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source: trunk/GSASIIIO.py @ 4548

Last change on this file since 4548 was 4548, checked in by vondreele, 3 years ago
Add csv exporter for reflectometry data
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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2020-08-19 13:14:36 +0000 (Wed, 19 Aug 2020) $
4	# $Author: vondreele $
5	# $Revision: 4548 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 4548 2020-08-19 13:14:36Z 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 class for data export routines (TODO: should move)
19
20	TODO: This module needs some work to separate wx from non-wx routines. GUI
21	routines should probably move to GSASIIctrlGUI.
22	'''
23
24	from __future__ import division, print_function
25
26	# Allow this to be imported without wx present. Was needed for G2scriptable, but is
27	# likely not needed anymore
28	try:
29	import wx
30	except ImportError:
31	# was needed by sphinx, but probably not anymore
32	class Placeholder(object):
33	def __init__(self):
34	self.Dialog = object
35	wx = Placeholder()
36	import math
37	import numpy as np
38	import numpy.ma as ma
39
40	import copy
41	import platform
42	if '2' in platform.python_version_tuple()[0]:
43	import cPickle
44	else:
45	import pickle as cPickle
46	import sys
47	import re
48	import random as ran
49	import GSASIIpath
50	GSASIIpath.SetVersionNumber("$Revision: 4548 $")
51	try:
52	import GSASIIdataGUI as G2gd
53	except ImportError:
54	pass
55	import GSASIIobj as G2obj
56	import GSASIIlattice as G2lat
57	try:
58	import GSASIIpwdGUI as G2pdG
59	import GSASIIimgGUI as G2imG
60	except ImportError:
61	pass
62	import GSASIIElem as G2el
63	import GSASIIstrIO as G2stIO
64	import GSASIImapvars as G2mv
65	import GSASIIfiles as G2fil
66	try:
67	import GSASIIctrlGUI as G2G
68	except ImportError:
69	pass
70	import os
71	import os.path as ospath
72
73	DEBUG = False #=True for various prints
74	TRANSP = False #=true to transpose images for testing
75	if GSASIIpath.GetConfigValue('Transpose'): TRANSP = True
76	npsind = lambda x: np.sin(x*np.pi/180.)
77
78	def sfloat(S):
79	'Convert a string to float. An empty field or a unconvertable value is treated as zero'
80	if S.strip():
81	try:
82	return float(S)
83	except ValueError:
84	pass
85	return 0.0
86
87	def sint(S):
88	'Convert a string to int. An empty field is treated as zero'
89	if S.strip():
90	return int(S)
91	else:
92	return 0
93
94	def trim(val):
95	'''Simplify a string containing leading and trailing spaces
96	as well as newlines, tabs, repeated spaces etc. into a shorter and
97	more simple string, by replacing all ranges of whitespace
98	characters with a single space.
99
100	:param str val: the string to be simplified
101
102	:returns: the (usually) shortened version of the string
103	'''
104	return re.sub('\s+', ' ', val).strip()
105
106	def FileDlgFixExt(dlg,file):
107	'this is needed to fix a problem in linux wx.FileDialog'
108	ext = dlg.GetWildcard().split('\|')[2dlg.GetFilterIndex()+1].strip('')
109	if ext not in file:
110	file += ext
111	return file
112
113	def GetPowderPeaks(fileName):
114	'Read powder peaks from a file'
115	sind = lambda x: math.sin(x*math.pi/180.)
116	asind = lambda x: 180.*math.asin(x)/math.pi
117	wave = 1.54052
118	File = open(fileName,'Ur')
119	Comments = []
120	peaks = []
121	S = File.readline()
122	while S:
123	if S[:1] == '#':
124	Comments.append(S[:-1])
125	else:
126	item = S.split()
127	if len(item) == 1:
128	peaks.append([float(item[0]),1.0])
129	elif len(item) > 1:
130	peaks.append([float(item[0]),float(item[0])])
131	S = File.readline()
132	File.close()
133	if Comments:
134	print ('Comments on file:')
135	for Comment in Comments:
136	print (Comment)
137	if 'wavelength' in Comment:
138	wave = float(Comment.split('=')[1])
139	Peaks = []
140	if peaks[0][0] > peaks[-1][0]: # d-spacings - assume CuKa
141	for peak in peaks:
142	dsp = peak[0]
143	sth = wave/(2.0*dsp)
144	if sth < 1.0:
145	tth = 2.0*asind(sth)
146	else:
147	break
148	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
149	else: #2-thetas - assume Cuka (for now)
150	for peak in peaks:
151	tth = peak[0]
152	dsp = wave/(2.0*sind(tth/2.0))
153	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
154	limits = [1000.,0.]
155	for peak in Peaks:
156	limits[0] = min(limits[0],peak[0])
157	limits[1] = max(limits[1],peak[0])
158	limits[0] = max(1.,(int(limits[0]-1.)/5)*5.)
159	limits[1] = min(170.,(int(limits[1]+1.)/5)*5.)
160	return Comments,Peaks,limits,wave
161
162	def GetCheckImageFile(G2frame,treeId):
163	'''Try to locate an image file if the project and image have been moved
164	together. If the image file cannot be found, request the location from
165	the user.
166
167	:param wx.Frame G2frame: main GSAS-II Frame and data object
168	:param wx.Id treeId: Id for the main tree item for the image
169	:returns: Npix,imagefile,imagetag with (Npix) number of pixels,
170	imagefile, if it exists, or the name of a file that does exist or False if the user presses Cancel
171	and (imagetag) an optional image number
172
173	'''
174	Npix,Imagefile,imagetag = G2frame.GPXtree.GetImageLoc(treeId)
175	if isinstance(Imagefile,list):
176	imagefile,imagetag = Imagefile
177	else:
178	imagefile = Imagefile
179	if not os.path.exists(imagefile):
180	print ('Image file '+imagefile+' not found')
181	fil = imagefile.replace('\\','/') # windows?!
182	# see if we can find a file with same name or in a similarly named sub-dir
183	pth,fil = os.path.split(fil)
184	prevpth = None
185	while pth and pth != prevpth:
186	prevpth = pth
187	if os.path.exists(os.path.join(G2frame.dirname,fil)):
188	print ('found image file '+os.path.join(G2frame.dirname,fil))
189	imagefile = os.path.join(G2frame.dirname,fil)
190	G2frame.GPXtree.UpdateImageLoc(treeId,imagefile)
191	return Npix,imagefile,imagetag
192	pth,enddir = os.path.split(pth)
193	fil = os.path.join(enddir,fil)
194	# not found as a subdirectory, drop common parts of path for last saved & image file names
195	# if image was .../A/B/C/imgs/ima.ge
196	# & GPX was .../A/B/C/refs/fil.gpx but is now .../NEW/TEST/TEST1
197	# will look for .../NEW/TEST/TEST1/imgs/ima.ge, .../NEW/TEST/imgs/ima.ge, .../NEW/imgs/ima.ge and so on
198	Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
199	gpxPath = Controls.get('LastSavedAs','').replace('\\','/').split('/') # blank in older .GPX files
200	imgPath = imagefile.replace('\\','/').split('/')
201	for p1,p2 in zip(gpxPath,imgPath):
202	if p1 == p2:
203	gpxPath.pop(0),imgPath.pop(0)
204	else:
205	break
206	fil = os.path.join(*imgPath) # file with non-common prefix elements
207	prevpth = None
208	pth = os.path.abspath(G2frame.dirname)
209	while pth and pth != prevpth:
210	prevpth = pth
211	if os.path.exists(os.path.join(pth,fil)):
212	print ('found image file '+os.path.join(pth,fil))
213	imagefile = os.path.join(pth,fil)
214	G2frame.GPXtree.UpdateImageLoc(treeId,imagefile)
215	return Npix,imagefile,imagetag
216	pth,enddir = os.path.split(pth)
217	#GSASIIpath.IPyBreak()
218
219	if not os.path.exists(imagefile):
220	# note that this fails (at least on Mac) to get an image during the GUI initialization
221	prevnam = os.path.split(imagefile)[1]
222	prevext = os.path.splitext(imagefile)[1]
223	wildcard = 'Image format ('+prevext+')\|'+prevext
224	dlg = wx.FileDialog(G2frame, 'Previous image file ('+prevnam+') not found; open here', '.', prevnam,
225	wildcard,wx.FD_OPEN)
226	try:
227	dlg.SetFilename(''+ospath.split(imagefile)[1])
228	if dlg.ShowModal() == wx.ID_OK:
229	imagefile = dlg.GetPath()
230	G2frame.GPXtree.UpdateImageLoc(treeId,imagefile)
231	else:
232	imagefile = None # was False
233	finally:
234	dlg.Destroy()
235	return Npix,imagefile,imagetag
236
237	def EditImageParms(parent,Data,Comments,Image,filename):
238	dlg = wx.Dialog(parent, wx.ID_ANY, 'Edit image parameters',
239	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
240	def onClose(event):
241	dlg.EndModal(wx.ID_OK)
242	mainsizer = wx.BoxSizer(wx.VERTICAL)
243	h,w = Image.shape[:2]
244	mainsizer.Add(wx.StaticText(dlg,wx.ID_ANY,'File '+str(filename)+'\nImage size: '+str(h)+' x '+str(w)),
245	0,wx.ALIGN_LEFT\|wx.ALL, 2)
246
247	vsizer = wx.BoxSizer(wx.HORIZONTAL)
248	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Wavelength (\xC5) '),
249	0,wx.ALIGN_LEFT\|wx.ALL, 2)
250	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'wavelength')
251	vsizer.Add(wdgt)
252	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
253
254	vsizer = wx.BoxSizer(wx.HORIZONTAL)
255	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Pixel size (\xb5m). Width '),
256	0,wx.ALIGN_LEFT\|wx.ALL, 2)
257	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],0,size=(50,-1))
258	vsizer.Add(wdgt)
259	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Height '),wx.ALIGN_LEFT\|wx.ALL, 2)
260	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],1,size=(50,-1))
261	vsizer.Add(wdgt)
262	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
263
264	vsizer = wx.BoxSizer(wx.HORIZONTAL)
265	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Sample to detector (mm) '),
266	0,wx.ALIGN_LEFT\|wx.ALL, 2)
267	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'distance')
268	vsizer.Add(wdgt)
269	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
270
271	vsizer = wx.BoxSizer(wx.HORIZONTAL)
272	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Beam center (pixels). X = '),
273	0,wx.ALIGN_LEFT\|wx.ALL, 2)
274	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],0,size=(75,-1))
275	vsizer.Add(wdgt)
276	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Y = '),wx.ALIGN_LEFT\|wx.ALL, 2)
277	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],1,size=(75,-1))
278	vsizer.Add(wdgt)
279	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
280
281	vsizer = wx.BoxSizer(wx.HORIZONTAL)
282	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Comments '),
283	0,wx.ALIGN_LEFT\|wx.ALL, 2)
284	wdgt = G2G.ValidatedTxtCtrl(dlg,Comments,0,size=(250,-1))
285	vsizer.Add(wdgt)
286	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
287
288	btnsizer = wx.StdDialogButtonSizer()
289	OKbtn = wx.Button(dlg, wx.ID_OK, 'Continue')
290	OKbtn.SetDefault()
291	OKbtn.Bind(wx.EVT_BUTTON,onClose)
292	btnsizer.AddButton(OKbtn) # not sure why this is needed
293	btnsizer.Realize()
294	mainsizer.Add(btnsizer, 1, wx.ALIGN_CENTER\|wx.ALL\|wx.EXPAND, 5)
295	dlg.SetSizer(mainsizer)
296	dlg.CenterOnParent()
297	dlg.ShowModal()
298
299	def LoadImage2Tree(imagefile,G2frame,Comments,Data,Npix,Image):
300	'''Load an image into the tree. Saves the location of the image, as well as the
301	ImageTag (where there is more than one image in the file), if defined.
302	'''
303	ImgNames = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',])
304	TreeLbl = 'IMG '+os.path.basename(imagefile)
305	ImageTag = Data.get('ImageTag')
306	if ImageTag:
307	TreeLbl += ' #'+'%04d'%(ImageTag)
308	imageInfo = (imagefile,ImageTag)
309	else:
310	imageInfo = imagefile
311	TreeName = G2obj.MakeUniqueLabel(TreeLbl,ImgNames)
312	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=TreeName)
313	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments)
314	Imax = np.amax(Image)
315	if G2frame.imageDefault:
316	Data = copy.copy(G2frame.imageDefault)
317	Data['showLines'] = True
318	Data['ring'] = []
319	Data['rings'] = []
320	Data['cutoff'] = 10.
321	Data['pixLimit'] = 20
322	Data['edgemin'] = 100000000
323	Data['calibdmin'] = 0.5
324	Data['calibskip'] = 0
325	Data['ellipses'] = []
326	Data['calibrant'] = ''
327	Data['GonioAngles'] = [0.,0.,0.]
328	Data['DetDepthRef'] = False
329	else:
330	Data['type'] = 'PWDR'
331	Data['color'] = GSASIIpath.GetConfigValue('Contour_color','Paired')
332	if 'tilt' not in Data: #defaults if not preset in e.g. Bruker importer
333	Data['tilt'] = 0.0
334	Data['rotation'] = 0.0
335	Data['pixLimit'] = 20
336	Data['calibdmin'] = 0.5
337	Data['cutoff'] = 10.
338	Data['showLines'] = False
339	Data['calibskip'] = 0
340	Data['ring'] = []
341	Data['rings'] = []
342	Data['edgemin'] = 100000000
343	Data['ellipses'] = []
344	Data['GonioAngles'] = [0.,0.,0.]
345	Data['DetDepth'] = 0.
346	Data['DetDepthRef'] = False
347	Data['calibrant'] = ''
348	Data['IOtth'] = [5.0,50.0]
349	if GSASIIpath.GetConfigValue('Image_2theta_min'):
350	try:
351	Data['IOtth'][0] = float(GSASIIpath.GetConfigValue('Image_2theta_min'))
352	except:
353	pass
354	if GSASIIpath.GetConfigValue('Image_2theta_max'):
355	try:
356	Data['IOtth'][1] = float(GSASIIpath.GetConfigValue('Image_2theta_max'))
357	except:
358	pass
359	Data['LRazimuth'] = [0.,180.]
360	Data['azmthOff'] = 0.0
361	Data['outChannels'] = 2500
362	Data['outAzimuths'] = 1
363	Data['centerAzm'] = False
364	Data['fullIntegrate'] = GSASIIpath.GetConfigValue('fullIntegrate',True)
365	Data['setRings'] = False
366	Data['background image'] = ['',-1.0]
367	Data['dark image'] = ['',-1.0]
368	Data['Flat Bkg'] = 0.0
369	Data['Oblique'] = [0.5,False]
370	Data['setDefault'] = False
371	Data['range'] = [(0,Imax),[0,Imax]]
372	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Image Controls'),Data)
373	Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],
374	'Thresholds':[(0,Imax),[0,Imax]],
375	'SpotMask':{'esdMul':3.,'spotMask':None}}
376	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Masks'),Masks)
377	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Stress/Strain'),
378	{'Type':'True','d-zero':[],'Sample phi':0.0,'Sample z':0.0,'Sample load':0.0})
379	G2frame.GPXtree.SetItemPyData(Id,[Npix,imageInfo])
380	G2frame.PickId = Id
381	G2frame.PickIdText = G2frame.GetTreeItemsList(G2frame.PickId)
382	G2frame.Image = Id
383
384	def GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None,FormatName=''):
385	'''Read a single image with an image importer. This is called to reread an image
386	after it has already been imported with :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`
387	(or :func:`ReadImages` in Auto Integration) so it is not necessary to reload metadata.
388
389	:param wx.Frame G2frame: main GSAS-II Frame and data object.
390	:param str imagefile: name of image file
391	:param bool imageOnly: If True return only the image,
392	otherwise (default) return more (see below)
393	:param int/str ImageTag: specifies a particular image to be read from a file.
394	First image is read if None (default).
395	:param str formatName: the image reader formatName
396
397	:returns: an image as a numpy array or a list of four items:
398	Comments, Data, Npix and the Image, as selected by imageOnly
399
400	'''
401	# determine which formats are compatible with this file
402	primaryReaders = []
403	secondaryReaders = []
404	for rd in G2frame.ImportImageReaderlist:
405	flag = rd.ExtensionValidator(imagefile)
406	if flag is None:
407	secondaryReaders.append(rd)
408	elif flag:
409	if not FormatName:
410	primaryReaders.append(rd)
411	elif FormatName == rd.formatName:
412	primaryReaders.append(rd)
413	if len(secondaryReaders) + len(primaryReaders) == 0:
414	print('Error: No matching format for file '+imagefile)
415	raise Exception('No image read')
416	errorReport = ''
417	if not imagefile:
418	return
419	for rd in primaryReaders+secondaryReaders:
420	rd.ReInitialize() # purge anything from a previous read
421	rd.errors = "" # clear out any old errors
422	if not rd.ContentsValidator(imagefile): # rejected on cursory check
423	errorReport += "\n "+rd.formatName + ' validator error'
424	if rd.errors:
425	errorReport += ': '+rd.errors
426	continue
427	if imageOnly:
428	ParentFrame = None # prevent GUI access on reread
429	else:
430	ParentFrame = G2frame
431	if GSASIIpath.GetConfigValue('debug'):
432	flag = rd.Reader(imagefile,ParentFrame,blocknum=ImageTag)
433	else:
434	flag = False
435	try:
436	flag = rd.Reader(imagefile,ParentFrame,blocknum=ImageTag)
437	except rd.ImportException as detail:
438	rd.errors += "\n Read exception: "+str(detail)
439	except Exception as detail:
440	import traceback
441	rd.errors += "\n Unhandled read exception: "+str(detail)
442	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
443	if flag: # this read succeeded
444	if rd.Image is None:
445	raise Exception('No image read. Strange!')
446	if GSASIIpath.GetConfigValue('Transpose'):
447	print ('Transposing Image!')
448	rd.Image = rd.Image.T
449	#rd.readfilename = imagefile
450	if imageOnly:
451	return rd.Image
452	else:
453	return rd.Comments,rd.Data,rd.Npix,rd.Image
454	else:
455	print('Error reading file '+imagefile)
456	print('Error messages(s)\n'+errorReport)
457	raise Exception('No image read')
458
459	def ReadImages(G2frame,imagefile):
460	'''Read one or more images from a file and put them into the Tree
461	using image importers. Called only in :meth:`AutoIntFrame.OnTimerLoop`.
462
463	ToDo: Images are most commonly read in :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`
464	which is called from :meth:`GSASIIdataGUI.GSASII.OnImportImage`
465	it would be good if these routines used a common code core so that changes need to
466	be made in only one place.
467
468	:param wx.Frame G2frame: main GSAS-II Frame and data object.
469	:param str imagefile: name of image file
470
471	:returns: a list of the id's of the IMG tree items created
472	'''
473	# determine which formats are compatible with this file
474	primaryReaders = []
475	secondaryReaders = []
476	for rd in G2frame.ImportImageReaderlist:
477	flag = rd.ExtensionValidator(imagefile)
478	if flag is None:
479	secondaryReaders.append(rd)
480	elif flag:
481	primaryReaders.append(rd)
482	if len(secondaryReaders) + len(primaryReaders) == 0:
483	print('Error: No matching format for file '+imagefile)
484	raise Exception('No image read')
485	errorReport = ''
486	rdbuffer = {} # create temporary storage for file reader
487	for rd in primaryReaders+secondaryReaders:
488	rd.ReInitialize() # purge anything from a previous read
489	rd.errors = "" # clear out any old errors
490	if not rd.ContentsValidator(imagefile): # rejected on cursory check
491	errorReport += "\n "+rd.formatName + ' validator error'
492	if rd.errors:
493	errorReport += ': '+rd.errors
494	continue
495	ParentFrame = G2frame
496	block = 0
497	repeat = True
498	CreatedIMGitems = []
499	while repeat: # loop if the reader asks for another pass on the file
500	block += 1
501	repeat = False
502	if GSASIIpath.GetConfigValue('debug'):
503	flag = rd.Reader(imagefile,ParentFrame,blocknum=block,Buffer=rdbuffer)
504	else:
505	flag = False
506	try:
507	flag = rd.Reader(imagefile,ParentFrame,blocknum=block,Buffer=rdbuffer)
508	except rd.ImportException as detail:
509	rd.errors += "\n Read exception: "+str(detail)
510	except Exception as detail:
511	import traceback
512	rd.errors += "\n Unhandled read exception: "+str(detail)
513	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
514	if flag: # this read succeeded
515	if rd.Image is None:
516	raise Exception('No image read. Strange!')
517	if GSASIIpath.GetConfigValue('Transpose'):
518	print ('Transposing Image!')
519	rd.Image = rd.Image.T
520	rd.Data['ImageTag'] = rd.repeatcount
521	rd.readfilename = imagefile
522	# Load generic metadata, as configured
523	G2fil.GetColumnMetadata(rd)
524	LoadImage2Tree(imagefile,G2frame,rd.Comments,rd.Data,rd.Npix,rd.Image)
525	repeat = rd.repeat
526	CreatedIMGitems.append(G2frame.Image)
527	if CreatedIMGitems: return CreatedIMGitems
528	else:
529	print('Error reading file '+imagefile)
530	print('Error messages(s)\n'+errorReport)
531	return []
532	#raise Exception('No image read')
533
534	def SaveMultipleImg(G2frame):
535	if not G2frame.GPXtree.GetCount():
536	print ('no images!')
537	return
538	choices = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',])
539	if len(choices) == 1:
540	names = choices
541	else:
542	dlg = G2G.G2MultiChoiceDialog(G2frame,'Stress/Strain fitting','Select images to fit:',choices)
543	dlg.SetSelections([])
544	names = []
545	if dlg.ShowModal() == wx.ID_OK:
546	names = [choices[sel] for sel in dlg.GetSelections()]
547	dlg.Destroy()
548	if not names: return
549	for name in names:
550	Id = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, name)
551	Npix,imagefile,imagetag = G2frame.GPXtree.GetImageLoc(Id)
552	imroot = os.path.splitext(imagefile)[0]
553	if imagetag:
554	imroot += '_' + str(imagetag)
555	Data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Image Controls'))
556	print('Writing '+imroot+'.imctrl')
557	File = open(imroot+'.imctrl','w')
558	keys = ['type','wavelength','calibrant','distance','center',
559	'tilt','rotation','azmthOff','fullIntegrate','LRazimuth',
560	'IOtth','outChannels','outAzimuths','invert_x','invert_y','DetDepth',
561	'calibskip','pixLimit','cutoff','calibdmin','chisq','Flat Bkg',
562	'binType','SampleShape','PolaVal','SampleAbs','dark image','background image']
563	for key in keys:
564	if key not in Data: continue #uncalibrated!
565	File.write(key+':'+str(Data[key])+'\n')
566	File.close()
567	mask = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Masks'))
568	G2imG.CleanupMasks(mask)
569	print('Writing '+imroot+'.immask')
570	File = open(imroot+'.immask','w')
571	for key in ['Points','Rings','Arcs','Polygons','Frames','Thresholds']:
572	File.write(key+':'+str(mask[key])+'\n')
573	File.close()
574
575	def PutG2Image(filename,Comments,Data,Npix,image):
576	'Write an image as a python pickle - might be better as an .edf file?'
577	File = open(filename,'wb')
578	cPickle.dump([Comments,Data,Npix,image],File,2)
579	File.close()
580	return
581
582	objectScanIgnore = [int,bool,float,str,np.float64,np.float32,np.int32,np.int64,np.ndarray,G2obj.G2VarObj,G2obj.ExpressionObj]
583	try:
584	objectScanIgnore += [ma.MaskedArray] # fails in doc builds
585	except AttributeError:
586	pass
587
588	if '2' in platform.python_version_tuple()[0]:
589	objectScanIgnore += [unicode,long,]
590
591	def objectScan(data,tag,indexStack=[]):
592	'''Recursively scan an object looking for unexpected data types.
593	This is used in debug mode to scan .gpx files for objects we did not
594	intend to be there.
595	'''
596	if type(data) is list or type(data) is tuple:
597	for i in range(len(data)):
598	val = objectScan(data[i],tag,indexStack+[i])
599	if val:
600	data[i] = val
601	print('...fixed')
602	elif type(data) is dict:
603	for key in data:
604	val = objectScan(data[key],tag,indexStack+[key])
605	if val:
606	data[key] = val
607	print('...fixed')
608	elif data is None:
609	return None
610	elif type(data) in objectScanIgnore:
611	return None
612	else:
613	s = 'unexpected object in '+tag
614	for i in indexStack:
615	s += "[{}]".format(i)
616	#print(s,data.__class__.__name__) # loses full name of class
617	print(s,type(data))
618	global unexpectedObject
619	unexpectedObject = True
620	# fix bad objects
621	if "gdi.Colour" in str(type(data)):
622	return tuple(data)
623	return
624
625	def cPickleLoad(fp):
626	if '2' in platform.python_version_tuple()[0]:
627	return cPickle.load(fp)
628	else:
629	return cPickle.load(fp,encoding='latin-1')
630
631	def ProjFileOpen(G2frame,showProvenance=True):
632	'Read a GSAS-II project file and load into the G2 data tree'
633	if not os.path.exists(G2frame.GSASprojectfile):
634	print ('\n*** Error attempt to open project file that does not exist:\n '+
635	str(G2frame.GSASprojectfile))
636	return
637	LastSavedUsing = None
638	filep = open(G2frame.GSASprojectfile,'rb')
639	if showProvenance: print ('loading from file: '+G2frame.GSASprojectfile)
640	GPXphase = os.path.splitext(G2frame.GSASprojectfile)[0]+'.seqPhase'
641	GPXhist = os.path.splitext(G2frame.GSASprojectfile)[0]+'.seqHist'
642	deleteSeq = False
643	hist = None
644	tmpHistIndex = {}
645	updateFromSeq = False
646	if os.path.exists(GPXphase) and os.path.exists(GPXhist):
647	dlg = wx.MessageDialog(G2frame,
648	'Load results from crashed sequential fit?\nNo deletes the files!', 'Recover partial sequential fit?', wx.YES \| wx.NO \| wx.CANCEL)
649	dlg.CenterOnParent()
650	try:
651	result = dlg.ShowModal()
652	deleteSeq = result != wx.ID_CANCEL
653	if result == wx.ID_YES:
654	updateFromSeq = True
655	fp = open(GPXphase,'rb')
656	data = cPickleLoad(fp) # first block in file should be Phases
657	if data[0][0] != 'Phases':
658	raise Exception('Unexpected block in {} file. How did this happen?'
659	.format(GPXphase))
660	Phases = {}
661	for name,vals in data[1:]:
662	Phases[name] = vals
663	name,CovData = cPickleLoad(fp)[0] # 2nd block in file should be Covariance
664	name,RigidBodies = cPickleLoad(fp)[0] # 3rd block in file should be Rigid Bodies
665	fp.close()
666	# index the histogram updates
667	hist = open(GPXhist,'rb')
668	try:
669	while True:
670	loc = hist.tell()
671	datum = cPickleLoad(hist)[0]
672	tmpHistIndex[datum[0]] = loc
673	except EOFError:
674	pass
675	finally:
676	dlg.Destroy()
677	wx.BeginBusyCursor()
678	try:
679	while True:
680	try:
681	data = cPickleLoad(filep)
682	except EOFError:
683	break
684	datum = data[0]
685	# scan the GPX file for unexpected objects
686	if GSASIIpath.GetConfigValue('debug'):
687	global unexpectedObject
688	unexpectedObject = False
689	objectScan(data,'tree item "{}" entry '.format(datum[0]))
690	#if unexpectedObject:
691	# print(datum[0])
692	# GSASIIpath.IPyBreak()
693	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=datum[0])
694	if updateFromSeq and datum[0] == 'Phases':
695	for pdata in data[1:]:
696	if pdata[0] in Phases:
697	pdata[1].update(Phases[pdata[0]])
698	elif updateFromSeq and datum[0] == 'Covariance':
699	data[0][1] = CovData
700	elif updateFromSeq and datum[0] == 'Rigid bodies':
701	data[0][1] = RigidBodies
702	elif updateFromSeq and datum[0] in tmpHistIndex:
703	hist.seek(tmpHistIndex[datum[0]])
704	hdata = cPickleLoad(hist)
705	if data[0][0] != hdata[0][0]:
706	print('Error! Updating {} with {}'.format(data[0][0],hdata[0][0]))
707	datum = hdata[0]
708	xferItems = ['Background','Instrument Parameters','Sample Parameters','Reflection Lists']
709	hItems = {name:j+1 for j,(name,val) in enumerate(hdata[1:]) if name in xferItems}
710	for j,(name,val) in enumerate(data[1:]):
711	if name not in xferItems: continue
712	data[j+1][1] = hdata[hItems[name]][1]
713	if datum[0].startswith('PWDR'):
714	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
715	datum[1][0]['ranId'] = ran.randint(0,sys.maxsize)
716	G2frame.GPXtree.SetItemPyData(Id,datum[1][:3]) #temp. trim off junk (patch?)
717	elif datum[0].startswith('HKLF'):
718	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
719	datum[1][0]['ranId'] = ran.randint(0,sys.maxsize)
720	G2frame.GPXtree.SetItemPyData(Id,datum[1])
721	else:
722	G2frame.GPXtree.SetItemPyData(Id,datum[1])
723	if datum[0] == 'Controls' and 'LastSavedUsing' in datum[1]:
724	LastSavedUsing = datum[1]['LastSavedUsing']
725	if datum[0] == 'Controls' and 'PythonVersions' in datum[1] and GSASIIpath.GetConfigValue('debug') and showProvenance:
726	print('DBG_Packages used to create .GPX file:')
727	if 'dict' in str(type(datum[1]['PythonVersions'])): #patch
728	for p in sorted(datum[1]['PythonVersions'],key=lambda s: s.lower()):
729	print(" {:<14s}: {:s}".format(p[0],p[1]))
730	else:
731	for p in datum[1]['PythonVersions']:
732	print(" {:<12s} {:s}".format(p[0]+':',p[1]))
733	oldPDF = False
734	for datus in data[1:]:
735	#patch - 1/23/17 PDF cleanup
736	if datus[0][:4] in ['I(Q)','S(Q)','F(Q)','G(R)']:
737	oldPDF = True
738	data[1][1][datus[0][:4]] = copy.deepcopy(datus[1][:2])
739	continue
740	#end PDF cleanup
741	sub = G2frame.GPXtree.AppendItem(Id,datus[0])
742	#patch
743	if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
744	if datum[0].startswith('PWDR'):
745	datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
746	else:
747	datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
748	for item in datus[1][0]: #zip makes tuples - now make lists!
749	datus[1][0][item] = list(datus[1][0][item])
750	#end patch
751	G2frame.GPXtree.SetItemPyData(sub,datus[1])
752	if 'PDF ' in datum[0][:4] and oldPDF:
753	sub = G2frame.GPXtree.AppendItem(Id,'PDF Peaks')
754	G2frame.GPXtree.SetItemPyData(sub,{'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]})
755	if datum [0].startswith('IMG'): #retrieve image default flag & data if set
756	Data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Image Controls'))
757	if Data['setDefault']:
758	G2frame.imageDefault = Data
759	if LastSavedUsing:
760	print('GPX load successful. Last saved with GSAS-II revision '+LastSavedUsing)
761	else:
762	print('project load successful')
763	G2frame.NewPlot = True
764	except Exception as errmsg:
765	if GSASIIpath.GetConfigValue('debug'):
766	print('\nError reading GPX file:',errmsg)
767	import traceback
768	print (traceback.format_exc())
769	msg = wx.MessageDialog(G2frame,message="Error reading file "+
770	str(G2frame.GSASprojectfile)+". This is not a current GSAS-II .gpx file",
771	caption="Load Error",style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
772	msg.ShowModal()
773	finally:
774	filep.close()
775	wx.EndBusyCursor()
776	G2frame.Status.SetStatusText('Mouse RB drag/drop to reorder',0)
777	if deleteSeq:
778	if hist: hist.close()
779	try:
780	os.remove(GPXphase)
781	except:
782	print('Warning: unable to delete {}'.format(GPXphase))
783	try:
784	os.remove(GPXhist)
785	except:
786	print('Warning: unable to delete {}'.format(GPXhist))
787	G2frame.SetTitleByGPX()
788
789	def ProjFileSave(G2frame):
790	'Save a GSAS-II project file'
791	if not G2frame.GPXtree.IsEmpty():
792	file = open(G2frame.GSASprojectfile,'wb')
793	print ('save to file: '+G2frame.GSASprojectfile)
794	# stick the file name into the tree and version info into tree so they are saved.
795	# (Controls should always be created at this point)
796	try:
797	Controls = G2frame.GPXtree.GetItemPyData(
798	G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
799	Controls['LastSavedAs'] = os.path.abspath(G2frame.GSASprojectfile)
800	Controls['LastSavedUsing'] = str(GSASIIpath.GetVersionNumber())
801	Controls['PythonVersions'] = G2frame.PackageVersions
802	except:
803	pass
804	wx.BeginBusyCursor()
805	try:
806	item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
807	while item:
808	data = []
809	name = G2frame.GPXtree.GetItemText(item)
810	data.append([name,G2frame.GPXtree.GetItemPyData(item)])
811	item2, cookie2 = G2frame.GPXtree.GetFirstChild(item)
812	while item2:
813	name = G2frame.GPXtree.GetItemText(item2)
814	data.append([name,G2frame.GPXtree.GetItemPyData(item2)])
815	item2, cookie2 = G2frame.GPXtree.GetNextChild(item, cookie2)
816	item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
817	cPickle.dump(data,file,2)
818	file.close()
819	pth = os.path.split(os.path.abspath(G2frame.GSASprojectfile))[0]
820	if GSASIIpath.GetConfigValue('Save_paths'): G2G.SaveGPXdirectory(pth)
821	G2frame.LastGPXdir = pth
822	finally:
823	wx.EndBusyCursor()
824	print('project save successful')
825
826	def SaveIntegration(G2frame,PickId,data,Overwrite=False):
827	'Save image integration results as powder pattern(s)'
828	waves = {'Cu':[1.54051,1.54433],'Ti':[2.74841,2.75207],'Cr':[2.28962,2.29351],
829	'Fe':[1.93597,1.93991],'Co':[1.78892,1.79278],'Mo':[0.70926,0.713543],
830	'Ag':[0.559363,0.563775]}
831	azms = G2frame.Integrate[1]
832	X = G2frame.Integrate[2][:-1]
833	N = len(X)
834	Id = G2frame.GPXtree.GetItemParent(PickId)
835	name = G2frame.GPXtree.GetItemText(Id)
836	name = name.replace('IMG ',data['type']+' ')
837	Comments = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Comments'))
838	Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
839	if 'PWDR' in name:
840	if 'target' in data:
841	names = ['Type','Lam1','Lam2','I(L2)/I(L1)','Zero','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth']
842	codes = [0 for i in range(14)]
843	else:
844	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth']
845	codes = [0 for i in range(12)]
846	elif 'SASD' in name:
847	names = ['Type','Lam','Zero','Azimuth']
848	codes = [0 for i in range(4)]
849	X = 4.np.pinpsind(X/2.)/data['wavelength'] #convert to q
850	Xminmax = [X[0],X[-1]]
851	Azms = np.zeros(data['outAzimuths'])
852	dazm = 0.
853	if data['outAzimuths'] > 1:
854	dazm = np.min(np.abs(np.diff(azms)))/2.
855	G2frame.IntgOutList = []
856	for i,azm in enumerate(azms[:-1]):
857	Aname = name+" Azm= %.2f"%((azm+dazm)%360.)
858	item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
859	# if Overwrite delete any duplicate
860	if Overwrite and G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname):
861	print('Replacing '+Aname)
862	item = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname)
863	G2frame.GPXtree.Delete(item)
864	else:
865	nOcc = 0
866	while item:
867	Name = G2frame.GPXtree.GetItemText(item)
868	if Aname in Name:
869	nOcc += 1
870	item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
871	if nOcc:
872	Aname += '(%d)'%(nOcc)
873	Sample = G2obj.SetDefaultSample() #set as Debye-Scherrer
874	Sample['Gonio. radius'] = data['distance']
875	Sample['Omega'] = data['GonioAngles'][0]
876	Sample['Chi'] = data['GonioAngles'][1]
877	Sample['Phi'] = data['GonioAngles'][2]
878	Sample['Azimuth'] = (azm+dazm)%360. #put here as bin center
879	polariz = data['PolaVal'][0]
880	for item in Comments:
881	for key in ('Temperature','Pressure','Time','FreePrm1','FreePrm2','FreePrm3','Omega',
882	'Chi','Phi'):
883	if key.lower() in item.lower():
884	try:
885	Sample[key] = float(item.split('=')[1])
886	except:
887	pass
888	if 'label_prm' in item.lower():
889	for num in ('1','2','3'):
890	if 'label_prm'+num in item.lower():
891	Controls['FreePrm'+num] = item.split('=')[1].strip()
892	if 'PWDR' in Aname:
893	if 'target' in data: #from lab x-ray 2D imaging data
894	wave1,wave2 = waves[data['target']]
895	parms = ['PXC',wave1,wave2,0.5,0.0,polariz,290.,-40.,30.,6.,-14.,0.0,0.0001,Azms[i]]
896	else:
897	parms = ['PXC',data['wavelength'],0.0,polariz,1.0,-0.10,0.4,0.30,1.0,0.0,0.0001,Azms[i]]
898	elif 'SASD' in Aname:
899	Sample['Trans'] = data['SampleAbs'][0]
900	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
901	Y = G2frame.Integrate[0][i]
902	Ymin = np.min(Y)
903	Ymax = np.max(Y)
904	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
905	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=Aname)
906	G2frame.IntgOutList.append(Id)
907	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments)
908	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Limits'),copy.deepcopy([tuple(Xminmax),Xminmax]))
909	if 'PWDR' in Aname:
910	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Background'),[['chebyschev-1',1,3,1.0,0.0,0.0],
911	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
912	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
913	for item in inst[0]:
914	inst[0][item] = list(inst[0][item])
915	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Instrument Parameters'),inst)
916	if 'PWDR' in Aname:
917	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample)
918	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
919	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Index Peak List'),[[],[]])
920	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Unit Cells List'),[])
921	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Reflection Lists'),{})
922	elif 'SASD' in Aname:
923	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
924	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample)
925	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
926	valuesdict = {
927	'wtFactor':1.0,'Dummy':False,'ranId':ran.randint(0,sys.maxsize),'Offset':[0.0,0.0],'delOffset':0.02*Ymax,
928	'refOffset':-0.1Ymax,'refDelt':0.1Ymax,'Yminmax':[Ymin,Ymax]}
929	G2frame.GPXtree.SetItemPyData(Id,[valuesdict,
930	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
931	return Id #last powder pattern generated
932
933	def XYsave(G2frame,XY,labelX='X',labelY='Y',names=[]):
934	'Save XY table data'
935	pth = G2G.GetExportPath(G2frame)
936	dlg = wx.FileDialog(
937	G2frame, 'Enter csv filename for XY table', pth, '',
938	'XY table file (.csv)\|.csv',wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
939	try:
940	if dlg.ShowModal() == wx.ID_OK:
941	filename = dlg.GetPath()
942	filename = os.path.splitext(filename)[0]+'.csv'
943	File = open(filename,'w')
944	else:
945	filename = None
946	finally:
947	dlg.Destroy()
948	if not filename:
949	return
950	for i in range(len(XY)):
951	if len(names):
952	header = '%s,%s(%s)\n'%(labelX,labelY,names[i])
953	else:
954	header = '%s,%s(%d)\n'%(labelX,labelY,i)
955	File.write(header)
956	for x,y in XY[i].T:
957	File.write('%.3f,%.3f\n'%(x,y))
958	File.close()
959	print (' XY data saved to: '+filename)
960
961	def PeakListSave(G2frame,file,peaks):
962	'Save powder peaks to a data file'
963	print ('save peak list to file: '+G2frame.peaklistfile)
964	if not peaks:
965	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
966	try:
967	dlg.ShowModal()
968	finally:
969	dlg.Destroy()
970	return
971	for peak in peaks:
972	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
973	(peak[0],peak[2],peak[4],peak[6]))
974	print ('peak list saved')
975
976	def IndexPeakListSave(G2frame,peaks):
977	'Save powder peaks from the indexing list'
978	file = open(G2frame.peaklistfile,'wa')
979	print ('save index peak list to file: '+G2frame.peaklistfile)
980	wx.BeginBusyCursor()
981	try:
982	if not peaks:
983	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
984	try:
985	dlg.ShowModal()
986	finally:
987	dlg.Destroy()
988	return
989	for peak in peaks:
990	file.write("%12.6f\n" % (peak[7]))
991	file.close()
992	finally:
993	wx.EndBusyCursor()
994	print ('index peak list saved')
995
996	def ExtractFileFromZip(filename, selection=None, confirmread=True,
997	confirmoverwrite=True, parent=None,
998	multipleselect=False):
999	'''If the filename is a zip file, extract a file from that
1000	archive.
1001
1002	:param list Selection: used to predefine the name of the file
1003	to be extracted. Filename case and zip directory name are
1004	ignored in selection; the first matching file is used.
1005
1006	:param bool confirmread: if True asks the user to confirm before expanding
1007	the only file in a zip
1008
1009	:param bool confirmoverwrite: if True asks the user to confirm
1010	before overwriting if the extracted file already exists
1011
1012	:param bool multipleselect: if True allows more than one zip
1013	file to be extracted, a list of file(s) is returned.
1014	If only one file is present, do not ask which one, otherwise
1015	offer a list of choices (unless selection is used).
1016
1017	:returns: the name of the file that has been created or a
1018	list of files (see multipleselect)
1019
1020	If the file is not a zipfile, return the name of the input file.
1021	If the zipfile is empty or no file has been selected, return None
1022	'''
1023	import zipfile # do this now, since we can save startup time by doing this only on need
1024	import shutil
1025	zloc = os.path.split(filename)[0]
1026	if not zipfile.is_zipfile(filename):
1027	#print("not zip")
1028	return filename
1029
1030	z = zipfile.ZipFile(filename,'r')
1031	zinfo = z.infolist()
1032
1033	if len(zinfo) == 0:
1034	#print('Zip has no files!')
1035	zlist = [-1]
1036	if selection:
1037	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1038	if selection.lower() in choices:
1039	zlist = [choices.index(selection.lower())]
1040	else:
1041	print('debug: file '+str(selection)+' was not found in '+str(filename))
1042	zlist = [-1]
1043	elif len(zinfo) == 1 and confirmread:
1044	result = wx.ID_NO
1045	dlg = wx.MessageDialog(
1046	parent,
1047	'Is file '+str(zinfo[0].filename)+
1048	' what you want to extract from '+
1049	str(os.path.split(filename)[1])+'?',
1050	'Confirm file',
1051	wx.YES_NO \| wx.ICON_QUESTION)
1052	try:
1053	result = dlg.ShowModal()
1054	finally:
1055	dlg.Destroy()
1056	if result == wx.ID_NO:
1057	zlist = [-1]
1058	else:
1059	zlist = [0]
1060	elif len(zinfo) == 1:
1061	zlist = [0]
1062	elif multipleselect:
1063	# select one or more from a from list
1064	choices = [i.filename for i in zinfo]
1065	dlg = G2G.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1066	'Choose file(s)',choices)
1067	if dlg.ShowModal() == wx.ID_OK:
1068	zlist = dlg.GetSelections()
1069	else:
1070	zlist = []
1071	dlg.Destroy()
1072	else:
1073	# select one from a from list
1074	choices = [i.filename for i in zinfo]
1075	dlg = wx.SingleChoiceDialog(parent,
1076	'Select file to extract from zip file'+str(filename),'Choose file',
1077	choices,)
1078	if dlg.ShowModal() == wx.ID_OK:
1079	zlist = [dlg.GetSelection()]
1080	else:
1081	zlist = [-1]
1082	dlg.Destroy()
1083
1084	outlist = []
1085	for zindex in zlist:
1086	if zindex >= 0:
1087	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1088	if os.path.exists(efil) and confirmoverwrite:
1089	result = wx.ID_NO
1090	dlg = wx.MessageDialog(parent,
1091	'File '+str(efil)+' already exists. OK to overwrite it?',
1092	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1093	try:
1094	result = dlg.ShowModal()
1095	finally:
1096	dlg.Destroy()
1097	if result == wx.ID_NO:
1098	zindex = -1
1099	if zindex >= 0:
1100	# extract the file to the current directory, regardless of it's original path
1101	#z.extract(zinfo[zindex],zloc)
1102	eloc,efil = os.path.split(zinfo[zindex].filename)
1103	outfile = os.path.join(zloc, efil)
1104	fpin = z.open(zinfo[zindex])
1105	fpout = open(outfile, "wb")
1106	shutil.copyfileobj(fpin, fpout)
1107	fpin.close()
1108	fpout.close()
1109	outlist.append(outfile)
1110	z.close()
1111	if multipleselect and len(outlist) >= 1:
1112	return outlist
1113	elif len(outlist) == 1:
1114	return outlist[0]
1115	else:
1116	return None
1117
1118	def striphist(var,insChar=''):
1119	'strip a histogram number from a var name'
1120	sv = var.split(':')
1121	if len(sv) <= 1: return var
1122	if sv[1]:
1123	sv[1] = insChar
1124	return ':'.join(sv)
1125
1126	######################################################################
1127	# base classes for reading various types of data files
1128	# not used directly, only by subclassing
1129	######################################################################
1130	class ExportBaseclass(object):
1131	'''Defines a base class for the exporting of GSAS-II results.
1132
1133	This class is subclassed in the various exports/G2export_*.py files. Those files
1134	are imported in :meth:`GSASIIdataGUI.GSASII._init_Exports` which defines the
1135	appropriate menu items for each one and the .Exporter method is called
1136	directly from the menu item.
1137
1138	Routines may also define a .Writer method, which is used to write a single
1139	file without invoking any GUI objects.
1140	'''
1141	# TODO: review exporters producing exceptions where .Writer can't be used where G2frame is None (see CIF)
1142	# TODO: review conflicting uses of .Writer with mode (SeqRef) & elsewhere
1143	# TODO: move this class to G2fil
1144	def __init__(self,G2frame,formatName,extension,longFormatName=None,):
1145	self.G2frame = G2frame
1146	self.formatName = formatName # short string naming file type
1147	self.extension = extension
1148	if longFormatName: # longer string naming file type
1149	self.longFormatName = longFormatName
1150	else:
1151	self.longFormatName = formatName
1152	self.OverallParms = {}
1153	self.Phases = {}
1154	self.Histograms = {}
1155	self.powderDict = {}
1156	self.sasdDict = {}
1157	self.refdDict = {}
1158	self.xtalDict = {}
1159	self.parmDict = {}
1160	self.sigDict = {}
1161	# updated in InitExport:
1162	self.currentExportType = None # type of export that has been requested
1163	# updated in ExportSelect (when used):
1164	self.phasenam = None # a list of selected phases
1165	self.histnam = None # a list of selected histograms
1166	self.filename = None # name of file to be written (single export) or template (multiple files)
1167	self.dirname = '' # name of directory where file(s) will be written
1168	self.fullpath = '' # name of file being written -- full path
1169
1170	# items that should be defined in a subclass of this class
1171	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1172	# The following types are defined: 'project', "phase", "powder", "single"
1173	self.multiple = False # set as True if the class can export multiple phases or histograms
1174	# self.multiple is ignored for "project" exports
1175
1176	def InitExport(self,event):
1177	'''Determines the type of menu that called the Exporter and
1178	misc initialization.
1179	'''
1180	self.filename = None # name of file to be written (single export)
1181	self.dirname = '' # name of file to be written (multiple export)
1182	if event:
1183	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1184
1185	def MakePWDRfilename(self,hist):
1186	'''Make a filename root (no extension) from a PWDR histogram name
1187
1188	:param str hist: the histogram name in data tree (starts with "PWDR ")
1189	'''
1190	file0 = ''
1191	file1 = hist[5:]
1192	# replace repeated blanks
1193	while file1 != file0:
1194	file0 = file1
1195	file1 = file0.replace(' ',' ').strip()
1196	file0 = file1.replace('Azm= ','A')
1197	# if angle has unneeded decimal places on aziumuth, remove them
1198	if file0[-3:] == '.00': file0 = file0[:-3]
1199	file0 = file0.replace('.','_')
1200	file0 = file0.replace(' ','_')
1201	return file0
1202
1203	def ExportSelect(self,AskFile='ask'):
1204	'''Selects histograms or phases when needed. Sets a default file name when
1205	requested into self.filename; always sets a default directory in self.dirname.
1206
1207	:param bool AskFile: Determines how this routine processes getting a
1208	location to store the current export(s).
1209
1210	* if AskFile is 'ask' (default option), get the name of the file to be written;
1211	self.filename and self.dirname are always set. In the case where
1212	multiple files must be generated, the export routine should do this
1213	based on self.filename as a template.
1214	* if AskFile is 'dir', get the name of the directory to be used;
1215	self.filename is not used, but self.dirname is always set. The export routine
1216	will always generate the file name.
1217	* if AskFile is 'single', get only the name of the directory to be used when
1218	multiple items will be written (as multiple files) are used
1219	or a complete file name is requested when a single file
1220	name is selected. self.dirname is always set and self.filename used
1221	only when a single file is selected.
1222	* if AskFile is 'default', creates a name of the file to be used from
1223	the name of the project (.gpx) file. If the project has not been saved,
1224	then the name of file is requested.
1225	self.filename and self.dirname are always set. In the case where
1226	multiple file names must be generated, the export routine should do this
1227	based on self.filename.
1228	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1229	file. If the project has not been saved, then a directory is requested.
1230	self.filename is not used.
1231
1232	:returns: True in case of an error
1233	'''
1234
1235	numselected = 1
1236	if self.currentExportType == 'phase':
1237	if len(self.Phases) == 0:
1238	self.G2frame.ErrorDialog(
1239	'Empty project',
1240	'Project does not contain any phases.')
1241	return True
1242	elif len(self.Phases) == 1:
1243	self.phasenam = list(self.Phases.keys())
1244	elif self.multiple:
1245	choices = sorted(self.Phases.keys())
1246	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1247	if phasenum is None: return True
1248	self.phasenam = [choices[i] for i in phasenum]
1249	if not self.phasenam: return True
1250	numselected = len(self.phasenam)
1251	else:
1252	choices = sorted(self.Phases.keys())
1253	phasenum = G2G.ItemSelector(choices,self.G2frame)
1254	if phasenum is None: return True
1255	self.phasenam = [choices[phasenum]]
1256	numselected = len(self.phasenam)
1257	elif self.currentExportType == 'single':
1258	if len(self.xtalDict) == 0:
1259	self.G2frame.ErrorDialog(
1260	'Empty project',
1261	'Project does not contain any single crystal data.')
1262	return True
1263	elif len(self.xtalDict) == 1:
1264	self.histnam = self.xtalDict.values()
1265	elif self.multiple:
1266	choices = sorted(self.xtalDict.values())
1267	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1268	if not hnum: return True
1269	self.histnam = [choices[i] for i in hnum]
1270	numselected = len(self.histnam)
1271	else:
1272	choices = sorted(self.xtalDict.values())
1273	hnum = G2G.ItemSelector(choices,self.G2frame)
1274	if hnum is None: return True
1275	self.histnam = [choices[hnum]]
1276	numselected = len(self.histnam)
1277	elif self.currentExportType == 'powder':
1278	if len(self.powderDict) == 0:
1279	self.G2frame.ErrorDialog(
1280	'Empty project',
1281	'Project does not contain any powder data.')
1282	return True
1283	elif len(self.powderDict) == 1:
1284	self.histnam = list(self.powderDict.values())
1285	elif self.multiple:
1286	choices = sorted(self.powderDict.values())
1287	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1288	if not hnum: return True
1289	self.histnam = [choices[i] for i in hnum]
1290	numselected = len(self.histnam)
1291	else:
1292	choices = sorted(self.powderDict.values())
1293	hnum = G2G.ItemSelector(choices,self.G2frame)
1294	if hnum is None: return True
1295	self.histnam = [choices[hnum]]
1296	numselected = len(self.histnam)
1297	elif self.currentExportType == 'sasd':
1298	if len(self.sasdDict) == 0:
1299	self.G2frame.ErrorDialog(
1300	'Empty project',
1301	'Project does not contain any small angle data.')
1302	return True
1303	elif len(self.sasdDict) == 1:
1304	self.histnam = self.sasdDict.values()
1305	elif self.multiple:
1306	choices = sorted(self.sasdDict.values())
1307	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1308	if not hnum: return True
1309	self.histnam = [choices[i] for i in hnum]
1310	numselected = len(self.histnam)
1311	else:
1312	choices = sorted(self.sasdDict.values())
1313	hnum = G2G.ItemSelector(choices,self.G2frame)
1314	if hnum is None: return True
1315	self.histnam = [choices[hnum]]
1316	numselected = len(self.histnam)
1317	elif self.currentExportType == 'refd':
1318	if len(self.refdDict) == 0:
1319	self.G2frame.ErrorDialog(
1320	'Empty project',
1321	'Project does not contain any reflectivity data.')
1322	return True
1323	elif len(self.refdDict) == 1:
1324	self.histnam = self.refdDict.values()
1325	elif self.multiple:
1326	choices = sorted(self.refdDict.values())
1327	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1328	if not hnum: return True
1329	self.histnam = [choices[i] for i in hnum]
1330	numselected = len(self.histnam)
1331	else:
1332	choices = sorted(self.refdDict.values())
1333	hnum = G2G.ItemSelector(choices,self.G2frame)
1334	if hnum is None: return True
1335	self.histnam = [choices[hnum]]
1336	numselected = len(self.histnam)
1337	elif self.currentExportType == 'image':
1338	if len(self.Histograms) == 0:
1339	self.G2frame.ErrorDialog(
1340	'Empty project',
1341	'Project does not contain any images.')
1342	return True
1343	elif len(self.Histograms) == 1:
1344	self.histnam = list(self.Histograms.keys())
1345	else:
1346	choices = sorted(self.Histograms.keys())
1347	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1348	if self.multiple:
1349	if not hnum: return True
1350	self.histnam = [choices[i] for i in hnum]
1351	else:
1352	if hnum is None: return True
1353	self.histnam = [choices[hnum]]
1354	numselected = len(self.histnam)
1355	if self.currentExportType == 'map':
1356	# search for phases with maps
1357	mapPhases = []
1358	choices = []
1359	for phasenam in sorted(self.Phases):
1360	phasedict = self.Phases[phasenam] # pointer to current phase info
1361	if len(phasedict['General']['Map'].get('rho',[])):
1362	mapPhases.append(phasenam)
1363	if phasedict['General']['Map'].get('Flip'):
1364	choices.append('Charge flip map: '+str(phasenam))
1365	elif phasedict['General']['Map'].get('MapType'):
1366	choices.append(
1367	str(phasedict['General']['Map'].get('MapType'))
1368	+ ' map: ' + str(phasenam))
1369	else:
1370	choices.append('unknown map: '+str(phasenam))
1371	# select a map if needed
1372	if len(mapPhases) == 0:
1373	self.G2frame.ErrorDialog(
1374	'Empty project',
1375	'Project does not contain any maps.')
1376	return True
1377	elif len(mapPhases) == 1:
1378	self.phasenam = mapPhases
1379	else:
1380	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1381	if self.multiple:
1382	if not phasenum: return True
1383	self.phasenam = [mapPhases[i] for i in phasenum]
1384	else:
1385	if phasenum is None: return True
1386	self.phasenam = [mapPhases[phasenum]]
1387	numselected = len(self.phasenam)
1388
1389	# items selected, now set self.dirname and usually self.filename
1390	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
1391	AskFile == 'default' and not self.G2frame.GSASprojectfile
1392	):
1393	filename = self.askSaveFile()
1394	if not filename: return True
1395	self.dirname,self.filename = os.path.split(filename)
1396	elif AskFile == 'dir' or AskFile == 'single' or (
1397	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
1398	):
1399	self.dirname = self.askSaveDirectory()
1400	if not self.dirname: return True
1401	elif AskFile == 'default-dir' or AskFile == 'default':
1402	self.dirname,self.filename = os.path.split(
1403	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
1404	)
1405	else:
1406	raise Exception('This should not happen!')
1407
1408	def loadParmDict(self):
1409	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
1410	refined values to those from the last cycle and set the uncertainties for the
1411	refined parameters in another dict (self.sigDict).
1412
1413	Expands the parm & sig dicts to include values derived from constraints.
1414
1415	This could be made faster for sequential fits by reducing the histogram list to only
1416	the active histogram being exported.
1417	'''
1418	self.G2frame.CheckNotebook()
1419	self.parmDict = {}
1420	self.sigDict = {}
1421	rigidbodyDict = {}
1422	covDict = {}
1423	consDict = {}
1424	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1425	if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1426	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1427	while item:
1428	name = self.G2frame.GPXtree.GetItemText(item)
1429	if name == 'Rigid bodies':
1430	rigidbodyDict = self.G2frame.GPXtree.GetItemPyData(item)
1431	elif name == 'Covariance':
1432	covDict = self.G2frame.GPXtree.GetItemPyData(item)
1433	elif name == 'Constraints':
1434	consDict = self.G2frame.GPXtree.GetItemPyData(item)
1435	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1436	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1437	self.parmDict.update(rbDict)
1438	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1439	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData(
1440	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
1441	self.parmDict.update(phaseDict)
1442	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
1443	Phases,Histograms,Print=False,resetRefList=False)
1444	self.parmDict.update(hapDict)
1445	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
1446	self.parmDict.update(histDict)
1447	self.parmDict.update(zip(
1448	covDict.get('varyList',[]),
1449	covDict.get('variables',[])))
1450	self.sigDict = dict(zip(
1451	covDict.get('varyList',[]),
1452	covDict.get('sig',[])))
1453	# expand to include constraints: first compile a list of constraints
1454	constList = []
1455	for item in consDict:
1456	if item.startswith('_'): continue
1457	constList += consDict[item]
1458	# now process the constraints
1459	G2mv.InitVars()
1460	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
1461	varyList = covDict.get('varyListStart')
1462	if varyList is None and len(constDict) == 0:
1463	# no constraints can use varyList
1464	varyList = covDict.get('varyList')
1465	elif varyList is None:
1466	# old GPX file from before pre-constraint varyList is saved
1467	print (' * Old refinement: Please use Calculate/Refine to redo *')
1468	raise Exception(' * Export aborted *')
1469	else:
1470	varyList = list(varyList)
1471	# add symmetry-generated constraints
1472	rigidbodyDict = self.G2frame.GPXtree.GetItemPyData(
1473	G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,'Rigid bodies'))
1474	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1475	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1476	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData(
1477	Phases,RestraintDict=None,rbIds=rbIds,Print=False) # generates atom symmetry constraints
1478	msg = G2mv.EvaluateMultipliers(constDict,phaseDict)
1479	if msg:
1480	print('Unable to interpret multiplier(s): '+msg)
1481	raise Exception(' * CIF creation aborted *')
1482	try:
1483	G2mv.GenerateConstraints(varyList,constDict,fixedList,self.parmDict)
1484	#print(G2mv.VarRemapShow(varyList))
1485	except:
1486	# this really should not happen
1487	print (' * ERROR - constraints are internally inconsistent *')
1488	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
1489	print ('Errors'+errmsg)
1490	if warnmsg: print ('Warnings'+warnmsg)
1491	raise Exception(' * CIF creation aborted *')
1492	# add the constrained values to the parameter dictionary
1493	G2mv.Dict2Map(self.parmDict,varyList)
1494	# and add their uncertainties into the esd dictionary (sigDict)
1495	if covDict.get('covMatrix') is not None:
1496	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
1497
1498	def loadTree(self):
1499	'''Load the contents of the data tree into a set of dicts
1500	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
1501	& self.xtalDict)
1502
1503	* The childrenless data tree items are overall parameters/controls for the
1504	entire project and are placed in self.OverallParms
1505	* Phase items are placed in self.Phases
1506	* Data items are placed in self.Histogram. The key for these data items
1507	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
1508	'''
1509	self.OverallParms = {}
1510	self.powderDict = {}
1511	self.sasdDict = {}
1512	self.refdDict = {}
1513	self.xtalDict = {}
1514	self.Phases = {}
1515	self.Histograms = {}
1516	self.SeqRefdata = None
1517	self.SeqRefhist = None
1518	if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1519	histType = None
1520	if self.currentExportType == 'phase':
1521	# if exporting phases load them here
1522	sub = G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,'Phases')
1523	if not sub:
1524	print ('no phases found')
1525	return True
1526	item, cookie = self.G2frame.GPXtree.GetFirstChild(sub)
1527	while item:
1528	phaseName = self.G2frame.GPXtree.GetItemText(item)
1529	self.Phases[phaseName] = self.G2frame.GPXtree.GetItemPyData(item)
1530	item, cookie = self.G2frame.GPXtree.GetNextChild(sub, cookie)
1531	return
1532	elif self.currentExportType == 'single':
1533	histType = 'HKLF'
1534	elif self.currentExportType == 'powder':
1535	histType = 'PWDR'
1536	elif self.currentExportType == 'image':
1537	histType = 'IMG'
1538	elif self.currentExportType == 'sasd':
1539	histType = 'SASD'
1540	elif self.currentExportType == 'refd':
1541	histType = 'REFD'
1542
1543	if histType: # Loading just one kind of tree entry
1544	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1545	while item:
1546	name = self.G2frame.GPXtree.GetItemText(item)
1547	if name.startswith(histType):
1548	if self.Histograms.get(name): # there is already an item with this name
1549	print('Histogram name '+str(name)+' is repeated. Renaming')
1550	if name[-1] == '9':
1551	name = name[:-1] + '10'
1552	elif name[-1] in '012345678':
1553	name = name[:-1] + str(int(name[-1])+1)
1554	else:
1555	name += '-1'
1556	self.Histograms[name] = {}
1557	# the main info goes into Data, but the 0th
1558	# element contains refinement results, carry
1559	# that over too now.
1560	self.Histograms[name]['Data'] = self.G2frame.GPXtree.GetItemPyData(item)[1]
1561	self.Histograms[name][0] = self.G2frame.GPXtree.GetItemPyData(item)[0]
1562	item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1563	while item2:
1564	child = self.G2frame.GPXtree.GetItemText(item2)
1565	self.Histograms[name][child] = self.G2frame.GPXtree.GetItemPyData(item2)
1566	item2, cookie2 = self.G2frame.GPXtree.GetNextChild(item, cookie2)
1567	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1568	# index powder and single crystal histograms by number
1569	for hist in self.Histograms:
1570	if hist.startswith("PWDR"):
1571	d = self.powderDict
1572	elif hist.startswith("HKLF"):
1573	d = self.xtalDict
1574	elif hist.startswith("SASD"):
1575	d = self.sasdDict
1576	elif hist.startswith("REFD"):
1577	d = self.refdDict
1578	else:
1579	return
1580	i = self.Histograms[hist].get('hId')
1581	if i is None and not d.keys():
1582	i = 0
1583	elif i is None or i in d.keys():
1584	i = max(d.keys())+1
1585	d[i] = hist
1586	return
1587	# else standard load: using all interlinked phases and histograms
1588	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1589	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1590	while item:
1591	name = self.G2frame.GPXtree.GetItemText(item)
1592	item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1593	if not item2:
1594	self.OverallParms[name] = self.G2frame.GPXtree.GetItemPyData(item)
1595	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1596	# index powder and single crystal histograms
1597	for hist in self.Histograms:
1598	i = self.Histograms[hist]['hId']
1599	if hist.startswith("PWDR"):
1600	self.powderDict[i] = hist
1601	elif hist.startswith("HKLF"):
1602	self.xtalDict[i] = hist
1603	elif hist.startswith("SASD"):
1604	self.sasdDict[i] = hist
1605	elif hist.startswith("REFD"):
1606	self.refdDict[i] = hist
1607
1608	def dumpTree(self,mode='type'):
1609	'''Print out information on the data tree dicts loaded in loadTree.
1610	Used for testing only.
1611	'''
1612	if self.SeqRefdata and self.SeqRefhist:
1613	print('Note that dumpTree does not show sequential results')
1614	print ('\nOverall')
1615	if mode == 'type':
1616	def Show(arg): return type(arg)
1617	else:
1618	def Show(arg): return arg
1619	for key in self.OverallParms:
1620	print (' '+key+Show(self.OverallParms[key]))
1621	print ('Phases')
1622	for key1 in self.Phases:
1623	print (' '+key1+Show(self.Phases[key1]))
1624	print ('Histogram')
1625	for key1 in self.Histograms:
1626	print (' '+key1+Show(self.Histograms[key1]))
1627	for key2 in self.Histograms[key1]:
1628	print (' '+key2+Show(self.Histograms[key1][key2]))
1629
1630	def defaultSaveFile(self):
1631	return os.path.abspath(
1632	os.path.splitext(self.G2frame.GSASprojectfile
1633	)[0]+self.extension)
1634
1635	def askSaveFile(self):
1636	'''Ask the user to supply a file name
1637
1638	:returns: a file name (str) or None if Cancel is pressed
1639
1640	'''
1641	#pth = G2G.GetExportPath(self.G2frame)
1642	if self.G2frame.GSASprojectfile:
1643	defnam = os.path.splitext(
1644	os.path.split(self.G2frame.GSASprojectfile)[1]
1645	)[0]+self.extension
1646	else:
1647	defnam = 'default' + self.extension
1648	return G2G.askSaveFile(self.G2frame,defnam,self.extension,self.longFormatName)
1649
1650	def askSaveDirectory(self):
1651	'''Ask the user to supply a directory name. Path name is used as the
1652	starting point for the next export path search.
1653
1654	:returns: a directory name (str) or None if Cancel is pressed
1655
1656	TODO: Can this be replaced with G2G.askSaveDirectory?
1657	'''
1658	pth = G2G.GetExportPath(self.G2frame)
1659	dlg = wx.DirDialog(
1660	self.G2frame, 'Input directory where file(s) will be written', pth,
1661	wx.DD_DEFAULT_STYLE)
1662	dlg.CenterOnParent()
1663	try:
1664	if dlg.ShowModal() == wx.ID_OK:
1665	filename = dlg.GetPath()
1666	self.G2frame.LastExportDir = filename
1667	else:
1668	filename = None
1669	finally:
1670	dlg.Destroy()
1671	return filename
1672
1673	# Tools for file writing.
1674	def OpenFile(self,fil=None,mode='w'):
1675	'''Open the output file
1676
1677	:param str fil: The name of the file to open. If None (default)
1678	the name defaults to self.dirname + self.filename.
1679	If an extension is supplied, it is not overridded,
1680	but if not, the default extension is used.
1681	:returns: the file object opened by the routine which is also
1682	saved as self.fp
1683	'''
1684	if mode == 'd': # debug mode
1685	self.fullpath = '(stdout)'
1686	self.fp = sys.stdout
1687	return
1688	if not fil:
1689	if not os.path.splitext(self.filename)[1]:
1690	self.filename += self.extension
1691	fil = os.path.join(self.dirname,self.filename)
1692	self.fullpath = os.path.abspath(fil)
1693	self.fp = open(self.fullpath,mode)
1694	return self.fp
1695
1696	def Write(self,line):
1697	'''write a line of output, attaching a line-end character
1698
1699	:param str line: the text to be written.
1700	'''
1701	self.fp.write(line+'\n')
1702
1703	def CloseFile(self,fp=None):
1704	'''Close a file opened in OpenFile
1705
1706	:param file fp: the file object to be closed. If None (default)
1707	file object self.fp is closed.
1708	'''
1709	if self.fp == sys.stdout: return # debug mode
1710	if fp is None:
1711	fp = self.fp
1712	self.fp = None
1713	if fp is not None: fp.close()
1714
1715	def SetSeqRef(self,data,hist):
1716	'''Set the exporter to retrieve results from a sequential refinement
1717	rather than the main tree
1718	'''
1719	self.SeqRefdata = data
1720	self.SeqRefhist = hist
1721	data_name = data[hist]
1722	for i,val in zip(data_name['varyList'],data_name['sig']):
1723	self.sigDict[i] = val
1724	self.sigDict[striphist(i)] = val
1725	for i in data_name['parmDict']:
1726	self.parmDict[striphist(i)] = data_name['parmDict'][i]
1727	self.parmDict[i] = data_name['parmDict'][i]
1728	# zero out the dA[xyz] terms, they would only bring confusion
1729	key = i.split(':')
1730	if len(key) < 3: continue
1731	if key[2].startswith('dA'):
1732	self.parmDict[i] = 0.0
1733	for i,(val,sig) in data_name.get('depParmDict',{}).items():
1734	self.parmDict[i] = val
1735	self.sigDict[i] = sig
1736	#GSASIIpath.IPyBreak()
1737
1738	# Tools to pull information out of the data arrays
1739	def GetCell(self,phasenam):
1740	"""Gets the unit cell parameters and their s.u.'s for a selected phase
1741
1742	:param str phasenam: the name for the selected phase
1743	:returns: `cellList,cellSig` where each is a 7 element list corresponding
1744	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1745	cell values and `cellSig` has their uncertainties.
1746	"""
1747	if self.SeqRefdata and self.SeqRefhist:
1748	return self.GetSeqCell(phasenam,self.SeqRefdata[self.SeqRefhist])
1749	phasedict = self.Phases[phasenam] # pointer to current phase info
1750	try:
1751	pfx = str(phasedict['pId'])+'::'
1752	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
1753	cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A,
1754	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
1755	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
1756	return cellList,cellSig
1757	except KeyError:
1758	cell = phasedict['General']['Cell'][1:]
1759	return cell,7*[0]
1760
1761	def GetSeqCell(self,phasenam,data_name):
1762	"""Gets the unit cell parameters and their s.u.'s for a selected phase
1763	and histogram in a sequential fit
1764
1765	:param str phasenam: the name for the selected phase
1766	:param dict data_name: the sequential refinement parameters for the selected histogram
1767	:returns: `cellList,cellSig` where each is a 7 element list corresponding
1768	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1769	cell values and `cellSig` has their uncertainties.
1770	"""
1771	phasedict = self.Phases[phasenam]
1772	SGdata = phasedict['General']['SGData']
1773	pId = phasedict['pId']
1774	RecpCellTerms = G2lat.cell2A(phasedict['General']['Cell'][1:7])
1775	ESDlookup = {}
1776	Dlookup = {}
1777	varied = [striphist(i) for i in data_name['varyList']]
1778	for item,val in data_name['newCellDict'].items():
1779	if item in varied:
1780	ESDlookup[val[0]] = item
1781	Dlookup[item] = val[0]
1782	A = RecpCellTerms[:]
1783	for i in range(6):
1784	var = str(pId)+'::A'+str(i)
1785	if var in ESDlookup:
1786	A[i] = data_name['newCellDict'][ESDlookup[var]][1] # override with refined value
1787	cellDict = dict(zip([str(pId)+'::A'+str(i) for i in range(6)],A))
1788	zeroDict = {i:0.0 for i in cellDict}
1789	A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata,cellDict,zeroDict)
1790	covData = {
1791	'varyList': [Dlookup.get(striphist(v),v) for v in data_name['varyList']],
1792	'covMatrix': data_name['covMatrix']
1793	}
1794	return list(G2lat.A2cell(A)) + [G2lat.calc_V(A)], G2stIO.getCellEsd(str(pId)+'::',SGdata,A,covData)
1795
1796	def GetAtoms(self,phasenam):
1797	"""Gets the atoms associated with a phase. Can be used with standard
1798	or macromolecular phases
1799
1800	:param str phasenam: the name for the selected phase
1801	:returns: a list of items for eac atom where each item is a list containing:
1802	label, typ, mult, xyz, and td, where
1803
1804	* label and typ are the atom label and the scattering factor type (str)
1805	* mult is the site multiplicity (int)
1806	* xyz is contains a list with four pairs of numbers:
1807	x, y, z and fractional occupancy and
1808	their standard uncertainty (or a negative value)
1809	* td is contains a list with either one or six pairs of numbers:
1810	if one number it is U\ :sub:`iso` and with six numbers it is
1811	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
1812	paired with their standard uncertainty (or a negative value)
1813	"""
1814	phasedict = self.Phases[phasenam] # pointer to current phase info
1815	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
1816	cfrac = cx+3
1817	fpfx = str(phasedict['pId'])+'::Afrac:'
1818	atomslist = []
1819	for i,at in enumerate(phasedict['Atoms']):
1820	if phasedict['General']['Type'] == 'macromolecular':
1821	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
1822	else:
1823	label = at[ct-1]
1824	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
1825	fsig = self.sigDict.get(fpfx+str(i),-0.009)
1826	mult = at[cs+1]
1827	typ = at[ct]
1828	xyz = []
1829	for j,v in enumerate(('x','y','z')):
1830	val = at[cx+j]
1831	pfx = str(phasedict['pId']) + '::A' + v + ':' + str(i)
1832	val = self.parmDict.get(pfx, val)
1833	dpfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
1834	sig = self.sigDict.get(dpfx,-0.000009)
1835	xyz.append((val,sig))
1836	xyz.append((fval,fsig))
1837	td = []
1838	if at[cia] == 'I':
1839	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
1840	val = self.parmDict.get(pfx,at[cia+1])
1841	sig = self.sigDict.get(pfx,-0.0009)
1842	td.append((val,sig))
1843	else:
1844	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
1845	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
1846	val = self.parmDict.get(pfx,at[cia+2+i])
1847	sig = self.sigDict.get(pfx,-0.0009)
1848	td.append((val,sig))
1849	atomslist.append((label,typ,mult,xyz,td))
1850	return atomslist
1851	######################################################################
1852	def ExportPowderList(G2frame):
1853	'''Returns a list of extensions supported by :func:`GSASIIIO:ExportPowder`
1854	along with their descriptions (note that a extension may be repeated
1855	but descriptions are unique).
1856	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
1857
1858	:param wx.Frame G2frame: the GSAS-II main data tree window
1859	'''
1860	extList = []
1861	extLabel = []
1862	for obj in G2frame.exporterlist:
1863	if 'powder' in obj.exporttype:
1864	try:
1865	obj.Writer
1866	extList.append(obj.extension)
1867	extLabel.append(obj.formatName)
1868	except AttributeError:
1869	pass
1870	return extList,extLabel
1871
1872	def ExportPowder(G2frame,TreeName,fileroot,extension,hint=''):
1873	'''Writes a single powder histogram using the Export routines.
1874	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
1875
1876	:param wx.Frame G2frame: the GSAS-II main data tree window
1877	:param str TreeName: the name of the histogram (PWDR ...) in the data tree
1878	:param str fileroot: name for file to be written, extension ignored
1879	:param str extension: extension for file to be written (start with '.'). Must
1880	match a powder export routine that has a Writer object.
1881	:param str hint: a string that must match the export's format
1882	'''
1883	filename = os.path.abspath(os.path.splitext(fileroot)[0]+extension)
1884	for obj in G2frame.exporterlist:
1885	if obj.extension == extension and 'powder' in obj.exporttype:
1886	if hint and hint not in obj.formatName: continue
1887	obj.currentExportType = 'powder'
1888	obj.InitExport(None)
1889	obj.loadTree() # load all histograms in tree into dicts
1890	if TreeName not in obj.Histograms:
1891	raise Exception('Histogram not found: '+str(TreeName))
1892	try:
1893	obj.Writer
1894	except AttributeError:
1895	continue
1896	try:
1897	obj.Writer(TreeName,filename)
1898	print('wrote file '+filename)
1899	return
1900	except Exception:
1901	print('Export Routine for '+extension+' failed.')
1902	else:
1903	print('No Export routine supports extension '+extension)
1904
1905	def ExportSequential(G2frame,data,obj,exporttype):
1906	'''
1907	Used to export from every phase/dataset in a sequential refinement using
1908	a .Writer method for either projects or phases. Prompts to select histograms
1909	and for phase exports, which phase(s).
1910
1911	:param wx.Frame G2frame: the GSAS-II main data tree window
1912	:param dict data: the sequential refinement data object
1913	:param str exporttype: indicates the type of export ('project' or 'phase')
1914	'''
1915	if len(data['histNames']) == 0:
1916	G2G.G2MessageBox(G2frame,'There are no sequential histograms','Warning')
1917	obj.InitExport(None)
1918	obj.loadTree()
1919	obj.loadParmDict()
1920	if len(data['histNames']) == 1:
1921	histlist = data['histNames']
1922	else:
1923	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select histograms to export from list',
1924	'Select histograms',data['histNames'])
1925	if dlg.ShowModal() == wx.ID_OK:
1926	histlist = [data['histNames'][l] for l in dlg.GetSelections()]
1927	dlg.Destroy()
1928	else:
1929	dlg.Destroy()
1930	return
1931	if exporttype == 'Phase':
1932	phaselist = list(obj.Phases.keys())
1933	if len(obj.Phases) == 0:
1934	G2G.G2MessageBox(G2frame,'There are no phases in sequential ref.','Warning')
1935	return
1936	elif len(obj.Phases) > 1:
1937	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select phases to export from list',
1938	'Select phases', phaselist)
1939	if dlg.ShowModal() == wx.ID_OK:
1940	phaselist = [phaselist[l] for l in dlg.GetSelections()]
1941	dlg.Destroy()
1942	else:
1943	dlg.Destroy()
1944	return
1945	filename = obj.askSaveFile()
1946	if not filename: return True
1947	obj.dirname,obj.filename = os.path.split(filename)
1948	print('Writing output to file '+str(obj.filename)+"...")
1949	mode = 'w'
1950	for p in phaselist:
1951	for h in histlist:
1952	obj.SetSeqRef(data,h)
1953	#GSASIIpath.IPyBreak()
1954	obj.Writer(h,phasenam=p,mode=mode)
1955	mode = 'a'
1956	print('...done')
1957	elif exporttype == 'Project': # note that the CIF exporter is not yet ready for this
1958	filename = obj.askSaveFile()
1959	if not filename: return True
1960	obj.dirname,obj.filename = os.path.split(filename)
1961	print('Writing output to file '+str(obj.filename)+"...")
1962	mode = 'w'
1963	for h in histlist:
1964	obj.SetSeqRef(data,h)
1965	obj.Writer(h,mode=mode)
1966	print('\t'+str(h)+' written')
1967	mode = 'a'
1968	print('...done')
1969	elif exporttype == 'Powder':
1970	filename = obj.askSaveFile()
1971	if not filename: return True
1972	obj.dirname,obj.filename = os.path.split(filename)
1973	print('Writing output to file '+str(obj.filename)+"...")
1974	mode = 'w'
1975	for h in histlist:
1976	obj.SetSeqRef(data,h)
1977	obj.Writer(h,mode=mode)
1978	print('\t'+str(h)+' written')
1979	mode = 'a'
1980	print('...done')
1981
1982	def ReadDIFFaX(DIFFaXfile):
1983	print ('read '+DIFFaXfile)
1984	Layer = {'Laue':'-1','Cell':[False,1.,1.,1.,90.,90.,90,1.],'Width':[[10.,10.],[False,False]],
1985	'Layers':[],'Stacking':[],'Transitions':[],'Toler':0.01,'AtInfo':{}}
1986	df = open(DIFFaXfile,'r')
1987	lines = df.readlines()
1988	df.close()
1989	struct = False
1990	Struct = []
1991	stack = False
1992	Stack = []
1993	trans = False
1994	Trans = []
1995	for diff in lines:
1996	diff = diff[:-1].lower()
1997	if '!' in diff:
1998	continue
1999	while '}' in diff: #strip comments
2000	iB = diff.index('{')
2001	iF = diff.index('}')+1
2002	if iB:
2003	diff = diff[:iB]
2004	else:
2005	diff = diff[iF:]
2006	if not diff:
2007	continue
2008	if diff.strip() == 'instrumental':
2009	continue
2010	if diff.strip() == 'structural':
2011	struct = True
2012	continue
2013	elif diff.strip() == 'stacking':
2014	struct = False
2015	stack = True
2016	continue
2017	elif diff.strip() == 'transitions':
2018	stack = False
2019	trans = True
2020	continue
2021	diff = diff.strip()
2022	if struct:
2023	if diff:
2024	Struct.append(diff)
2025	elif stack:
2026	if diff:
2027	Stack.append(diff)
2028	elif trans:
2029	if diff:
2030	Trans.append(diff)
2031
2032	#STRUCTURE records
2033	laueRec = Struct[1].split()
2034	Layer['Laue'] = laueRec[0]
2035	if Layer['Laue'] == 'unknown' and len(laueRec) > 1:
2036	Layer['Toler'] = float(laueRec[1]) #tolerance for 'unknown'?
2037	if Layer['Laue'] == '2/m(1)': Layer['Laue'] = '2/m(c)'
2038	if Layer['Laue'] == '2/m(2)': Layer['Laue'] = '2/m(ab)'
2039	cell = Struct[0].split()
2040	Layer['Cell'] = [False,float(cell[0]),float(cell[1]),float(cell[2]),90.,90.,float(cell[3]),1.0]
2041	nLayers = int(Struct[2])
2042	N = 3
2043	if 'layer' not in Struct[3]:
2044	N = 4
2045	if Struct[3] != 'infinite':
2046	width = Struct[3].split()
2047	Layer['Width'][0] = [float(width[0]),float(width[1])]
2048	for nL in range(nLayers):
2049	if '=' in Struct[N]:
2050	name = Struct[N].split('=')
2051	sameas = int(name[1])-1
2052	Layer['Layers'].append({'Name':name[0],'SameAs':Layer['Layers'][sameas]['Name'],'Symm':'None','Atoms':[]})
2053	N += 1
2054	continue
2055	Symm = 'None'
2056	if 'centro' in Struct[N+1]: Symm = '-1'
2057	Layer['Layers'].append({'Name':Struct[N],'SameAs':'','Symm':Symm,'Atoms':[]})
2058	N += 2
2059	while 'layer' not in Struct[N]:
2060	atom = Struct[N][4:].split()
2061	atomType = G2el.FixValence(Struct[N][:4].replace(' ','').strip().capitalize())
2062	if atomType not in Layer['AtInfo']:
2063	Layer['AtInfo'][atomType] = G2el.GetAtomInfo(atomType)
2064	atomName = '%s(%s)'%(atomType,atom[0])
2065	newVals = []
2066	for val in atom[1:6]:
2067	if '/' in val:
2068	newVals.append(eval(val+'.'))
2069	else:
2070	newVals.append(float(val))
2071	atomRec = [atomName,atomType,newVals[0],newVals[1],newVals[2],newVals[4],newVals[3]/78.9568]
2072	Layer['Layers'][-1]['Atoms'].append(atomRec)
2073	N += 1
2074	if N > len(Struct)-1:
2075	break
2076	#TRANSITIONS records
2077	transArray = []
2078	N = 0
2079	for i in range(nLayers):
2080	transArray.append([])
2081	for j in range(nLayers):
2082	vals = Trans[N].split()
2083	newVals = []
2084	for val in vals[:4]:
2085	if '/' in val:
2086	newVals.append(eval(val+'.'))
2087	else:
2088	newVals.append(float(val))
2089	transArray[-1].append(newVals+['',False])
2090	N += 1
2091	Layer['Transitions'] = transArray
2092	#STACKING records
2093	Layer['Stacking'] = [Stack[0],'']
2094	if Stack[0] == 'recursive':
2095	Layer['Stacking'][1] = Stack[1]
2096	elif Stack[0] == 'explicit':
2097	if Stack[1] == 'random':
2098	Layer['Stacking'][1] = Stack[1]
2099	else:
2100	Layer['Stacking'][1] = 'list'
2101	Layer['Stacking'].append('')
2102	for stack in Stack[2:]:
2103	Layer['Stacking'][2] += ' '+stack
2104	return Layer
2105
2106	def postURL(URL,postdict):
2107	'''Posts a set of values as from a web form. If access fails to an https
2108	site the access is retried with http.
2109
2110	:param str URL: the URL to post; typically something
2111	like 'http://www.../dir/page?'
2112	:param dict postdict: contains keywords and values, such
2113	as {'centrosymmetry': '0', 'crystalsystem': '0', ...}
2114	:returns: a string with the response from the web server or None
2115	if access fails.
2116	'''
2117	try:
2118	import requests # delay this until now, since rarely needed
2119	except:
2120	# this import seems to fail with the Anaconda pythonw on
2121	# macs; it should not!
2122	print('Warning: failed to import requests. Python config error')
2123	return None
2124
2125	repeat = True
2126	while repeat:
2127	r = None
2128	repeat = False
2129	try:
2130	r = requests.get(URL,params=postdict)
2131	if r.status_code == 200:
2132	print('request OK')
2133	page = r.text
2134	return page # success
2135	else:
2136	print('request to {} failed. Reason={}'.format(URL,r.reason))
2137	except Exception as msg: #ConnectionError?
2138	print('connection error - not on internet?')
2139	if GSASIIpath.GetConfigValue('debug'): print(msg)
2140	finally:
2141	if r: r.close()
2142	if URL.startswith('https:'):
2143	repeat = True
2144	URL = URL.replace('https:','http:')
2145	else:
2146	return None
2147
2148	if __name__ == '__main__':
2149	import GSASIIdataGUI
2150	application = GSASIIdataGUI.GSASIImain(0)
2151	G2frame = application.main
2152	#app = wx.PySimpleApp()
2153	#G2frame = wx.Frame(None) # create a frame
2154	#frm.Show(True)
2155	#filename = '/tmp/notzip.zip'
2156	#filename = '/tmp/all.zip'
2157	#filename = '/tmp/11bmb_7652.zip'
2158
2159	#selection=None, confirmoverwrite=True, parent=None
2160	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2161	#print ExtractFileFromZip(filename,multipleselect=True)
2162	# #confirmread=False, confirmoverwrite=False)
2163
2164	# choicelist=[ ('a','b','c'),
2165	# ('test1','test2'),('no choice',)]
2166	# titles = [ 'a, b or c', 'tests', 'No option here']
2167	# dlg = MultipleChoicesDialog(
2168	# choicelist,titles,
2169	# parent=frm)
2170	# if dlg.ShowModal() == wx.ID_OK:
2171	# print 'Got OK'
2172	imagefile = '/tmp/NDC5_00237_3.ge3'
2173	Comments, Data, Npix, Image = GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None)
2174
2175	print("\n\nResults loaded to Comments, Data, Npix and Image\n\n")
2176
2177	GSASIIpath.IPyBreak_base()

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