalData = phasedict['General']
1296	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
1297	cn = ct-1
1298	fpfx = str(phasedict['pId'])+'::Afrac:'
1299	cfrac = cx+3
1300	DisAglData = {}
1301	DisAglCtls = {}
1302	# create a list of atoms, but skip atoms with zero occupancy
1303	xyz = []
1304	fpfx = str(phasedict['pId'])+'::Afrac:'
1305	for i,atom in enumerate(Atoms):
1306	if self.parmDict.get(fpfx+str(i),atom[cfrac]) == 0.0: continue
1307	xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3])
1308	if 'DisAglCtls' in generalData:
1309	DisAglCtls = generalData['DisAglCtls']
1310	else:
1311	dlg = G2gd.DisAglDialog(self.G2frame,DisAglCtls,generalData)
1312	if dlg.ShowModal() == wx.ID_OK:
1313	DisAglCtls = dlg.GetData()
1314	generalData['DisAglCtls'] = DisAglCtls
1315	else:
1316	dlg.Destroy()
1317	return
1318	dlg.Destroy()
1319	DisAglData['OrigAtoms'] = xyz
1320	DisAglData['TargAtoms'] = xyz
1321	SymOpList,offsetList,symOpList,G2oprList = G2spc.AllOps(
1322	generalData['SGData'])
1323
1324	xpandSGdata = generalData['SGData'].copy()
1325	xpandSGdata.update({'SGOps':symOpList,
1326	'SGInv':False,
1327	'SGLatt':'P',
1328	'SGCen':np.array([[0, 0, 0]]),})
1329	DisAglData['SGData'] = xpandSGdata
1330
1331	DisAglData['Cell'] = generalData['Cell'][1:] #+ volume
1332	if 'pId' in phasedict:
1333	DisAglData['pId'] = phasedict['pId']
1334	DisAglData['covData'] = self.OverallParms['Covariance']
1335	try:
1336	AtomLabels,DistArray,AngArray = G2stMn.RetDistAngle(DisAglCtls,DisAglData)
1337	except KeyError: # inside DistAngle for missing atom types in DisAglCtls
1338	print('** ERROR - try again but do "Reset" to fill in missing atom types **')
1339
1340	# loop over interatomic distances for this phase
1341	WriteCIFitem('\n# MOLECULAR GEOMETRY')
1342	WriteCIFitem('loop_' +
1343	'\n\t_geom_bond_atom_site_label_1' +
1344	'\n\t_geom_bond_atom_site_label_2' +
1345	'\n\t_geom_bond_distance' +
1346	'\n\t_geom_bond_site_symmetry_1' +
1347	'\n\t_geom_bond_site_symmetry_2' +
1348	'\n\t_geom_bond_publ_flag')
1349
1350	for i in sorted(AtomLabels.keys()):
1351	Dist = DistArray[i]
1352	for D in Dist:
1353	line = ' '+PutInCol(AtomLabels[i],6)+PutInCol(AtomLabels[D[0]],6)
1354	sig = D[4]
1355	if sig == 0: sig = -0.00009
1356	line += PutInCol(G2mth.ValEsd(D[3],sig,True),10)
1357	line += " 1_555 "
1358	line += " {:3d}_".format(D[2])
1359	for d in D[1]:
1360	line += "{:1d}".format(d+5)
1361	line += " yes"
1362	WriteCIFitem(line)
1363
1364	# loop over interatomic angles for this phase
1365	WriteCIFitem('\nloop_' +
1366	'\n\t_geom_angle_atom_site_label_1' +
1367	'\n\t_geom_angle_atom_site_label_2' +
1368	'\n\t_geom_angle_atom_site_label_3' +
1369	'\n\t_geom_angle' +
1370	'\n\t_geom_angle_site_symmetry_1' +
1371	'\n\t_geom_angle_site_symmetry_2' +
1372	'\n\t_geom_angle_site_symmetry_3' +
1373	'\n\t_geom_angle_publ_flag')
1374
1375	for i in sorted(AtomLabels.keys()):
1376	Dist = DistArray[i]
1377	for k,j,tup in AngArray[i]:
1378	Dj = Dist[j]
1379	Dk = Dist[k]
1380	line = ' '+PutInCol(AtomLabels[Dj[0]],6)+PutInCol(AtomLabels[i],6)+PutInCol(AtomLabels[Dk[0]],6)
1381	sig = tup[1]
1382	if sig == 0: sig = -0.009
1383	line += PutInCol(G2mth.ValEsd(tup[0],sig,True),10)
1384	line += " {:3d}_".format(Dj[2])
1385	for d in Dj[1]:
1386	line += "{:1d}".format(d+5)
1387	line += " 1_555 "
1388	line += " {:3d}_".format(Dk[2])
1389	for d in Dk[1]:
1390	line += "{:1d}".format(d+5)
1391	line += " yes"
1392	WriteCIFitem(line)
1393
1394	def WritePhaseInfo(phasenam):
1395	WriteCIFitem('\n# phase info for '+str(phasenam) + ' follows')
1396	phasedict = self.Phases[phasenam] # pointer to current phase info
1397	WriteCIFitem('_pd_phase_name', phasenam)
1398	pfx = str(phasedict['pId'])+'::'
1399	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
1400	cellSig = G2stIO.getCellEsd(pfx,
1401	phasedict['General']['SGData'],A,
1402	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
1403	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
1404	defsigL = 3[-0.00001] + 3[-0.001] + [-0.01] # significance to use when no sigma
1405	names = ['length_a','length_b','length_c',
1406	'angle_alpha','angle_beta ','angle_gamma',
1407	'volume']
1408	prevsig = 0
1409	for lbl,defsig,val,sig in zip(names,defsigL,cellList,cellSig):
1410	if sig:
1411	txt = G2mth.ValEsd(val,sig)
1412	prevsig = -sig # use this as the significance for next value
1413	else:
1414	txt = G2mth.ValEsd(val,min(defsig,prevsig),True)
1415	WriteCIFitem('_cell_'+lbl,txt)
1416
1417	WriteCIFitem('_symmetry_cell_setting',
1418	phasedict['General']['SGData']['SGSys'])
1419
1420	spacegroup = phasedict['General']['SGData']['SpGrp'].strip()
1421	# regularize capitalization and remove trailing H/R
1422	spacegroup = spacegroup[0].upper() + spacegroup[1:].lower().rstrip('rh ')
1423	WriteCIFitem('_symmetry_space_group_name_H-M',spacegroup)
1424
1425	# generate symmetry operations including centering and center of symmetry
1426	SymOpList,offsetList,symOpList,G2oprList = G2spc.AllOps(
1427	phasedict['General']['SGData'])
1428	WriteCIFitem('loop_\n _space_group_symop_id\n _space_group_symop_operation_xyz')
1429	for i,op in enumerate(SymOpList,start=1):
1430	WriteCIFitem(' {:3d} {:}'.format(i,op.lower()))
1431
1432	# loop over histogram(s) used in this phase
1433	if not oneblock and not self.quickmode:
1434	# report pointers to the histograms used in this phase
1435	histlist = []
1436	for hist in self.Phases[phasenam]['Histograms']:
1437	if self.Phases[phasenam]['Histograms'][hist]['Use']:
1438	if phasebyhistDict.get(hist):
1439	phasebyhistDict[hist].append(phasenam)
1440	else:
1441	phasebyhistDict[hist] = [phasenam,]
1442	blockid = datablockidDict.get(hist)
1443	if not blockid:
1444	print("Internal error: no block for data. Phase "+str(
1445	phasenam)+" histogram "+str(hist))
1446	histlist = []
1447	break
1448	histlist.append(blockid)
1449
1450	if len(histlist) == 0:
1451	WriteCIFitem('# Note: phase has no associated data')
1452
1453	# report atom params
1454	if phasedict['General']['Type'] == 'nuclear': #this needs macromolecular variant, etc!
1455	WriteAtomsNuclear(phasenam)
1456	else:
1457	raise Exception,"no export for mm coordinates implemented"
1458	# report cell contents
1459	WriteComposition(phasenam)
1460	if not self.quickmode: # report distances and angles
1461	WriteDistances(phasenam,SymOpList,offsetList,symOpList,G2oprList)
1462
1463	def Yfmt(ndec,val):
1464	'Format intensity values'
1465	out = ("{:."+str(ndec)+"f}").format(val)
1466	out = out.rstrip('0') # strip zeros to right of decimal
1467	return out.rstrip('.') # and decimal place when not needed
1468
1469	def WriteReflStat(refcount,hklmin,hklmax,dmin,dmax,nRefSets=1):
1470	WriteCIFitem('_reflns_number_total', str(refcount))
1471	if hklmin is not None and nRefSets == 1: # hkl range has no meaning with multiple phases
1472	WriteCIFitem('_reflns_limit_h_min', str(int(hklmin[0])))
1473	WriteCIFitem('_reflns_limit_h_max', str(int(hklmax[0])))
1474	WriteCIFitem('_reflns_limit_k_min', str(int(hklmin[1])))
1475	WriteCIFitem('_reflns_limit_k_max', str(int(hklmax[1])))
1476	WriteCIFitem('_reflns_limit_l_min', str(int(hklmin[2])))
1477	WriteCIFitem('_reflns_limit_l_max', str(int(hklmax[2])))
1478	if hklmin is not None:
1479	WriteCIFitem('_reflns_d_resolution_low ', G2mth.ValEsd(dmax,-0.009))
1480	WriteCIFitem('_reflns_d_resolution_high ', G2mth.ValEsd(dmin,-0.009))
1481
1482	def WritePowderData(histlbl):
1483	histblk = self.Histograms[histlbl]
1484	inst = histblk['Instrument Parameters'][0]
1485	hId = histblk['hId']
1486	pfx = ':' + str(hId) + ':'
1487
1488	if 'Lam1' in inst:
1489	ratio = self.parmDict.get('I(L2)/I(L1)',inst['I(L2)/I(L1)'][1])
1490	sratio = self.sigDict.get('I(L2)/I(L1)',-0.0009)
1491	lam1 = self.parmDict.get('Lam1',inst['Lam1'][1])
1492	slam1 = self.sigDict.get('Lam1',-0.00009)
1493	lam2 = self.parmDict.get('Lam2',inst['Lam2'][1])
1494	slam2 = self.sigDict.get('Lam2',-0.00009)
1495	# always assume Ka1 & Ka2 if two wavelengths are present
1496	WriteCIFitem('_diffrn_radiation_type','K\\a~1,2~')
1497	WriteCIFitem('loop_' +
1498	'\n\t_diffrn_radiation_wavelength' +
1499	'\n\t_diffrn_radiation_wavelength_wt' +
1500	'\n\t_diffrn_radiation_wavelength_id')
1501	WriteCIFitem(' ' + PutInCol(G2mth.ValEsd(lam1,slam1),15)+
1502	PutInCol('1.0',15) +
1503	PutInCol('1',5))
1504	WriteCIFitem(' ' + PutInCol(G2mth.ValEsd(lam2,slam2),15)+
1505	PutInCol(G2mth.ValEsd(ratio,sratio),15)+
1506	PutInCol('2',5))
1507	else:
1508	lam1 = self.parmDict.get('Lam',inst['Lam'][1])
1509	slam1 = self.sigDict.get('Lam',-0.00009)
1510	WriteCIFitem('_diffrn_radiation_wavelength',G2mth.ValEsd(lam1,slam1))
1511
1512	if not oneblock:
1513	if not phasebyhistDict.get(histlbl):
1514	WriteCIFitem('\n# No phases associated with this data set')
1515	else:
1516	WriteCIFitem('\n# PHASE TABLE')
1517	WriteCIFitem('loop_' +
1518	'\n\t_pd_phase_id' +
1519	'\n\t_pd_phase_block_id' +
1520	'\n\t_pd_phase_mass_%')
1521	wtFrSum = 0.
1522	for phasenam in phasebyhistDict.get(histlbl):
1523	hapData = self.Phases[phasenam]['Histograms'][histlbl]
1524	General = self.Phases[phasenam]['General']
1525	wtFrSum += hapData['Scale'][0]*General['Mass']
1526
1527	for phasenam in phasebyhistDict.get(histlbl):
1528	hapData = self.Phases[phasenam]['Histograms'][histlbl]
1529	General = self.Phases[phasenam]['General']
1530	wtFr = hapData['Scale'][0]*General['Mass']/wtFrSum
1531	pfx = str(self.Phases[phasenam]['pId'])+':'+str(hId)+':'
1532	if pfx+'Scale' in self.sigDict:
1533	sig = self.sigDict[pfx+'Scale']*wtFr/hapData['Scale'][0]
1534	else:
1535	sig = -0.0001
1536	WriteCIFitem(
1537	' '+
1538	str(self.Phases[phasenam]['pId']) +
1539	' '+datablockidDict[phasenam]+
1540	' '+G2mth.ValEsd(wtFr,sig)
1541	)
1542	WriteCIFitem('loop_' +
1543	'\n\t_gsas_proc_phase_R_F_factor' +
1544	'\n\t_gsas_proc_phase_R_Fsqd_factor' +
1545	'\n\t_gsas_proc_phase_id' +
1546	'\n\t_gsas_proc_phase_block_id')
1547	for phasenam in phasebyhistDict.get(histlbl):
1548	pfx = str(self.Phases[phasenam]['pId'])+':'+str(hId)+':'
1549	WriteCIFitem(
1550	' '+
1551	' '+G2mth.ValEsd(histblk[pfx+'Rf']/100.,-.00009) +
1552	' '+G2mth.ValEsd(histblk[pfx+'Rf^2']/100.,-.00009)+
1553	' '+str(self.Phases[phasenam]['pId'])+
1554	' '+datablockidDict[phasenam]
1555	)
1556	else:
1557	# single phase in this histogram
1558	pfx = '0:'+str(hId)+':'
1559	WriteCIFitem('_refine_ls_R_F_factor ','%.5f'%(histblk[pfx+'Rf']/100.))
1560	WriteCIFitem('_refine_ls_R_Fsqd_factor ','%.5f'%(histblk[pfx+'Rf^2']/100.))
1561
1562	WriteCIFitem('_pd_proc_ls_prof_R_factor ','%.5f'%(histblk['R']/100.))
1563	WriteCIFitem('_pd_proc_ls_prof_wR_factor ','%.5f'%(histblk['wR']/100.))
1564	WriteCIFitem('_gsas_proc_ls_prof_R_B_factor ','%.5f'%(histblk['Rb']/100.))
1565	WriteCIFitem('_gsas_proc_ls_prof_wR_B_factor','%.5f'%(histblk['wRb']/100.))
1566	WriteCIFitem('_pd_proc_ls_prof_wR_expected','%.5f'%(histblk['wRmin']/100.))
1567
1568	if histblk['Instrument Parameters'][0]['Type'][1][1] == 'X':
1569	WriteCIFitem('_diffrn_radiation_probe','x-ray')
1570	pola = histblk['Instrument Parameters'][0].get('Polariz.')
1571	if pola:
1572	pfx = ':' + str(hId) + ':'
1573	sig = self.sigDict.get(pfx+'Polariz.',-0.0009)
1574	txt = G2mth.ValEsd(pola[1],sig)
1575	WriteCIFitem('_diffrn_radiation_polarisn_ratio',txt)
1576	elif histblk['Instrument Parameters'][0]['Type'][1][1] == 'N':
1577	WriteCIFitem('_diffrn_radiation_probe','neutron')
1578	# TOF (note that this may not be defined)
1579	#if histblk['Instrument Parameters'][0]['Type'][1][2] == 'T':
1580	# WriteCIFitem('_pd_meas_2theta_fixed',text)
1581
1582
1583	# TODO: this will need help from Bob
1584	#if not oneblock:
1585	#WriteCIFitem('\n# SCATTERING FACTOR INFO')
1586	#WriteCIFitem('loop_ _atom_type_symbol')
1587	#if histblk['Instrument Parameters'][0]['Type'][1][1] == 'X':
1588	# WriteCIFitem(' _atom_type_scat_dispersion_real')
1589	# WriteCIFitem(' _atom_type_scat_dispersion_imag')
1590	# for lbl in ('a1','a2','a3', 'a4', 'b1', 'b2', 'b3', 'b4', 'c'):
1591	# WriteCIFitem(' _atom_type_scat_Cromer_Mann_'+lbl)
1592	#elif histblk['Instrument Parameters'][0]['Type'][1][1] == 'N':
1593	# WriteCIFitem(' _atom_type_scat_length_neutron')
1594	#WriteCIFitem(' _atom_type_scat_source')
1595
1596	WriteCIFitem('_pd_proc_ls_background_function',FormatBackground(histblk['Background'],histblk['hId']))
1597
1598	# TODO: this will need help from Bob
1599	#WriteCIFitem('_exptl_absorpt_process_details','?')
1600	#WriteCIFitem('_exptl_absorpt_correction_T_min','?')
1601	#WriteCIFitem('_exptl_absorpt_correction_T_max','?')
1602	#C extinction
1603	#WRITE(IUCIF,'(A)') '# Extinction correction'
1604	#CALL WRVAL(IUCIF,'_gsas_exptl_extinct_corr_T_min',TEXT(1:10))
1605	#CALL WRVAL(IUCIF,'_gsas_exptl_extinct_corr_T_max',TEXT(11:20))
1606
1607	if not oneblock: # instrumental profile terms go here
1608	WriteCIFitem('_pd_proc_ls_profile_function',
1609	FormatInstProfile(histblk["Instrument Parameters"],histblk['hId']))
1610
1611	#refprx = '_refln.' # mm
1612	refprx = '_refln_' # normal
1613	WriteCIFitem('\n# STRUCTURE FACTOR TABLE')
1614	# compute maximum intensity reflection
1615	Imax = 0
1616	for phasenam in histblk['Reflection Lists']:
1617	scale = self.Phases[phasenam]['Histograms'][histlbl]['Scale'][0]
1618	Icorr = np.array([refl[13] for refl in histblk['Reflection Lists'][phasenam]])[0]
1619	FO2 = np.array([refl[8] for refl in histblk['Reflection Lists'][phasenam]])
1620	I100 = scaleFO2Icorr
1621	Imax = max(Imax,max(I100))
1622
1623	WriteCIFitem('loop_')
1624	if len(histblk['Reflection Lists'].keys()) > 1:
1625	WriteCIFitem('\t_pd_refln_phase_id')
1626	WriteCIFitem('\t' + refprx + 'index_h' +
1627	'\n\t' + refprx + 'index_k' +
1628	'\n\t' + refprx + 'index_l' +
1629	'\n\t' + refprx + 'F_squared_meas' +
1630	'\n\t' + refprx + 'F_squared_calc' +
1631	'\n\t' + refprx + 'phase_calc' +
1632	'\n\t_pd_refln_d_spacing')
1633	if Imax > 0:
1634	WriteCIFitem('\t_gsas_i100_meas')
1635
1636	refcount = 0
1637	hklmin = None
1638	hklmax = None
1639	dmax = None
1640	dmin = None
1641	for phasenam in histblk['Reflection Lists']:
1642	scale = self.Phases[phasenam]['Histograms'][histlbl]['Scale'][0]
1643	phaseid = self.Phases[phasenam]['pId']
1644	refcount += len(histblk['Reflection Lists'][phasenam])
1645	for ref in histblk['Reflection Lists'][phasenam]:
1646	if DEBUG:
1647	print('DEBUG: skipping reflection list')
1648	break
1649	if hklmin is None:
1650	hklmin = ref[0:3]
1651	hklmax = ref[0:3]
1652	dmax = dmin = ref[4]
1653	if len(histblk['Reflection Lists'].keys()) > 1:
1654	s = PutInCol(phaseid,2)
1655	else:
1656	s = ""
1657	for i,hkl in enumerate(ref[0:3]):
1658	hklmax[i] = max(hkl,hklmax[i])
1659	hklmin[i] = min(hkl,hklmin[i])
1660	s += PutInCol(int(hkl),4)
1661	for I in ref[8:10]:
1662	s += PutInCol(G2mth.ValEsd(I,-0.0009),10)
1663	s += PutInCol(G2mth.ValEsd(ref[10],-0.9),7)
1664	dmax = max(dmax,ref[4])
1665	dmin = min(dmin,ref[4])
1666	s += PutInCol(G2mth.ValEsd(ref[4],-0.009),8)
1667	if Imax > 0:
1668	I100 = 100.scaleref[8]*ref[13]/Imax
1669	s += PutInCol(G2mth.ValEsd(I100,-0.09),6)
1670	WriteCIFitem(" "+s)
1671
1672	WriteReflStat(refcount,hklmin,hklmax,dmin,dmax,len(histblk['Reflection Lists']))
1673	WriteCIFitem('\n# POWDER DATA TABLE')
1674	# is data fixed step? If the step varies by <0.01% treat as fixed step
1675	steps = histblk['Data'][0][1:] - histblk['Data'][0][:-1]
1676	if abs(max(steps)-min(steps)) > abs(max(steps))/10000.:
1677	fixedstep = False
1678	else:
1679	fixedstep = True
1680
1681	if fixedstep: # and not TOF
1682	WriteCIFitem('_pd_meas_2theta_range_min', G2mth.ValEsd(histblk['Data'][0][0],-0.00009))
1683	WriteCIFitem('_pd_meas_2theta_range_max', G2mth.ValEsd(histblk['Data'][0][-1],-0.00009))
1684	WriteCIFitem('_pd_meas_2theta_range_inc', G2mth.ValEsd(steps.sum()/len(steps),-0.00009))
1685	# zero correct, if defined
1686	zero = None
1687	zerolst = histblk['Instrument Parameters'][0].get('Zero')
1688	if zerolst: zero = zerolst[1]
1689	zero = self.parmDict.get('Zero',zero)
1690	if zero:
1691	WriteCIFitem('_pd_proc_2theta_range_min', G2mth.ValEsd(histblk['Data'][0][0]-zero,-0.00009))
1692	WriteCIFitem('_pd_proc_2theta_range_max', G2mth.ValEsd(histblk['Data'][0][-1]-zero,-0.00009))
1693	WriteCIFitem('_pd_proc_2theta_range_inc', G2mth.ValEsd(steps.sum()/len(steps),-0.00009))
1694
1695	if zero:
1696	WriteCIFitem('_pd_proc_number_of_points', str(len(histblk['Data'][0])))
1697	else:
1698	WriteCIFitem('_pd_meas_number_of_points', str(len(histblk['Data'][0])))
1699	WriteCIFitem('\nloop_')
1700	# WriteCIFitem('\t_pd_proc_d_spacing') # need easy way to get this
1701	if not fixedstep:
1702	if zero:
1703	WriteCIFitem('\t_pd_proc_2theta_corrected')
1704	else:
1705	WriteCIFitem('\t_pd_meas_2theta_scan')
1706	# at least for now, always report weights.
1707	#if countsdata:
1708	# WriteCIFitem('\t_pd_meas_counts_total')
1709	#else:
1710	WriteCIFitem('\t_pd_meas_intensity_total')
1711	WriteCIFitem('\t_pd_calc_intensity_total')
1712	WriteCIFitem('\t_pd_proc_intensity_bkg_calc')
1713	WriteCIFitem('\t_pd_proc_ls_weight')
1714	maxY = max(histblk['Data'][1].max(),histblk['Data'][3].max())
1715	if maxY < 0: maxY *= -10 # this should never happen, but...
1716	ndec = max(0,10-int(np.log10(maxY))-1) # 10 sig figs should be enough
1717	maxSU = histblk['Data'][2].max()
1718	if maxSU < 0: maxSU *= -1 # this should never happen, but...
1719	ndecSU = max(0,8-int(np.log10(maxSU))-1) # 8 sig figs should be enough
1720	lowlim,highlim = histblk['Limits'][1]
1721
1722	if DEBUG:
1723	print('DEBUG: skipping profile list')
1724	else:
1725	for x,yobs,yw,ycalc,ybkg in zip(histblk['Data'][0],
1726	histblk['Data'][1],
1727	histblk['Data'][2],
1728	histblk['Data'][3],
1729	histblk['Data'][4]):
1730	if lowlim <= x <= highlim:
1731	pass
1732	else:
1733	yw = 0.0 # show the point is not in use
1734
1735	if fixedstep:
1736	s = ""
1737	else:
1738	s = PutInCol(G2mth.ValEsd(x-zero,-0.00009),10)
1739	s += PutInCol(Yfmt(ndec,yobs),12)
1740	s += PutInCol(Yfmt(ndec,ycalc),12)
1741	s += PutInCol(Yfmt(ndec,ybkg),11)
1742	s += PutInCol(Yfmt(ndecSU,yw),9)
1743	WriteCIFitem(" "+s)
1744
1745	def WriteSingleXtalData(histlbl):
1746	histblk = self.Histograms[histlbl]
1747	#refprx = '_refln.' # mm
1748	refprx = '_refln_' # normal
1749
1750	WriteCIFitem('\n# STRUCTURE FACTOR TABLE')
1751	WriteCIFitem('loop_' +
1752	'\n\t' + refprx + 'index_h' +
1753	'\n\t' + refprx + 'index_k' +
1754	'\n\t' + refprx + 'index_l' +
1755	'\n\t' + refprx + 'F_squared_meas' +
1756	'\n\t' + refprx + 'F_squared_sigma' +
1757	'\n\t' + refprx + 'F_squared_calc' +
1758	'\n\t' + refprx + 'phase_calc'
1759	)
1760
1761	hklmin = None
1762	hklmax = None
1763	dmax = None
1764	dmin = None
1765	refcount = len(histblk['Data'])
1766	for ref in histblk['Data']:
1767	s = " "
1768	if hklmin is None:
1769	hklmin = ref[0:3]
1770	hklmax = ref[0:3]
1771	dmax = dmin = ref[4]
1772	for i,hkl in enumerate(ref[0:3]):
1773	hklmax[i] = max(hkl,hklmax[i])
1774	hklmin[i] = min(hkl,hklmin[i])
1775	s += PutInCol(int(hkl),4)
1776	sig = ref[6] * ref[8] / ref[5]
1777	s += PutInCol(G2mth.ValEsd(ref[8],-abs(sig/10)),12)
1778	s += PutInCol(G2mth.ValEsd(sig,-abs(sig)/10.),10)
1779	s += PutInCol(G2mth.ValEsd(ref[9],-abs(sig/10)),12)
1780	s += PutInCol(G2mth.ValEsd(ref[10],-0.9),7)
1781	dmax = max(dmax,ref[4])
1782	dmin = min(dmin,ref[4])
1783	WriteCIFitem(s)
1784	WriteReflStat(refcount,hklmin,hklmax,dmin,dmax)
1785	hId = histblk['hId']
1786	pfx = '0:'+str(hId)+':'
1787	WriteCIFitem('_reflns_wR_factor_obs ','%.4f'%(histblk['wR']/100.))
1788	WriteCIFitem('_reflns_R_F_factor_obs ','%.4f'%(histblk[pfx+'Rf']/100.))
1789	WriteCIFitem('_reflns_R_Fsqd_factor_obs','%.4f'%(histblk[pfx+'Rf^2']/100.))
1790	def EditAuthor(event=None):
1791	'Edit the CIF author name'
1792	dlg = G2gd.SingleStringDialog(self.G2frame,
1793	'Get CIF Author',
1794	'Provide CIF Author name (Last, First)',
1795	value=self.author)
1796	if not dlg.Show():
1797	dlg.Destroy()
1798	return False # cancel was pressed
1799	self.author = dlg.GetValue()
1800	dlg.Destroy()
1801	try:
1802	self.OverallParms['Controls']["Author"] = self.author # save for future
1803	except KeyError:
1804	pass
1805	return True
1806	def EditInstNames(event=None):
1807	'Provide a dialog for editing instrument names'
1808	dictlist = []
1809	keylist = []
1810	lbllist = []
1811	for hist in self.Histograms:
1812	if hist.startswith("PWDR"):
1813	key2 = "Sample Parameters"
1814	d = self.Histograms[hist][key2]
1815	elif hist.startswith("HKLF"):
1816	key2 = "Instrument Parameters"
1817	d = self.Histograms[hist][key2][0]
1818
1819	lbllist.append(hist)
1820	dictlist.append(d)
1821	keylist.append('InstrName')
1822	instrname = d.get('InstrName')
1823	if instrname is None:
1824	d['InstrName'] = ''
1825	return G2gd.CallScrolledMultiEditor(
1826	self.G2frame,dictlist,keylist,
1827	prelbl=range(1,len(dictlist)+1),
1828	postlbl=lbllist,
1829	title='Instrument names',
1830	header="Edit instrument names. Note that a non-blank\nname is required for all histograms",
1831	CopyButton=True)
1832
1833	def EditRanges(event):
1834	but = event.GetEventObject()
1835	phasedict = but.phasedict
1836	dlg = G2gd.DisAglDialog(self.G2frame,{},phasedict['General'])
1837	if dlg.ShowModal() == wx.ID_OK:
1838	phasedict['General']['DisAglCtls'] = dlg.GetData()
1839	dlg.Destroy()
1840
1841	def EditCIFDefaults():
1842	'Fills the CIF Defaults window'
1843	import wx.lib.scrolledpanel as wxscroll
1844	self.cifdefs.DestroyChildren()
1845	self.cifdefs.SetTitle('Edit CIF settings')
1846	vbox = wx.BoxSizer(wx.VERTICAL)
1847	but = wx.Button(self.cifdefs, wx.ID_ANY,'Edit CIF Author')
1848	but.Bind(wx.EVT_BUTTON,EditAuthor)
1849	vbox.Add(but,0,wx.ALIGN_CENTER,3)
1850	but = wx.Button(self.cifdefs, wx.ID_ANY,'Edit Instrument Name(s)')
1851	but.Bind(wx.EVT_BUTTON,EditInstNames)
1852	vbox.Add(but,0,wx.ALIGN_CENTER,3)
1853	cpnl = wxscroll.ScrolledPanel(self.cifdefs,size=(300,300))
1854	cbox = wx.BoxSizer(wx.VERTICAL)
1855	G2gd.HorizontalLine(cbox,cpnl)
1856	cbox.Add(
1857	CIFtemplateSelect(self.cifdefs,
1858	cpnl,'publ',self.OverallParms['Controls'],
1859	EditCIFDefaults,
1860	"Publication (overall) template",
1861	),
1862	0,wx.EXPAND\|wx.ALIGN_LEFT\|wx.ALL)
1863	for phasenam in sorted(self.Phases.keys()):
1864	G2gd.HorizontalLine(cbox,cpnl)
1865	title = 'Phase '+phasenam
1866	phasedict = self.Phases[phasenam] # pointer to current phase info
1867	cbox.Add(
1868	CIFtemplateSelect(self.cifdefs,
1869	cpnl,'phase',phasedict['General'],
1870	EditCIFDefaults,
1871	title,
1872	phasenam),
1873	0,wx.EXPAND\|wx.ALIGN_LEFT\|wx.ALL)
1874	cpnl.SetSizer(cbox)
1875	but = wx.Button(cpnl, wx.ID_ANY,'Edit distance/angle ranges')
1876	#cbox.Add(but,0,wx.ALIGN_CENTER,3)
1877	cbox.Add((-1,2))
1878	cbox.Add(but,0,wx.ALIGN_LEFT,0)
1879	but.phasedict = self.Phases[phasenam] # set a pointer to current phase info
1880	but.Bind(wx.EVT_BUTTON,EditRanges) # phase bond/angle ranges
1881	for i in sorted(self.powderDict.keys()):
1882	G2gd.HorizontalLine(cbox,cpnl)
1883	hist = self.powderDict[i]
1884	histblk = self.Histograms[hist]
1885	title = 'Powder dataset '+hist[5:]
1886	cbox.Add(
1887	CIFtemplateSelect(self.cifdefs,
1888	cpnl,'powder',histblk["Sample Parameters"],
1889	EditCIFDefaults,
1890	title,
1891	histblk["Sample Parameters"]['InstrName']),
1892	0,wx.EXPAND\|wx.ALIGN_LEFT\|wx.ALL)
1893	cpnl.SetSizer(cbox)
1894	for i in sorted(self.xtalDict.keys()):
1895	G2gd.HorizontalLine(cbox,cpnl)
1896	hist = self.xtalDict[i]
1897	histblk = self.Histograms[hist]
1898	title = 'Single Xtal dataset '+hist[5:]
1899	cbox.Add(
1900	CIFtemplateSelect(self.cifdefs,
1901	cpnl,'single',histblk["Instrument Parameters"][0],
1902	EditCIFDefaults,
1903	title,
1904	histblk["Instrument Parameters"][0]['InstrName']),
1905	0,wx.EXPAND\|wx.ALIGN_LEFT\|wx.ALL)
1906	cpnl.SetSizer(cbox)
1907
1908	cpnl.SetAutoLayout(1)
1909	cpnl.SetupScrolling()
1910	#cpnl.Bind(rw.EVT_RW_LAYOUT_NEEDED, self.OnLayoutNeeded) # needed if sizes change
1911	cpnl.Layout()
1912
1913	vbox.Add(cpnl, 1, wx.ALIGN_LEFT\|wx.ALL\|wx.EXPAND, 0)
1914	btnsizer = wx.StdDialogButtonSizer()
1915	btn = wx.Button(self.cifdefs, wx.ID_OK, "Create CIF")
1916	btn.SetDefault()
1917	btnsizer.AddButton(btn)
1918	btn = wx.Button(self.cifdefs, wx.ID_CANCEL)
1919	btnsizer.AddButton(btn)
1920	btnsizer.Realize()
1921	vbox.Add(btnsizer, 0, wx.ALIGN_CENTER\|wx.ALL, 5)
1922	self.cifdefs.SetSizer(vbox)
1923	vbox.Fit(self.cifdefs)
1924	self.cifdefs.Layout()
1925
1926	# ===== end of functions for export method =======================================
1927	#=================================================================================
1928
1929	# the export process starts here
1930	# load all of the tree into a set of dicts
1931	self.loadTree()
1932	# create a dict with refined values and their uncertainties
1933	self.loadParmDict()
1934
1935	# Someday: get restraint & constraint info
1936	#restraintDict = self.OverallParms.get('Restraints',{})
1937	#for i in self.OverallParms['Constraints']:
1938	# print i
1939	# for j in self.OverallParms['Constraints'][i]:
1940	# print j
1941
1942	self.CIFdate = dt.datetime.strftime(dt.datetime.now(),"%Y-%m-%dT%H:%M")
1943	# index powder and single crystal histograms
1944	self.powderDict = {}
1945	self.xtalDict = {}
1946	for hist in self.Histograms:
1947	i = self.Histograms[hist]['hId']
1948	if hist.startswith("PWDR"):
1949	self.powderDict[i] = hist
1950	elif hist.startswith("HKLF"):
1951	self.xtalDict[i] = hist
1952	# is there anything to export?
1953	if len(self.Phases) == len(self.powderDict) == len(self.xtalDict) == 0:
1954	self.G2frame.ErrorDialog(
1955	'Empty project',
1956	'Project does not contain interconnected data & phase(s)')
1957	return
1958	# get the project file name
1959	self.CIFname = os.path.splitext(
1960	os.path.split(self.G2frame.GSASprojectfile)[1]
1961	)[0]
1962	self.CIFname = self.CIFname.replace(' ','')
1963	if not self.CIFname: # none defined & needed, save as GPX to get one
1964	self.G2frame.OnFileSaveas(None)
1965	if not self.G2frame.GSASprojectfile: return
1966	self.CIFname = os.path.splitext(
1967	os.path.split(self.G2frame.GSASprojectfile)[1]
1968	)[0]
1969	self.CIFname = self.CIFname.replace(' ','')
1970	# test for quick CIF mode or no data
1971	self.quickmode = False
1972	phasenam = phasenum = None # include all phases
1973	if mode != "full" or len(self.powderDict) + len(self.xtalDict) == 0:
1974	self.quickmode = True
1975	oneblock = True
1976	if len(self.Phases) == 0:
1977	self.G2frame.ErrorDialog(
1978	'No phase present',
1979	'Cannot create a coordinates CIF with no phases')
1980	return
1981	elif len(self.Phases) > 1: # quick mode: choose one phase
1982	choices = sorted(self.Phases.keys())
1983	phasenum = G2gd.ItemSelector(choices,self.G2frame)
1984	if phasenum is None: return
1985	phasenam = choices[phasenum]
1986	# will this require a multiblock CIF?
1987	elif len(self.Phases) > 1:
1988	oneblock = False
1989	elif len(self.powderDict) + len(self.xtalDict) > 1:
1990	oneblock = False
1991	else: # one phase, one dataset, Full CIF
1992	oneblock = True
1993
1994	# make sure needed infomation is present
1995	# get CIF author name -- required for full CIFs
1996	try:
1997	self.author = self.OverallParms['Controls'].get("Author",'').strip()
1998	except KeyError:
1999	pass
2000	while not (self.author or self.quickmode):
2001	if not EditAuthor(): return
2002	self.shortauthorname = self.author.replace(',','').replace(' ','')[:20]
2003
2004	# check there is an instrument name for every histogram
2005	if not self.quickmode:
2006	invalid = 0
2007	key3 = 'InstrName'
2008	for hist in self.Histograms:
2009	if hist.startswith("PWDR"):
2010	key2 = "Sample Parameters"
2011	d = self.Histograms[hist][key2]
2012	elif hist.startswith("HKLF"):
2013	key2 = "Instrument Parameters"
2014	d = self.Histograms[hist][key2][0]
2015	instrname = d.get(key3)
2016	if instrname is None:
2017	d[key3] = ''
2018	invalid += 1
2019	elif instrname.strip() == '':
2020	invalid += 1
2021	if invalid:
2022	msg = ""
2023	if invalid > 3: msg = (
2024	"\n\nNote: it may be faster to set the name for\n"
2025	"one histogram for each instrument and use the\n"
2026	"File/Copy option to duplicate the name"
2027	)
2028	if not EditInstNames(): return
2029	# check for a distance-angle range search range for each phase
2030	if not self.quickmode:
2031	for phasenam in sorted(self.Phases.keys()):
2032	#i = self.Phases[phasenam]['pId']
2033	phasedict = self.Phases[phasenam] # pointer to current phase info
2034	if 'DisAglCtls' not in phasedict['General']:
2035	dlg = G2gd.DisAglDialog(self.G2frame,{},phasedict['General'])
2036	if dlg.ShowModal() == wx.ID_OK:
2037	phasedict['General']['DisAglCtls'] = dlg.GetData()
2038	else:
2039	dlg.Destroy()
2040	return
2041	dlg.Destroy()
2042
2043	if oneblock and not self.quickmode:
2044	# select a dataset to use (there should only be one set in one block,
2045	# but take whatever comes 1st)
2046	for hist in self.Histograms:
2047	histblk = self.Histograms[hist]
2048	if hist.startswith("PWDR"):
2049	instnam = histblk["Sample Parameters"]['InstrName']
2050	break # ignore all but 1st data histogram
2051	elif hist.startswith("HKLF"):
2052	instnam = histblk["Instrument Parameters"][0]['InstrName']
2053	break # ignore all but 1st data histogram
2054	if self.quickmode:
2055	fil = self.askSaveFile()
2056	else:
2057	fil = self.defSaveFile()
2058	if not fil: return
2059	if not self.quickmode: # give the user a chance to edit all defaults
2060	self.cifdefs = wx.Dialog(
2061	self.G2frame,style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
2062	EditCIFDefaults()
2063	val = self.cifdefs.ShowModal()
2064	self.cifdefs.Destroy()
2065	if val != wx.ID_OK:
2066	return
2067	#======================================================================
2068	# Start writing the CIF - single block
2069	#======================================================================
2070	openCIF(fil)
2071	if oneblock:
2072	WriteCIFitem('data_'+self.CIFname)
2073	if phasenam is None: # if not already selected, select the first phase (should be one)
2074	phasenam = self.Phases.keys()[0]
2075	#print 'phasenam',phasenam
2076	phaseblk = self.Phases[phasenam] # pointer to current phase info
2077	if not self.quickmode:
2078	instnam = instnam.replace(' ','')
2079	WriteCIFitem('_pd_block_id',
2080	str(self.CIFdate) + "\|" + str(self.CIFname) + "\|" +
2081	str(self.shortauthorname) + "\|" + instnam)
2082	WriteAudit()
2083	WritePubTemplate()
2084	WriteOverall()
2085	WritePhaseTemplate(phasenam)
2086	# report the phase info
2087	WritePhaseInfo(phasenam)
2088	if hist.startswith("PWDR") and not self.quickmode:
2089	# preferred orientation
2090	SH = FormatSH(phasenam)
2091	MD = FormatHAPpo(phasenam)
2092	if SH and MD:
2093	WriteCIFitem('_pd_proc_ls_pref_orient_corr', SH + '\n' + MD)
2094	elif SH or MD:
2095	WriteCIFitem('_pd_proc_ls_pref_orient_corr', SH + MD)
2096	else:
2097	WriteCIFitem('_pd_proc_ls_pref_orient_corr', 'none')
2098	# report profile, since one-block: include both histogram and phase info
2099	WriteCIFitem('_pd_proc_ls_profile_function',
2100	FormatInstProfile(histblk["Instrument Parameters"],histblk['hId'])
2101	+'\n'+FormatPhaseProfile(phasenam))
2102	WritePowderTemplate(hist)
2103	WritePowderData(hist)
2104	elif hist.startswith("HKLF") and not self.quickmode:
2105	WriteSnglXtalTemplate(hist)
2106	WriteSingleXtalData(hist)
2107	else:
2108	#======================================================================
2109	# Start writing the CIF - multiblock
2110	#======================================================================
2111	# publication info
2112	WriteCIFitem('\ndata_'+self.CIFname+'_publ')
2113	WriteAudit()
2114	WriteCIFitem('_pd_block_id',
2115	str(self.CIFdate) + "\|" + str(self.CIFname) + "\|" +
2116	str(self.shortauthorname) + "\|Overall")
2117	WritePubTemplate()
2118	# overall info
2119	WriteCIFitem('data_'+str(self.CIFname)+'_overall')
2120	WriteOverall()
2121	#============================================================
2122	WriteCIFitem('# POINTERS TO PHASE AND HISTOGRAM BLOCKS')
2123	datablockidDict = {} # save block names here -- N.B. check for conflicts between phase & hist names (unlikely!)
2124	# loop over phase blocks
2125	if len(self.Phases) > 1:
2126	loopprefix = ''
2127	WriteCIFitem('loop_ _pd_phase_block_id')
2128	else:
2129	loopprefix = '_pd_phase_block_id'
2130
2131	for phasenam in sorted(self.Phases.keys()):
2132	i = self.Phases[phasenam]['pId']
2133	datablockidDict[phasenam] = (str(self.CIFdate) + "\|" + str(self.CIFname) + "\|" +
2134	'phase_'+ str(i) + '\|' + str(self.shortauthorname))
2135	WriteCIFitem(loopprefix,datablockidDict[phasenam])
2136	# loop over data blocks
2137	if len(self.powderDict) + len(self.xtalDict) > 1:
2138	loopprefix = ''
2139	WriteCIFitem('loop_ _pd_block_diffractogram_id')
2140	else:
2141	loopprefix = '_pd_block_diffractogram_id'
2142	for i in sorted(self.powderDict.keys()):
2143	hist = self.powderDict[i]
2144	histblk = self.Histograms[hist]
2145	instnam = histblk["Sample Parameters"]['InstrName']
2146	instnam = instnam.replace(' ','')
2147	i = histblk['hId']
2148	datablockidDict[hist] = (str(self.CIFdate) + "\|" + str(self.CIFname) + "\|" +
2149	str(self.shortauthorname) + "\|" +
2150	instnam + "_hist_"+str(i))
2151	WriteCIFitem(loopprefix,datablockidDict[hist])
2152	for i in sorted(self.xtalDict.keys()):
2153	hist = self.xtalDict[i]
2154	histblk = self.Histograms[hist]
2155	instnam = histblk["Instrument Parameters"][0]['InstrName']
2156	instnam = instnam.replace(' ','')
2157	i = histblk['hId']
2158	datablockidDict[hist] = (str(self.CIFdate) + "\|" + str(self.CIFname) + "\|" +
2159	str(self.shortauthorname) + "\|" +
2160	instnam + "_hist_"+str(i))
2161	WriteCIFitem(loopprefix,datablockidDict[hist])
2162	#============================================================
2163	# loop over phases, exporting them
2164	phasebyhistDict = {} # create a cross-reference to phases by histogram
2165	for j,phasenam in enumerate(sorted(self.Phases.keys())):
2166	i = self.Phases[phasenam]['pId']
2167	WriteCIFitem('\ndata_'+self.CIFname+"_phase_"+str(i))
2168	WriteCIFitem('# Information for phase '+str(i))
2169	WriteCIFitem('_pd_block_id',datablockidDict[phasenam])
2170	# report the phase
2171	WritePhaseTemplate(phasenam)
2172	WritePhaseInfo(phasenam)
2173	# preferred orientation
2174	SH = FormatSH(phasenam)
2175	MD = FormatHAPpo(phasenam)
2176	if SH and MD:
2177	WriteCIFitem('_pd_proc_ls_pref_orient_corr', SH + '\n' + MD)
2178	elif SH or MD:
2179	WriteCIFitem('_pd_proc_ls_pref_orient_corr', SH + MD)
2180	else:
2181	WriteCIFitem('_pd_proc_ls_pref_orient_corr', 'none')
2182	# report sample profile terms
2183	PP = FormatPhaseProfile(phasenam)
2184	if PP:
2185	WriteCIFitem('_pd_proc_ls_profile_function',PP)
2186
2187	#============================================================
2188	# loop over histograms, exporting them
2189	for i in sorted(self.powderDict.keys()):
2190	hist = self.powderDict[i]
2191	histblk = self.Histograms[hist]
2192	if hist.startswith("PWDR"):
2193	WriteCIFitem('\ndata_'+self.CIFname+"_pwd_"+str(i))
2194	#instnam = histblk["Sample Parameters"]['InstrName']
2195	# report instrumental profile terms
2196	WriteCIFitem('_pd_proc_ls_profile_function',
2197	FormatInstProfile(histblk["Instrument Parameters"],histblk['hId']))
2198	WriteCIFitem('# Information for histogram '+str(i)+': '+hist)
2199	WriteCIFitem('_pd_block_id',datablockidDict[hist])
2200	WritePowderTemplate(hist)
2201	WritePowderData(hist)
2202	for i in sorted(self.xtalDict.keys()):
2203	hist = self.xtalDict[i]
2204	histblk = self.Histograms[hist]
2205	if hist.startswith("HKLF"):
2206	WriteCIFitem('\ndata_'+self.CIFname+"_sx_"+str(i))
2207	#instnam = histblk["Instrument Parameters"][0]['InstrName']
2208	WriteCIFitem('# Information for histogram '+str(i)+': '+hist)
2209	WriteCIFitem('_pd_block_id',datablockidDict[hist])
2210	WriteSnglXtalTemplate(hist)
2211	WriteSingleXtalData(hist)
2212
2213	WriteCIFitem('#--' + 15*'eof--' + '#')
2214	closeCIF()

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