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source: trunk/GSASIIIO.py @ 3246

Last change on this file since 3246 was 3246, checked in by toby, 5 years ago
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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2018-01-29 02:56:19 +0000 (Mon, 29 Jan 2018) $
4	# $Author: toby $
5	# $Revision: 3246 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 3246 2018-01-29 02:56:19Z toby $
8	########### SVN repository information ###################
9	'''
10	GSASIIIO: Misc I/O routines
11	=============================
12
13	Module with miscellaneous routines for input and output. Many
14	are GUI routines to interact with user.
15
16	Includes support for image reading.
17
18	Also includes base classes for data import routines.
19
20	This module needs some work to separate wx from non-wx routines
21	'''
22	# If this is being used for GSASIIscriptable, don't depend on wx
23	from __future__ import division, print_function
24	try:
25	import wx
26	except ImportError:
27	class Placeholder(object):
28	def __init__(self):
29	self.Dialog = object
30	wx = Placeholder()
31	import math
32	import numpy as np
33	import copy
34	import platform
35	if '2' in platform.python_version_tuple()[0]:
36	import cPickle
37	else:
38	import _pickle as cPickle
39	import sys
40	import re
41	import glob
42	import random as ran
43	import GSASIIpath
44	GSASIIpath.SetVersionNumber("$Revision: 3246 $")
45	try:
46	import GSASIIdataGUI as G2gd
47	except ImportError:
48	pass
49	import GSASIIobj as G2obj
50	import GSASIIlattice as G2lat
51	import GSASIImath as G2mth
52	try:
53	import GSASIIpwdGUI as G2pdG
54	import GSASIIimgGUI as G2imG
55	except ImportError:
56	pass
57	import GSASIIimage as G2img
58	import GSASIIElem as G2el
59	import GSASIIstrIO as G2stIO
60	import GSASIImapvars as G2mv
61	try:
62	import GSASIIctrlGUI as G2G
63	except ImportError:
64	pass
65	import os
66	import os.path as ospath
67
68	DEBUG = False #=True for various prints
69	TRANSP = False #=true to transpose images for testing
70	if GSASIIpath.GetConfigValue('Transpose'): TRANSP = True
71	npsind = lambda x: np.sin(x*np.pi/180.)
72
73	def sfloat(S):
74	'Convert a string to float. An empty field or a unconvertable value is treated as zero'
75	if S.strip():
76	try:
77	return float(S)
78	except ValueError:
79	pass
80	return 0.0
81
82	def sint(S):
83	'Convert a string to int. An empty field is treated as zero'
84	if S.strip():
85	return int(S)
86	else:
87	return 0
88
89	def trim(val):
90	'''Simplify a string containing leading and trailing spaces
91	as well as newlines, tabs, repeated spaces etc. into a shorter and
92	more simple string, by replacing all ranges of whitespace
93	characters with a single space.
94
95	:param str val: the string to be simplified
96
97	:returns: the (usually) shortened version of the string
98	'''
99	return re.sub('\s+', ' ', val).strip()
100
101	def FileDlgFixExt(dlg,file):
102	'this is needed to fix a problem in linux wx.FileDialog'
103	ext = dlg.GetWildcard().split('\|')[2dlg.GetFilterIndex()+1].strip('')
104	if ext not in file:
105	file += ext
106	return file
107
108	def GetPowderPeaks(fileName):
109	'Read powder peaks from a file'
110	sind = lambda x: math.sin(x*math.pi/180.)
111	asind = lambda x: 180.*math.asin(x)/math.pi
112	wave = 1.54052
113	File = open(fileName,'Ur')
114	Comments = []
115	peaks = []
116	S = File.readline()
117	while S:
118	if S[:1] == '#':
119	Comments.append(S[:-1])
120	else:
121	item = S.split()
122	if len(item) == 1:
123	peaks.append([float(item[0]),1.0])
124	elif len(item) > 1:
125	peaks.append([float(item[0]),float(item[0])])
126	S = File.readline()
127	File.close()
128	if Comments:
129	print ('Comments on file:')
130	for Comment in Comments:
131	print (Comment)
132	if 'wavelength' in Comment:
133	wave = float(Comment.split('=')[1])
134	Peaks = []
135	if peaks[0][0] > peaks[-1][0]: # d-spacings - assume CuKa
136	for peak in peaks:
137	dsp = peak[0]
138	sth = wave/(2.0*dsp)
139	if sth < 1.0:
140	tth = 2.0*asind(sth)
141	else:
142	break
143	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
144	else: #2-thetas - assume Cuka (for now)
145	for peak in peaks:
146	tth = peak[0]
147	dsp = wave/(2.0*sind(tth/2.0))
148	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
149	limits = [1000.,0.]
150	for peak in Peaks:
151	limits[0] = min(limits[0],peak[0])
152	limits[1] = max(limits[1],peak[0])
153	limits[0] = max(1.,(int(limits[0]-1.)/5)*5.)
154	limits[1] = min(170.,(int(limits[1]+1.)/5)*5.)
155	return Comments,Peaks,limits,wave
156
157	def GetCheckImageFile(G2frame,treeId):
158	'''Try to locate an image file if the project and image have been moved
159	together. If the image file cannot be found, request the location from
160	the user.
161
162	:param wx.Frame G2frame: main GSAS-II Frame and data object
163	:param wx.Id treeId: Id for the main tree item for the image
164	:returns: Npix,imagefile,imagetag with (Npix) number of pixels,
165	imagefile, if it exists, or the name of a file that does exist or False if the user presses Cancel
166	and (imagetag) an optional image number
167
168	'''
169	Npix,Imagefile,imagetag = G2frame.GPXtree.GetImageLoc(treeId)
170	if isinstance(Imagefile,list):
171	imagefile,imagetag = Imagefile
172	else:
173	imagefile = Imagefile
174	if not os.path.exists(imagefile):
175	print ('Image file '+imagefile+' not found')
176	fil = imagefile.replace('\\','/') # windows?!
177	# see if we can find a file with same name or in a similarly named sub-dir
178	pth,fil = os.path.split(fil)
179	prevpth = None
180	while pth and pth != prevpth:
181	prevpth = pth
182	if os.path.exists(os.path.join(G2frame.dirname,fil)):
183	print ('found image file '+os.path.join(G2frame.dirname,fil))
184	imagefile = os.path.join(G2frame.dirname,fil)
185	G2frame.GPXtree.UpdateImageLoc(treeId,imagefile)
186	return Npix,imagefile,imagetag
187	pth,enddir = os.path.split(pth)
188	fil = os.path.join(enddir,fil)
189	# not found as a subdirectory, drop common parts of path for last saved & image file names
190	# if image was .../A/B/C/imgs/ima.ge
191	# & GPX was .../A/B/C/refs/fil.gpx but is now .../NEW/TEST/TEST1
192	# will look for .../NEW/TEST/TEST1/imgs/ima.ge, .../NEW/TEST/imgs/ima.ge, .../NEW/imgs/ima.ge and so on
193	Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
194	gpxPath = Controls.get('LastSavedAs','').replace('\\','/').split('/') # blank in older .GPX files
195	imgPath = imagefile.replace('\\','/').split('/')
196	for p1,p2 in zip(gpxPath,imgPath):
197	if p1 == p2:
198	gpxPath.pop(0),imgPath.pop(0)
199	else:
200	break
201	fil = os.path.join(*imgPath) # file with non-common prefix elements
202	prevpth = None
203	pth = os.path.abspath(G2frame.dirname)
204	while pth and pth != prevpth:
205	prevpth = pth
206	if os.path.exists(os.path.join(pth,fil)):
207	print ('found image file '+os.path.join(pth,fil))
208	imagefile = os.path.join(pth,fil)
209	G2frame.GPXtree.UpdateImageLoc(treeId,imagefile)
210	return Npix,imagefile,imagetag
211	pth,enddir = os.path.split(pth)
212	#GSASIIpath.IPyBreak()
213
214	if not os.path.exists(imagefile):
215	# note that this fails (at least on Mac) to get an image during the GUI initialization
216	prevnam = os.path.split(imagefile)[1]
217	prevext = os.path.splitext(imagefile)[1]
218	wildcard = 'Image format ('+prevext+')\|'+prevext
219	dlg = wx.FileDialog(G2frame, 'Previous image file ('+prevnam+') not found; open here', '.', prevnam,
220	wildcard,wx.FD_OPEN)
221	try:
222	dlg.SetFilename(''+ospath.split(imagefile)[1])
223	if dlg.ShowModal() == wx.ID_OK:
224	imagefile = dlg.GetPath()
225	G2frame.GPXtree.UpdateImageLoc(treeId,imagefile)
226	else:
227	imagefile = False
228	finally:
229	dlg.Destroy()
230	return Npix,imagefile,imagetag
231
232	def EditImageParms(parent,Data,Comments,Image,filename):
233	dlg = wx.Dialog(parent, wx.ID_ANY, 'Edit image parameters',
234	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
235	def onClose(event):
236	dlg.EndModal(wx.ID_OK)
237	mainsizer = wx.BoxSizer(wx.VERTICAL)
238	h,w = Image.shape[:2]
239	mainsizer.Add(wx.StaticText(dlg,wx.ID_ANY,'File '+str(filename)+'\nImage size: '+str(h)+' x '+str(w)),
240	0,wx.ALIGN_LEFT\|wx.ALL, 2)
241
242	vsizer = wx.BoxSizer(wx.HORIZONTAL)
243	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Wavelength (\xC5) '),
244	0,wx.ALIGN_LEFT\|wx.ALL, 2)
245	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'wavelength')
246	vsizer.Add(wdgt)
247	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
248
249	vsizer = wx.BoxSizer(wx.HORIZONTAL)
250	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Pixel size (\xb5m). Width '),
251	0,wx.ALIGN_LEFT\|wx.ALL, 2)
252	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],0,
253	size=(50,-1))
254	vsizer.Add(wdgt)
255	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Height '),wx.ALIGN_LEFT\|wx.ALL, 2)
256	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],1,size=(50,-1))
257	vsizer.Add(wdgt)
258	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
259
260	vsizer = wx.BoxSizer(wx.HORIZONTAL)
261	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Sample to detector (mm) '),
262	0,wx.ALIGN_LEFT\|wx.ALL, 2)
263	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'distance')
264	vsizer.Add(wdgt)
265	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
266
267	vsizer = wx.BoxSizer(wx.HORIZONTAL)
268	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Beam center (pixels). X = '),
269	0,wx.ALIGN_LEFT\|wx.ALL, 2)
270	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],0,size=(75,-1))
271	vsizer.Add(wdgt)
272	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Y = '),wx.ALIGN_LEFT\|wx.ALL, 2)
273	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],1,size=(75,-1))
274	vsizer.Add(wdgt)
275	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
276
277	vsizer = wx.BoxSizer(wx.HORIZONTAL)
278	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Comments '),
279	0,wx.ALIGN_LEFT\|wx.ALL, 2)
280	wdgt = G2G.ValidatedTxtCtrl(dlg,Comments,0,size=(250,-1))
281	vsizer.Add(wdgt)
282	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
283
284	btnsizer = wx.StdDialogButtonSizer()
285	OKbtn = wx.Button(dlg, wx.ID_OK, 'Continue')
286	OKbtn.SetDefault()
287	OKbtn.Bind(wx.EVT_BUTTON,onClose)
288	btnsizer.AddButton(OKbtn) # not sure why this is needed
289	btnsizer.Realize()
290	mainsizer.Add(btnsizer, 1, wx.ALIGN_CENTER\|wx.ALL\|wx.EXPAND, 5)
291	dlg.SetSizer(mainsizer)
292	dlg.CenterOnParent()
293	dlg.ShowModal()
294
295	def LoadImage2Tree(imagefile,G2frame,Comments,Data,Npix,Image):
296	'''Load an image into the tree. Saves the location of the image, as well as the
297	ImageTag (where there is more than one image in the file), if defined.
298	'''
299	ImgNames = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',])
300	TreeLbl = 'IMG '+os.path.basename(imagefile)
301	ImageTag = Data.get('ImageTag')
302	if ImageTag:
303	TreeLbl += ' #'+'%04d'%(ImageTag)
304	imageInfo = (imagefile,ImageTag)
305	else:
306	imageInfo = imagefile
307	TreeName = G2obj.MakeUniqueLabel(TreeLbl,ImgNames)
308	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=TreeName)
309	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments)
310	Imax = np.amax(Image)
311	if G2frame.imageDefault:
312	Data = copy.copy(G2frame.imageDefault)
313	Data['showLines'] = True
314	Data['ring'] = []
315	Data['rings'] = []
316	Data['cutoff'] = 10
317	Data['pixLimit'] = 20
318	Data['edgemin'] = 100000000
319	Data['calibdmin'] = 0.5
320	Data['calibskip'] = 0
321	Data['ellipses'] = []
322	Data['calibrant'] = ''
323	Data['GonioAngles'] = [0.,0.,0.]
324	Data['DetDepthRef'] = False
325	else:
326	Data['type'] = 'PWDR'
327	Data['color'] = GSASIIpath.GetConfigValue('Contour_color','Paired')
328	Data['tilt'] = 0.0
329	Data['rotation'] = 0.0
330	Data['showLines'] = False
331	Data['ring'] = []
332	Data['rings'] = []
333	Data['cutoff'] = 10
334	Data['pixLimit'] = 20
335	Data['calibdmin'] = 0.5
336	Data['calibskip'] = 0
337	Data['edgemin'] = 100000000
338	Data['ellipses'] = []
339	Data['GonioAngles'] = [0.,0.,0.]
340	Data['DetDepth'] = 0.
341	Data['DetDepthRef'] = False
342	Data['calibrant'] = ''
343	Data['IOtth'] = [2.0,5.0]
344	Data['LRazimuth'] = [0.,180.]
345	Data['azmthOff'] = 0.0
346	Data['outChannels'] = 2500
347	Data['outAzimuths'] = 1
348	Data['centerAzm'] = False
349	Data['fullIntegrate'] = False
350	Data['setRings'] = False
351	Data['background image'] = ['',-1.0]
352	Data['dark image'] = ['',-1.0]
353	Data['Flat Bkg'] = 0.0
354	Data['setDefault'] = False
355	Data['range'] = [(0,Imax),[0,Imax]]
356	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Image Controls'),Data)
357	Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],'Thresholds':[(0,Imax),[0,Imax]]}
358	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Masks'),Masks)
359	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Stress/Strain'),
360	{'Type':'True','d-zero':[],'Sample phi':0.0,'Sample z':0.0,'Sample load':0.0})
361	G2frame.GPXtree.SetItemPyData(Id,[Npix,imageInfo])
362	G2frame.PickId = Id
363	G2frame.PickIdText = G2frame.GetTreeItemsList(G2frame.PickId)
364	G2frame.Image = Id
365
366	def GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None,FormatName=''):
367	'''Read a single image with an image importer. This is called to reread an image
368	after it has already been imported with :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`
369	(or :func:`ReadImages` in Auto Integration) so it is not necessary to reload metadata.
370
371	:param wx.Frame G2frame: main GSAS-II Frame and data object.
372	:param str imagefile: name of image file
373	:param bool imageOnly: If True return only the image,
374	otherwise (default) return more (see below)
375	:param int/str ImageTag: specifies a particular image to be read from a file.
376	First image is read if None (default).
377	:param str formatName: the image reader formatName
378
379	:returns: an image as a numpy array or a list of four items:
380	Comments, Data, Npix and the Image, as selected by imageOnly
381
382	'''
383	# determine which formats are compatible with this file
384	primaryReaders = []
385	secondaryReaders = []
386	for rd in G2frame.ImportImageReaderlist:
387	flag = rd.ExtensionValidator(imagefile)
388	if flag is None:
389	secondaryReaders.append(rd)
390	elif flag:
391	if not FormatName:
392	primaryReaders.append(rd)
393	elif FormatName == rd.formatName:
394	primaryReaders.append(rd)
395	if len(secondaryReaders) + len(primaryReaders) == 0:
396	print('Error: No matching format for file '+imagefile)
397	raise Exception('No image read')
398	errorReport = ''
399	if not imagefile:
400	return
401	for rd in primaryReaders+secondaryReaders:
402	rd.ReInitialize() # purge anything from a previous read
403	rd.errors = "" # clear out any old errors
404	if not rd.ContentsValidator(imagefile): # rejected on cursory check
405	errorReport += "\n "+rd.formatName + ' validator error'
406	if rd.errors:
407	errorReport += ': '+rd.errors
408	continue
409	if imageOnly:
410	ParentFrame = None # prevent GUI access on reread
411	else:
412	ParentFrame = G2frame
413	if GSASIIpath.GetConfigValue('debug'):
414	flag = rd.Reader(imagefile,ParentFrame,blocknum=ImageTag)
415	else:
416	flag = False
417	try:
418	flag = rd.Reader(imagefile,ParentFrame,blocknum=ImageTag)
419	except rd.ImportException as detail:
420	rd.errors += "\n Read exception: "+str(detail)
421	except Exception as detail:
422	import traceback
423	rd.errors += "\n Unhandled read exception: "+str(detail)
424	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
425	if flag: # this read succeeded
426	if rd.Image is None:
427	raise Exception('No image read. Strange!')
428	if GSASIIpath.GetConfigValue('Transpose'):
429	print ('Transposing Image!')
430	rd.Image = rd.Image.T
431	#rd.readfilename = imagefile
432	if imageOnly:
433	return rd.Image
434	else:
435	return rd.Comments,rd.Data,rd.Npix,rd.Image
436	else:
437	print('Error reading file '+imagefile)
438	print('Error messages(s)\n'+errorReport)
439	raise Exception('No image read')
440
441	def ReadImages(G2frame,imagefile):
442	'''Read one or more images from a file and put them into the Tree
443	using image importers. Called only in :meth:`AutoIntFrame.OnTimerLoop`.
444
445	ToDo: Images are most commonly read in :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`
446	which is called from :meth:`GSASIIdataGUI.GSASII.OnImportImage`
447	it would be good if these routines used a common code core so that changes need to
448	be made in only one place.
449
450	:param wx.Frame G2frame: main GSAS-II Frame and data object.
451	:param str imagefile: name of image file
452
453	:returns: a list of the id's of the IMG tree items created
454	'''
455	# determine which formats are compatible with this file
456	primaryReaders = []
457	secondaryReaders = []
458	for rd in G2frame.ImportImageReaderlist:
459	flag = rd.ExtensionValidator(imagefile)
460	if flag is None:
461	secondaryReaders.append(rd)
462	elif flag:
463	primaryReaders.append(rd)
464	if len(secondaryReaders) + len(primaryReaders) == 0:
465	print('Error: No matching format for file '+imagefile)
466	raise Exception('No image read')
467	errorReport = ''
468	rdbuffer = {} # create temporary storage for file reader
469	for rd in primaryReaders+secondaryReaders:
470	rd.ReInitialize() # purge anything from a previous read
471	rd.errors = "" # clear out any old errors
472	if not rd.ContentsValidator(imagefile): # rejected on cursory check
473	errorReport += "\n "+rd.formatName + ' validator error'
474	if rd.errors:
475	errorReport += ': '+rd.errors
476	continue
477	ParentFrame = G2frame
478	block = 0
479	repeat = True
480	CreatedIMGitems = []
481	while repeat: # loop if the reader asks for another pass on the file
482	block += 1
483	repeat = False
484	if GSASIIpath.GetConfigValue('debug'):
485	flag = rd.Reader(imagefile,ParentFrame,blocknum=block,Buffer=rdbuffer)
486	else:
487	flag = False
488	try:
489	flag = rd.Reader(imagefile,ParentFrame,blocknum=block,Buffer=rdbuffer)
490	except rd.ImportException as detail:
491	rd.errors += "\n Read exception: "+str(detail)
492	except Exception as detail:
493	import traceback
494	rd.errors += "\n Unhandled read exception: "+str(detail)
495	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
496	if flag: # this read succeeded
497	if rd.Image is None:
498	raise Exception('No image read. Strange!')
499	if GSASIIpath.GetConfigValue('Transpose'):
500	print ('Transposing Image!')
501	rd.Image = rd.Image.T
502	rd.Data['ImageTag'] = rd.repeatcount
503	rd.readfilename = imagefile
504	# Load generic metadata, as configured
505	GetColumnMetadata(rd)
506	LoadImage2Tree(imagefile,G2frame,rd.Comments,rd.Data,rd.Npix,rd.Image)
507	repeat = rd.repeat
508	CreatedIMGitems.append(G2frame.Image)
509	if CreatedIMGitems: return CreatedIMGitems
510	else:
511	print('Error reading file '+imagefile)
512	print('Error messages(s)\n'+errorReport)
513	return []
514	#raise Exception('No image read')
515
516	def SaveMultipleImg(G2frame):
517	if not G2frame.GPXtree.GetCount():
518	print ('no images!')
519	return
520	choices = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',])
521	if len(choices) == 1:
522	names = choices
523	else:
524	dlg = G2G.G2MultiChoiceDialog(G2frame,'Stress/Strain fitting','Select images to fit:',choices)
525	dlg.SetSelections([])
526	names = []
527	if dlg.ShowModal() == wx.ID_OK:
528	names = [choices[sel] for sel in dlg.GetSelections()]
529	dlg.Destroy()
530	if not names: return
531	for name in names:
532	Id = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, name)
533	Npix,imagefile,imagetag = G2frame.GPXtree.GetImageLoc(Id)
534	imroot = os.path.splitext(imagefile)[0]
535	if imagetag:
536	imroot += '_' + str(imagetag)
537	Data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Image Controls'))
538	print('Writing '+imroot+'.imctrl')
539	File = open(imroot+'.imctrl','w')
540	keys = ['type','wavelength','calibrant','distance','center',
541	'tilt','rotation','azmthOff','fullIntegrate','LRazimuth',
542	'IOtth','outChannels','outAzimuths','invert_x','invert_y','DetDepth',
543	'calibskip','pixLimit','cutoff','calibdmin','chisq','Flat Bkg',
544	'binType','SampleShape','PolaVal','SampleAbs','dark image','background image']
545	for key in keys:
546	if key not in Data: continue #uncalibrated!
547	File.write(key+':'+str(Data[key])+'\n')
548	File.close()
549	mask = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Masks'))
550	G2imG.CleanupMasks(mask)
551	print('Writing '+imroot+'.immask')
552	File = open(imroot+'.immask','w')
553	for key in ['Points','Rings','Arcs','Polygons','Frames','Thresholds']:
554	File.write(key+':'+str(mask[key])+'\n')
555	File.close()
556
557	def PutG2Image(filename,Comments,Data,Npix,image):
558	'Write an image as a python pickle - might be better as an .edf file?'
559	File = open(filename,'wb')
560	cPickle.dump([Comments,Data,Npix,image],File,2)
561	File.close()
562	return
563
564	def ProjFileOpen(G2frame,showProvenance=True):
565	'Read a GSAS-II project file and load into the G2 data tree'
566	if not os.path.exists(G2frame.GSASprojectfile):
567	print ('\n*** Error attempt to open project file that does not exist:\n '+
568	str(G2frame.GSASprojectfile))
569	return
570	LastSavedUsing = None
571	file = open(G2frame.GSASprojectfile,'rb')
572	if showProvenance: print ('loading from file: '+G2frame.GSASprojectfile)
573	#G2frame.SetTitle("GSAS-II data tree: "+
574	# os.path.split(G2frame.GSASprojectfile)[1])
575	G2frame.SetTitle("GSAS-II data tree: "+
576	os.path.split(G2frame.GSASprojectfile)[1],1)
577	wx.BeginBusyCursor()
578	try:
579	while True:
580	try:
581	if '2' in platform.python_version_tuple()[0]:
582	data = cPickle.load(file)
583	else:
584	data = cPickle.load(file,encoding='latin-1')
585	except EOFError:
586	break
587	datum = data[0]
588
589	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=datum[0])
590	if datum[0].startswith('PWDR'):
591	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
592	datum[1][0]['ranId'] = ran.randint(0,sys.maxsize)
593	G2frame.GPXtree.SetItemPyData(Id,datum[1][:3]) #temp. trim off junk (patch?)
594	elif datum[0].startswith('HKLF'):
595	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
596	datum[1][0]['ranId'] = ran.randint(0,sys.maxsize)
597	G2frame.GPXtree.SetItemPyData(Id,datum[1])
598	else:
599	G2frame.GPXtree.SetItemPyData(Id,datum[1])
600	if datum[0] == 'Controls' and 'LastSavedUsing' in datum[1]:
601	LastSavedUsing = datum[1]['LastSavedUsing']
602	if datum[0] == 'Controls' and 'PythonVersions' in datum[1] and GSASIIpath.GetConfigValue('debug') and showProvenance:
603	print('Packages used to create .GPX file:')
604	if 'dict' in str(type(datum[1]['PythonVersions'])): #patch
605	for p in sorted(datum[1]['PythonVersions'],key=lambda s: s.lower()):
606	print(" {:<14s}: {:s}".format(p[0],p[1]))
607	else:
608	for p in datum[1]['PythonVersions']:
609	print(" {:<12s} {:s}".format(p[0]+':',p[1]))
610	oldPDF = False
611	for datus in data[1:]:
612	#patch - 1/23/17 PDF cleanup
613	if datus[0][:4] in ['I(Q)','S(Q)','F(Q)','G(R)']:
614	oldPDF = True
615	data[1][1][datus[0][:4]] = copy.deepcopy(datus[1][:2])
616	continue
617	#end PDF cleanup
618	sub = G2frame.GPXtree.AppendItem(Id,datus[0])
619	#patch
620	if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
621	if datum[0].startswith('PWDR'):
622	datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
623	else:
624	datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
625	for item in datus[1][0]: #zip makes tuples - now make lists!
626	datus[1][0][item] = list(datus[1][0][item])
627	#end patch
628	G2frame.GPXtree.SetItemPyData(sub,datus[1])
629	if 'PDF ' in datum[0][:4] and oldPDF:
630	sub = G2frame.GPXtree.AppendItem(Id,'PDF Peaks')
631	G2frame.GPXtree.SetItemPyData(sub,{'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]})
632	if datum[0].startswith('IMG'): #retrieve image default flag & data if set
633	Data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Image Controls'))
634	if Data['setDefault']:
635	G2frame.imageDefault = Data
636	file.close()
637	if LastSavedUsing:
638	print('GPX load successful. Last saved with GSAS-II revision '+LastSavedUsing)
639	else:
640	print('project load successful')
641	G2frame.NewPlot = True
642	except:
643	msg = wx.MessageDialog(G2frame,message="Error reading file "+
644	str(G2frame.GSASprojectfile)+". This is not a GSAS-II .gpx file",
645	caption="Load Error",style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
646	msg.ShowModal()
647	finally:
648	wx.EndBusyCursor()
649	G2frame.Status.SetStatusText('Mouse RB drag/drop to reorder',0)
650
651	def ProjFileSave(G2frame):
652	'Save a GSAS-II project file'
653	if not G2frame.GPXtree.IsEmpty():
654	file = open(G2frame.GSASprojectfile,'wb')
655	print ('save to file: '+G2frame.GSASprojectfile)
656	# stick the file name into the tree and version info into tree so they are saved.
657	# (Controls should always be created at this point)
658	try:
659	Controls = G2frame.GPXtree.GetItemPyData(
660	G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
661	Controls['LastSavedAs'] = os.path.abspath(G2frame.GSASprojectfile)
662	Controls['LastSavedUsing'] = str(GSASIIpath.GetVersionNumber())
663	Controls['PythonVersions'] = G2frame.PackageVersions
664	except:
665	pass
666	wx.BeginBusyCursor()
667	try:
668	item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
669	while item:
670	data = []
671	name = G2frame.GPXtree.GetItemText(item)
672	data.append([name,G2frame.GPXtree.GetItemPyData(item)])
673	item2, cookie2 = G2frame.GPXtree.GetFirstChild(item)
674	while item2:
675	name = G2frame.GPXtree.GetItemText(item2)
676	data.append([name,G2frame.GPXtree.GetItemPyData(item2)])
677	item2, cookie2 = G2frame.GPXtree.GetNextChild(item, cookie2)
678	item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
679	cPickle.dump(data,file,2)
680	file.close()
681	pth = os.path.split(os.path.abspath(G2frame.GSASprojectfile))[0]
682	if GSASIIpath.GetConfigValue('Save_paths'): G2G.SaveGPXdirectory(pth)
683	G2frame.LastGPXdir = pth
684	finally:
685	wx.EndBusyCursor()
686	print('project save successful')
687
688	def SaveIntegration(G2frame,PickId,data,Overwrite=False):
689	'Save image integration results as powder pattern(s)'
690	azms = G2frame.Integrate[1]
691	X = G2frame.Integrate[2][:-1]
692	N = len(X)
693	Id = G2frame.GPXtree.GetItemParent(PickId)
694	name = G2frame.GPXtree.GetItemText(Id)
695	name = name.replace('IMG ',data['type']+' ')
696	Comments = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Comments'))
697	Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
698	if 'PWDR' in name:
699	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth']
700	codes = [0 for i in range(12)]
701	elif 'SASD' in name:
702	names = ['Type','Lam','Zero','Azimuth']
703	codes = [0 for i in range(4)]
704	X = 4.np.pinpsind(X/2.)/data['wavelength'] #convert to q
705	Xminmax = [X[0],X[-1]]
706	Azms = []
707	dazm = 0.
708	if data['fullIntegrate'] and data['outAzimuths'] == 1:
709	Azms = [45.0,] #a poor man's average?
710	else:
711	for i,azm in enumerate(azms[:-1]):
712	if azm > 360. and azms[i+1] > 360.:
713	Azms.append(G2img.meanAzm(azm%360.,azms[i+1]%360.))
714	else:
715	Azms.append(G2img.meanAzm(azm,azms[i+1]))
716	dazm = np.min(np.abs(np.diff(azms)))/2.
717	G2frame.IntgOutList = []
718	for i,azm in enumerate(azms[:-1]):
719	Aname = name+" Azm= %.2f"%((azm+dazm)%360.)
720	item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
721	# if Overwrite delete any duplicate
722	if Overwrite and G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname):
723	print('Replacing '+Aname)
724	item = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname)
725	G2frame.GPXtree.Delete(item)
726	else:
727	nOcc = 0
728	while item:
729	Name = G2frame.GPXtree.GetItemText(item)
730	if Aname in Name:
731	nOcc += 1
732	item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
733	if nOcc:
734	Aname += '(%d)'%(nOcc)
735	Sample = G2obj.SetDefaultSample() #set as Debye-Scherrer
736	Sample['Gonio. radius'] = data['distance']
737	Sample['Omega'] = data['GonioAngles'][0]
738	Sample['Chi'] = data['GonioAngles'][1]
739	Sample['Phi'] = data['GonioAngles'][2]
740	Sample['Azimuth'] = (azm+dazm)%360. #put here as bin center
741	polariz = 0.99 #set default polarization for synchrotron radiation!
742	for item in Comments:
743	if 'polariz' in item:
744	try:
745	polariz = float(item.split('=')[1])
746	except:
747	polariz = 0.99
748	for key in ('Temperature','Pressure','Time','FreePrm1','FreePrm2','FreePrm3','Omega',
749	'Chi','Phi'):
750	if key.lower() in item.lower():
751	try:
752	Sample[key] = float(item.split('=')[1])
753	except:
754	pass
755	if 'label_prm' in item.lower():
756	for num in ('1','2','3'):
757	if 'label_prm'+num in item.lower():
758	Controls['FreePrm'+num] = item.split('=')[1].strip()
759	if 'PWDR' in Aname:
760	parms = ['PXC',data['wavelength'],0.0,polariz,1.0,-0.10,0.4,0.30,1.0,0.0,0.0001,Azms[i]]
761	elif 'SASD' in Aname:
762	Sample['Trans'] = data['SampleAbs'][0]
763	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
764	Y = G2frame.Integrate[0][i]
765	Ymin = np.min(Y)
766	Ymax = np.max(Y)
767	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
768	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=Aname)
769	G2frame.IntgOutList.append(Id)
770	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments)
771	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Limits'),copy.deepcopy([tuple(Xminmax),Xminmax]))
772	if 'PWDR' in Aname:
773	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Background'),[['chebyschev',1,3,1.0,0.0,0.0],
774	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
775	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
776	for item in inst[0]:
777	inst[0][item] = list(inst[0][item])
778	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Instrument Parameters'),inst)
779	if 'PWDR' in Aname:
780	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample)
781	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
782	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Index Peak List'),[[],[]])
783	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Unit Cells List'),[])
784	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Reflection Lists'),{})
785	elif 'SASD' in Aname:
786	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
787	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample)
788	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
789	valuesdict = {
790	'wtFactor':1.0,
791	'Dummy':False,
792	'ranId':ran.randint(0,sys.maxsize),
793	'Offset':[0.0,0.0],'delOffset':0.02Ymax,'refOffset':-0.1Ymax,'refDelt':0.1*Ymax,
794	'qPlot':False,'dPlot':False,'sqrtPlot':False,'Yminmax':[Ymin,Ymax]
795	}
796	G2frame.GPXtree.SetItemPyData(
797	Id,[valuesdict,
798	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
799	return Id #last powder pattern generated
800
801	def XYsave(G2frame,XY,labelX='X',labelY='Y',names=None):
802	'Save XY table data'
803	pth = G2G.GetExportPath(G2frame)
804	dlg = wx.FileDialog(
805	G2frame, 'Enter csv filename for XY table', pth, '',
806	'XY table file (.csv)\|.csv',wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
807	try:
808	if dlg.ShowModal() == wx.ID_OK:
809	filename = dlg.GetPath()
810	filename = os.path.splitext(filename)[0]+'.csv'
811	File = open(filename,'w')
812	else:
813	filename = None
814	finally:
815	dlg.Destroy()
816	if not filename:
817	return
818	for i in range(len(XY)):
819	if names != None:
820	header = '%s,%s(%s)\n'%(labelX,labelY,names[i])
821	else:
822	header = '%s,%s(%d)\n'%(labelX,labelY,i)
823	File.write(header)
824	for x,y in XY[i].T:
825	File.write('%.3f,%.3f\n'%(x,y))
826	File.close()
827	print (' XY data saved to: '+filename)
828
829	def askSaveDirectory(G2frame):
830	'''Ask the user to supply a directory name. Path name is used as the
831	starting point for the next export path search.
832
833	:returns: a directory name (str) or None if Cancel is pressed
834	'''
835	pth = G2G.GetExportPath(G2frame)
836	dlg = wx.DirDialog(
837	G2frame, 'Input directory where file(s) will be written', pth,
838	wx.DD_DEFAULT_STYLE)
839	dlg.CenterOnParent()
840	try:
841	if dlg.ShowModal() == wx.ID_OK:
842	filename = dlg.GetPath()
843	G2frame.LastExportDir = filename
844	else:
845	filename = None
846	finally:
847	dlg.Destroy()
848	return filename
849
850	def askSaveFile(G2frame,defnam,extension,longFormatName):
851	'''Ask the user to supply a file name
852
853	:returns: a file name (str) or None if Cancel is pressed
854	'''
855
856	pth = G2G.GetExportPath(G2frame)
857	dlg = wx.FileDialog(
858	G2frame, 'Input name for file to write', pth, defnam,
859	longFormatName+' ('+extension+')\|'+extension,
860	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
861	dlg.CenterOnParent()
862	try:
863	if dlg.ShowModal() == wx.ID_OK:
864	filename = dlg.GetPath()
865	G2frame.LastExportDir = os.path.split(filename)[0]
866	filename = os.path.splitext(filename)[0]+extension # make sure extension is correct
867	else:
868	filename = None
869	finally:
870	dlg.Destroy()
871	return filename
872
873	def PDFSave(G2frame,exports,PDFsaves):
874	'Save a PDF I(Q), S(Q), F(Q) and G(r) in column formats'
875	import scipy.interpolate as scintp
876	if len(exports) > 1:
877	dirname = askSaveDirectory(G2frame)
878	if not dirname: return
879	else:
880	defnam = exports[0].replace(' ','_')[5:]
881	filename = askSaveFile(G2frame,defnam,'.gr','G(r) file, etc.')
882	if not filename: return
883	dirname,filename = os.path.split(filename)
884	filename = os.path.splitext(filename)[0]
885	for export in exports:
886	if len(exports) > 1:
887	filename = export.replace(' ','_')[5:]
888	PickId = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, export)
889	PDFControls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame, PickId,'PDF Controls'))
890	if PDFsaves[0]: #I(Q)
891	iqfilename = ospath.join(dirname,filename+'.iq')
892	iqdata = PDFControls['I(Q)'][0]
893	iqfxn = scintp.interp1d(iqdata[0],iqdata[1],kind='linear')
894	iqfile = open(iqfilename,'w')
895	iqfile.write('#T I(Q) %s\n'%(export))
896	iqfile.write('#L Q I(Q)\n')
897	qnew = np.arange(iqdata[0][0],iqdata[0][-1],0.005)
898	iqnew = zip(qnew,iqfxn(qnew))
899	for q,iq in iqnew:
900	iqfile.write("%15.6g %15.6g\n" % (q,iq))
901	iqfile.close()
902	print (' I(Q) saved to: '+iqfilename)
903
904	if PDFsaves[1]: #S(Q)
905	sqfilename = ospath.join(dirname,filename+'.sq')
906	sqdata = PDFControls['S(Q)'][1]
907	sqfxn = scintp.interp1d(sqdata[0],sqdata[1],kind='linear')
908	sqfile = open(sqfilename,'w')
909	sqfile.write('#T S(Q) %s\n'%(export))
910	sqfile.write('#L Q S(Q)\n')
911	qnew = np.arange(sqdata[0][0],sqdata[0][-1],0.005)
912	sqnew = zip(qnew,sqfxn(qnew))
913	for q,sq in sqnew:
914	sqfile.write("%15.6g %15.6g\n" % (q,sq))
915	sqfile.close()
916	print (' S(Q) saved to: '+sqfilename)
917
918	if PDFsaves[2]: #F(Q)
919	fqfilename = ospath.join(dirname,filename+'.fq')
920	fqdata = PDFControls['F(Q)'][1]
921	fqfxn = scintp.interp1d(fqdata[0],fqdata[1],kind='linear')
922	fqfile = open(fqfilename,'w')
923	fqfile.write('#T F(Q) %s\n'%(export))
924	fqfile.write('#L Q F(Q)\n')
925	qnew = np.arange(fqdata[0][0],fqdata[0][-1],0.005)
926	fqnew = zip(qnew,fqfxn(qnew))
927	for q,fq in fqnew:
928	fqfile.write("%15.6g %15.6g\n" % (q,fq))
929	fqfile.close()
930	print (' F(Q) saved to: '+fqfilename)
931
932	if PDFsaves[3]: #G(R)
933	grfilename = ospath.join(dirname,filename+'.gr')
934	grdata = PDFControls['G(R)'][1]
935	grfxn = scintp.interp1d(grdata[0],grdata[1],kind='linear')
936	grfile = open(grfilename,'w')
937	grfile.write('#T G(R) %s\n'%(export))
938	grfile.write('#L R G(R)\n')
939	rnew = np.arange(grdata[0][0],grdata[0][-1],0.010)
940	grnew = zip(rnew,grfxn(rnew))
941	for r,gr in grnew:
942	grfile.write("%15.6g %15.6g\n" % (r,gr))
943	grfile.close()
944	print (' G(R) saved to: '+grfilename)
945
946	if PDFsaves[4]: #pdfGUI file for G(R)
947	pId = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, 'PWDR'+export[4:])
948	Inst = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame, pId,'Instrument Parameters'))[0]
949	Limits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame, pId,'Limits'))
950	grfilename = ospath.join(dirname,filename+'.gr')
951	grdata = PDFControls['G(R)'][1]
952	qdata = PDFControls['I(Q)'][1][0]
953	grfxn = scintp.interp1d(grdata[0],grdata[1],kind='linear')
954	grfile = open(grfilename,'w')
955	rnew = np.arange(grdata[0][0],grdata[0][-1],0.010)
956	grnew = zip(rnew,grfxn(rnew))
957
958	grfile.write('[DEFAULT]\n')
959	grfile.write('\n')
960	grfile.write('version = GSAS-II-v'+str(GSASIIpath.GetVersionNumber())+'\n')
961	grfile.write('\n')
962	grfile.write('# input and output specifications\n')
963	grfile.write('dataformat = Qnm\n')
964	grfile.write('inputfile = %s\n'%(PDFControls['Sample']['Name']))
965	grfile.write('backgroundfile = %s\n'%(PDFControls['Sample Bkg.']['Name']))
966	grfile.write('outputtype = gr\n')
967	grfile.write('\n')
968	grfile.write('# PDF calculation setup\n')
969	if 'x' in Inst['Type']:
970	grfile.write('mode = %s\n'%('xray'))
971	elif 'N' in Inst['Type']:
972	grfile.write('mode = %s\n'%('neutron'))
973	wave = G2mth.getMeanWave(Inst)
974	grfile.write('wavelength = %.5f\n'%(wave))
975	formula = ''
976	for el in PDFControls['ElList']:
977	formula += el
978	num = PDFControls['ElList'][el]['FormulaNo']
979	if num == round(num):
980	formula += '%d'%(int(num))
981	else:
982	formula += '%.2f'%(num)
983	grfile.write('composition = %s\n'%(formula))
984	grfile.write('bgscale = %.3f\n'%(-PDFControls['Sample Bkg.']['Mult']))
985	highQ = 2.*np.pi/G2lat.Pos2dsp(Inst,Limits[1][1])
986	grfile.write('qmaxinst = %.2f\n'%(highQ))
987	grfile.write('qmin = %.5f\n'%(qdata[0]))
988	grfile.write('qmax = %.4f\n'%(qdata[-1]))
989	grfile.write('rmin = %.2f\n'%(PDFControls['Rmin']))
990	grfile.write('rmax = %.2f\n'%(PDFControls['Rmax']))
991	grfile.write('rstep = 0.01\n')
992
993
994	grfile.write('\n')
995	grfile.write('# End of config '+63*'-')
996	grfile.write('\n')
997	grfile.write('#### start data\n')
998	grfile.write('#S 1\n')
999	grfile.write('#L r($\AA$) G($\AA^{-2}$)\n')
1000	for r,gr in grnew:
1001	grfile.write("%15.2F %15.6F\n" % (r,gr))
1002	grfile.close()
1003	print (' G(R) saved to: '+grfilename)
1004
1005	def PeakListSave(G2frame,file,peaks):
1006	'Save powder peaks to a data file'
1007	print ('save peak list to file: '+G2frame.peaklistfile)
1008	if not peaks:
1009	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1010	try:
1011	dlg.ShowModal()
1012	finally:
1013	dlg.Destroy()
1014	return
1015	for peak in peaks:
1016	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
1017	(peak[0],peak[2],peak[4],peak[6]))
1018	print ('peak list saved')
1019
1020	def IndexPeakListSave(G2frame,peaks):
1021	'Save powder peaks from the indexing list'
1022	file = open(G2frame.peaklistfile,'wa')
1023	print ('save index peak list to file: '+G2frame.peaklistfile)
1024	wx.BeginBusyCursor()
1025	try:
1026	if not peaks:
1027	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1028	try:
1029	dlg.ShowModal()
1030	finally:
1031	dlg.Destroy()
1032	return
1033	for peak in peaks:
1034	file.write("%12.6f\n" % (peak[7]))
1035	file.close()
1036	finally:
1037	wx.EndBusyCursor()
1038	print ('index peak list saved')
1039
1040	class MultipleChoicesDialog(wx.Dialog):
1041	'''A dialog that offers a series of choices, each with a
1042	title and a wx.Choice widget. Intended to be used Modally.
1043	typical input:
1044
1045	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1046	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1047
1048	selections are placed in self.chosen when OK is pressed
1049
1050	Also see GSASIIctrlGUI
1051	'''
1052	def __init__(self,choicelist,headinglist,
1053	head='Select options',
1054	title='Please select from options below',
1055	parent=None):
1056	self.chosen = []
1057	wx.Dialog.__init__(
1058	self,parent,wx.ID_ANY,head,
1059	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
1060	panel = wx.Panel(self)
1061	mainSizer = wx.BoxSizer(wx.VERTICAL)
1062	mainSizer.Add((10,10),1)
1063	topLabl = wx.StaticText(panel,wx.ID_ANY,title)
1064	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.CENTER,10)
1065	self.ChItems = []
1066	for choice,lbl in zip(choicelist,headinglist):
1067	mainSizer.Add((10,10),1)
1068	self.chosen.append(0)
1069	topLabl = wx.StaticText(panel,wx.ID_ANY,' '+lbl)
1070	mainSizer.Add(topLabl,0,wx.ALIGN_LEFT,10)
1071	self.ChItems.append(wx.Choice(self, wx.ID_ANY, (100, 50), choices = choice))
1072	mainSizer.Add(self.ChItems[-1],0,wx.ALIGN_CENTER,10)
1073
1074	OkBtn = wx.Button(panel,-1,"Ok")
1075	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
1076	cancelBtn = wx.Button(panel,-1,"Cancel")
1077	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
1078	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1079	btnSizer.Add((20,20),1)
1080	btnSizer.Add(OkBtn)
1081	btnSizer.Add((20,20),1)
1082	btnSizer.Add(cancelBtn)
1083	btnSizer.Add((20,20),1)
1084	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1085	panel.SetSizer(mainSizer)
1086	panel.Fit()
1087	self.Fit()
1088
1089	def OnOk(self,event):
1090	parent = self.GetParent()
1091	if parent is not None: parent.Raise()
1092	# save the results from the choice widgets
1093	self.chosen = []
1094	for w in self.ChItems:
1095	self.chosen.append(w.GetSelection())
1096	self.EndModal(wx.ID_OK)
1097
1098	def OnCancel(self,event):
1099	parent = self.GetParent()
1100	if parent is not None: parent.Raise()
1101	self.chosen = []
1102	self.EndModal(wx.ID_CANCEL)
1103
1104	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1105	confirmoverwrite=True, parent=None,
1106	multipleselect=False):
1107	'''If the filename is a zip file, extract a file from that
1108	archive.
1109
1110	:param list Selection: used to predefine the name of the file
1111	to be extracted. Filename case and zip directory name are
1112	ignored in selection; the first matching file is used.
1113
1114	:param bool confirmread: if True asks the user to confirm before expanding
1115	the only file in a zip
1116
1117	:param bool confirmoverwrite: if True asks the user to confirm
1118	before overwriting if the extracted file already exists
1119
1120	:param bool multipleselect: if True allows more than one zip
1121	file to be extracted, a list of file(s) is returned.
1122	If only one file is present, do not ask which one, otherwise
1123	offer a list of choices (unless selection is used).
1124
1125	:returns: the name of the file that has been created or a
1126	list of files (see multipleselect)
1127
1128	If the file is not a zipfile, return the name of the input file.
1129	If the zipfile is empty or no file has been selected, return None
1130	'''
1131	import zipfile # do this now, since we can save startup time by doing this only on need
1132	import shutil
1133	zloc = os.path.split(filename)[0]
1134	if not zipfile.is_zipfile(filename):
1135	#print("not zip")
1136	return filename
1137
1138	z = zipfile.ZipFile(filename,'r')
1139	zinfo = z.infolist()
1140
1141	if len(zinfo) == 0:
1142	#print('Zip has no files!')
1143	zlist = [-1]
1144	if selection:
1145	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1146	if selection.lower() in choices:
1147	zlist = [choices.index(selection.lower())]
1148	else:
1149	print('debug: file '+str(selection)+' was not found in '+str(filename))
1150	zlist = [-1]
1151	elif len(zinfo) == 1 and confirmread:
1152	result = wx.ID_NO
1153	dlg = wx.MessageDialog(
1154	parent,
1155	'Is file '+str(zinfo[0].filename)+
1156	' what you want to extract from '+
1157	str(os.path.split(filename)[1])+'?',
1158	'Confirm file',
1159	wx.YES_NO \| wx.ICON_QUESTION)
1160	try:
1161	result = dlg.ShowModal()
1162	finally:
1163	dlg.Destroy()
1164	if result == wx.ID_NO:
1165	zlist = [-1]
1166	else:
1167	zlist = [0]
1168	elif len(zinfo) == 1:
1169	zlist = [0]
1170	elif multipleselect:
1171	# select one or more from a from list
1172	choices = [i.filename for i in zinfo]
1173	dlg = G2G.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1174	'Choose file(s)',choices)
1175	if dlg.ShowModal() == wx.ID_OK:
1176	zlist = dlg.GetSelections()
1177	else:
1178	zlist = []
1179	dlg.Destroy()
1180	else:
1181	# select one from a from list
1182	choices = [i.filename for i in zinfo]
1183	dlg = wx.SingleChoiceDialog(parent,
1184	'Select file to extract from zip file'+str(filename),'Choose file',
1185	choices,)
1186	if dlg.ShowModal() == wx.ID_OK:
1187	zlist = [dlg.GetSelection()]
1188	else:
1189	zlist = [-1]
1190	dlg.Destroy()
1191
1192	outlist = []
1193	for zindex in zlist:
1194	if zindex >= 0:
1195	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1196	if os.path.exists(efil) and confirmoverwrite:
1197	result = wx.ID_NO
1198	dlg = wx.MessageDialog(parent,
1199	'File '+str(efil)+' already exists. OK to overwrite it?',
1200	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1201	try:
1202	result = dlg.ShowModal()
1203	finally:
1204	dlg.Destroy()
1205	if result == wx.ID_NO:
1206	zindex = -1
1207	if zindex >= 0:
1208	# extract the file to the current directory, regardless of it's original path
1209	#z.extract(zinfo[zindex],zloc)
1210	eloc,efil = os.path.split(zinfo[zindex].filename)
1211	outfile = os.path.join(zloc, efil)
1212	fpin = z.open(zinfo[zindex])
1213	fpout = file(outfile, "wb")
1214	shutil.copyfileobj(fpin, fpout)
1215	fpin.close()
1216	fpout.close()
1217	outlist.append(outfile)
1218	z.close()
1219	if multipleselect and len(outlist) >= 1:
1220	return outlist
1221	elif len(outlist) == 1:
1222	return outlist[0]
1223	else:
1224	return None
1225
1226	######################################################################
1227	# base classes for reading various types of data files
1228	# not used directly, only by subclassing
1229	######################################################################
1230	def BlockSelector(ChoiceList, ParentFrame=None,title='Select a block',
1231	size=None, header='Block Selector',useCancel=True):
1232	''' Provide a wx dialog to select a block if the file contains more
1233	than one set of data and one must be selected
1234	'''
1235	if useCancel:
1236	dlg = wx.SingleChoiceDialog(
1237	ParentFrame,title, header,ChoiceList)
1238	else:
1239	dlg = wx.SingleChoiceDialog(
1240	ParentFrame,title, header,ChoiceList,
1241	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.OK\|wx.CENTRE)
1242	if size: dlg.SetSize(size)
1243	dlg.CenterOnParent()
1244	if dlg.ShowModal() == wx.ID_OK:
1245	sel = dlg.GetSelection()
1246	return sel
1247	else:
1248	return None
1249	dlg.Destroy()
1250
1251	def MultipleBlockSelector(ChoiceList, ParentFrame=None,
1252	title='Select a block',size=None, header='Block Selector'):
1253	'''Provide a wx dialog to select a block of data if the
1254	file contains more than one set of data and one must be
1255	selected.
1256
1257	:returns: a list of the selected blocks
1258	'''
1259	dlg = wx.MultiChoiceDialog(ParentFrame,title, header,ChoiceList+['Select all'],
1260	wx.CHOICEDLG_STYLE)
1261	dlg.CenterOnScreen()
1262	if size: dlg.SetSize(size)
1263	if dlg.ShowModal() == wx.ID_OK:
1264	sel = dlg.GetSelections()
1265	else:
1266	return []
1267	dlg.Destroy()
1268	selected = []
1269	if len(ChoiceList) in sel:
1270	return range(len(ChoiceList))
1271	else:
1272	return sel
1273	return selected
1274
1275	def MultipleChoicesSelector(choicelist, headinglist, ParentFrame=None, **kwargs):
1276	'''A modal dialog that offers a series of choices, each with a title and a wx.Choice
1277	widget. Typical input:
1278
1279	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1280
1281	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1282
1283	optional keyword parameters are: head (window title) and title
1284	returns a list of selected indicies for each choice (or None)
1285	'''
1286	result = None
1287	dlg = MultipleChoicesDialog(choicelist,headinglist,
1288	parent=ParentFrame, **kwargs)
1289	dlg.CenterOnParent()
1290	if dlg.ShowModal() == wx.ID_OK:
1291	result = dlg.chosen
1292	dlg.Destroy()
1293	return result
1294
1295	def PhaseSelector(ChoiceList, ParentFrame=None,
1296	title='Select a phase', size=None,header='Phase Selector'):
1297	''' Provide a wx dialog to select a phase if the file contains more
1298	than one phase
1299	'''
1300	return BlockSelector(ChoiceList,ParentFrame,title,
1301	size,header)
1302
1303	######################################################################
1304	def striphist(var,insChar=''):
1305	'strip a histogram number from a var name'
1306	sv = var.split(':')
1307	if len(sv) <= 1: return var
1308	if sv[1]:
1309	sv[1] = insChar
1310	return ':'.join(sv)
1311	class ExportBaseclass(object):
1312	'''Defines a base class for the exporting of GSAS-II results.
1313
1314	This class is subclassed in the various exports/G2export_*.py files. Those files
1315	are imported in :meth:`GSASIIdataGUI.GSASII._init_Exports` which defines the
1316	appropriate menu items for each one and the .Exporter method is called
1317	directly from the menu item.
1318
1319	Routines may also define a .Writer method, which is used to write a single
1320	file without invoking any GUI objects.
1321	'''
1322	# TODO: review exporters producing exceptions where .Writer can't be used where G2frame is None (see CIF)
1323	# TODO: review conflicting uses of .Writer with mode (SeqRef) & elsewhere
1324	# TODO: move this class to G2fil
1325	def __init__(self,G2frame,formatName,extension,longFormatName=None,):
1326	self.G2frame = G2frame
1327	self.formatName = formatName # short string naming file type
1328	self.extension = extension
1329	if longFormatName: # longer string naming file type
1330	self.longFormatName = longFormatName
1331	else:
1332	self.longFormatName = formatName
1333	self.OverallParms = {}
1334	self.Phases = {}
1335	self.Histograms = {}
1336	self.powderDict = {}
1337	self.xtalDict = {}
1338	self.parmDict = {}
1339	self.sigDict = {}
1340	# updated in InitExport:
1341	self.currentExportType = None # type of export that has been requested
1342	# updated in ExportSelect (when used):
1343	self.phasenam = None # a list of selected phases
1344	self.histnam = None # a list of selected histograms
1345	self.filename = None # name of file to be written (single export) or template (multiple files)
1346	self.dirname = '' # name of directory where file(s) will be written
1347	self.fullpath = '' # name of file being written -- full path
1348
1349	# items that should be defined in a subclass of this class
1350	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1351	# The following types are defined: 'project', "phase", "powder", "single"
1352	self.multiple = False # set as True if the class can export multiple phases or histograms
1353	# self.multiple is ignored for "project" exports
1354
1355	def InitExport(self,event):
1356	'''Determines the type of menu that called the Exporter and
1357	misc initialization.
1358	'''
1359	self.filename = None # name of file to be written (single export)
1360	self.dirname = '' # name of file to be written (multiple export)
1361	if event:
1362	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1363
1364	def MakePWDRfilename(self,hist):
1365	'''Make a filename root (no extension) from a PWDR histogram name
1366
1367	:param str hist: the histogram name in data tree (starts with "PWDR ")
1368	'''
1369	file0 = ''
1370	file1 = hist[5:]
1371	# replace repeated blanks
1372	while file1 != file0:
1373	file0 = file1
1374	file1 = file0.replace(' ',' ').strip()
1375	file0 = file1.replace('Azm= ','A')
1376	# if angle has unneeded decimal places on aziumuth, remove them
1377	if file0[-3:] == '.00': file0 = file0[:-3]
1378	file0 = file0.replace('.','_')
1379	file0 = file0.replace(' ','_')
1380	return file0
1381
1382	def ExportSelect(self,AskFile='ask'):
1383	'''Selects histograms or phases when needed. Sets a default file name when
1384	requested into self.filename; always sets a default directory in self.dirname.
1385
1386	:param bool AskFile: Determines how this routine processes getting a
1387	location to store the current export(s).
1388
1389	* if AskFile is 'ask' (default option), get the name of the file to be written;
1390	self.filename and self.dirname are always set. In the case where
1391	multiple files must be generated, the export routine should do this
1392	based on self.filename as a template.
1393	* if AskFile is 'dir', get the name of the directory to be used;
1394	self.filename is not used, but self.dirname is always set. The export routine
1395	will always generate the file name.
1396	* if AskFile is 'single', get only the name of the directory to be used when
1397	multiple items will be written (as multiple files) are used
1398	or a complete file name is requested when a single file
1399	name is selected. self.dirname is always set and self.filename used
1400	only when a single file is selected.
1401	* if AskFile is 'default', creates a name of the file to be used from
1402	the name of the project (.gpx) file. If the project has not been saved,
1403	then the name of file is requested.
1404	self.filename and self.dirname are always set. In the case where
1405	multiple file names must be generated, the export routine should do this
1406	based on self.filename.
1407	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1408	file. If the project has not been saved, then a directory is requested.
1409	self.filename is not used.
1410
1411	:returns: True in case of an error
1412	'''
1413
1414	numselected = 1
1415	if self.currentExportType == 'phase':
1416	if len(self.Phases) == 0:
1417	self.G2frame.ErrorDialog(
1418	'Empty project',
1419	'Project does not contain any phases.')
1420	return True
1421	elif len(self.Phases) == 1:
1422	self.phasenam = list(self.Phases.keys())
1423	elif self.multiple:
1424	choices = sorted(self.Phases.keys())
1425	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1426	if phasenum is None: return True
1427	self.phasenam = [choices[i] for i in phasenum]
1428	if not self.phasenam: return True
1429	numselected = len(self.phasenam)
1430	else:
1431	choices = sorted(self.Phases.keys())
1432	phasenum = G2G.ItemSelector(choices,self.G2frame)
1433	if phasenum is None: return True
1434	self.phasenam = [choices[phasenum]]
1435	numselected = len(self.phasenam)
1436	elif self.currentExportType == 'single':
1437	if len(self.xtalDict) == 0:
1438	self.G2frame.ErrorDialog(
1439	'Empty project',
1440	'Project does not contain any single crystal data.')
1441	return True
1442	elif len(self.xtalDict) == 1:
1443	self.histnam = self.xtalDict.values()
1444	elif self.multiple:
1445	choices = sorted(self.xtalDict.values())
1446	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1447	if not hnum: return True
1448	self.histnam = [choices[i] for i in hnum]
1449	numselected = len(self.histnam)
1450	else:
1451	choices = sorted(self.xtalDict.values())
1452	hnum = G2G.ItemSelector(choices,self.G2frame)
1453	if hnum is None: return True
1454	self.histnam = [choices[hnum]]
1455	numselected = len(self.histnam)
1456	elif self.currentExportType == 'powder':
1457	if len(self.powderDict) == 0:
1458	self.G2frame.ErrorDialog(
1459	'Empty project',
1460	'Project does not contain any powder data.')
1461	return True
1462	elif len(self.powderDict) == 1:
1463	self.histnam = self.powderDict.values()
1464	elif self.multiple:
1465	choices = sorted(self.powderDict.values())
1466	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1467	if not hnum: return True
1468	self.histnam = [choices[i] for i in hnum]
1469	numselected = len(self.histnam)
1470	else:
1471	choices = sorted(self.powderDict.values())
1472	hnum = G2G.ItemSelector(choices,self.G2frame)
1473	if hnum is None: return True
1474	self.histnam = [choices[hnum]]
1475	numselected = len(self.histnam)
1476	elif self.currentExportType == 'image':
1477	if len(self.Histograms) == 0:
1478	self.G2frame.ErrorDialog(
1479	'Empty project',
1480	'Project does not contain any images.')
1481	return True
1482	elif len(self.Histograms) == 1:
1483	self.histnam = list(self.Histograms.keys())
1484	else:
1485	choices = sorted(self.Histograms.keys())
1486	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1487	if self.multiple:
1488	if not hnum: return True
1489	self.histnam = [choices[i] for i in hnum]
1490	else:
1491	if hnum is None: return True
1492	self.histnam = [choices[hnum]]
1493	numselected = len(self.histnam)
1494	if self.currentExportType == 'map':
1495	# search for phases with maps
1496	mapPhases = []
1497	choices = []
1498	for phasenam in sorted(self.Phases):
1499	phasedict = self.Phases[phasenam] # pointer to current phase info
1500	if len(phasedict['General']['Map'].get('rho',[])):
1501	mapPhases.append(phasenam)
1502	if phasedict['General']['Map'].get('Flip'):
1503	choices.append('Charge flip map: '+str(phasenam))
1504	elif phasedict['General']['Map'].get('MapType'):
1505	choices.append(
1506	str(phasedict['General']['Map'].get('MapType'))
1507	+ ' map: ' + str(phasenam))
1508	else:
1509	choices.append('unknown map: '+str(phasenam))
1510	# select a map if needed
1511	if len(mapPhases) == 0:
1512	self.G2frame.ErrorDialog(
1513	'Empty project',
1514	'Project does not contain any maps.')
1515	return True
1516	elif len(mapPhases) == 1:
1517	self.phasenam = mapPhases
1518	else:
1519	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1520	if self.multiple:
1521	if not phasenum: return True
1522	self.phasenam = [mapPhases[i] for i in phasenum]
1523	else:
1524	if phasenum is None: return True
1525	self.phasenam = [mapPhases[phasenum]]
1526	numselected = len(self.phasenam)
1527
1528	# items selected, now set self.dirname and usually self.filename
1529	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
1530	AskFile == 'default' and not self.G2frame.GSASprojectfile
1531	):
1532	filename = self.askSaveFile()
1533	if not filename: return True
1534	self.dirname,self.filename = os.path.split(filename)
1535	elif AskFile == 'dir' or AskFile == 'single' or (
1536	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
1537	):
1538	self.dirname = self.askSaveDirectory()
1539	if not self.dirname: return True
1540	elif AskFile == 'default-dir' or AskFile == 'default':
1541	self.dirname,self.filename = os.path.split(
1542	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
1543	)
1544	else:
1545	raise Exception('This should not happen!')
1546
1547	def loadParmDict(self):
1548	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
1549	refined values to those from the last cycle and set the uncertainties for the
1550	refined parameters in another dict (self.sigDict).
1551
1552	Expands the parm & sig dicts to include values derived from constraints.
1553	'''
1554	self.parmDict = {}
1555	self.sigDict = {}
1556	rigidbodyDict = {}
1557	covDict = {}
1558	consDict = {}
1559	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1560	if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1561	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1562	while item:
1563	name = self.G2frame.GPXtree.GetItemText(item)
1564	if name == 'Rigid bodies':
1565	rigidbodyDict = self.G2frame.GPXtree.GetItemPyData(item)
1566	elif name == 'Covariance':
1567	covDict = self.G2frame.GPXtree.GetItemPyData(item)
1568	elif name == 'Constraints':
1569	consDict = self.G2frame.GPXtree.GetItemPyData(item)
1570	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1571	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1572	self.parmDict.update(rbDict)
1573	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1574	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData(
1575	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
1576	self.parmDict.update(phaseDict)
1577	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
1578	Phases,Histograms,Print=False,resetRefList=False)
1579	self.parmDict.update(hapDict)
1580	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
1581	self.parmDict.update(histDict)
1582	self.parmDict.update(zip(
1583	covDict.get('varyList',[]),
1584	covDict.get('variables',[])))
1585	self.sigDict = dict(zip(
1586	covDict.get('varyList',[]),
1587	covDict.get('sig',[])))
1588	# expand to include constraints: first compile a list of constraints
1589	constList = []
1590	for item in consDict:
1591	if item.startswith('_'): continue
1592	constList += consDict[item]
1593	# now process the constraints
1594	G2mv.InitVars()
1595	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
1596	varyList = covDict.get('varyListStart')
1597	if varyList is None and len(constDict) == 0:
1598	# no constraints can use varyList
1599	varyList = covDict.get('varyList')
1600	elif varyList is None:
1601	# old GPX file from before pre-constraint varyList is saved
1602	print (' * Old refinement: Please use Calculate/Refine to redo *')
1603	raise Exception(' * Export aborted *')
1604	else:
1605	varyList = list(varyList)
1606	# add symmetry-generated constraints
1607	rigidbodyDict = self.G2frame.GPXtree.GetItemPyData(
1608	G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,'Rigid bodies'))
1609	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1610	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1611	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData(
1612	Phases,RestraintDict=None,rbIds=rbIds,Print=False) # generates atom symmetry constraints
1613	try:
1614	groups,parmlist = G2mv.GroupConstraints(constDict)
1615	G2mv.GenerateConstraints(groups,parmlist,varyList,constDict,fixedList,self.parmDict)
1616	#print(G2mv.VarRemapShow(varyList))
1617	except:
1618	# this really should not happen
1619	print (' * ERROR - constraints are internally inconsistent *')
1620	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
1621	print ('Errors'+errmsg)
1622	if warnmsg: print ('Warnings'+warnmsg)
1623	raise Exception(' * CIF creation aborted *')
1624	# add the constrained values to the parameter dictionary
1625	G2mv.Dict2Map(self.parmDict,varyList)
1626	# and add their uncertainties into the esd dictionary (sigDict)
1627	if covDict.get('covMatrix') is not None:
1628	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
1629
1630	def loadTree(self):
1631	'''Load the contents of the data tree into a set of dicts
1632	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
1633	& self.xtalDict)
1634
1635	* The childrenless data tree items are overall parameters/controls for the
1636	entire project and are placed in self.OverallParms
1637	* Phase items are placed in self.Phases
1638	* Data items are placed in self.Histogram. The key for these data items
1639	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
1640	'''
1641	self.OverallParms = {}
1642	self.powderDict = {}
1643	self.xtalDict = {}
1644	self.Phases = {}
1645	self.Histograms = {}
1646	self.SeqRefdata = None
1647	self.SeqRefhist = None
1648	if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1649	histType = None
1650	if self.currentExportType == 'phase':
1651	# if exporting phases load them here
1652	sub = G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,'Phases')
1653	if not sub:
1654	print ('no phases found')
1655	return True
1656	item, cookie = self.G2frame.GPXtree.GetFirstChild(sub)
1657	while item:
1658	phaseName = self.G2frame.GPXtree.GetItemText(item)
1659	self.Phases[phaseName] = self.G2frame.GPXtree.GetItemPyData(item)
1660	item, cookie = self.G2frame.GPXtree.GetNextChild(sub, cookie)
1661	return
1662	elif self.currentExportType == 'single':
1663	histType = 'HKLF'
1664	elif self.currentExportType == 'powder':
1665	histType = 'PWDR'
1666	elif self.currentExportType == 'image':
1667	histType = 'IMG'
1668
1669	if histType: # Loading just one kind of tree entry
1670	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1671	while item:
1672	name = self.G2frame.GPXtree.GetItemText(item)
1673	if name.startswith(histType):
1674	if self.Histograms.get(name): # there is already an item with this name
1675	print('Histogram name '+str(name)+' is repeated. Renaming')
1676	if name[-1] == '9':
1677	name = name[:-1] + '10'
1678	elif name[-1] in '012345678':
1679	name = name[:-1] + str(int(name[-1])+1)
1680	else:
1681	name += '-1'
1682	self.Histograms[name] = {}
1683	# the main info goes into Data, but the 0th
1684	# element contains refinement results, carry
1685	# that over too now.
1686	self.Histograms[name]['Data'] = self.G2frame.GPXtree.GetItemPyData(item)[1]
1687	self.Histograms[name][0] = self.G2frame.GPXtree.GetItemPyData(item)[0]
1688	item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1689	while item2:
1690	child = self.G2frame.GPXtree.GetItemText(item2)
1691	self.Histograms[name][child] = self.G2frame.GPXtree.GetItemPyData(item2)
1692	item2, cookie2 = self.G2frame.GPXtree.GetNextChild(item, cookie2)
1693	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1694	# index powder and single crystal histograms by number
1695	for hist in self.Histograms:
1696	if hist.startswith("PWDR"):
1697	d = self.powderDict
1698	elif hist.startswith("HKLF"):
1699	d = self.xtalDict
1700	else:
1701	return
1702	i = self.Histograms[hist].get('hId')
1703	if i is None and not d.keys():
1704	i = 0
1705	elif i is None or i in d.keys():
1706	i = max(d.keys())+1
1707	d[i] = hist
1708	return
1709	# else standard load: using all interlinked phases and histograms
1710	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1711	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1712	while item:
1713	name = self.G2frame.GPXtree.GetItemText(item)
1714	item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1715	if not item2:
1716	self.OverallParms[name] = self.G2frame.GPXtree.GetItemPyData(item)
1717	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1718	# index powder and single crystal histograms
1719	for hist in self.Histograms:
1720	i = self.Histograms[hist]['hId']
1721	if hist.startswith("PWDR"):
1722	self.powderDict[i] = hist
1723	elif hist.startswith("HKLF"):
1724	self.xtalDict[i] = hist
1725
1726	def dumpTree(self,mode='type'):
1727	'''Print out information on the data tree dicts loaded in loadTree.
1728	Used for testing only.
1729	'''
1730	if self.SeqRefdata and self.SeqRefhist:
1731	print('Note that dumpTree does not show sequential results')
1732	print ('\nOverall')
1733	if mode == 'type':
1734	def Show(arg): return type(arg)
1735	else:
1736	def Show(arg): return arg
1737	for key in self.OverallParms:
1738	print (' '+key+Show(self.OverallParms[key]))
1739	print ('Phases')
1740	for key1 in self.Phases:
1741	print (' '+key1+Show(self.Phases[key1]))
1742	print ('Histogram')
1743	for key1 in self.Histograms:
1744	print (' '+key1+Show(self.Histograms[key1]))
1745	for key2 in self.Histograms[key1]:
1746	print (' '+key2+Show(self.Histograms[key1][key2]))
1747
1748	def defaultSaveFile(self):
1749	return os.path.abspath(
1750	os.path.splitext(self.G2frame.GSASprojectfile
1751	)[0]+self.extension)
1752
1753	def askSaveFile(self):
1754	'''Ask the user to supply a file name
1755
1756	:returns: a file name (str) or None if Cancel is pressed
1757	'''
1758
1759	pth = G2G.GetExportPath(self.G2frame)
1760	defnam = os.path.splitext(
1761	os.path.split(self.G2frame.GSASprojectfile)[1]
1762	)[0]+self.extension
1763	dlg = wx.FileDialog(
1764	self.G2frame, 'Input name for file to write', pth, defnam,
1765	self.longFormatName+' ('+self.extension+')\|'+self.extension,
1766	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
1767	dlg.CenterOnParent()
1768	try:
1769	if dlg.ShowModal() == wx.ID_OK:
1770	filename = dlg.GetPath()
1771	self.G2frame.LastExportDir = os.path.split(filename)[0]
1772	filename = os.path.splitext(filename)[0]+self.extension # make sure extension is correct
1773	else:
1774	filename = None
1775	finally:
1776	dlg.Destroy()
1777	return filename
1778
1779	def askSaveDirectory(self):
1780	'''Ask the user to supply a directory name. Path name is used as the
1781	starting point for the next export path search.
1782
1783	:returns: a directory name (str) or None if Cancel is pressed
1784	'''
1785	pth = G2G.GetExportPath(self.G2frame)
1786	dlg = wx.DirDialog(
1787	self.G2frame, 'Input directory where file(s) will be written', pth,
1788	wx.DD_DEFAULT_STYLE)
1789	dlg.CenterOnParent()
1790	try:
1791	if dlg.ShowModal() == wx.ID_OK:
1792	filename = dlg.GetPath()
1793	self.G2frame.LastExportDir = filename
1794	else:
1795	filename = None
1796	finally:
1797	dlg.Destroy()
1798	return filename
1799
1800	# Tools for file writing.
1801	def OpenFile(self,fil=None,mode='w'):
1802	'''Open the output file
1803
1804	:param str fil: The name of the file to open. If None (default)
1805	the name defaults to self.dirname + self.filename.
1806	If an extension is supplied, it is not overridded,
1807	but if not, the default extension is used.
1808	:returns: the file object opened by the routine which is also
1809	saved as self.fp
1810	'''
1811	if mode == 'd': # debug mode
1812	self.fullpath = '(stdout)'
1813	self.fp = sys.stdout
1814	return
1815	if not fil:
1816	if not os.path.splitext(self.filename)[1]:
1817	self.filename += self.extension
1818	fil = os.path.join(self.dirname,self.filename)
1819	self.fullpath = os.path.abspath(fil)
1820	self.fp = open(self.fullpath,mode)
1821	return self.fp
1822
1823	def Write(self,line):
1824	'''write a line of output, attaching a line-end character
1825
1826	:param str line: the text to be written.
1827	'''
1828	self.fp.write(line+'\n')
1829
1830	def CloseFile(self,fp=None):
1831	'''Close a file opened in OpenFile
1832
1833	:param file fp: the file object to be closed. If None (default)
1834	file object self.fp is closed.
1835	'''
1836	if self.fp == sys.stdout: return # debug mode
1837	if fp is None:
1838	fp = self.fp
1839	self.fp = None
1840	if fp is not None: fp.close()
1841
1842	def SetSeqRef(self,data,hist):
1843	'''Set the exporter to retrieve results from a sequential refinement
1844	rather than the main tree
1845	'''
1846	self.SeqRefdata = data
1847	self.SeqRefhist = hist
1848	data_name = data[hist]
1849	for i,val in zip(data_name['varyList'],data_name['sig']):
1850	self.sigDict[i] = val
1851	self.sigDict[striphist(i)] = val
1852	for i in data_name['parmDict']:
1853	self.parmDict[striphist(i)] = data_name['parmDict'][i]
1854	self.parmDict[i] = data_name['parmDict'][i]
1855	# zero out the dA[xyz] terms, they would only bring confusion
1856	key = i.split(':')
1857	if len(key) < 3: continue
1858	if key[2].startswith('dA'):
1859	self.parmDict[i] = 0.0
1860	for i,(val,sig) in data_name.get('depParmDict',{}).iteritems():
1861	self.parmDict[i] = val
1862	self.sigDict[i] = sig
1863	#GSASIIpath.IPyBreak()
1864
1865	def SetFromArray(self,hist,histname):
1866	'''Load a histogram into the exporter in preparation for use of the .Writer
1867	rather than the main tree. This is used in GSASIIscriptable when wx
1868	is not present.
1869	'''
1870	self.Histograms[histname] = {}
1871	self.Histograms[histname]['Data'] = hist['data'][1]
1872	self.Histograms[histname]['Instrument Parameters'] = hist['Instrument Parameters']
1873	self.Histograms[histname]['Sample Parameters'] = hist['Sample Parameters']
1874
1875	# Tools to pull information out of the data arrays
1876	def GetCell(self,phasenam):
1877	"""Gets the unit cell parameters and their s.u.'s for a selected phase
1878
1879	:param str phasenam: the name for the selected phase
1880	:returns: `cellList,cellSig` where each is a 7 element list corresponding
1881	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1882	cell values and `cellSig` has their uncertainties.
1883	"""
1884	if self.SeqRefdata and self.SeqRefhist:
1885	return self.GetSeqCell(phasenam,self.SeqRefdata[self.SeqRefhist])
1886	phasedict = self.Phases[phasenam] # pointer to current phase info
1887	try:
1888	pfx = str(phasedict['pId'])+'::'
1889	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
1890	cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A,
1891	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
1892	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
1893	return cellList,cellSig
1894	except KeyError:
1895	cell = phasedict['General']['Cell'][1:]
1896	return cell,7*[0]
1897
1898	def GetSeqCell(self,phasenam,data_name):
1899	"""Gets the unit cell parameters and their s.u.'s for a selected phase
1900	and histogram in a sequential fit
1901
1902	:param str phasenam: the name for the selected phase
1903	:param dict data_name: the sequential refinement parameters for the selected histogram
1904	:returns: `cellList,cellSig` where each is a 7 element list corresponding
1905	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1906	cell values and `cellSig` has their uncertainties.
1907	"""
1908	phasedict = self.Phases[phasenam]
1909	SGdata = phasedict['General']['SGData']
1910	pId = phasedict['pId']
1911	RecpCellTerms = G2lat.cell2A(phasedict['General']['Cell'][1:7])
1912	ESDlookup = {}
1913	Dlookup = {}
1914	varied = [striphist(i) for i in data_name['varyList']]
1915	for item,val in data_name['newCellDict'].iteritems():
1916	if item in varied:
1917	ESDlookup[val[0]] = item
1918	Dlookup[item] = val[0]
1919	A = RecpCellTerms[:]
1920	for i in range(6):
1921	var = str(pId)+'::A'+str(i)
1922	if var in ESDlookup:
1923	A[i] = data_name['newCellDict'][ESDlookup[var]][1] # override with refined value
1924	cellDict = dict(zip([str(pId)+'::A'+str(i) for i in range(6)],A))
1925	zeroDict = {i:0.0 for i in cellDict}
1926	A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata,cellDict,zeroDict)
1927	covData = {
1928	'varyList': [Dlookup.get(striphist(v),v) for v in data_name['varyList']],
1929	'covMatrix': data_name['covMatrix']
1930	}
1931	return list(G2lat.A2cell(A)) + [G2lat.calc_V(A)], G2stIO.getCellEsd(str(pId)+'::',SGdata,A,covData)
1932
1933	def GetAtoms(self,phasenam):
1934	"""Gets the atoms associated with a phase. Can be used with standard
1935	or macromolecular phases
1936
1937	:param str phasenam: the name for the selected phase
1938	:returns: a list of items for eac atom where each item is a list containing:
1939	label, typ, mult, xyz, and td, where
1940
1941	* label and typ are the atom label and the scattering factor type (str)
1942	* mult is the site multiplicity (int)
1943	* xyz is contains a list with four pairs of numbers:
1944	x, y, z and fractional occupancy and
1945	their standard uncertainty (or a negative value)
1946	* td is contains a list with either one or six pairs of numbers:
1947	if one number it is U\ :sub:`iso` and with six numbers it is
1948	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
1949	paired with their standard uncertainty (or a negative value)
1950	"""
1951	phasedict = self.Phases[phasenam] # pointer to current phase info
1952	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
1953	cfrac = cx+3
1954	fpfx = str(phasedict['pId'])+'::Afrac:'
1955	atomslist = []
1956	for i,at in enumerate(phasedict['Atoms']):
1957	if phasedict['General']['Type'] == 'macromolecular':
1958	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
1959	else:
1960	label = at[ct-1]
1961	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
1962	fsig = self.sigDict.get(fpfx+str(i),-0.009)
1963	mult = at[cs+1]
1964	typ = at[ct]
1965	xyz = []
1966	for j,v in enumerate(('x','y','z')):
1967	val = at[cx+j]
1968	pfx = str(phasedict['pId']) + '::A' + v + ':' + str(i)
1969	val = self.parmDict.get(pfx, val)
1970	dpfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
1971	sig = self.sigDict.get(dpfx,-0.000009)
1972	xyz.append((val,sig))
1973	xyz.append((fval,fsig))
1974	td = []
1975	if at[cia] == 'I':
1976	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
1977	val = self.parmDict.get(pfx,at[cia+1])
1978	sig = self.sigDict.get(pfx,-0.0009)
1979	td.append((val,sig))
1980	else:
1981	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
1982	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
1983	val = self.parmDict.get(pfx,at[cia+2+i])
1984	sig = self.sigDict.get(pfx,-0.0009)
1985	td.append((val,sig))
1986	atomslist.append((label,typ,mult,xyz,td))
1987	return atomslist
1988	######################################################################
1989	def ExportPowderList(G2frame):
1990	'''Returns a list of extensions supported by :func:`GSASIIIO:ExportPowder`
1991	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
1992
1993	:param wx.Frame G2frame: the GSAS-II main data tree window
1994	'''
1995	extList = []
1996	for obj in G2frame.exporterlist:
1997	if 'powder' in obj.exporttype:
1998	try:
1999	obj.Writer
2000	extList.append(obj.extension)
2001	except AttributeError:
2002	pass
2003	return extList
2004
2005	def ExportPowder(G2frame,TreeName,fileroot,extension):
2006	'''Writes a single powder histogram using the Export routines.
2007	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
2008
2009	:param wx.Frame G2frame: the GSAS-II main data tree window
2010	:param str TreeName: the name of the histogram (PWDR ...) in the data tree
2011	:param str fileroot: name for file to be written, extension ignored
2012	:param str extension: extension for file to be written (start with '.'). Must
2013	match a powder export routine that has a Writer object.
2014	'''
2015	filename = os.path.abspath(os.path.splitext(fileroot)[0]+extension)
2016	for obj in G2frame.exporterlist:
2017	if obj.extension == extension and 'powder' in obj.exporttype:
2018	obj.currentExportType = 'powder'
2019	obj.InitExport(None)
2020	obj.loadTree() # load all histograms in tree into dicts
2021	if TreeName not in obj.Histograms:
2022	raise Exception('Histogram not found: '+str(TreeName))
2023	try:
2024	obj.Writer
2025	except AttributeError:
2026	continue
2027	try:
2028	obj.Writer(TreeName,filename)
2029	print('wrote file '+filename)
2030	return
2031	except Exception:
2032	print('Export Routine for '+extension+' failed.')
2033	else:
2034	print('No Export routine supports extension '+extension)
2035
2036	def ExportSequential(G2frame,data,obj,exporttype):
2037	'''
2038	Used to export from every phase/dataset in a sequential refinement using
2039	a .Writer method for either projects or phases. Prompts to select histograms
2040	and for phase exports, which phase(s).
2041
2042	:param wx.Frame G2frame: the GSAS-II main data tree window
2043	:param dict data: the sequential refinement data object
2044	:param str exporttype: indicates the type of export ('project' or 'phase')
2045	'''
2046	if len(data['histNames']) == 0:
2047	G2G.G2MessageBox(G2frame,'There are no sequential histograms','Warning')
2048	obj.InitExport(None)
2049	obj.loadTree()
2050	obj.loadParmDict()
2051	if len(data['histNames']) == 1:
2052	histlist = data['histNames']
2053	else:
2054	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select histograms to export from list',
2055	'Select histograms',data['histNames'])
2056	if dlg.ShowModal() == wx.ID_OK:
2057	histlist = [data['histNames'][l] for l in dlg.GetSelections()]
2058	dlg.Destroy()
2059	else:
2060	dlg.Destroy()
2061	return
2062	if exporttype == 'Phase':
2063	phaselist = list(obj.Phases.keys())
2064	if len(obj.Phases) == 0:
2065	G2G.G2MessageBox(G2frame,'There are no phases in sequential ref.','Warning')
2066	return
2067	elif len(obj.Phases) > 1:
2068	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select phases to export from list',
2069	'Select phases', phaselist)
2070	if dlg.ShowModal() == wx.ID_OK:
2071	phaselist = [phaselist[l] for l in dlg.GetSelections()]
2072	dlg.Destroy()
2073	else:
2074	dlg.Destroy()
2075	return
2076	filename = obj.askSaveFile()
2077	if not filename: return True
2078	obj.dirname,obj.filename = os.path.split(filename)
2079	print('Writing output to file '+str(obj.filename)+"...")
2080	mode = 'w'
2081	for p in phaselist:
2082	for h in histlist:
2083	obj.SetSeqRef(data,h)
2084	#GSASIIpath.IPyBreak()
2085	obj.Writer(h,phasenam=p,mode=mode)
2086	mode = 'a'
2087	print('...done')
2088	elif exporttype == 'Project': # note that the CIF exporter is not yet ready for this
2089	filename = obj.askSaveFile()
2090	if not filename: return True
2091	obj.dirname,obj.filename = os.path.split(filename)
2092	print('Writing output to file '+str(obj.filename)+"...")
2093	mode = 'w'
2094	for h in histlist:
2095	obj.SetSeqRef(data,h)
2096	obj.Writer(h,mode=mode)
2097	print('\t'+str(h)+' written')
2098	mode = 'a'
2099	print('...done')
2100	elif exporttype == 'Powder':
2101	filename = obj.askSaveFile()
2102	if not filename: return True
2103	obj.dirname,obj.filename = os.path.split(filename)
2104	print('Writing output to file '+str(obj.filename)+"...")
2105	mode = 'w'
2106	for h in histlist:
2107	obj.SetSeqRef(data,h)
2108	obj.Writer(h,mode=mode)
2109	print('\t'+str(h)+' written')
2110	mode = 'a'
2111	print('...done')
2112
2113	def ReadDIFFaX(DIFFaXfile):
2114	print ('read '+DIFFaXfile)
2115	Layer = {'Laue':'-1','Cell':[False,1.,1.,1.,90.,90.,90,1.],'Width':[[10.,10.],[False,False]],
2116	'Layers':[],'Stacking':[],'Transitions':[],'Toler':0.01,'AtInfo':{}}
2117	df = open(DIFFaXfile,'r')
2118	lines = df.readlines()
2119	df.close()
2120	struct = False
2121	Struct = []
2122	stack = False
2123	Stack = []
2124	trans = False
2125	Trans = []
2126	for diff in lines:
2127	diff = diff[:-1].lower()
2128	if '!' in diff:
2129	continue
2130	while '}' in diff: #strip comments
2131	iB = diff.index('{')
2132	iF = diff.index('}')+1
2133	if iB:
2134	diff = diff[:iB]
2135	else:
2136	diff = diff[iF:]
2137	if not diff:
2138	continue
2139	if diff.strip() == 'instrumental':
2140	continue
2141	if diff.strip() == 'structural':
2142	struct = True
2143	continue
2144	elif diff.strip() == 'stacking':
2145	struct = False
2146	stack = True
2147	continue
2148	elif diff.strip() == 'transitions':
2149	stack = False
2150	trans = True
2151	continue
2152	diff = diff.strip()
2153	if struct:
2154	if diff:
2155	Struct.append(diff)
2156	elif stack:
2157	if diff:
2158	Stack.append(diff)
2159	elif trans:
2160	if diff:
2161	Trans.append(diff)
2162
2163	#STRUCTURE records
2164	laueRec = Struct[1].split()
2165	Layer['Laue'] = laueRec[0]
2166	if Layer['Laue'] == 'unknown' and len(laueRec) > 1:
2167	Layer['Toler'] = float(laueRec[1]) #tolerance for 'unknown'?
2168	if Layer['Laue'] == '2/m(1)': Layer['Laue'] = '2/m(c)'
2169	if Layer['Laue'] == '2/m(2)': Layer['Laue'] = '2/m(ab)'
2170	cell = Struct[0].split()
2171	Layer['Cell'] = [False,float(cell[0]),float(cell[1]),float(cell[2]),90.,90.,float(cell[3]),1.0]
2172	nLayers = int(Struct[2])
2173	N = 3
2174	if 'layer' not in Struct[3]:
2175	N = 4
2176	if Struct[3] != 'infinite':
2177	width = Struct[3].split()
2178	Layer['Width'][0] = [float(width[0]),float(width[1])]
2179	for nL in range(nLayers):
2180	if '=' in Struct[N]:
2181	name = Struct[N].split('=')
2182	sameas = int(name[1])-1
2183	Layer['Layers'].append({'Name':name[0],'SameAs':Layer['Layers'][sameas]['Name'],'Symm':'None','Atoms':[]})
2184	N += 1
2185	continue
2186	Symm = 'None'
2187	if 'centro' in Struct[N+1]: Symm = '-1'
2188	Layer['Layers'].append({'Name':Struct[N],'SameAs':'','Symm':Symm,'Atoms':[]})
2189	N += 2
2190	while 'layer' not in Struct[N]:
2191	atom = Struct[N][4:].split()
2192	atomType = G2el.FixValence(Struct[N][:4].replace(' ','').strip().capitalize())
2193	if atomType not in Layer['AtInfo']:
2194	Layer['AtInfo'][atomType] = G2el.GetAtomInfo(atomType)
2195	atomName = '%s(%s)'%(atomType,atom[0])
2196	newVals = []
2197	for val in atom[1:6]:
2198	if '/' in val:
2199	newVals.append(eval(val+'.'))
2200	else:
2201	newVals.append(float(val))
2202	atomRec = [atomName,atomType,newVals[0],newVals[1],newVals[2],newVals[4],newVals[3]/78.9568]
2203	Layer['Layers'][-1]['Atoms'].append(atomRec)
2204	N += 1
2205	if N > len(Struct)-1:
2206	break
2207	#TRANSITIONS records
2208	transArray = []
2209	N = 0
2210	for i in range(nLayers):
2211	transArray.append([])
2212	for j in range(nLayers):
2213	vals = Trans[N].split()
2214	newVals = []
2215	for val in vals[:4]:
2216	if '/' in val:
2217	newVals.append(eval(val+'.'))
2218	else:
2219	newVals.append(float(val))
2220	transArray[-1].append(newVals+['',False])
2221	N += 1
2222	Layer['Transitions'] = transArray
2223	#STACKING records
2224	Layer['Stacking'] = [Stack[0],'']
2225	if Stack[0] == 'recursive':
2226	Layer['Stacking'][1] = Stack[1]
2227	elif Stack[0] == 'explicit':
2228	if Stack[1] == 'random':
2229	Layer['Stacking'][1] = Stack[1]
2230	else:
2231	Layer['Stacking'][1] = 'list'
2232	Layer['Stacking'].append('')
2233	for stack in Stack[2:]:
2234	Layer['Stacking'][2] += ' '+stack
2235	return Layer
2236
2237	def readColMetadata(imagefile):
2238	'''Reads image metadata from a column-oriented metadata table
2239	(1-ID style .par file). Called by :func:`GetColumnMetadata`
2240
2241	The .par file has any number of columns separated by spaces.
2242	The directory for the file must be specified in
2243	Config variable ``Column_Metadata_directory``.
2244	As an index to the .par file a second "label file" must be specified with the
2245	same file root name as the .par file but the extension must be .XXX_lbls (where
2246	.XXX is the extension of the image) or if that is not present extension
2247	.lbls.
2248
2249	:param str imagefile: the full name of the image file (with extension, directory optional)
2250
2251	:returns: a dict with parameter values. Named parameters will have the type based on
2252	the specified Python function, named columns will be character strings
2253
2254	The contents of the label file will look like this::
2255
2256	# define keywords
2257	filename:lambda x,y: "{}_{:0>6}".format(x,y)\|33,34
2258	distance: float \| 75
2259	wavelength:lambda keV: 12.398425/float(keV)\|9
2260	pixelSize:lambda x: [74.8, 74.8]\|0
2261	ISOlikeDate: lambda dow,m,d,t,y:"{}-{}-{}T{} ({})".format(y,m,d,t,dow)\|0,1,2,3,4
2262	Temperature: float\|53
2263	FreePrm2: int \| 34 \| Free Parm2 Label
2264	# define other variables
2265	0:day
2266	1:month
2267	2:date
2268	3:time
2269	4:year
2270	7:I_ring
2271
2272	This file contains three types of lines in any order.
2273	* Named parameters are evaluated with user-supplied Python code (see
2274	subsequent information). Specific named parameters are used
2275	to determine values that are used for image interpretation (see table,
2276	below). Any others are copied to the Comments subsection of the Image
2277	tree item.
2278	* Column labels are defined with a column number (integer) followed by
2279	a colon (:) and a label to be assigned to that column. All labeled
2280	columns are copied to the Image's Comments subsection.
2281	* Comments are any line that does not contain a colon.
2282
2283	Note that columns are numbered starting at zero.
2284
2285	Any named parameter may be defined provided it is not a valid integer,
2286	but the named parameters in the table have special meanings, as descibed.
2287	The parameter name is followed by a colon. After the colon, specify
2288	Python code that defines or specifies a function that will be called to
2289	generate a value for that parameter.
2290
2291	Note that several keywords, if defined in the Comments, will be found and
2292	placed in the appropriate section of the powder histogram(s)'s Sample
2293	Parameters after an integration: ``Temperature``,``Pressure``,``Time``,
2294	``FreePrm1``,``FreePrm2``,``FreePrm3``,``Omega``,``Chi``, and ``Phi``.
2295
2296	After the Python code, supply a vertical bar (\|) and then a list of one
2297	more more columns that will be supplied as arguments to that function.
2298
2299	Note that the labels for the three FreePrm items can be changed by
2300	including that label as a third item with an additional vertical bar. Labels
2301	will be ignored for any other named parameters.
2302
2303	The examples above are discussed here:
2304
2305	``filename:lambda x,y: "{}_{:0>6}".format(x,y)\|33,34``
2306	Here the function to be used is defined with a lambda statement::
2307
2308	lambda x,y: "{}_{:0>6}".format(x,y)
2309
2310	This function will use the format function to create a file name from the
2311	contents of columns 33 and 34. The first parameter (x, col. 33) is inserted directly into
2312	the file name, followed by a underscore (_), followed by the second parameter (y, col. 34),
2313	which will be left-padded with zeros to six characters (format directive ``:0>6``).
2314
2315	When there will be more than one image generated per line in the .par file, an alternate way to
2316	generate list of file names takes into account the number of images generated::
2317
2318	lambda x,y,z: ["{}_{:0>6}".format(x,int(y)+i) for i in range(int(z))]
2319
2320	Here a third parameter is used to specify the number of images generated, where
2321	the image number is incremented for each image.
2322
2323	``distance: float \| 75``
2324	Here the contents of column 75 will be converted to a floating point number
2325	by calling float on it. Note that the spaces here are ignored.
2326
2327	``wavelength:lambda keV: 12.398425/float(keV)\|9``
2328	Here we define an algebraic expression to convert an energy in keV to a
2329	wavelength and pass the contents of column 9 as that input energy
2330
2331	``pixelSize:lambda x: [74.8, 74.8]\|0``
2332	In this case the pixel size is a constant (a list of two numbers). The first
2333	column is passed as an argument as at least one argument is required, but that
2334	value is not used in the expression.
2335
2336	``ISOlikeDate: lambda dow,m,d,t,y:"{}-{}-{}T{} ({})".format(y,m,d,t,dow)\|0,1,2,3,4``
2337	This example defines a parameter that takes items in the first five columns
2338	and formats them in a different way. This parameter is not one of the pre-defined
2339	parameter names below. Some external code could be used to change the month string
2340	(argument ``m``) to a integer from 1 to 12.
2341
2342	``FreePrm2: int \| 34 \| Free Parm2 Label``
2343	In this example, the contents of column 34 will be converted to an integer and
2344	placed as the second free-named parameter in the Sample Parameters after an
2345	integration. The label for this parameter will be changed to "Free Parm2 Label".
2346
2347	Pre-defined parameter names
2348
2349	============= ========= ======== =====================================================
2350	keyword required type Description
2351	============= ========= ======== =====================================================
2352	filename yes str or generates the file name prefix for the matching image
2353	list file (MyImage001 for file /tmp/MyImage001.tif) or
2354	a list of file names.
2355	polarization no float generates the polarization expected based on the
2356	monochromator angle, defaults to 0.99.
2357	center no list of generates the approximate beam center on the detector
2358	2 floats in mm, such as [204.8, 204.8].
2359	distance yes float generates the distance from the sample to the detector
2360	in mm
2361	pixelSize no list of generates the size of the pixels in microns such as
2362	2 floats [200.0, 200.0].
2363	wavelength yes float generates the wavelength in Angstroms
2364	============= ========= ======== =====================================================
2365
2366	'''
2367	dir,fil = os.path.split(os.path.abspath(imagefile))
2368	imageName,ext = os.path.splitext(fil)
2369	if not GSASIIpath.GetConfigValue('Column_Metadata_directory'): return
2370	parfiles = glob.glob(os.path.join(GSASIIpath.GetConfigValue('Column_Metadata_directory'),'*.par'))
2371	if len(parfiles) == 0:
2372	print('Sorry, No Column metadata (.par) file found in '+
2373	GSASIIpath.GetConfigValue('Column_Metadata_directory'))
2374	return {}
2375	for parFil in parfiles: # loop over all .par files (hope just 1) in image dir until image is found
2376	parRoot = os.path.splitext(parFil)[0]
2377	for e in (ext+'_lbls','.lbls'):
2378	if os.path.exists(parRoot+e):
2379	lblFil = parRoot+e
2380	break
2381	else:
2382	print('Warning: No labels definitions found for '+parFil)
2383	continue
2384	labels,lbldict,keyCols,keyExp,errors = readColMetadataLabels(lblFil)
2385	if errors:
2386	print('Errors in labels file '+lblFil)
2387	for i in errors: print(' '+i)
2388	continue
2389	else:
2390	print('Read '+lblFil)
2391	# scan through each line in this .par file, looking for the matching image rootname
2392	fp = open(parFil,'Ur')
2393	for iline,line in enumerate(fp):
2394	items = line.strip().split(' ')
2395	nameList = keyExp['filename'](*[items[j] for j in keyCols['filename']])
2396	if type(nameList) is str:
2397	if nameList != imageName: continue
2398	name = nameList
2399	else:
2400	for name in nameList:
2401	if name == imageName: break # got a match
2402	else:
2403	continue
2404	# parse the line and finish
2405	metadata = evalColMetadataDicts(items,labels,lbldict,keyCols,keyExp)
2406	metadata['par file'] = parFil
2407	metadata['lbls file'] = lblFil
2408	print("Metadata read from {} line {}".format(parFil,iline+1))
2409	fp.close()
2410	return metadata
2411	else:
2412	print("Image {} not found in {}".format(imageName,parFil))
2413	fp.close()
2414	continue
2415	fp.close()
2416	else:
2417	print("Warning: No .par metadata for image {}".format(imageName))
2418	return {}
2419
2420	def readColMetadataLabels(lblFil):
2421	'''Read the .*lbls file and setup for metadata assignments
2422	'''
2423	lbldict = {}
2424	keyExp = {}
2425	keyCols = {}
2426	labels = {}
2427	errors = []
2428	fp = open(lblFil,'Ur') # read column labels
2429	for iline,line in enumerate(fp): # read label definitions
2430	line = line.strip()
2431	if not line or line[0] == '#': continue # comments
2432	items = line.split(':')
2433	if len(items) < 2: continue # lines with no colon are also comments
2434	# does this line a definition for a named parameter?
2435	key = items[0]
2436	try:
2437	int(key)
2438	except ValueError: # try as named parameter since not a valid number
2439	items = line.split(':',1)[1].split('\|')
2440	try:
2441	f = eval(items[0]) # compile the expression
2442	if not callable(f):
2443	errors += ['Expression "{}" for key {} is not a function (line {})'.
2444	format(items[0],key,iline)]
2445	continue
2446	keyExp[key] = f
2447	except Exception as msg:
2448	errors += ['Expression "{}" for key {} is not valid (line {})'.
2449	format(items[0],key,iline)]
2450	errors += [str(msg)]
2451	continue
2452	keyCols[key] = [int(i) for i in items[1].strip().split(',')]
2453	if key.lower().startswith('freeprm') and len(items) > 2:
2454	labels[key] = items[2]
2455	continue
2456	if len(items) == 2: # simple column definition
2457	lbldict[int(items[0])] = items[1]
2458	fp.close()
2459	if 'filename' not in keyExp:
2460	errors += ["File {} is invalid. No valid filename expression.".format(lblFil)]
2461	return labels,lbldict,keyCols,keyExp,errors
2462
2463	def evalColMetadataDicts(items,labels,lbldict,keyCols,keyExp,ShowError=False):
2464	'''Evaluate the metadata for a line in the .par file
2465	'''
2466	metadata = {lbldict[j]:items[j] for j in lbldict}
2467	named = {}
2468	for key in keyExp:
2469	try:
2470	res = keyExp[key](*[items[j] for j in keyCols[key]])
2471	except:
2472	if ShowError:
2473	res = "* error *"
2474	else:
2475	continue
2476	named[key] = res
2477	metadata.update(named)
2478	for lbl in labels: # add labels for FreePrm's
2479	metadata['label_'+lbl[4:].lower()] = labels[lbl]
2480	return metadata
2481
2482	def GetColumnMetadata(reader):
2483	'''Add metadata to an image from a column-type metadata file
2484	using :func:`readColMetadata`
2485
2486	:param reader: a reader object from reading an image
2487
2488	'''
2489	if not GSASIIpath.GetConfigValue('Column_Metadata_directory'): return
2490	parParms = readColMetadata(reader.readfilename)
2491	if not parParms: return # check for read failure
2492	specialKeys = ('filename',"polarization", "center", "distance", "pixelSize", "wavelength",)
2493	reader.Comments = ['Metadata from {} assigned by {}'.format(parParms['par file'],parParms['lbls file'])]
2494	for key in parParms:
2495	if key in specialKeys+('par file','lbls file'): continue
2496	reader.Comments += ["{} = {}".format(key,parParms[key])]
2497	if "polarization" in parParms:
2498	reader.Data['PolaVal'][0] = parParms["polarization"]
2499	else:
2500	reader.Data['PolaVal'][0] = 0.99
2501	if "center" in parParms:
2502	reader.Data['center'] = parParms["center"]
2503	if "pixelSize" in parParms:
2504	reader.Data['pixelSize'] = parParms["pixelSize"]
2505	if "wavelength" in parParms:
2506	reader.Data['wavelength'] = parParms['wavelength']
2507	else:
2508	print('Error: wavelength not defined in {}'.format(parParms['lbls file']))
2509	if "distance" in parParms:
2510	reader.Data['distance'] = parParms['distance']
2511	reader.Data['setdist'] = parParms['distance']
2512	else:
2513	print('Error: distance not defined in {}'.format(parParms['lbls file']))
2514
2515	def testColumnMetadata(G2frame):
2516	'''Test the column-oriented metadata parsing, as implemented at 1-ID, by showing results
2517	when using a .par and .lbls pair.
2518
2519	* Select a .par file, if more than one in selected dir.
2520	* Select the .*lbls file, if more than one matching .par file.
2521	* Parse the .lbls file, showing errors if encountered; loop until errors are fixed.
2522	* Search for an image or a line in the .par file and show the results when interpreted
2523
2524	See :func:`readColMetadata` for more details.
2525	'''
2526	if not GSASIIpath.GetConfigValue('Column_Metadata_directory'):
2527	G2G.G2MessageBox(G2frame,'The configuration option for I-ID Metadata is not set.\n'+
2528	'Please use the File/Preferences menu to set Column_Metadata_directory',
2529	'Warning')
2530	return
2531	parFiles = glob.glob(os.path.join(GSASIIpath.GetConfigValue('Column_Metadata_directory'),'*.par'))
2532	if not parFiles:
2533	G2G.G2MessageBox(G2frame,'No .par files found in directory {}. '
2534	.format(GSASIIpath.GetConfigValue('Column_Metadata_directory'))+
2535	'\nThis is set by config variable Column_Metadata_directory '+
2536	'(Set in File/Preferences menu).',
2537	'Warning')
2538	return
2539	parList = []
2540	for parFile in parFiles:
2541	lblList = []
2542	parRoot = os.path.splitext(parFile)[0]
2543	for f in glob.glob(parRoot+'.*lbls'):
2544	if os.path.exists(f): lblList.append(f)
2545	if not len(lblList):
2546	continue
2547	parList.append(parFile)
2548	if len(parList) == 0:
2549	G2G.G2MessageBox(G2frame,'No .lbls or .EXT_lbls file found for .par file(s) in directory {}. '
2550	.format(GSASIIpath.GetConfigValue('Column_Metadata_directory'))+
2551	'\nThis is set by config variable Column_Metadata_directory '+
2552	'(Set in File/Preferences menu).',
2553	'Warning')
2554	return
2555	elif len(parList) == 1:
2556	parFile = parList[0]
2557	else:
2558	dlg = G2G.G2SingleChoiceDialog(G2frame,
2559	'More than 1 .par file found. (Better if only 1!). Choose the one to test in '+
2560	GSASIIpath.GetConfigValue('Column_Metadata_directory'),
2561	'Choose .par file', [os.path.split(i)[1] for i in parList])
2562	if dlg.ShowModal() == wx.ID_OK:
2563	parFile = parList[dlg.GetSelection()]
2564	dlg.Destroy()
2565	else:
2566	dlg.Destroy()
2567	return
2568	# got .par file; now work on .*lbls file
2569	lblList = []
2570	parRoot = os.path.splitext(parFile)[0]
2571	for f in glob.glob(parRoot+'.*lbls'):
2572	if os.path.exists(f): lblList.append(f)
2573	if not len(lblList):
2574	raise Exception('How did this happen! No .*lbls files for '+parFile)
2575	elif len(lblList) == 1:
2576	lblFile = lblList[0]
2577	else:
2578	dlg = G2G.G2SingleChoiceDialog(G2frame,
2579	'Select label file for .par file '+parFile,
2580	'Choose label file', [os.path.split(i)[1] for i in lblList])
2581	if dlg.ShowModal() == wx.ID_OK:
2582	lblFile = lblList[dlg.GetSelection()]
2583	dlg.Destroy()
2584	else:
2585	dlg.Destroy()
2586	return
2587	# parse the labels file
2588	errors = True
2589	while errors:
2590	labels,lbldict,keyCols,keyExp,errors = readColMetadataLabels(lblFile)
2591	if errors:
2592	t = "Error reading file "+lblFile
2593	for l in errors:
2594	t += '\n'
2595	t += l
2596	t += "\n\nPlease edit the file and press OK (or Cancel to quit)"
2597	dlg = wx.MessageDialog(G2frame,message=t,
2598	caption="Read Error",style=wx.ICON_ERROR\| wx.OK\|wx.STAY_ON_TOP\|wx.CANCEL)
2599	if dlg.ShowModal() != wx.ID_OK: return
2600	# request a line number, read that line
2601	dlg = G2G.SingleStringDialog(G2frame,'Read what',
2602	'Enter a line number or an image file name (-1=last line)',
2603	'-1',size=(400,-1))
2604	if dlg.Show():
2605	fileorline = dlg.GetValue()
2606	dlg.Destroy()
2607	else:
2608	dlg.Destroy()
2609	return
2610	# and report the generated key pairs in metadata dict
2611	linenum = None
2612	try:
2613	linenum = int(fileorline)
2614	except:
2615	imageName = os.path.splitext(os.path.split(fileorline)[1])[0]
2616
2617	fp = open(parFile,'Ur')
2618	for iline,line in enumerate(fp):
2619	if linenum is not None:
2620	if iline == linenum:
2621	items = line.strip().split(' ')
2622	n = "Line {}".format(iline)
2623	break
2624	else:
2625	continue
2626	else:
2627	items = line.strip().split(' ')
2628	nameList = keyExp['filename'](*[items[j] for j in keyCols['filename']])
2629	if type(nameList) is str:
2630	if nameList != imageName: continue
2631	name = nameList
2632	break
2633	else:
2634	for name in nameList:
2635	print (name,name == imageName)
2636	if name == imageName:
2637	n = "Image {} found in line {}".format(imageName,iline)
2638	break # got a match
2639	else:
2640	continue
2641	break
2642	else:
2643	if linenum is not None:
2644	n = "Line {}".format(iline)
2645	else:
2646	n = "Image {} not found. Reporting line {}".format(imageName,iline)
2647	items = line.strip().split(' ')
2648	fp.close()
2649	metadata = evalColMetadataDicts(items,labels,lbldict,keyCols,keyExp,True)
2650	title = "Results: ("+n+")"
2651	t = ['Files: '+parFile,lblFile,' ']
2652	n = ["Named parameters:"]
2653	l = ['',"Labeled columns:"]
2654	for key in sorted(metadata):
2655	if key == "filename" or key.startswith('label_prm'): continue
2656	if key in keyCols:
2657	n += [" {} = {}".format(key,metadata[key])]
2658	elif key in lbldict.values():
2659	l += [" {} = {}".format(key,metadata[key])]
2660	else:
2661	t += ["** Unexpected: {}".format(key,metadata[key])]
2662	if type(metadata['filename']) is str:
2663	l += ["","Filename: "+ metadata['filename']]
2664	else:
2665	l += ["","Filename(s): "]
2666	for i,j in enumerate(metadata['filename']):
2667	if i: l[-1] += ', '
2668	l[-1] += j
2669	t += n + l + ['','Unused columns:']
2670	usedCols = list(lbldict.keys())
2671	for i in keyCols.values(): usedCols += i
2672	for i in range(len(items)):
2673	if i in usedCols: continue
2674	t += [" {}: {}".format(i,items[i])]
2675	dlg = G2G.G2SingleChoiceDialog(None,title,'Column metadata parse results',t,
2676	monoFont=True,filterBox=False,size=(400,600),
2677	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.CENTRE\|wx.OK)
2678	dlg.ShowModal()
2679
2680	if __name__ == '__main__':
2681	import GSASIIdataGUI
2682	application = GSASIIdataGUI.GSASIImain(0)
2683	G2frame = application.main
2684	#app = wx.PySimpleApp()
2685	#G2frame = wx.Frame(None) # create a frame
2686	#frm.Show(True)
2687	#filename = '/tmp/notzip.zip'
2688	#filename = '/tmp/all.zip'
2689	#filename = '/tmp/11bmb_7652.zip'
2690
2691	#selection=None, confirmoverwrite=True, parent=None
2692	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2693	#print ExtractFileFromZip(filename,multipleselect=True)
2694	# #confirmread=False, confirmoverwrite=False)
2695
2696	# choicelist=[ ('a','b','c'),
2697	# ('test1','test2'),('no choice',)]
2698	# titles = [ 'a, b or c', 'tests', 'No option here']
2699	# dlg = MultipleChoicesDialog(
2700	# choicelist,titles,
2701	# parent=frm)
2702	# if dlg.ShowModal() == wx.ID_OK:
2703	# print 'Got OK'
2704	imagefile = '/tmp/NDC5_00237_3.ge3'
2705	Comments, Data, Npix, Image = GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None)
2706
2707	print("\n\nResults loaded to Comments, Data, Npix and Image\n\n")
2708
2709	GSASIIpath.IPyBreak_base()

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