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source: trunk/GSASIIIO.py @ 3173

Last change on this file since 3173 was 3173, checked in by vondreele, 5 years ago
ensure limits on multiple powder patterns from integration are independent Integrate All & Auto integrate now reuse x,y --> 2th,azm maps if image controls unchanged - much faster multiple integrations
Property svn:eol-style set to `native` Property svn:keywords set to `Date Author Revision URL Id`
File size: 90.6 KB

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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2017-12-05 21:23:50 +0000 (Tue, 05 Dec 2017) $
4	# $Author: vondreele $
5	# $Revision: 3173 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 3173 2017-12-05 21:23:50Z 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	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 copy
34	import platform
35	if '2' in platform.python_version_tuple()[0]:
36	import cPickle
37	else:
38	import _pickle as cPickle
39	import sys
40	import re
41	import random as ran
42	import GSASIIpath
43	GSASIIpath.SetVersionNumber("$Revision: 3173 $")
44	try:
45	import GSASIIdataGUI as G2gd
46	except ImportError:
47	pass
48	import GSASIIobj as G2obj
49	import GSASIIlattice as G2lat
50	import GSASIImath as G2mth
51	try:
52	import GSASIIpwdGUI as G2pdG
53	import GSASIIimgGUI as G2imG
54	except ImportError:
55	pass
56	import GSASIIimage as G2img
57	import GSASIIElem as G2el
58	import GSASIIstrIO as G2stIO
59	import GSASIImapvars as G2mv
60	try:
61	import GSASIIctrlGUI as G2G
62	except ImportError:
63	pass
64	import os
65	import os.path as ospath
66
67	DEBUG = False #=True for various prints
68	TRANSP = False #=true to transpose images for testing
69	if GSASIIpath.GetConfigValue('Transpose'): TRANSP = True
70	npsind = lambda x: np.sin(x*np.pi/180.)
71
72	def sfloat(S):
73	'Convert a string to float. An empty field or a unconvertable value is treated as zero'
74	if S.strip():
75	try:
76	return float(S)
77	except ValueError:
78	pass
79	return 0.0
80
81	def sint(S):
82	'Convert a string to int. An empty field is treated as zero'
83	if S.strip():
84	return int(S)
85	else:
86	return 0
87
88	def trim(val):
89	'''Simplify a string containing leading and trailing spaces
90	as well as newlines, tabs, repeated spaces etc. into a shorter and
91	more simple string, by replacing all ranges of whitespace
92	characters with a single space.
93
94	:param str val: the string to be simplified
95
96	:returns: the (usually) shortened version of the string
97	'''
98	return re.sub('\s+', ' ', val).strip()
99
100	def FileDlgFixExt(dlg,file):
101	'this is needed to fix a problem in linux wx.FileDialog'
102	ext = dlg.GetWildcard().split('\|')[2dlg.GetFilterIndex()+1].strip('')
103	if ext not in file:
104	file += ext
105	return file
106
107	def GetPowderPeaks(fileName):
108	'Read powder peaks from a file'
109	sind = lambda x: math.sin(x*math.pi/180.)
110	asind = lambda x: 180.*math.asin(x)/math.pi
111	wave = 1.54052
112	File = open(fileName,'Ur')
113	Comments = []
114	peaks = []
115	S = File.readline()
116	while S:
117	if S[:1] == '#':
118	Comments.append(S[:-1])
119	else:
120	item = S.split()
121	if len(item) == 1:
122	peaks.append([float(item[0]),1.0])
123	elif len(item) > 1:
124	peaks.append([float(item[0]),float(item[0])])
125	S = File.readline()
126	File.close()
127	if Comments:
128	print ('Comments on file:')
129	for Comment in Comments:
130	print (Comment)
131	if 'wavelength' in Comment:
132	wave = float(Comment.split('=')[1])
133	Peaks = []
134	if peaks[0][0] > peaks[-1][0]: # d-spacings - assume CuKa
135	for peak in peaks:
136	dsp = peak[0]
137	sth = wave/(2.0*dsp)
138	if sth < 1.0:
139	tth = 2.0*asind(sth)
140	else:
141	break
142	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
143	else: #2-thetas - assume Cuka (for now)
144	for peak in peaks:
145	tth = peak[0]
146	dsp = wave/(2.0*sind(tth/2.0))
147	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
148	limits = [1000.,0.]
149	for peak in Peaks:
150	limits[0] = min(limits[0],peak[0])
151	limits[1] = max(limits[1],peak[0])
152	limits[0] = max(1.,(int(limits[0]-1.)/5)*5.)
153	limits[1] = min(170.,(int(limits[1]+1.)/5)*5.)
154	return Comments,Peaks,limits,wave
155
156	def GetCheckImageFile(G2frame,treeId):
157	'''Try to locate an image file if the project and image have been moved
158	together. If the image file cannot be found, request the location from
159	the user.
160
161	:param wx.Frame G2frame: main GSAS-II Frame and data object
162	:param wx.Id treeId: Id for the main tree item for the image
163	:returns: Npix,imagefile,imagetag with (Npix) number of pixels,
164	imagefile, if it exists, or the name of a file that does exist or False if the user presses Cancel
165	and (imagetag) an optional image number
166
167	'''
168	Npix,Imagefile,imagetag = G2frame.GPXtree.GetImageLoc(treeId)
169	if isinstance(Imagefile,list):
170	imagefile,imagetag = Imagefile
171	else:
172	imagefile = Imagefile
173	if not os.path.exists(imagefile):
174	print ('Image file '+imagefile+' not found')
175	fil = imagefile.replace('\\','/') # windows?!
176	# see if we can find a file with same name or in a similarly named sub-dir
177	pth,fil = os.path.split(fil)
178	prevpth = None
179	while pth and pth != prevpth:
180	prevpth = pth
181	if os.path.exists(os.path.join(G2frame.dirname,fil)):
182	print ('found image file '+os.path.join(G2frame.dirname,fil))
183	imagefile = os.path.join(G2frame.dirname,fil)
184	G2frame.GPXtree.UpdateImageLoc(treeId,imagefile)
185	return Npix,imagefile,imagetag
186	pth,enddir = os.path.split(pth)
187	fil = os.path.join(enddir,fil)
188	# not found as a subdirectory, drop common parts of path for last saved & image file names
189	# if image was .../A/B/C/imgs/ima.ge
190	# & GPX was .../A/B/C/refs/fil.gpx but is now .../NEW/TEST/TEST1
191	# will look for .../NEW/TEST/TEST1/imgs/ima.ge, .../NEW/TEST/imgs/ima.ge, .../NEW/imgs/ima.ge and so on
192	Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
193	gpxPath = Controls.get('LastSavedAs','').replace('\\','/').split('/') # blank in older .GPX files
194	imgPath = imagefile.replace('\\','/').split('/')
195	for p1,p2 in zip(gpxPath,imgPath):
196	if p1 == p2:
197	gpxPath.pop(0),imgPath.pop(0)
198	else:
199	break
200	fil = os.path.join(*imgPath) # file with non-common prefix elements
201	prevpth = None
202	pth = os.path.abspath(G2frame.dirname)
203	while pth and pth != prevpth:
204	prevpth = pth
205	if os.path.exists(os.path.join(pth,fil)):
206	print ('found image file '+os.path.join(pth,fil))
207	imagefile = os.path.join(pth,fil)
208	G2frame.GPXtree.UpdateImageLoc(treeId,imagefile)
209	return Npix,imagefile,imagetag
210	pth,enddir = os.path.split(pth)
211	#GSASIIpath.IPyBreak()
212
213	if not os.path.exists(imagefile):
214	prevnam = os.path.split(imagefile)[1]
215	prevext = os.path.splitext(imagefile)[1]
216	wildcard = 'Image format ('+prevext+')\|'+prevext
217	dlg = wx.FileDialog(G2frame, 'Previous image file ('+prevnam+') not found; open here', '.', prevnam,
218	wildcard,wx.FD_OPEN)
219	try:
220	dlg.SetFilename(''+ospath.split(imagefile)[1])
221	if dlg.ShowModal() == wx.ID_OK:
222	imagefile = dlg.GetPath()
223	G2frame.GPXtree.UpdateImageLoc(treeId,imagefile)
224	else:
225	imagefile = False
226	finally:
227	dlg.Destroy()
228	return Npix,imagefile,imagetag
229
230	def EditImageParms(parent,Data,Comments,Image,filename):
231	dlg = wx.Dialog(parent, wx.ID_ANY, 'Edit image parameters',
232	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
233	def onClose(event):
234	dlg.EndModal(wx.ID_OK)
235	mainsizer = wx.BoxSizer(wx.VERTICAL)
236	h,w = Image.shape[:2]
237	mainsizer.Add(wx.StaticText(dlg,wx.ID_ANY,'File '+str(filename)+'\nImage size: '+str(h)+' x '+str(w)),
238	0,wx.ALIGN_LEFT\|wx.ALL, 2)
239
240	vsizer = wx.BoxSizer(wx.HORIZONTAL)
241	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Wavelength (\xC5) '),
242	0,wx.ALIGN_LEFT\|wx.ALL, 2)
243	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'wavelength')
244	vsizer.Add(wdgt)
245	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
246
247	vsizer = wx.BoxSizer(wx.HORIZONTAL)
248	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Pixel size (\xb5m). Width '),
249	0,wx.ALIGN_LEFT\|wx.ALL, 2)
250	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],0,
251	size=(50,-1))
252	vsizer.Add(wdgt)
253	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Height '),wx.ALIGN_LEFT\|wx.ALL, 2)
254	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],1,size=(50,-1))
255	vsizer.Add(wdgt)
256	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
257
258	vsizer = wx.BoxSizer(wx.HORIZONTAL)
259	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Sample to detector (mm) '),
260	0,wx.ALIGN_LEFT\|wx.ALL, 2)
261	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'distance')
262	vsizer.Add(wdgt)
263	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
264
265	vsizer = wx.BoxSizer(wx.HORIZONTAL)
266	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Beam center (pixels). X = '),
267	0,wx.ALIGN_LEFT\|wx.ALL, 2)
268	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],0,size=(75,-1))
269	vsizer.Add(wdgt)
270	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Y = '),wx.ALIGN_LEFT\|wx.ALL, 2)
271	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],1,size=(75,-1))
272	vsizer.Add(wdgt)
273	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
274
275	vsizer = wx.BoxSizer(wx.HORIZONTAL)
276	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Comments '),
277	0,wx.ALIGN_LEFT\|wx.ALL, 2)
278	wdgt = G2G.ValidatedTxtCtrl(dlg,Comments,0,size=(250,-1))
279	vsizer.Add(wdgt)
280	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
281
282	btnsizer = wx.StdDialogButtonSizer()
283	OKbtn = wx.Button(dlg, wx.ID_OK, 'Continue')
284	OKbtn.SetDefault()
285	OKbtn.Bind(wx.EVT_BUTTON,onClose)
286	btnsizer.AddButton(OKbtn) # not sure why this is needed
287	btnsizer.Realize()
288	mainsizer.Add(btnsizer, 1, wx.ALIGN_CENTER\|wx.ALL\|wx.EXPAND, 5)
289	dlg.SetSizer(mainsizer)
290	dlg.CenterOnParent()
291	dlg.ShowModal()
292
293	def LoadImage2Tree(imagefile,G2frame,Comments,Data,Npix,Image):
294	'''Load an image into the tree. Saves the location of the image, as well as the
295	ImageTag (where there is more than one image in the file), if defined.
296	'''
297	ImgNames = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',])
298	TreeLbl = 'IMG '+os.path.basename(imagefile)
299	ImageTag = Data.get('ImageTag')
300	if ImageTag:
301	TreeLbl += ' #'+'%04d'%(ImageTag)
302	imageInfo = (imagefile,ImageTag)
303	else:
304	imageInfo = imagefile
305	TreeName = G2obj.MakeUniqueLabel(TreeLbl,ImgNames)
306	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=TreeName)
307	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments)
308	Imax = np.amax(Image)
309	if G2frame.imageDefault:
310	Data = copy.copy(G2frame.imageDefault)
311	Data['showLines'] = True
312	Data['ring'] = []
313	Data['rings'] = []
314	Data['cutoff'] = 10
315	Data['pixLimit'] = 20
316	Data['edgemin'] = 100000000
317	Data['calibdmin'] = 0.5
318	Data['calibskip'] = 0
319	Data['ellipses'] = []
320	Data['calibrant'] = ''
321	Data['GonioAngles'] = [0.,0.,0.]
322	Data['DetDepthRef'] = False
323	else:
324	Data['type'] = 'PWDR'
325	Data['color'] = GSASIIpath.GetConfigValue('Contour_color','Paired')
326	Data['tilt'] = 0.0
327	Data['rotation'] = 0.0
328	Data['showLines'] = False
329	Data['ring'] = []
330	Data['rings'] = []
331	Data['cutoff'] = 10
332	Data['pixLimit'] = 20
333	Data['calibdmin'] = 0.5
334	Data['calibskip'] = 0
335	Data['edgemin'] = 100000000
336	Data['ellipses'] = []
337	Data['GonioAngles'] = [0.,0.,0.]
338	Data['DetDepth'] = 0.
339	Data['DetDepthRef'] = False
340	Data['calibrant'] = ''
341	Data['IOtth'] = [2.0,5.0]
342	Data['LRazimuth'] = [0.,180.]
343	Data['azmthOff'] = 0.0
344	Data['outChannels'] = 2500
345	Data['outAzimuths'] = 1
346	Data['centerAzm'] = False
347	Data['fullIntegrate'] = False
348	Data['setRings'] = False
349	Data['background image'] = ['',-1.0]
350	Data['dark image'] = ['',-1.0]
351	Data['Flat Bkg'] = 0.0
352	Data['setDefault'] = False
353	Data['range'] = [(0,Imax),[0,Imax]]
354	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Image Controls'),Data)
355	Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],'Thresholds':[(0,Imax),[0,Imax]]}
356	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Masks'),Masks)
357	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Stress/Strain'),
358	{'Type':'True','d-zero':[],'Sample phi':0.0,'Sample z':0.0,'Sample load':0.0})
359	G2frame.GPXtree.SetItemPyData(Id,[Npix,imageInfo])
360	G2frame.PickId = Id
361	G2frame.PickIdText = G2frame.GetTreeItemsList(G2frame.PickId)
362	G2frame.Image = Id
363
364	def GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None,FormatName=''):
365	'''Read a single image with an image importer.
366
367	:param wx.Frame G2frame: main GSAS-II Frame and data object.
368	:param str imagefile: name of image file
369	:param bool imageOnly: If True return only the image,
370	otherwise (default) return more (see below)
371	:param int/str ImageTag: specifies a particular image to be read from a file.
372	First image is read if None (default).
373	:param str formatName: the image reader formatName
374
375	:returns: an image as a numpy array or a list of four items:
376	Comments, Data, Npix and the Image, as selected by imageOnly
377
378	'''
379	# determine which formats are compatible with this file
380	primaryReaders = []
381	secondaryReaders = []
382	for rd in G2frame.ImportImageReaderlist:
383	flag = rd.ExtensionValidator(imagefile)
384	if flag is None:
385	secondaryReaders.append(rd)
386	elif flag:
387	if not FormatName:
388	primaryReaders.append(rd)
389	elif FormatName == rd.formatName:
390	primaryReaders.append(rd)
391	if len(secondaryReaders) + len(primaryReaders) == 0:
392	print('Error: No matching format for file '+imagefile)
393	raise Exception('No image read')
394	errorReport = ''
395	if not imagefile:
396	return
397	for rd in primaryReaders+secondaryReaders:
398	rd.ReInitialize() # purge anything from a previous read
399	rd.errors = "" # clear out any old errors
400	if not rd.ContentsValidator(imagefile): # rejected on cursory check
401	errorReport += "\n "+rd.formatName + ' validator error'
402	if rd.errors:
403	errorReport += ': '+rd.errors
404	continue
405	if imageOnly:
406	ParentFrame = None # prevent GUI access on reread
407	else:
408	ParentFrame = G2frame
409	if GSASIIpath.GetConfigValue('debug'):
410	flag = rd.Reader(imagefile,ParentFrame,blocknum=ImageTag)
411	else:
412	flag = False
413	try:
414	flag = rd.Reader(imagefile,ParentFrame,blocknum=ImageTag)
415	except rd.ImportException as detail:
416	rd.errors += "\n Read exception: "+str(detail)
417	except Exception as detail:
418	import traceback
419	rd.errors += "\n Unhandled read exception: "+str(detail)
420	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
421	if flag: # this read succeeded
422	if rd.Image is None:
423	raise Exception('No image read. Strange!')
424	if GSASIIpath.GetConfigValue('Transpose'):
425	print ('Transposing Image!')
426	rd.Image = rd.Image.T
427	#rd.readfilename = imagefile
428	if imageOnly:
429	return rd.Image
430	else:
431	return rd.Comments,rd.Data,rd.Npix,rd.Image
432	else:
433	print('Error reading file '+imagefile)
434	print('Error messages(s)\n'+errorReport)
435	raise Exception('No image read')
436
437	def ReadImages(G2frame,imagefile):
438	'''Read one or more images from a file and put them into the Tree
439	using image importers. Called only in :meth:`AutoIntFrame.OnTimerLoop`.
440
441	:param wx.Frame G2frame: main GSAS-II Frame and data object.
442	:param str imagefile: name of image file
443
444	:returns: a list of the id's of the IMG tree items created
445	'''
446	# determine which formats are compatible with this file
447	primaryReaders = []
448	secondaryReaders = []
449	for rd in G2frame.ImportImageReaderlist:
450	flag = rd.ExtensionValidator(imagefile)
451	if flag is None:
452	secondaryReaders.append(rd)
453	elif flag:
454	primaryReaders.append(rd)
455	if len(secondaryReaders) + len(primaryReaders) == 0:
456	print('Error: No matching format for file '+imagefile)
457	raise Exception('No image read')
458	errorReport = ''
459	rdbuffer = {} # create temporary storage for file reader
460	for rd in primaryReaders+secondaryReaders:
461	rd.ReInitialize() # purge anything from a previous read
462	rd.errors = "" # clear out any old errors
463	if not rd.ContentsValidator(imagefile): # rejected on cursory check
464	errorReport += "\n "+rd.formatName + ' validator error'
465	if rd.errors:
466	errorReport += ': '+rd.errors
467	continue
468	ParentFrame = G2frame
469	block = 0
470	repeat = True
471	CreatedIMGitems = []
472	while repeat: # loop if the reader asks for another pass on the file
473	block += 1
474	repeat = False
475	if GSASIIpath.GetConfigValue('debug'):
476	flag = rd.Reader(imagefile,ParentFrame,blocknum=block,Buffer=rdbuffer)
477	else:
478	flag = False
479	try:
480	flag = rd.Reader(imagefile,ParentFrame,blocknum=block,Buffer=rdbuffer)
481	except rd.ImportException as detail:
482	rd.errors += "\n Read exception: "+str(detail)
483	except Exception as detail:
484	import traceback
485	rd.errors += "\n Unhandled read exception: "+str(detail)
486	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
487	if flag: # this read succeeded
488	if rd.Image is None:
489	raise Exception('No image read. Strange!')
490	if GSASIIpath.GetConfigValue('Transpose'):
491	print ('Transposing Image!')
492	rd.Image = rd.Image.T
493	rd.Data['ImageTag'] = rd.repeatcount
494	LoadImage2Tree(imagefile,G2frame,rd.Comments,rd.Data,rd.Npix,rd.Image)
495	repeat = rd.repeat
496	CreatedIMGitems.append(G2frame.Image)
497	if CreatedIMGitems: return CreatedIMGitems
498	else:
499	print('Error reading file '+imagefile)
500	print('Error messages(s)\n'+errorReport)
501	return []
502	#raise Exception('No image read')
503
504	def SaveMultipleImg(G2frame):
505	if not G2frame.GPXtree.GetCount():
506	print ('no images!')
507	return
508	choices = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',])
509	if len(choices) == 1:
510	names = choices
511	else:
512	dlg = G2G.G2MultiChoiceDialog(G2frame,'Stress/Strain fitting','Select images to fit:',choices)
513	dlg.SetSelections([])
514	names = []
515	if dlg.ShowModal() == wx.ID_OK:
516	names = [choices[sel] for sel in dlg.GetSelections()]
517	dlg.Destroy()
518	if not names: return
519	for name in names:
520	Id = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, name)
521	Npix,imagefile,imagetag = G2frame.GPXtree.GetImageLoc(Id)
522	imroot = os.path.splitext(imagefile)[0]
523	if imagetag:
524	imroot += '_' + str(imagetag)
525	Data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Image Controls'))
526	print('Writing '+imroot+'.imctrl')
527	File = open(imroot+'.imctrl','w')
528	keys = ['type','wavelength','calibrant','distance','center',
529	'tilt','rotation','azmthOff','fullIntegrate','LRazimuth',
530	'IOtth','outChannels','outAzimuths','invert_x','invert_y','DetDepth',
531	'calibskip','pixLimit','cutoff','calibdmin','chisq','Flat Bkg',
532	'binType','SampleShape','PolaVal','SampleAbs','dark image','background image']
533	for key in keys:
534	if key not in Data: continue #uncalibrated!
535	File.write(key+':'+str(Data[key])+'\n')
536	File.close()
537	mask = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Masks'))
538	G2imG.CleanupMasks(mask)
539	print('Writing '+imroot+'.immask')
540	File = open(imroot+'.immask','w')
541	for key in ['Points','Rings','Arcs','Polygons','Frames','Thresholds']:
542	File.write(key+':'+str(mask[key])+'\n')
543	File.close()
544
545	def PutG2Image(filename,Comments,Data,Npix,image):
546	'Write an image as a python pickle - might be better as an .edf file?'
547	File = open(filename,'wb')
548	cPickle.dump([Comments,Data,Npix,image],File,2)
549	File.close()
550	return
551
552	def ProjFileOpen(G2frame,showProvenance=True):
553	'Read a GSAS-II project file and load into the G2 data tree'
554	if not os.path.exists(G2frame.GSASprojectfile):
555	print ('\n*** Error attempt to open project file that does not exist:\n '+
556	str(G2frame.GSASprojectfile))
557	return
558	LastSavedUsing = None
559	file = open(G2frame.GSASprojectfile,'rb')
560	if showProvenance: print ('loading from file: '+G2frame.GSASprojectfile)
561	#G2frame.SetTitle("GSAS-II data tree: "+
562	# os.path.split(G2frame.GSASprojectfile)[1])
563	G2frame.SetTitle("GSAS-II data tree: "+
564	os.path.split(G2frame.GSASprojectfile)[1],1)
565	wx.BeginBusyCursor()
566	try:
567	while True:
568	try:
569	if '2' in platform.python_version_tuple()[0]:
570	data = cPickle.load(file)
571	else:
572	data = cPickle.load(file,encoding='latin-1')
573	except EOFError:
574	break
575	datum = data[0]
576
577	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=datum[0])
578	if datum[0].startswith('PWDR'):
579	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
580	datum[1][0]['ranId'] = ran.randint(0,sys.maxsize)
581	G2frame.GPXtree.SetItemPyData(Id,datum[1][:3]) #temp. trim off junk (patch?)
582	elif datum[0].startswith('HKLF'):
583	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
584	datum[1][0]['ranId'] = ran.randint(0,sys.maxsize)
585	G2frame.GPXtree.SetItemPyData(Id,datum[1])
586	else:
587	G2frame.GPXtree.SetItemPyData(Id,datum[1])
588	if datum[0] == 'Controls' and 'LastSavedUsing' in datum[1]:
589	LastSavedUsing = datum[1]['LastSavedUsing']
590	if datum[0] == 'Controls' and 'PythonVersions' in datum[1] and GSASIIpath.GetConfigValue('debug') and showProvenance:
591	print('Packages used to create .GPX file:')
592	if 'dict' in str(type(datum[1]['PythonVersions'])): #patch
593	for p in sorted(datum[1]['PythonVersions'],key=lambda s: s.lower()):
594	print(" {:<14s}: {:s}".format(p[0],p[1]))
595	else:
596	for p in datum[1]['PythonVersions']:
597	print(" {:<12s} {:s}".format(p[0]+':',p[1]))
598	oldPDF = False
599	for datus in data[1:]:
600	#patch - 1/23/17 PDF cleanup
601	if datus[0][:4] in ['I(Q)','S(Q)','F(Q)','G(R)']:
602	oldPDF = True
603	data[1][1][datus[0][:4]] = copy.deepcopy(datus[1][:2])
604	continue
605	#end PDF cleanup
606	sub = G2frame.GPXtree.AppendItem(Id,datus[0])
607	#patch
608	if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
609	if datum[0].startswith('PWDR'):
610	datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
611	else:
612	datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
613	for item in datus[1][0]: #zip makes tuples - now make lists!
614	datus[1][0][item] = list(datus[1][0][item])
615	#end patch
616	G2frame.GPXtree.SetItemPyData(sub,datus[1])
617	if 'PDF ' in datum[0][:4] and oldPDF:
618	sub = G2frame.GPXtree.AppendItem(Id,'PDF Peaks')
619	G2frame.GPXtree.SetItemPyData(sub,{'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]})
620	if datum[0].startswith('IMG'): #retrieve image default flag & data if set
621	Data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Image Controls'))
622	if Data['setDefault']:
623	G2frame.imageDefault = Data
624	file.close()
625	if LastSavedUsing:
626	print('GPX load successful. Last saved with GSAS-II revision '+LastSavedUsing)
627	else:
628	print('project load successful')
629	G2frame.NewPlot = True
630	except:
631	msg = wx.MessageDialog(G2frame,message="Error reading file "+
632	str(G2frame.GSASprojectfile)+". This is not a GSAS-II .gpx file",
633	caption="Load Error",style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
634	msg.ShowModal()
635	finally:
636	wx.EndBusyCursor()
637	G2frame.Status.SetStatusText('Mouse RB drag/drop to reorder',0)
638
639	def ProjFileSave(G2frame):
640	'Save a GSAS-II project file'
641	if not G2frame.GPXtree.IsEmpty():
642	file = open(G2frame.GSASprojectfile,'wb')
643	print ('save to file: '+G2frame.GSASprojectfile)
644	# stick the file name into the tree and version info into tree so they are saved.
645	# (Controls should always be created at this point)
646	try:
647	Controls = G2frame.GPXtree.GetItemPyData(
648	G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
649	Controls['LastSavedAs'] = os.path.abspath(G2frame.GSASprojectfile)
650	Controls['LastSavedUsing'] = str(GSASIIpath.GetVersionNumber())
651	Controls['PythonVersions'] = G2frame.PackageVersions
652	except:
653	pass
654	wx.BeginBusyCursor()
655	try:
656	item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
657	while item:
658	data = []
659	name = G2frame.GPXtree.GetItemText(item)
660	data.append([name,G2frame.GPXtree.GetItemPyData(item)])
661	item2, cookie2 = G2frame.GPXtree.GetFirstChild(item)
662	while item2:
663	name = G2frame.GPXtree.GetItemText(item2)
664	data.append([name,G2frame.GPXtree.GetItemPyData(item2)])
665	item2, cookie2 = G2frame.GPXtree.GetNextChild(item, cookie2)
666	item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
667	cPickle.dump(data,file,2)
668	file.close()
669	pth = os.path.split(os.path.abspath(G2frame.GSASprojectfile))[0]
670	if GSASIIpath.GetConfigValue('Save_paths'): G2G.SaveGPXdirectory(pth)
671	G2frame.LastGPXdir = pth
672	finally:
673	wx.EndBusyCursor()
674	print('project save successful')
675
676	def SaveIntegration(G2frame,PickId,data,Overwrite=False):
677	'Save image integration results as powder pattern(s)'
678	azms = G2frame.Integrate[1]
679	X = G2frame.Integrate[2][:-1]
680	N = len(X)
681	Id = G2frame.GPXtree.GetItemParent(PickId)
682	name = G2frame.GPXtree.GetItemText(Id)
683	name = name.replace('IMG ',data['type']+' ')
684	Comments = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Comments'))
685	if 'PWDR' in name:
686	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth']
687	codes = [0 for i in range(12)]
688	elif 'SASD' in name:
689	names = ['Type','Lam','Zero','Azimuth']
690	codes = [0 for i in range(4)]
691	X = 4.np.pinpsind(X/2.)/data['wavelength'] #convert to q
692	Xminmax = [X[0],X[-1]]
693	Azms = []
694	dazm = 0.
695	if data['fullIntegrate'] and data['outAzimuths'] == 1:
696	Azms = [45.0,] #a poor man's average?
697	else:
698	for i,azm in enumerate(azms[:-1]):
699	if azm > 360. and azms[i+1] > 360.:
700	Azms.append(G2img.meanAzm(azm%360.,azms[i+1]%360.))
701	else:
702	Azms.append(G2img.meanAzm(azm,azms[i+1]))
703	dazm = np.min(np.abs(np.diff(azms)))/2.
704	G2frame.IntgOutList = []
705	for i,azm in enumerate(azms[:-1]):
706	Aname = name+" Azm= %.2f"%((azm+dazm)%360.)
707	item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
708	# if Overwrite delete any duplicate
709	if Overwrite and G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname):
710	print('Replacing '+Aname)
711	item = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname)
712	G2frame.GPXtree.Delete(item)
713	else:
714	nOcc = 0
715	while item:
716	Name = G2frame.GPXtree.GetItemText(item)
717	if Aname in Name:
718	nOcc += 1
719	item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
720	if nOcc:
721	Aname += '(%d)'%(nOcc)
722	Sample = G2obj.SetDefaultSample() #set as Debye-Scherrer
723	Sample['Gonio. radius'] = data['distance']
724	Sample['Omega'] = data['GonioAngles'][0]
725	Sample['Chi'] = data['GonioAngles'][1]
726	Sample['Phi'] = data['GonioAngles'][2]
727	Sample['Azimuth'] = (azm+dazm)%360. #put here as bin center
728	polariz = 0.99 #set default polarization for synchrotron radiation!
729	for item in Comments:
730	if 'polariz' in item:
731	try:
732	polariz = float(item.split('=')[1])
733	except:
734	polariz = 0.99
735	if 'PWDR' in Aname:
736	parms = ['PXC',data['wavelength'],0.0,polariz,1.0,-0.10,0.4,0.30,1.0,0.0,0.0001,Azms[i]]
737	elif 'SASD' in Aname:
738	Sample['Trans'] = data['SampleAbs'][0]
739	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
740	Y = G2frame.Integrate[0][i]
741	Ymin = np.min(Y)
742	Ymax = np.max(Y)
743	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
744	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=Aname)
745	G2frame.IntgOutList.append(Id)
746	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments)
747	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Limits'),copy.deepcopy([tuple(Xminmax),Xminmax]))
748	if 'PWDR' in Aname:
749	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Background'),[['chebyschev',1,3,1.0,0.0,0.0],
750	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
751	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
752	for item in inst[0]:
753	inst[0][item] = list(inst[0][item])
754	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Instrument Parameters'),inst)
755	if 'PWDR' in Aname:
756	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample)
757	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
758	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Index Peak List'),[[],[]])
759	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Unit Cells List'),[])
760	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Reflection Lists'),{})
761	elif 'SASD' in Aname:
762	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
763	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample)
764	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
765	valuesdict = {
766	'wtFactor':1.0,
767	'Dummy':False,
768	'ranId':ran.randint(0,sys.maxsize),
769	'Offset':[0.0,0.0],'delOffset':0.02Ymax,'refOffset':-0.1Ymax,'refDelt':0.1*Ymax,
770	'qPlot':False,'dPlot':False,'sqrtPlot':False,'Yminmax':[Ymin,Ymax]
771	}
772	G2frame.GPXtree.SetItemPyData(
773	Id,[valuesdict,
774	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
775	return Id #last powder pattern generated
776
777	def XYsave(G2frame,XY,labelX='X',labelY='Y',names=None):
778	'Save XY table data'
779	pth = G2G.GetExportPath(G2frame)
780	dlg = wx.FileDialog(
781	G2frame, 'Enter csv filename for XY table', pth, '',
782	'XY table file (.csv)\|.csv',wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
783	try:
784	if dlg.ShowModal() == wx.ID_OK:
785	filename = dlg.GetPath()
786	filename = os.path.splitext(filename)[0]+'.csv'
787	File = open(filename,'w')
788	else:
789	filename = None
790	finally:
791	dlg.Destroy()
792	if not filename:
793	return
794	for i in range(len(XY)):
795	if names != None:
796	header = '%s,%s(%s)\n'%(labelX,labelY,names[i])
797	else:
798	header = '%s,%s(%d)\n'%(labelX,labelY,i)
799	File.write(header)
800	for x,y in XY[i].T:
801	File.write('%.3f,%.3f\n'%(x,y))
802	File.close()
803	print (' XY data saved to: '+filename)
804
805	def PDFSave(G2frame,exports,PDFsaves):
806	'Save a PDF I(Q), S(Q), F(Q) and G(r) in column formats'
807	import scipy.interpolate as scintp
808	for export in exports:
809	PickId = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, export)
810	PDFControls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame, PickId,'PDF Controls'))
811	if PDFsaves[0]: #I(Q)
812	iqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.iq')
813	iqdata = PDFControls['I(Q)'][0]
814	iqfxn = scintp.interp1d(iqdata[0],iqdata[1],kind='linear')
815	iqfile = open(iqfilename,'w')
816	iqfile.write('#T I(Q) %s\n'%(export))
817	iqfile.write('#L Q I(Q)\n')
818	qnew = np.arange(iqdata[0][0],iqdata[0][-1],0.005)
819	iqnew = zip(qnew,iqfxn(qnew))
820	for q,iq in iqnew:
821	iqfile.write("%15.6g %15.6g\n" % (q,iq))
822	iqfile.close()
823	print (' I(Q) saved to: '+iqfilename)
824
825	if PDFsaves[1]: #S(Q)
826	sqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.sq')
827	sqdata = PDFControls['S(Q)'][1]
828	sqfxn = scintp.interp1d(sqdata[0],sqdata[1],kind='linear')
829	sqfile = open(sqfilename,'w')
830	sqfile.write('#T S(Q) %s\n'%(export))
831	sqfile.write('#L Q S(Q)\n')
832	qnew = np.arange(sqdata[0][0],sqdata[0][-1],0.005)
833	sqnew = zip(qnew,sqfxn(qnew))
834	for q,sq in sqnew:
835	sqfile.write("%15.6g %15.6g\n" % (q,sq))
836	sqfile.close()
837	print (' S(Q) saved to: '+sqfilename)
838
839	if PDFsaves[2]: #F(Q)
840	fqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.fq')
841	fqdata = PDFControls['F(Q)'][1]
842	fqfxn = scintp.interp1d(fqdata[0],fqdata[1],kind='linear')
843	fqfile = open(sqfilename,'w')
844	fqfile.write('#T F(Q) %s\n'%(export))
845	fqfile.write('#L Q F(Q)\n')
846	qnew = np.arange(sqdata[0][0],sqdata[0][-1],0.005)
847	fqnew = zip(qnew,fqfxn(qnew))
848	for q,fq in fqnew:
849	fqfile.write("%15.6g %15.6g\n" % (q,fq))
850	fqfile.close()
851	print (' F(Q) saved to: '+fqfilename)
852
853	if PDFsaves[3]: #G(R)
854	grfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.gr')
855	grdata = PDFControls['G(R)'][1]
856	grfxn = scintp.interp1d(grdata[0],grdata[1],kind='linear')
857	grfile = open(grfilename,'w')
858	grfile.write('#T G(R) %s\n'%(export))
859	grfile.write('#L R G(R)\n')
860	rnew = np.arange(grdata[0][0],grdata[0][-1],0.010)
861	grnew = zip(rnew,grfxn(rnew))
862	for r,gr in grnew:
863	grfile.write("%15.6g %15.6g\n" % (r,gr))
864	grfile.close()
865	print (' G(R) saved to: '+grfilename)
866
867	if PDFsaves[4]: #pdfGUI file for G(R)
868	pId = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, 'PWDR'+export[4:])
869	Inst = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame, pId,'Instrument Parameters'))[0]
870	Limits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame, pId,'Limits'))
871	grfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.gr')
872	grdata = PDFControls['G(R)'][1]
873	qdata = PDFControls['I(Q)'][1][0]
874	grfxn = scintp.interp1d(grdata[0],grdata[1],kind='linear')
875	grfile = open(grfilename,'w')
876	rnew = np.arange(grdata[0][0],grdata[0][-1],0.010)
877	grnew = zip(rnew,grfxn(rnew))
878
879	grfile.write('[DEFAULT]\n')
880	grfile.write('\n')
881	grfile.write('version = GSAS-II-v'+str(GSASIIpath.GetVersionNumber())+'\n')
882	grfile.write('\n')
883	grfile.write('# input and output specifications\n')
884	grfile.write('dataformat = Qnm\n')
885	grfile.write('inputfile = %s\n'%(PDFControls['Sample']['Name']))
886	grfile.write('backgroundfile = %s\n'%(PDFControls['Sample Bkg.']['Name']))
887	grfile.write('outputtype = gr\n')
888	grfile.write('\n')
889	grfile.write('# PDF calculation setup\n')
890	if 'x' in Inst['Type']:
891	grfile.write('mode = %s\n'%('xray'))
892	elif 'N' in Inst['Type']:
893	grfile.write('mode = %s\n'%('neutron'))
894	wave = G2mth.getMeanWave(Inst)
895	grfile.write('wavelength = %.5f\n'%(wave))
896	formula = ''
897	for el in PDFControls['ElList']:
898	formula += el
899	num = PDFControls['ElList'][el]['FormulaNo']
900	if num == round(num):
901	formula += '%d'%(int(num))
902	else:
903	formula += '%.2f'%(num)
904	grfile.write('composition = %s\n'%(formula))
905	grfile.write('bgscale = %.3f\n'%(-PDFControls['Sample Bkg.']['Mult']))
906	highQ = 2.*np.pi/G2lat.Pos2dsp(Inst,Limits[1][1])
907	grfile.write('qmaxinst = %.2f\n'%(highQ))
908	grfile.write('qmin = %.5f\n'%(qdata[0]))
909	grfile.write('qmax = %.4f\n'%(qdata[-1]))
910	grfile.write('rmin = %.2f\n'%(PDFControls['Rmin']))
911	grfile.write('rmax = %.2f\n'%(PDFControls['Rmax']))
912	grfile.write('rstep = 0.01\n')
913
914
915	grfile.write('\n')
916	grfile.write('# End of config '+63*'-')
917	grfile.write('\n')
918	grfile.write('#### start data\n')
919	grfile.write('#S 1\n')
920	grfile.write('#L r($\AA$) G($\AA^{-2}$)\n')
921	for r,gr in grnew:
922	grfile.write("%15.2F %15.6F\n" % (r,gr))
923	grfile.close()
924	print (' G(R) saved to: '+grfilename)
925
926	def PeakListSave(G2frame,file,peaks):
927	'Save powder peaks to a data file'
928	print ('save peak list to file: '+G2frame.peaklistfile)
929	if not peaks:
930	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
931	try:
932	dlg.ShowModal()
933	finally:
934	dlg.Destroy()
935	return
936	for peak in peaks:
937	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
938	(peak[0],peak[2],peak[4],peak[6]))
939	print ('peak list saved')
940
941	def IndexPeakListSave(G2frame,peaks):
942	'Save powder peaks from the indexing list'
943	file = open(G2frame.peaklistfile,'wa')
944	print ('save index peak list to file: '+G2frame.peaklistfile)
945	wx.BeginBusyCursor()
946	try:
947	if not peaks:
948	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
949	try:
950	dlg.ShowModal()
951	finally:
952	dlg.Destroy()
953	return
954	for peak in peaks:
955	file.write("%12.6f\n" % (peak[7]))
956	file.close()
957	finally:
958	wx.EndBusyCursor()
959	print ('index peak list saved')
960
961	class MultipleChoicesDialog(wx.Dialog):
962	'''A dialog that offers a series of choices, each with a
963	title and a wx.Choice widget. Intended to be used Modally.
964	typical input:
965
966	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
967	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
968
969	selections are placed in self.chosen when OK is pressed
970
971	Also see GSASIIctrlGUI
972	'''
973	def __init__(self,choicelist,headinglist,
974	head='Select options',
975	title='Please select from options below',
976	parent=None):
977	self.chosen = []
978	wx.Dialog.__init__(
979	self,parent,wx.ID_ANY,head,
980	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
981	panel = wx.Panel(self)
982	mainSizer = wx.BoxSizer(wx.VERTICAL)
983	mainSizer.Add((10,10),1)
984	topLabl = wx.StaticText(panel,wx.ID_ANY,title)
985	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.CENTER,10)
986	self.ChItems = []
987	for choice,lbl in zip(choicelist,headinglist):
988	mainSizer.Add((10,10),1)
989	self.chosen.append(0)
990	topLabl = wx.StaticText(panel,wx.ID_ANY,' '+lbl)
991	mainSizer.Add(topLabl,0,wx.ALIGN_LEFT,10)
992	self.ChItems.append(wx.Choice(self, wx.ID_ANY, (100, 50), choices = choice))
993	mainSizer.Add(self.ChItems[-1],0,wx.ALIGN_CENTER,10)
994
995	OkBtn = wx.Button(panel,-1,"Ok")
996	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
997	cancelBtn = wx.Button(panel,-1,"Cancel")
998	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
999	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1000	btnSizer.Add((20,20),1)
1001	btnSizer.Add(OkBtn)
1002	btnSizer.Add((20,20),1)
1003	btnSizer.Add(cancelBtn)
1004	btnSizer.Add((20,20),1)
1005	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1006	panel.SetSizer(mainSizer)
1007	panel.Fit()
1008	self.Fit()
1009
1010	def OnOk(self,event):
1011	parent = self.GetParent()
1012	if parent is not None: parent.Raise()
1013	# save the results from the choice widgets
1014	self.chosen = []
1015	for w in self.ChItems:
1016	self.chosen.append(w.GetSelection())
1017	self.EndModal(wx.ID_OK)
1018
1019	def OnCancel(self,event):
1020	parent = self.GetParent()
1021	if parent is not None: parent.Raise()
1022	self.chosen = []
1023	self.EndModal(wx.ID_CANCEL)
1024
1025	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1026	confirmoverwrite=True, parent=None,
1027	multipleselect=False):
1028	'''If the filename is a zip file, extract a file from that
1029	archive.
1030
1031	:param list Selection: used to predefine the name of the file
1032	to be extracted. Filename case and zip directory name are
1033	ignored in selection; the first matching file is used.
1034
1035	:param bool confirmread: if True asks the user to confirm before expanding
1036	the only file in a zip
1037
1038	:param bool confirmoverwrite: if True asks the user to confirm
1039	before overwriting if the extracted file already exists
1040
1041	:param bool multipleselect: if True allows more than one zip
1042	file to be extracted, a list of file(s) is returned.
1043	If only one file is present, do not ask which one, otherwise
1044	offer a list of choices (unless selection is used).
1045
1046	:returns: the name of the file that has been created or a
1047	list of files (see multipleselect)
1048
1049	If the file is not a zipfile, return the name of the input file.
1050	If the zipfile is empty or no file has been selected, return None
1051	'''
1052	import zipfile # do this now, since we can save startup time by doing this only on need
1053	import shutil
1054	zloc = os.path.split(filename)[0]
1055	if not zipfile.is_zipfile(filename):
1056	#print("not zip")
1057	return filename
1058
1059	z = zipfile.ZipFile(filename,'r')
1060	zinfo = z.infolist()
1061
1062	if len(zinfo) == 0:
1063	#print('Zip has no files!')
1064	zlist = [-1]
1065	if selection:
1066	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1067	if selection.lower() in choices:
1068	zlist = [choices.index(selection.lower())]
1069	else:
1070	print('debug: file '+str(selection)+' was not found in '+str(filename))
1071	zlist = [-1]
1072	elif len(zinfo) == 1 and confirmread:
1073	result = wx.ID_NO
1074	dlg = wx.MessageDialog(
1075	parent,
1076	'Is file '+str(zinfo[0].filename)+
1077	' what you want to extract from '+
1078	str(os.path.split(filename)[1])+'?',
1079	'Confirm file',
1080	wx.YES_NO \| wx.ICON_QUESTION)
1081	try:
1082	result = dlg.ShowModal()
1083	finally:
1084	dlg.Destroy()
1085	if result == wx.ID_NO:
1086	zlist = [-1]
1087	else:
1088	zlist = [0]
1089	elif len(zinfo) == 1:
1090	zlist = [0]
1091	elif multipleselect:
1092	# select one or more from a from list
1093	choices = [i.filename for i in zinfo]
1094	dlg = G2G.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1095	'Choose file(s)',choices)
1096	if dlg.ShowModal() == wx.ID_OK:
1097	zlist = dlg.GetSelections()
1098	else:
1099	zlist = []
1100	dlg.Destroy()
1101	else:
1102	# select one from a from list
1103	choices = [i.filename for i in zinfo]
1104	dlg = wx.SingleChoiceDialog(parent,
1105	'Select file to extract from zip file'+str(filename),'Choose file',
1106	choices,)
1107	if dlg.ShowModal() == wx.ID_OK:
1108	zlist = [dlg.GetSelection()]
1109	else:
1110	zlist = [-1]
1111	dlg.Destroy()
1112
1113	outlist = []
1114	for zindex in zlist:
1115	if zindex >= 0:
1116	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1117	if os.path.exists(efil) and confirmoverwrite:
1118	result = wx.ID_NO
1119	dlg = wx.MessageDialog(parent,
1120	'File '+str(efil)+' already exists. OK to overwrite it?',
1121	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1122	try:
1123	result = dlg.ShowModal()
1124	finally:
1125	dlg.Destroy()
1126	if result == wx.ID_NO:
1127	zindex = -1
1128	if zindex >= 0:
1129	# extract the file to the current directory, regardless of it's original path
1130	#z.extract(zinfo[zindex],zloc)
1131	eloc,efil = os.path.split(zinfo[zindex].filename)
1132	outfile = os.path.join(zloc, efil)
1133	fpin = z.open(zinfo[zindex])
1134	fpout = file(outfile, "wb")
1135	shutil.copyfileobj(fpin, fpout)
1136	fpin.close()
1137	fpout.close()
1138	outlist.append(outfile)
1139	z.close()
1140	if multipleselect and len(outlist) >= 1:
1141	return outlist
1142	elif len(outlist) == 1:
1143	return outlist[0]
1144	else:
1145	return None
1146
1147	######################################################################
1148	# base classes for reading various types of data files
1149	# not used directly, only by subclassing
1150	######################################################################
1151	def BlockSelector(ChoiceList, ParentFrame=None,title='Select a block',
1152	size=None, header='Block Selector',useCancel=True):
1153	''' Provide a wx dialog to select a block if the file contains more
1154	than one set of data and one must be selected
1155	'''
1156	if useCancel:
1157	dlg = wx.SingleChoiceDialog(
1158	ParentFrame,title, header,ChoiceList)
1159	else:
1160	dlg = wx.SingleChoiceDialog(
1161	ParentFrame,title, header,ChoiceList,
1162	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.OK\|wx.CENTRE)
1163	if size: dlg.SetSize(size)
1164	dlg.CenterOnParent()
1165	if dlg.ShowModal() == wx.ID_OK:
1166	sel = dlg.GetSelection()
1167	return sel
1168	else:
1169	return None
1170	dlg.Destroy()
1171
1172	def MultipleBlockSelector(ChoiceList, ParentFrame=None,
1173	title='Select a block',size=None, header='Block Selector'):
1174	'''Provide a wx dialog to select a block of data if the
1175	file contains more than one set of data and one must be
1176	selected.
1177
1178	:returns: a list of the selected blocks
1179	'''
1180	dlg = wx.MultiChoiceDialog(ParentFrame,title, header,ChoiceList+['Select all'],
1181	wx.CHOICEDLG_STYLE)
1182	dlg.CenterOnScreen()
1183	if size: dlg.SetSize(size)
1184	if dlg.ShowModal() == wx.ID_OK:
1185	sel = dlg.GetSelections()
1186	else:
1187	return []
1188	dlg.Destroy()
1189	selected = []
1190	if len(ChoiceList) in sel:
1191	return range(len(ChoiceList))
1192	else:
1193	return sel
1194	return selected
1195
1196	def MultipleChoicesSelector(choicelist, headinglist, ParentFrame=None, **kwargs):
1197	'''A modal dialog that offers a series of choices, each with a title and a wx.Choice
1198	widget. Typical input:
1199
1200	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1201
1202	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1203
1204	optional keyword parameters are: head (window title) and title
1205	returns a list of selected indicies for each choice (or None)
1206	'''
1207	result = None
1208	dlg = MultipleChoicesDialog(choicelist,headinglist,
1209	parent=ParentFrame, **kwargs)
1210	dlg.CenterOnParent()
1211	if dlg.ShowModal() == wx.ID_OK:
1212	result = dlg.chosen
1213	dlg.Destroy()
1214	return result
1215
1216	def PhaseSelector(ChoiceList, ParentFrame=None,
1217	title='Select a phase', size=None,header='Phase Selector'):
1218	''' Provide a wx dialog to select a phase if the file contains more
1219	than one phase
1220	'''
1221	return BlockSelector(ChoiceList,ParentFrame,title,
1222	size,header)
1223
1224	######################################################################
1225	def striphist(var,insChar=''):
1226	'strip a histogram number from a var name'
1227	sv = var.split(':')
1228	if len(sv) <= 1: return var
1229	if sv[1]:
1230	sv[1] = insChar
1231	return ':'.join(sv)
1232	class ExportBaseclass(object):
1233	'''Defines a base class for the exporting of GSAS-II results.
1234
1235	This class is subclassed in the various exports/G2export_*.py files. Those files
1236	are imported in :meth:`GSASIIdataGUI.GSASII._init_Exports` which defines the
1237	appropriate menu items for each one and the .Exporter method is called
1238	directly from the menu item.
1239
1240	Routines may also define a .Writer method, which is used to write a single
1241	file without invoking any GUI objects.
1242	'''
1243	def __init__(self,G2frame,formatName,extension,longFormatName=None,):
1244	self.G2frame = G2frame
1245	self.formatName = formatName # short string naming file type
1246	self.extension = extension
1247	if longFormatName: # longer string naming file type
1248	self.longFormatName = longFormatName
1249	else:
1250	self.longFormatName = formatName
1251	self.OverallParms = {}
1252	self.Phases = {}
1253	self.Histograms = {}
1254	self.powderDict = {}
1255	self.xtalDict = {}
1256	self.parmDict = {}
1257	self.sigDict = {}
1258	# updated in InitExport:
1259	self.currentExportType = None # type of export that has been requested
1260	# updated in ExportSelect (when used):
1261	self.phasenam = None # a list of selected phases
1262	self.histnam = None # a list of selected histograms
1263	self.filename = None # name of file to be written (single export) or template (multiple files)
1264	self.dirname = '' # name of directory where file(s) will be written
1265	self.fullpath = '' # name of file being written -- full path
1266
1267	# items that should be defined in a subclass of this class
1268	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1269	# The following types are defined: 'project', "phase", "powder", "single"
1270	self.multiple = False # set as True if the class can export multiple phases or histograms
1271	# self.multiple is ignored for "project" exports
1272
1273	def InitExport(self,event):
1274	'''Determines the type of menu that called the Exporter and
1275	misc initialization.
1276	'''
1277	self.filename = None # name of file to be written (single export)
1278	self.dirname = '' # name of file to be written (multiple export)
1279	if event:
1280	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1281
1282	def MakePWDRfilename(self,hist):
1283	'''Make a filename root (no extension) from a PWDR histogram name
1284
1285	:param str hist: the histogram name in data tree (starts with "PWDR ")
1286	'''
1287	file0 = ''
1288	file1 = hist[5:]
1289	# replace repeated blanks
1290	while file1 != file0:
1291	file0 = file1
1292	file1 = file0.replace(' ',' ').strip()
1293	file0 = file1.replace('Azm= ','A')
1294	# if angle has unneeded decimal places on aziumuth, remove them
1295	if file0[-3:] == '.00': file0 = file0[:-3]
1296	file0 = file0.replace('.','_')
1297	file0 = file0.replace(' ','_')
1298	return file0
1299
1300	def ExportSelect(self,AskFile='ask'):
1301	'''Selects histograms or phases when needed. Sets a default file name when
1302	requested into self.filename; always sets a default directory in self.dirname.
1303
1304	:param bool AskFile: Determines how this routine processes getting a
1305	location to store the current export(s).
1306
1307	* if AskFile is 'ask' (default option), get the name of the file to be written;
1308	self.filename and self.dirname are always set. In the case where
1309	multiple files must be generated, the export routine should do this
1310	based on self.filename as a template.
1311	* if AskFile is 'dir', get the name of the directory to be used;
1312	self.filename is not used, but self.dirname is always set. The export routine
1313	will always generate the file name.
1314	* if AskFile is 'single', get only the name of the directory to be used when
1315	multiple items will be written (as multiple files) are used
1316	or a complete file name is requested when a single file
1317	name is selected. self.dirname is always set and self.filename used
1318	only when a single file is selected.
1319	* if AskFile is 'default', creates a name of the file to be used from
1320	the name of the project (.gpx) file. If the project has not been saved,
1321	then the name of file is requested.
1322	self.filename and self.dirname are always set. In the case where
1323	multiple file names must be generated, the export routine should do this
1324	based on self.filename.
1325	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1326	file. If the project has not been saved, then a directory is requested.
1327	self.filename is not used.
1328
1329	:returns: True in case of an error
1330	'''
1331
1332	numselected = 1
1333	if self.currentExportType == 'phase':
1334	if len(self.Phases) == 0:
1335	self.G2frame.ErrorDialog(
1336	'Empty project',
1337	'Project does not contain any phases.')
1338	return True
1339	elif len(self.Phases) == 1:
1340	self.phasenam = self.Phases.keys()
1341	elif self.multiple:
1342	choices = sorted(self.Phases.keys())
1343	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1344	if phasenum is None: return True
1345	self.phasenam = [choices[i] for i in phasenum]
1346	if not self.phasenam: return True
1347	numselected = len(self.phasenam)
1348	else:
1349	choices = sorted(self.Phases.keys())
1350	phasenum = G2G.ItemSelector(choices,self.G2frame)
1351	if phasenum is None: return True
1352	self.phasenam = [choices[phasenum]]
1353	numselected = len(self.phasenam)
1354	elif self.currentExportType == 'single':
1355	if len(self.xtalDict) == 0:
1356	self.G2frame.ErrorDialog(
1357	'Empty project',
1358	'Project does not contain any single crystal data.')
1359	return True
1360	elif len(self.xtalDict) == 1:
1361	self.histnam = self.xtalDict.values()
1362	elif self.multiple:
1363	choices = sorted(self.xtalDict.values())
1364	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1365	if not hnum: return True
1366	self.histnam = [choices[i] for i in hnum]
1367	numselected = len(self.histnam)
1368	else:
1369	choices = sorted(self.xtalDict.values())
1370	hnum = G2G.ItemSelector(choices,self.G2frame)
1371	if hnum is None: return True
1372	self.histnam = [choices[hnum]]
1373	numselected = len(self.histnam)
1374	elif self.currentExportType == 'powder':
1375	if len(self.powderDict) == 0:
1376	self.G2frame.ErrorDialog(
1377	'Empty project',
1378	'Project does not contain any powder data.')
1379	return True
1380	elif len(self.powderDict) == 1:
1381	self.histnam = self.powderDict.values()
1382	elif self.multiple:
1383	choices = sorted(self.powderDict.values())
1384	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1385	if not hnum: return True
1386	self.histnam = [choices[i] for i in hnum]
1387	numselected = len(self.histnam)
1388	else:
1389	choices = sorted(self.powderDict.values())
1390	hnum = G2G.ItemSelector(choices,self.G2frame)
1391	if hnum is None: return True
1392	self.histnam = [choices[hnum]]
1393	numselected = len(self.histnam)
1394	elif self.currentExportType == 'image':
1395	if len(self.Histograms) == 0:
1396	self.G2frame.ErrorDialog(
1397	'Empty project',
1398	'Project does not contain any images.')
1399	return True
1400	elif len(self.Histograms) == 1:
1401	self.histnam = self.Histograms.keys()
1402	else:
1403	choices = sorted(self.Histograms.keys())
1404	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1405	if self.multiple:
1406	if not hnum: return True
1407	self.histnam = [choices[i] for i in hnum]
1408	else:
1409	if hnum is None: return True
1410	self.histnam = [choices[hnum]]
1411	numselected = len(self.histnam)
1412	if self.currentExportType == 'map':
1413	# search for phases with maps
1414	mapPhases = []
1415	choices = []
1416	for phasenam in sorted(self.Phases):
1417	phasedict = self.Phases[phasenam] # pointer to current phase info
1418	if len(phasedict['General']['Map'].get('rho',[])):
1419	mapPhases.append(phasenam)
1420	if phasedict['General']['Map'].get('Flip'):
1421	choices.append('Charge flip map: '+str(phasenam))
1422	elif phasedict['General']['Map'].get('MapType'):
1423	choices.append(
1424	str(phasedict['General']['Map'].get('MapType'))
1425	+ ' map: ' + str(phasenam))
1426	else:
1427	choices.append('unknown map: '+str(phasenam))
1428	# select a map if needed
1429	if len(mapPhases) == 0:
1430	self.G2frame.ErrorDialog(
1431	'Empty project',
1432	'Project does not contain any maps.')
1433	return True
1434	elif len(mapPhases) == 1:
1435	self.phasenam = mapPhases
1436	else:
1437	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1438	if self.multiple:
1439	if not phasenum: return True
1440	self.phasenam = [mapPhases[i] for i in phasenum]
1441	else:
1442	if phasenum is None: return True
1443	self.phasenam = [mapPhases[phasenum]]
1444	numselected = len(self.phasenam)
1445
1446	# items selected, now set self.dirname and usually self.filename
1447	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
1448	AskFile == 'default' and not self.G2frame.GSASprojectfile
1449	):
1450	filename = self.askSaveFile()
1451	if not filename: return True
1452	self.dirname,self.filename = os.path.split(filename)
1453	elif AskFile == 'dir' or AskFile == 'single' or (
1454	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
1455	):
1456	self.dirname = self.askSaveDirectory()
1457	if not self.dirname: return True
1458	elif AskFile == 'default-dir' or AskFile == 'default':
1459	self.dirname,self.filename = os.path.split(
1460	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
1461	)
1462	else:
1463	raise Exception('This should not happen!')
1464
1465	def loadParmDict(self):
1466	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
1467	refined values to those from the last cycle and set the uncertainties for the
1468	refined parameters in another dict (self.sigDict).
1469
1470	Expands the parm & sig dicts to include values derived from constraints.
1471	'''
1472	self.parmDict = {}
1473	self.sigDict = {}
1474	rigidbodyDict = {}
1475	covDict = {}
1476	consDict = {}
1477	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1478	if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1479	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1480	while item:
1481	name = self.G2frame.GPXtree.GetItemText(item)
1482	if name == 'Rigid bodies':
1483	rigidbodyDict = self.G2frame.GPXtree.GetItemPyData(item)
1484	elif name == 'Covariance':
1485	covDict = self.G2frame.GPXtree.GetItemPyData(item)
1486	elif name == 'Constraints':
1487	consDict = self.G2frame.GPXtree.GetItemPyData(item)
1488	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1489	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1490	self.parmDict.update(rbDict)
1491	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1492	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData(
1493	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
1494	self.parmDict.update(phaseDict)
1495	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
1496	Phases,Histograms,Print=False,resetRefList=False)
1497	self.parmDict.update(hapDict)
1498	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
1499	self.parmDict.update(histDict)
1500	self.parmDict.update(zip(
1501	covDict.get('varyList',[]),
1502	covDict.get('variables',[])))
1503	self.sigDict = dict(zip(
1504	covDict.get('varyList',[]),
1505	covDict.get('sig',[])))
1506	# expand to include constraints: first compile a list of constraints
1507	constList = []
1508	for item in consDict:
1509	if item.startswith('_'): continue
1510	constList += consDict[item]
1511	# now process the constraints
1512	G2mv.InitVars()
1513	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
1514	varyList = covDict.get('varyListStart')
1515	if varyList is None and len(constDict) == 0:
1516	# no constraints can use varyList
1517	varyList = covDict.get('varyList')
1518	elif varyList is None:
1519	# old GPX file from before pre-constraint varyList is saved
1520	print (' * Old refinement: Please use Calculate/Refine to redo *')
1521	raise Exception(' * Export aborted *')
1522	else:
1523	varyList = list(varyList)
1524	try:
1525	groups,parmlist = G2mv.GroupConstraints(constDict)
1526	G2mv.GenerateConstraints(groups,parmlist,varyList,constDict,fixedList,self.parmDict)
1527	except:
1528	# this really should not happen
1529	print (' * ERROR - constraints are internally inconsistent *')
1530	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
1531	print ('Errors'+errmsg)
1532	if warnmsg: print ('Warnings'+warnmsg)
1533	raise Exception(' * CIF creation aborted *')
1534	# add the constrained values to the parameter dictionary
1535	G2mv.Dict2Map(self.parmDict,varyList)
1536	# and add their uncertainties into the esd dictionary (sigDict)
1537	if covDict.get('covMatrix') is not None:
1538	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
1539
1540	def loadTree(self):
1541	'''Load the contents of the data tree into a set of dicts
1542	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
1543	& self.xtalDict)
1544
1545	* The childrenless data tree items are overall parameters/controls for the
1546	entire project and are placed in self.OverallParms
1547	* Phase items are placed in self.Phases
1548	* Data items are placed in self.Histogram. The key for these data items
1549	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
1550	'''
1551	self.OverallParms = {}
1552	self.powderDict = {}
1553	self.xtalDict = {}
1554	self.Phases = {}
1555	self.Histograms = {}
1556	self.SeqRefdata = None
1557	self.SeqRefhist = None
1558	if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1559	histType = None
1560	if self.currentExportType == 'phase':
1561	# if exporting phases load them here
1562	sub = G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,'Phases')
1563	if not sub:
1564	print ('no phases found')
1565	return True
1566	item, cookie = self.G2frame.GPXtree.GetFirstChild(sub)
1567	while item:
1568	phaseName = self.G2frame.GPXtree.GetItemText(item)
1569	self.Phases[phaseName] = self.G2frame.GPXtree.GetItemPyData(item)
1570	item, cookie = self.G2frame.GPXtree.GetNextChild(sub, cookie)
1571	return
1572	elif self.currentExportType == 'single':
1573	histType = 'HKLF'
1574	elif self.currentExportType == 'powder':
1575	histType = 'PWDR'
1576	elif self.currentExportType == 'image':
1577	histType = 'IMG'
1578
1579	if histType: # Loading just one kind of tree entry
1580	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1581	while item:
1582	name = self.G2frame.GPXtree.GetItemText(item)
1583	if name.startswith(histType):
1584	if self.Histograms.get(name): # there is already an item with this name
1585	print('Histogram name '+str(name)+' is repeated. Renaming')
1586	if name[-1] == '9':
1587	name = name[:-1] + '10'
1588	elif name[-1] in '012345678':
1589	name = name[:-1] + str(int(name[-1])+1)
1590	else:
1591	name += '-1'
1592	self.Histograms[name] = {}
1593	# the main info goes into Data, but the 0th
1594	# element contains refinement results, carry
1595	# that over too now.
1596	self.Histograms[name]['Data'] = self.G2frame.GPXtree.GetItemPyData(item)[1]
1597	self.Histograms[name][0] = self.G2frame.GPXtree.GetItemPyData(item)[0]
1598	item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1599	while item2:
1600	child = self.G2frame.GPXtree.GetItemText(item2)
1601	self.Histograms[name][child] = self.G2frame.GPXtree.GetItemPyData(item2)
1602	item2, cookie2 = self.G2frame.GPXtree.GetNextChild(item, cookie2)
1603	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1604	# index powder and single crystal histograms by number
1605	for hist in self.Histograms:
1606	if hist.startswith("PWDR"):
1607	d = self.powderDict
1608	elif hist.startswith("HKLF"):
1609	d = self.xtalDict
1610	else:
1611	return
1612	i = self.Histograms[hist].get('hId')
1613	if i is None and not d.keys():
1614	i = 0
1615	elif i is None or i in d.keys():
1616	i = max(d.keys())+1
1617	d[i] = hist
1618	return
1619	# else standard load: using all interlinked phases and histograms
1620	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1621	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1622	while item:
1623	name = self.G2frame.GPXtree.GetItemText(item)
1624	item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1625	if not item2:
1626	self.OverallParms[name] = self.G2frame.GPXtree.GetItemPyData(item)
1627	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1628	# index powder and single crystal histograms
1629	for hist in self.Histograms:
1630	i = self.Histograms[hist]['hId']
1631	if hist.startswith("PWDR"):
1632	self.powderDict[i] = hist
1633	elif hist.startswith("HKLF"):
1634	self.xtalDict[i] = hist
1635
1636	def dumpTree(self,mode='type'):
1637	'''Print out information on the data tree dicts loaded in loadTree.
1638	Used for testing only.
1639	'''
1640	if self.SeqRefdata and self.SeqRefhist:
1641	print('Note that dumpTree does not show sequential results')
1642	print ('\nOverall')
1643	if mode == 'type':
1644	def Show(arg): return type(arg)
1645	else:
1646	def Show(arg): return arg
1647	for key in self.OverallParms:
1648	print (' '+key+Show(self.OverallParms[key]))
1649	print ('Phases')
1650	for key1 in self.Phases:
1651	print (' '+key1+Show(self.Phases[key1]))
1652	print ('Histogram')
1653	for key1 in self.Histograms:
1654	print (' '+key1+Show(self.Histograms[key1]))
1655	for key2 in self.Histograms[key1]:
1656	print (' '+key2+Show(self.Histograms[key1][key2]))
1657
1658	def defaultSaveFile(self):
1659	return os.path.abspath(
1660	os.path.splitext(self.G2frame.GSASprojectfile
1661	)[0]+self.extension)
1662
1663	def askSaveFile(self):
1664	'''Ask the user to supply a file name
1665
1666	:returns: a file name (str) or None if Cancel is pressed
1667	'''
1668
1669	pth = G2G.GetExportPath(self.G2frame)
1670	defnam = os.path.splitext(
1671	os.path.split(self.G2frame.GSASprojectfile)[1]
1672	)[0]+self.extension
1673	dlg = wx.FileDialog(
1674	self.G2frame, 'Input name for file to write', pth, defnam,
1675	self.longFormatName+' ('+self.extension+')\|'+self.extension,
1676	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
1677	dlg.CenterOnParent()
1678	try:
1679	if dlg.ShowModal() == wx.ID_OK:
1680	filename = dlg.GetPath()
1681	self.G2frame.LastExportDir = os.path.split(filename)[0]
1682	filename = os.path.splitext(filename)[0]+self.extension # make sure extension is correct
1683	else:
1684	filename = None
1685	finally:
1686	dlg.Destroy()
1687	return filename
1688
1689	def askSaveDirectory(self):
1690	'''Ask the user to supply a directory name. Path name is used as the
1691	starting point for the next export path search.
1692
1693	:returns: a directory name (str) or None if Cancel is pressed
1694	'''
1695	pth = G2G.GetExportPath(self.G2frame)
1696	dlg = wx.DirDialog(
1697	self.G2frame, 'Input directory where file(s) will be written', pth,
1698	wx.DD_DEFAULT_STYLE)
1699	dlg.CenterOnParent()
1700	try:
1701	if dlg.ShowModal() == wx.ID_OK:
1702	filename = dlg.GetPath()
1703	self.G2frame.LastExportDir = filename
1704	else:
1705	filename = None
1706	finally:
1707	dlg.Destroy()
1708	return filename
1709
1710	# Tools for file writing.
1711	def OpenFile(self,fil=None,mode='w'):
1712	'''Open the output file
1713
1714	:param str fil: The name of the file to open. If None (default)
1715	the name defaults to self.dirname + self.filename.
1716	If an extension is supplied, it is not overridded,
1717	but if not, the default extension is used.
1718	:returns: the file object opened by the routine which is also
1719	saved as self.fp
1720	'''
1721	if mode == 'd': # debug mode
1722	self.fullpath = '(stdout)'
1723	self.fp = sys.stdout
1724	return
1725	if not fil:
1726	if not os.path.splitext(self.filename)[1]:
1727	self.filename += self.extension
1728	fil = os.path.join(self.dirname,self.filename)
1729	self.fullpath = os.path.abspath(fil)
1730	self.fp = open(self.fullpath,mode)
1731	return self.fp
1732
1733	def Write(self,line):
1734	'''write a line of output, attaching a line-end character
1735
1736	:param str line: the text to be written.
1737	'''
1738	self.fp.write(line+'\n')
1739
1740	def CloseFile(self,fp=None):
1741	'''Close a file opened in OpenFile
1742
1743	:param file fp: the file object to be closed. If None (default)
1744	file object self.fp is closed.
1745	'''
1746	if self.fp == sys.stdout: return # debug mode
1747	if fp is None:
1748	fp = self.fp
1749	self.fp = None
1750	if fp is not None: fp.close()
1751
1752	def SetSeqRef(self,data,hist):
1753	'''Set the exporter to retrieve results from a sequential refinement
1754	rather than the main tree
1755	'''
1756	self.SeqRefdata = data
1757	self.SeqRefhist = hist
1758	data_name = data[hist]
1759	for i,val in zip(data_name['varyList'],data_name['sig']):
1760	self.sigDict[i] = val
1761	self.sigDict[striphist(i)] = val
1762	for i in data_name['parmDict']:
1763	self.parmDict[striphist(i)] = data_name['parmDict'][i]
1764	self.parmDict[i] = data_name['parmDict'][i]
1765	# zero out the dA[xyz] terms, they would only bring confusion
1766	key = i.split(':')
1767	if len(key) < 3: continue
1768	if key[2].startswith('dA'):
1769	self.parmDict[i] = 0.0
1770	for i,(val,sig) in data_name.get('depParmDict',{}).iteritems():
1771	self.parmDict[i] = val
1772	self.sigDict[i] = sig
1773	#GSASIIpath.IPyBreak()
1774
1775	# Tools to pull information out of the data arrays
1776	def GetCell(self,phasenam):
1777	"""Gets the unit cell parameters and their s.u.'s for a selected phase
1778
1779	:param str phasenam: the name for the selected phase
1780	:returns: `cellList,cellSig` where each is a 7 element list corresponding
1781	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1782	cell values and `cellSig` has their uncertainties.
1783	"""
1784	if self.SeqRefdata and self.SeqRefhist:
1785	return self.GetSeqCell(phasenam,self.SeqRefdata[self.SeqRefhist])
1786	phasedict = self.Phases[phasenam] # pointer to current phase info
1787	try:
1788	pfx = str(phasedict['pId'])+'::'
1789	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
1790	cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A,
1791	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
1792	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
1793	return cellList,cellSig
1794	except KeyError:
1795	cell = phasedict['General']['Cell'][1:]
1796	return cell,7*[0]
1797
1798	def GetSeqCell(self,phasenam,data_name):
1799	"""Gets the unit cell parameters and their s.u.'s for a selected phase
1800	and histogram in a sequential fit
1801
1802	:param str phasenam: the name for the selected phase
1803	:param dict data_name: the sequential refinement parameters for the selected histogram
1804	:returns: `cellList,cellSig` where each is a 7 element list corresponding
1805	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1806	cell values and `cellSig` has their uncertainties.
1807	"""
1808	phasedict = self.Phases[phasenam]
1809	SGdata = phasedict['General']['SGData']
1810	pId = phasedict['pId']
1811	RecpCellTerms = G2lat.cell2A(phasedict['General']['Cell'][1:7])
1812	ESDlookup = {}
1813	Dlookup = {}
1814	varied = [striphist(i) for i in data_name['varyList']]
1815	for item,val in data_name['newCellDict'].iteritems():
1816	if item in varied:
1817	ESDlookup[val[0]] = item
1818	Dlookup[item] = val[0]
1819	A = RecpCellTerms[:]
1820	for i in range(6):
1821	var = str(pId)+'::A'+str(i)
1822	if var in ESDlookup:
1823	A[i] = data_name['newCellDict'][ESDlookup[var]][1] # override with refined value
1824	cellDict = dict(zip([str(pId)+'::A'+str(i) for i in range(6)],A))
1825	zeroDict = {i:0.0 for i in cellDict}
1826	A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata,cellDict,zeroDict)
1827	covData = {
1828	'varyList': [Dlookup.get(striphist(v),v) for v in data_name['varyList']],
1829	'covMatrix': data_name['covMatrix']
1830	}
1831	return list(G2lat.A2cell(A)) + [G2lat.calc_V(A)], G2stIO.getCellEsd(str(pId)+'::',SGdata,A,covData)
1832
1833	def GetAtoms(self,phasenam):
1834	"""Gets the atoms associated with a phase. Can be used with standard
1835	or macromolecular phases
1836
1837	:param str phasenam: the name for the selected phase
1838	:returns: a list of items for eac atom where each item is a list containing:
1839	label, typ, mult, xyz, and td, where
1840
1841	* label and typ are the atom label and the scattering factor type (str)
1842	* mult is the site multiplicity (int)
1843	* xyz is contains a list with four pairs of numbers:
1844	x, y, z and fractional occupancy and
1845	their standard uncertainty (or a negative value)
1846	* td is contains a list with either one or six pairs of numbers:
1847	if one number it is U\ :sub:`iso` and with six numbers it is
1848	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
1849	paired with their standard uncertainty (or a negative value)
1850	"""
1851	phasedict = self.Phases[phasenam] # pointer to current phase info
1852	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
1853	cfrac = cx+3
1854	fpfx = str(phasedict['pId'])+'::Afrac:'
1855	atomslist = []
1856	for i,at in enumerate(phasedict['Atoms']):
1857	if phasedict['General']['Type'] == 'macromolecular':
1858	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
1859	else:
1860	label = at[ct-1]
1861	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
1862	fsig = self.sigDict.get(fpfx+str(i),-0.009)
1863	mult = at[cs+1]
1864	typ = at[ct]
1865	xyz = []
1866	for j,v in enumerate(('x','y','z')):
1867	val = at[cx+j]
1868	pfx = str(phasedict['pId']) + '::A' + v + ':' + str(i)
1869	val = self.parmDict.get(pfx, val)
1870	dpfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
1871	sig = self.sigDict.get(dpfx,-0.000009)
1872	xyz.append((val,sig))
1873	xyz.append((fval,fsig))
1874	td = []
1875	if at[cia] == 'I':
1876	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
1877	val = self.parmDict.get(pfx,at[cia+1])
1878	sig = self.sigDict.get(pfx,-0.0009)
1879	td.append((val,sig))
1880	else:
1881	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
1882	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
1883	val = self.parmDict.get(pfx,at[cia+2+i])
1884	sig = self.sigDict.get(pfx,-0.0009)
1885	td.append((val,sig))
1886	atomslist.append((label,typ,mult,xyz,td))
1887	return atomslist
1888	######################################################################
1889	def ExportPowderList(G2frame):
1890	'''Returns a list of extensions supported by :func:`GSASIIIO:ExportPowder`
1891	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
1892
1893	:param wx.Frame G2frame: the GSAS-II main data tree window
1894	'''
1895	extList = []
1896	for obj in G2frame.exporterlist:
1897	if 'powder' in obj.exporttype:
1898	try:
1899	obj.Writer
1900	extList.append(obj.extension)
1901	except AttributeError:
1902	pass
1903	return extList
1904
1905	def ExportPowder(G2frame,TreeName,fileroot,extension):
1906	'''Writes a single powder histogram using the Export routines.
1907	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
1908
1909	:param wx.Frame G2frame: the GSAS-II main data tree window
1910	:param str TreeName: the name of the histogram (PWDR ...) in the data tree
1911	:param str fileroot: name for file to be written, extension ignored
1912	:param str extension: extension for file to be written (start with '.'). Must
1913	match a powder export routine that has a Writer object.
1914	'''
1915	filename = os.path.abspath(os.path.splitext(fileroot)[0]+extension)
1916	for obj in G2frame.exporterlist:
1917	if obj.extension == extension and 'powder' in obj.exporttype:
1918	obj.currentExportType = 'powder'
1919	obj.InitExport(None)
1920	obj.loadTree() # load all histograms in tree into dicts
1921	if TreeName not in obj.Histograms:
1922	raise Exception('Histogram not found: '+str(TreeName))
1923	try:
1924	obj.Writer
1925	except AttributeError:
1926	continue
1927	try:
1928	obj.Writer(TreeName,filename)
1929	return
1930	except Exception:
1931	print('Export Routine for '+extension+' failed.')
1932	else:
1933	print('No Export routine supports extension '+extension)
1934
1935	def ExportSequential(G2frame,data,obj,exporttype):
1936	'''
1937	Used to export from every phase/dataset in a sequential refinement using
1938	a .Writer method for either projects or phases. Prompts to select histograms
1939	and for phase exports, which phase(s).
1940
1941	:param wx.Frame G2frame: the GSAS-II main data tree window
1942	:param dict data: the sequential refinement data object
1943	:param str exporttype: indicates the type of export ('project' or 'phase')
1944	'''
1945	if len(data['histNames']) == 0:
1946	G2G.G2MessageBox(G2frame,'There are no sequential histograms','Warning')
1947	obj.InitExport(None)
1948	obj.loadTree()
1949	obj.loadParmDict()
1950	if len(data['histNames']) == 1:
1951	histlist = data['histNames']
1952	else:
1953	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select histograms to export from list',
1954	'Select histograms',data['histNames'])
1955	if dlg.ShowModal() == wx.ID_OK:
1956	histlist = [data['histNames'][l] for l in dlg.GetSelections()]
1957	dlg.Destroy()
1958	else:
1959	dlg.Destroy()
1960	return
1961	if exporttype == 'Phase':
1962	phaselist = list(obj.Phases.keys())
1963	if len(obj.Phases) == 0:
1964	G2G.G2MessageBox(G2frame,'There are no phases in sequential ref.','Warning')
1965	return
1966	elif len(obj.Phases) > 1:
1967	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select phases to export from list',
1968	'Select phases', phaselist)
1969	if dlg.ShowModal() == wx.ID_OK:
1970	phaselist = [phaselist[l] for l in dlg.GetSelections()]
1971	dlg.Destroy()
1972	else:
1973	dlg.Destroy()
1974	return
1975	filename = obj.askSaveFile()
1976	if not filename: return True
1977	obj.dirname,obj.filename = os.path.split(filename)
1978	print('Writing output to file '+str(obj.filename)+"...")
1979	mode = 'w'
1980	for p in phaselist:
1981	for h in histlist:
1982	obj.SetSeqRef(data,h)
1983	#GSASIIpath.IPyBreak()
1984	obj.Writer(h,phasenam=p,mode=mode)
1985	mode = 'a'
1986	print('...done')
1987	elif exporttype == 'Project': # note that the CIF exporter is not yet ready for this
1988	filename = obj.askSaveFile()
1989	if not filename: return True
1990	obj.dirname,obj.filename = os.path.split(filename)
1991	print('Writing output to file '+str(obj.filename)+"...")
1992	mode = 'w'
1993	for h in histlist:
1994	obj.SetSeqRef(data,h)
1995	obj.Writer(h,mode=mode)
1996	print('\t'+str(h)+' written')
1997	mode = 'a'
1998	print('...done')
1999	elif exporttype == 'Powder':
2000	filename = obj.askSaveFile()
2001	if not filename: return True
2002	obj.dirname,obj.filename = os.path.split(filename)
2003	print('Writing output to file '+str(obj.filename)+"...")
2004	mode = 'w'
2005	for h in histlist:
2006	obj.SetSeqRef(data,h)
2007	obj.Writer(h,mode=mode)
2008	print('\t'+str(h)+' written')
2009	mode = 'a'
2010	print('...done')
2011
2012	def ReadDIFFaX(DIFFaXfile):
2013	print ('read '+DIFFaXfile)
2014	Layer = {'Laue':'-1','Cell':[False,1.,1.,1.,90.,90.,90,1.],'Width':[[10.,10.],[False,False]],
2015	'Layers':[],'Stacking':[],'Transitions':[],'Toler':0.01,'AtInfo':{}}
2016	df = open(DIFFaXfile,'r')
2017	lines = df.readlines()
2018	df.close()
2019	struct = False
2020	Struct = []
2021	stack = False
2022	Stack = []
2023	trans = False
2024	Trans = []
2025	for diff in lines:
2026	diff = diff[:-1].lower()
2027	if '!' in diff:
2028	continue
2029	while '}' in diff: #strip comments
2030	iB = diff.index('{')
2031	iF = diff.index('}')+1
2032	if iB:
2033	diff = diff[:iB]
2034	else:
2035	diff = diff[iF:]
2036	if not diff:
2037	continue
2038	if diff.strip() == 'instrumental':
2039	continue
2040	if diff.strip() == 'structural':
2041	struct = True
2042	continue
2043	elif diff.strip() == 'stacking':
2044	struct = False
2045	stack = True
2046	continue
2047	elif diff.strip() == 'transitions':
2048	stack = False
2049	trans = True
2050	continue
2051	diff = diff.strip()
2052	if struct:
2053	if diff:
2054	Struct.append(diff)
2055	elif stack:
2056	if diff:
2057	Stack.append(diff)
2058	elif trans:
2059	if diff:
2060	Trans.append(diff)
2061
2062	#STRUCTURE records
2063	laueRec = Struct[1].split()
2064	Layer['Laue'] = laueRec[0]
2065	if Layer['Laue'] == 'unknown' and len(laueRec) > 1:
2066	Layer['Toler'] = float(laueRec[1]) #tolerance for 'unknown'?
2067	if Layer['Laue'] == '2/m(1)': Layer['Laue'] = '2/m(c)'
2068	if Layer['Laue'] == '2/m(2)': Layer['Laue'] = '2/m(ab)'
2069	cell = Struct[0].split()
2070	Layer['Cell'] = [False,float(cell[0]),float(cell[1]),float(cell[2]),90.,90.,float(cell[3]),1.0]
2071	nLayers = int(Struct[2])
2072	N = 3
2073	if 'layer' not in Struct[3]:
2074	N = 4
2075	if Struct[3] != 'infinite':
2076	width = Struct[3].split()
2077	Layer['Width'][0] = [float(width[0]),float(width[1])]
2078	for nL in range(nLayers):
2079	if '=' in Struct[N]:
2080	name = Struct[N].split('=')
2081	sameas = int(name[1])-1
2082	Layer['Layers'].append({'Name':name[0],'SameAs':Layer['Layers'][sameas]['Name'],'Symm':'None','Atoms':[]})
2083	N += 1
2084	continue
2085	Symm = 'None'
2086	if 'centro' in Struct[N+1]: Symm = '-1'
2087	Layer['Layers'].append({'Name':Struct[N],'SameAs':'','Symm':Symm,'Atoms':[]})
2088	N += 2
2089	while 'layer' not in Struct[N]:
2090	atom = Struct[N][4:].split()
2091	atomType = G2el.FixValence(Struct[N][:4].replace(' ','').strip().capitalize())
2092	if atomType not in Layer['AtInfo']:
2093	Layer['AtInfo'][atomType] = G2el.GetAtomInfo(atomType)
2094	atomName = '%s(%s)'%(atomType,atom[0])
2095	newVals = []
2096	for val in atom[1:6]:
2097	if '/' in val:
2098	newVals.append(eval(val+'.'))
2099	else:
2100	newVals.append(float(val))
2101	atomRec = [atomName,atomType,newVals[0],newVals[1],newVals[2],newVals[4],newVals[3]/78.9568]
2102	Layer['Layers'][-1]['Atoms'].append(atomRec)
2103	N += 1
2104	if N > len(Struct)-1:
2105	break
2106	#TRANSITIONS records
2107	transArray = []
2108	N = 0
2109	for i in range(nLayers):
2110	transArray.append([])
2111	for j in range(nLayers):
2112	vals = Trans[N].split()
2113	newVals = []
2114	for val in vals[:4]:
2115	if '/' in val:
2116	newVals.append(eval(val+'.'))
2117	else:
2118	newVals.append(float(val))
2119	transArray[-1].append(newVals+['',False])
2120	N += 1
2121	Layer['Transitions'] = transArray
2122	#STACKING records
2123	Layer['Stacking'] = [Stack[0],'']
2124	if Stack[0] == 'recursive':
2125	Layer['Stacking'][1] = Stack[1]
2126	elif Stack[0] == 'explicit':
2127	if Stack[1] == 'random':
2128	Layer['Stacking'][1] = Stack[1]
2129	else:
2130	Layer['Stacking'][1] = 'list'
2131	Layer['Stacking'].append('')
2132	for stack in Stack[2:]:
2133	Layer['Stacking'][2] += ' '+stack
2134	return Layer
2135
2136	if __name__ == '__main__':
2137	import GSASIIdataGUI
2138	application = GSASIIdataGUI.GSASIImain(0)
2139	G2frame = application.main
2140	#app = wx.PySimpleApp()
2141	#G2frame = wx.Frame(None) # create a frame
2142	#frm.Show(True)
2143	#filename = '/tmp/notzip.zip'
2144	#filename = '/tmp/all.zip'
2145	#filename = '/tmp/11bmb_7652.zip'
2146
2147	#selection=None, confirmoverwrite=True, parent=None
2148	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2149	#print ExtractFileFromZip(filename,multipleselect=True)
2150	# #confirmread=False, confirmoverwrite=False)
2151
2152	# choicelist=[ ('a','b','c'),
2153	# ('test1','test2'),('no choice',)]
2154	# titles = [ 'a, b or c', 'tests', 'No option here']
2155	# dlg = MultipleChoicesDialog(
2156	# choicelist,titles,
2157	# parent=frm)
2158	# if dlg.ShowModal() == wx.ID_OK:
2159	# print 'Got OK'
2160	imagefile = '/tmp/NDC5_00237_3.ge3'
2161	Comments, Data, Npix, Image = GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None)
2162
2163	print("\n\nResults loaded to Comments, Data, Npix and Image\n\n")
2164
2165	GSASIIpath.IPyBreak_base()

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