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source: trunk/GSASIIIO.py @ 2757

Last change on this file since 2757 was 2754, checked in by vondreele, 8 years ago
fix "off-by-one" problem in powder profiles; calc missed last point - now fixed. add import of reflectometry data - same as small angle data implement plotting of reflectometry data & all the scale options set up the Model page for reflectometry (Layers is missing)
Property svn:eol-style set to `native` Property svn:keywords set to `Date Author Revision URL Id`
File size: 117.5 KB

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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2017-03-14 15:19:59 +0000 (Tue, 14 Mar 2017) $
4	# $Author: vondreele $
5	# $Revision: 2754 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 2754 2017-03-14 15:19:59Z vondreele $
8	########### SVN repository information ###################
9	'''
10	GSASIIIO: Misc I/O routines
11	=============================
12
13	Module with miscellaneous routines for input and output. Many
14	are GUI routines to interact with user.
15
16	Includes support for image reading.
17
18	Also includes base classes for data import routines.
19
20	'''
21	"""GSASIIIO: functions for IO of data
22	Copyright: 2008, Robert B. Von Dreele (Argonne National Laboratory)
23	"""
24	import wx
25	import math
26	import numpy as np
27	import copy
28	import cPickle
29	import sys
30	import re
31	import random as ran
32	import GSASIIpath
33	GSASIIpath.SetVersionNumber("$Revision: 2754 $")
34	import GSASIIgrid as G2gd
35	import GSASIIspc as G2spc
36	import GSASIIobj as G2obj
37	import GSASIIlattice as G2lat
38	import GSASIImath as G2mth
39	import GSASIIpwdGUI as G2pdG
40	import GSASIIimgGUI as G2imG
41	import GSASIIimage as G2img
42	import GSASIIElem as G2el
43	import GSASIIstrIO as G2stIO
44	import GSASIImapvars as G2mv
45	import GSASIIctrls as G2G
46	import os
47	import os.path as ospath
48
49	DEBUG = False #=True for various prints
50	TRANSP = False #=true to transpose images for testing
51	if GSASIIpath.GetConfigValue('Transpose'): TRANSP = True
52	npsind = lambda x: np.sin(x*np.pi/180.)
53
54	def sfloat(S):
55	'Convert a string to float. An empty field or a unconvertable value is treated as zero'
56	if S.strip():
57	try:
58	return float(S)
59	except ValueError:
60	pass
61	return 0.0
62
63	def sint(S):
64	'Convert a string to int. An empty field is treated as zero'
65	if S.strip():
66	return int(S)
67	else:
68	return 0
69
70	def trim(val):
71	'''Simplify a string containing leading and trailing spaces
72	as well as newlines, tabs, repeated spaces etc. into a shorter and
73	more simple string, by replacing all ranges of whitespace
74	characters with a single space.
75
76	:param str val: the string to be simplified
77
78	:returns: the (usually) shortened version of the string
79	'''
80	return re.sub('\s+', ' ', val).strip()
81
82	def makeInstDict(names,data,codes):
83	inst = dict(zip(names,zip(data,data,codes)))
84	for item in inst:
85	inst[item] = list(inst[item])
86	return inst
87
88	def FileDlgFixExt(dlg,file):
89	'this is needed to fix a problem in linux wx.FileDialog'
90	ext = dlg.GetWildcard().split('\|')[2dlg.GetFilterIndex()+1].strip('')
91	if ext not in file:
92	file += ext
93	return file
94
95	def GetPowderPeaks(fileName):
96	'Read powder peaks from a file'
97	sind = lambda x: math.sin(x*math.pi/180.)
98	asind = lambda x: 180.*math.asin(x)/math.pi
99	wave = 1.54052
100	File = open(fileName,'Ur')
101	Comments = []
102	peaks = []
103	S = File.readline()
104	while S:
105	if S[:1] == '#':
106	Comments.append(S[:-1])
107	else:
108	item = S.split()
109	if len(item) == 1:
110	peaks.append([float(item[0]),1.0])
111	elif len(item) > 1:
112	peaks.append([float(item[0]),float(item[0])])
113	S = File.readline()
114	File.close()
115	if Comments:
116	print 'Comments on file:'
117	for Comment in Comments:
118	print Comment
119	if 'wavelength' in Comment:
120	wave = float(Comment.split('=')[1])
121	Peaks = []
122	if peaks[0][0] > peaks[-1][0]: # d-spacings - assume CuKa
123	for peak in peaks:
124	dsp = peak[0]
125	sth = wave/(2.0*dsp)
126	if sth < 1.0:
127	tth = 2.0*asind(sth)
128	else:
129	break
130	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
131	else: #2-thetas - assume Cuka (for now)
132	for peak in peaks:
133	tth = peak[0]
134	dsp = wave/(2.0*sind(tth/2.0))
135	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
136	limits = [1000.,0.]
137	for peak in Peaks:
138	limits[0] = min(limits[0],peak[0])
139	limits[1] = max(limits[1],peak[0])
140	limits[0] = max(1.,(int(limits[0]-1.)/5)*5.)
141	limits[1] = min(170.,(int(limits[1]+1.)/5)*5.)
142	return Comments,Peaks,limits,wave
143
144	def GetCheckImageFile(G2frame,treeId):
145	'''Try to locate an image file if the project and image have been moved
146	together. If the image file cannot be found, request the location from
147	the user.
148
149	:param wx.Frame G2frame: main GSAS-II Frame and data object
150	:param wx.Id treeId: Id for the main tree item for the image
151	:returns: Npix,imagefile,imagetag with (Npix) number of pixels,
152	imagefile, if it exists, or the name of a file that does exist or False if the user presses Cancel
153	and (imagetag) an optional image number
154
155	'''
156	Npix,Imagefile,imagetag = G2frame.PatternTree.GetImageLoc(treeId)
157	if isinstance(Imagefile,list):
158	imagefile,imagetag = Imagefile
159	else:
160	imagefile = Imagefile
161	if not os.path.exists(imagefile):
162	print 'Image file '+imagefile+' not found'
163	fil = imagefile.replace('\\','/') # windows?!
164	# see if we can find a file with same name or in a similarly named sub-dir
165	pth,fil = os.path.split(fil)
166	prevpth = None
167	while pth and pth != prevpth:
168	prevpth = pth
169	if os.path.exists(os.path.join(G2frame.dirname,fil)):
170	print 'found image file '+os.path.join(G2frame.dirname,fil)
171	imagefile = os.path.join(G2frame.dirname,fil)
172	G2frame.PatternTree.UpdateImageLoc(treeId,imagefile)
173	return Npix,imagefile,imagetag
174	pth,enddir = os.path.split(pth)
175	fil = os.path.join(enddir,fil)
176	# not found as a subdirectory, drop common parts of path for last saved & image file names
177	# if image was .../A/B/C/imgs/ima.ge
178	# & GPX was .../A/B/C/refs/fil.gpx but is now .../NEW/TEST/TEST1
179	# will look for .../NEW/TEST/TEST1/imgs/ima.ge, .../NEW/TEST/imgs/ima.ge, .../NEW/imgs/ima.ge and so on
180	Controls = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
181	gpxPath = Controls.get('LastSavedAs','').replace('\\','/').split('/') # blank in older .GPX files
182	imgPath = imagefile.replace('\\','/').split('/')
183	for p1,p2 in zip(gpxPath,imgPath):
184	if p1 == p2:
185	gpxPath.pop(0),imgPath.pop(0)
186	else:
187	break
188	fil = os.path.join(*imgPath) # file with non-common prefix elements
189	prevpth = None
190	pth = os.path.abspath(G2frame.dirname)
191	while pth and pth != prevpth:
192	prevpth = pth
193	if os.path.exists(os.path.join(pth,fil)):
194	print 'found image file '+os.path.join(pth,fil)
195	imagefile = os.path.join(pth,fil)
196	G2frame.PatternTree.UpdateImageLoc(treeId,imagefile)
197	return Npix,imagefile,imagetag
198	pth,enddir = os.path.split(pth)
199	#GSASIIpath.IPyBreak()
200
201	if not os.path.exists(imagefile):
202	prevnam = os.path.split(imagefile)[1]
203	prevext = os.path.splitext(imagefile)[1]
204	wildcard = 'Image format ('+prevext+')\|'+prevext
205	dlg = wx.FileDialog(G2frame, 'Previous image file ('+prevnam+') not found; open here', '.', prevnam,
206	wildcard,wx.OPEN)
207	try:
208	dlg.SetFilename(''+ospath.split(imagefile)[1])
209	if dlg.ShowModal() == wx.ID_OK:
210	imagefile = dlg.GetPath()
211	G2frame.PatternTree.UpdateImageLoc(treeId,imagefile)
212	else:
213	imagefile = False
214	finally:
215	dlg.Destroy()
216	return Npix,imagefile,imagetag
217
218	def EditImageParms(parent,Data,Comments,Image,filename):
219	dlg = wx.Dialog(parent, wx.ID_ANY, 'Edit image parameters',
220	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
221	def onClose(event):
222	dlg.EndModal(wx.ID_OK)
223	mainsizer = wx.BoxSizer(wx.VERTICAL)
224	h,w = Image.shape[:2]
225	mainsizer.Add(wx.StaticText(dlg,wx.ID_ANY,
226	'File '+str(filename)+'\nImage size: '+str(h)+' x '+str(w)),
227	0,wx.ALIGN_LEFT\|wx.ALL, 2)
228
229	vsizer = wx.BoxSizer(wx.HORIZONTAL)
230	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Wavelength (\xC5) '),
231	0,wx.ALIGN_LEFT\|wx.ALL, 2)
232	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'wavelength')
233	vsizer.Add(wdgt)
234	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
235
236	vsizer = wx.BoxSizer(wx.HORIZONTAL)
237	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Pixel size (\xb5m). Width '),
238	0,wx.ALIGN_LEFT\|wx.ALL, 2)
239	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],0,
240	size=(50,-1))
241	vsizer.Add(wdgt)
242	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Height '),
243	wx.ALIGN_LEFT\|wx.ALL, 2)
244	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],1,
245	size=(50,-1))
246	vsizer.Add(wdgt)
247	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
248
249	vsizer = wx.BoxSizer(wx.HORIZONTAL)
250	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Sample to detector (mm) '),
251	0,wx.ALIGN_LEFT\|wx.ALL, 2)
252	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'distance')
253	vsizer.Add(wdgt)
254	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
255
256	vsizer = wx.BoxSizer(wx.HORIZONTAL)
257	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Beam center (pixels). X = '),
258	0,wx.ALIGN_LEFT\|wx.ALL, 2)
259	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],0,
260	size=(75,-1))
261	vsizer.Add(wdgt)
262	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Y = '),
263	wx.ALIGN_LEFT\|wx.ALL, 2)
264	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],1,
265	size=(75,-1))
266	vsizer.Add(wdgt)
267	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
268
269	vsizer = wx.BoxSizer(wx.HORIZONTAL)
270	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Comments '),
271	0,wx.ALIGN_LEFT\|wx.ALL, 2)
272	wdgt = G2G.ValidatedTxtCtrl(dlg,Comments,0,size=(250,-1))
273	vsizer.Add(wdgt)
274	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
275
276	btnsizer = wx.StdDialogButtonSizer()
277	OKbtn = wx.Button(dlg, wx.ID_OK, 'Continue')
278	OKbtn.SetDefault()
279	OKbtn.Bind(wx.EVT_BUTTON,onClose)
280	btnsizer.AddButton(OKbtn) # not sure why this is needed
281	btnsizer.Realize()
282	mainsizer.Add(btnsizer, 1, wx.ALIGN_CENTER\|wx.ALL\|wx.EXPAND, 5)
283	dlg.SetSizer(mainsizer)
284	dlg.CenterOnParent()
285	dlg.ShowModal()
286
287	def LoadImage2Tree(imagefile,G2frame,Comments,Data,Npix,Image):
288	'''Load an image into the tree. Saves the location of the image, as well as the
289	ImageTag (where there is more than one image in the file), if defined.
290	'''
291	ImgNames = G2gd.GetPatternTreeDataNames(G2frame,['IMG ',])
292	TreeLbl = 'IMG '+os.path.basename(imagefile)
293	ImageTag = Data.get('ImageTag')
294	if ImageTag:
295	TreeLbl += ' #'+'%04d'%(ImageTag)
296	imageInfo = (imagefile,ImageTag)
297	else:
298	imageInfo = imagefile
299	TreeName = G2obj.MakeUniqueLabel(TreeLbl,ImgNames)
300	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=TreeName)
301	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
302	Imax = np.amax(Image)
303	if G2frame.imageDefault:
304	Data = copy.copy(G2frame.imageDefault)
305	Data['showLines'] = True
306	Data['ring'] = []
307	Data['rings'] = []
308	Data['cutoff'] = 10
309	Data['pixLimit'] = 20
310	Data['edgemin'] = 100000000
311	Data['calibdmin'] = 0.5
312	Data['calibskip'] = 0
313	Data['ellipses'] = []
314	Data['calibrant'] = ''
315	Data['GonioAngles'] = [0.,0.,0.]
316	Data['DetDepthRef'] = False
317	else:
318	Data['type'] = 'PWDR'
319	Data['color'] = 'Paired'
320	Data['tilt'] = 0.0
321	Data['rotation'] = 0.0
322	Data['showLines'] = False
323	Data['ring'] = []
324	Data['rings'] = []
325	Data['cutoff'] = 10
326	Data['pixLimit'] = 20
327	Data['calibdmin'] = 0.5
328	Data['calibskip'] = 0
329	Data['edgemin'] = 100000000
330	Data['ellipses'] = []
331	Data['GonioAngles'] = [0.,0.,0.]
332	Data['DetDepth'] = 0.
333	Data['DetDepthRef'] = False
334	Data['calibrant'] = ''
335	Data['IOtth'] = [2.0,5.0]
336	Data['LRazimuth'] = [0.,180.]
337	Data['azmthOff'] = 0.0
338	Data['outChannels'] = 2500
339	Data['outAzimuths'] = 1
340	Data['centerAzm'] = False
341	Data['fullIntegrate'] = False
342	Data['setRings'] = False
343	Data['background image'] = ['',-1.0]
344	Data['dark image'] = ['',-1.0]
345	Data['Flat Bkg'] = 0.0
346	Data['setDefault'] = False
347	Data['range'] = [(0,Imax),[0,Imax]]
348	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Image Controls'),Data)
349	Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],'Thresholds':[(0,Imax),[0,Imax]]}
350	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Masks'),Masks)
351	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Stress/Strain'),
352	{'Type':'True','d-zero':[],'Sample phi':0.0,'Sample z':0.0,'Sample load':0.0})
353	G2frame.PatternTree.SetItemPyData(Id,[Npix,imageInfo])
354	G2frame.PickId = Id
355	G2frame.PickIdText = G2frame.GetTreeItemsList(G2frame.PickId)
356	G2frame.Image = Id
357
358	def GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None,FormatName=''):
359	'''Read a single image with an image importer.
360
361	:param wx.Frame G2frame: main GSAS-II Frame and data object.
362	:param str imagefile: name of image file
363	:param bool imageOnly: If True return only the image,
364	otherwise (default) return more (see below)
365	:param int/str ImageTag: specifies a particular image to be read from a file.
366	First image is read if None (default).
367	:param str formatName: the image reader formatName
368
369	:returns: an image as a numpy array or a list of four items:
370	Comments, Data, Npix and the Image, as selected by imageOnly
371
372	'''
373	# determine which formats are compatible with this file
374	primaryReaders = []
375	secondaryReaders = []
376	for rd in G2frame.ImportImageReaderlist:
377	flag = rd.ExtensionValidator(imagefile)
378	if flag is None:
379	secondaryReaders.append(rd)
380	elif flag:
381	if not FormatName:
382	primaryReaders.append(rd)
383	elif FormatName == rd.formatName:
384	primaryReaders.append(rd)
385	if len(secondaryReaders) + len(primaryReaders) == 0:
386	print('Error: No matching format for file '+imagefile)
387	raise Exception('No image read')
388	fp = None
389	errorReport = ''
390	if not imagefile:
391	return
392	fp = open(imagefile,'Ur')
393	for rd in primaryReaders+secondaryReaders:
394	rd.ReInitialize() # purge anything from a previous read
395	fp.seek(0) # rewind
396	rd.errors = "" # clear out any old errors
397	if not rd.ContentsValidator(fp): # rejected on cursory check
398	errorReport += "\n "+rd.formatName + ' validator error'
399	if rd.errors:
400	errorReport += ': '+rd.errors
401	continue
402	if imageOnly:
403	ParentFrame = None # prevent GUI access on reread
404	else:
405	ParentFrame = G2frame
406	if GSASIIpath.GetConfigValue('debug'):
407	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=ImageTag)
408	else:
409	flag = False
410	try:
411	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=ImageTag)
412	except rd.ImportException as detail:
413	rd.errors += "\n Read exception: "+str(detail)
414	except Exception as detail:
415	import traceback
416	rd.errors += "\n Unhandled read exception: "+str(detail)
417	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
418	if flag: # this read succeeded
419	if rd.Image is None:
420	raise Exception('No image read. Strange!')
421	if GSASIIpath.GetConfigValue('Transpose'):
422	print 'Transposing Image!'
423	rd.Image = rd.Image.T
424	#rd.readfilename = imagefile
425	if imageOnly:
426	return rd.Image
427	else:
428	return rd.Comments,rd.Data,rd.Npix,rd.Image
429	else:
430	print('Error reading file '+imagefile)
431	print('Error messages(s)\n'+errorReport)
432	raise Exception('No image read')
433
434	def ReadImages(G2frame,imagefile):
435	'''Read one or more images from a file and put them into the Tree
436	using image importers. Called only in :meth:`AutoIntFrame.OnTimerLoop`.
437
438	:param wx.Frame G2frame: main GSAS-II Frame and data object.
439	:param str imagefile: name of image file
440
441	:returns: a list of the id's of the IMG tree items created
442	'''
443	# determine which formats are compatible with this file
444	primaryReaders = []
445	secondaryReaders = []
446	for rd in G2frame.ImportImageReaderlist:
447	flag = rd.ExtensionValidator(imagefile)
448	if flag is None:
449	secondaryReaders.append(rd)
450	elif flag:
451	primaryReaders.append(rd)
452	if len(secondaryReaders) + len(primaryReaders) == 0:
453	print('Error: No matching format for file '+imagefile)
454	raise Exception('No image read')
455	errorReport = ''
456	fp = open(imagefile,'Ur')
457	rdbuffer = {} # create temporary storage for file reader
458	for rd in primaryReaders+secondaryReaders:
459	rd.ReInitialize() # purge anything from a previous read
460	fp.seek(0) # rewind
461	rd.errors = "" # clear out any old errors
462	if not rd.ContentsValidator(fp): # rejected on cursory check
463	errorReport += "\n "+rd.formatName + ' validator error'
464	if rd.errors:
465	errorReport += ': '+rd.errors
466	continue
467	ParentFrame = G2frame
468	block = 0
469	repeat = True
470	CreatedIMGitems = []
471	while repeat: # loop if the reader asks for another pass on the file
472	block += 1
473	repeat = False
474	if GSASIIpath.GetConfigValue('debug'):
475	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=block,Buffer=rdbuffer)
476	else:
477	flag = False
478	try:
479	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=block,Buffer=rdbuffer)
480	except rd.ImportException as detail:
481	rd.errors += "\n Read exception: "+str(detail)
482	except Exception as detail:
483	import traceback
484	rd.errors += "\n Unhandled read exception: "+str(detail)
485	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
486	if flag: # this read succeeded
487	if rd.Image is None:
488	raise Exception('No image read. Strange!')
489	if GSASIIpath.GetConfigValue('Transpose'):
490	print 'Transposing Image!'
491	rd.Image = rd.Image.T
492	rd.Data['ImageTag'] = rd.repeatcount
493	LoadImage2Tree(imagefile,G2frame,rd.Comments,rd.Data,rd.Npix,rd.Image)
494	repeat = rd.repeat
495	CreatedIMGitems.append(G2frame.Image)
496	if CreatedIMGitems: return CreatedIMGitems
497	else:
498	print('Error reading file '+imagefile)
499	print('Error messages(s)\n'+errorReport)
500	return []
501	#raise Exception('No image read')
502
503	def SaveMultipleImg(G2frame):
504	if not G2frame.PatternTree.GetCount():
505	print 'no images!'
506	return
507	choices = G2gd.GetPatternTreeDataNames(G2frame,['IMG ',])
508	if len(choices) == 1:
509	names = choices
510	else:
511	dlg = G2G.G2MultiChoiceDialog(G2frame,'Stress/Strain fitting','Select images to fit:',choices)
512	dlg.SetSelections([])
513	names = []
514	if dlg.ShowModal() == wx.ID_OK:
515	names = [choices[sel] for sel in dlg.GetSelections()]
516	dlg.Destroy()
517	if not names: return
518	for name in names:
519	Id = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, name)
520	Npix,imagefile,imagetag = G2frame.PatternTree.GetImageLoc(Id)
521	imroot = os.path.splitext(imagefile)[0]
522	if imagetag:
523	imroot += '_' + str(imagetag)
524	Data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Image Controls'))
525	print('Writing '+imroot+'.imctrl')
526	File = open(imroot+'.imctrl','w')
527	keys = ['type','wavelength','calibrant','distance','center',
528	'tilt','rotation','azmthOff','fullIntegrate','LRazimuth',
529	'IOtth','outChannels','outAzimuths','invert_x','invert_y','DetDepth',
530	'calibskip','pixLimit','cutoff','calibdmin','chisq','Flat Bkg',
531	'binType','SampleShape','PolaVal','SampleAbs','dark image','background image']
532	for key in keys:
533	if key not in Data: continue #uncalibrated!
534	File.write(key+':'+str(Data[key])+'\n')
535	File.close()
536	mask = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Masks'))
537	G2imG.CleanupMasks(mask)
538	print('Writing '+imroot+'.immask')
539	File = open(imroot+'.immask','w')
540	for key in ['Points','Rings','Arcs','Polygons','Frames','Thresholds']:
541	File.write(key+':'+str(mask[key])+'\n')
542	File.close()
543
544	def PutG2Image(filename,Comments,Data,Npix,image):
545	'Write an image as a python pickle - might be better as an .edf file?'
546	File = open(filename,'wb')
547	cPickle.dump([Comments,Data,Npix,image],File,1)
548	File.close()
549	return
550
551	# should get moved to importer when ready to test
552	def GetEdfData(filename,imageOnly=False):
553	'Read European detector data edf file'
554	if not imageOnly:
555	print 'Read European detector data edf file: ',filename
556	File = open(filename,'rb')
557	fileSize = os.stat(filename).st_size
558	head = File.read(3072)
559	lines = head.split('\n')
560	sizexy = [0,0]
561	pixSize = [154,154] #Pixium4700?
562	cent = [0,0]
563	wave = 1.54187 #default <CuKa>
564	dist = 1000.
565	head = ['European detector data',]
566	for line in lines:
567	line = line.replace(';',' ').strip()
568	fields = line.split()
569	if 'Dim_1' in line:
570	sizexy[0] = int(fields[2])
571	elif 'Dim_2' in line:
572	sizexy[1] = int(fields[2])
573	elif 'DataType' in line:
574	dType = fields[2]
575	elif 'wavelength' in line:
576	wave = float(fields[2])
577	elif 'Size' in line:
578	imSize = int(fields[2])
579	# elif 'DataType' in lines:
580	# dType = fields[2]
581	elif 'pixel_size_x' in line:
582	pixSize[0] = float(fields[2])
583	elif 'pixel_size_y' in line:
584	pixSize[1] = float(fields[2])
585	elif 'beam_center_x' in line:
586	cent[0] = float(fields[2])
587	elif 'beam_center_y' in line:
588	cent[1] = float(fields[2])
589	elif 'refined_distance' in line:
590	dist = float(fields[2])
591	if line:
592	head.append(line)
593	else: #blank line at end of header
594	break
595	File.seek(fileSize-imSize)
596	if dType == 'UnsignedShort':
597	image = np.array(np.frombuffer(File.read(imSize),dtype=np.int16),dtype=np.int32)
598	else:
599	image = np.array(np.frombuffer(File.read(imSize),dtype=np.int32),dtype=np.int32)
600	image = np.reshape(image,(sizexy[1],sizexy[0]))
601	data = {'pixelSize':pixSize,'wavelength':wave,'distance':dist,'center':cent,'size':sizexy}
602	Npix = sizexy[0]*sizexy[1]
603	File.close()
604	if imageOnly:
605	return image
606	else:
607	return head,data,Npix,image
608
609	# should get moved to importer when ready to test
610	def GetRigaku(filename,imageOnly=False):
611	'Read Rigaku R-Axis IV image file'
612	import array as ar
613	if not imageOnly:
614	print 'Read Rigaku R-Axis IV file: ',filename
615	File = open(filename,'rb')
616	fileSize = os.stat(filename).st_size
617	Npix = (fileSize-6000)/2
618	File.read(6000)
619	head = ['Rigaku R-Axis IV detector data',]
620	image = np.array(ar.array('H',File.read(fileSize-6000)),dtype=np.int32)
621	print fileSize,image.shape
622	print head
623	if Npix == 9000000:
624	sizexy = [3000,3000]
625	pixSize = [100.,100.]
626	elif Npix == 2250000:
627	sizexy = [1500,1500]
628	pixSize = [200.,200.]
629	else:
630	sizexy = [6000,6000]
631	pixSize = [50.,50.]
632	image = np.reshape(image,(sizexy[1],sizexy[0]))
633	data = {'pixelSize':pixSize,'wavelength':1.5428,'distance':250.0,'center':[150.,150.],'size':sizexy}
634	File.close()
635	if imageOnly:
636	return image
637	else:
638	return head,data,Npix,image
639
640	# should get moved to importer when ready to test
641	def GetImgData(filename,imageOnly=False):
642	'Read an ADSC image file'
643	import array as ar
644	if not imageOnly:
645	print 'Read ADSC img file: ',filename
646	File = open(filename,'rb')
647	head = File.read(511)
648	lines = head.split('\n')
649	head = []
650	center = [0,0]
651	for line in lines[1:-2]:
652	line = line.strip()[:-1]
653	if line:
654	if 'SIZE1' in line:
655	size = int(line.split('=')[1])
656	Npix = size*size
657	elif 'WAVELENGTH' in line:
658	wave = float(line.split('=')[1])
659	elif 'BIN' in line:
660	if line.split('=')[1] == '2x2':
661	pixel=(102,102)
662	else:
663	pixel = (51,51)
664	elif 'DISTANCE' in line:
665	distance = float(line.split('=')[1])
666	elif 'CENTER_X' in line:
667	center[0] = float(line.split('=')[1])
668	elif 'CENTER_Y' in line:
669	center[1] = float(line.split('=')[1])
670	head.append(line)
671	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center,'size':[size,size]}
672	image = []
673	pos = 512
674	File.seek(pos)
675	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
676	image = np.reshape(image,(size,size))
677	# image = np.zeros(shape=(size,size),dtype=np.int32)
678	# while row < size:
679	# File.seek(pos)
680	# line = ar.array('H',File.read(2*size))
681	# image[row] = np.asarray(line)
682	# row += 1
683	# pos += 2*size
684	File.close()
685	if imageOnly:
686	return image
687	else:
688	return lines[1:-2],data,Npix,image
689
690	# should get moved to importer when ready to test
691	def GetMAR345Data(filename,imageOnly=False):
692	'Read a MAR-345 image plate image'
693	try:
694	import pack_f as pf
695	except:
696	msg = wx.MessageDialog(None, message="Unable to load the GSAS MAR image decompression, pack_f",
697	caption="Import Error",
698	style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
699	msg.ShowModal()
700	return None,None,None,None
701
702	if not imageOnly:
703	print 'Read Mar345 file: ',filename
704	File = open(filename,'rb')
705	head = File.read(4095)
706	lines = head[128:].split('\n')
707	head = []
708	for line in lines:
709	line = line.strip()
710	if 'PIXEL' in line:
711	values = line.split()
712	pixel = (int(values[2]),int(values[4])) #in microns
713	elif 'WAVELENGTH' in line:
714	wave = float(line.split()[1])
715	elif 'DISTANCE' in line:
716	distance = float(line.split()[1]) #in mm
717	if not distance:
718	distance = 500.
719	elif 'CENTER' in line:
720	values = line.split()
721	center = [float(values[2])/10.,float(values[4])/10.] #make in mm from pixels
722	if line:
723	head.append(line)
724	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center}
725	for line in head:
726	if 'FORMAT' in line[0:6]:
727	items = line.split()
728	sizex = int(items[1])
729	Npix = int(items[3])
730	sizey = int(Npix/sizex)
731	pos = 4096
732	data['size'] = [sizex,sizey]
733	File.seek(pos)
734	line = File.read(8)
735	while 'CCP4' not in line: #get past overflow list for now
736	line = File.read(8)
737	pos += 8
738	pos += 37
739	File.seek(pos)
740	raw = File.read()
741	File.close()
742	image = np.zeros(shape=(sizex,sizey),dtype=np.int32)
743
744	image = np.flipud(pf.pack_f(len(raw),raw,sizex,sizey,image).T) #transpose to get it right way around & flip
745	if imageOnly:
746	return image
747	else:
748	return head,data,Npix,image
749
750	def ProjFileOpen(G2frame,showProvenance=True):
751	'Read a GSAS-II project file and load into the G2 data tree'
752	if not os.path.exists(G2frame.GSASprojectfile):
753	print ('\n*** Error attempt to open project file that does not exist:\n '+
754	str(G2frame.GSASprojectfile))
755	return
756	LastSavedUsing = None
757	file = open(G2frame.GSASprojectfile,'rb')
758	if showProvenance: print 'loading from file: ',G2frame.GSASprojectfile
759	G2frame.SetTitle("GSAS-II data tree: "+
760	os.path.split(G2frame.GSASprojectfile)[1])
761	wx.BeginBusyCursor()
762	try:
763	while True:
764	try:
765	data = cPickle.load(file)
766	except EOFError:
767	break
768	datum = data[0]
769
770	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=datum[0])
771	if datum[0].startswith('PWDR'):
772	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
773	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
774	G2frame.PatternTree.SetItemPyData(Id,datum[1][:3]) #temp. trim off junk (patch?)
775	elif datum[0].startswith('HKLF'):
776	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
777	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
778	G2frame.PatternTree.SetItemPyData(Id,datum[1])
779	else:
780	G2frame.PatternTree.SetItemPyData(Id,datum[1])
781	if datum[0] == 'Controls' and 'LastSavedUsing' in datum[1]:
782	LastSavedUsing = datum[1]['LastSavedUsing']
783	if datum[0] == 'Controls' and 'PythonVersions' in datum[1] and GSASIIpath.GetConfigValue('debug') and showProvenance:
784	print('Packages used to create .GPX file:')
785	if 'dict' in str(type(datum[1]['PythonVersions'])): #patch
786	for p in sorted(datum[1]['PythonVersions'],key=lambda s: s.lower()):
787	print(" {:<14s}: {:s}".format(p[0],p[1]))
788	else:
789	for p in datum[1]['PythonVersions']:
790	print(" {:<12s} {:s}".format(p[0]+':',p[1]))
791	oldPDF = False
792	for datus in data[1:]:
793	#patch - 1/23/17 PDF cleanup
794	if datus[0][:4] in ['I(Q)','S(Q)','F(Q)','G(R)']:
795	oldPDF = True
796	data[1][1][datus[0][:4]] = copy.deepcopy(datus[1][:2])
797	continue
798	#end PDF cleanup
799	sub = G2frame.PatternTree.AppendItem(Id,datus[0])
800	#patch
801	if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
802	if datum[0].startswith('PWDR'):
803	datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
804	else:
805	datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
806	for item in datus[1][0]: #zip makes tuples - now make lists!
807	datus[1][0][item] = list(datus[1][0][item])
808	#end patch
809	G2frame.PatternTree.SetItemPyData(sub,datus[1])
810	if 'PDF ' in datum[0][:4] and oldPDF:
811	sub = G2frame.PatternTree.AppendItem(Id,'PDF Peaks')
812	G2frame.PatternTree.SetItemPyData(sub,{'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]})
813	if datum[0].startswith('IMG'): #retrieve image default flag & data if set
814	Data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Image Controls'))
815	if Data['setDefault']:
816	G2frame.imageDefault = Data
817	file.close()
818	if LastSavedUsing:
819	print('GPX load successful. Last saved with GSAS-II revision '+LastSavedUsing)
820	else:
821	print('project load successful')
822	G2frame.NewPlot = True
823	except:
824	msg = wx.MessageDialog(G2frame,message="Error reading file "+
825	str(G2frame.GSASprojectfile)+". This is not a GSAS-II .gpx file",
826	caption="Load Error",style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
827	msg.ShowModal()
828	finally:
829	wx.EndBusyCursor()
830	G2frame.Status.SetStatusText('Mouse RB click item to refresh/raise; RB drag/drop to reorder')
831
832	def ProjFileSave(G2frame):
833	'Save a GSAS-II project file'
834	if not G2frame.PatternTree.IsEmpty():
835	file = open(G2frame.GSASprojectfile,'wb')
836	print 'save to file: ',G2frame.GSASprojectfile
837	# stick the file name into the tree and version info into tree so they are saved.
838	# (Controls should always be created at this point)
839	try:
840	Controls = G2frame.PatternTree.GetItemPyData(
841	G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
842	Controls['LastSavedAs'] = os.path.abspath(G2frame.GSASprojectfile)
843	Controls['LastSavedUsing'] = str(GSASIIpath.GetVersionNumber())
844	Controls['PythonVersions'] = G2frame.PackageVersions
845	except:
846	pass
847	wx.BeginBusyCursor()
848	try:
849	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
850	while item:
851	data = []
852	name = G2frame.PatternTree.GetItemText(item)
853	data.append([name,G2frame.PatternTree.GetItemPyData(item)])
854	item2, cookie2 = G2frame.PatternTree.GetFirstChild(item)
855	while item2:
856	name = G2frame.PatternTree.GetItemText(item2)
857	data.append([name,G2frame.PatternTree.GetItemPyData(item2)])
858	item2, cookie2 = G2frame.PatternTree.GetNextChild(item, cookie2)
859	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
860	cPickle.dump(data,file,1)
861	file.close()
862	pth = os.path.split(os.path.abspath(G2frame.GSASprojectfile))[0]
863	if GSASIIpath.GetConfigValue('Save_paths'): G2G.SaveGPXdirectory(pth)
864	G2frame.LastGPXdir = pth
865	finally:
866	wx.EndBusyCursor()
867	print('project save successful')
868
869	def SaveIntegration(G2frame,PickId,data,Overwrite=False):
870	'Save image integration results as powder pattern(s)'
871	azms = G2frame.Integrate[1]
872	X = G2frame.Integrate[2][:-1]
873	N = len(X)
874	Id = G2frame.PatternTree.GetItemParent(PickId)
875	name = G2frame.PatternTree.GetItemText(Id)
876	name = name.replace('IMG ',data['type']+' ')
877	Comments = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Comments'))
878	if 'PWDR' in name:
879	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','SH/L','Azimuth']
880	codes = [0 for i in range(11)]
881	elif 'SASD' in name:
882	names = ['Type','Lam','Zero','Azimuth']
883	codes = [0 for i in range(4)]
884	X = 4.np.pinpsind(X/2.)/data['wavelength'] #convert to q
885	Xminmax = [X[0],X[-1]]
886	Azms = []
887	dazm = 0.
888	if data['fullIntegrate'] and data['outAzimuths'] == 1:
889	Azms = [45.0,] #a poor man's average?
890	else:
891	for i,azm in enumerate(azms[:-1]):
892	if azm > 360. and azms[i+1] > 360.:
893	Azms.append(G2img.meanAzm(azm%360.,azms[i+1]%360.))
894	else:
895	Azms.append(G2img.meanAzm(azm,azms[i+1]))
896	dazm = np.min(np.abs(np.diff(azms)))/2.
897	G2frame.IntgOutList = []
898	for i,azm in enumerate(azms[:-1]):
899	Aname = name+" Azm= %.2f"%((azm+dazm)%360.)
900	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
901	# if Overwrite delete any duplicate
902	if Overwrite and G2gd.GetPatternTreeItemId(G2frame,G2frame.root,Aname):
903	print('Replacing '+Aname)
904	item = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,Aname)
905	G2frame.PatternTree.Delete(item)
906	else:
907	nOcc = 0
908	while item:
909	Name = G2frame.PatternTree.GetItemText(item)
910	if Aname in Name:
911	nOcc += 1
912	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
913	if nOcc:
914	Aname += '(%d)'%(nOcc)
915	Sample = G2pdG.SetDefaultSample() #set as Debye-Scherrer
916	Sample['Gonio. radius'] = data['distance']
917	Sample['Omega'] = data['GonioAngles'][0]
918	Sample['Chi'] = data['GonioAngles'][1]
919	Sample['Phi'] = data['GonioAngles'][2]
920	Sample['Azimuth'] = (azm+dazm)%360. #put here as bin center
921	polariz = 0.99 #set default polarization for synchrotron radiation!
922	for item in Comments:
923	if 'polariz' in item:
924	try:
925	polariz = float(item.split('=')[1])
926	except:
927	polariz = 0.99
928	if 'PWDR' in Aname:
929	parms = ['PXC',data['wavelength'],0.0,polariz,1.0,-0.10,0.4,0.30,1.0,0.0001,Azms[i]]
930	elif 'SASD' in Aname:
931	Sample['Trans'] = data['SampleAbs'][0]
932	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
933	Y = G2frame.Integrate[0][i]
934	Ymin = np.min(Y)
935	Ymax = np.max(Y)
936	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
937	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=Aname)
938	G2frame.IntgOutList.append(Id)
939	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
940	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Limits'),[tuple(Xminmax),Xminmax])
941	if 'PWDR' in Aname:
942	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Background'),[['chebyschev',1,3,1.0,0.0,0.0],
943	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
944	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
945	for item in inst[0]:
946	inst[0][item] = list(inst[0][item])
947	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Instrument Parameters'),inst)
948	if 'PWDR' in Aname:
949	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
950	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
951	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Index Peak List'),[[],[]])
952	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Unit Cells List'),[])
953	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Reflection Lists'),{})
954	elif 'SASD' in Aname:
955	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
956	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
957	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
958	valuesdict = {
959	'wtFactor':1.0,
960	'Dummy':False,
961	'ranId':ran.randint(0,sys.maxint),
962	'Offset':[0.0,0.0],'delOffset':0.02Ymax,'refOffset':-0.1Ymax,'refDelt':0.1*Ymax,
963	'qPlot':False,'dPlot':False,'sqrtPlot':False,'Yminmax':[Ymin,Ymax]
964	}
965	G2frame.PatternTree.SetItemPyData(
966	Id,[valuesdict,
967	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
968	return Id #last powder pattern generated
969
970	def XYsave(G2frame,XY,labelX='X',labelY='Y',names=None):
971	'Save XY table data'
972	pth = G2G.GetExportPath(G2frame)
973	dlg = wx.FileDialog(
974	G2frame, 'Enter csv filename for XY table', pth, '',
975	'XY table file (.csv)\|.csv',wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
976	try:
977	if dlg.ShowModal() == wx.ID_OK:
978	filename = dlg.GetPath()
979	filename = os.path.splitext(filename)[0]+'.csv'
980	File = open(filename,'w')
981	else:
982	filename = None
983	finally:
984	dlg.Destroy()
985	if not filename:
986	return
987	for i in range(len(XY)):
988	if names != None:
989	header = '%s,%s(%s)\n'%(labelX,labelY,names[i])
990	else:
991	header = '%s,%s(%d)\n'%(labelX,labelY,i)
992	File.write(header)
993	for x,y in XY[i].T:
994	File.write('%.3f,%.3f\n'%(x,y))
995	File.close()
996	print ' XY data saved to: ',filename
997
998	def PDFSave(G2frame,exports,PDFsaves):
999	'Save a PDF I(Q), S(Q), F(Q) and G(r) in column formats'
1000	import scipy.interpolate as scintp
1001	for export in exports:
1002	PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1003	PDFControls = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame, PickId,'PDF Controls'))
1004	if PDFsaves[0]: #I(Q)
1005	iqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.iq')
1006	iqdata = PDFControls['I(Q)'][0]
1007	iqfxn = scintp.interp1d(iqdata[0],iqdata[1],kind='linear')
1008	iqfile = open(iqfilename,'w')
1009	iqfile.write('#T I(Q) %s\n'%(export))
1010	iqfile.write('#L Q I(Q)\n')
1011	qnew = np.arange(iqdata[0][0],iqdata[0][-1],0.005)
1012	iqnew = zip(qnew,iqfxn(qnew))
1013	for q,iq in iqnew:
1014	iqfile.write("%15.6g %15.6g\n" % (q,iq))
1015	iqfile.close()
1016	print ' I(Q) saved to: ',iqfilename
1017
1018	if PDFsaves[1]: #S(Q)
1019	sqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.sq')
1020	sqdata = PDFControls['S(Q)'][1]
1021	sqfxn = scintp.interp1d(sqdata[0],sqdata[1],kind='linear')
1022	sqfile = open(sqfilename,'w')
1023	sqfile.write('#T S(Q) %s\n'%(export))
1024	sqfile.write('#L Q S(Q)\n')
1025	qnew = np.arange(sqdata[0][0],sqdata[0][-1],0.005)
1026	sqnew = zip(qnew,sqfxn(qnew))
1027	for q,sq in sqnew:
1028	sqfile.write("%15.6g %15.6g\n" % (q,sq))
1029	sqfile.close()
1030	print ' S(Q) saved to: ',sqfilename
1031
1032	if PDFsaves[2]: #F(Q)
1033	fqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.fq')
1034	fqdata = PDFControls['F(Q)'][1]
1035	fqfxn = scintp.interp1d(fqdata[0],fqdata[1],kind='linear')
1036	fqfile = open(sqfilename,'w')
1037	fqfile.write('#T F(Q) %s\n'%(export))
1038	fqfile.write('#L Q F(Q)\n')
1039	qnew = np.arange(sqdata[0][0],sqdata[0][-1],0.005)
1040	fqnew = zip(qnew,fqfxn(qnew))
1041	for q,fq in fqnew:
1042	fqfile.write("%15.6g %15.6g\n" % (q,fq))
1043	fqfile.close()
1044	print ' F(Q) saved to: ',fqfilename
1045
1046	if PDFsaves[3]: #G(R)
1047	grfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.gr')
1048	grdata = PDFControls['G(R)'][1]
1049	grfxn = scintp.interp1d(grdata[0],grdata[1],kind='linear')
1050	grfile = open(grfilename,'w')
1051	grfile.write('#T G(R) %s\n'%(export))
1052	grfile.write('#L R G(R)\n')
1053	rnew = np.arange(grdata[0][0],grdata[0][-1],0.010)
1054	grnew = zip(rnew,grfxn(rnew))
1055	for r,gr in grnew:
1056	grfile.write("%15.6g %15.6g\n" % (r,gr))
1057	grfile.close()
1058	print ' G(R) saved to: ',grfilename
1059
1060	if PDFsaves[4]: #pdfGUI file for G(R)
1061	pId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, 'PWDR'+export[4:])
1062	Inst = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame, pId,'Instrument Parameters'))[0]
1063	Limits = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame, pId,'Limits'))
1064	grfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.gr')
1065	grdata = PDFControls['G(R)'][1]
1066	qdata = PDFControls['I(Q)'][1][0]
1067	grfxn = scintp.interp1d(grdata[0],grdata[1],kind='linear')
1068	grfile = open(grfilename,'w')
1069	rnew = np.arange(grdata[0][0],grdata[0][-1],0.010)
1070	grnew = zip(rnew,grfxn(rnew))
1071
1072	grfile.write('[DEFAULT]\n')
1073	grfile.write('\n')
1074	grfile.write('version = GSAS-II-v'+str(GSASIIpath.GetVersionNumber())+'\n')
1075	grfile.write('\n')
1076	grfile.write('# input and output specifications\n')
1077	grfile.write('dataformat = Qnm\n')
1078	grfile.write('inputfile = %s\n'%(PDFControls['Sample']['Name']))
1079	grfile.write('backgroundfile = %s\n'%(PDFControls['Sample Bkg.']['Name']))
1080	grfile.write('outputtype = gr\n')
1081	grfile.write('\n')
1082	grfile.write('# PDF calculation setup\n')
1083	if 'x' in Inst['Type']:
1084	grfile.write('mode = %s\n'%('xray'))
1085	elif 'N' in Inst['Type']:
1086	grfile.write('mode = %s\n'%('neutron'))
1087	wave = G2mth.getMeanWave(Inst)
1088	grfile.write('wavelength = %.5f\n'%(wave))
1089	formula = ''
1090	for el in PDFControls['ElList']:
1091	formula += el
1092	num = PDFControls['ElList'][el]['FormulaNo']
1093	if num == round(num):
1094	formula += '%d'%(int(num))
1095	else:
1096	formula += '%.2f'%(num)
1097	grfile.write('composition = %s\n'%(formula))
1098	grfile.write('bgscale = %.3f\n'%(-PDFControls['Sample Bkg.']['Mult']))
1099	highQ = 2.*np.pi/G2lat.Pos2dsp(Inst,Limits[1][1])
1100	grfile.write('qmaxinst = %.2f\n'%(highQ))
1101	grfile.write('qmin = %.5f\n'%(qdata[0]))
1102	grfile.write('qmax = %.4f\n'%(qdata[-1]))
1103	grfile.write('rmin = %.2f\n'%(PDFControls['Rmin']))
1104	grfile.write('rmax = %.2f\n'%(PDFControls['Rmax']))
1105	grfile.write('rstep = 0.01\n')
1106
1107
1108	grfile.write('\n')
1109	grfile.write('# End of config '+63*'-')
1110	grfile.write('\n')
1111	grfile.write('#### start data\n')
1112	grfile.write('#S 1\n')
1113	grfile.write('#L r($\AA$) G($\AA^{-2}$)\n')
1114	for r,gr in grnew:
1115	grfile.write("%15.2F %15.6F\n" % (r,gr))
1116	grfile.close()
1117	print ' G(R) saved to: ',grfilename
1118
1119
1120
1121
1122	def PeakListSave(G2frame,file,peaks):
1123	'Save powder peaks to a data file'
1124	print 'save peak list to file: ',G2frame.peaklistfile
1125	if not peaks:
1126	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1127	try:
1128	dlg.ShowModal()
1129	finally:
1130	dlg.Destroy()
1131	return
1132	for peak in peaks:
1133	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
1134	(peak[0],peak[2],peak[4],peak[6]))
1135	print 'peak list saved'
1136
1137	def IndexPeakListSave(G2frame,peaks):
1138	'Save powder peaks from the indexing list'
1139	file = open(G2frame.peaklistfile,'wa')
1140	print 'save index peak list to file: ',G2frame.peaklistfile
1141	wx.BeginBusyCursor()
1142	try:
1143	if not peaks:
1144	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1145	try:
1146	dlg.ShowModal()
1147	finally:
1148	dlg.Destroy()
1149	return
1150	for peak in peaks:
1151	file.write("%12.6f\n" % (peak[7]))
1152	file.close()
1153	finally:
1154	wx.EndBusyCursor()
1155	print 'index peak list saved'
1156
1157	def SetNewPhase(Name='New Phase',SGData=None,cell=None,Super=None):
1158	'''Create a new phase dict with default values for various parameters
1159
1160	:param str Name: Name for new Phase
1161
1162	:param dict SGData: space group data from :func:`GSASIIspc:SpcGroup`;
1163	defaults to data for P 1
1164
1165	:param list cell: unit cell parameter list; defaults to
1166	[1.0,1.0,1.0,90.,90,90.,1.]
1167
1168	'''
1169	if SGData is None: SGData = G2spc.SpcGroup('P 1')[1]
1170	if cell is None: cell=[1.0,1.0,1.0,90.,90,90.,1.]
1171	phaseData = {
1172	'ranId':ran.randint(0,sys.maxint),
1173	'General':{
1174	'Name':Name,
1175	'Type':'nuclear',
1176	'Modulated':False,
1177	'AtomPtrs':[3,1,7,9],
1178	'SGData':SGData,
1179	'Cell':[False,]+cell,
1180	'Pawley dmin':1.0,
1181	'Data plot type':'None',
1182	'SH Texture':{
1183	'Order':0,
1184	'Model':'cylindrical',
1185	'Sample omega':[False,0.0],
1186	'Sample chi':[False,0.0],
1187	'Sample phi':[False,0.0],
1188	'SH Coeff':[False,{}],
1189	'SHShow':False,
1190	'PFhkl':[0,0,1],
1191	'PFxyz':[0,0,1],
1192	'PlotType':'Pole figure',
1193	'Penalty':[['',],0.1,False,1.0]}},
1194	'Atoms':[],
1195	'Drawing':{},
1196	'Histograms':{},
1197	'Pawley ref':[],
1198	'RBModels':{},
1199	}
1200	if Super and Super.get('Use',False):
1201	phaseData['General'].update({'Modulated':True,'Super':True,'SuperSg':Super['ssSymb']})
1202	phaseData['General']['SSGData'] = G2spc.SSpcGroup(SGData,Super['ssSymb'])
1203	phaseData['General']['SuperVec'] = [Super['ModVec'],False,Super['maxH']]
1204
1205	return phaseData
1206
1207	class MultipleChoicesDialog(wx.Dialog):
1208	'''A dialog that offers a series of choices, each with a
1209	title and a wx.Choice widget. Intended to be used Modally.
1210	typical input:
1211
1212	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1213	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1214
1215	selections are placed in self.chosen when OK is pressed
1216
1217	Also see GSASIIctrls
1218	'''
1219	def __init__(self,choicelist,headinglist,
1220	head='Select options',
1221	title='Please select from options below',
1222	parent=None):
1223	self.chosen = []
1224	wx.Dialog.__init__(
1225	self,parent,wx.ID_ANY,head,
1226	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
1227	panel = wx.Panel(self)
1228	mainSizer = wx.BoxSizer(wx.VERTICAL)
1229	mainSizer.Add((10,10),1)
1230	topLabl = wx.StaticText(panel,wx.ID_ANY,title)
1231	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.CENTER,10)
1232	self.ChItems = []
1233	for choice,lbl in zip(choicelist,headinglist):
1234	mainSizer.Add((10,10),1)
1235	self.chosen.append(0)
1236	topLabl = wx.StaticText(panel,wx.ID_ANY,' '+lbl)
1237	mainSizer.Add(topLabl,0,wx.ALIGN_LEFT,10)
1238	self.ChItems.append(wx.Choice(self, wx.ID_ANY, (100, 50), choices = choice))
1239	mainSizer.Add(self.ChItems[-1],0,wx.ALIGN_CENTER,10)
1240
1241	OkBtn = wx.Button(panel,-1,"Ok")
1242	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
1243	cancelBtn = wx.Button(panel,-1,"Cancel")
1244	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
1245	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1246	btnSizer.Add((20,20),1)
1247	btnSizer.Add(OkBtn)
1248	btnSizer.Add((20,20),1)
1249	btnSizer.Add(cancelBtn)
1250	btnSizer.Add((20,20),1)
1251	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1252	panel.SetSizer(mainSizer)
1253	panel.Fit()
1254	self.Fit()
1255
1256	def OnOk(self,event):
1257	parent = self.GetParent()
1258	if parent is not None: parent.Raise()
1259	# save the results from the choice widgets
1260	self.chosen = []
1261	for w in self.ChItems:
1262	self.chosen.append(w.GetSelection())
1263	self.EndModal(wx.ID_OK)
1264
1265	def OnCancel(self,event):
1266	parent = self.GetParent()
1267	if parent is not None: parent.Raise()
1268	self.chosen = []
1269	self.EndModal(wx.ID_CANCEL)
1270
1271	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1272	confirmoverwrite=True, parent=None,
1273	multipleselect=False):
1274	'''If the filename is a zip file, extract a file from that
1275	archive.
1276
1277	:param list Selection: used to predefine the name of the file
1278	to be extracted. Filename case and zip directory name are
1279	ignored in selection; the first matching file is used.
1280
1281	:param bool confirmread: if True asks the user to confirm before expanding
1282	the only file in a zip
1283
1284	:param bool confirmoverwrite: if True asks the user to confirm
1285	before overwriting if the extracted file already exists
1286
1287	:param bool multipleselect: if True allows more than one zip
1288	file to be extracted, a list of file(s) is returned.
1289	If only one file is present, do not ask which one, otherwise
1290	offer a list of choices (unless selection is used).
1291
1292	:returns: the name of the file that has been created or a
1293	list of files (see multipleselect)
1294
1295	If the file is not a zipfile, return the name of the input file.
1296	If the zipfile is empty or no file has been selected, return None
1297	'''
1298	import zipfile # do this now, since we can save startup time by doing this only on need
1299	import shutil
1300	zloc = os.path.split(filename)[0]
1301	if not zipfile.is_zipfile(filename):
1302	#print("not zip")
1303	return filename
1304
1305	z = zipfile.ZipFile(filename,'r')
1306	zinfo = z.infolist()
1307
1308	if len(zinfo) == 0:
1309	#print('Zip has no files!')
1310	zlist = [-1]
1311	if selection:
1312	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1313	if selection.lower() in choices:
1314	zlist = [choices.index(selection.lower())]
1315	else:
1316	print('debug: file '+str(selection)+' was not found in '+str(filename))
1317	zlist = [-1]
1318	elif len(zinfo) == 1 and confirmread:
1319	result = wx.ID_NO
1320	dlg = wx.MessageDialog(
1321	parent,
1322	'Is file '+str(zinfo[0].filename)+
1323	' what you want to extract from '+
1324	str(os.path.split(filename)[1])+'?',
1325	'Confirm file',
1326	wx.YES_NO \| wx.ICON_QUESTION)
1327	try:
1328	result = dlg.ShowModal()
1329	finally:
1330	dlg.Destroy()
1331	if result == wx.ID_NO:
1332	zlist = [-1]
1333	else:
1334	zlist = [0]
1335	elif len(zinfo) == 1:
1336	zlist = [0]
1337	elif multipleselect:
1338	# select one or more from a from list
1339	choices = [i.filename for i in zinfo]
1340	dlg = G2G.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1341	'Choose file(s)',choices)
1342	if dlg.ShowModal() == wx.ID_OK:
1343	zlist = dlg.GetSelections()
1344	else:
1345	zlist = []
1346	dlg.Destroy()
1347	else:
1348	# select one from a from list
1349	choices = [i.filename for i in zinfo]
1350	dlg = wx.SingleChoiceDialog(parent,
1351	'Select file to extract from zip file'+str(filename),'Choose file',
1352	choices,)
1353	if dlg.ShowModal() == wx.ID_OK:
1354	zlist = [dlg.GetSelection()]
1355	else:
1356	zlist = [-1]
1357	dlg.Destroy()
1358
1359	outlist = []
1360	for zindex in zlist:
1361	if zindex >= 0:
1362	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1363	if os.path.exists(efil) and confirmoverwrite:
1364	result = wx.ID_NO
1365	dlg = wx.MessageDialog(parent,
1366	'File '+str(efil)+' already exists. OK to overwrite it?',
1367	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1368	try:
1369	result = dlg.ShowModal()
1370	finally:
1371	dlg.Destroy()
1372	if result == wx.ID_NO:
1373	zindex = -1
1374	if zindex >= 0:
1375	# extract the file to the current directory, regardless of it's original path
1376	#z.extract(zinfo[zindex],zloc)
1377	eloc,efil = os.path.split(zinfo[zindex].filename)
1378	outfile = os.path.join(zloc, efil)
1379	fpin = z.open(zinfo[zindex])
1380	fpout = file(outfile, "wb")
1381	shutil.copyfileobj(fpin, fpout)
1382	fpin.close()
1383	fpout.close()
1384	outlist.append(outfile)
1385	z.close()
1386	if multipleselect and len(outlist) >= 1:
1387	return outlist
1388	elif len(outlist) == 1:
1389	return outlist[0]
1390	else:
1391	return None
1392
1393	######################################################################
1394	# base classes for reading various types of data files
1395	# not used directly, only by subclassing
1396	######################################################################
1397	try:
1398	E,SGData = G2spc.SpcGroup('P 1') # data structure for default space group
1399	except: # errors on doc build
1400	SGData = None
1401	P1SGData = SGData
1402	######################################################################
1403	class ImportBaseclass(object):
1404	'''Defines a base class for the reading of input files (diffraction
1405	data, coordinates,...). See :ref:`Writing a Import Routine<Import_routines>`
1406	for an explanation on how to use a subclass of this class.
1407	'''
1408	class ImportException(Exception):
1409	'''Defines an Exception that is used when an import routine hits an expected error,
1410	usually in .Reader.
1411
1412	Good practice is that the Reader should define a value in self.errors that
1413	tells the user some information about what is wrong with their file.
1414	'''
1415	pass
1416
1417	UseReader = True # in __init__ set value of self.UseReader to False to skip use of current importer
1418	def __init__(self,formatName,longFormatName=None,
1419	extensionlist=[],strictExtension=False,):
1420	self.formatName = formatName # short string naming file type
1421	if longFormatName: # longer string naming file type
1422	self.longFormatName = longFormatName
1423	else:
1424	self.longFormatName = formatName
1425	# define extensions that are allowed for the file type
1426	# for windows, remove any extensions that are duplicate, as case is ignored
1427	if sys.platform == 'windows' and extensionlist:
1428	extensionlist = list(set([s.lower() for s in extensionlist]))
1429	self.extensionlist = extensionlist
1430	# If strictExtension is True, the file will not be read, unless
1431	# the extension matches one in the extensionlist
1432	self.strictExtension = strictExtension
1433	self.errors = ''
1434	self.warnings = ''
1435	# used for readers that will use multiple passes to read
1436	# more than one data block
1437	self.repeat = False
1438	self.selections = []
1439	self.repeatcount = 0
1440	self.readfilename = '?'
1441	#print 'created',self.__class__
1442
1443	def ReInitialize(self):
1444	'Reinitialize the Reader to initial settings'
1445	self.errors = ''
1446	self.warnings = ''
1447	self.repeat = False
1448	self.repeatcount = 0
1449	self.readfilename = '?'
1450
1451	def BlockSelector(self, ChoiceList, ParentFrame=None,title='Select a block',
1452	size=None, header='Block Selector',useCancel=True):
1453	''' Provide a wx dialog to select a block if the file contains more
1454	than one set of data and one must be selected
1455	'''
1456	if useCancel:
1457	dlg = wx.SingleChoiceDialog(
1458	ParentFrame,title, header,ChoiceList)
1459	else:
1460	dlg = wx.SingleChoiceDialog(
1461	ParentFrame,title, header,ChoiceList,
1462	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.OK\|wx.CENTRE)
1463	if size: dlg.SetSize(size)
1464	dlg.CenterOnParent()
1465	if dlg.ShowModal() == wx.ID_OK:
1466	sel = dlg.GetSelection()
1467	return sel
1468	else:
1469	return None
1470	dlg.Destroy()
1471
1472	def MultipleBlockSelector(self, ChoiceList, ParentFrame=None,
1473	title='Select a block',size=None, header='Block Selector'):
1474	'''Provide a wx dialog to select a block of data if the
1475	file contains more than one set of data and one must be
1476	selected.
1477
1478	:returns: a list of the selected blocks
1479	'''
1480	dlg = wx.MultiChoiceDialog(ParentFrame,title, header,ChoiceList+['Select all'],
1481	wx.CHOICEDLG_STYLE)
1482	dlg.CenterOnScreen()
1483	if size: dlg.SetSize(size)
1484	if dlg.ShowModal() == wx.ID_OK:
1485	sel = dlg.GetSelections()
1486	else:
1487	return []
1488	dlg.Destroy()
1489	selected = []
1490	if len(ChoiceList) in sel:
1491	return range(len(ChoiceList))
1492	else:
1493	return sel
1494	return selected
1495
1496	def MultipleChoicesDialog(self, choicelist, headinglist, ParentFrame=None, **kwargs):
1497	'''A modal dialog that offers a series of choices, each with a title and a wx.Choice
1498	widget. Typical input:
1499
1500	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1501
1502	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1503
1504	optional keyword parameters are: head (window title) and title
1505	returns a list of selected indicies for each choice (or None)
1506	'''
1507	result = None
1508	dlg = MultipleChoicesDialog(choicelist,headinglist,
1509	parent=ParentFrame, **kwargs)
1510	dlg.CenterOnParent()
1511	if dlg.ShowModal() == wx.ID_OK:
1512	result = dlg.chosen
1513	dlg.Destroy()
1514	return result
1515
1516	def ShowBusy(self):
1517	wx.BeginBusyCursor()
1518	# wx.Yield() # make it happen now!
1519
1520	def DoneBusy(self):
1521	wx.EndBusyCursor()
1522	wx.Yield() # make it happen now!
1523
1524	# def Reader(self, filename, filepointer, ParentFrame=None, **unused):
1525	# '''This method must be supplied in the child class to read the file.
1526	# if the read fails either return False or raise an Exception
1527	# preferably of type ImportException.
1528	# '''
1529	# #start reading
1530	# raise ImportException("Error occurred while...")
1531	# self.errors += "Hint for user on why the error occur
1532	# return False # if an error occurs
1533	# return True # if read OK
1534
1535	def ExtensionValidator(self, filename):
1536	'''This methods checks if the file has the correct extension
1537	Return False if this filename will not be supported by this reader
1538	Return True if the extension matches the list supplied by the reader
1539	Return None if the reader allows un-registered extensions
1540	'''
1541	if filename:
1542	ext = os.path.splitext(filename)[1]
1543	if sys.platform == 'windows': ext = ext.lower()
1544	if ext in self.extensionlist: return True
1545	if self.strictExtension: return False
1546	return None
1547
1548	def ContentsValidator(self, filepointer):
1549	'''This routine will attempt to determine if the file can be read
1550	with the current format.
1551	This will typically be overridden with a method that
1552	takes a quick scan of [some of]
1553	the file contents to do a "sanity" check if the file
1554	appears to match the selected format.
1555	Expected to be called via self.Validator()
1556	'''
1557	#filepointer.seek(0) # rewind the file pointer
1558	return True
1559
1560	def CIFValidator(self, filepointer):
1561	'''A :meth:`ContentsValidator` for use to validate CIF files.
1562	'''
1563	for i,l in enumerate(filepointer):
1564	if i >= 1000: return True
1565	'''Encountered only blank lines or comments in first 1000
1566	lines. This is unlikely, but assume it is CIF anyway, since we are
1567	even less likely to find a file with nothing but hashes and
1568	blank lines'''
1569	line = l.strip()
1570	if len(line) == 0: # ignore blank lines
1571	continue
1572	elif line.startswith('#'): # ignore comments
1573	continue
1574	elif line.startswith('data_'): # on the right track, accept this file
1575	return True
1576	else: # found something invalid
1577	self.errors = 'line '+str(i+1)+' contains unexpected data:\n'
1578	if all([ord(c) < 128 and ord(c) != 0 for c in str(l)]): # show only if ASCII
1579	self.errors += ' '+str(l)
1580	else:
1581	self.errors += ' (binary)'
1582	self.errors += '\n Note: a CIF should only have blank lines or comments before'
1583	self.errors += '\n a data_ statement begins a block.'
1584	return False
1585
1586	######################################################################
1587	class ImportPhase(ImportBaseclass):
1588	'''Defines a base class for the reading of files with coordinates
1589
1590	Objects constructed that subclass this (in import/G2phase_*.py etc.) will be used
1591	in :meth:`GSASII.GSASII.OnImportPhase`.
1592	See :ref:`Writing a Import Routine<Import_Routines>`
1593	for an explanation on how to use this class.
1594
1595	'''
1596	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1597	strictExtension=False,):
1598	# call parent __init__
1599	ImportBaseclass.__init__(self,formatName,longFormatName,
1600	extensionlist,strictExtension)
1601	self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
1602	self.Constraints = None
1603
1604	def PhaseSelector(self, ChoiceList, ParentFrame=None,
1605	title='Select a phase', size=None,header='Phase Selector'):
1606	''' Provide a wx dialog to select a phase if the file contains more
1607	than one phase
1608	'''
1609	return self.BlockSelector(ChoiceList,ParentFrame,title,
1610	size,header)
1611
1612	######################################################################
1613	class ImportStructFactor(ImportBaseclass):
1614	'''Defines a base class for the reading of files with tables
1615	of structure factors.
1616
1617	Structure factors are read with a call to :meth:`GSASII.GSASII.OnImportSfact`
1618	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`, which calls
1619	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1620	:meth:`Reader`.
1621
1622	See :ref:`Writing a Import Routine<Import_Routines>`
1623	for an explanation on how to use import classes in general. The specifics
1624	for reading a structure factor histogram require that
1625	the ``Reader()`` routine in the import
1626	class need to do only a few things: It
1627	should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
1628	and set :attr:`Parameters` with the instrument parameters
1629	(initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
1630	'''
1631	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1632	strictExtension=False,):
1633	ImportBaseclass.__init__(self,formatName,longFormatName,
1634	extensionlist,strictExtension)
1635
1636	# define contents of Structure Factor entry
1637	self.Parameters = []
1638	'self.Parameters is a list with two dicts for data parameter settings'
1639	self.InitParameters()
1640	self.RefDict = {'RefList':[],'FF':{},'Super':0}
1641	self.Banks = [] #for multi bank data (usually TOF)
1642	'''self.RefDict is a dict containing the reflection information, as read from the file.
1643	Item 'RefList' contains the reflection information. See the
1644	:ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
1645	for the contents of each row. Dict element 'FF'
1646	contains the form factor values for each element type; if this entry
1647	is left as initialized (an empty list) it will be initialized as needed later.
1648	'''
1649	def ReInitialize(self):
1650	'Reinitialize the Reader to initial settings'
1651	ImportBaseclass.ReInitialize(self)
1652	self.InitParameters()
1653	self.Banks = [] #for multi bank data (usually TOF)
1654	self.RefDict = {'RefList':[],'FF':{},'Super':0}
1655
1656	def InitParameters(self):
1657	'initialize the instrument parameters structure'
1658	Lambda = 0.70926
1659	HistType = 'SXC'
1660	self.Parameters = [{'Type':[HistType,HistType], # create the structure
1661	'Lam':[Lambda,Lambda]
1662	}, {}]
1663	'Parameters is a list with two dicts for data parameter settings'
1664
1665	def UpdateParameters(self,Type=None,Wave=None):
1666	'Revise the instrument parameters'
1667	if Type is not None:
1668	self.Parameters[0]['Type'] = [Type,Type]
1669	if Wave is not None:
1670	self.Parameters[0]['Lam'] = [Wave,Wave]
1671
1672	######################################################################
1673	class ImportPowderData(ImportBaseclass):
1674	'''Defines a base class for the reading of files with powder data.
1675
1676	Objects constructed that subclass this (in import/G2pwd_*.py etc.) will be used
1677	in :meth:`GSASII.GSASII.OnImportPowder`.
1678	See :ref:`Writing a Import Routine<Import_Routines>`
1679	for an explanation on how to use this class.
1680	'''
1681	def __init__(self,formatName,longFormatName=None,
1682	extensionlist=[],strictExtension=False,):
1683	ImportBaseclass.__init__(self,formatName,longFormatName,
1684	extensionlist,strictExtension)
1685	self.clockWd = None # used in TOF
1686	self.ReInitialize()
1687
1688	def ReInitialize(self):
1689	'Reinitialize the Reader to initial settings'
1690	ImportBaseclass.ReInitialize(self)
1691	self.powderentry = ['',None,None] # (filename,Pos,Bank)
1692	self.powderdata = [] # Powder dataset
1693	'''A powder data set is a list with items [x,y,w,yc,yb,yd]:
1694	np.array(x), # x-axis values
1695	np.array(y), # powder pattern intensities
1696	np.array(w), # 1/sig(intensity)^2 values (weights)
1697	np.array(yc), # calc. intensities (zero)
1698	np.array(yb), # calc. background (zero)
1699	np.array(yd), # obs-calc profiles
1700	'''
1701	self.comments = []
1702	self.idstring = ''
1703	self.Sample = G2pdG.SetDefaultSample() # default sample parameters
1704	self.Controls = {} # items to be placed in top-level Controls
1705	self.GSAS = None # used in TOF
1706	self.repeat_instparm = True # Should a parm file be
1707	# used for multiple histograms?
1708	self.instparm = None # name hint from file of instparm to use
1709	self.instfile = '' # full path name to instrument parameter file
1710	self.instbank = '' # inst parm bank number
1711	self.instmsg = '' # a label that gets printed to show
1712	# where instrument parameters are from
1713	self.numbanks = 1
1714	self.instdict = {} # place items here that will be transferred to the instrument parameters
1715	self.pwdparms = {} # place parameters that are transferred directly to the tree
1716	# here (typically from an existing GPX file)
1717	######################################################################
1718	class ImportSmallAngleData(ImportBaseclass):
1719	'''Defines a base class for the reading of files with small angle data.
1720	See :ref:`Writing a Import Routine<Import_Routines>`
1721	for an explanation on how to use this class.
1722	'''
1723	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1724	strictExtension=False,):
1725
1726	ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
1727	strictExtension)
1728	self.ReInitialize()
1729
1730	def ReInitialize(self):
1731	'Reinitialize the Reader to initial settings'
1732	ImportBaseclass.ReInitialize(self)
1733	self.smallangleentry = ['',None,None] # (filename,Pos,Bank)
1734	self.smallangledata = [] # SASD dataset
1735	'''A small angle data set is a list with items [x,y,w,yc,yd]:
1736	np.array(x), # x-axis values
1737	np.array(y), # powder pattern intensities
1738	np.array(w), # 1/sig(intensity)^2 values (weights)
1739	np.array(yc), # calc. intensities (zero)
1740	np.array(yd), # obs-calc profiles
1741	np.array(yb), # preset bkg
1742	'''
1743	self.comments = []
1744	self.idstring = ''
1745	self.Sample = G2pdG.SetDefaultSample()
1746	self.GSAS = None # used in TOF
1747	self.clockWd = None # used in TOF
1748	self.numbanks = 1
1749	self.instdict = {} # place items here that will be transferred to the instrument parameters
1750
1751	######################################################################
1752	class ImportReflectometryData(ImportBaseclass):
1753	'''Defines a base class for the reading of files with small angle data.
1754	See :ref:`Writing a Import Routine<Import_Routines>`
1755	for an explanation on how to use this class.
1756	'''
1757	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1758	strictExtension=False,):
1759
1760	ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
1761	strictExtension)
1762	self.ReInitialize()
1763
1764	def ReInitialize(self):
1765	'Reinitialize the Reader to initial settings'
1766	ImportBaseclass.ReInitialize(self)
1767	self.reflectometryentry = ['',None,None] # (filename,Pos,Bank)
1768	self.reflectometrydata = [] # SASD dataset
1769	'''A small angle data set is a list with items [x,y,w,yc,yd]:
1770	np.array(x), # x-axis values
1771	np.array(y), # powder pattern intensities
1772	np.array(w), # 1/sig(intensity)^2 values (weights)
1773	np.array(yc), # calc. intensities (zero)
1774	np.array(yd), # obs-calc profiles
1775	np.array(yb), # preset bkg
1776	'''
1777	self.comments = []
1778	self.idstring = ''
1779	self.Sample = G2pdG.SetDefaultSample()
1780	self.GSAS = None # used in TOF
1781	self.clockWd = None # used in TOF
1782	self.numbanks = 1
1783	self.instdict = {} # place items here that will be transferred to the instrument parameters
1784
1785	######################################################################
1786	class ImportImage(ImportBaseclass):
1787	'''Defines a base class for the reading of images
1788
1789	Images are read in only these places:
1790
1791	* Initial reading is typically done from a menu item
1792	with a call to :meth:`GSASII.GSASII.OnImportImage`
1793	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`. That calls
1794	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1795	:meth:`Reader`. This returns a list of reader objects for each read image.
1796
1797	* Images are read alternatively in :func:`GSASIIIO.ReadImages`, which puts image info
1798	directly into the data tree.
1799
1800	* Images are reloaded with :func:`GSASIIIO.GetImageData`.
1801
1802	.. _Image_import_routines:
1803
1804	When reading an image, the ``Reader()`` routine in the ImportImage class
1805	should set:
1806
1807	* :attr:`Comments`: a list of strings (str),
1808	* :attr:`Npix`: the number of pixels in the image (int),
1809	* :attr:`Image`: the actual image as a numpy array (np.array)
1810	* :attr:`Data`: a dict defining image parameters (dict). Within this dict the following
1811	data items are needed:
1812
1813	* 'pixelSize': size of each pixel in microns (such as ``[200,200]``.
1814	* 'wavelength': wavelength in Angstoms.
1815	* 'distance': distance of detector from sample in cm.
1816	* 'center': uncalibrated center of beam on detector (such as ``[204.8,204.8]``.
1817	* 'size': size of image (such as ``[2048,2048]``).
1818	* 'ImageTag': image number or other keyword used to retrieve image from
1819	a multi-image data file (defaults to ``1`` if not specified).
1820	* 'sumfile': holds sum image file name if a sum was produced from a multi image file
1821
1822	optional data items:
1823
1824	* :attr:`repeat`: set to True if there are additional images to
1825	read in the file, False otherwise
1826	* :attr:`repeatcount`: set to the number of the image.
1827
1828	Note that the above is initialized with :meth:`InitParameters`.
1829	(Also see :ref:`Writing a Import Routine<Import_Routines>`
1830	for an explanation on how to use import classes in general.)
1831	'''
1832	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1833	strictExtension=False,):
1834	ImportBaseclass.__init__(self,formatName,longFormatName,
1835	extensionlist,strictExtension)
1836	self.InitParameters()
1837
1838	def ReInitialize(self):
1839	'Reinitialize the Reader to initial settings -- not used at present'
1840	ImportBaseclass.ReInitialize(self)
1841	self.InitParameters()
1842
1843	def InitParameters(self):
1844	'initialize the instrument parameters structure'
1845	self.Comments = ['No comments']
1846	self.Data = {}
1847	self.Npix = 0
1848	self.Image = None
1849	self.repeat = False
1850	self.repeatcount = 1
1851	self.sumfile = ''
1852
1853	def LoadImage(self,ParentFrame,imagefile,imagetag=None):
1854	'''Optionally, call this after reading in an image to load it into the tree.
1855	This saves time by preventing a reread of the same information.
1856	'''
1857	if ParentFrame:
1858	ParentFrame.ImageZ = self.Image # store the image for plotting
1859	ParentFrame.oldImagefile = imagefile # save the name of the last image file read
1860	ParentFrame.oldImageTag = imagetag # save the tag of the last image file read
1861
1862	######################################################################
1863	def striphist(var,insChar=''):
1864	'strip a histogram number from a var name'
1865	sv = var.split(':')
1866	if len(sv) <= 1: return var
1867	if sv[1]:
1868	sv[1] = insChar
1869	return ':'.join(sv)
1870	class ExportBaseclass(object):
1871	'''Defines a base class for the exporting of GSAS-II results.
1872
1873	This class is subclassed in the various exports/G2export_*.py files. Those files
1874	are imported in :meth:`GSASII.GSASII._init_Exports` which defines the
1875	appropriate menu items for each one and the .Exporter method is called
1876	directly from the menu item.
1877
1878	Routines may also define a .Writer method, which is used to write a single
1879	file without invoking any GUI objects.
1880	'''
1881	def __init__(self,G2frame,formatName,extension,longFormatName=None,):
1882	self.G2frame = G2frame
1883	self.formatName = formatName # short string naming file type
1884	self.extension = extension
1885	if longFormatName: # longer string naming file type
1886	self.longFormatName = longFormatName
1887	else:
1888	self.longFormatName = formatName
1889	self.OverallParms = {}
1890	self.Phases = {}
1891	self.Histograms = {}
1892	self.powderDict = {}
1893	self.xtalDict = {}
1894	self.parmDict = {}
1895	self.sigDict = {}
1896	# updated in InitExport:
1897	self.currentExportType = None # type of export that has been requested
1898	# updated in ExportSelect (when used):
1899	self.phasenam = None # a list of selected phases
1900	self.histnam = None # a list of selected histograms
1901	self.filename = None # name of file to be written (single export) or template (multiple files)
1902	self.dirname = '' # name of directory where file(s) will be written
1903	self.fullpath = '' # name of file being written -- full path
1904
1905	# items that should be defined in a subclass of this class
1906	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1907	# The following types are defined: 'project', "phase", "powder", "single"
1908	self.multiple = False # set as True if the class can export multiple phases or histograms
1909	# self.multiple is ignored for "project" exports
1910
1911	def InitExport(self,event):
1912	'''Determines the type of menu that called the Exporter and
1913	misc initialization.
1914	'''
1915	self.filename = None # name of file to be written (single export)
1916	self.dirname = '' # name of file to be written (multiple export)
1917	if event:
1918	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1919
1920	def MakePWDRfilename(self,hist):
1921	'''Make a filename root (no extension) from a PWDR histogram name
1922
1923	:param str hist: the histogram name in data tree (starts with "PWDR ")
1924	'''
1925	file0 = ''
1926	file1 = hist[5:]
1927	# replace repeated blanks
1928	while file1 != file0:
1929	file0 = file1
1930	file1 = file0.replace(' ',' ').strip()
1931	file0 = file1.replace('Azm= ','A')
1932	# if angle has unneeded decimal places on aziumuth, remove them
1933	if file0[-3:] == '.00': file0 = file0[:-3]
1934	file0 = file0.replace('.','_')
1935	file0 = file0.replace(' ','_')
1936	return file0
1937
1938	def ExportSelect(self,AskFile='ask'):
1939	'''Selects histograms or phases when needed. Sets a default file name when
1940	requested into self.filename; always sets a default directory in self.dirname.
1941
1942	:param bool AskFile: Determines how this routine processes getting a
1943	location to store the current export(s).
1944
1945	* if AskFile is 'ask' (default option), get the name of the file to be written;
1946	self.filename and self.dirname are always set. In the case where
1947	multiple files must be generated, the export routine should do this
1948	based on self.filename as a template.
1949	* if AskFile is 'dir', get the name of the directory to be used;
1950	self.filename is not used, but self.dirname is always set. The export routine
1951	will always generate the file name.
1952	* if AskFile is 'single', get only the name of the directory to be used when
1953	multiple items will be written (as multiple files) are used
1954	or a complete file name is requested when a single file
1955	name is selected. self.dirname is always set and self.filename used
1956	only when a single file is selected.
1957	* if AskFile is 'default', creates a name of the file to be used from
1958	the name of the project (.gpx) file. If the project has not been saved,
1959	then the name of file is requested.
1960	self.filename and self.dirname are always set. In the case where
1961	multiple file names must be generated, the export routine should do this
1962	based on self.filename.
1963	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1964	file. If the project has not been saved, then a directory is requested.
1965	self.filename is not used.
1966
1967	:returns: True in case of an error
1968	'''
1969
1970	numselected = 1
1971	if self.currentExportType == 'phase':
1972	if len(self.Phases) == 0:
1973	self.G2frame.ErrorDialog(
1974	'Empty project',
1975	'Project does not contain any phases.')
1976	return True
1977	elif len(self.Phases) == 1:
1978	self.phasenam = self.Phases.keys()
1979	elif self.multiple:
1980	choices = sorted(self.Phases.keys())
1981	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1982	if phasenum is None: return True
1983	self.phasenam = [choices[i] for i in phasenum]
1984	if not self.phasenam: return True
1985	numselected = len(self.phasenam)
1986	else:
1987	choices = sorted(self.Phases.keys())
1988	phasenum = G2G.ItemSelector(choices,self.G2frame)
1989	if phasenum is None: return True
1990	self.phasenam = [choices[phasenum]]
1991	numselected = len(self.phasenam)
1992	elif self.currentExportType == 'single':
1993	if len(self.xtalDict) == 0:
1994	self.G2frame.ErrorDialog(
1995	'Empty project',
1996	'Project does not contain any single crystal data.')
1997	return True
1998	elif len(self.xtalDict) == 1:
1999	self.histnam = self.xtalDict.values()
2000	elif self.multiple:
2001	choices = sorted(self.xtalDict.values())
2002	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
2003	if not hnum: return True
2004	self.histnam = [choices[i] for i in hnum]
2005	numselected = len(self.histnam)
2006	else:
2007	choices = sorted(self.xtalDict.values())
2008	hnum = G2G.ItemSelector(choices,self.G2frame)
2009	if hnum is None: return True
2010	self.histnam = [choices[hnum]]
2011	numselected = len(self.histnam)
2012	elif self.currentExportType == 'powder':
2013	if len(self.powderDict) == 0:
2014	self.G2frame.ErrorDialog(
2015	'Empty project',
2016	'Project does not contain any powder data.')
2017	return True
2018	elif len(self.powderDict) == 1:
2019	self.histnam = self.powderDict.values()
2020	elif self.multiple:
2021	choices = sorted(self.powderDict.values())
2022	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
2023	if not hnum: return True
2024	self.histnam = [choices[i] for i in hnum]
2025	numselected = len(self.histnam)
2026	else:
2027	choices = sorted(self.powderDict.values())
2028	hnum = G2G.ItemSelector(choices,self.G2frame)
2029	if hnum is None: return True
2030	self.histnam = [choices[hnum]]
2031	numselected = len(self.histnam)
2032	elif self.currentExportType == 'image':
2033	if len(self.Histograms) == 0:
2034	self.G2frame.ErrorDialog(
2035	'Empty project',
2036	'Project does not contain any images.')
2037	return True
2038	elif len(self.Histograms) == 1:
2039	self.histnam = self.Histograms.keys()
2040	else:
2041	choices = sorted(self.Histograms.keys())
2042	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
2043	if self.multiple:
2044	if not hnum: return True
2045	self.histnam = [choices[i] for i in hnum]
2046	else:
2047	if hnum is None: return True
2048	self.histnam = [choices[hnum]]
2049	numselected = len(self.histnam)
2050	if self.currentExportType == 'map':
2051	# search for phases with maps
2052	mapPhases = []
2053	choices = []
2054	for phasenam in sorted(self.Phases):
2055	phasedict = self.Phases[phasenam] # pointer to current phase info
2056	if len(phasedict['General']['Map'].get('rho',[])):
2057	mapPhases.append(phasenam)
2058	if phasedict['General']['Map'].get('Flip'):
2059	choices.append('Charge flip map: '+str(phasenam))
2060	elif phasedict['General']['Map'].get('MapType'):
2061	choices.append(
2062	str(phasedict['General']['Map'].get('MapType'))
2063	+ ' map: ' + str(phasenam))
2064	else:
2065	choices.append('unknown map: '+str(phasenam))
2066	# select a map if needed
2067	if len(mapPhases) == 0:
2068	self.G2frame.ErrorDialog(
2069	'Empty project',
2070	'Project does not contain any maps.')
2071	return True
2072	elif len(mapPhases) == 1:
2073	self.phasenam = mapPhases
2074	else:
2075	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
2076	if self.multiple:
2077	if not phasenum: return True
2078	self.phasenam = [mapPhases[i] for i in phasenum]
2079	else:
2080	if phasenum is None: return True
2081	self.phasenam = [mapPhases[phasenum]]
2082	numselected = len(self.phasenam)
2083
2084	# items selected, now set self.dirname and usually self.filename
2085	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
2086	AskFile == 'default' and not self.G2frame.GSASprojectfile
2087	):
2088	filename = self.askSaveFile()
2089	if not filename: return True
2090	self.dirname,self.filename = os.path.split(filename)
2091	elif AskFile == 'dir' or AskFile == 'single' or (
2092	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
2093	):
2094	self.dirname = self.askSaveDirectory()
2095	if not self.dirname: return True
2096	elif AskFile == 'default-dir' or AskFile == 'default':
2097	self.dirname,self.filename = os.path.split(
2098	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
2099	)
2100	else:
2101	raise Exception('This should not happen!')
2102
2103	def loadParmDict(self):
2104	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
2105	refined values to those from the last cycle and set the uncertainties for the
2106	refined parameters in another dict (self.sigDict).
2107
2108	Expands the parm & sig dicts to include values derived from constraints.
2109	'''
2110	self.parmDict = {}
2111	self.sigDict = {}
2112	rigidbodyDict = {}
2113	covDict = {}
2114	consDict = {}
2115	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2116	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2117	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2118	while item:
2119	name = self.G2frame.PatternTree.GetItemText(item)
2120	if name == 'Rigid bodies':
2121	rigidbodyDict = self.G2frame.PatternTree.GetItemPyData(item)
2122	elif name == 'Covariance':
2123	covDict = self.G2frame.PatternTree.GetItemPyData(item)
2124	elif name == 'Constraints':
2125	consDict = self.G2frame.PatternTree.GetItemPyData(item)
2126	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2127	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
2128	self.parmDict.update(rbDict)
2129	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
2130	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData(
2131	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
2132	self.parmDict.update(phaseDict)
2133	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
2134	Phases,Histograms,Print=False,resetRefList=False)
2135	self.parmDict.update(hapDict)
2136	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
2137	self.parmDict.update(histDict)
2138	self.parmDict.update(zip(
2139	covDict.get('varyList',[]),
2140	covDict.get('variables',[])))
2141	self.sigDict = dict(zip(
2142	covDict.get('varyList',[]),
2143	covDict.get('sig',[])))
2144	# expand to include constraints: first compile a list of constraints
2145	constList = []
2146	for item in consDict:
2147	if item.startswith('_'): continue
2148	constList += consDict[item]
2149	# now process the constraints
2150	G2mv.InitVars()
2151	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
2152	varyList = covDict.get('varyListStart')
2153	if varyList is None and len(constDict) == 0:
2154	# no constraints can use varyList
2155	varyList = covDict.get('varyList')
2156	elif varyList is None:
2157	# old GPX file from before pre-constraint varyList is saved
2158	print ' * Old refinement: Please use Calculate/Refine to redo *'
2159	raise Exception(' * Export aborted *')
2160	else:
2161	varyList = list(varyList)
2162	try:
2163	groups,parmlist = G2mv.GroupConstraints(constDict)
2164	G2mv.GenerateConstraints(groups,parmlist,varyList,constDict,fixedList,self.parmDict)
2165	except:
2166	# this really should not happen
2167	print ' * ERROR - constraints are internally inconsistent *'
2168	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
2169	print 'Errors',errmsg
2170	if warnmsg: print 'Warnings',warnmsg
2171	raise Exception(' * CIF creation aborted *')
2172	# add the constrained values to the parameter dictionary
2173	G2mv.Dict2Map(self.parmDict,varyList)
2174	# and add their uncertainties into the esd dictionary (sigDict)
2175	if covDict.get('covMatrix') is not None:
2176	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
2177
2178	def loadTree(self):
2179	'''Load the contents of the data tree into a set of dicts
2180	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
2181	& self.xtalDict)
2182
2183	* The childrenless data tree items are overall parameters/controls for the
2184	entire project and are placed in self.OverallParms
2185	* Phase items are placed in self.Phases
2186	* Data items are placed in self.Histogram. The key for these data items
2187	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
2188	'''
2189	self.OverallParms = {}
2190	self.powderDict = {}
2191	self.xtalDict = {}
2192	self.Phases = {}
2193	self.Histograms = {}
2194	self.SeqRefdata = None
2195	self.SeqRefhist = None
2196	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2197	histType = None
2198	if self.currentExportType == 'phase':
2199	# if exporting phases load them here
2200	sub = G2gd.GetPatternTreeItemId(self.G2frame,self.G2frame.root,'Phases')
2201	if not sub:
2202	print 'no phases found'
2203	return True
2204	item, cookie = self.G2frame.PatternTree.GetFirstChild(sub)
2205	while item:
2206	phaseName = self.G2frame.PatternTree.GetItemText(item)
2207	self.Phases[phaseName] = self.G2frame.PatternTree.GetItemPyData(item)
2208	item, cookie = self.G2frame.PatternTree.GetNextChild(sub, cookie)
2209	return
2210	elif self.currentExportType == 'single':
2211	histType = 'HKLF'
2212	elif self.currentExportType == 'powder':
2213	histType = 'PWDR'
2214	elif self.currentExportType == 'image':
2215	histType = 'IMG'
2216
2217	if histType: # Loading just one kind of tree entry
2218	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2219	while item:
2220	name = self.G2frame.PatternTree.GetItemText(item)
2221	if name.startswith(histType):
2222	if self.Histograms.get(name): # there is already an item with this name
2223	print('Histogram name '+str(name)+' is repeated. Renaming')
2224	if name[-1] == '9':
2225	name = name[:-1] + '10'
2226	elif name[-1] in '012345678':
2227	name = name[:-1] + str(int(name[-1])+1)
2228	else:
2229	name += '-1'
2230	self.Histograms[name] = {}
2231	# the main info goes into Data, but the 0th
2232	# element contains refinement results, carry
2233	# that over too now.
2234	self.Histograms[name]['Data'] = self.G2frame.PatternTree.GetItemPyData(item)[1]
2235	self.Histograms[name][0] = self.G2frame.PatternTree.GetItemPyData(item)[0]
2236	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2237	while item2:
2238	child = self.G2frame.PatternTree.GetItemText(item2)
2239	self.Histograms[name][child] = self.G2frame.PatternTree.GetItemPyData(item2)
2240	item2, cookie2 = self.G2frame.PatternTree.GetNextChild(item, cookie2)
2241	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2242	# index powder and single crystal histograms by number
2243	for hist in self.Histograms:
2244	if hist.startswith("PWDR"):
2245	d = self.powderDict
2246	elif hist.startswith("HKLF"):
2247	d = self.xtalDict
2248	else:
2249	return
2250	i = self.Histograms[hist].get('hId')
2251	if i is None and not d.keys():
2252	i = 0
2253	elif i is None or i in d.keys():
2254	i = max(d.keys())+1
2255	d[i] = hist
2256	return
2257	# else standard load: using all interlinked phases and histograms
2258	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2259	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2260	while item:
2261	name = self.G2frame.PatternTree.GetItemText(item)
2262	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2263	if not item2:
2264	self.OverallParms[name] = self.G2frame.PatternTree.GetItemPyData(item)
2265	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2266	# index powder and single crystal histograms
2267	for hist in self.Histograms:
2268	i = self.Histograms[hist]['hId']
2269	if hist.startswith("PWDR"):
2270	self.powderDict[i] = hist
2271	elif hist.startswith("HKLF"):
2272	self.xtalDict[i] = hist
2273
2274	def dumpTree(self,mode='type'):
2275	'''Print out information on the data tree dicts loaded in loadTree.
2276	Used for testing only.
2277	'''
2278	if self.SeqRefdata and self.SeqRefhist:
2279	print('Note that dumpTree does not show sequential results')
2280	print '\nOverall'
2281	if mode == 'type':
2282	def Show(arg): return type(arg)
2283	else:
2284	def Show(arg): return arg
2285	for key in self.OverallParms:
2286	print ' ',key,Show(self.OverallParms[key])
2287	print 'Phases'
2288	for key1 in self.Phases:
2289	print ' ',key1,Show(self.Phases[key1])
2290	print 'Histogram'
2291	for key1 in self.Histograms:
2292	print ' ',key1,Show(self.Histograms[key1])
2293	for key2 in self.Histograms[key1]:
2294	print ' ',key2,Show(self.Histograms[key1][key2])
2295
2296	def defaultSaveFile(self):
2297	return os.path.abspath(
2298	os.path.splitext(self.G2frame.GSASprojectfile
2299	)[0]+self.extension)
2300
2301	def askSaveFile(self):
2302	'''Ask the user to supply a file name
2303
2304	:returns: a file name (str) or None if Cancel is pressed
2305	'''
2306
2307	pth = G2G.GetExportPath(self.G2frame)
2308	defnam = os.path.splitext(
2309	os.path.split(self.G2frame.GSASprojectfile)[1]
2310	)[0]+self.extension
2311	dlg = wx.FileDialog(
2312	self.G2frame, 'Input name for file to write', pth, defnam,
2313	self.longFormatName+' ('+self.extension+')\|'+self.extension,
2314	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
2315	dlg.CenterOnParent()
2316	try:
2317	if dlg.ShowModal() == wx.ID_OK:
2318	filename = dlg.GetPath()
2319	self.G2frame.LastExportDir = os.path.split(filename)[0]
2320	filename = os.path.splitext(filename)[0]+self.extension # make sure extension is correct
2321	else:
2322	filename = None
2323	finally:
2324	dlg.Destroy()
2325	return filename
2326
2327	def askSaveDirectory(self):
2328	'''Ask the user to supply a directory name. Path name is used as the
2329	starting point for the next export path search.
2330
2331	:returns: a directory name (str) or None if Cancel is pressed
2332	'''
2333	pth = G2G.GetExportPath(self.G2frame)
2334	dlg = wx.DirDialog(
2335	self.G2frame, 'Input directory where file(s) will be written', pth,
2336	wx.DD_DEFAULT_STYLE)
2337	dlg.CenterOnParent()
2338	try:
2339	if dlg.ShowModal() == wx.ID_OK:
2340	filename = dlg.GetPath()
2341	self.G2frame.LastExportDir = filename
2342	else:
2343	filename = None
2344	finally:
2345	dlg.Destroy()
2346	return filename
2347
2348	# Tools for file writing.
2349	def OpenFile(self,fil=None,mode='w'):
2350	'''Open the output file
2351
2352	:param str fil: The name of the file to open. If None (default)
2353	the name defaults to self.dirname + self.filename.
2354	If an extension is supplied, it is not overridded,
2355	but if not, the default extension is used.
2356	:returns: the file object opened by the routine which is also
2357	saved as self.fp
2358	'''
2359	if mode == 'd': # debug mode
2360	self.fullpath = '(stdout)'
2361	self.fp = sys.stdout
2362	return
2363	if not fil:
2364	if not os.path.splitext(self.filename)[1]:
2365	self.filename += self.extension
2366	fil = os.path.join(self.dirname,self.filename)
2367	self.fullpath = os.path.abspath(fil)
2368	self.fp = open(self.fullpath,mode)
2369	return self.fp
2370
2371	def Write(self,line):
2372	'''write a line of output, attaching a line-end character
2373
2374	:param str line: the text to be written.
2375	'''
2376	self.fp.write(line+'\n')
2377
2378	def CloseFile(self,fp=None):
2379	'''Close a file opened in OpenFile
2380
2381	:param file fp: the file object to be closed. If None (default)
2382	file object self.fp is closed.
2383	'''
2384	if self.fp == sys.stdout: return # debug mode
2385	if fp is None:
2386	fp = self.fp
2387	self.fp = None
2388	fp.close()
2389
2390	def SetSeqRef(self,data,hist):
2391	'''Set the exporter to retrieve results from a sequential refinement
2392	rather than the main tree
2393	'''
2394	self.SeqRefdata = data
2395	self.SeqRefhist = hist
2396	data_name = data[hist]
2397	for i,val in zip(data_name['varyList'],data_name['sig']):
2398	self.sigDict[i] = val
2399	self.sigDict[striphist(i)] = val
2400	for i in data_name['parmDict']:
2401	self.parmDict[striphist(i)] = data_name['parmDict'][i]
2402	self.parmDict[i] = data_name['parmDict'][i]
2403	# zero out the dA[xyz] terms, they would only bring confusion
2404	key = i.split(':')
2405	if len(key) < 3: continue
2406	if key[2].startswith('dA'):
2407	self.parmDict[i] = 0.0
2408	for i,(val,sig) in data_name.get('depParmDict',{}).iteritems():
2409	self.parmDict[i] = val
2410	self.sigDict[i] = sig
2411	#GSASIIpath.IPyBreak()
2412
2413	# Tools to pull information out of the data arrays
2414	def GetCell(self,phasenam):
2415	"""Gets the unit cell parameters and their s.u.'s for a selected phase
2416
2417	:param str phasenam: the name for the selected phase
2418	:returns: `cellList,cellSig` where each is a 7 element list corresponding
2419	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
2420	cell values and `cellSig` has their uncertainties.
2421	"""
2422	if self.SeqRefdata and self.SeqRefhist:
2423	return self.GetSeqCell(phasenam,self.SeqRefdata[self.SeqRefhist])
2424	phasedict = self.Phases[phasenam] # pointer to current phase info
2425	try:
2426	pfx = str(phasedict['pId'])+'::'
2427	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
2428	cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A,
2429	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
2430	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
2431	return cellList,cellSig
2432	except KeyError:
2433	cell = phasedict['General']['Cell'][1:]
2434	return cell,7*[0]
2435
2436	def GetSeqCell(self,phasenam,data_name):
2437	"""Gets the unit cell parameters and their s.u.'s for a selected phase
2438	and histogram in a sequential fit
2439
2440	:param str phasenam: the name for the selected phase
2441	:param dict data_name: the sequential refinement parameters for the selected histogram
2442	:returns: `cellList,cellSig` where each is a 7 element list corresponding
2443	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
2444	cell values and `cellSig` has their uncertainties.
2445	"""
2446	phasedict = self.Phases[phasenam]
2447	SGdata = phasedict['General']['SGData']
2448	pId = phasedict['pId']
2449	RecpCellTerms = G2lat.cell2A(phasedict['General']['Cell'][1:7])
2450	ESDlookup = {}
2451	Dlookup = {}
2452	varied = [striphist(i) for i in data_name['varyList']]
2453	for item,val in data_name['newCellDict'].iteritems():
2454	if item in varied:
2455	ESDlookup[val[0]] = item
2456	Dlookup[item] = val[0]
2457	A = RecpCellTerms[:]
2458	for i in range(6):
2459	var = str(pId)+'::A'+str(i)
2460	if var in ESDlookup:
2461	A[i] = data_name['newCellDict'][ESDlookup[var]][1] # override with refined value
2462	cellDict = dict(zip([str(pId)+'::A'+str(i) for i in range(6)],A))
2463	zeroDict = {i:0.0 for i in cellDict}
2464	A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata,cellDict,zeroDict)
2465	covData = {
2466	'varyList': [Dlookup.get(striphist(v),v) for v in data_name['varyList']],
2467	'covMatrix': data_name['covMatrix']
2468	}
2469	return list(G2lat.A2cell(A)) + [G2lat.calc_V(A)], G2stIO.getCellEsd(str(pId)+'::',SGdata,A,covData)
2470
2471	def GetAtoms(self,phasenam):
2472	"""Gets the atoms associated with a phase. Can be used with standard
2473	or macromolecular phases
2474
2475	:param str phasenam: the name for the selected phase
2476	:returns: a list of items for eac atom where each item is a list containing:
2477	label, typ, mult, xyz, and td, where
2478
2479	* label and typ are the atom label and the scattering factor type (str)
2480	* mult is the site multiplicity (int)
2481	* xyz is contains a list with four pairs of numbers:
2482	x, y, z and fractional occupancy and
2483	their standard uncertainty (or a negative value)
2484	* td is contains a list with either one or six pairs of numbers:
2485	if one number it is U\ :sub:`iso` and with six numbers it is
2486	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
2487	paired with their standard uncertainty (or a negative value)
2488	"""
2489	phasedict = self.Phases[phasenam] # pointer to current phase info
2490	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
2491	cfrac = cx+3
2492	fpfx = str(phasedict['pId'])+'::Afrac:'
2493	atomslist = []
2494	for i,at in enumerate(phasedict['Atoms']):
2495	if phasedict['General']['Type'] == 'macromolecular':
2496	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
2497	else:
2498	label = at[ct-1]
2499	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
2500	fsig = self.sigDict.get(fpfx+str(i),-0.009)
2501	mult = at[cs+1]
2502	typ = at[ct]
2503	xyz = []
2504	for j,v in enumerate(('x','y','z')):
2505	val = at[cx+j]
2506	pfx = str(phasedict['pId']) + '::A' + v + ':' + str(i)
2507	val = self.parmDict.get(pfx, val)
2508	dpfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
2509	sig = self.sigDict.get(dpfx,-0.000009)
2510	xyz.append((val,sig))
2511	xyz.append((fval,fsig))
2512	td = []
2513	if at[cia] == 'I':
2514	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
2515	val = self.parmDict.get(pfx,at[cia+1])
2516	sig = self.sigDict.get(pfx,-0.0009)
2517	td.append((val,sig))
2518	else:
2519	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
2520	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
2521	val = self.parmDict.get(pfx,at[cia+2+i])
2522	sig = self.sigDict.get(pfx,-0.0009)
2523	td.append((val,sig))
2524	atomslist.append((label,typ,mult,xyz,td))
2525	return atomslist
2526	######################################################################
2527	def ExportPowderList(G2frame):
2528	'''Returns a list of extensions supported by :func:`GSASIIIO:ExportPowder`
2529	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
2530
2531	:param wx.Frame G2frame: the GSAS-II main data tree window
2532	'''
2533	extList = []
2534	for obj in G2frame.exporterlist:
2535	if 'powder' in obj.exporttype:
2536	try:
2537	obj.Writer
2538	extList.append(obj.extension)
2539	except AttributeError:
2540	pass
2541	return extList
2542
2543	def ExportPowder(G2frame,TreeName,fileroot,extension):
2544	'''Writes a single powder histogram using the Export routines.
2545	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
2546
2547	:param wx.Frame G2frame: the GSAS-II main data tree window
2548	:param str TreeName: the name of the histogram (PWDR ...) in the data tree
2549	:param str fileroot: name for file to be written, extension ignored
2550	:param str extension: extension for file to be written (start with '.'). Must
2551	match a powder export routine that has a Writer object.
2552	'''
2553	filename = os.path.abspath(os.path.splitext(fileroot)[0]+extension)
2554	for obj in G2frame.exporterlist:
2555	if obj.extension == extension and 'powder' in obj.exporttype:
2556	obj.currentExportType = 'powder'
2557	obj.InitExport(None)
2558	obj.loadTree() # load all histograms in tree into dicts
2559	if TreeName not in obj.Histograms:
2560	raise Exception('Histogram not found: '+str(TreeName))
2561	try:
2562	obj.Writer
2563	except AttributeError:
2564	continue
2565	try:
2566	obj.Writer(TreeName,filename)
2567	return
2568	except Exception,err:
2569	print('Export Routine for '+extension+' failed.')
2570	print err
2571	else:
2572	print('No Export routine supports extension '+extension)
2573
2574	def ExportSequential(G2frame,data,obj,exporttype):
2575	'''
2576	Used to export from every phase/dataset in a sequential refinement using
2577	a .Writer method for either projects or phases. Prompts to select histograms
2578	and for phase exports, which phase(s).
2579
2580	:param wx.Frame G2frame: the GSAS-II main data tree window
2581	:param dict data: the sequential refinement data object
2582	:param str exporttype: indicates the type of export ('project' or 'phase')
2583	'''
2584	if len(data['histNames']) == 0:
2585	G2G.G2MessageBox(G2frame,'There are no sequential histograms','Warning')
2586	obj.InitExport(None)
2587	obj.loadTree()
2588	obj.loadParmDict()
2589	if len(data['histNames']) == 1:
2590	histlist = data['histNames']
2591	else:
2592	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select histograms to export from list',
2593	'Select histograms',data['histNames'])
2594	if dlg.ShowModal() == wx.ID_OK:
2595	histlist = [data['histNames'][l] for l in dlg.GetSelections()]
2596	dlg.Destroy()
2597	else:
2598	dlg.Destroy()
2599	return
2600	if exporttype == 'Phase':
2601	phaselist = obj.Phases.keys()
2602	if len(obj.Phases) == 0:
2603	G2G.G2MessageBox(G2frame,'There are no phases in sequential ref.','Warning')
2604	return
2605	elif len(obj.Phases) > 1:
2606	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select phases to export from list',
2607	'Select phases', phaselist)
2608	if dlg.ShowModal() == wx.ID_OK:
2609	phaselist = [phaselist[l] for l in dlg.GetSelections()]
2610	dlg.Destroy()
2611	else:
2612	dlg.Destroy()
2613	return
2614	filename = obj.askSaveFile()
2615	if not filename: return True
2616	obj.dirname,obj.filename = os.path.split(filename)
2617	print('Writing output to file '+str(obj.filename)+"...")
2618	mode = 'w'
2619	for p in phaselist:
2620	for h in histlist:
2621	obj.SetSeqRef(data,h)
2622	#GSASIIpath.IPyBreak()
2623	obj.Writer(h,phasenam=p,mode=mode)
2624	mode = 'a'
2625	print('...done')
2626	elif exporttype == 'Project':
2627	filename = obj.askSaveFile()
2628	if not filename: return True
2629	obj.dirname,obj.filename = os.path.split(filename)
2630	print('Writing output to file '+str(obj.filename)+"...")
2631	mode = 'w'
2632	for h in histlist:
2633	obj.SetSeqRef(data,h)
2634	obj.Writer(h,mode=mode)
2635	print('\t'+str(h)+' written')
2636	mode = 'a'
2637	print('...done')
2638
2639	def ReadDIFFaX(DIFFaXfile):
2640	print 'read ',DIFFaXfile
2641	Layer = {'Laue':'-1','Cell':[False,1.,1.,1.,90.,90.,90,1.],'Width':[[10.,10.],[False,False]],
2642	'Layers':[],'Stacking':[],'Transitions':[],'Toler':0.01,'AtInfo':{}}
2643	df = open(DIFFaXfile,'r')
2644	lines = df.readlines()
2645	df.close()
2646	struct = False
2647	Struct = []
2648	stack = False
2649	Stack = []
2650	trans = False
2651	Trans = []
2652	for diff in lines:
2653	diff = diff[:-1].lower()
2654	if '!' in diff:
2655	continue
2656	while '}' in diff: #strip comments
2657	iB = diff.index('{')
2658	iF = diff.index('}')+1
2659	if iB:
2660	diff = diff[:iB]
2661	else:
2662	diff = diff[iF:]
2663	if not diff:
2664	continue
2665	if diff.strip() == 'instrumental':
2666	continue
2667	if diff.strip() == 'structural':
2668	struct = True
2669	continue
2670	elif diff.strip() == 'stacking':
2671	struct = False
2672	stack = True
2673	continue
2674	elif diff.strip() == 'transitions':
2675	stack = False
2676	trans = True
2677	continue
2678	diff = diff.strip()
2679	if struct:
2680	if diff:
2681	Struct.append(diff)
2682	elif stack:
2683	if diff:
2684	Stack.append(diff)
2685	elif trans:
2686	if diff:
2687	Trans.append(diff)
2688
2689	#STRUCTURE records
2690	laueRec = Struct[1].split()
2691	Layer['Laue'] = laueRec[0]
2692	if Layer['Laue'] == 'unknown' and len(laueRec) > 1:
2693	Layer['Toler'] = float(laueRec[1]) #tolerance for 'unknown'?
2694	if Layer['Laue'] == '2/m(1)': Layer['Laue'] = '2/m(c)'
2695	if Layer['Laue'] == '2/m(2)': Layer['Laue'] = '2/m(ab)'
2696	cell = Struct[0].split()
2697	Layer['Cell'] = [False,float(cell[0]),float(cell[1]),float(cell[2]),90.,90.,float(cell[3]),1.0]
2698	nLayers = int(Struct[2])
2699	N = 3
2700	if 'layer' not in Struct[3]:
2701	N = 4
2702	if Struct[3] != 'infinite':
2703	width = Struct[3].split()
2704	Layer['Width'][0] = [float(width[0]),float(width[1])]
2705	for nL in range(nLayers):
2706	if '=' in Struct[N]:
2707	name = Struct[N].split('=')
2708	sameas = int(name[1])-1
2709	Layer['Layers'].append({'Name':name[0],'SameAs':Layer['Layers'][sameas]['Name'],'Symm':'None','Atoms':[]})
2710	N += 1
2711	continue
2712	Symm = 'None'
2713	if 'centro' in Struct[N+1]: Symm = '-1'
2714	Layer['Layers'].append({'Name':Struct[N],'SameAs':'','Symm':Symm,'Atoms':[]})
2715	N += 2
2716	while 'layer' not in Struct[N]:
2717	atom = Struct[N][4:].split()
2718	atomType = G2el.FixValence(Struct[N][:4].replace(' ','').strip().capitalize())
2719	if atomType not in Layer['AtInfo']:
2720	Layer['AtInfo'][atomType] = G2el.GetAtomInfo(atomType)
2721	atomName = '%s(%s)'%(atomType,atom[0])
2722	newVals = []
2723	for val in atom[1:6]:
2724	if '/' in val:
2725	newVals.append(eval(val+'.'))
2726	else:
2727	newVals.append(float(val))
2728	atomRec = [atomName,atomType,newVals[0],newVals[1],newVals[2],newVals[4],newVals[3]/78.9568]
2729	Layer['Layers'][-1]['Atoms'].append(atomRec)
2730	N += 1
2731	if N > len(Struct)-1:
2732	break
2733	#TRANSITIONS records
2734	transArray = []
2735	N = 0
2736	for i in range(nLayers):
2737	transArray.append([])
2738	for j in range(nLayers):
2739	vals = Trans[N].split()
2740	newVals = []
2741	for val in vals[:4]:
2742	if '/' in val:
2743	newVals.append(eval(val+'.'))
2744	else:
2745	newVals.append(float(val))
2746	transArray[-1].append(newVals+['',False])
2747	N += 1
2748	Layer['Transitions'] = transArray
2749	#STACKING records
2750	Layer['Stacking'] = [Stack[0],'']
2751	if Stack[0] == 'recursive':
2752	Layer['Stacking'][1] = Stack[1]
2753	elif Stack[0] == 'explicit':
2754	if Stack[1] == 'random':
2755	Layer['Stacking'][1] = Stack[1]
2756	else:
2757	Layer['Stacking'][1] = 'list'
2758	Layer['Stacking'].append('')
2759	for stack in Stack[2:]:
2760	Layer['Stacking'][2] += ' '+stack
2761	return Layer
2762
2763	def ReadCIF(URLorFile):
2764	'''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
2765	(from James Hester).
2766	The open routine gets confused with DOS names that begin with a letter and colon
2767	"C:\dir\" so this routine will try to open the passed name as a file and if that
2768	fails, try it as a URL
2769
2770	:param str URLorFile: string containing a URL or a file name. Code will try first
2771	to open it as a file and then as a URL.
2772
2773	:returns: a PyCifRW CIF object.
2774	'''
2775	import CifFile as cif # PyCifRW from James Hester
2776
2777	# alternate approach:
2778	#import urllib
2779	#ciffile = 'file:'+urllib.pathname2url(filename)
2780
2781	try:
2782	fp = open(URLorFile,'r')
2783	cf = cif.ReadCif(fp)
2784	fp.close()
2785	return cf
2786	except IOError:
2787	return cif.ReadCif(URLorFile)
2788
2789	if __name__ == '__main__':
2790	import GSASII
2791	application = GSASII.GSASIImain(0)
2792	G2frame = application.main
2793	#app = wx.PySimpleApp()
2794	#G2frame = wx.Frame(None) # create a frame
2795	#frm.Show(True)
2796	#filename = '/tmp/notzip.zip'
2797	#filename = '/tmp/all.zip'
2798	#filename = '/tmp/11bmb_7652.zip'
2799
2800	#selection=None, confirmoverwrite=True, parent=None
2801	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2802	#print ExtractFileFromZip(filename,multipleselect=True)
2803	# #confirmread=False, confirmoverwrite=False)
2804
2805	# choicelist=[ ('a','b','c'),
2806	# ('test1','test2'),('no choice',)]
2807	# titles = [ 'a, b or c', 'tests', 'No option here']
2808	# dlg = MultipleChoicesDialog(
2809	# choicelist,titles,
2810	# parent=frm)
2811	# if dlg.ShowModal() == wx.ID_OK:
2812	# print 'Got OK'
2813	imagefile = '/tmp/NDC5_00237_3.ge3'
2814	Comments, Data, Npix, Image = GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None)
2815
2816	print("\n\nResults loaded to Comments, Data, Npix and Image\n\n")
2817
2818	GSASIIpath.IPyBreak_base()

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