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source: trunk/GSASIIIO.py @ 4184

Last change on this file since 4184 was 4184, checked in by toby, 4 years ago
fix GPX files with a colour object in them
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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2019-10-21 17:02:18 +0000 (Mon, 21 Oct 2019) $
4	# $Author: toby $
5	# $Revision: 4184 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 4184 2019-10-21 17:02:18Z toby $
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	This module needs some work to separate wx from non-wx routines
21	'''
22	# If this is being used for GSASIIscriptable, don't depend on wx
23	from __future__ import division, print_function
24	try:
25	import wx
26	except ImportError:
27	class Placeholder(object):
28	def __init__(self):
29	self.Dialog = object
30	wx = Placeholder()
31	import math
32	import numpy as np
33	import numpy.ma as ma
34
35	import copy
36	import platform
37	if '2' in platform.python_version_tuple()[0]:
38	import cPickle
39	else:
40	import pickle as cPickle
41	import sys
42	import re
43	import glob
44	import random as ran
45	import GSASIIpath
46	GSASIIpath.SetVersionNumber("$Revision: 4184 $")
47	try:
48	import GSASIIdataGUI as G2gd
49	except ImportError:
50	pass
51	import GSASIIobj as G2obj
52	import GSASIIlattice as G2lat
53	try:
54	import GSASIIpwdGUI as G2pdG
55	import GSASIIimgGUI as G2imG
56	except ImportError:
57	pass
58	import GSASIIimage as G2img
59	import GSASIIElem as G2el
60	import GSASIIstrIO as G2stIO
61	import GSASIImapvars as G2mv
62	import GSASIIfiles as G2fil
63	try:
64	import GSASIIctrlGUI as G2G
65	except ImportError:
66	pass
67	import os
68	import os.path as ospath
69
70	DEBUG = False #=True for various prints
71	TRANSP = False #=true to transpose images for testing
72	if GSASIIpath.GetConfigValue('Transpose'): TRANSP = True
73	npsind = lambda x: np.sin(x*np.pi/180.)
74
75	def sfloat(S):
76	'Convert a string to float. An empty field or a unconvertable value is treated as zero'
77	if S.strip():
78	try:
79	return float(S)
80	except ValueError:
81	pass
82	return 0.0
83
84	def sint(S):
85	'Convert a string to int. An empty field is treated as zero'
86	if S.strip():
87	return int(S)
88	else:
89	return 0
90
91	def trim(val):
92	'''Simplify a string containing leading and trailing spaces
93	as well as newlines, tabs, repeated spaces etc. into a shorter and
94	more simple string, by replacing all ranges of whitespace
95	characters with a single space.
96
97	:param str val: the string to be simplified
98
99	:returns: the (usually) shortened version of the string
100	'''
101	return re.sub('\s+', ' ', val).strip()
102
103	def FileDlgFixExt(dlg,file):
104	'this is needed to fix a problem in linux wx.FileDialog'
105	ext = dlg.GetWildcard().split('\|')[2dlg.GetFilterIndex()+1].strip('')
106	if ext not in file:
107	file += ext
108	return file
109
110	def GetPowderPeaks(fileName):
111	'Read powder peaks from a file'
112	sind = lambda x: math.sin(x*math.pi/180.)
113	asind = lambda x: 180.*math.asin(x)/math.pi
114	wave = 1.54052
115	File = open(fileName,'Ur')
116	Comments = []
117	peaks = []
118	S = File.readline()
119	while S:
120	if S[:1] == '#':
121	Comments.append(S[:-1])
122	else:
123	item = S.split()
124	if len(item) == 1:
125	peaks.append([float(item[0]),1.0])
126	elif len(item) > 1:
127	peaks.append([float(item[0]),float(item[0])])
128	S = File.readline()
129	File.close()
130	if Comments:
131	print ('Comments on file:')
132	for Comment in Comments:
133	print (Comment)
134	if 'wavelength' in Comment:
135	wave = float(Comment.split('=')[1])
136	Peaks = []
137	if peaks[0][0] > peaks[-1][0]: # d-spacings - assume CuKa
138	for peak in peaks:
139	dsp = peak[0]
140	sth = wave/(2.0*dsp)
141	if sth < 1.0:
142	tth = 2.0*asind(sth)
143	else:
144	break
145	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
146	else: #2-thetas - assume Cuka (for now)
147	for peak in peaks:
148	tth = peak[0]
149	dsp = wave/(2.0*sind(tth/2.0))
150	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
151	limits = [1000.,0.]
152	for peak in Peaks:
153	limits[0] = min(limits[0],peak[0])
154	limits[1] = max(limits[1],peak[0])
155	limits[0] = max(1.,(int(limits[0]-1.)/5)*5.)
156	limits[1] = min(170.,(int(limits[1]+1.)/5)*5.)
157	return Comments,Peaks,limits,wave
158
159	def GetCheckImageFile(G2frame,treeId):
160	'''Try to locate an image file if the project and image have been moved
161	together. If the image file cannot be found, request the location from
162	the user.
163
164	:param wx.Frame G2frame: main GSAS-II Frame and data object
165	:param wx.Id treeId: Id for the main tree item for the image
166	:returns: Npix,imagefile,imagetag with (Npix) number of pixels,
167	imagefile, if it exists, or the name of a file that does exist or False if the user presses Cancel
168	and (imagetag) an optional image number
169
170	'''
171	Npix,Imagefile,imagetag = G2frame.GPXtree.GetImageLoc(treeId)
172	if isinstance(Imagefile,list):
173	imagefile,imagetag = Imagefile
174	else:
175	imagefile = Imagefile
176	if not os.path.exists(imagefile):
177	print ('Image file '+imagefile+' not found')
178	fil = imagefile.replace('\\','/') # windows?!
179	# see if we can find a file with same name or in a similarly named sub-dir
180	pth,fil = os.path.split(fil)
181	prevpth = None
182	while pth and pth != prevpth:
183	prevpth = pth
184	if os.path.exists(os.path.join(G2frame.dirname,fil)):
185	print ('found image file '+os.path.join(G2frame.dirname,fil))
186	imagefile = os.path.join(G2frame.dirname,fil)
187	G2frame.GPXtree.UpdateImageLoc(treeId,imagefile)
188	return Npix,imagefile,imagetag
189	pth,enddir = os.path.split(pth)
190	fil = os.path.join(enddir,fil)
191	# not found as a subdirectory, drop common parts of path for last saved & image file names
192	# if image was .../A/B/C/imgs/ima.ge
193	# & GPX was .../A/B/C/refs/fil.gpx but is now .../NEW/TEST/TEST1
194	# will look for .../NEW/TEST/TEST1/imgs/ima.ge, .../NEW/TEST/imgs/ima.ge, .../NEW/imgs/ima.ge and so on
195	Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
196	gpxPath = Controls.get('LastSavedAs','').replace('\\','/').split('/') # blank in older .GPX files
197	imgPath = imagefile.replace('\\','/').split('/')
198	for p1,p2 in zip(gpxPath,imgPath):
199	if p1 == p2:
200	gpxPath.pop(0),imgPath.pop(0)
201	else:
202	break
203	fil = os.path.join(*imgPath) # file with non-common prefix elements
204	prevpth = None
205	pth = os.path.abspath(G2frame.dirname)
206	while pth and pth != prevpth:
207	prevpth = pth
208	if os.path.exists(os.path.join(pth,fil)):
209	print ('found image file '+os.path.join(pth,fil))
210	imagefile = os.path.join(pth,fil)
211	G2frame.GPXtree.UpdateImageLoc(treeId,imagefile)
212	return Npix,imagefile,imagetag
213	pth,enddir = os.path.split(pth)
214	#GSASIIpath.IPyBreak()
215
216	if not os.path.exists(imagefile):
217	# note that this fails (at least on Mac) to get an image during the GUI initialization
218	prevnam = os.path.split(imagefile)[1]
219	prevext = os.path.splitext(imagefile)[1]
220	wildcard = 'Image format ('+prevext+')\|'+prevext
221	dlg = wx.FileDialog(G2frame, 'Previous image file ('+prevnam+') not found; open here', '.', prevnam,
222	wildcard,wx.FD_OPEN)
223	try:
224	dlg.SetFilename(''+ospath.split(imagefile)[1])
225	if dlg.ShowModal() == wx.ID_OK:
226	imagefile = dlg.GetPath()
227	G2frame.GPXtree.UpdateImageLoc(treeId,imagefile)
228	else:
229	imagefile = None # was False
230	finally:
231	dlg.Destroy()
232	return Npix,imagefile,imagetag
233
234	def EditImageParms(parent,Data,Comments,Image,filename):
235	dlg = wx.Dialog(parent, wx.ID_ANY, 'Edit image parameters',
236	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
237	def onClose(event):
238	dlg.EndModal(wx.ID_OK)
239	mainsizer = wx.BoxSizer(wx.VERTICAL)
240	h,w = Image.shape[:2]
241	mainsizer.Add(wx.StaticText(dlg,wx.ID_ANY,'File '+str(filename)+'\nImage size: '+str(h)+' x '+str(w)),
242	0,wx.ALIGN_LEFT\|wx.ALL, 2)
243
244	vsizer = wx.BoxSizer(wx.HORIZONTAL)
245	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Wavelength (\xC5) '),
246	0,wx.ALIGN_LEFT\|wx.ALL, 2)
247	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'wavelength')
248	vsizer.Add(wdgt)
249	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
250
251	vsizer = wx.BoxSizer(wx.HORIZONTAL)
252	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Pixel size (\xb5m). Width '),
253	0,wx.ALIGN_LEFT\|wx.ALL, 2)
254	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],0,
255	size=(50,-1))
256	vsizer.Add(wdgt)
257	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Height '),wx.ALIGN_LEFT\|wx.ALL, 2)
258	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],1,size=(50,-1))
259	vsizer.Add(wdgt)
260	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
261
262	vsizer = wx.BoxSizer(wx.HORIZONTAL)
263	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Sample to detector (mm) '),
264	0,wx.ALIGN_LEFT\|wx.ALL, 2)
265	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'distance')
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'Beam center (pixels). X = '),
271	0,wx.ALIGN_LEFT\|wx.ALL, 2)
272	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],0,size=(75,-1))
273	vsizer.Add(wdgt)
274	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Y = '),wx.ALIGN_LEFT\|wx.ALL, 2)
275	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],1,size=(75,-1))
276	vsizer.Add(wdgt)
277	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
278
279	vsizer = wx.BoxSizer(wx.HORIZONTAL)
280	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Comments '),
281	0,wx.ALIGN_LEFT\|wx.ALL, 2)
282	wdgt = G2G.ValidatedTxtCtrl(dlg,Comments,0,size=(250,-1))
283	vsizer.Add(wdgt)
284	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
285
286	btnsizer = wx.StdDialogButtonSizer()
287	OKbtn = wx.Button(dlg, wx.ID_OK, 'Continue')
288	OKbtn.SetDefault()
289	OKbtn.Bind(wx.EVT_BUTTON,onClose)
290	btnsizer.AddButton(OKbtn) # not sure why this is needed
291	btnsizer.Realize()
292	mainsizer.Add(btnsizer, 1, wx.ALIGN_CENTER\|wx.ALL\|wx.EXPAND, 5)
293	dlg.SetSizer(mainsizer)
294	dlg.CenterOnParent()
295	dlg.ShowModal()
296
297	def LoadImage2Tree(imagefile,G2frame,Comments,Data,Npix,Image):
298	'''Load an image into the tree. Saves the location of the image, as well as the
299	ImageTag (where there is more than one image in the file), if defined.
300	'''
301	ImgNames = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',])
302	TreeLbl = 'IMG '+os.path.basename(imagefile)
303	ImageTag = Data.get('ImageTag')
304	if ImageTag:
305	TreeLbl += ' #'+'%04d'%(ImageTag)
306	imageInfo = (imagefile,ImageTag)
307	else:
308	imageInfo = imagefile
309	TreeName = G2obj.MakeUniqueLabel(TreeLbl,ImgNames)
310	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=TreeName)
311	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments)
312	Imax = np.amax(Image)
313	if G2frame.imageDefault:
314	Data = copy.copy(G2frame.imageDefault)
315	Data['showLines'] = True
316	Data['ring'] = []
317	Data['rings'] = []
318	Data['cutoff'] = 10.
319	Data['pixLimit'] = 20
320	Data['edgemin'] = 100000000
321	Data['calibdmin'] = 0.5
322	Data['calibskip'] = 0
323	Data['ellipses'] = []
324	Data['calibrant'] = ''
325	Data['GonioAngles'] = [0.,0.,0.]
326	Data['DetDepthRef'] = False
327	else:
328	Data['type'] = 'PWDR'
329	Data['color'] = GSASIIpath.GetConfigValue('Contour_color','Paired')
330	if 'tilt' not in Data: #defaults if not preset in e.g. Bruker importer
331	Data['tilt'] = 0.0
332	Data['rotation'] = 0.0
333	Data['pixLimit'] = 20
334	Data['calibdmin'] = 0.5
335	Data['cutoff'] = 10.
336	Data['showLines'] = False
337	Data['calibskip'] = 0
338	Data['ring'] = []
339	Data['rings'] = []
340	Data['edgemin'] = 100000000
341	Data['ellipses'] = []
342	Data['GonioAngles'] = [0.,0.,0.]
343	Data['DetDepth'] = 0.
344	Data['DetDepthRef'] = False
345	Data['calibrant'] = ''
346	Data['IOtth'] = [5.0,50.0]
347	Data['LRazimuth'] = [0.,180.]
348	Data['azmthOff'] = 0.0
349	Data['outChannels'] = 2500
350	Data['outAzimuths'] = 1
351	Data['centerAzm'] = False
352	Data['fullIntegrate'] = GSASIIpath.GetConfigValue('fullIntegrate',True)
353	Data['setRings'] = False
354	Data['background image'] = ['',-1.0]
355	Data['dark image'] = ['',-1.0]
356	Data['Flat Bkg'] = 0.0
357	Data['Oblique'] = [0.5,False]
358	Data['setDefault'] = False
359	Data['range'] = [(0,Imax),[0,Imax]]
360	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Image Controls'),Data)
361	Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],'Thresholds':[(0,Imax),[0,Imax]]}
362	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Masks'),Masks)
363	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Stress/Strain'),
364	{'Type':'True','d-zero':[],'Sample phi':0.0,'Sample z':0.0,'Sample load':0.0})
365	G2frame.GPXtree.SetItemPyData(Id,[Npix,imageInfo])
366	G2frame.PickId = Id
367	G2frame.PickIdText = G2frame.GetTreeItemsList(G2frame.PickId)
368	G2frame.Image = Id
369
370	def GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None,FormatName=''):
371	'''Read a single image with an image importer. This is called to reread an image
372	after it has already been imported with :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`
373	(or :func:`ReadImages` in Auto Integration) so it is not necessary to reload metadata.
374
375	:param wx.Frame G2frame: main GSAS-II Frame and data object.
376	:param str imagefile: name of image file
377	:param bool imageOnly: If True return only the image,
378	otherwise (default) return more (see below)
379	:param int/str ImageTag: specifies a particular image to be read from a file.
380	First image is read if None (default).
381	:param str formatName: the image reader formatName
382
383	:returns: an image as a numpy array or a list of four items:
384	Comments, Data, Npix and the Image, as selected by imageOnly
385
386	'''
387	# determine which formats are compatible with this file
388	primaryReaders = []
389	secondaryReaders = []
390	for rd in G2frame.ImportImageReaderlist:
391	flag = rd.ExtensionValidator(imagefile)
392	if flag is None:
393	secondaryReaders.append(rd)
394	elif flag:
395	if not FormatName:
396	primaryReaders.append(rd)
397	elif FormatName == rd.formatName:
398	primaryReaders.append(rd)
399	if len(secondaryReaders) + len(primaryReaders) == 0:
400	print('Error: No matching format for file '+imagefile)
401	raise Exception('No image read')
402	errorReport = ''
403	if not imagefile:
404	return
405	for rd in primaryReaders+secondaryReaders:
406	rd.ReInitialize() # purge anything from a previous read
407	rd.errors = "" # clear out any old errors
408	if not rd.ContentsValidator(imagefile): # rejected on cursory check
409	errorReport += "\n "+rd.formatName + ' validator error'
410	if rd.errors:
411	errorReport += ': '+rd.errors
412	continue
413	if imageOnly:
414	ParentFrame = None # prevent GUI access on reread
415	else:
416	ParentFrame = G2frame
417	if GSASIIpath.GetConfigValue('debug'):
418	flag = rd.Reader(imagefile,ParentFrame,blocknum=ImageTag)
419	else:
420	flag = False
421	try:
422	flag = rd.Reader(imagefile,ParentFrame,blocknum=ImageTag)
423	except rd.ImportException as detail:
424	rd.errors += "\n Read exception: "+str(detail)
425	except Exception as detail:
426	import traceback
427	rd.errors += "\n Unhandled read exception: "+str(detail)
428	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
429	if flag: # this read succeeded
430	if rd.Image is None:
431	raise Exception('No image read. Strange!')
432	if GSASIIpath.GetConfigValue('Transpose'):
433	print ('Transposing Image!')
434	rd.Image = rd.Image.T
435	#rd.readfilename = imagefile
436	if imageOnly:
437	return rd.Image
438	else:
439	return rd.Comments,rd.Data,rd.Npix,rd.Image
440	else:
441	print('Error reading file '+imagefile)
442	print('Error messages(s)\n'+errorReport)
443	raise Exception('No image read')
444
445	def ReadImages(G2frame,imagefile):
446	'''Read one or more images from a file and put them into the Tree
447	using image importers. Called only in :meth:`AutoIntFrame.OnTimerLoop`.
448
449	ToDo: Images are most commonly read in :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`
450	which is called from :meth:`GSASIIdataGUI.GSASII.OnImportImage`
451	it would be good if these routines used a common code core so that changes need to
452	be made in only one place.
453
454	:param wx.Frame G2frame: main GSAS-II Frame and data object.
455	:param str imagefile: name of image file
456
457	:returns: a list of the id's of the IMG tree items created
458	'''
459	# determine which formats are compatible with this file
460	primaryReaders = []
461	secondaryReaders = []
462	for rd in G2frame.ImportImageReaderlist:
463	flag = rd.ExtensionValidator(imagefile)
464	if flag is None:
465	secondaryReaders.append(rd)
466	elif flag:
467	primaryReaders.append(rd)
468	if len(secondaryReaders) + len(primaryReaders) == 0:
469	print('Error: No matching format for file '+imagefile)
470	raise Exception('No image read')
471	errorReport = ''
472	rdbuffer = {} # create temporary storage for file reader
473	for rd in primaryReaders+secondaryReaders:
474	rd.ReInitialize() # purge anything from a previous read
475	rd.errors = "" # clear out any old errors
476	if not rd.ContentsValidator(imagefile): # rejected on cursory check
477	errorReport += "\n "+rd.formatName + ' validator error'
478	if rd.errors:
479	errorReport += ': '+rd.errors
480	continue
481	ParentFrame = G2frame
482	block = 0
483	repeat = True
484	CreatedIMGitems = []
485	while repeat: # loop if the reader asks for another pass on the file
486	block += 1
487	repeat = False
488	if GSASIIpath.GetConfigValue('debug'):
489	flag = rd.Reader(imagefile,ParentFrame,blocknum=block,Buffer=rdbuffer)
490	else:
491	flag = False
492	try:
493	flag = rd.Reader(imagefile,ParentFrame,blocknum=block,Buffer=rdbuffer)
494	except rd.ImportException as detail:
495	rd.errors += "\n Read exception: "+str(detail)
496	except Exception as detail:
497	import traceback
498	rd.errors += "\n Unhandled read exception: "+str(detail)
499	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
500	if flag: # this read succeeded
501	if rd.Image is None:
502	raise Exception('No image read. Strange!')
503	if GSASIIpath.GetConfigValue('Transpose'):
504	print ('Transposing Image!')
505	rd.Image = rd.Image.T
506	rd.Data['ImageTag'] = rd.repeatcount
507	rd.readfilename = imagefile
508	# Load generic metadata, as configured
509	G2fil.GetColumnMetadata(rd)
510	LoadImage2Tree(imagefile,G2frame,rd.Comments,rd.Data,rd.Npix,rd.Image)
511	repeat = rd.repeat
512	CreatedIMGitems.append(G2frame.Image)
513	if CreatedIMGitems: return CreatedIMGitems
514	else:
515	print('Error reading file '+imagefile)
516	print('Error messages(s)\n'+errorReport)
517	return []
518	#raise Exception('No image read')
519
520	def SaveMultipleImg(G2frame):
521	if not G2frame.GPXtree.GetCount():
522	print ('no images!')
523	return
524	choices = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',])
525	if len(choices) == 1:
526	names = choices
527	else:
528	dlg = G2G.G2MultiChoiceDialog(G2frame,'Stress/Strain fitting','Select images to fit:',choices)
529	dlg.SetSelections([])
530	names = []
531	if dlg.ShowModal() == wx.ID_OK:
532	names = [choices[sel] for sel in dlg.GetSelections()]
533	dlg.Destroy()
534	if not names: return
535	for name in names:
536	Id = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, name)
537	Npix,imagefile,imagetag = G2frame.GPXtree.GetImageLoc(Id)
538	imroot = os.path.splitext(imagefile)[0]
539	if imagetag:
540	imroot += '_' + str(imagetag)
541	Data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Image Controls'))
542	print('Writing '+imroot+'.imctrl')
543	File = open(imroot+'.imctrl','w')
544	keys = ['type','wavelength','calibrant','distance','center',
545	'tilt','rotation','azmthOff','fullIntegrate','LRazimuth',
546	'IOtth','outChannels','outAzimuths','invert_x','invert_y','DetDepth',
547	'calibskip','pixLimit','cutoff','calibdmin','chisq','Flat Bkg',
548	'binType','SampleShape','PolaVal','SampleAbs','dark image','background image']
549	for key in keys:
550	if key not in Data: continue #uncalibrated!
551	File.write(key+':'+str(Data[key])+'\n')
552	File.close()
553	mask = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Masks'))
554	G2imG.CleanupMasks(mask)
555	print('Writing '+imroot+'.immask')
556	File = open(imroot+'.immask','w')
557	for key in ['Points','Rings','Arcs','Polygons','Frames','Thresholds']:
558	File.write(key+':'+str(mask[key])+'\n')
559	File.close()
560
561	def PutG2Image(filename,Comments,Data,Npix,image):
562	'Write an image as a python pickle - might be better as an .edf file?'
563	File = open(filename,'wb')
564	cPickle.dump([Comments,Data,Npix,image],File,2)
565	File.close()
566	return
567
568	objectScanIgnore = [int,bool,float,str,np.float64,np.float32,np.int32,np.int64,np.ndarray,G2obj.G2VarObj,G2obj.ExpressionObj]
569	try:
570	objectScanIgnore += [ma.MaskedArray] # fails in doc builds
571	except AttributeError:
572	pass
573
574	if '2' in platform.python_version_tuple()[0]:
575	objectScanIgnore += [unicode,long,]
576
577	def objectScan(data,tag,indexStack=[]):
578	'''Recursively scan an object looking for unexpected data types.
579	This is used in debug mode to scan .gpx files for objects we did not
580	intend to be there.
581	'''
582	if type(data) is list or type(data) is tuple:
583	for i in range(len(data)):
584	val = objectScan(data[i],tag,indexStack+[i])
585	if val:
586	data[i] = val
587	print('...fixed')
588	elif type(data) is dict:
589	for key in data:
590	val = objectScan(data[key],tag,indexStack+[key])
591	if val:
592	data[key] = val
593	print('...fixed')
594	elif data is None:
595	return None
596	elif type(data) in objectScanIgnore:
597	return None
598	else:
599	s = 'unexpected object in '+tag
600	for i in indexStack:
601	s += "[{}]".format(i)
602	#print(s,data.__class__.__name__) # loses full name of class
603	print(s,type(data))
604	global unexpectedObject
605	unexpectedObject = True
606	# fix bad objects
607	if "gdi.Colour" in str(type(data)):
608	return tuple(data)
609	return
610
611	def cPickleLoad(fp):
612	if '2' in platform.python_version_tuple()[0]:
613	return cPickle.load(fp)
614	else:
615	return cPickle.load(fp,encoding='latin-1')
616
617	def ProjFileOpen(G2frame,showProvenance=True):
618	'Read a GSAS-II project file and load into the G2 data tree'
619	if not os.path.exists(G2frame.GSASprojectfile):
620	print ('\n*** Error attempt to open project file that does not exist:\n '+
621	str(G2frame.GSASprojectfile))
622	return
623	LastSavedUsing = None
624	filep = open(G2frame.GSASprojectfile,'rb')
625	if showProvenance: print ('loading from file: '+G2frame.GSASprojectfile)
626	GPXphase = os.path.splitext(G2frame.GSASprojectfile)[0]+'.seqPhase'
627	GPXhist = os.path.splitext(G2frame.GSASprojectfile)[0]+'.seqHist'
628	deleteSeq = False
629	hist = None
630	tmpHistIndex = {}
631	updateFromSeq = False
632	if os.path.exists(GPXphase) and os.path.exists(GPXhist):
633	dlg = wx.MessageDialog(G2frame,
634	'Load results from crashed sequential fit?\nNo deletes the files!', 'Recover partial sequential fit?', wx.YES \| wx.NO \| wx.CANCEL)
635	dlg.CenterOnParent()
636	try:
637	result = dlg.ShowModal()
638	deleteSeq = result != wx.ID_CANCEL
639	if result == wx.ID_YES:
640	updateFromSeq = True
641	fp = open(GPXphase,'rb')
642	data = cPickleLoad(fp) # first block in file should be Phases
643	if data[0][0] != 'Phases':
644	raise Exception('Unexpected block in {} file. How did this happen?'
645	.format(GPXphase))
646	Phases = {}
647	for name,vals in data[1:]:
648	Phases[name] = vals
649	name,CovData = cPickleLoad(fp)[0] # 2nd block in file should be Covariance
650	name,RigidBodies = cPickleLoad(fp)[0] # 3rd block in file should be Rigid Bodies
651	fp.close()
652	# index the histogram updates
653	hist = open(GPXhist,'rb')
654	try:
655	while True:
656	loc = hist.tell()
657	datum = cPickleLoad(hist)[0]
658	tmpHistIndex[datum[0]] = loc
659	except EOFError:
660	pass
661	finally:
662	dlg.Destroy()
663	wx.BeginBusyCursor()
664	try:
665	while True:
666	try:
667	data = cPickleLoad(filep)
668	except EOFError:
669	break
670	datum = data[0]
671	# scan the GPX file for unexpected objects
672	if GSASIIpath.GetConfigValue('debug'):
673	global unexpectedObject
674	unexpectedObject = False
675	objectScan(data,'tree item "{}" entry '.format(datum[0]))
676	#if unexpectedObject:
677	# print(datum[0])
678	# GSASIIpath.IPyBreak()
679	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=datum[0])
680	if updateFromSeq and datum[0] == 'Phases':
681	for pdata in data[1:]:
682	if pdata[0] in Phases:
683	pdata[1].update(Phases[pdata[0]])
684	elif updateFromSeq and datum[0] == 'Covariance':
685	data[0][1] = CovData
686	elif updateFromSeq and datum[0] == 'Rigid bodies':
687	data[0][1] = RigidBodies
688	elif updateFromSeq and datum[0] in tmpHistIndex:
689	hist.seek(tmpHistIndex[datum[0]])
690	hdata = cPickleLoad(hist)
691	if data[0][0] != hdata[0][0]:
692	print('Error! Updating {} with {}'.format(data[0][0],hdata[0][0]))
693	datum = hdata[0]
694	xferItems = ['Background','Instrument Parameters','Sample Parameters','Reflection Lists']
695	hItems = {name:j+1 for j,(name,val) in enumerate(hdata[1:]) if name in xferItems}
696	for j,(name,val) in enumerate(data[1:]):
697	if name not in xferItems: continue
698	data[j+1][1] = hdata[hItems[name]][1]
699	if datum[0].startswith('PWDR'):
700	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
701	datum[1][0]['ranId'] = ran.randint(0,sys.maxsize)
702	G2frame.GPXtree.SetItemPyData(Id,datum[1][:3]) #temp. trim off junk (patch?)
703	elif datum[0].startswith('HKLF'):
704	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
705	datum[1][0]['ranId'] = ran.randint(0,sys.maxsize)
706	G2frame.GPXtree.SetItemPyData(Id,datum[1])
707	else:
708	G2frame.GPXtree.SetItemPyData(Id,datum[1])
709	if datum[0] == 'Controls' and 'LastSavedUsing' in datum[1]:
710	LastSavedUsing = datum[1]['LastSavedUsing']
711	if datum[0] == 'Controls' and 'PythonVersions' in datum[1] and GSASIIpath.GetConfigValue('debug') and showProvenance:
712	print('DBG_Packages used to create .GPX file:')
713	if 'dict' in str(type(datum[1]['PythonVersions'])): #patch
714	for p in sorted(datum[1]['PythonVersions'],key=lambda s: s.lower()):
715	print(" {:<14s}: {:s}".format(p[0],p[1]))
716	else:
717	for p in datum[1]['PythonVersions']:
718	print(" {:<12s} {:s}".format(p[0]+':',p[1]))
719	oldPDF = False
720	for datus in data[1:]:
721	#patch - 1/23/17 PDF cleanup
722	if datus[0][:4] in ['I(Q)','S(Q)','F(Q)','G(R)']:
723	oldPDF = True
724	data[1][1][datus[0][:4]] = copy.deepcopy(datus[1][:2])
725	continue
726	#end PDF cleanup
727	sub = G2frame.GPXtree.AppendItem(Id,datus[0])
728	#patch
729	if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
730	if datum[0].startswith('PWDR'):
731	datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
732	else:
733	datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
734	for item in datus[1][0]: #zip makes tuples - now make lists!
735	datus[1][0][item] = list(datus[1][0][item])
736	#end patch
737	G2frame.GPXtree.SetItemPyData(sub,datus[1])
738	if 'PDF ' in datum[0][:4] and oldPDF:
739	sub = G2frame.GPXtree.AppendItem(Id,'PDF Peaks')
740	G2frame.GPXtree.SetItemPyData(sub,{'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]})
741	if datum [0].startswith('IMG'): #retrieve image default flag & data if set
742	Data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Image Controls'))
743	if Data['setDefault']:
744	G2frame.imageDefault = Data
745	if LastSavedUsing:
746	print('GPX load successful. Last saved with GSAS-II revision '+LastSavedUsing)
747	else:
748	print('project load successful')
749	G2frame.NewPlot = True
750	except Exception as errmsg:
751	if GSASIIpath.GetConfigValue('debug'):
752	print('\nError reading GPX file:',errmsg)
753	import traceback
754	print (traceback.format_exc())
755	msg = wx.MessageDialog(G2frame,message="Error reading file "+
756	str(G2frame.GSASprojectfile)+". This is not a current GSAS-II .gpx file",
757	caption="Load Error",style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
758	msg.ShowModal()
759	finally:
760	filep.close()
761	wx.EndBusyCursor()
762	G2frame.Status.SetStatusText('Mouse RB drag/drop to reorder',0)
763	if deleteSeq:
764	if hist: hist.close()
765	try:
766	os.remove(GPXphase)
767	except:
768	print('Warning: unable to delete {}'.format(GPXphase))
769	try:
770	os.remove(GPXhist)
771	except:
772	print('Warning: unable to delete {}'.format(GPXhist))
773	G2frame.SetTitleByGPX()
774
775	def ProjFileSave(G2frame):
776	'Save a GSAS-II project file'
777	if not G2frame.GPXtree.IsEmpty():
778	file = open(G2frame.GSASprojectfile,'wb')
779	print ('save to file: '+G2frame.GSASprojectfile)
780	# stick the file name into the tree and version info into tree so they are saved.
781	# (Controls should always be created at this point)
782	try:
783	Controls = G2frame.GPXtree.GetItemPyData(
784	G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
785	Controls['LastSavedAs'] = os.path.abspath(G2frame.GSASprojectfile)
786	Controls['LastSavedUsing'] = str(GSASIIpath.GetVersionNumber())
787	Controls['PythonVersions'] = G2frame.PackageVersions
788	except:
789	pass
790	wx.BeginBusyCursor()
791	try:
792	item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
793	while item:
794	data = []
795	name = G2frame.GPXtree.GetItemText(item)
796	data.append([name,G2frame.GPXtree.GetItemPyData(item)])
797	item2, cookie2 = G2frame.GPXtree.GetFirstChild(item)
798	while item2:
799	name = G2frame.GPXtree.GetItemText(item2)
800	data.append([name,G2frame.GPXtree.GetItemPyData(item2)])
801	item2, cookie2 = G2frame.GPXtree.GetNextChild(item, cookie2)
802	item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
803	cPickle.dump(data,file,2)
804	file.close()
805	pth = os.path.split(os.path.abspath(G2frame.GSASprojectfile))[0]
806	if GSASIIpath.GetConfigValue('Save_paths'): G2G.SaveGPXdirectory(pth)
807	G2frame.LastGPXdir = pth
808	finally:
809	wx.EndBusyCursor()
810	print('project save successful')
811
812	def SaveIntegration(G2frame,PickId,data,Overwrite=False):
813	'Save image integration results as powder pattern(s)'
814	waves = {'Cu':[1.54051,1.54433],'Ti':[2.74841,2.75207],'Cr':[2.28962,2.29351],
815	'Fe':[1.93597,1.93991],'Co':[1.78892,1.79278],'Mo':[0.70926,0.713543],
816	'Ag':[0.559363,0.563775]}
817	azms = G2frame.Integrate[1]
818	X = G2frame.Integrate[2][:-1]
819	N = len(X)
820	Id = G2frame.GPXtree.GetItemParent(PickId)
821	name = G2frame.GPXtree.GetItemText(Id)
822	name = name.replace('IMG ',data['type']+' ')
823	Comments = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Comments'))
824	Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
825	if 'PWDR' in name:
826	if 'target' in data:
827	names = ['Type','Lam1','Lam2','I(L2)/I(L1)','Zero','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth']
828	codes = [0 for i in range(14)]
829	else:
830	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth']
831	codes = [0 for i in range(12)]
832	elif 'SASD' in name:
833	names = ['Type','Lam','Zero','Azimuth']
834	codes = [0 for i in range(4)]
835	X = 4.np.pinpsind(X/2.)/data['wavelength'] #convert to q
836	Xminmax = [X[0],X[-1]]
837	Azms = np.zeros(data['outAzimuths'])
838	dazm = 0.
839	# if data['fullIntegrate'] and data['outAzimuths'] == 1:
840	# Azms = [0.0,] #a poor man's average?
841	# else:
842	## for i,azm in enumerate(azms[:-1]):
843	## if azm > 360. and azms[i+1] > 360.:
844	## Azms.append(G2img.meanAzm(azm%360.,azms[i+1]%360.))
845	## else:
846	## Azms.append(G2img.meanAzm(azm,azms[i+1]))
847	if data['outAzimuths'] > 1:
848	dazm = np.min(np.abs(np.diff(azms)))/2.
849	G2frame.IntgOutList = []
850	for i,azm in enumerate(azms[:-1]):
851	Aname = name+" Azm= %.2f"%((azm+dazm)%360.)
852	item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
853	# if Overwrite delete any duplicate
854	if Overwrite and G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname):
855	print('Replacing '+Aname)
856	item = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname)
857	G2frame.GPXtree.Delete(item)
858	else:
859	nOcc = 0
860	while item:
861	Name = G2frame.GPXtree.GetItemText(item)
862	if Aname in Name:
863	nOcc += 1
864	item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
865	if nOcc:
866	Aname += '(%d)'%(nOcc)
867	Sample = G2obj.SetDefaultSample() #set as Debye-Scherrer
868	Sample['Gonio. radius'] = data['distance']
869	Sample['Omega'] = data['GonioAngles'][0]
870	Sample['Chi'] = data['GonioAngles'][1]
871	Sample['Phi'] = data['GonioAngles'][2]
872	Sample['Azimuth'] = (azm+dazm)%360. #put here as bin center
873	polariz = 0.99 #set default polarization for synchrotron radiation!
874	for item in Comments:
875	if 'polariz' in item:
876	try:
877	polariz = float(item.split('=')[1])
878	except:
879	polariz = 0.99
880	for key in ('Temperature','Pressure','Time','FreePrm1','FreePrm2','FreePrm3','Omega',
881	'Chi','Phi'):
882	if key.lower() in item.lower():
883	try:
884	Sample[key] = float(item.split('=')[1])
885	except:
886	pass
887	if 'label_prm' in item.lower():
888	for num in ('1','2','3'):
889	if 'label_prm'+num in item.lower():
890	Controls['FreePrm'+num] = item.split('=')[1].strip()
891	if 'PWDR' in Aname:
892	if 'target' in data: #from lab x-ray 2D imaging data
893	wave1,wave2 = waves[data['target']]
894	parms = ['PXC',wave1,wave2,0.5,0.0,polariz,290.,-40.,30.,6.,-14.,0.0,0.0001,Azms[i]]
895	else:
896	parms = ['PXC',data['wavelength'],0.0,polariz,1.0,-0.10,0.4,0.30,1.0,0.0,0.0001,Azms[i]]
897	elif 'SASD' in Aname:
898	Sample['Trans'] = data['SampleAbs'][0]
899	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
900	Y = G2frame.Integrate[0][i]
901	Ymin = np.min(Y)
902	Ymax = np.max(Y)
903	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
904	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=Aname)
905	G2frame.IntgOutList.append(Id)
906	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments)
907	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Limits'),copy.deepcopy([tuple(Xminmax),Xminmax]))
908	if 'PWDR' in Aname:
909	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Background'),[['chebyschev',1,3,1.0,0.0,0.0],
910	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
911	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
912	for item in inst[0]:
913	inst[0][item] = list(inst[0][item])
914	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Instrument Parameters'),inst)
915	if 'PWDR' in Aname:
916	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample)
917	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
918	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Index Peak List'),[[],[]])
919	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Unit Cells List'),[])
920	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Reflection Lists'),{})
921	elif 'SASD' in Aname:
922	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
923	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample)
924	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
925	valuesdict = {
926	'wtFactor':1.0,'Dummy':False,'ranId':ran.randint(0,sys.maxsize),'Offset':[0.0,0.0],'delOffset':0.02*Ymax,
927	'refOffset':-0.1Ymax,'refDelt':0.1Ymax,'Yminmax':[Ymin,Ymax]}
928	G2frame.GPXtree.SetItemPyData(Id,[valuesdict,
929	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
930	return Id #last powder pattern generated
931
932	def XYsave(G2frame,XY,labelX='X',labelY='Y',names=[]):
933	'Save XY table data'
934	pth = G2G.GetExportPath(G2frame)
935	dlg = wx.FileDialog(
936	G2frame, 'Enter csv filename for XY table', pth, '',
937	'XY table file (.csv)\|.csv',wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
938	try:
939	if dlg.ShowModal() == wx.ID_OK:
940	filename = dlg.GetPath()
941	filename = os.path.splitext(filename)[0]+'.csv'
942	File = open(filename,'w')
943	else:
944	filename = None
945	finally:
946	dlg.Destroy()
947	if not filename:
948	return
949	for i in range(len(XY)):
950	if len(names):
951	header = '%s,%s(%s)\n'%(labelX,labelY,names[i])
952	else:
953	header = '%s,%s(%d)\n'%(labelX,labelY,i)
954	File.write(header)
955	for x,y in XY[i].T:
956	File.write('%.3f,%.3f\n'%(x,y))
957	File.close()
958	print (' XY data saved to: '+filename)
959
960	def PeakListSave(G2frame,file,peaks):
961	'Save powder peaks to a data file'
962	print ('save peak list to file: '+G2frame.peaklistfile)
963	if not peaks:
964	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
965	try:
966	dlg.ShowModal()
967	finally:
968	dlg.Destroy()
969	return
970	for peak in peaks:
971	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
972	(peak[0],peak[2],peak[4],peak[6]))
973	print ('peak list saved')
974
975	def IndexPeakListSave(G2frame,peaks):
976	'Save powder peaks from the indexing list'
977	file = open(G2frame.peaklistfile,'wa')
978	print ('save index peak list to file: '+G2frame.peaklistfile)
979	wx.BeginBusyCursor()
980	try:
981	if not peaks:
982	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
983	try:
984	dlg.ShowModal()
985	finally:
986	dlg.Destroy()
987	return
988	for peak in peaks:
989	file.write("%12.6f\n" % (peak[7]))
990	file.close()
991	finally:
992	wx.EndBusyCursor()
993	print ('index peak list saved')
994
995	class MultipleChoicesDialog(wx.Dialog):
996	'''A dialog that offers a series of choices, each with a
997	title and a wx.Choice widget. Intended to be used Modally.
998	typical input:
999
1000	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1001	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1002
1003	selections are placed in self.chosen when OK is pressed
1004
1005	Also see GSASIIctrlGUI
1006	'''
1007	def __init__(self,choicelist,headinglist,
1008	head='Select options',
1009	title='Please select from options below',
1010	parent=None):
1011	self.chosen = []
1012	wx.Dialog.__init__(
1013	self,parent,wx.ID_ANY,head,
1014	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
1015	panel = wx.Panel(self)
1016	mainSizer = wx.BoxSizer(wx.VERTICAL)
1017	mainSizer.Add((10,10),1)
1018	topLabl = wx.StaticText(panel,wx.ID_ANY,title)
1019	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.CENTER,10)
1020	self.ChItems = []
1021	for choice,lbl in zip(choicelist,headinglist):
1022	mainSizer.Add((10,10),1)
1023	self.chosen.append(0)
1024	topLabl = wx.StaticText(panel,wx.ID_ANY,' '+lbl)
1025	mainSizer.Add(topLabl,0,wx.ALIGN_LEFT,10)
1026	self.ChItems.append(wx.Choice(self, wx.ID_ANY, (100, 50), choices = choice))
1027	mainSizer.Add(self.ChItems[-1],0,wx.ALIGN_CENTER,10)
1028
1029	OkBtn = wx.Button(panel,-1,"Ok")
1030	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
1031	cancelBtn = wx.Button(panel,-1,"Cancel")
1032	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
1033	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1034	btnSizer.Add((20,20),1)
1035	btnSizer.Add(OkBtn)
1036	btnSizer.Add((20,20),1)
1037	btnSizer.Add(cancelBtn)
1038	btnSizer.Add((20,20),1)
1039	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1040	panel.SetSizer(mainSizer)
1041	panel.Fit()
1042	self.Fit()
1043
1044	def OnOk(self,event):
1045	parent = self.GetParent()
1046	if parent is not None: parent.Raise()
1047	# save the results from the choice widgets
1048	self.chosen = []
1049	for w in self.ChItems:
1050	self.chosen.append(w.GetSelection())
1051	self.EndModal(wx.ID_OK)
1052
1053	def OnCancel(self,event):
1054	parent = self.GetParent()
1055	if parent is not None: parent.Raise()
1056	self.chosen = []
1057	self.EndModal(wx.ID_CANCEL)
1058
1059	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1060	confirmoverwrite=True, parent=None,
1061	multipleselect=False):
1062	'''If the filename is a zip file, extract a file from that
1063	archive.
1064
1065	:param list Selection: used to predefine the name of the file
1066	to be extracted. Filename case and zip directory name are
1067	ignored in selection; the first matching file is used.
1068
1069	:param bool confirmread: if True asks the user to confirm before expanding
1070	the only file in a zip
1071
1072	:param bool confirmoverwrite: if True asks the user to confirm
1073	before overwriting if the extracted file already exists
1074
1075	:param bool multipleselect: if True allows more than one zip
1076	file to be extracted, a list of file(s) is returned.
1077	If only one file is present, do not ask which one, otherwise
1078	offer a list of choices (unless selection is used).
1079
1080	:returns: the name of the file that has been created or a
1081	list of files (see multipleselect)
1082
1083	If the file is not a zipfile, return the name of the input file.
1084	If the zipfile is empty or no file has been selected, return None
1085	'''
1086	import zipfile # do this now, since we can save startup time by doing this only on need
1087	import shutil
1088	zloc = os.path.split(filename)[0]
1089	if not zipfile.is_zipfile(filename):
1090	#print("not zip")
1091	return filename
1092
1093	z = zipfile.ZipFile(filename,'r')
1094	zinfo = z.infolist()
1095
1096	if len(zinfo) == 0:
1097	#print('Zip has no files!')
1098	zlist = [-1]
1099	if selection:
1100	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1101	if selection.lower() in choices:
1102	zlist = [choices.index(selection.lower())]
1103	else:
1104	print('debug: file '+str(selection)+' was not found in '+str(filename))
1105	zlist = [-1]
1106	elif len(zinfo) == 1 and confirmread:
1107	result = wx.ID_NO
1108	dlg = wx.MessageDialog(
1109	parent,
1110	'Is file '+str(zinfo[0].filename)+
1111	' what you want to extract from '+
1112	str(os.path.split(filename)[1])+'?',
1113	'Confirm file',
1114	wx.YES_NO \| wx.ICON_QUESTION)
1115	try:
1116	result = dlg.ShowModal()
1117	finally:
1118	dlg.Destroy()
1119	if result == wx.ID_NO:
1120	zlist = [-1]
1121	else:
1122	zlist = [0]
1123	elif len(zinfo) == 1:
1124	zlist = [0]
1125	elif multipleselect:
1126	# select one or more from a from list
1127	choices = [i.filename for i in zinfo]
1128	dlg = G2G.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1129	'Choose file(s)',choices)
1130	if dlg.ShowModal() == wx.ID_OK:
1131	zlist = dlg.GetSelections()
1132	else:
1133	zlist = []
1134	dlg.Destroy()
1135	else:
1136	# select one from a from list
1137	choices = [i.filename for i in zinfo]
1138	dlg = wx.SingleChoiceDialog(parent,
1139	'Select file to extract from zip file'+str(filename),'Choose file',
1140	choices,)
1141	if dlg.ShowModal() == wx.ID_OK:
1142	zlist = [dlg.GetSelection()]
1143	else:
1144	zlist = [-1]
1145	dlg.Destroy()
1146
1147	outlist = []
1148	for zindex in zlist:
1149	if zindex >= 0:
1150	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1151	if os.path.exists(efil) and confirmoverwrite:
1152	result = wx.ID_NO
1153	dlg = wx.MessageDialog(parent,
1154	'File '+str(efil)+' already exists. OK to overwrite it?',
1155	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1156	try:
1157	result = dlg.ShowModal()
1158	finally:
1159	dlg.Destroy()
1160	if result == wx.ID_NO:
1161	zindex = -1
1162	if zindex >= 0:
1163	# extract the file to the current directory, regardless of it's original path
1164	#z.extract(zinfo[zindex],zloc)
1165	eloc,efil = os.path.split(zinfo[zindex].filename)
1166	outfile = os.path.join(zloc, efil)
1167	fpin = z.open(zinfo[zindex])
1168	fpout = open(outfile, "wb")
1169	shutil.copyfileobj(fpin, fpout)
1170	fpin.close()
1171	fpout.close()
1172	outlist.append(outfile)
1173	z.close()
1174	if multipleselect and len(outlist) >= 1:
1175	return outlist
1176	elif len(outlist) == 1:
1177	return outlist[0]
1178	else:
1179	return None
1180
1181	######################################################################
1182	# base classes for reading various types of data files
1183	# not used directly, only by subclassing
1184	######################################################################
1185	def BlockSelector(ChoiceList, ParentFrame=None,title='Select a block',
1186	size=None, header='Block Selector',useCancel=True):
1187	''' Provide a wx dialog to select a block if the file contains more
1188	than one set of data and one must be selected
1189	'''
1190	if useCancel:
1191	dlg = wx.SingleChoiceDialog(
1192	ParentFrame,title, header,ChoiceList)
1193	else:
1194	dlg = wx.SingleChoiceDialog(
1195	ParentFrame,title, header,ChoiceList,
1196	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.OK\|wx.CENTRE)
1197	if size: dlg.SetSize(size)
1198	dlg.CenterOnParent()
1199	if dlg.ShowModal() == wx.ID_OK:
1200	sel = dlg.GetSelection()
1201	return sel
1202	else:
1203	return None
1204	dlg.Destroy()
1205
1206	def MultipleBlockSelector(ChoiceList, ParentFrame=None,
1207	title='Select a block',size=None, header='Block Selector'):
1208	'''Provide a wx dialog to select a block of data if the
1209	file contains more than one set of data and one must be
1210	selected.
1211
1212	:returns: a list of the selected blocks
1213	'''
1214	dlg = wx.MultiChoiceDialog(ParentFrame,title, header,ChoiceList+['Select all'],
1215	wx.CHOICEDLG_STYLE)
1216	dlg.CenterOnScreen()
1217	if size: dlg.SetSize(size)
1218	if dlg.ShowModal() == wx.ID_OK:
1219	sel = dlg.GetSelections()
1220	else:
1221	return []
1222	dlg.Destroy()
1223	selected = []
1224	if len(ChoiceList) in sel:
1225	return range(len(ChoiceList))
1226	else:
1227	return sel
1228	return selected
1229
1230	def MultipleChoicesSelector(choicelist, headinglist, ParentFrame=None, **kwargs):
1231	'''A modal dialog that offers a series of choices, each with a title and a wx.Choice
1232	widget. Typical input:
1233
1234	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1235
1236	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1237
1238	optional keyword parameters are: head (window title) and title
1239	returns a list of selected indicies for each choice (or None)
1240	'''
1241	result = None
1242	dlg = MultipleChoicesDialog(choicelist,headinglist,
1243	parent=ParentFrame, **kwargs)
1244	dlg.CenterOnParent()
1245	if dlg.ShowModal() == wx.ID_OK:
1246	result = dlg.chosen
1247	dlg.Destroy()
1248	return result
1249
1250	def PhaseSelector(ChoiceList, ParentFrame=None,
1251	title='Select a phase', size=None,header='Phase Selector'):
1252	''' Provide a wx dialog to select a phase if the file contains more
1253	than one phase
1254	'''
1255	return BlockSelector(ChoiceList,ParentFrame,title,
1256	size,header)
1257
1258	######################################################################
1259	def striphist(var,insChar=''):
1260	'strip a histogram number from a var name'
1261	sv = var.split(':')
1262	if len(sv) <= 1: return var
1263	if sv[1]:
1264	sv[1] = insChar
1265	return ':'.join(sv)
1266	class ExportBaseclass(object):
1267	'''Defines a base class for the exporting of GSAS-II results.
1268
1269	This class is subclassed in the various exports/G2export_*.py files. Those files
1270	are imported in :meth:`GSASIIdataGUI.GSASII._init_Exports` which defines the
1271	appropriate menu items for each one and the .Exporter method is called
1272	directly from the menu item.
1273
1274	Routines may also define a .Writer method, which is used to write a single
1275	file without invoking any GUI objects.
1276	'''
1277	# TODO: review exporters producing exceptions where .Writer can't be used where G2frame is None (see CIF)
1278	# TODO: review conflicting uses of .Writer with mode (SeqRef) & elsewhere
1279	# TODO: move this class to G2fil
1280	def __init__(self,G2frame,formatName,extension,longFormatName=None,):
1281	self.G2frame = G2frame
1282	self.formatName = formatName # short string naming file type
1283	self.extension = extension
1284	if longFormatName: # longer string naming file type
1285	self.longFormatName = longFormatName
1286	else:
1287	self.longFormatName = formatName
1288	self.OverallParms = {}
1289	self.Phases = {}
1290	self.Histograms = {}
1291	self.powderDict = {}
1292	self.sasdDict = {}
1293	self.xtalDict = {}
1294	self.parmDict = {}
1295	self.sigDict = {}
1296	# updated in InitExport:
1297	self.currentExportType = None # type of export that has been requested
1298	# updated in ExportSelect (when used):
1299	self.phasenam = None # a list of selected phases
1300	self.histnam = None # a list of selected histograms
1301	self.filename = None # name of file to be written (single export) or template (multiple files)
1302	self.dirname = '' # name of directory where file(s) will be written
1303	self.fullpath = '' # name of file being written -- full path
1304
1305	# items that should be defined in a subclass of this class
1306	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1307	# The following types are defined: 'project', "phase", "powder", "single"
1308	self.multiple = False # set as True if the class can export multiple phases or histograms
1309	# self.multiple is ignored for "project" exports
1310
1311	def InitExport(self,event):
1312	'''Determines the type of menu that called the Exporter and
1313	misc initialization.
1314	'''
1315	self.filename = None # name of file to be written (single export)
1316	self.dirname = '' # name of file to be written (multiple export)
1317	if event:
1318	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1319
1320	def MakePWDRfilename(self,hist):
1321	'''Make a filename root (no extension) from a PWDR histogram name
1322
1323	:param str hist: the histogram name in data tree (starts with "PWDR ")
1324	'''
1325	file0 = ''
1326	file1 = hist[5:]
1327	# replace repeated blanks
1328	while file1 != file0:
1329	file0 = file1
1330	file1 = file0.replace(' ',' ').strip()
1331	file0 = file1.replace('Azm= ','A')
1332	# if angle has unneeded decimal places on aziumuth, remove them
1333	if file0[-3:] == '.00': file0 = file0[:-3]
1334	file0 = file0.replace('.','_')
1335	file0 = file0.replace(' ','_')
1336	return file0
1337
1338	def ExportSelect(self,AskFile='ask'):
1339	'''Selects histograms or phases when needed. Sets a default file name when
1340	requested into self.filename; always sets a default directory in self.dirname.
1341
1342	:param bool AskFile: Determines how this routine processes getting a
1343	location to store the current export(s).
1344
1345	* if AskFile is 'ask' (default option), get the name of the file to be written;
1346	self.filename and self.dirname are always set. In the case where
1347	multiple files must be generated, the export routine should do this
1348	based on self.filename as a template.
1349	* if AskFile is 'dir', get the name of the directory to be used;
1350	self.filename is not used, but self.dirname is always set. The export routine
1351	will always generate the file name.
1352	* if AskFile is 'single', get only the name of the directory to be used when
1353	multiple items will be written (as multiple files) are used
1354	or a complete file name is requested when a single file
1355	name is selected. self.dirname is always set and self.filename used
1356	only when a single file is selected.
1357	* if AskFile is 'default', creates a name of the file to be used from
1358	the name of the project (.gpx) file. If the project has not been saved,
1359	then the name of file is requested.
1360	self.filename and self.dirname are always set. In the case where
1361	multiple file names must be generated, the export routine should do this
1362	based on self.filename.
1363	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1364	file. If the project has not been saved, then a directory is requested.
1365	self.filename is not used.
1366
1367	:returns: True in case of an error
1368	'''
1369
1370	numselected = 1
1371	if self.currentExportType == 'phase':
1372	if len(self.Phases) == 0:
1373	self.G2frame.ErrorDialog(
1374	'Empty project',
1375	'Project does not contain any phases.')
1376	return True
1377	elif len(self.Phases) == 1:
1378	self.phasenam = list(self.Phases.keys())
1379	elif self.multiple:
1380	choices = sorted(self.Phases.keys())
1381	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1382	if phasenum is None: return True
1383	self.phasenam = [choices[i] for i in phasenum]
1384	if not self.phasenam: return True
1385	numselected = len(self.phasenam)
1386	else:
1387	choices = sorted(self.Phases.keys())
1388	phasenum = G2G.ItemSelector(choices,self.G2frame)
1389	if phasenum is None: return True
1390	self.phasenam = [choices[phasenum]]
1391	numselected = len(self.phasenam)
1392	elif self.currentExportType == 'single':
1393	if len(self.xtalDict) == 0:
1394	self.G2frame.ErrorDialog(
1395	'Empty project',
1396	'Project does not contain any single crystal data.')
1397	return True
1398	elif len(self.xtalDict) == 1:
1399	self.histnam = self.xtalDict.values()
1400	elif self.multiple:
1401	choices = sorted(self.xtalDict.values())
1402	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1403	if not hnum: return True
1404	self.histnam = [choices[i] for i in hnum]
1405	numselected = len(self.histnam)
1406	else:
1407	choices = sorted(self.xtalDict.values())
1408	hnum = G2G.ItemSelector(choices,self.G2frame)
1409	if hnum is None: return True
1410	self.histnam = [choices[hnum]]
1411	numselected = len(self.histnam)
1412	elif self.currentExportType == 'powder':
1413	if len(self.powderDict) == 0:
1414	self.G2frame.ErrorDialog(
1415	'Empty project',
1416	'Project does not contain any powder data.')
1417	return True
1418	elif len(self.powderDict) == 1:
1419	self.histnam = self.powderDict.values()
1420	elif self.multiple:
1421	choices = sorted(self.powderDict.values())
1422	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1423	if not hnum: return True
1424	self.histnam = [choices[i] for i in hnum]
1425	numselected = len(self.histnam)
1426	else:
1427	choices = sorted(self.powderDict.values())
1428	hnum = G2G.ItemSelector(choices,self.G2frame)
1429	if hnum is None: return True
1430	self.histnam = [choices[hnum]]
1431	numselected = len(self.histnam)
1432	elif self.currentExportType == 'sasd':
1433	if len(self.sasdDict) == 0:
1434	self.G2frame.ErrorDialog(
1435	'Empty project',
1436	'Project does not contain any small angle data.')
1437	return True
1438	elif len(self.sasdDict) == 1:
1439	self.histnam = self.sasdDict.values()
1440	elif self.multiple:
1441	choices = sorted(self.sasdDict.values())
1442	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1443	if not hnum: return True
1444	self.histnam = [choices[i] for i in hnum]
1445	numselected = len(self.histnam)
1446	else:
1447	choices = sorted(self.sasdDict.values())
1448	hnum = G2G.ItemSelector(choices,self.G2frame)
1449	if hnum is None: return True
1450	self.histnam = [choices[hnum]]
1451	numselected = len(self.histnam)
1452	elif self.currentExportType == 'image':
1453	if len(self.Histograms) == 0:
1454	self.G2frame.ErrorDialog(
1455	'Empty project',
1456	'Project does not contain any images.')
1457	return True
1458	elif len(self.Histograms) == 1:
1459	self.histnam = list(self.Histograms.keys())
1460	else:
1461	choices = sorted(self.Histograms.keys())
1462	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1463	if self.multiple:
1464	if not hnum: return True
1465	self.histnam = [choices[i] for i in hnum]
1466	else:
1467	if hnum is None: return True
1468	self.histnam = [choices[hnum]]
1469	numselected = len(self.histnam)
1470	if self.currentExportType == 'map':
1471	# search for phases with maps
1472	mapPhases = []
1473	choices = []
1474	for phasenam in sorted(self.Phases):
1475	phasedict = self.Phases[phasenam] # pointer to current phase info
1476	if len(phasedict['General']['Map'].get('rho',[])):
1477	mapPhases.append(phasenam)
1478	if phasedict['General']['Map'].get('Flip'):
1479	choices.append('Charge flip map: '+str(phasenam))
1480	elif phasedict['General']['Map'].get('MapType'):
1481	choices.append(
1482	str(phasedict['General']['Map'].get('MapType'))
1483	+ ' map: ' + str(phasenam))
1484	else:
1485	choices.append('unknown map: '+str(phasenam))
1486	# select a map if needed
1487	if len(mapPhases) == 0:
1488	self.G2frame.ErrorDialog(
1489	'Empty project',
1490	'Project does not contain any maps.')
1491	return True
1492	elif len(mapPhases) == 1:
1493	self.phasenam = mapPhases
1494	else:
1495	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1496	if self.multiple:
1497	if not phasenum: return True
1498	self.phasenam = [mapPhases[i] for i in phasenum]
1499	else:
1500	if phasenum is None: return True
1501	self.phasenam = [mapPhases[phasenum]]
1502	numselected = len(self.phasenam)
1503
1504	# items selected, now set self.dirname and usually self.filename
1505	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
1506	AskFile == 'default' and not self.G2frame.GSASprojectfile
1507	):
1508	filename = self.askSaveFile()
1509	if not filename: return True
1510	self.dirname,self.filename = os.path.split(filename)
1511	elif AskFile == 'dir' or AskFile == 'single' or (
1512	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
1513	):
1514	self.dirname = self.askSaveDirectory()
1515	if not self.dirname: return True
1516	elif AskFile == 'default-dir' or AskFile == 'default':
1517	self.dirname,self.filename = os.path.split(
1518	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
1519	)
1520	else:
1521	raise Exception('This should not happen!')
1522
1523	def loadParmDict(self):
1524	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
1525	refined values to those from the last cycle and set the uncertainties for the
1526	refined parameters in another dict (self.sigDict).
1527
1528	Expands the parm & sig dicts to include values derived from constraints.
1529
1530	This could be made faster for sequential fits by reducing the histogram list to only
1531	the active histogram being exported.
1532	'''
1533	self.parmDict = {}
1534	self.sigDict = {}
1535	rigidbodyDict = {}
1536	covDict = {}
1537	consDict = {}
1538	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1539	if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1540	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1541	while item:
1542	name = self.G2frame.GPXtree.GetItemText(item)
1543	if name == 'Rigid bodies':
1544	rigidbodyDict = self.G2frame.GPXtree.GetItemPyData(item)
1545	elif name == 'Covariance':
1546	covDict = self.G2frame.GPXtree.GetItemPyData(item)
1547	elif name == 'Constraints':
1548	consDict = self.G2frame.GPXtree.GetItemPyData(item)
1549	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1550	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1551	self.parmDict.update(rbDict)
1552	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1553	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData(
1554	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
1555	self.parmDict.update(phaseDict)
1556	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
1557	Phases,Histograms,Print=False,resetRefList=False)
1558	self.parmDict.update(hapDict)
1559	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
1560	self.parmDict.update(histDict)
1561	self.parmDict.update(zip(
1562	covDict.get('varyList',[]),
1563	covDict.get('variables',[])))
1564	self.sigDict = dict(zip(
1565	covDict.get('varyList',[]),
1566	covDict.get('sig',[])))
1567	# expand to include constraints: first compile a list of constraints
1568	constList = []
1569	for item in consDict:
1570	if item.startswith('_'): continue
1571	constList += consDict[item]
1572	# now process the constraints
1573	G2mv.InitVars()
1574	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
1575	varyList = covDict.get('varyListStart')
1576	if varyList is None and len(constDict) == 0:
1577	# no constraints can use varyList
1578	varyList = covDict.get('varyList')
1579	elif varyList is None:
1580	# old GPX file from before pre-constraint varyList is saved
1581	print (' * Old refinement: Please use Calculate/Refine to redo *')
1582	raise Exception(' * Export aborted *')
1583	else:
1584	varyList = list(varyList)
1585	# add symmetry-generated constraints
1586	rigidbodyDict = self.G2frame.GPXtree.GetItemPyData(
1587	G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,'Rigid bodies'))
1588	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1589	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1590	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData(
1591	Phases,RestraintDict=None,rbIds=rbIds,Print=False) # generates atom symmetry constraints
1592	msg = G2mv.EvaluateMultipliers(constDict,phaseDict)
1593	if msg:
1594	print('Unable to interpret multiplier(s): '+msg)
1595	raise Exception(' * CIF creation aborted *')
1596	try:
1597	G2mv.GenerateConstraints(varyList,constDict,fixedList,self.parmDict)
1598	#print(G2mv.VarRemapShow(varyList))
1599	except:
1600	# this really should not happen
1601	print (' * ERROR - constraints are internally inconsistent *')
1602	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
1603	print ('Errors'+errmsg)
1604	if warnmsg: print ('Warnings'+warnmsg)
1605	raise Exception(' * CIF creation aborted *')
1606	# add the constrained values to the parameter dictionary
1607	G2mv.Dict2Map(self.parmDict,varyList)
1608	# and add their uncertainties into the esd dictionary (sigDict)
1609	if covDict.get('covMatrix') is not None:
1610	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
1611
1612	def loadTree(self):
1613	'''Load the contents of the data tree into a set of dicts
1614	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
1615	& self.xtalDict)
1616
1617	* The childrenless data tree items are overall parameters/controls for the
1618	entire project and are placed in self.OverallParms
1619	* Phase items are placed in self.Phases
1620	* Data items are placed in self.Histogram. The key for these data items
1621	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
1622	'''
1623	self.OverallParms = {}
1624	self.powderDict = {}
1625	self.sasdDict = {}
1626	self.xtalDict = {}
1627	self.Phases = {}
1628	self.Histograms = {}
1629	self.SeqRefdata = None
1630	self.SeqRefhist = None
1631	if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1632	histType = None
1633	if self.currentExportType == 'phase':
1634	# if exporting phases load them here
1635	sub = G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,'Phases')
1636	if not sub:
1637	print ('no phases found')
1638	return True
1639	item, cookie = self.G2frame.GPXtree.GetFirstChild(sub)
1640	while item:
1641	phaseName = self.G2frame.GPXtree.GetItemText(item)
1642	self.Phases[phaseName] = self.G2frame.GPXtree.GetItemPyData(item)
1643	item, cookie = self.G2frame.GPXtree.GetNextChild(sub, cookie)
1644	return
1645	elif self.currentExportType == 'single':
1646	histType = 'HKLF'
1647	elif self.currentExportType == 'powder':
1648	histType = 'PWDR'
1649	elif self.currentExportType == 'image':
1650	histType = 'IMG'
1651	elif self.currentExportType == 'sasd':
1652	histType = 'SASD'
1653
1654	if histType: # Loading just one kind of tree entry
1655	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1656	while item:
1657	name = self.G2frame.GPXtree.GetItemText(item)
1658	if name.startswith(histType):
1659	if self.Histograms.get(name): # there is already an item with this name
1660	print('Histogram name '+str(name)+' is repeated. Renaming')
1661	if name[-1] == '9':
1662	name = name[:-1] + '10'
1663	elif name[-1] in '012345678':
1664	name = name[:-1] + str(int(name[-1])+1)
1665	else:
1666	name += '-1'
1667	self.Histograms[name] = {}
1668	# the main info goes into Data, but the 0th
1669	# element contains refinement results, carry
1670	# that over too now.
1671	self.Histograms[name]['Data'] = self.G2frame.GPXtree.GetItemPyData(item)[1]
1672	self.Histograms[name][0] = self.G2frame.GPXtree.GetItemPyData(item)[0]
1673	item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1674	while item2:
1675	child = self.G2frame.GPXtree.GetItemText(item2)
1676	self.Histograms[name][child] = self.G2frame.GPXtree.GetItemPyData(item2)
1677	item2, cookie2 = self.G2frame.GPXtree.GetNextChild(item, cookie2)
1678	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1679	# index powder and single crystal histograms by number
1680	for hist in self.Histograms:
1681	if hist.startswith("PWDR"):
1682	d = self.powderDict
1683	elif hist.startswith("HKLF"):
1684	d = self.xtalDict
1685	elif hist.startswith("SASD"):
1686	d = self.sasdDict
1687	else:
1688	return
1689	i = self.Histograms[hist].get('hId')
1690	if i is None and not d.keys():
1691	i = 0
1692	elif i is None or i in d.keys():
1693	i = max(d.keys())+1
1694	d[i] = hist
1695	return
1696	# else standard load: using all interlinked phases and histograms
1697	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1698	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1699	while item:
1700	name = self.G2frame.GPXtree.GetItemText(item)
1701	item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1702	if not item2:
1703	self.OverallParms[name] = self.G2frame.GPXtree.GetItemPyData(item)
1704	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1705	# index powder and single crystal histograms
1706	for hist in self.Histograms:
1707	i = self.Histograms[hist]['hId']
1708	if hist.startswith("PWDR"):
1709	self.powderDict[i] = hist
1710	elif hist.startswith("HKLF"):
1711	self.xtalDict[i] = hist
1712	elif hist.startswith("SASD"):
1713	self.sasdDict[i] = hist
1714
1715	def dumpTree(self,mode='type'):
1716	'''Print out information on the data tree dicts loaded in loadTree.
1717	Used for testing only.
1718	'''
1719	if self.SeqRefdata and self.SeqRefhist:
1720	print('Note that dumpTree does not show sequential results')
1721	print ('\nOverall')
1722	if mode == 'type':
1723	def Show(arg): return type(arg)
1724	else:
1725	def Show(arg): return arg
1726	for key in self.OverallParms:
1727	print (' '+key+Show(self.OverallParms[key]))
1728	print ('Phases')
1729	for key1 in self.Phases:
1730	print (' '+key1+Show(self.Phases[key1]))
1731	print ('Histogram')
1732	for key1 in self.Histograms:
1733	print (' '+key1+Show(self.Histograms[key1]))
1734	for key2 in self.Histograms[key1]:
1735	print (' '+key2+Show(self.Histograms[key1][key2]))
1736
1737	def defaultSaveFile(self):
1738	return os.path.abspath(
1739	os.path.splitext(self.G2frame.GSASprojectfile
1740	)[0]+self.extension)
1741
1742	def askSaveFile(self):
1743	'''Ask the user to supply a file name
1744
1745	:returns: a file name (str) or None if Cancel is pressed
1746
1747	'''
1748	pth = G2G.GetExportPath(self.G2frame)
1749	if self.G2frame.GSASprojectfile:
1750	defnam = os.path.splitext(
1751	os.path.split(self.G2frame.GSASprojectfile)[1]
1752	)[0]+self.extension
1753	else:
1754	defnam = 'default' + self.extension
1755	return G2G.askSaveFile(self.G2frame,defnam,self.extension,self.longFormatName)
1756
1757	def askSaveDirectory(self):
1758	'''Ask the user to supply a directory name. Path name is used as the
1759	starting point for the next export path search.
1760
1761	:returns: a directory name (str) or None if Cancel is pressed
1762
1763	TODO: Can this be replaced with G2G.askSaveDirectory?
1764	'''
1765	pth = G2G.GetExportPath(self.G2frame)
1766	dlg = wx.DirDialog(
1767	self.G2frame, 'Input directory where file(s) will be written', pth,
1768	wx.DD_DEFAULT_STYLE)
1769	dlg.CenterOnParent()
1770	try:
1771	if dlg.ShowModal() == wx.ID_OK:
1772	filename = dlg.GetPath()
1773	self.G2frame.LastExportDir = filename
1774	else:
1775	filename = None
1776	finally:
1777	dlg.Destroy()
1778	return filename
1779
1780	# Tools for file writing.
1781	def OpenFile(self,fil=None,mode='w'):
1782	'''Open the output file
1783
1784	:param str fil: The name of the file to open. If None (default)
1785	the name defaults to self.dirname + self.filename.
1786	If an extension is supplied, it is not overridded,
1787	but if not, the default extension is used.
1788	:returns: the file object opened by the routine which is also
1789	saved as self.fp
1790	'''
1791	if mode == 'd': # debug mode
1792	self.fullpath = '(stdout)'
1793	self.fp = sys.stdout
1794	return
1795	if not fil:
1796	if not os.path.splitext(self.filename)[1]:
1797	self.filename += self.extension
1798	fil = os.path.join(self.dirname,self.filename)
1799	self.fullpath = os.path.abspath(fil)
1800	self.fp = open(self.fullpath,mode)
1801	return self.fp
1802
1803	def Write(self,line):
1804	'''write a line of output, attaching a line-end character
1805
1806	:param str line: the text to be written.
1807	'''
1808	self.fp.write(line+'\n')
1809
1810	def CloseFile(self,fp=None):
1811	'''Close a file opened in OpenFile
1812
1813	:param file fp: the file object to be closed. If None (default)
1814	file object self.fp is closed.
1815	'''
1816	if self.fp == sys.stdout: return # debug mode
1817	if fp is None:
1818	fp = self.fp
1819	self.fp = None
1820	if fp is not None: fp.close()
1821
1822	def SetSeqRef(self,data,hist):
1823	'''Set the exporter to retrieve results from a sequential refinement
1824	rather than the main tree
1825	'''
1826	self.SeqRefdata = data
1827	self.SeqRefhist = hist
1828	data_name = data[hist]
1829	for i,val in zip(data_name['varyList'],data_name['sig']):
1830	self.sigDict[i] = val
1831	self.sigDict[striphist(i)] = val
1832	for i in data_name['parmDict']:
1833	self.parmDict[striphist(i)] = data_name['parmDict'][i]
1834	self.parmDict[i] = data_name['parmDict'][i]
1835	# zero out the dA[xyz] terms, they would only bring confusion
1836	key = i.split(':')
1837	if len(key) < 3: continue
1838	if key[2].startswith('dA'):
1839	self.parmDict[i] = 0.0
1840	for i,(val,sig) in data_name.get('depParmDict',{}).items():
1841	self.parmDict[i] = val
1842	self.sigDict[i] = sig
1843	#GSASIIpath.IPyBreak()
1844
1845	# Tools to pull information out of the data arrays
1846	def GetCell(self,phasenam):
1847	"""Gets the unit cell parameters and their s.u.'s for a selected phase
1848
1849	:param str phasenam: the name for the selected phase
1850	:returns: `cellList,cellSig` where each is a 7 element list corresponding
1851	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1852	cell values and `cellSig` has their uncertainties.
1853	"""
1854	if self.SeqRefdata and self.SeqRefhist:
1855	return self.GetSeqCell(phasenam,self.SeqRefdata[self.SeqRefhist])
1856	phasedict = self.Phases[phasenam] # pointer to current phase info
1857	try:
1858	pfx = str(phasedict['pId'])+'::'
1859	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
1860	cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A,
1861	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
1862	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
1863	return cellList,cellSig
1864	except KeyError:
1865	cell = phasedict['General']['Cell'][1:]
1866	return cell,7*[0]
1867
1868	def GetSeqCell(self,phasenam,data_name):
1869	"""Gets the unit cell parameters and their s.u.'s for a selected phase
1870	and histogram in a sequential fit
1871
1872	:param str phasenam: the name for the selected phase
1873	:param dict data_name: the sequential refinement parameters for the selected histogram
1874	:returns: `cellList,cellSig` where each is a 7 element list corresponding
1875	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1876	cell values and `cellSig` has their uncertainties.
1877	"""
1878	phasedict = self.Phases[phasenam]
1879	SGdata = phasedict['General']['SGData']
1880	pId = phasedict['pId']
1881	RecpCellTerms = G2lat.cell2A(phasedict['General']['Cell'][1:7])
1882	ESDlookup = {}
1883	Dlookup = {}
1884	varied = [striphist(i) for i in data_name['varyList']]
1885	for item,val in data_name['newCellDict'].items():
1886	if item in varied:
1887	ESDlookup[val[0]] = item
1888	Dlookup[item] = val[0]
1889	A = RecpCellTerms[:]
1890	for i in range(6):
1891	var = str(pId)+'::A'+str(i)
1892	if var in ESDlookup:
1893	A[i] = data_name['newCellDict'][ESDlookup[var]][1] # override with refined value
1894	cellDict = dict(zip([str(pId)+'::A'+str(i) for i in range(6)],A))
1895	zeroDict = {i:0.0 for i in cellDict}
1896	A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata,cellDict,zeroDict)
1897	covData = {
1898	'varyList': [Dlookup.get(striphist(v),v) for v in data_name['varyList']],
1899	'covMatrix': data_name['covMatrix']
1900	}
1901	return list(G2lat.A2cell(A)) + [G2lat.calc_V(A)], G2stIO.getCellEsd(str(pId)+'::',SGdata,A,covData)
1902
1903	def GetAtoms(self,phasenam):
1904	"""Gets the atoms associated with a phase. Can be used with standard
1905	or macromolecular phases
1906
1907	:param str phasenam: the name for the selected phase
1908	:returns: a list of items for eac atom where each item is a list containing:
1909	label, typ, mult, xyz, and td, where
1910
1911	* label and typ are the atom label and the scattering factor type (str)
1912	* mult is the site multiplicity (int)
1913	* xyz is contains a list with four pairs of numbers:
1914	x, y, z and fractional occupancy and
1915	their standard uncertainty (or a negative value)
1916	* td is contains a list with either one or six pairs of numbers:
1917	if one number it is U\ :sub:`iso` and with six numbers it is
1918	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
1919	paired with their standard uncertainty (or a negative value)
1920	"""
1921	phasedict = self.Phases[phasenam] # pointer to current phase info
1922	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
1923	cfrac = cx+3
1924	fpfx = str(phasedict['pId'])+'::Afrac:'
1925	atomslist = []
1926	for i,at in enumerate(phasedict['Atoms']):
1927	if phasedict['General']['Type'] == 'macromolecular':
1928	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
1929	else:
1930	label = at[ct-1]
1931	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
1932	fsig = self.sigDict.get(fpfx+str(i),-0.009)
1933	mult = at[cs+1]
1934	typ = at[ct]
1935	xyz = []
1936	for j,v in enumerate(('x','y','z')):
1937	val = at[cx+j]
1938	pfx = str(phasedict['pId']) + '::A' + v + ':' + str(i)
1939	val = self.parmDict.get(pfx, val)
1940	dpfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
1941	sig = self.sigDict.get(dpfx,-0.000009)
1942	xyz.append((val,sig))
1943	xyz.append((fval,fsig))
1944	td = []
1945	if at[cia] == 'I':
1946	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
1947	val = self.parmDict.get(pfx,at[cia+1])
1948	sig = self.sigDict.get(pfx,-0.0009)
1949	td.append((val,sig))
1950	else:
1951	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
1952	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
1953	val = self.parmDict.get(pfx,at[cia+2+i])
1954	sig = self.sigDict.get(pfx,-0.0009)
1955	td.append((val,sig))
1956	atomslist.append((label,typ,mult,xyz,td))
1957	return atomslist
1958	######################################################################
1959	def ExportPowderList(G2frame):
1960	'''Returns a list of extensions supported by :func:`GSASIIIO:ExportPowder`
1961	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
1962
1963	:param wx.Frame G2frame: the GSAS-II main data tree window
1964	'''
1965	extList = []
1966	for obj in G2frame.exporterlist:
1967	if 'powder' in obj.exporttype:
1968	try:
1969	obj.Writer
1970	extList.append(obj.extension)
1971	except AttributeError:
1972	pass
1973	return extList
1974
1975	def ExportPowder(G2frame,TreeName,fileroot,extension):
1976	'''Writes a single powder histogram using the Export routines.
1977	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
1978
1979	:param wx.Frame G2frame: the GSAS-II main data tree window
1980	:param str TreeName: the name of the histogram (PWDR ...) in the data tree
1981	:param str fileroot: name for file to be written, extension ignored
1982	:param str extension: extension for file to be written (start with '.'). Must
1983	match a powder export routine that has a Writer object.
1984	'''
1985	filename = os.path.abspath(os.path.splitext(fileroot)[0]+extension)
1986	for obj in G2frame.exporterlist:
1987	if obj.extension == extension and 'powder' in obj.exporttype:
1988	obj.currentExportType = 'powder'
1989	obj.InitExport(None)
1990	obj.loadTree() # load all histograms in tree into dicts
1991	if TreeName not in obj.Histograms:
1992	raise Exception('Histogram not found: '+str(TreeName))
1993	try:
1994	obj.Writer
1995	except AttributeError:
1996	continue
1997	try:
1998	obj.Writer(TreeName,filename)
1999	print('wrote file '+filename)
2000	return
2001	except Exception:
2002	print('Export Routine for '+extension+' failed.')
2003	else:
2004	print('No Export routine supports extension '+extension)
2005
2006	def ExportSequential(G2frame,data,obj,exporttype):
2007	'''
2008	Used to export from every phase/dataset in a sequential refinement using
2009	a .Writer method for either projects or phases. Prompts to select histograms
2010	and for phase exports, which phase(s).
2011
2012	:param wx.Frame G2frame: the GSAS-II main data tree window
2013	:param dict data: the sequential refinement data object
2014	:param str exporttype: indicates the type of export ('project' or 'phase')
2015	'''
2016	if len(data['histNames']) == 0:
2017	G2G.G2MessageBox(G2frame,'There are no sequential histograms','Warning')
2018	obj.InitExport(None)
2019	obj.loadTree()
2020	obj.loadParmDict()
2021	if len(data['histNames']) == 1:
2022	histlist = data['histNames']
2023	else:
2024	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select histograms to export from list',
2025	'Select histograms',data['histNames'])
2026	if dlg.ShowModal() == wx.ID_OK:
2027	histlist = [data['histNames'][l] for l in dlg.GetSelections()]
2028	dlg.Destroy()
2029	else:
2030	dlg.Destroy()
2031	return
2032	if exporttype == 'Phase':
2033	phaselist = list(obj.Phases.keys())
2034	if len(obj.Phases) == 0:
2035	G2G.G2MessageBox(G2frame,'There are no phases in sequential ref.','Warning')
2036	return
2037	elif len(obj.Phases) > 1:
2038	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select phases to export from list',
2039	'Select phases', phaselist)
2040	if dlg.ShowModal() == wx.ID_OK:
2041	phaselist = [phaselist[l] for l in dlg.GetSelections()]
2042	dlg.Destroy()
2043	else:
2044	dlg.Destroy()
2045	return
2046	filename = obj.askSaveFile()
2047	if not filename: return True
2048	obj.dirname,obj.filename = os.path.split(filename)
2049	print('Writing output to file '+str(obj.filename)+"...")
2050	mode = 'w'
2051	for p in phaselist:
2052	for h in histlist:
2053	obj.SetSeqRef(data,h)
2054	#GSASIIpath.IPyBreak()
2055	obj.Writer(h,phasenam=p,mode=mode)
2056	mode = 'a'
2057	print('...done')
2058	elif exporttype == 'Project': # note that the CIF exporter is not yet ready for this
2059	filename = obj.askSaveFile()
2060	if not filename: return True
2061	obj.dirname,obj.filename = os.path.split(filename)
2062	print('Writing output to file '+str(obj.filename)+"...")
2063	mode = 'w'
2064	for h in histlist:
2065	obj.SetSeqRef(data,h)
2066	obj.Writer(h,mode=mode)
2067	print('\t'+str(h)+' written')
2068	mode = 'a'
2069	print('...done')
2070	elif exporttype == 'Powder':
2071	filename = obj.askSaveFile()
2072	if not filename: return True
2073	obj.dirname,obj.filename = os.path.split(filename)
2074	print('Writing output to file '+str(obj.filename)+"...")
2075	mode = 'w'
2076	for h in histlist:
2077	obj.SetSeqRef(data,h)
2078	obj.Writer(h,mode=mode)
2079	print('\t'+str(h)+' written')
2080	mode = 'a'
2081	print('...done')
2082
2083	def ReadDIFFaX(DIFFaXfile):
2084	print ('read '+DIFFaXfile)
2085	Layer = {'Laue':'-1','Cell':[False,1.,1.,1.,90.,90.,90,1.],'Width':[[10.,10.],[False,False]],
2086	'Layers':[],'Stacking':[],'Transitions':[],'Toler':0.01,'AtInfo':{}}
2087	df = open(DIFFaXfile,'r')
2088	lines = df.readlines()
2089	df.close()
2090	struct = False
2091	Struct = []
2092	stack = False
2093	Stack = []
2094	trans = False
2095	Trans = []
2096	for diff in lines:
2097	diff = diff[:-1].lower()
2098	if '!' in diff:
2099	continue
2100	while '}' in diff: #strip comments
2101	iB = diff.index('{')
2102	iF = diff.index('}')+1
2103	if iB:
2104	diff = diff[:iB]
2105	else:
2106	diff = diff[iF:]
2107	if not diff:
2108	continue
2109	if diff.strip() == 'instrumental':
2110	continue
2111	if diff.strip() == 'structural':
2112	struct = True
2113	continue
2114	elif diff.strip() == 'stacking':
2115	struct = False
2116	stack = True
2117	continue
2118	elif diff.strip() == 'transitions':
2119	stack = False
2120	trans = True
2121	continue
2122	diff = diff.strip()
2123	if struct:
2124	if diff:
2125	Struct.append(diff)
2126	elif stack:
2127	if diff:
2128	Stack.append(diff)
2129	elif trans:
2130	if diff:
2131	Trans.append(diff)
2132
2133	#STRUCTURE records
2134	laueRec = Struct[1].split()
2135	Layer['Laue'] = laueRec[0]
2136	if Layer['Laue'] == 'unknown' and len(laueRec) > 1:
2137	Layer['Toler'] = float(laueRec[1]) #tolerance for 'unknown'?
2138	if Layer['Laue'] == '2/m(1)': Layer['Laue'] = '2/m(c)'
2139	if Layer['Laue'] == '2/m(2)': Layer['Laue'] = '2/m(ab)'
2140	cell = Struct[0].split()
2141	Layer['Cell'] = [False,float(cell[0]),float(cell[1]),float(cell[2]),90.,90.,float(cell[3]),1.0]
2142	nLayers = int(Struct[2])
2143	N = 3
2144	if 'layer' not in Struct[3]:
2145	N = 4
2146	if Struct[3] != 'infinite':
2147	width = Struct[3].split()
2148	Layer['Width'][0] = [float(width[0]),float(width[1])]
2149	for nL in range(nLayers):
2150	if '=' in Struct[N]:
2151	name = Struct[N].split('=')
2152	sameas = int(name[1])-1
2153	Layer['Layers'].append({'Name':name[0],'SameAs':Layer['Layers'][sameas]['Name'],'Symm':'None','Atoms':[]})
2154	N += 1
2155	continue
2156	Symm = 'None'
2157	if 'centro' in Struct[N+1]: Symm = '-1'
2158	Layer['Layers'].append({'Name':Struct[N],'SameAs':'','Symm':Symm,'Atoms':[]})
2159	N += 2
2160	while 'layer' not in Struct[N]:
2161	atom = Struct[N][4:].split()
2162	atomType = G2el.FixValence(Struct[N][:4].replace(' ','').strip().capitalize())
2163	if atomType not in Layer['AtInfo']:
2164	Layer['AtInfo'][atomType] = G2el.GetAtomInfo(atomType)
2165	atomName = '%s(%s)'%(atomType,atom[0])
2166	newVals = []
2167	for val in atom[1:6]:
2168	if '/' in val:
2169	newVals.append(eval(val+'.'))
2170	else:
2171	newVals.append(float(val))
2172	atomRec = [atomName,atomType,newVals[0],newVals[1],newVals[2],newVals[4],newVals[3]/78.9568]
2173	Layer['Layers'][-1]['Atoms'].append(atomRec)
2174	N += 1
2175	if N > len(Struct)-1:
2176	break
2177	#TRANSITIONS records
2178	transArray = []
2179	N = 0
2180	for i in range(nLayers):
2181	transArray.append([])
2182	for j in range(nLayers):
2183	vals = Trans[N].split()
2184	newVals = []
2185	for val in vals[:4]:
2186	if '/' in val:
2187	newVals.append(eval(val+'.'))
2188	else:
2189	newVals.append(float(val))
2190	transArray[-1].append(newVals+['',False])
2191	N += 1
2192	Layer['Transitions'] = transArray
2193	#STACKING records
2194	Layer['Stacking'] = [Stack[0],'']
2195	if Stack[0] == 'recursive':
2196	Layer['Stacking'][1] = Stack[1]
2197	elif Stack[0] == 'explicit':
2198	if Stack[1] == 'random':
2199	Layer['Stacking'][1] = Stack[1]
2200	else:
2201	Layer['Stacking'][1] = 'list'
2202	Layer['Stacking'].append('')
2203	for stack in Stack[2:]:
2204	Layer['Stacking'][2] += ' '+stack
2205	return Layer
2206
2207	if __name__ == '__main__':
2208	import GSASIIdataGUI
2209	application = GSASIIdataGUI.GSASIImain(0)
2210	G2frame = application.main
2211	#app = wx.PySimpleApp()
2212	#G2frame = wx.Frame(None) # create a frame
2213	#frm.Show(True)
2214	#filename = '/tmp/notzip.zip'
2215	#filename = '/tmp/all.zip'
2216	#filename = '/tmp/11bmb_7652.zip'
2217
2218	#selection=None, confirmoverwrite=True, parent=None
2219	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2220	#print ExtractFileFromZip(filename,multipleselect=True)
2221	# #confirmread=False, confirmoverwrite=False)
2222
2223	# choicelist=[ ('a','b','c'),
2224	# ('test1','test2'),('no choice',)]
2225	# titles = [ 'a, b or c', 'tests', 'No option here']
2226	# dlg = MultipleChoicesDialog(
2227	# choicelist,titles,
2228	# parent=frm)
2229	# if dlg.ShowModal() == wx.ID_OK:
2230	# print 'Got OK'
2231	imagefile = '/tmp/NDC5_00237_3.ge3'
2232	Comments, Data, Npix, Image = GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None)
2233
2234	print("\n\nResults loaded to Comments, Data, Npix and Image\n\n")
2235
2236	GSASIIpath.IPyBreak_base()

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