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source: trunk/GSASIIIO.py @ 5042

Last change on this file since 5042 was 5042, checked in by toby, 4 years ago
implement sequential CIF export; minor CIF bug fixes; add su to seq res for WtFrac?; Add new sequential project export menu items; move some lattice labels to G2lat; Use G2strIO (not G2strIO) throughout
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: 2021-10-04 22:14:24 +0000 (Mon, 04 Oct 2021) $
4	# $Author: toby $
5	# $Revision: 5042 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 5042 2021-10-04 22:14:24Z toby $
8	########### SVN repository information ###################
9	'''
10	GSASIIIO: Misc I/O routines
11	=============================
12
13	Module with miscellaneous routines for input and output. Many
14	are GUI routines to interact with user.
15
16	Includes support for image reading.
17
18	Also includes base 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: 5042 $")
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,'r')
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.size[: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.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.update(copy.deepcopy(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 in rd.formatName: #This is a kluge because the rd.formatName was changed!
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	if GSASIIpath.GetConfigValue('show_gpxSize'):
680	posPrev = 0
681	sizeList = {}
682	while True:
683	try:
684	data = cPickleLoad(filep)
685	except EOFError:
686	break
687	datum = data[0]
688	if GSASIIpath.GetConfigValue('show_gpxSize'):
689	sizeList[datum[0]] = filep.tell()-posPrev
690	posPrev = filep.tell()
691	# scan the GPX file for unexpected objects
692	if GSASIIpath.GetConfigValue('debug'):
693	global unexpectedObject
694	unexpectedObject = False
695	objectScan(data,'tree item "{}" entry '.format(datum[0]))
696	#if unexpectedObject:
697	# print(datum[0])
698	# GSASIIpath.IPyBreak()
699	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=datum[0])
700	if datum[0] == 'Phases' and GSASIIpath.GetConfigValue('SeparateHistPhaseTreeItem',False):
701	G2frame.GPXtree.AppendItem(parent=G2frame.root,text='Hist/Phase')
702	if updateFromSeq and datum[0] == 'Phases':
703	for pdata in data[1:]:
704	if pdata[0] in Phases:
705	pdata[1].update(Phases[pdata[0]])
706	elif updateFromSeq and datum[0] == 'Covariance':
707	data[0][1] = CovData
708	elif updateFromSeq and datum[0] == 'Rigid bodies':
709	data[0][1] = RigidBodies
710	elif updateFromSeq and datum[0] in tmpHistIndex:
711	hist.seek(tmpHistIndex[datum[0]])
712	hdata = cPickleLoad(hist)
713	if data[0][0] != hdata[0][0]:
714	print('Error! Updating {} with {}'.format(data[0][0],hdata[0][0]))
715	datum = hdata[0]
716	xferItems = ['Background','Instrument Parameters','Sample Parameters','Reflection Lists']
717	hItems = {name:j+1 for j,(name,val) in enumerate(hdata[1:]) if name in xferItems}
718	for j,(name,val) in enumerate(data[1:]):
719	if name not in xferItems: continue
720	data[j+1][1] = hdata[hItems[name]][1]
721	if datum[0].startswith('PWDR'):
722	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
723	datum[1][0]['ranId'] = ran.randint(0,sys.maxsize)
724	G2frame.GPXtree.SetItemPyData(Id,datum[1][:3]) #temp. trim off junk (patch?)
725	elif datum[0].startswith('HKLF'):
726	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
727	datum[1][0]['ranId'] = ran.randint(0,sys.maxsize)
728	G2frame.GPXtree.SetItemPyData(Id,datum[1])
729	else:
730	G2frame.GPXtree.SetItemPyData(Id,datum[1])
731	if datum[0] == 'Controls' and 'LastSavedUsing' in datum[1]:
732	LastSavedUsing = datum[1]['LastSavedUsing']
733	if datum[0] == 'Controls' and 'PythonVersions' in datum[1] and GSASIIpath.GetConfigValue('debug') and showProvenance:
734	print('DBG_Packages used to create .GPX file:')
735	if 'dict' in str(type(datum[1]['PythonVersions'])): #patch
736	for p in sorted(datum[1]['PythonVersions'],key=lambda s: s.lower()):
737	print(" {:<14s}: {:s}".format(p[0],p[1]))
738	else:
739	for p in datum[1]['PythonVersions']:
740	print(" {:<12s} {:s}".format(p[0]+':',p[1]))
741	oldPDF = False
742	for datus in data[1:]:
743	#patch - 1/23/17 PDF cleanup
744	if datus[0][:4] in ['I(Q)','S(Q)','F(Q)','G(R)']:
745	oldPDF = True
746	data[1][1][datus[0][:4]] = copy.deepcopy(datus[1][:2])
747	continue
748	#end PDF cleanup
749	sub = G2frame.GPXtree.AppendItem(Id,datus[0])
750	#patch
751	if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
752	if datum[0].startswith('PWDR'):
753	datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
754	else:
755	datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
756	for item in datus[1][0]: #zip makes tuples - now make lists!
757	datus[1][0][item] = list(datus[1][0][item])
758	#end patch
759	G2frame.GPXtree.SetItemPyData(sub,datus[1])
760	if 'PDF ' in datum[0][:4] and oldPDF:
761	sub = G2frame.GPXtree.AppendItem(Id,'PDF Peaks')
762	G2frame.GPXtree.SetItemPyData(sub,{'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]})
763	if datum [0].startswith('IMG'): #retrieve image default flag & data if set
764	Data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Image Controls'))
765	if Data['setDefault']:
766	G2frame.imageDefault = Data
767	G2frame.imageDefault['setDefault'] = False
768	if 'formatName' in G2frame.imageDefault: del G2frame.imageDefault['formatName']
769	if LastSavedUsing:
770	print('GPX load successful. Last saved with GSAS-II revision '+LastSavedUsing)
771	else:
772	print('project load successful')
773	if GSASIIpath.GetConfigValue('show_gpxSize'):
774	print(50*'=')
775	print('File section sizes (Kb)')
776	for item in sizeList:
777	print(' {:20s} {:10.3f}'.format(
778	item[:20],sizeList[item]/1024.))
779	print(50*'=')
780	G2frame.NewPlot = True
781	except Exception as errmsg:
782	if GSASIIpath.GetConfigValue('debug'):
783	print('\nError reading GPX file:',errmsg)
784	import traceback
785	print (traceback.format_exc())
786	msg = wx.MessageDialog(G2frame,message="Error reading file "+
787	str(G2frame.GSASprojectfile)+". This is not a current GSAS-II .gpx file",
788	caption="Load Error",style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
789	msg.ShowModal()
790	finally:
791	filep.close()
792	wx.EndBusyCursor()
793	G2frame.Status.SetStatusText('Mouse RB drag/drop to reorder',0)
794	if deleteSeq:
795	if hist: hist.close()
796	try:
797	os.remove(GPXphase)
798	except:
799	print('Warning: unable to delete {}'.format(GPXphase))
800	try:
801	os.remove(GPXhist)
802	except:
803	print('Warning: unable to delete {}'.format(GPXhist))
804	G2frame.SetTitleByGPX()
805	if LastSavedUsing:
806	try:
807	G2G.updateNotifier(G2frame,int(LastSavedUsing))
808	except:
809	pass
810
811	def ProjFileSave(G2frame):
812	'Save a GSAS-II project file'
813	if not G2frame.GPXtree.IsEmpty():
814	file = open(G2frame.GSASprojectfile,'wb')
815	print ('save to file: '+G2frame.GSASprojectfile)
816	# stick the file name into the tree and version info into tree so they are saved.
817	# (Controls should always be created at this point)
818	try:
819	Controls = G2frame.GPXtree.GetItemPyData(
820	G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
821	Controls['LastSavedAs'] = os.path.abspath(G2frame.GSASprojectfile)
822	Controls['LastSavedUsing'] = str(GSASIIpath.GetVersionNumber())
823	Controls['PythonVersions'] = G2frame.PackageVersions
824	except:
825	pass
826	wx.BeginBusyCursor()
827	try:
828	item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
829	while item:
830	data = []
831	name = G2frame.GPXtree.GetItemText(item)
832	if name.startswith('Hist/Phase'): # skip over this
833	item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
834	continue
835	data.append([name,G2frame.GPXtree.GetItemPyData(item)])
836	item2, cookie2 = G2frame.GPXtree.GetFirstChild(item)
837	while item2:
838	name = G2frame.GPXtree.GetItemText(item2)
839	data.append([name,G2frame.GPXtree.GetItemPyData(item2)])
840	item2, cookie2 = G2frame.GPXtree.GetNextChild(item, cookie2)
841	item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
842	cPickle.dump(data,file,2)
843	file.close()
844	pth = os.path.split(os.path.abspath(G2frame.GSASprojectfile))[0]
845	if GSASIIpath.GetConfigValue('Save_paths'): G2G.SaveGPXdirectory(pth)
846	G2frame.LastGPXdir = pth
847	finally:
848	wx.EndBusyCursor()
849	print('project save successful')
850
851	def SaveIntegration(G2frame,PickId,data,Overwrite=False):
852	'Save image integration results as powder pattern(s)'
853	waves = {'Cu':[1.54051,1.54433],'Ti':[2.74841,2.75207],'Cr':[2.28962,2.29351],
854	'Fe':[1.93597,1.93991],'Co':[1.78892,1.79278],'Mo':[0.70926,0.713543],
855	'Ag':[0.559363,0.563775]}
856	azms = G2frame.Integrate[1]
857	X = G2frame.Integrate[2][:-1]
858	N = len(X)
859	Id = G2frame.GPXtree.GetItemParent(PickId)
860	name = G2frame.GPXtree.GetItemText(Id)
861	name = name.replace('IMG ',data['type']+' ')
862	Comments = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Comments'))
863	Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
864	Comments.append('Dark image = %s\n'%str(data['dark image']))
865	Comments.append('Background image = %s\n'%str(data['background image']))
866	Comments.append('Gain map = %s\n'%str(data['Gain map']))
867
868	if 'PWDR' in name:
869	if 'target' in data:
870	names = ['Type','Lam1','Lam2','I(L2)/I(L1)','Zero','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth']
871	codes = [0 for i in range(14)]
872	else:
873	if data.get('IfPink',False):
874	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','Z','alpha-0','alpha-1','beta-0','beta-1','Azimuth']
875	codes = [0 for i in range(15)]
876	else:
877	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth']
878	codes = [0 for i in range(12)]
879	elif 'SASD' in name:
880	names = ['Type','Lam','Zero','Azimuth']
881	codes = [0 for i in range(4)]
882	X = 4.np.pinpsind(X/2.)/data['wavelength'] #convert to q
883	Xminmax = [X[0],X[-1]]
884	Azms = np.zeros(data['outAzimuths'])
885	dazm = 0.
886	if data['outAzimuths'] > 1:
887	dazm = np.min(np.abs(np.diff(azms)))/2.
888	G2frame.IntgOutList = []
889	for i,azm in enumerate(azms[:-1]):
890	Aname = name+" Azm= %.2f"%((azm+dazm)%360.)
891	item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
892	# if Overwrite delete any duplicate
893	if Overwrite and G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname):
894	print('Replacing '+Aname)
895	item = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname)
896	G2frame.GPXtree.Delete(item)
897	else:
898	nOcc = 0
899	while item:
900	Name = G2frame.GPXtree.GetItemText(item)
901	if Aname in Name:
902	nOcc += 1
903	item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
904	if nOcc:
905	Aname += '(%d)'%(nOcc)
906	Sample = G2obj.SetDefaultSample() #set as Debye-Scherrer
907	Sample['Gonio. radius'] = data['distance']
908	Sample['Omega'] = data['GonioAngles'][0]
909	Sample['Chi'] = data['GonioAngles'][1]
910	Sample['Phi'] = data['GonioAngles'][2]
911	Sample['Azimuth'] = (azm+dazm)%360. #put here as bin center
912	polariz = data['PolaVal'][0]
913	for item in Comments:
914	for key in ('Temperature','Pressure','Time','FreePrm1','FreePrm2','FreePrm3','Omega',
915	'Chi','Phi'):
916	if key.lower() in item.lower():
917	try:
918	Sample[key] = float(item.split('=')[1])
919	except:
920	pass
921	if 'label_prm' in item.lower():
922	for num in ('1','2','3'):
923	if 'label_prm'+num in item.lower():
924	Controls['FreePrm'+num] = item.split('=')[1].strip()
925	if 'PWDR' in Aname:
926	if 'target' in data: #from lab x-ray 2D imaging data
927	wave1,wave2 = waves[data['target']]
928	parms = ['PXC',wave1,wave2,0.5,0.0,polariz,290.,-40.,30.,6.,-14.,0.0,0.0001,Azms[i]]
929	else:
930	if data.get('IfPink',False):
931	parms = ['PXB',data['wavelength'],0.0,polariz,0.,8000.,-150.,-24.,0.,0.,0.,13.,-1300.,3.,-7.,Azms[i]] #from Sect 35 LSS
932	else:
933	parms = ['PXC',data['wavelength'],0.0,polariz,1.0,-0.10,0.4,0.30,1.0,0.0,0.0001,Azms[i]]
934	elif 'SASD' in Aname:
935	Sample['Trans'] = data['SampleAbs'][0]
936	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
937	Y = G2frame.Integrate[0][i]
938	Ymin = np.min(Y)
939	Ymax = np.max(Y)
940	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
941	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=Aname)
942	G2frame.IntgOutList.append(Id)
943	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments)
944	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Limits'),copy.deepcopy([tuple(Xminmax),Xminmax]))
945	if 'PWDR' in Aname:
946	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Background'),[['chebyschev-1',1,3,1.0,0.0,0.0],
947	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[],'background PWDR':['',1.0,False]}])
948	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
949	for item in inst[0]:
950	inst[0][item] = list(inst[0][item])
951	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Instrument Parameters'),inst)
952	if 'PWDR' in Aname:
953	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample)
954	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
955	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Index Peak List'),[[],[]])
956	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Unit Cells List'),[])
957	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Reflection Lists'),{})
958	elif 'SASD' in Aname:
959	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
960	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample)
961	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
962	valuesdict = {
963	'wtFactor':1.0,'Dummy':False,'ranId':ran.randint(0,sys.maxsize),'Offset':[0.0,0.0],'delOffset':0.02*Ymax,
964	'refOffset':-0.1Ymax,'refDelt':0.1Ymax,'Yminmax':[Ymin,Ymax]}
965	G2frame.GPXtree.SetItemPyData(Id,[valuesdict,
966	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
967	return Id #last powder pattern generated
968
969	def XYsave(G2frame,XY,labelX='X',labelY='Y',names=[]):
970	'Save XY table data'
971	pth = G2G.GetExportPath(G2frame)
972	dlg = wx.FileDialog(
973	G2frame, 'Enter csv filename for XY table', pth, '',
974	'XY table file (.csv)\|.csv',wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
975	try:
976	if dlg.ShowModal() == wx.ID_OK:
977	filename = dlg.GetPath()
978	filename = os.path.splitext(filename)[0]+'.csv'
979	File = open(filename,'w')
980	else:
981	filename = None
982	finally:
983	dlg.Destroy()
984	if not filename:
985	return
986	for i in range(len(XY)):
987	if len(names):
988	header = '%s,%s(%s)\n'%(labelX,labelY,names[i])
989	else:
990	header = '%s,%s(%d)\n'%(labelX,labelY,i)
991	File.write(header)
992	for x,y in XY[i].T:
993	File.write('%.3f,%.3f\n'%(x,y))
994	File.close()
995	print (' XY data saved to: '+filename)
996
997	def PeakListSave(G2frame,file,peaks):
998	'Save powder peaks to a data file'
999	print ('save peak list to file: '+G2frame.peaklistfile)
1000	if not peaks:
1001	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1002	try:
1003	dlg.ShowModal()
1004	finally:
1005	dlg.Destroy()
1006	return
1007	for peak in peaks:
1008	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
1009	(peak[0],peak[2],peak[4],peak[6]))
1010	print ('peak list saved')
1011
1012	def IndexPeakListSave(G2frame,peaks):
1013	'Save powder peaks from the indexing list'
1014	file = open(G2frame.peaklistfile,'wa')
1015	print ('save index peak list to file: '+G2frame.peaklistfile)
1016	wx.BeginBusyCursor()
1017	try:
1018	if not peaks:
1019	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1020	try:
1021	dlg.ShowModal()
1022	finally:
1023	dlg.Destroy()
1024	return
1025	for peak in peaks:
1026	file.write("%12.6f\n" % (peak[7]))
1027	file.close()
1028	finally:
1029	wx.EndBusyCursor()
1030	print ('index peak list saved')
1031
1032	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1033	confirmoverwrite=True, parent=None,
1034	multipleselect=False):
1035	'''If the filename is a zip file, extract a file from that
1036	archive.
1037
1038	:param list Selection: used to predefine the name of the file
1039	to be extracted. Filename case and zip directory name are
1040	ignored in selection; the first matching file is used.
1041
1042	:param bool confirmread: if True asks the user to confirm before expanding
1043	the only file in a zip
1044
1045	:param bool confirmoverwrite: if True asks the user to confirm
1046	before overwriting if the extracted file already exists
1047
1048	:param bool multipleselect: if True allows more than one zip
1049	file to be extracted, a list of file(s) is returned.
1050	If only one file is present, do not ask which one, otherwise
1051	offer a list of choices (unless selection is used).
1052
1053	:returns: the name of the file that has been created or a
1054	list of files (see multipleselect)
1055
1056	If the file is not a zipfile, return the name of the input file.
1057	If the zipfile is empty or no file has been selected, return None
1058	'''
1059	import zipfile # do this now, since we can save startup time by doing this only on need
1060	import shutil
1061	zloc = os.path.split(filename)[0]
1062	if not zipfile.is_zipfile(filename):
1063	#print("not zip")
1064	return filename
1065
1066	z = zipfile.ZipFile(filename,'r')
1067	zinfo = z.infolist()
1068
1069	if len(zinfo) == 0:
1070	#print('Zip has no files!')
1071	zlist = [-1]
1072	if selection:
1073	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1074	if selection.lower() in choices:
1075	zlist = [choices.index(selection.lower())]
1076	else:
1077	print('debug: file '+str(selection)+' was not found in '+str(filename))
1078	zlist = [-1]
1079	elif len(zinfo) == 1 and confirmread:
1080	result = wx.ID_NO
1081	dlg = wx.MessageDialog(
1082	parent,
1083	'Is file '+str(zinfo[0].filename)+
1084	' what you want to extract from '+
1085	str(os.path.split(filename)[1])+'?',
1086	'Confirm file',
1087	wx.YES_NO \| wx.ICON_QUESTION)
1088	try:
1089	result = dlg.ShowModal()
1090	finally:
1091	dlg.Destroy()
1092	if result == wx.ID_NO:
1093	zlist = [-1]
1094	else:
1095	zlist = [0]
1096	elif len(zinfo) == 1:
1097	zlist = [0]
1098	elif multipleselect:
1099	# select one or more from a from list
1100	choices = [i.filename for i in zinfo]
1101	dlg = G2G.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1102	'Choose file(s)',choices)
1103	if dlg.ShowModal() == wx.ID_OK:
1104	zlist = dlg.GetSelections()
1105	else:
1106	zlist = []
1107	dlg.Destroy()
1108	else:
1109	# select one from a from list
1110	choices = [i.filename for i in zinfo]
1111	dlg = wx.SingleChoiceDialog(parent,
1112	'Select file to extract from zip file'+str(filename),'Choose file',
1113	choices,)
1114	if dlg.ShowModal() == wx.ID_OK:
1115	zlist = [dlg.GetSelection()]
1116	else:
1117	zlist = [-1]
1118	dlg.Destroy()
1119
1120	outlist = []
1121	for zindex in zlist:
1122	if zindex >= 0:
1123	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1124	if os.path.exists(efil) and confirmoverwrite:
1125	result = wx.ID_NO
1126	dlg = wx.MessageDialog(parent,
1127	'File '+str(efil)+' already exists. OK to overwrite it?',
1128	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1129	try:
1130	result = dlg.ShowModal()
1131	finally:
1132	dlg.Destroy()
1133	if result == wx.ID_NO:
1134	zindex = -1
1135	if zindex >= 0:
1136	# extract the file to the current directory, regardless of it's original path
1137	#z.extract(zinfo[zindex],zloc)
1138	eloc,efil = os.path.split(zinfo[zindex].filename)
1139	outfile = os.path.join(zloc, efil)
1140	fpin = z.open(zinfo[zindex])
1141	fpout = open(outfile, "wb")
1142	shutil.copyfileobj(fpin, fpout)
1143	fpin.close()
1144	fpout.close()
1145	outlist.append(outfile)
1146	z.close()
1147	if multipleselect and len(outlist) >= 1:
1148	return outlist
1149	elif len(outlist) == 1:
1150	return outlist[0]
1151	else:
1152	return None
1153
1154	def striphist(var,insChar=''):
1155	'strip a histogram number from a var name'
1156	sv = var.split(':')
1157	if len(sv) <= 1: return var
1158	if sv[1]:
1159	sv[1] = insChar
1160	return ':'.join(sv)
1161
1162	######################################################################
1163	# base classes for reading various types of data files
1164	# not used directly, only by subclassing
1165	######################################################################
1166	class ExportBaseclass(object):
1167	'''Defines a base class for the exporting of GSAS-II results.
1168
1169	This class is subclassed in the various exports/G2export_*.py files. Those files
1170	are imported in :meth:`GSASIIdataGUI.GSASII._init_Exports` which defines the
1171	appropriate menu items for each one and the .Exporter method is called
1172	directly from the menu item.
1173
1174	Routines may also define a .Writer method, which is used to write a single
1175	file without invoking any GUI objects.
1176	'''
1177	# TODO: review exporters producing exceptions where .Writer can't be used where G2frame is None (see CIF)
1178	# TODO: review conflicting uses of .Writer with mode (SeqRef) & elsewhere
1179	# TODO: move this class to G2fil
1180	def __init__(self,G2frame,formatName,extension,longFormatName=None,):
1181	self.G2frame = G2frame
1182	self.formatName = formatName # short string naming file type
1183	self.extension = extension
1184	if longFormatName: # longer string naming file type
1185	self.longFormatName = longFormatName
1186	else:
1187	self.longFormatName = formatName
1188	self.OverallParms = {}
1189	self.Phases = {}
1190	self.Histograms = {}
1191	self.powderDict = {}
1192	self.sasdDict = {}
1193	self.refdDict = {}
1194	self.xtalDict = {}
1195	self.parmDict = {}
1196	self.sigDict = {}
1197	self.fp = None
1198	# updated in InitExport:
1199	self.currentExportType = None # type of export that has been requested
1200	# updated in ExportSelect (when used):
1201	self.phasenam = None # a list of selected phases
1202	self.histnam = None # a list of selected histograms
1203	self.filename = None # name of file to be written (single export) or template (multiple files)
1204	self.dirname = '' # name of directory where file(s) will be written
1205	self.fullpath = '' # name of file being written -- full path
1206
1207	# items that should be defined in a subclass of this class
1208	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1209	# The following types are defined: 'project', "phase", "powder", "single"
1210	self.multiple = False # set as True if the class can export multiple phases or histograms
1211	# self.multiple is ignored for "project" exports
1212
1213	def InitExport(self,event):
1214	'''Determines the type of menu that called the Exporter and
1215	misc initialization.
1216	'''
1217	self.filename = None # name of file to be written (single export)
1218	self.dirname = '' # name of file to be written (multiple export)
1219	if event:
1220	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1221
1222	def MakePWDRfilename(self,hist):
1223	'''Make a filename root (no extension) from a PWDR histogram name
1224
1225	:param str hist: the histogram name in data tree (starts with "PWDR ")
1226	'''
1227	file0 = ''
1228	file1 = hist[5:]
1229	# replace repeated blanks
1230	while file1 != file0:
1231	file0 = file1
1232	file1 = file0.replace(' ',' ').strip()
1233	file0 = file1.replace('Azm= ','A')
1234	# if angle has unneeded decimal places on aziumuth, remove them
1235	if file0[-3:] == '.00': file0 = file0[:-3]
1236	file0 = file0.replace('.','_')
1237	file0 = file0.replace(' ','_')
1238	return file0
1239
1240	def ExportSelect(self,AskFile='ask'):
1241	'''Selects histograms or phases when needed. Sets a default file name when
1242	requested into self.filename; always sets a default directory in self.dirname.
1243
1244	:param bool AskFile: Determines how this routine processes getting a
1245	location to store the current export(s).
1246
1247	* if AskFile is 'ask' (default option), get the name of the file to be written;
1248	self.filename and self.dirname are always set. In the case where
1249	multiple files must be generated, the export routine should do this
1250	based on self.filename as a template.
1251	* if AskFile is 'dir', get the name of the directory to be used;
1252	self.filename is not used, but self.dirname is always set. The export routine
1253	will always generate the file name.
1254	* if AskFile is 'single', get only the name of the directory to be used when
1255	multiple items will be written (as multiple files) are used
1256	or a complete file name is requested when a single file
1257	name is selected. self.dirname is always set and self.filename used
1258	only when a single file is selected.
1259	* if AskFile is 'default', creates a name of the file to be used from
1260	the name of the project (.gpx) file. If the project has not been saved,
1261	then the name of file is requested.
1262	self.filename and self.dirname are always set. In the case where
1263	multiple file names must be generated, the export routine should do this
1264	based on self.filename.
1265	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1266	file. If the project has not been saved, then a directory is requested.
1267	self.filename is not used.
1268
1269	:returns: True in case of an error
1270	'''
1271
1272	numselected = 1
1273	if self.currentExportType == 'phase':
1274	if len(self.Phases) == 0:
1275	self.G2frame.ErrorDialog(
1276	'Empty project',
1277	'Project does not contain any phases.')
1278	return True
1279	elif len(self.Phases) == 1:
1280	self.phasenam = list(self.Phases.keys())
1281	elif self.multiple:
1282	choices = sorted(self.Phases.keys())
1283	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1284	if phasenum is None: return True
1285	self.phasenam = [choices[i] for i in phasenum]
1286	if not self.phasenam: return True
1287	numselected = len(self.phasenam)
1288	else:
1289	choices = sorted(self.Phases.keys())
1290	phasenum = G2G.ItemSelector(choices,self.G2frame)
1291	if phasenum is None: return True
1292	self.phasenam = [choices[phasenum]]
1293	numselected = len(self.phasenam)
1294	elif self.currentExportType == 'single':
1295	if len(self.xtalDict) == 0:
1296	self.G2frame.ErrorDialog(
1297	'Empty project',
1298	'Project does not contain any single crystal data.')
1299	return True
1300	elif len(self.xtalDict) == 1:
1301	self.histnam = self.xtalDict.values()
1302	elif self.multiple:
1303	choices = sorted(self.xtalDict.values())
1304	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1305	if not hnum: return True
1306	self.histnam = [choices[i] for i in hnum]
1307	numselected = len(self.histnam)
1308	else:
1309	choices = sorted(self.xtalDict.values())
1310	hnum = G2G.ItemSelector(choices,self.G2frame)
1311	if hnum is None: return True
1312	self.histnam = [choices[hnum]]
1313	numselected = len(self.histnam)
1314	elif self.currentExportType == 'powder':
1315	if len(self.powderDict) == 0:
1316	self.G2frame.ErrorDialog(
1317	'Empty project',
1318	'Project does not contain any powder data.')
1319	return True
1320	elif len(self.powderDict) == 1:
1321	self.histnam = list(self.powderDict.values())
1322	elif self.multiple:
1323	choices = sorted(self.powderDict.values())
1324	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1325	if not hnum: return True
1326	self.histnam = [choices[i] for i in hnum]
1327	numselected = len(self.histnam)
1328	else:
1329	choices = sorted(self.powderDict.values())
1330	hnum = G2G.ItemSelector(choices,self.G2frame)
1331	if hnum is None: return True
1332	self.histnam = [choices[hnum]]
1333	numselected = len(self.histnam)
1334	elif self.currentExportType == 'sasd':
1335	if len(self.sasdDict) == 0:
1336	self.G2frame.ErrorDialog(
1337	'Empty project',
1338	'Project does not contain any small angle data.')
1339	return True
1340	elif len(self.sasdDict) == 1:
1341	self.histnam = self.sasdDict.values()
1342	elif self.multiple:
1343	choices = sorted(self.sasdDict.values())
1344	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1345	if not hnum: return True
1346	self.histnam = [choices[i] for i in hnum]
1347	numselected = len(self.histnam)
1348	else:
1349	choices = sorted(self.sasdDict.values())
1350	hnum = G2G.ItemSelector(choices,self.G2frame)
1351	if hnum is None: return True
1352	self.histnam = [choices[hnum]]
1353	numselected = len(self.histnam)
1354	elif self.currentExportType == 'refd':
1355	if len(self.refdDict) == 0:
1356	self.G2frame.ErrorDialog(
1357	'Empty project',
1358	'Project does not contain any reflectivity data.')
1359	return True
1360	elif len(self.refdDict) == 1:
1361	self.histnam = self.refdDict.values()
1362	elif self.multiple:
1363	choices = sorted(self.refdDict.values())
1364	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1365	if not hnum: return True
1366	self.histnam = [choices[i] for i in hnum]
1367	numselected = len(self.histnam)
1368	else:
1369	choices = sorted(self.refdDict.values())
1370	hnum = G2G.ItemSelector(choices,self.G2frame)
1371	if hnum is None: return True
1372	self.histnam = [choices[hnum]]
1373	numselected = len(self.histnam)
1374	elif self.currentExportType == 'image':
1375	if len(self.Histograms) == 0:
1376	self.G2frame.ErrorDialog(
1377	'Empty project',
1378	'Project does not contain any images.')
1379	return True
1380	elif len(self.Histograms) == 1:
1381	self.histnam = list(self.Histograms.keys())
1382	else:
1383	choices = sorted(self.Histograms.keys())
1384	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1385	if self.multiple:
1386	if not hnum: return True
1387	self.histnam = [choices[i] for i in hnum]
1388	else:
1389	if hnum is None: return True
1390	self.histnam = [choices[hnum]]
1391	numselected = len(self.histnam)
1392	if self.currentExportType == 'map':
1393	# search for phases with maps
1394	mapPhases = []
1395	choices = []
1396	for phasenam in sorted(self.Phases):
1397	phasedict = self.Phases[phasenam] # pointer to current phase info
1398	if len(phasedict['General']['Map'].get('rho',[])):
1399	mapPhases.append(phasenam)
1400	if phasedict['General']['Map'].get('Flip'):
1401	choices.append('Charge flip map: '+str(phasenam))
1402	elif phasedict['General']['Map'].get('MapType'):
1403	choices.append(
1404	str(phasedict['General']['Map'].get('MapType'))
1405	+ ' map: ' + str(phasenam))
1406	else:
1407	choices.append('unknown map: '+str(phasenam))
1408	# select a map if needed
1409	if len(mapPhases) == 0:
1410	self.G2frame.ErrorDialog(
1411	'Empty project',
1412	'Project does not contain any maps.')
1413	return True
1414	elif len(mapPhases) == 1:
1415	self.phasenam = mapPhases
1416	else:
1417	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1418	if self.multiple:
1419	if not phasenum: return True
1420	self.phasenam = [mapPhases[i] for i in phasenum]
1421	else:
1422	if phasenum is None: return True
1423	self.phasenam = [mapPhases[phasenum]]
1424	numselected = len(self.phasenam)
1425
1426	# items selected, now set self.dirname and usually self.filename
1427	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
1428	AskFile == 'default' and not self.G2frame.GSASprojectfile
1429	):
1430	filename = self.askSaveFile()
1431	if not filename: return True
1432	self.dirname,self.filename = os.path.split(filename)
1433	elif AskFile == 'dir' or AskFile == 'single' or (
1434	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
1435	):
1436	self.dirname = self.askSaveDirectory()
1437	if not self.dirname: return True
1438	elif AskFile == 'default-dir' or AskFile == 'default':
1439	self.dirname,self.filename = os.path.split(
1440	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
1441	)
1442	else:
1443	raise Exception('This should not happen!')
1444
1445	def loadParmDict(self):
1446	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
1447	refined values to those from the last cycle and set the uncertainties for the
1448	refined parameters in another dict (self.sigDict).
1449
1450	Expands the parm & sig dicts to include values derived from constraints.
1451
1452	This could be made faster for sequential fits by reducing the histogram list to only
1453	the active histogram being exported.
1454	'''
1455	# TODO: this does not expand wild-card constraints properly for sequential fits.
1456	# this needs revisiting for sequential exports if constraints need to be generated correctly.
1457
1458	self.G2frame.CheckNotebook()
1459	self.parmDict = {}
1460	self.sigDict = {}
1461	rigidbodyDict = {}
1462	covDict = {}
1463	consDict = {}
1464	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1465	if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1466	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1467	while item:
1468	name = self.G2frame.GPXtree.GetItemText(item)
1469	if name == 'Rigid bodies':
1470	rigidbodyDict = self.G2frame.GPXtree.GetItemPyData(item)
1471	elif name == 'Covariance':
1472	covDict = self.G2frame.GPXtree.GetItemPyData(item)
1473	elif name == 'Constraints':
1474	consDict = self.G2frame.GPXtree.GetItemPyData(item)
1475	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1476	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1477	self.parmDict.update(rbDict)
1478	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1479	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData(
1480	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
1481	self.parmDict.update(phaseDict)
1482	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
1483	Phases,Histograms,Print=False,resetRefList=False)
1484	self.parmDict.update(hapDict)
1485	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
1486	self.parmDict.update(histDict)
1487	self.parmDict.update(zip(
1488	covDict.get('varyList',[]),
1489	covDict.get('variables',[])))
1490	self.sigDict = dict(zip(
1491	covDict.get('varyList',[]),
1492	covDict.get('sig',[])))
1493	# expand to include constraints: first compile a list of constraints
1494	constList = []
1495	for item in consDict:
1496	if item.startswith('_'): continue
1497	constList += consDict[item]
1498	# now process the constraints
1499	G2mv.InitVars()
1500	constrDict,fixedList,ignored = G2mv.ProcessConstraints(constList)
1501	varyList = covDict.get('varyListStart')
1502	if varyList is None and len(constrDict) == 0:
1503	# no constraints can use varyList
1504	varyList = covDict.get('varyList')
1505	elif varyList is None:
1506	# old GPX file from before pre-constraint varyList is saved
1507	print (' * Old refinement: Please use Calculate/Refine to redo *')
1508	raise Exception(' * Export aborted *')
1509	else:
1510	varyList = list(varyList)
1511	# add symmetry-generated constraints
1512	rigidbodyDict = self.G2frame.GPXtree.GetItemPyData(
1513	G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,'Rigid bodies'))
1514	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1515	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False) # done twice, needed?
1516	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData(
1517	Phases,RestraintDict=None,rbIds=rbIds,Print=False) # generates atom symmetry constraints
1518	msg = G2mv.EvaluateMultipliers(constrDict,phaseDict)
1519	if msg:
1520	print('Unable to interpret multiplier(s): '+msg)
1521	raise Exception(' * CIF creation aborted *')
1522	errmsg,warnmsg,groups,parmlist = G2mv.GenerateConstraints(varyList,constrDict,fixedList,self.parmDict)
1523	if errmsg:
1524	# this really should not happen
1525	print (' * ERROR - constraints are internally inconsistent *')
1526	print ('Errors: ',errmsg)
1527	if warnmsg: print ('Warnings'+warnmsg)
1528	raise Exception(' * CIF creation aborted *')
1529	G2mv.Map2Dict(self.parmDict,varyList) # changes varyList
1530	G2mv.Dict2Map(self.parmDict) # add the constrained values to the parameter dictionary
1531	# and add their uncertainties into the esd dictionary (sigDict)
1532	if covDict.get('covMatrix') is not None:
1533	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
1534
1535	def loadTree(self):
1536	'''Load the contents of the data tree into a set of dicts
1537	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
1538	& self.xtalDict)
1539
1540	* The childrenless data tree items are overall parameters/controls for the
1541	entire project and are placed in self.OverallParms
1542	* Phase items are placed in self.Phases
1543	* Data items are placed in self.Histogram. The key for these data items
1544	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
1545	'''
1546	self.OverallParms = {}
1547	self.powderDict = {}
1548	self.sasdDict = {}
1549	self.refdDict = {}
1550	self.xtalDict = {}
1551	self.Phases = {}
1552	self.Histograms = {}
1553	self.SeqRefdata = None
1554	self.SeqRefhist = None
1555	if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1556	histType = None
1557	if self.currentExportType == 'phase':
1558	# if exporting phases load them here
1559	sub = G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,'Phases')
1560	if not sub:
1561	print ('no phases found')
1562	return True
1563	item, cookie = self.G2frame.GPXtree.GetFirstChild(sub)
1564	while item:
1565	phaseName = self.G2frame.GPXtree.GetItemText(item)
1566	self.Phases[phaseName] = self.G2frame.GPXtree.GetItemPyData(item)
1567	item, cookie = self.G2frame.GPXtree.GetNextChild(sub, cookie)
1568	# Get rigid body info into self.OverallParms
1569	for key in ('Rigid bodies','Covariance'):
1570	item = G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,key)
1571	if item:
1572	self.OverallParms[key] = self.G2frame.GPXtree.GetItemPyData(item)
1573	item, cookie = self.G2frame.GPXtree.GetNextChild(sub, cookie)
1574	return
1575	elif self.currentExportType == 'single':
1576	histType = 'HKLF'
1577	elif self.currentExportType == 'powder':
1578	histType = 'PWDR'
1579	elif self.currentExportType == 'image':
1580	histType = 'IMG'
1581	elif self.currentExportType == 'sasd':
1582	histType = 'SASD'
1583	elif self.currentExportType == 'refd':
1584	histType = 'REFD'
1585
1586	if histType: # Loading just one kind of tree entry
1587	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1588	while item:
1589	name = self.G2frame.GPXtree.GetItemText(item)
1590	if name.startswith(histType):
1591	if self.Histograms.get(name): # there is already an item with this name
1592	print('Histogram name '+str(name)+' is repeated. Renaming')
1593	if name[-1] == '9':
1594	name = name[:-1] + '10'
1595	elif name[-1] in '012345678':
1596	name = name[:-1] + str(int(name[-1])+1)
1597	else:
1598	name += '-1'
1599	self.Histograms[name] = {}
1600	# the main info goes into Data, but the 0th
1601	# element contains refinement results, carry
1602	# that over too now.
1603	self.Histograms[name]['Data'] = self.G2frame.GPXtree.GetItemPyData(item)[1]
1604	self.Histograms[name][0] = self.G2frame.GPXtree.GetItemPyData(item)[0]
1605	item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1606	while item2:
1607	child = self.G2frame.GPXtree.GetItemText(item2)
1608	self.Histograms[name][child] = self.G2frame.GPXtree.GetItemPyData(item2)
1609	item2, cookie2 = self.G2frame.GPXtree.GetNextChild(item, cookie2)
1610	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1611	# index powder and single crystal histograms by number
1612	for hist in self.Histograms:
1613	if hist.startswith("PWDR"):
1614	d = self.powderDict
1615	elif hist.startswith("HKLF"):
1616	d = self.xtalDict
1617	elif hist.startswith("SASD"):
1618	d = self.sasdDict
1619	elif hist.startswith("REFD"):
1620	d = self.refdDict
1621	else:
1622	return
1623	i = self.Histograms[hist].get('hId')
1624	if i is None and not d.keys():
1625	i = 0
1626	elif i is None or i in d.keys():
1627	i = max(d.keys())+1
1628	d[i] = hist
1629	return
1630	# else standard load: using all interlinked phases and histograms
1631	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1632	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1633	while item:
1634	name = self.G2frame.GPXtree.GetItemText(item)
1635	item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1636	if not item2:
1637	self.OverallParms[name] = self.G2frame.GPXtree.GetItemPyData(item)
1638	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1639	# index powder and single crystal histograms
1640	for hist in self.Histograms:
1641	i = self.Histograms[hist]['hId']
1642	if hist.startswith("PWDR"):
1643	self.powderDict[i] = hist
1644	elif hist.startswith("HKLF"):
1645	self.xtalDict[i] = hist
1646	elif hist.startswith("SASD"):
1647	self.sasdDict[i] = hist
1648	elif hist.startswith("REFD"):
1649	self.refdDict[i] = hist
1650
1651	def dumpTree(self,mode='type'):
1652	'''Print out information on the data tree dicts loaded in loadTree.
1653	Used for testing only.
1654	'''
1655	if self.SeqRefdata and self.SeqRefhist:
1656	print('Note that dumpTree does not show sequential results')
1657	print ('\nOverall')
1658	if mode == 'type':
1659	def Show(arg): return type(arg)
1660	else:
1661	def Show(arg): return arg
1662	for key in self.OverallParms:
1663	print (' '+key+Show(self.OverallParms[key]))
1664	print ('Phases')
1665	for key1 in self.Phases:
1666	print (' '+key1+Show(self.Phases[key1]))
1667	print ('Histogram')
1668	for key1 in self.Histograms:
1669	print (' '+key1+Show(self.Histograms[key1]))
1670	for key2 in self.Histograms[key1]:
1671	print (' '+key2+Show(self.Histograms[key1][key2]))
1672
1673	def defaultSaveFile(self):
1674	return os.path.abspath(
1675	os.path.splitext(self.G2frame.GSASprojectfile
1676	)[0]+self.extension)
1677
1678	def askSaveFile(self):
1679	'''Ask the user to supply a file name
1680
1681	:returns: a file name (str) or None if Cancel is pressed
1682
1683	'''
1684	#pth = G2G.GetExportPath(self.G2frame)
1685	if self.G2frame.GSASprojectfile:
1686	defnam = os.path.splitext(
1687	os.path.split(self.G2frame.GSASprojectfile)[1]
1688	)[0]+self.extension
1689	else:
1690	defnam = 'default' + self.extension
1691	return G2G.askSaveFile(self.G2frame,defnam,self.extension,self.longFormatName)
1692
1693	def askSaveDirectory(self):
1694	'''Ask the user to supply a directory name. Path name is used as the
1695	starting point for the next export path search.
1696
1697	:returns: a directory name (str) or None if Cancel is pressed
1698
1699	TODO: Can this be replaced with G2G.askSaveDirectory?
1700	'''
1701	pth = G2G.GetExportPath(self.G2frame)
1702	dlg = wx.DirDialog(
1703	self.G2frame, 'Input directory where file(s) will be written', pth,
1704	wx.DD_DEFAULT_STYLE)
1705	dlg.CenterOnParent()
1706	try:
1707	if dlg.ShowModal() == wx.ID_OK:
1708	filename = dlg.GetPath()
1709	self.G2frame.LastExportDir = filename
1710	else:
1711	filename = None
1712	finally:
1713	dlg.Destroy()
1714	return filename
1715
1716	# Tools for file writing.
1717	def OpenFile(self,fil=None,mode='w'):
1718	'''Open the output file
1719
1720	:param str fil: The name of the file to open. If None (default)
1721	the name defaults to self.dirname + self.filename.
1722	If an extension is supplied, it is not overridded,
1723	but if not, the default extension is used.
1724	:param str mode: The mode can 'w' to write a file, or 'a' to append to it. If
1725	the mode is 'd' (for debug), output is displayed on the console.
1726	:returns: the file object opened by the routine which is also
1727	saved as self.fp
1728	'''
1729	if mode == 'd': # debug mode
1730	self.fullpath = '(stdout)'
1731	self.fp = sys.stdout
1732	return
1733	if not fil:
1734	if not os.path.splitext(self.filename)[1]:
1735	self.filename += self.extension
1736	fil = os.path.join(self.dirname,self.filename)
1737	self.fullpath = os.path.abspath(fil)
1738	self.fp = open(self.fullpath,mode)
1739	return self.fp
1740
1741	def Write(self,line):
1742	'''write a line of output, attaching a line-end character
1743
1744	:param str line: the text to be written.
1745	'''
1746	if self.fp is None:
1747	raise Exception('Attempt to Write without use of OpenFile')
1748	self.fp.write(line+'\n')
1749
1750	def CloseFile(self,fp=None):
1751	'''Close a file opened in OpenFile
1752
1753	:param file fp: the file object to be closed. If None (default)
1754	file object self.fp is closed.
1755	'''
1756	if self.fp is None:
1757	raise Exception('Attempt to CloseFile without use of OpenFile')
1758	if self.fp == sys.stdout: return # debug mode
1759	if fp is None:
1760	fp = self.fp
1761	self.fp = None
1762	if fp is not None: fp.close()
1763
1764	def SetSeqRef(self,data,hist):
1765	'''Set the exporter to retrieve results from a sequential refinement
1766	rather than the main tree
1767	'''
1768	self.SeqRefdata = data
1769	self.SeqRefhist = hist
1770	data_name = data[hist]
1771	for i,val in zip(data_name['varyList'],data_name['sig']):
1772	self.sigDict[i] = val
1773	self.sigDict[striphist(i)] = val
1774	for i in data_name['parmDict']:
1775	self.parmDict[striphist(i)] = data_name['parmDict'][i]
1776	self.parmDict[i] = data_name['parmDict'][i]
1777	# zero out the dA[xyz] terms, they would only bring confusion
1778	key = i.split(':')
1779	if len(key) < 3: continue
1780	if key[2].startswith('dA'):
1781	self.parmDict[i] = 0.0
1782	for i,(val,sig) in data_name.get('depParmDict',{}).items():
1783	self.parmDict[i] = val
1784	self.sigDict[i] = sig
1785	#GSASIIpath.IPyBreak()
1786
1787	# Tools to pull information out of the data arrays
1788	def GetCell(self,phasenam):
1789	"""Gets the unit cell parameters and their s.u.'s for a selected phase
1790
1791	:param str phasenam: the name for the selected phase
1792	:returns: `cellList,cellSig` where each is a 7 element list corresponding
1793	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1794	cell values and `cellSig` has their uncertainties.
1795	"""
1796	if self.SeqRefdata and self.SeqRefhist:
1797	return self.GetSeqCell(phasenam,self.SeqRefdata[self.SeqRefhist])
1798	phasedict = self.Phases[phasenam] # pointer to current phase info
1799	try:
1800	pfx = str(phasedict['pId'])+'::'
1801	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
1802	cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A,
1803	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
1804	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
1805	return cellList,cellSig
1806	except KeyError:
1807	cell = phasedict['General']['Cell'][1:]
1808	return cell,7*[0]
1809
1810	def GetSeqCell(self,phasenam,data_name):
1811	"""Gets the unit cell parameters and their s.u.'s for a selected phase
1812	and histogram in a sequential fit
1813
1814	:param str phasenam: the name for the selected phase
1815	:param dict data_name: the sequential refinement parameters for the selected histogram
1816	:returns: `cellList,cellSig` where each is a 7 element list corresponding
1817	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1818	cell values and `cellSig` has their uncertainties.
1819	"""
1820	phasedict = self.Phases[phasenam]
1821	SGdata = phasedict['General']['SGData']
1822	pId = phasedict['pId']
1823	RecpCellTerms = G2lat.cell2A(phasedict['General']['Cell'][1:7])
1824	ESDlookup = {}
1825	Dlookup = {}
1826	varied = [striphist(i) for i in data_name['varyList']]
1827	for item,val in data_name['newCellDict'].items():
1828	if item in varied:
1829	ESDlookup[val[0]] = item
1830	Dlookup[item] = val[0]
1831	A = RecpCellTerms[:]
1832	for i in range(6):
1833	var = str(pId)+'::A'+str(i)
1834	if var in ESDlookup:
1835	A[i] = data_name['newCellDict'][ESDlookup[var]][1] # override with refined value
1836	cellDict = dict(zip([str(pId)+'::A'+str(i) for i in range(6)],A))
1837	zeroDict = {i:0.0 for i in cellDict}
1838	A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata,cellDict,zeroDict)
1839	covData = {
1840	'varyList': [Dlookup.get(striphist(v),v) for v in data_name['varyList']],
1841	'covMatrix': data_name['covMatrix']
1842	}
1843	return list(G2lat.A2cell(A)) + [G2lat.calc_V(A)], G2stIO.getCellEsd(str(pId)+'::',SGdata,A,covData)
1844
1845	def GetAtoms(self,phasenam):
1846	"""Gets the atoms associated with a phase. Can be used with standard
1847	or macromolecular phases
1848
1849	:param str phasenam: the name for the selected phase
1850	:returns: a list of items for eac atom where each item is a list containing:
1851	label, typ, mult, xyz, and td, where
1852
1853	* label and typ are the atom label and the scattering factor type (str)
1854	* mult is the site multiplicity (int)
1855	* xyz is contains a list with four pairs of numbers:
1856	x, y, z and fractional occupancy and
1857	their standard uncertainty (or a negative value)
1858	* td is contains a list with either one or six pairs of numbers:
1859	if one number it is U\\ :sub:`iso` and with six numbers it is
1860	U\\ :sub:`11`, U\\ :sub:`22`, U\\ :sub:`33`, U\\ :sub:`12`, U\\ :sub:`13` & U\\ :sub:`23`
1861	paired with their standard uncertainty (or a negative value)
1862	"""
1863	phasedict = self.Phases[phasenam] # pointer to current phase info
1864	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
1865	cfrac = cx+3
1866	fpfx = str(phasedict['pId'])+'::Afrac:'
1867	atomslist = []
1868	for i,at in enumerate(phasedict['Atoms']):
1869	if phasedict['General']['Type'] == 'macromolecular':
1870	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
1871	else:
1872	label = at[ct-1]
1873	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
1874	fsig = self.sigDict.get(fpfx+str(i),-0.009)
1875	mult = at[cs+1]
1876	typ = at[ct]
1877	xyz = []
1878	for j,v in enumerate(('x','y','z')):
1879	val = at[cx+j]
1880	pfx = str(phasedict['pId']) + '::A' + v + ':' + str(i)
1881	val = self.parmDict.get(pfx, val)
1882	dpfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
1883	sig = self.sigDict.get(dpfx,-0.000009)
1884	xyz.append((val,sig))
1885	xyz.append((fval,fsig))
1886	td = []
1887	if at[cia] == 'I':
1888	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
1889	val = self.parmDict.get(pfx,at[cia+1])
1890	sig = self.sigDict.get(pfx,-0.0009)
1891	td.append((val,sig))
1892	else:
1893	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
1894	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
1895	val = self.parmDict.get(pfx,at[cia+2+i])
1896	sig = self.sigDict.get(pfx,-0.0009)
1897	td.append((val,sig))
1898	atomslist.append((label,typ,mult,xyz,td))
1899	return atomslist
1900	######################################################################
1901	def ExportPowderList(G2frame):
1902	'''Returns a list of extensions supported by :func:`GSASIIIO:ExportPowder`
1903	along with their descriptions (note that a extension may be repeated
1904	but descriptions are unique).
1905	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
1906
1907	:param wx.Frame G2frame: the GSAS-II main data tree window
1908	'''
1909	extList = []
1910	extLabel = []
1911	for obj in G2frame.exporterlist:
1912	if 'powder' in obj.exporttype:
1913	try:
1914	obj.Writer
1915	extList.append(obj.extension)
1916	extLabel.append(obj.formatName)
1917	except AttributeError:
1918	pass
1919	return extList,extLabel
1920
1921	def ExportPowder(G2frame,TreeName,fileroot,extension,hint=''):
1922	'''Writes a single powder histogram using the Export routines.
1923	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
1924
1925	:param wx.Frame G2frame: the GSAS-II main data tree window
1926	:param str TreeName: the name of the histogram (PWDR ...) in the data tree
1927	:param str fileroot: name for file to be written, extension ignored
1928	:param str extension: extension for file to be written (start with '.'). Must
1929	match a powder export routine that has a Writer object.
1930	:param str hint: a string that must match the export's format
1931	'''
1932	filename = os.path.abspath(os.path.splitext(fileroot)[0]+extension)
1933	for obj in G2frame.exporterlist:
1934	if obj.extension == extension and 'powder' in obj.exporttype:
1935	if hint and hint not in obj.formatName: continue
1936	obj.currentExportType = 'powder'
1937	obj.InitExport(None)
1938	obj.loadTree() # load all histograms in tree into dicts
1939	if TreeName not in obj.Histograms:
1940	raise Exception('Histogram not found: '+str(TreeName))
1941	try:
1942	obj.Writer
1943	except AttributeError:
1944	continue
1945	try:
1946	obj.Writer(TreeName,filename)
1947	print('wrote file '+filename)
1948	return
1949	except Exception:
1950	print('Export Routine for '+extension+' failed.')
1951	else:
1952	print('No Export routine supports extension '+extension)
1953
1954	def ExportSequentialFullCIF(G2frame,seqData,Controls):
1955	'''Handles access to CIF exporter a bit differently for sequential fits, as this is
1956	not accessed via the usual export menus
1957	'''
1958	import G2export_CIF
1959	#import imp
1960	#imp.reload(G2export_CIF) #TODO for debug
1961	obj = G2export_CIF.ExportProjectCIF(G2frame)
1962	obj.Exporter(None,seqData=seqData,Controls=Controls)
1963
1964	def ExportSequential(G2frame,data,obj,exporttype):
1965	'''
1966	Used to export from every phase/dataset in a sequential refinement using
1967	a .Writer method for either projects or phases. Prompts to select histograms
1968	and for phase exports, which phase(s).
1969
1970	:param wx.Frame G2frame: the GSAS-II main data tree window
1971	:param dict data: the sequential refinement data object
1972	:param exporter obj: an exporter object
1973	:param str exporttype: indicates the type of export ('project' or 'phase')
1974	'''
1975	if len(data['histNames']) == 0:
1976	G2G.G2MessageBox(G2frame,'There are no sequential histograms','Warning')
1977	obj.InitExport(None)
1978	obj.loadTree()
1979	obj.loadParmDict()
1980	if len(data['histNames']) == 1:
1981	histlist = data['histNames']
1982	else:
1983	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select histograms to export from list',
1984	'Select histograms',data['histNames'])
1985	if dlg.ShowModal() == wx.ID_OK:
1986	histlist = [data['histNames'][l] for l in dlg.GetSelections()]
1987	dlg.Destroy()
1988	else:
1989	dlg.Destroy()
1990	return
1991	if exporttype == 'Phase':
1992	phaselist = list(obj.Phases.keys())
1993	if len(obj.Phases) == 0:
1994	G2G.G2MessageBox(G2frame,'There are no phases in sequential ref.','Warning')
1995	return
1996	elif len(obj.Phases) > 1:
1997	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select phases to export from list',
1998	'Select phases', phaselist)
1999	if dlg.ShowModal() == wx.ID_OK:
2000	phaselist = [phaselist[l] for l in dlg.GetSelections()]
2001	dlg.Destroy()
2002	else:
2003	dlg.Destroy()
2004	return
2005	filename = obj.askSaveFile()
2006	if not filename: return True
2007	obj.dirname,obj.filename = os.path.split(filename)
2008	print('Writing output to file '+str(obj.filename)+"...")
2009	mode = 'w'
2010	for p in phaselist:
2011	for h in histlist:
2012	obj.SetSeqRef(data,h)
2013	#GSASIIpath.IPyBreak()
2014	obj.Writer(h,phasenam=p,mode=mode)
2015	mode = 'a'
2016	print('...done')
2017	elif exporttype == 'Project': # note that the CIF exporter is not yet ready for this
2018	filename = obj.askSaveFile()
2019	if not filename: return True
2020	obj.dirname,obj.filename = os.path.split(filename)
2021	print('Writing output to file '+str(obj.filename)+"...")
2022	mode = 'w'
2023	for h in histlist:
2024	obj.SetSeqRef(data,h)
2025	obj.Writer(h,mode=mode)
2026	print('\t'+str(h)+' written')
2027	mode = 'a'
2028	print('...done')
2029	elif exporttype == 'Powder':
2030	filename = obj.askSaveFile()
2031	if not filename: return True
2032	obj.dirname,obj.filename = os.path.split(filename)
2033	print('Writing output to file '+str(obj.filename)+"...")
2034	mode = 'w'
2035	for h in histlist:
2036	obj.SetSeqRef(data,h)
2037	obj.Writer(h,mode=mode)
2038	print('\t'+str(h)+' written')
2039	mode = 'a'
2040	print('...done')
2041
2042	def ReadDIFFaX(DIFFaXfile):
2043	print ('read '+DIFFaXfile)
2044	Layer = {'Laue':'-1','Cell':[False,1.,1.,1.,90.,90.,90,1.],'Width':[[10.,10.],[False,False]],
2045	'Layers':[],'Stacking':[],'Transitions':[],'Toler':0.01,'AtInfo':{}}
2046	df = open(DIFFaXfile,'r')
2047	lines = df.readlines()
2048	df.close()
2049	struct = False
2050	Struct = []
2051	stack = False
2052	Stack = []
2053	trans = False
2054	Trans = []
2055	for diff in lines:
2056	diff = diff[:-1].lower()
2057	if '!' in diff:
2058	continue
2059	while '}' in diff: #strip comments
2060	iB = diff.index('{')
2061	iF = diff.index('}')+1
2062	if iB:
2063	diff = diff[:iB]
2064	else:
2065	diff = diff[iF:]
2066	if not diff:
2067	continue
2068	if diff.strip() == 'instrumental':
2069	continue
2070	if diff.strip() == 'structural':
2071	struct = True
2072	continue
2073	elif diff.strip() == 'stacking':
2074	struct = False
2075	stack = True
2076	continue
2077	elif diff.strip() == 'transitions':
2078	stack = False
2079	trans = True
2080	continue
2081	diff = diff.strip()
2082	if struct:
2083	if diff:
2084	Struct.append(diff)
2085	elif stack:
2086	if diff:
2087	Stack.append(diff)
2088	elif trans:
2089	if diff:
2090	Trans.append(diff)
2091
2092	#STRUCTURE records
2093	laueRec = Struct[1].split()
2094	Layer['Laue'] = laueRec[0]
2095	if Layer['Laue'] == 'unknown' and len(laueRec) > 1:
2096	Layer['Toler'] = float(laueRec[1]) #tolerance for 'unknown'?
2097	if Layer['Laue'] == '2/m(1)': Layer['Laue'] = '2/m(c)'
2098	if Layer['Laue'] == '2/m(2)': Layer['Laue'] = '2/m(ab)'
2099	cell = Struct[0].split()
2100	Layer['Cell'] = [False,float(cell[0]),float(cell[1]),float(cell[2]),90.,90.,float(cell[3]),1.0]
2101	nLayers = int(Struct[2])
2102	N = 3
2103	if 'layer' not in Struct[3]:
2104	N = 4
2105	if Struct[3] != 'infinite':
2106	width = Struct[3].split()
2107	Layer['Width'][0] = [float(width[0]),float(width[1])]
2108	for nL in range(nLayers):
2109	if '=' in Struct[N]:
2110	name = Struct[N].split('=')
2111	sameas = int(name[1])-1
2112	Layer['Layers'].append({'Name':name[0],'SameAs':Layer['Layers'][sameas]['Name'],'Symm':'None','Atoms':[]})
2113	N += 1
2114	continue
2115	Symm = 'None'
2116	if 'centro' in Struct[N+1]: Symm = '-1'
2117	Layer['Layers'].append({'Name':Struct[N],'SameAs':'','Symm':Symm,'Atoms':[]})
2118	N += 2
2119	while 'layer' not in Struct[N]:
2120	atom = Struct[N][4:].split()
2121	atomType = G2el.FixValence(Struct[N][:4].replace(' ','').strip().capitalize())
2122	if atomType not in Layer['AtInfo']:
2123	Layer['AtInfo'][atomType] = G2el.GetAtomInfo(atomType)
2124	atomName = '%s(%s)'%(atomType,atom[0])
2125	newVals = []
2126	for val in atom[1:6]:
2127	if '/' in val:
2128	newVals.append(eval(val+'.'))
2129	else:
2130	newVals.append(float(val))
2131	atomRec = [atomName,atomType,newVals[0],newVals[1],newVals[2],newVals[4],newVals[3]/78.9568]
2132	Layer['Layers'][-1]['Atoms'].append(atomRec)
2133	N += 1
2134	if N > len(Struct)-1:
2135	break
2136	#TRANSITIONS records
2137	transArray = []
2138	N = 0
2139	for i in range(nLayers):
2140	transArray.append([])
2141	for j in range(nLayers):
2142	vals = Trans[N].split()
2143	newVals = []
2144	for val in vals[:4]:
2145	if '/' in val:
2146	newVals.append(eval(val+'.'))
2147	else:
2148	newVals.append(float(val))
2149	transArray[-1].append(newVals+['',False])
2150	N += 1
2151	Layer['Transitions'] = transArray
2152	#STACKING records
2153	Layer['Stacking'] = [Stack[0],'']
2154	if Stack[0] == 'recursive':
2155	Layer['Stacking'][1] = Stack[1]
2156	elif Stack[0] == 'explicit':
2157	if Stack[1] == 'random':
2158	Layer['Stacking'][1] = Stack[1]
2159	else:
2160	Layer['Stacking'][1] = 'list'
2161	Layer['Stacking'].append('')
2162	for stack in Stack[2:]:
2163	Layer['Stacking'][2] += ' '+stack
2164	return Layer
2165
2166	def postURL(URL,postdict):
2167	'''Posts a set of values as from a web form. If access fails to an https
2168	site the access is retried with http.
2169
2170	:param str URL: the URL to post; typically something
2171	like 'http://www.../dir/page?'
2172	:param dict postdict: contains keywords and values, such
2173	as {'centrosymmetry': '0', 'crystalsystem': '0', ...}
2174	:returns: a string with the response from the web server or None
2175	if access fails.
2176	'''
2177	try:
2178	import requests # delay this until now, since rarely needed
2179	except:
2180	# this import seems to fail with the Anaconda pythonw on
2181	# macs; it should not!
2182	print('Warning: failed to import requests. Python config error')
2183	return None
2184
2185	repeat = True
2186	while repeat:
2187	r = None
2188	repeat = False
2189	try:
2190	r = requests.get(URL,params=postdict)
2191	if r.status_code == 200:
2192	print('request OK')
2193	page = r.text
2194	return page # success
2195	else:
2196	print('request to {} failed. Reason={}'.format(URL,r.reason))
2197	except Exception as msg: #ConnectionError?
2198	print('connection error - not on internet?')
2199	if GSASIIpath.GetConfigValue('debug'): print(msg)
2200	finally:
2201	if r: r.close()
2202	if URL.startswith('https:'):
2203	repeat = True
2204	URL = URL.replace('https:','http:')
2205	else:
2206	return None
2207
2208	if __name__ == '__main__':
2209	import GSASIIdataGUI
2210	application = GSASIIdataGUI.GSASIImain(0)
2211	G2frame = application.main
2212	#app = wx.PySimpleApp()
2213	#G2frame = wx.Frame(None) # create a frame
2214	#frm.Show(True)
2215	#filename = '/tmp/notzip.zip'
2216	#filename = '/tmp/all.zip'
2217	#filename = '/tmp/11bmb_7652.zip'
2218
2219	#selection=None, confirmoverwrite=True, parent=None
2220	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2221	#print ExtractFileFromZip(filename,multipleselect=True)
2222	# #confirmread=False, confirmoverwrite=False)
2223
2224	# choicelist=[ ('a','b','c'),
2225	# ('test1','test2'),('no choice',)]
2226	# titles = [ 'a, b or c', 'tests', 'No option here']
2227	# dlg = MultipleChoicesDialog(
2228	# choicelist,titles,
2229	# parent=frm)
2230	# if dlg.ShowModal() == wx.ID_OK:
2231	# print 'Got OK'
2232	imagefile = '/tmp/NDC5_00237_3.ge3'
2233	Comments, Data, Npix, Image = GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None)
2234
2235	print("\n\nResults loaded to Comments, Data, Npix and Image\n\n")
2236
2237	GSASIIpath.IPyBreak_base()

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