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source: trunk/GSASIIIO.py @ 4619

Last change on this file since 4619 was 4619, checked in by vondreele, 2 years ago
Add pink beam check box to image data GUI When selected, integration will set inst parms to pink beam defaults based on Sector 35 LSS data
Property svn:eol-style set to `native` Property svn:keywords set to `Date Author Revision URL Id`
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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2020-10-23 14:53:06 +0000 (Fri, 23 Oct 2020) $
4	# $Author: vondreele $
5	# $Revision: 4619 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 4619 2020-10-23 14:53:06Z 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: 4619 $")
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	if data.get('IfPink',False):
845	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','Z','alpha-0','alpha-1','beta-0','beta-1','Azimuth']
846	codes = [0 for i in range(15)]
847	else:
848	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth']
849	codes = [0 for i in range(12)]
850	elif 'SASD' in name:
851	names = ['Type','Lam','Zero','Azimuth']
852	codes = [0 for i in range(4)]
853	X = 4.np.pinpsind(X/2.)/data['wavelength'] #convert to q
854	Xminmax = [X[0],X[-1]]
855	Azms = np.zeros(data['outAzimuths'])
856	dazm = 0.
857	if data['outAzimuths'] > 1:
858	dazm = np.min(np.abs(np.diff(azms)))/2.
859	G2frame.IntgOutList = []
860	for i,azm in enumerate(azms[:-1]):
861	Aname = name+" Azm= %.2f"%((azm+dazm)%360.)
862	item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
863	# if Overwrite delete any duplicate
864	if Overwrite and G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname):
865	print('Replacing '+Aname)
866	item = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname)
867	G2frame.GPXtree.Delete(item)
868	else:
869	nOcc = 0
870	while item:
871	Name = G2frame.GPXtree.GetItemText(item)
872	if Aname in Name:
873	nOcc += 1
874	item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
875	if nOcc:
876	Aname += '(%d)'%(nOcc)
877	Sample = G2obj.SetDefaultSample() #set as Debye-Scherrer
878	Sample['Gonio. radius'] = data['distance']
879	Sample['Omega'] = data['GonioAngles'][0]
880	Sample['Chi'] = data['GonioAngles'][1]
881	Sample['Phi'] = data['GonioAngles'][2]
882	Sample['Azimuth'] = (azm+dazm)%360. #put here as bin center
883	polariz = data['PolaVal'][0]
884	for item in Comments:
885	for key in ('Temperature','Pressure','Time','FreePrm1','FreePrm2','FreePrm3','Omega',
886	'Chi','Phi'):
887	if key.lower() in item.lower():
888	try:
889	Sample[key] = float(item.split('=')[1])
890	except:
891	pass
892	if 'label_prm' in item.lower():
893	for num in ('1','2','3'):
894	if 'label_prm'+num in item.lower():
895	Controls['FreePrm'+num] = item.split('=')[1].strip()
896	if 'PWDR' in Aname:
897	if 'target' in data: #from lab x-ray 2D imaging data
898	wave1,wave2 = waves[data['target']]
899	parms = ['PXC',wave1,wave2,0.5,0.0,polariz,290.,-40.,30.,6.,-14.,0.0,0.0001,Azms[i]]
900	else:
901	if data.get('IfPink',False):
902	parms = ['PXB',data['wavelength'],0.0,polariz,0.,8000.,-150.,-24.,0.,0.,0.,13.,-1300.,3.,-7.,Azms[i]] #from Sect 35 LSS
903	else:
904	parms = ['PXC',data['wavelength'],0.0,polariz,1.0,-0.10,0.4,0.30,1.0,0.0,0.0001,Azms[i]]
905	elif 'SASD' in Aname:
906	Sample['Trans'] = data['SampleAbs'][0]
907	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
908	Y = G2frame.Integrate[0][i]
909	Ymin = np.min(Y)
910	Ymax = np.max(Y)
911	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
912	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=Aname)
913	G2frame.IntgOutList.append(Id)
914	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments)
915	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Limits'),copy.deepcopy([tuple(Xminmax),Xminmax]))
916	if 'PWDR' in Aname:
917	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Background'),[['chebyschev-1',1,3,1.0,0.0,0.0],
918	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
919	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
920	for item in inst[0]:
921	inst[0][item] = list(inst[0][item])
922	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Instrument Parameters'),inst)
923	if 'PWDR' in Aname:
924	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample)
925	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
926	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Index Peak List'),[[],[]])
927	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Unit Cells List'),[])
928	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Reflection Lists'),{})
929	elif 'SASD' in Aname:
930	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
931	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample)
932	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
933	valuesdict = {
934	'wtFactor':1.0,'Dummy':False,'ranId':ran.randint(0,sys.maxsize),'Offset':[0.0,0.0],'delOffset':0.02*Ymax,
935	'refOffset':-0.1Ymax,'refDelt':0.1Ymax,'Yminmax':[Ymin,Ymax]}
936	G2frame.GPXtree.SetItemPyData(Id,[valuesdict,
937	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
938	return Id #last powder pattern generated
939
940	def XYsave(G2frame,XY,labelX='X',labelY='Y',names=[]):
941	'Save XY table data'
942	pth = G2G.GetExportPath(G2frame)
943	dlg = wx.FileDialog(
944	G2frame, 'Enter csv filename for XY table', pth, '',
945	'XY table file (.csv)\|.csv',wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
946	try:
947	if dlg.ShowModal() == wx.ID_OK:
948	filename = dlg.GetPath()
949	filename = os.path.splitext(filename)[0]+'.csv'
950	File = open(filename,'w')
951	else:
952	filename = None
953	finally:
954	dlg.Destroy()
955	if not filename:
956	return
957	for i in range(len(XY)):
958	if len(names):
959	header = '%s,%s(%s)\n'%(labelX,labelY,names[i])
960	else:
961	header = '%s,%s(%d)\n'%(labelX,labelY,i)
962	File.write(header)
963	for x,y in XY[i].T:
964	File.write('%.3f,%.3f\n'%(x,y))
965	File.close()
966	print (' XY data saved to: '+filename)
967
968	def PeakListSave(G2frame,file,peaks):
969	'Save powder peaks to a data file'
970	print ('save peak list to file: '+G2frame.peaklistfile)
971	if not peaks:
972	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
973	try:
974	dlg.ShowModal()
975	finally:
976	dlg.Destroy()
977	return
978	for peak in peaks:
979	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
980	(peak[0],peak[2],peak[4],peak[6]))
981	print ('peak list saved')
982
983	def IndexPeakListSave(G2frame,peaks):
984	'Save powder peaks from the indexing list'
985	file = open(G2frame.peaklistfile,'wa')
986	print ('save index peak list to file: '+G2frame.peaklistfile)
987	wx.BeginBusyCursor()
988	try:
989	if not peaks:
990	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
991	try:
992	dlg.ShowModal()
993	finally:
994	dlg.Destroy()
995	return
996	for peak in peaks:
997	file.write("%12.6f\n" % (peak[7]))
998	file.close()
999	finally:
1000	wx.EndBusyCursor()
1001	print ('index peak list saved')
1002
1003	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1004	confirmoverwrite=True, parent=None,
1005	multipleselect=False):
1006	'''If the filename is a zip file, extract a file from that
1007	archive.
1008
1009	:param list Selection: used to predefine the name of the file
1010	to be extracted. Filename case and zip directory name are
1011	ignored in selection; the first matching file is used.
1012
1013	:param bool confirmread: if True asks the user to confirm before expanding
1014	the only file in a zip
1015
1016	:param bool confirmoverwrite: if True asks the user to confirm
1017	before overwriting if the extracted file already exists
1018
1019	:param bool multipleselect: if True allows more than one zip
1020	file to be extracted, a list of file(s) is returned.
1021	If only one file is present, do not ask which one, otherwise
1022	offer a list of choices (unless selection is used).
1023
1024	:returns: the name of the file that has been created or a
1025	list of files (see multipleselect)
1026
1027	If the file is not a zipfile, return the name of the input file.
1028	If the zipfile is empty or no file has been selected, return None
1029	'''
1030	import zipfile # do this now, since we can save startup time by doing this only on need
1031	import shutil
1032	zloc = os.path.split(filename)[0]
1033	if not zipfile.is_zipfile(filename):
1034	#print("not zip")
1035	return filename
1036
1037	z = zipfile.ZipFile(filename,'r')
1038	zinfo = z.infolist()
1039
1040	if len(zinfo) == 0:
1041	#print('Zip has no files!')
1042	zlist = [-1]
1043	if selection:
1044	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1045	if selection.lower() in choices:
1046	zlist = [choices.index(selection.lower())]
1047	else:
1048	print('debug: file '+str(selection)+' was not found in '+str(filename))
1049	zlist = [-1]
1050	elif len(zinfo) == 1 and confirmread:
1051	result = wx.ID_NO
1052	dlg = wx.MessageDialog(
1053	parent,
1054	'Is file '+str(zinfo[0].filename)+
1055	' what you want to extract from '+
1056	str(os.path.split(filename)[1])+'?',
1057	'Confirm file',
1058	wx.YES_NO \| wx.ICON_QUESTION)
1059	try:
1060	result = dlg.ShowModal()
1061	finally:
1062	dlg.Destroy()
1063	if result == wx.ID_NO:
1064	zlist = [-1]
1065	else:
1066	zlist = [0]
1067	elif len(zinfo) == 1:
1068	zlist = [0]
1069	elif multipleselect:
1070	# select one or more from a from list
1071	choices = [i.filename for i in zinfo]
1072	dlg = G2G.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1073	'Choose file(s)',choices)
1074	if dlg.ShowModal() == wx.ID_OK:
1075	zlist = dlg.GetSelections()
1076	else:
1077	zlist = []
1078	dlg.Destroy()
1079	else:
1080	# select one from a from list
1081	choices = [i.filename for i in zinfo]
1082	dlg = wx.SingleChoiceDialog(parent,
1083	'Select file to extract from zip file'+str(filename),'Choose file',
1084	choices,)
1085	if dlg.ShowModal() == wx.ID_OK:
1086	zlist = [dlg.GetSelection()]
1087	else:
1088	zlist = [-1]
1089	dlg.Destroy()
1090
1091	outlist = []
1092	for zindex in zlist:
1093	if zindex >= 0:
1094	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1095	if os.path.exists(efil) and confirmoverwrite:
1096	result = wx.ID_NO
1097	dlg = wx.MessageDialog(parent,
1098	'File '+str(efil)+' already exists. OK to overwrite it?',
1099	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1100	try:
1101	result = dlg.ShowModal()
1102	finally:
1103	dlg.Destroy()
1104	if result == wx.ID_NO:
1105	zindex = -1
1106	if zindex >= 0:
1107	# extract the file to the current directory, regardless of it's original path
1108	#z.extract(zinfo[zindex],zloc)
1109	eloc,efil = os.path.split(zinfo[zindex].filename)
1110	outfile = os.path.join(zloc, efil)
1111	fpin = z.open(zinfo[zindex])
1112	fpout = open(outfile, "wb")
1113	shutil.copyfileobj(fpin, fpout)
1114	fpin.close()
1115	fpout.close()
1116	outlist.append(outfile)
1117	z.close()
1118	if multipleselect and len(outlist) >= 1:
1119	return outlist
1120	elif len(outlist) == 1:
1121	return outlist[0]
1122	else:
1123	return None
1124
1125	def striphist(var,insChar=''):
1126	'strip a histogram number from a var name'
1127	sv = var.split(':')
1128	if len(sv) <= 1: return var
1129	if sv[1]:
1130	sv[1] = insChar
1131	return ':'.join(sv)
1132
1133	######################################################################
1134	# base classes for reading various types of data files
1135	# not used directly, only by subclassing
1136	######################################################################
1137	class ExportBaseclass(object):
1138	'''Defines a base class for the exporting of GSAS-II results.
1139
1140	This class is subclassed in the various exports/G2export_*.py files. Those files
1141	are imported in :meth:`GSASIIdataGUI.GSASII._init_Exports` which defines the
1142	appropriate menu items for each one and the .Exporter method is called
1143	directly from the menu item.
1144
1145	Routines may also define a .Writer method, which is used to write a single
1146	file without invoking any GUI objects.
1147	'''
1148	# TODO: review exporters producing exceptions where .Writer can't be used where G2frame is None (see CIF)
1149	# TODO: review conflicting uses of .Writer with mode (SeqRef) & elsewhere
1150	# TODO: move this class to G2fil
1151	def __init__(self,G2frame,formatName,extension,longFormatName=None,):
1152	self.G2frame = G2frame
1153	self.formatName = formatName # short string naming file type
1154	self.extension = extension
1155	if longFormatName: # longer string naming file type
1156	self.longFormatName = longFormatName
1157	else:
1158	self.longFormatName = formatName
1159	self.OverallParms = {}
1160	self.Phases = {}
1161	self.Histograms = {}
1162	self.powderDict = {}
1163	self.sasdDict = {}
1164	self.refdDict = {}
1165	self.xtalDict = {}
1166	self.parmDict = {}
1167	self.sigDict = {}
1168	self.fp = None
1169	# updated in InitExport:
1170	self.currentExportType = None # type of export that has been requested
1171	# updated in ExportSelect (when used):
1172	self.phasenam = None # a list of selected phases
1173	self.histnam = None # a list of selected histograms
1174	self.filename = None # name of file to be written (single export) or template (multiple files)
1175	self.dirname = '' # name of directory where file(s) will be written
1176	self.fullpath = '' # name of file being written -- full path
1177
1178	# items that should be defined in a subclass of this class
1179	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1180	# The following types are defined: 'project', "phase", "powder", "single"
1181	self.multiple = False # set as True if the class can export multiple phases or histograms
1182	# self.multiple is ignored for "project" exports
1183
1184	def InitExport(self,event):
1185	'''Determines the type of menu that called the Exporter and
1186	misc initialization.
1187	'''
1188	self.filename = None # name of file to be written (single export)
1189	self.dirname = '' # name of file to be written (multiple export)
1190	if event:
1191	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1192
1193	def MakePWDRfilename(self,hist):
1194	'''Make a filename root (no extension) from a PWDR histogram name
1195
1196	:param str hist: the histogram name in data tree (starts with "PWDR ")
1197	'''
1198	file0 = ''
1199	file1 = hist[5:]
1200	# replace repeated blanks
1201	while file1 != file0:
1202	file0 = file1
1203	file1 = file0.replace(' ',' ').strip()
1204	file0 = file1.replace('Azm= ','A')
1205	# if angle has unneeded decimal places on aziumuth, remove them
1206	if file0[-3:] == '.00': file0 = file0[:-3]
1207	file0 = file0.replace('.','_')
1208	file0 = file0.replace(' ','_')
1209	return file0
1210
1211	def ExportSelect(self,AskFile='ask'):
1212	'''Selects histograms or phases when needed. Sets a default file name when
1213	requested into self.filename; always sets a default directory in self.dirname.
1214
1215	:param bool AskFile: Determines how this routine processes getting a
1216	location to store the current export(s).
1217
1218	* if AskFile is 'ask' (default option), get the name of the file to be written;
1219	self.filename and self.dirname are always set. In the case where
1220	multiple files must be generated, the export routine should do this
1221	based on self.filename as a template.
1222	* if AskFile is 'dir', get the name of the directory to be used;
1223	self.filename is not used, but self.dirname is always set. The export routine
1224	will always generate the file name.
1225	* if AskFile is 'single', get only the name of the directory to be used when
1226	multiple items will be written (as multiple files) are used
1227	or a complete file name is requested when a single file
1228	name is selected. self.dirname is always set and self.filename used
1229	only when a single file is selected.
1230	* if AskFile is 'default', creates a name of the file to be used from
1231	the name of the project (.gpx) file. If the project has not been saved,
1232	then the name of file is requested.
1233	self.filename and self.dirname are always set. In the case where
1234	multiple file names must be generated, the export routine should do this
1235	based on self.filename.
1236	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1237	file. If the project has not been saved, then a directory is requested.
1238	self.filename is not used.
1239
1240	:returns: True in case of an error
1241	'''
1242
1243	numselected = 1
1244	if self.currentExportType == 'phase':
1245	if len(self.Phases) == 0:
1246	self.G2frame.ErrorDialog(
1247	'Empty project',
1248	'Project does not contain any phases.')
1249	return True
1250	elif len(self.Phases) == 1:
1251	self.phasenam = list(self.Phases.keys())
1252	elif self.multiple:
1253	choices = sorted(self.Phases.keys())
1254	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1255	if phasenum is None: return True
1256	self.phasenam = [choices[i] for i in phasenum]
1257	if not self.phasenam: return True
1258	numselected = len(self.phasenam)
1259	else:
1260	choices = sorted(self.Phases.keys())
1261	phasenum = G2G.ItemSelector(choices,self.G2frame)
1262	if phasenum is None: return True
1263	self.phasenam = [choices[phasenum]]
1264	numselected = len(self.phasenam)
1265	elif self.currentExportType == 'single':
1266	if len(self.xtalDict) == 0:
1267	self.G2frame.ErrorDialog(
1268	'Empty project',
1269	'Project does not contain any single crystal data.')
1270	return True
1271	elif len(self.xtalDict) == 1:
1272	self.histnam = self.xtalDict.values()
1273	elif self.multiple:
1274	choices = sorted(self.xtalDict.values())
1275	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1276	if not hnum: return True
1277	self.histnam = [choices[i] for i in hnum]
1278	numselected = len(self.histnam)
1279	else:
1280	choices = sorted(self.xtalDict.values())
1281	hnum = G2G.ItemSelector(choices,self.G2frame)
1282	if hnum is None: return True
1283	self.histnam = [choices[hnum]]
1284	numselected = len(self.histnam)
1285	elif self.currentExportType == 'powder':
1286	if len(self.powderDict) == 0:
1287	self.G2frame.ErrorDialog(
1288	'Empty project',
1289	'Project does not contain any powder data.')
1290	return True
1291	elif len(self.powderDict) == 1:
1292	self.histnam = list(self.powderDict.values())
1293	elif self.multiple:
1294	choices = sorted(self.powderDict.values())
1295	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1296	if not hnum: return True
1297	self.histnam = [choices[i] for i in hnum]
1298	numselected = len(self.histnam)
1299	else:
1300	choices = sorted(self.powderDict.values())
1301	hnum = G2G.ItemSelector(choices,self.G2frame)
1302	if hnum is None: return True
1303	self.histnam = [choices[hnum]]
1304	numselected = len(self.histnam)
1305	elif self.currentExportType == 'sasd':
1306	if len(self.sasdDict) == 0:
1307	self.G2frame.ErrorDialog(
1308	'Empty project',
1309	'Project does not contain any small angle data.')
1310	return True
1311	elif len(self.sasdDict) == 1:
1312	self.histnam = self.sasdDict.values()
1313	elif self.multiple:
1314	choices = sorted(self.sasdDict.values())
1315	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1316	if not hnum: return True
1317	self.histnam = [choices[i] for i in hnum]
1318	numselected = len(self.histnam)
1319	else:
1320	choices = sorted(self.sasdDict.values())
1321	hnum = G2G.ItemSelector(choices,self.G2frame)
1322	if hnum is None: return True
1323	self.histnam = [choices[hnum]]
1324	numselected = len(self.histnam)
1325	elif self.currentExportType == 'refd':
1326	if len(self.refdDict) == 0:
1327	self.G2frame.ErrorDialog(
1328	'Empty project',
1329	'Project does not contain any reflectivity data.')
1330	return True
1331	elif len(self.refdDict) == 1:
1332	self.histnam = self.refdDict.values()
1333	elif self.multiple:
1334	choices = sorted(self.refdDict.values())
1335	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1336	if not hnum: return True
1337	self.histnam = [choices[i] for i in hnum]
1338	numselected = len(self.histnam)
1339	else:
1340	choices = sorted(self.refdDict.values())
1341	hnum = G2G.ItemSelector(choices,self.G2frame)
1342	if hnum is None: return True
1343	self.histnam = [choices[hnum]]
1344	numselected = len(self.histnam)
1345	elif self.currentExportType == 'image':
1346	if len(self.Histograms) == 0:
1347	self.G2frame.ErrorDialog(
1348	'Empty project',
1349	'Project does not contain any images.')
1350	return True
1351	elif len(self.Histograms) == 1:
1352	self.histnam = list(self.Histograms.keys())
1353	else:
1354	choices = sorted(self.Histograms.keys())
1355	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1356	if self.multiple:
1357	if not hnum: return True
1358	self.histnam = [choices[i] for i in hnum]
1359	else:
1360	if hnum is None: return True
1361	self.histnam = [choices[hnum]]
1362	numselected = len(self.histnam)
1363	if self.currentExportType == 'map':
1364	# search for phases with maps
1365	mapPhases = []
1366	choices = []
1367	for phasenam in sorted(self.Phases):
1368	phasedict = self.Phases[phasenam] # pointer to current phase info
1369	if len(phasedict['General']['Map'].get('rho',[])):
1370	mapPhases.append(phasenam)
1371	if phasedict['General']['Map'].get('Flip'):
1372	choices.append('Charge flip map: '+str(phasenam))
1373	elif phasedict['General']['Map'].get('MapType'):
1374	choices.append(
1375	str(phasedict['General']['Map'].get('MapType'))
1376	+ ' map: ' + str(phasenam))
1377	else:
1378	choices.append('unknown map: '+str(phasenam))
1379	# select a map if needed
1380	if len(mapPhases) == 0:
1381	self.G2frame.ErrorDialog(
1382	'Empty project',
1383	'Project does not contain any maps.')
1384	return True
1385	elif len(mapPhases) == 1:
1386	self.phasenam = mapPhases
1387	else:
1388	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1389	if self.multiple:
1390	if not phasenum: return True
1391	self.phasenam = [mapPhases[i] for i in phasenum]
1392	else:
1393	if phasenum is None: return True
1394	self.phasenam = [mapPhases[phasenum]]
1395	numselected = len(self.phasenam)
1396
1397	# items selected, now set self.dirname and usually self.filename
1398	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
1399	AskFile == 'default' and not self.G2frame.GSASprojectfile
1400	):
1401	filename = self.askSaveFile()
1402	if not filename: return True
1403	self.dirname,self.filename = os.path.split(filename)
1404	elif AskFile == 'dir' or AskFile == 'single' or (
1405	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
1406	):
1407	self.dirname = self.askSaveDirectory()
1408	if not self.dirname: return True
1409	elif AskFile == 'default-dir' or AskFile == 'default':
1410	self.dirname,self.filename = os.path.split(
1411	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
1412	)
1413	else:
1414	raise Exception('This should not happen!')
1415
1416	def loadParmDict(self):
1417	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
1418	refined values to those from the last cycle and set the uncertainties for the
1419	refined parameters in another dict (self.sigDict).
1420
1421	Expands the parm & sig dicts to include values derived from constraints.
1422
1423	This could be made faster for sequential fits by reducing the histogram list to only
1424	the active histogram being exported.
1425	'''
1426	self.G2frame.CheckNotebook()
1427	self.parmDict = {}
1428	self.sigDict = {}
1429	rigidbodyDict = {}
1430	covDict = {}
1431	consDict = {}
1432	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1433	if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1434	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1435	while item:
1436	name = self.G2frame.GPXtree.GetItemText(item)
1437	if name == 'Rigid bodies':
1438	rigidbodyDict = self.G2frame.GPXtree.GetItemPyData(item)
1439	elif name == 'Covariance':
1440	covDict = self.G2frame.GPXtree.GetItemPyData(item)
1441	elif name == 'Constraints':
1442	consDict = self.G2frame.GPXtree.GetItemPyData(item)
1443	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1444	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1445	self.parmDict.update(rbDict)
1446	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1447	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData(
1448	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
1449	self.parmDict.update(phaseDict)
1450	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
1451	Phases,Histograms,Print=False,resetRefList=False)
1452	self.parmDict.update(hapDict)
1453	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
1454	self.parmDict.update(histDict)
1455	self.parmDict.update(zip(
1456	covDict.get('varyList',[]),
1457	covDict.get('variables',[])))
1458	self.sigDict = dict(zip(
1459	covDict.get('varyList',[]),
1460	covDict.get('sig',[])))
1461	# expand to include constraints: first compile a list of constraints
1462	constList = []
1463	for item in consDict:
1464	if item.startswith('_'): continue
1465	constList += consDict[item]
1466	# now process the constraints
1467	G2mv.InitVars()
1468	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
1469	varyList = covDict.get('varyListStart')
1470	if varyList is None and len(constDict) == 0:
1471	# no constraints can use varyList
1472	varyList = covDict.get('varyList')
1473	elif varyList is None:
1474	# old GPX file from before pre-constraint varyList is saved
1475	print (' * Old refinement: Please use Calculate/Refine to redo *')
1476	raise Exception(' * Export aborted *')
1477	else:
1478	varyList = list(varyList)
1479	# add symmetry-generated constraints
1480	rigidbodyDict = self.G2frame.GPXtree.GetItemPyData(
1481	G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,'Rigid bodies'))
1482	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1483	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1484	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData(
1485	Phases,RestraintDict=None,rbIds=rbIds,Print=False) # generates atom symmetry constraints
1486	msg = G2mv.EvaluateMultipliers(constDict,phaseDict)
1487	if msg:
1488	print('Unable to interpret multiplier(s): '+msg)
1489	raise Exception(' * CIF creation aborted *')
1490	try:
1491	G2mv.GenerateConstraints(varyList,constDict,fixedList,self.parmDict)
1492	#print(G2mv.VarRemapShow(varyList))
1493	except:
1494	# this really should not happen
1495	print (' * ERROR - constraints are internally inconsistent *')
1496	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
1497	print ('Errors'+errmsg)
1498	if warnmsg: print ('Warnings'+warnmsg)
1499	raise Exception(' * CIF creation aborted *')
1500	# add the constrained values to the parameter dictionary
1501	G2mv.Dict2Map(self.parmDict,varyList)
1502	# and add their uncertainties into the esd dictionary (sigDict)
1503	if covDict.get('covMatrix') is not None:
1504	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
1505
1506	def loadTree(self):
1507	'''Load the contents of the data tree into a set of dicts
1508	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
1509	& self.xtalDict)
1510
1511	* The childrenless data tree items are overall parameters/controls for the
1512	entire project and are placed in self.OverallParms
1513	* Phase items are placed in self.Phases
1514	* Data items are placed in self.Histogram. The key for these data items
1515	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
1516	'''
1517	self.OverallParms = {}
1518	self.powderDict = {}
1519	self.sasdDict = {}
1520	self.refdDict = {}
1521	self.xtalDict = {}
1522	self.Phases = {}
1523	self.Histograms = {}
1524	self.SeqRefdata = None
1525	self.SeqRefhist = None
1526	if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1527	histType = None
1528	if self.currentExportType == 'phase':
1529	# if exporting phases load them here
1530	sub = G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,'Phases')
1531	if not sub:
1532	print ('no phases found')
1533	return True
1534	item, cookie = self.G2frame.GPXtree.GetFirstChild(sub)
1535	while item:
1536	phaseName = self.G2frame.GPXtree.GetItemText(item)
1537	self.Phases[phaseName] = self.G2frame.GPXtree.GetItemPyData(item)
1538	item, cookie = self.G2frame.GPXtree.GetNextChild(sub, cookie)
1539	return
1540	elif self.currentExportType == 'single':
1541	histType = 'HKLF'
1542	elif self.currentExportType == 'powder':
1543	histType = 'PWDR'
1544	elif self.currentExportType == 'image':
1545	histType = 'IMG'
1546	elif self.currentExportType == 'sasd':
1547	histType = 'SASD'
1548	elif self.currentExportType == 'refd':
1549	histType = 'REFD'
1550
1551	if histType: # Loading just one kind of tree entry
1552	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1553	while item:
1554	name = self.G2frame.GPXtree.GetItemText(item)
1555	if name.startswith(histType):
1556	if self.Histograms.get(name): # there is already an item with this name
1557	print('Histogram name '+str(name)+' is repeated. Renaming')
1558	if name[-1] == '9':
1559	name = name[:-1] + '10'
1560	elif name[-1] in '012345678':
1561	name = name[:-1] + str(int(name[-1])+1)
1562	else:
1563	name += '-1'
1564	self.Histograms[name] = {}
1565	# the main info goes into Data, but the 0th
1566	# element contains refinement results, carry
1567	# that over too now.
1568	self.Histograms[name]['Data'] = self.G2frame.GPXtree.GetItemPyData(item)[1]
1569	self.Histograms[name][0] = self.G2frame.GPXtree.GetItemPyData(item)[0]
1570	item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1571	while item2:
1572	child = self.G2frame.GPXtree.GetItemText(item2)
1573	self.Histograms[name][child] = self.G2frame.GPXtree.GetItemPyData(item2)
1574	item2, cookie2 = self.G2frame.GPXtree.GetNextChild(item, cookie2)
1575	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1576	# index powder and single crystal histograms by number
1577	for hist in self.Histograms:
1578	if hist.startswith("PWDR"):
1579	d = self.powderDict
1580	elif hist.startswith("HKLF"):
1581	d = self.xtalDict
1582	elif hist.startswith("SASD"):
1583	d = self.sasdDict
1584	elif hist.startswith("REFD"):
1585	d = self.refdDict
1586	else:
1587	return
1588	i = self.Histograms[hist].get('hId')
1589	if i is None and not d.keys():
1590	i = 0
1591	elif i is None or i in d.keys():
1592	i = max(d.keys())+1
1593	d[i] = hist
1594	return
1595	# else standard load: using all interlinked phases and histograms
1596	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1597	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1598	while item:
1599	name = self.G2frame.GPXtree.GetItemText(item)
1600	item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1601	if not item2:
1602	self.OverallParms[name] = self.G2frame.GPXtree.GetItemPyData(item)
1603	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1604	# index powder and single crystal histograms
1605	for hist in self.Histograms:
1606	i = self.Histograms[hist]['hId']
1607	if hist.startswith("PWDR"):
1608	self.powderDict[i] = hist
1609	elif hist.startswith("HKLF"):
1610	self.xtalDict[i] = hist
1611	elif hist.startswith("SASD"):
1612	self.sasdDict[i] = hist
1613	elif hist.startswith("REFD"):
1614	self.refdDict[i] = hist
1615
1616	def dumpTree(self,mode='type'):
1617	'''Print out information on the data tree dicts loaded in loadTree.
1618	Used for testing only.
1619	'''
1620	if self.SeqRefdata and self.SeqRefhist:
1621	print('Note that dumpTree does not show sequential results')
1622	print ('\nOverall')
1623	if mode == 'type':
1624	def Show(arg): return type(arg)
1625	else:
1626	def Show(arg): return arg
1627	for key in self.OverallParms:
1628	print (' '+key+Show(self.OverallParms[key]))
1629	print ('Phases')
1630	for key1 in self.Phases:
1631	print (' '+key1+Show(self.Phases[key1]))
1632	print ('Histogram')
1633	for key1 in self.Histograms:
1634	print (' '+key1+Show(self.Histograms[key1]))
1635	for key2 in self.Histograms[key1]:
1636	print (' '+key2+Show(self.Histograms[key1][key2]))
1637
1638	def defaultSaveFile(self):
1639	return os.path.abspath(
1640	os.path.splitext(self.G2frame.GSASprojectfile
1641	)[0]+self.extension)
1642
1643	def askSaveFile(self):
1644	'''Ask the user to supply a file name
1645
1646	:returns: a file name (str) or None if Cancel is pressed
1647
1648	'''
1649	#pth = G2G.GetExportPath(self.G2frame)
1650	if self.G2frame.GSASprojectfile:
1651	defnam = os.path.splitext(
1652	os.path.split(self.G2frame.GSASprojectfile)[1]
1653	)[0]+self.extension
1654	else:
1655	defnam = 'default' + self.extension
1656	return G2G.askSaveFile(self.G2frame,defnam,self.extension,self.longFormatName)
1657
1658	def askSaveDirectory(self):
1659	'''Ask the user to supply a directory name. Path name is used as the
1660	starting point for the next export path search.
1661
1662	:returns: a directory name (str) or None if Cancel is pressed
1663
1664	TODO: Can this be replaced with G2G.askSaveDirectory?
1665	'''
1666	pth = G2G.GetExportPath(self.G2frame)
1667	dlg = wx.DirDialog(
1668	self.G2frame, 'Input directory where file(s) will be written', pth,
1669	wx.DD_DEFAULT_STYLE)
1670	dlg.CenterOnParent()
1671	try:
1672	if dlg.ShowModal() == wx.ID_OK:
1673	filename = dlg.GetPath()
1674	self.G2frame.LastExportDir = filename
1675	else:
1676	filename = None
1677	finally:
1678	dlg.Destroy()
1679	return filename
1680
1681	# Tools for file writing.
1682	def OpenFile(self,fil=None,mode='w'):
1683	'''Open the output file
1684
1685	:param str fil: The name of the file to open. If None (default)
1686	the name defaults to self.dirname + self.filename.
1687	If an extension is supplied, it is not overridded,
1688	but if not, the default extension is used.
1689	:returns: the file object opened by the routine which is also
1690	saved as self.fp
1691	'''
1692	if mode == 'd': # debug mode
1693	self.fullpath = '(stdout)'
1694	self.fp = sys.stdout
1695	return
1696	if not fil:
1697	if not os.path.splitext(self.filename)[1]:
1698	self.filename += self.extension
1699	fil = os.path.join(self.dirname,self.filename)
1700	self.fullpath = os.path.abspath(fil)
1701	self.fp = open(self.fullpath,mode)
1702	return self.fp
1703
1704	def Write(self,line):
1705	'''write a line of output, attaching a line-end character
1706
1707	:param str line: the text to be written.
1708	'''
1709	if self.fp is None:
1710	raise Exception('Attempt to Write without use of OpenFile')
1711	self.fp.write(line+'\n')
1712
1713	def CloseFile(self,fp=None):
1714	'''Close a file opened in OpenFile
1715
1716	:param file fp: the file object to be closed. If None (default)
1717	file object self.fp is closed.
1718	'''
1719	if self.fp is None:
1720	raise Exception('Attempt to CloseFile without use of OpenFile')
1721	if self.fp == sys.stdout: return # debug mode
1722	if fp is None:
1723	fp = self.fp
1724	self.fp = None
1725	if fp is not None: fp.close()
1726
1727	def SetSeqRef(self,data,hist):
1728	'''Set the exporter to retrieve results from a sequential refinement
1729	rather than the main tree
1730	'''
1731	self.SeqRefdata = data
1732	self.SeqRefhist = hist
1733	data_name = data[hist]
1734	for i,val in zip(data_name['varyList'],data_name['sig']):
1735	self.sigDict[i] = val
1736	self.sigDict[striphist(i)] = val
1737	for i in data_name['parmDict']:
1738	self.parmDict[striphist(i)] = data_name['parmDict'][i]
1739	self.parmDict[i] = data_name['parmDict'][i]
1740	# zero out the dA[xyz] terms, they would only bring confusion
1741	key = i.split(':')
1742	if len(key) < 3: continue
1743	if key[2].startswith('dA'):
1744	self.parmDict[i] = 0.0
1745	for i,(val,sig) in data_name.get('depParmDict',{}).items():
1746	self.parmDict[i] = val
1747	self.sigDict[i] = sig
1748	#GSASIIpath.IPyBreak()
1749
1750	# Tools to pull information out of the data arrays
1751	def GetCell(self,phasenam):
1752	"""Gets the unit cell parameters and their s.u.'s for a selected phase
1753
1754	:param str phasenam: the name for the selected phase
1755	:returns: `cellList,cellSig` where each is a 7 element list corresponding
1756	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1757	cell values and `cellSig` has their uncertainties.
1758	"""
1759	if self.SeqRefdata and self.SeqRefhist:
1760	return self.GetSeqCell(phasenam,self.SeqRefdata[self.SeqRefhist])
1761	phasedict = self.Phases[phasenam] # pointer to current phase info
1762	try:
1763	pfx = str(phasedict['pId'])+'::'
1764	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
1765	cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A,
1766	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
1767	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
1768	return cellList,cellSig
1769	except KeyError:
1770	cell = phasedict['General']['Cell'][1:]
1771	return cell,7*[0]
1772
1773	def GetSeqCell(self,phasenam,data_name):
1774	"""Gets the unit cell parameters and their s.u.'s for a selected phase
1775	and histogram in a sequential fit
1776
1777	:param str phasenam: the name for the selected phase
1778	:param dict data_name: the sequential refinement parameters for the selected histogram
1779	:returns: `cellList,cellSig` where each is a 7 element list corresponding
1780	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1781	cell values and `cellSig` has their uncertainties.
1782	"""
1783	phasedict = self.Phases[phasenam]
1784	SGdata = phasedict['General']['SGData']
1785	pId = phasedict['pId']
1786	RecpCellTerms = G2lat.cell2A(phasedict['General']['Cell'][1:7])
1787	ESDlookup = {}
1788	Dlookup = {}
1789	varied = [striphist(i) for i in data_name['varyList']]
1790	for item,val in data_name['newCellDict'].items():
1791	if item in varied:
1792	ESDlookup[val[0]] = item
1793	Dlookup[item] = val[0]
1794	A = RecpCellTerms[:]
1795	for i in range(6):
1796	var = str(pId)+'::A'+str(i)
1797	if var in ESDlookup:
1798	A[i] = data_name['newCellDict'][ESDlookup[var]][1] # override with refined value
1799	cellDict = dict(zip([str(pId)+'::A'+str(i) for i in range(6)],A))
1800	zeroDict = {i:0.0 for i in cellDict}
1801	A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata,cellDict,zeroDict)
1802	covData = {
1803	'varyList': [Dlookup.get(striphist(v),v) for v in data_name['varyList']],
1804	'covMatrix': data_name['covMatrix']
1805	}
1806	return list(G2lat.A2cell(A)) + [G2lat.calc_V(A)], G2stIO.getCellEsd(str(pId)+'::',SGdata,A,covData)
1807
1808	def GetAtoms(self,phasenam):
1809	"""Gets the atoms associated with a phase. Can be used with standard
1810	or macromolecular phases
1811
1812	:param str phasenam: the name for the selected phase
1813	:returns: a list of items for eac atom where each item is a list containing:
1814	label, typ, mult, xyz, and td, where
1815
1816	* label and typ are the atom label and the scattering factor type (str)
1817	* mult is the site multiplicity (int)
1818	* xyz is contains a list with four pairs of numbers:
1819	x, y, z and fractional occupancy and
1820	their standard uncertainty (or a negative value)
1821	* td is contains a list with either one or six pairs of numbers:
1822	if one number it is U\\ :sub:`iso` and with six numbers it is
1823	U\\ :sub:`11`, U\\ :sub:`22`, U\\ :sub:`33`, U\\ :sub:`12`, U\\ :sub:`13` & U\\ :sub:`23`
1824	paired with their standard uncertainty (or a negative value)
1825	"""
1826	phasedict = self.Phases[phasenam] # pointer to current phase info
1827	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
1828	cfrac = cx+3
1829	fpfx = str(phasedict['pId'])+'::Afrac:'
1830	atomslist = []
1831	for i,at in enumerate(phasedict['Atoms']):
1832	if phasedict['General']['Type'] == 'macromolecular':
1833	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
1834	else:
1835	label = at[ct-1]
1836	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
1837	fsig = self.sigDict.get(fpfx+str(i),-0.009)
1838	mult = at[cs+1]
1839	typ = at[ct]
1840	xyz = []
1841	for j,v in enumerate(('x','y','z')):
1842	val = at[cx+j]
1843	pfx = str(phasedict['pId']) + '::A' + v + ':' + str(i)
1844	val = self.parmDict.get(pfx, val)
1845	dpfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
1846	sig = self.sigDict.get(dpfx,-0.000009)
1847	xyz.append((val,sig))
1848	xyz.append((fval,fsig))
1849	td = []
1850	if at[cia] == 'I':
1851	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
1852	val = self.parmDict.get(pfx,at[cia+1])
1853	sig = self.sigDict.get(pfx,-0.0009)
1854	td.append((val,sig))
1855	else:
1856	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
1857	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
1858	val = self.parmDict.get(pfx,at[cia+2+i])
1859	sig = self.sigDict.get(pfx,-0.0009)
1860	td.append((val,sig))
1861	atomslist.append((label,typ,mult,xyz,td))
1862	return atomslist
1863	######################################################################
1864	def ExportPowderList(G2frame):
1865	'''Returns a list of extensions supported by :func:`GSASIIIO:ExportPowder`
1866	along with their descriptions (note that a extension may be repeated
1867	but descriptions are unique).
1868	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
1869
1870	:param wx.Frame G2frame: the GSAS-II main data tree window
1871	'''
1872	extList = []
1873	extLabel = []
1874	for obj in G2frame.exporterlist:
1875	if 'powder' in obj.exporttype:
1876	try:
1877	obj.Writer
1878	extList.append(obj.extension)
1879	extLabel.append(obj.formatName)
1880	except AttributeError:
1881	pass
1882	return extList,extLabel
1883
1884	def ExportPowder(G2frame,TreeName,fileroot,extension,hint=''):
1885	'''Writes a single powder histogram using the Export routines.
1886	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
1887
1888	:param wx.Frame G2frame: the GSAS-II main data tree window
1889	:param str TreeName: the name of the histogram (PWDR ...) in the data tree
1890	:param str fileroot: name for file to be written, extension ignored
1891	:param str extension: extension for file to be written (start with '.'). Must
1892	match a powder export routine that has a Writer object.
1893	:param str hint: a string that must match the export's format
1894	'''
1895	filename = os.path.abspath(os.path.splitext(fileroot)[0]+extension)
1896	for obj in G2frame.exporterlist:
1897	if obj.extension == extension and 'powder' in obj.exporttype:
1898	if hint and hint not in obj.formatName: continue
1899	obj.currentExportType = 'powder'
1900	obj.InitExport(None)
1901	obj.loadTree() # load all histograms in tree into dicts
1902	if TreeName not in obj.Histograms:
1903	raise Exception('Histogram not found: '+str(TreeName))
1904	try:
1905	obj.Writer
1906	except AttributeError:
1907	continue
1908	try:
1909	obj.Writer(TreeName,filename)
1910	print('wrote file '+filename)
1911	return
1912	except Exception:
1913	print('Export Routine for '+extension+' failed.')
1914	else:
1915	print('No Export routine supports extension '+extension)
1916
1917	def ExportSequential(G2frame,data,obj,exporttype):
1918	'''
1919	Used to export from every phase/dataset in a sequential refinement using
1920	a .Writer method for either projects or phases. Prompts to select histograms
1921	and for phase exports, which phase(s).
1922
1923	:param wx.Frame G2frame: the GSAS-II main data tree window
1924	:param dict data: the sequential refinement data object
1925	:param str exporttype: indicates the type of export ('project' or 'phase')
1926	'''
1927	if len(data['histNames']) == 0:
1928	G2G.G2MessageBox(G2frame,'There are no sequential histograms','Warning')
1929	obj.InitExport(None)
1930	obj.loadTree()
1931	obj.loadParmDict()
1932	if len(data['histNames']) == 1:
1933	histlist = data['histNames']
1934	else:
1935	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select histograms to export from list',
1936	'Select histograms',data['histNames'])
1937	if dlg.ShowModal() == wx.ID_OK:
1938	histlist = [data['histNames'][l] for l in dlg.GetSelections()]
1939	dlg.Destroy()
1940	else:
1941	dlg.Destroy()
1942	return
1943	if exporttype == 'Phase':
1944	phaselist = list(obj.Phases.keys())
1945	if len(obj.Phases) == 0:
1946	G2G.G2MessageBox(G2frame,'There are no phases in sequential ref.','Warning')
1947	return
1948	elif len(obj.Phases) > 1:
1949	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select phases to export from list',
1950	'Select phases', phaselist)
1951	if dlg.ShowModal() == wx.ID_OK:
1952	phaselist = [phaselist[l] for l in dlg.GetSelections()]
1953	dlg.Destroy()
1954	else:
1955	dlg.Destroy()
1956	return
1957	filename = obj.askSaveFile()
1958	if not filename: return True
1959	obj.dirname,obj.filename = os.path.split(filename)
1960	print('Writing output to file '+str(obj.filename)+"...")
1961	mode = 'w'
1962	for p in phaselist:
1963	for h in histlist:
1964	obj.SetSeqRef(data,h)
1965	#GSASIIpath.IPyBreak()
1966	obj.Writer(h,phasenam=p,mode=mode)
1967	mode = 'a'
1968	print('...done')
1969	elif exporttype == 'Project': # note that the CIF exporter is not yet ready for this
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	elif exporttype == 'Powder':
1982	filename = obj.askSaveFile()
1983	if not filename: return True
1984	obj.dirname,obj.filename = os.path.split(filename)
1985	print('Writing output to file '+str(obj.filename)+"...")
1986	mode = 'w'
1987	for h in histlist:
1988	obj.SetSeqRef(data,h)
1989	obj.Writer(h,mode=mode)
1990	print('\t'+str(h)+' written')
1991	mode = 'a'
1992	print('...done')
1993
1994	def ReadDIFFaX(DIFFaXfile):
1995	print ('read '+DIFFaXfile)
1996	Layer = {'Laue':'-1','Cell':[False,1.,1.,1.,90.,90.,90,1.],'Width':[[10.,10.],[False,False]],
1997	'Layers':[],'Stacking':[],'Transitions':[],'Toler':0.01,'AtInfo':{}}
1998	df = open(DIFFaXfile,'r')
1999	lines = df.readlines()
2000	df.close()
2001	struct = False
2002	Struct = []
2003	stack = False
2004	Stack = []
2005	trans = False
2006	Trans = []
2007	for diff in lines:
2008	diff = diff[:-1].lower()
2009	if '!' in diff:
2010	continue
2011	while '}' in diff: #strip comments
2012	iB = diff.index('{')
2013	iF = diff.index('}')+1
2014	if iB:
2015	diff = diff[:iB]
2016	else:
2017	diff = diff[iF:]
2018	if not diff:
2019	continue
2020	if diff.strip() == 'instrumental':
2021	continue
2022	if diff.strip() == 'structural':
2023	struct = True
2024	continue
2025	elif diff.strip() == 'stacking':
2026	struct = False
2027	stack = True
2028	continue
2029	elif diff.strip() == 'transitions':
2030	stack = False
2031	trans = True
2032	continue
2033	diff = diff.strip()
2034	if struct:
2035	if diff:
2036	Struct.append(diff)
2037	elif stack:
2038	if diff:
2039	Stack.append(diff)
2040	elif trans:
2041	if diff:
2042	Trans.append(diff)
2043
2044	#STRUCTURE records
2045	laueRec = Struct[1].split()
2046	Layer['Laue'] = laueRec[0]
2047	if Layer['Laue'] == 'unknown' and len(laueRec) > 1:
2048	Layer['Toler'] = float(laueRec[1]) #tolerance for 'unknown'?
2049	if Layer['Laue'] == '2/m(1)': Layer['Laue'] = '2/m(c)'
2050	if Layer['Laue'] == '2/m(2)': Layer['Laue'] = '2/m(ab)'
2051	cell = Struct[0].split()
2052	Layer['Cell'] = [False,float(cell[0]),float(cell[1]),float(cell[2]),90.,90.,float(cell[3]),1.0]
2053	nLayers = int(Struct[2])
2054	N = 3
2055	if 'layer' not in Struct[3]:
2056	N = 4
2057	if Struct[3] != 'infinite':
2058	width = Struct[3].split()
2059	Layer['Width'][0] = [float(width[0]),float(width[1])]
2060	for nL in range(nLayers):
2061	if '=' in Struct[N]:
2062	name = Struct[N].split('=')
2063	sameas = int(name[1])-1
2064	Layer['Layers'].append({'Name':name[0],'SameAs':Layer['Layers'][sameas]['Name'],'Symm':'None','Atoms':[]})
2065	N += 1
2066	continue
2067	Symm = 'None'
2068	if 'centro' in Struct[N+1]: Symm = '-1'
2069	Layer['Layers'].append({'Name':Struct[N],'SameAs':'','Symm':Symm,'Atoms':[]})
2070	N += 2
2071	while 'layer' not in Struct[N]:
2072	atom = Struct[N][4:].split()
2073	atomType = G2el.FixValence(Struct[N][:4].replace(' ','').strip().capitalize())
2074	if atomType not in Layer['AtInfo']:
2075	Layer['AtInfo'][atomType] = G2el.GetAtomInfo(atomType)
2076	atomName = '%s(%s)'%(atomType,atom[0])
2077	newVals = []
2078	for val in atom[1:6]:
2079	if '/' in val:
2080	newVals.append(eval(val+'.'))
2081	else:
2082	newVals.append(float(val))
2083	atomRec = [atomName,atomType,newVals[0],newVals[1],newVals[2],newVals[4],newVals[3]/78.9568]
2084	Layer['Layers'][-1]['Atoms'].append(atomRec)
2085	N += 1
2086	if N > len(Struct)-1:
2087	break
2088	#TRANSITIONS records
2089	transArray = []
2090	N = 0
2091	for i in range(nLayers):
2092	transArray.append([])
2093	for j in range(nLayers):
2094	vals = Trans[N].split()
2095	newVals = []
2096	for val in vals[:4]:
2097	if '/' in val:
2098	newVals.append(eval(val+'.'))
2099	else:
2100	newVals.append(float(val))
2101	transArray[-1].append(newVals+['',False])
2102	N += 1
2103	Layer['Transitions'] = transArray
2104	#STACKING records
2105	Layer['Stacking'] = [Stack[0],'']
2106	if Stack[0] == 'recursive':
2107	Layer['Stacking'][1] = Stack[1]
2108	elif Stack[0] == 'explicit':
2109	if Stack[1] == 'random':
2110	Layer['Stacking'][1] = Stack[1]
2111	else:
2112	Layer['Stacking'][1] = 'list'
2113	Layer['Stacking'].append('')
2114	for stack in Stack[2:]:
2115	Layer['Stacking'][2] += ' '+stack
2116	return Layer
2117
2118	def postURL(URL,postdict):
2119	'''Posts a set of values as from a web form. If access fails to an https
2120	site the access is retried with http.
2121
2122	:param str URL: the URL to post; typically something
2123	like 'http://www.../dir/page?'
2124	:param dict postdict: contains keywords and values, such
2125	as {'centrosymmetry': '0', 'crystalsystem': '0', ...}
2126	:returns: a string with the response from the web server or None
2127	if access fails.
2128	'''
2129	try:
2130	import requests # delay this until now, since rarely needed
2131	except:
2132	# this import seems to fail with the Anaconda pythonw on
2133	# macs; it should not!
2134	print('Warning: failed to import requests. Python config error')
2135	return None
2136
2137	repeat = True
2138	while repeat:
2139	r = None
2140	repeat = False
2141	try:
2142	r = requests.get(URL,params=postdict)
2143	if r.status_code == 200:
2144	print('request OK')
2145	page = r.text
2146	return page # success
2147	else:
2148	print('request to {} failed. Reason={}'.format(URL,r.reason))
2149	except Exception as msg: #ConnectionError?
2150	print('connection error - not on internet?')
2151	if GSASIIpath.GetConfigValue('debug'): print(msg)
2152	finally:
2153	if r: r.close()
2154	if URL.startswith('https:'):
2155	repeat = True
2156	URL = URL.replace('https:','http:')
2157	else:
2158	return None
2159
2160	if __name__ == '__main__':
2161	import GSASIIdataGUI
2162	application = GSASIIdataGUI.GSASIImain(0)
2163	G2frame = application.main
2164	#app = wx.PySimpleApp()
2165	#G2frame = wx.Frame(None) # create a frame
2166	#frm.Show(True)
2167	#filename = '/tmp/notzip.zip'
2168	#filename = '/tmp/all.zip'
2169	#filename = '/tmp/11bmb_7652.zip'
2170
2171	#selection=None, confirmoverwrite=True, parent=None
2172	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2173	#print ExtractFileFromZip(filename,multipleselect=True)
2174	# #confirmread=False, confirmoverwrite=False)
2175
2176	# choicelist=[ ('a','b','c'),
2177	# ('test1','test2'),('no choice',)]
2178	# titles = [ 'a, b or c', 'tests', 'No option here']
2179	# dlg = MultipleChoicesDialog(
2180	# choicelist,titles,
2181	# parent=frm)
2182	# if dlg.ShowModal() == wx.ID_OK:
2183	# print 'Got OK'
2184	imagefile = '/tmp/NDC5_00237_3.ge3'
2185	Comments, Data, Npix, Image = GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None)
2186
2187	print("\n\nResults loaded to Comments, Data, Npix and Image\n\n")
2188
2189	GSASIIpath.IPyBreak_base()

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