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source: trunk/GSASIIIO.py @ 3189

Last change on this file since 3189 was 3189, checked in by toby, 5 years ago
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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2017-12-10 16:34:39 +0000 (Sun, 10 Dec 2017) $
4	# $Author: toby $
5	# $Revision: 3189 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 3189 2017-12-10 16:34:39Z 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: 3189 $")
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	prevnam = os.path.split(imagefile)[1]
216	prevext = os.path.splitext(imagefile)[1]
217	wildcard = 'Image format ('+prevext+')\|'+prevext
218	dlg = wx.FileDialog(G2frame, 'Previous image file ('+prevnam+') not found; open here', '.', prevnam,
219	wildcard,wx.FD_OPEN)
220	try:
221	dlg.SetFilename(''+ospath.split(imagefile)[1])
222	if dlg.ShowModal() == wx.ID_OK:
223	imagefile = dlg.GetPath()
224	G2frame.GPXtree.UpdateImageLoc(treeId,imagefile)
225	else:
226	imagefile = False
227	finally:
228	dlg.Destroy()
229	return Npix,imagefile,imagetag
230
231	def EditImageParms(parent,Data,Comments,Image,filename):
232	dlg = wx.Dialog(parent, wx.ID_ANY, 'Edit image parameters',
233	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
234	def onClose(event):
235	dlg.EndModal(wx.ID_OK)
236	mainsizer = wx.BoxSizer(wx.VERTICAL)
237	h,w = Image.shape[:2]
238	mainsizer.Add(wx.StaticText(dlg,wx.ID_ANY,'File '+str(filename)+'\nImage size: '+str(h)+' x '+str(w)),
239	0,wx.ALIGN_LEFT\|wx.ALL, 2)
240
241	vsizer = wx.BoxSizer(wx.HORIZONTAL)
242	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Wavelength (\xC5) '),
243	0,wx.ALIGN_LEFT\|wx.ALL, 2)
244	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'wavelength')
245	vsizer.Add(wdgt)
246	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
247
248	vsizer = wx.BoxSizer(wx.HORIZONTAL)
249	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Pixel size (\xb5m). Width '),
250	0,wx.ALIGN_LEFT\|wx.ALL, 2)
251	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],0,
252	size=(50,-1))
253	vsizer.Add(wdgt)
254	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Height '),wx.ALIGN_LEFT\|wx.ALL, 2)
255	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],1,size=(50,-1))
256	vsizer.Add(wdgt)
257	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
258
259	vsizer = wx.BoxSizer(wx.HORIZONTAL)
260	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Sample to detector (mm) '),
261	0,wx.ALIGN_LEFT\|wx.ALL, 2)
262	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'distance')
263	vsizer.Add(wdgt)
264	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
265
266	vsizer = wx.BoxSizer(wx.HORIZONTAL)
267	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Beam center (pixels). X = '),
268	0,wx.ALIGN_LEFT\|wx.ALL, 2)
269	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],0,size=(75,-1))
270	vsizer.Add(wdgt)
271	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Y = '),wx.ALIGN_LEFT\|wx.ALL, 2)
272	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],1,size=(75,-1))
273	vsizer.Add(wdgt)
274	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
275
276	vsizer = wx.BoxSizer(wx.HORIZONTAL)
277	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Comments '),
278	0,wx.ALIGN_LEFT\|wx.ALL, 2)
279	wdgt = G2G.ValidatedTxtCtrl(dlg,Comments,0,size=(250,-1))
280	vsizer.Add(wdgt)
281	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
282
283	btnsizer = wx.StdDialogButtonSizer()
284	OKbtn = wx.Button(dlg, wx.ID_OK, 'Continue')
285	OKbtn.SetDefault()
286	OKbtn.Bind(wx.EVT_BUTTON,onClose)
287	btnsizer.AddButton(OKbtn) # not sure why this is needed
288	btnsizer.Realize()
289	mainsizer.Add(btnsizer, 1, wx.ALIGN_CENTER\|wx.ALL\|wx.EXPAND, 5)
290	dlg.SetSizer(mainsizer)
291	dlg.CenterOnParent()
292	dlg.ShowModal()
293
294	def LoadImage2Tree(imagefile,G2frame,Comments,Data,Npix,Image):
295	'''Load an image into the tree. Saves the location of the image, as well as the
296	ImageTag (where there is more than one image in the file), if defined.
297	'''
298	ImgNames = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',])
299	TreeLbl = 'IMG '+os.path.basename(imagefile)
300	ImageTag = Data.get('ImageTag')
301	if ImageTag:
302	TreeLbl += ' #'+'%04d'%(ImageTag)
303	imageInfo = (imagefile,ImageTag)
304	else:
305	imageInfo = imagefile
306	TreeName = G2obj.MakeUniqueLabel(TreeLbl,ImgNames)
307	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=TreeName)
308	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments)
309	Imax = np.amax(Image)
310	if G2frame.imageDefault:
311	Data = copy.copy(G2frame.imageDefault)
312	Data['showLines'] = True
313	Data['ring'] = []
314	Data['rings'] = []
315	Data['cutoff'] = 10
316	Data['pixLimit'] = 20
317	Data['edgemin'] = 100000000
318	Data['calibdmin'] = 0.5
319	Data['calibskip'] = 0
320	Data['ellipses'] = []
321	Data['calibrant'] = ''
322	Data['GonioAngles'] = [0.,0.,0.]
323	Data['DetDepthRef'] = False
324	else:
325	Data['type'] = 'PWDR'
326	Data['color'] = GSASIIpath.GetConfigValue('Contour_color','Paired')
327	Data['tilt'] = 0.0
328	Data['rotation'] = 0.0
329	Data['showLines'] = False
330	Data['ring'] = []
331	Data['rings'] = []
332	Data['cutoff'] = 10
333	Data['pixLimit'] = 20
334	Data['calibdmin'] = 0.5
335	Data['calibskip'] = 0
336	Data['edgemin'] = 100000000
337	Data['ellipses'] = []
338	Data['GonioAngles'] = [0.,0.,0.]
339	Data['DetDepth'] = 0.
340	Data['DetDepthRef'] = False
341	Data['calibrant'] = ''
342	Data['IOtth'] = [2.0,5.0]
343	Data['LRazimuth'] = [0.,180.]
344	Data['azmthOff'] = 0.0
345	Data['outChannels'] = 2500
346	Data['outAzimuths'] = 1
347	Data['centerAzm'] = False
348	Data['fullIntegrate'] = False
349	Data['setRings'] = False
350	Data['background image'] = ['',-1.0]
351	Data['dark image'] = ['',-1.0]
352	Data['Flat Bkg'] = 0.0
353	Data['setDefault'] = False
354	Data['range'] = [(0,Imax),[0,Imax]]
355	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Image Controls'),Data)
356	Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],'Thresholds':[(0,Imax),[0,Imax]]}
357	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Masks'),Masks)
358	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Stress/Strain'),
359	{'Type':'True','d-zero':[],'Sample phi':0.0,'Sample z':0.0,'Sample load':0.0})
360	G2frame.GPXtree.SetItemPyData(Id,[Npix,imageInfo])
361	G2frame.PickId = Id
362	G2frame.PickIdText = G2frame.GetTreeItemsList(G2frame.PickId)
363	G2frame.Image = Id
364
365	def GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None,FormatName=''):
366	'''Read a single image with an image importer. This is called to reread an image
367	after it has already been imported with :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`
368	(or :func:`ReadImages` in Auto Integration) so it is not necessary to reload metadata.
369
370	:param wx.Frame G2frame: main GSAS-II Frame and data object.
371	:param str imagefile: name of image file
372	:param bool imageOnly: If True return only the image,
373	otherwise (default) return more (see below)
374	:param int/str ImageTag: specifies a particular image to be read from a file.
375	First image is read if None (default).
376	:param str formatName: the image reader formatName
377
378	:returns: an image as a numpy array or a list of four items:
379	Comments, Data, Npix and the Image, as selected by imageOnly
380
381	'''
382	# determine which formats are compatible with this file
383	primaryReaders = []
384	secondaryReaders = []
385	for rd in G2frame.ImportImageReaderlist:
386	flag = rd.ExtensionValidator(imagefile)
387	if flag is None:
388	secondaryReaders.append(rd)
389	elif flag:
390	if not FormatName:
391	primaryReaders.append(rd)
392	elif FormatName == rd.formatName:
393	primaryReaders.append(rd)
394	if len(secondaryReaders) + len(primaryReaders) == 0:
395	print('Error: No matching format for file '+imagefile)
396	raise Exception('No image read')
397	errorReport = ''
398	if not imagefile:
399	return
400	for rd in primaryReaders+secondaryReaders:
401	rd.ReInitialize() # purge anything from a previous read
402	rd.errors = "" # clear out any old errors
403	if not rd.ContentsValidator(imagefile): # rejected on cursory check
404	errorReport += "\n "+rd.formatName + ' validator error'
405	if rd.errors:
406	errorReport += ': '+rd.errors
407	continue
408	if imageOnly:
409	ParentFrame = None # prevent GUI access on reread
410	else:
411	ParentFrame = G2frame
412	if GSASIIpath.GetConfigValue('debug'):
413	flag = rd.Reader(imagefile,ParentFrame,blocknum=ImageTag)
414	else:
415	flag = False
416	try:
417	flag = rd.Reader(imagefile,ParentFrame,blocknum=ImageTag)
418	except rd.ImportException as detail:
419	rd.errors += "\n Read exception: "+str(detail)
420	except Exception as detail:
421	import traceback
422	rd.errors += "\n Unhandled read exception: "+str(detail)
423	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
424	if flag: # this read succeeded
425	if rd.Image is None:
426	raise Exception('No image read. Strange!')
427	if GSASIIpath.GetConfigValue('Transpose'):
428	print ('Transposing Image!')
429	rd.Image = rd.Image.T
430	#rd.readfilename = imagefile
431	if imageOnly:
432	return rd.Image
433	else:
434	return rd.Comments,rd.Data,rd.Npix,rd.Image
435	else:
436	print('Error reading file '+imagefile)
437	print('Error messages(s)\n'+errorReport)
438	raise Exception('No image read')
439
440	def ReadImages(G2frame,imagefile):
441	'''Read one or more images from a file and put them into the Tree
442	using image importers. Called only in :meth:`AutoIntFrame.OnTimerLoop`.
443
444	ToDo: Images are most commonly read in :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`
445	which is called from :meth:`GSASIIdataGUI.GSASII.OnImportImage`
446	it would be good if these routines used a common code core so that changes need to
447	be made in only one place.
448
449	:param wx.Frame G2frame: main GSAS-II Frame and data object.
450	:param str imagefile: name of image file
451
452	:returns: a list of the id's of the IMG tree items created
453	'''
454	# determine which formats are compatible with this file
455	primaryReaders = []
456	secondaryReaders = []
457	for rd in G2frame.ImportImageReaderlist:
458	flag = rd.ExtensionValidator(imagefile)
459	if flag is None:
460	secondaryReaders.append(rd)
461	elif flag:
462	primaryReaders.append(rd)
463	if len(secondaryReaders) + len(primaryReaders) == 0:
464	print('Error: No matching format for file '+imagefile)
465	raise Exception('No image read')
466	errorReport = ''
467	rdbuffer = {} # create temporary storage for file reader
468	for rd in primaryReaders+secondaryReaders:
469	rd.ReInitialize() # purge anything from a previous read
470	rd.errors = "" # clear out any old errors
471	if not rd.ContentsValidator(imagefile): # rejected on cursory check
472	errorReport += "\n "+rd.formatName + ' validator error'
473	if rd.errors:
474	errorReport += ': '+rd.errors
475	continue
476	ParentFrame = G2frame
477	block = 0
478	repeat = True
479	CreatedIMGitems = []
480	while repeat: # loop if the reader asks for another pass on the file
481	block += 1
482	repeat = False
483	if GSASIIpath.GetConfigValue('debug'):
484	flag = rd.Reader(imagefile,ParentFrame,blocknum=block,Buffer=rdbuffer)
485	else:
486	flag = False
487	try:
488	flag = rd.Reader(imagefile,ParentFrame,blocknum=block,Buffer=rdbuffer)
489	except rd.ImportException as detail:
490	rd.errors += "\n Read exception: "+str(detail)
491	except Exception as detail:
492	import traceback
493	rd.errors += "\n Unhandled read exception: "+str(detail)
494	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
495	if flag: # this read succeeded
496	if rd.Image is None:
497	raise Exception('No image read. Strange!')
498	if GSASIIpath.GetConfigValue('Transpose'):
499	print ('Transposing Image!')
500	rd.Image = rd.Image.T
501	rd.Data['ImageTag'] = rd.repeatcount
502	if GSASIIpath.GetConfigValue('Image_1IDmetadata'):
503	rd.readfilename = imagefile
504	Get1IDMetadata(rd)
505	LoadImage2Tree(imagefile,G2frame,rd.Comments,rd.Data,rd.Npix,rd.Image)
506	repeat = rd.repeat
507	CreatedIMGitems.append(G2frame.Image)
508	if CreatedIMGitems: return CreatedIMGitems
509	else:
510	print('Error reading file '+imagefile)
511	print('Error messages(s)\n'+errorReport)
512	return []
513	#raise Exception('No image read')
514
515	def SaveMultipleImg(G2frame):
516	if not G2frame.GPXtree.GetCount():
517	print ('no images!')
518	return
519	choices = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',])
520	if len(choices) == 1:
521	names = choices
522	else:
523	dlg = G2G.G2MultiChoiceDialog(G2frame,'Stress/Strain fitting','Select images to fit:',choices)
524	dlg.SetSelections([])
525	names = []
526	if dlg.ShowModal() == wx.ID_OK:
527	names = [choices[sel] for sel in dlg.GetSelections()]
528	dlg.Destroy()
529	if not names: return
530	for name in names:
531	Id = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, name)
532	Npix,imagefile,imagetag = G2frame.GPXtree.GetImageLoc(Id)
533	imroot = os.path.splitext(imagefile)[0]
534	if imagetag:
535	imroot += '_' + str(imagetag)
536	Data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Image Controls'))
537	print('Writing '+imroot+'.imctrl')
538	File = open(imroot+'.imctrl','w')
539	keys = ['type','wavelength','calibrant','distance','center',
540	'tilt','rotation','azmthOff','fullIntegrate','LRazimuth',
541	'IOtth','outChannels','outAzimuths','invert_x','invert_y','DetDepth',
542	'calibskip','pixLimit','cutoff','calibdmin','chisq','Flat Bkg',
543	'binType','SampleShape','PolaVal','SampleAbs','dark image','background image']
544	for key in keys:
545	if key not in Data: continue #uncalibrated!
546	File.write(key+':'+str(Data[key])+'\n')
547	File.close()
548	mask = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Masks'))
549	G2imG.CleanupMasks(mask)
550	print('Writing '+imroot+'.immask')
551	File = open(imroot+'.immask','w')
552	for key in ['Points','Rings','Arcs','Polygons','Frames','Thresholds']:
553	File.write(key+':'+str(mask[key])+'\n')
554	File.close()
555
556	def PutG2Image(filename,Comments,Data,Npix,image):
557	'Write an image as a python pickle - might be better as an .edf file?'
558	File = open(filename,'wb')
559	cPickle.dump([Comments,Data,Npix,image],File,2)
560	File.close()
561	return
562
563	def ProjFileOpen(G2frame,showProvenance=True):
564	'Read a GSAS-II project file and load into the G2 data tree'
565	if not os.path.exists(G2frame.GSASprojectfile):
566	print ('\n*** Error attempt to open project file that does not exist:\n '+
567	str(G2frame.GSASprojectfile))
568	return
569	LastSavedUsing = None
570	file = open(G2frame.GSASprojectfile,'rb')
571	if showProvenance: print ('loading from file: '+G2frame.GSASprojectfile)
572	#G2frame.SetTitle("GSAS-II data tree: "+
573	# os.path.split(G2frame.GSASprojectfile)[1])
574	G2frame.SetTitle("GSAS-II data tree: "+
575	os.path.split(G2frame.GSASprojectfile)[1],1)
576	wx.BeginBusyCursor()
577	try:
578	while True:
579	try:
580	if '2' in platform.python_version_tuple()[0]:
581	data = cPickle.load(file)
582	else:
583	data = cPickle.load(file,encoding='latin-1')
584	except EOFError:
585	break
586	datum = data[0]
587
588	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=datum[0])
589	if datum[0].startswith('PWDR'):
590	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
591	datum[1][0]['ranId'] = ran.randint(0,sys.maxsize)
592	G2frame.GPXtree.SetItemPyData(Id,datum[1][:3]) #temp. trim off junk (patch?)
593	elif datum[0].startswith('HKLF'):
594	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
595	datum[1][0]['ranId'] = ran.randint(0,sys.maxsize)
596	G2frame.GPXtree.SetItemPyData(Id,datum[1])
597	else:
598	G2frame.GPXtree.SetItemPyData(Id,datum[1])
599	if datum[0] == 'Controls' and 'LastSavedUsing' in datum[1]:
600	LastSavedUsing = datum[1]['LastSavedUsing']
601	if datum[0] == 'Controls' and 'PythonVersions' in datum[1] and GSASIIpath.GetConfigValue('debug') and showProvenance:
602	print('Packages used to create .GPX file:')
603	if 'dict' in str(type(datum[1]['PythonVersions'])): #patch
604	for p in sorted(datum[1]['PythonVersions'],key=lambda s: s.lower()):
605	print(" {:<14s}: {:s}".format(p[0],p[1]))
606	else:
607	for p in datum[1]['PythonVersions']:
608	print(" {:<12s} {:s}".format(p[0]+':',p[1]))
609	oldPDF = False
610	for datus in data[1:]:
611	#patch - 1/23/17 PDF cleanup
612	if datus[0][:4] in ['I(Q)','S(Q)','F(Q)','G(R)']:
613	oldPDF = True
614	data[1][1][datus[0][:4]] = copy.deepcopy(datus[1][:2])
615	continue
616	#end PDF cleanup
617	sub = G2frame.GPXtree.AppendItem(Id,datus[0])
618	#patch
619	if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
620	if datum[0].startswith('PWDR'):
621	datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
622	else:
623	datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
624	for item in datus[1][0]: #zip makes tuples - now make lists!
625	datus[1][0][item] = list(datus[1][0][item])
626	#end patch
627	G2frame.GPXtree.SetItemPyData(sub,datus[1])
628	if 'PDF ' in datum[0][:4] and oldPDF:
629	sub = G2frame.GPXtree.AppendItem(Id,'PDF Peaks')
630	G2frame.GPXtree.SetItemPyData(sub,{'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]})
631	if datum[0].startswith('IMG'): #retrieve image default flag & data if set
632	Data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Image Controls'))
633	if Data['setDefault']:
634	G2frame.imageDefault = Data
635	file.close()
636	if LastSavedUsing:
637	print('GPX load successful. Last saved with GSAS-II revision '+LastSavedUsing)
638	else:
639	print('project load successful')
640	G2frame.NewPlot = True
641	except:
642	msg = wx.MessageDialog(G2frame,message="Error reading file "+
643	str(G2frame.GSASprojectfile)+". This is not a GSAS-II .gpx file",
644	caption="Load Error",style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
645	msg.ShowModal()
646	finally:
647	wx.EndBusyCursor()
648	G2frame.Status.SetStatusText('Mouse RB drag/drop to reorder',0)
649
650	def ProjFileSave(G2frame):
651	'Save a GSAS-II project file'
652	if not G2frame.GPXtree.IsEmpty():
653	file = open(G2frame.GSASprojectfile,'wb')
654	print ('save to file: '+G2frame.GSASprojectfile)
655	# stick the file name into the tree and version info into tree so they are saved.
656	# (Controls should always be created at this point)
657	try:
658	Controls = G2frame.GPXtree.GetItemPyData(
659	G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
660	Controls['LastSavedAs'] = os.path.abspath(G2frame.GSASprojectfile)
661	Controls['LastSavedUsing'] = str(GSASIIpath.GetVersionNumber())
662	Controls['PythonVersions'] = G2frame.PackageVersions
663	except:
664	pass
665	wx.BeginBusyCursor()
666	try:
667	item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
668	while item:
669	data = []
670	name = G2frame.GPXtree.GetItemText(item)
671	data.append([name,G2frame.GPXtree.GetItemPyData(item)])
672	item2, cookie2 = G2frame.GPXtree.GetFirstChild(item)
673	while item2:
674	name = G2frame.GPXtree.GetItemText(item2)
675	data.append([name,G2frame.GPXtree.GetItemPyData(item2)])
676	item2, cookie2 = G2frame.GPXtree.GetNextChild(item, cookie2)
677	item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
678	cPickle.dump(data,file,2)
679	file.close()
680	pth = os.path.split(os.path.abspath(G2frame.GSASprojectfile))[0]
681	if GSASIIpath.GetConfigValue('Save_paths'): G2G.SaveGPXdirectory(pth)
682	G2frame.LastGPXdir = pth
683	finally:
684	wx.EndBusyCursor()
685	print('project save successful')
686
687	def SaveIntegration(G2frame,PickId,data,Overwrite=False):
688	'Save image integration results as powder pattern(s)'
689	azms = G2frame.Integrate[1]
690	X = G2frame.Integrate[2][:-1]
691	N = len(X)
692	Id = G2frame.GPXtree.GetItemParent(PickId)
693	name = G2frame.GPXtree.GetItemText(Id)
694	name = name.replace('IMG ',data['type']+' ')
695	Comments = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Comments'))
696	if 'PWDR' in name:
697	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth']
698	codes = [0 for i in range(12)]
699	elif 'SASD' in name:
700	names = ['Type','Lam','Zero','Azimuth']
701	codes = [0 for i in range(4)]
702	X = 4.np.pinpsind(X/2.)/data['wavelength'] #convert to q
703	Xminmax = [X[0],X[-1]]
704	Azms = []
705	dazm = 0.
706	if data['fullIntegrate'] and data['outAzimuths'] == 1:
707	Azms = [45.0,] #a poor man's average?
708	else:
709	for i,azm in enumerate(azms[:-1]):
710	if azm > 360. and azms[i+1] > 360.:
711	Azms.append(G2img.meanAzm(azm%360.,azms[i+1]%360.))
712	else:
713	Azms.append(G2img.meanAzm(azm,azms[i+1]))
714	dazm = np.min(np.abs(np.diff(azms)))/2.
715	G2frame.IntgOutList = []
716	for i,azm in enumerate(azms[:-1]):
717	Aname = name+" Azm= %.2f"%((azm+dazm)%360.)
718	item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
719	# if Overwrite delete any duplicate
720	if Overwrite and G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname):
721	print('Replacing '+Aname)
722	item = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname)
723	G2frame.GPXtree.Delete(item)
724	else:
725	nOcc = 0
726	while item:
727	Name = G2frame.GPXtree.GetItemText(item)
728	if Aname in Name:
729	nOcc += 1
730	item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
731	if nOcc:
732	Aname += '(%d)'%(nOcc)
733	Sample = G2obj.SetDefaultSample() #set as Debye-Scherrer
734	Sample['Gonio. radius'] = data['distance']
735	Sample['Omega'] = data['GonioAngles'][0]
736	Sample['Chi'] = data['GonioAngles'][1]
737	Sample['Phi'] = data['GonioAngles'][2]
738	Sample['Azimuth'] = (azm+dazm)%360. #put here as bin center
739	polariz = 0.99 #set default polarization for synchrotron radiation!
740	for item in Comments:
741	if 'polariz' in item:
742	try:
743	polariz = float(item.split('=')[1])
744	except:
745	polariz = 0.99
746	if 'PWDR' in Aname:
747	parms = ['PXC',data['wavelength'],0.0,polariz,1.0,-0.10,0.4,0.30,1.0,0.0,0.0001,Azms[i]]
748	elif 'SASD' in Aname:
749	Sample['Trans'] = data['SampleAbs'][0]
750	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
751	Y = G2frame.Integrate[0][i]
752	Ymin = np.min(Y)
753	Ymax = np.max(Y)
754	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
755	Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=Aname)
756	G2frame.IntgOutList.append(Id)
757	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments)
758	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Limits'),copy.deepcopy([tuple(Xminmax),Xminmax]))
759	if 'PWDR' in Aname:
760	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Background'),[['chebyschev',1,3,1.0,0.0,0.0],
761	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
762	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
763	for item in inst[0]:
764	inst[0][item] = list(inst[0][item])
765	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Instrument Parameters'),inst)
766	if 'PWDR' in Aname:
767	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample)
768	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
769	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Index Peak List'),[[],[]])
770	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Unit Cells List'),[])
771	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Reflection Lists'),{})
772	elif 'SASD' in Aname:
773	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
774	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample)
775	G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
776	valuesdict = {
777	'wtFactor':1.0,
778	'Dummy':False,
779	'ranId':ran.randint(0,sys.maxsize),
780	'Offset':[0.0,0.0],'delOffset':0.02Ymax,'refOffset':-0.1Ymax,'refDelt':0.1*Ymax,
781	'qPlot':False,'dPlot':False,'sqrtPlot':False,'Yminmax':[Ymin,Ymax]
782	}
783	G2frame.GPXtree.SetItemPyData(
784	Id,[valuesdict,
785	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
786	return Id #last powder pattern generated
787
788	def XYsave(G2frame,XY,labelX='X',labelY='Y',names=None):
789	'Save XY table data'
790	pth = G2G.GetExportPath(G2frame)
791	dlg = wx.FileDialog(
792	G2frame, 'Enter csv filename for XY table', pth, '',
793	'XY table file (.csv)\|.csv',wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
794	try:
795	if dlg.ShowModal() == wx.ID_OK:
796	filename = dlg.GetPath()
797	filename = os.path.splitext(filename)[0]+'.csv'
798	File = open(filename,'w')
799	else:
800	filename = None
801	finally:
802	dlg.Destroy()
803	if not filename:
804	return
805	for i in range(len(XY)):
806	if names != None:
807	header = '%s,%s(%s)\n'%(labelX,labelY,names[i])
808	else:
809	header = '%s,%s(%d)\n'%(labelX,labelY,i)
810	File.write(header)
811	for x,y in XY[i].T:
812	File.write('%.3f,%.3f\n'%(x,y))
813	File.close()
814	print (' XY data saved to: '+filename)
815
816	def PDFSave(G2frame,exports,PDFsaves):
817	'Save a PDF I(Q), S(Q), F(Q) and G(r) in column formats'
818	import scipy.interpolate as scintp
819	for export in exports:
820	PickId = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, export)
821	PDFControls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame, PickId,'PDF Controls'))
822	if PDFsaves[0]: #I(Q)
823	iqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.iq')
824	iqdata = PDFControls['I(Q)'][0]
825	iqfxn = scintp.interp1d(iqdata[0],iqdata[1],kind='linear')
826	iqfile = open(iqfilename,'w')
827	iqfile.write('#T I(Q) %s\n'%(export))
828	iqfile.write('#L Q I(Q)\n')
829	qnew = np.arange(iqdata[0][0],iqdata[0][-1],0.005)
830	iqnew = zip(qnew,iqfxn(qnew))
831	for q,iq in iqnew:
832	iqfile.write("%15.6g %15.6g\n" % (q,iq))
833	iqfile.close()
834	print (' I(Q) saved to: '+iqfilename)
835
836	if PDFsaves[1]: #S(Q)
837	sqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.sq')
838	sqdata = PDFControls['S(Q)'][1]
839	sqfxn = scintp.interp1d(sqdata[0],sqdata[1],kind='linear')
840	sqfile = open(sqfilename,'w')
841	sqfile.write('#T S(Q) %s\n'%(export))
842	sqfile.write('#L Q S(Q)\n')
843	qnew = np.arange(sqdata[0][0],sqdata[0][-1],0.005)
844	sqnew = zip(qnew,sqfxn(qnew))
845	for q,sq in sqnew:
846	sqfile.write("%15.6g %15.6g\n" % (q,sq))
847	sqfile.close()
848	print (' S(Q) saved to: '+sqfilename)
849
850	if PDFsaves[2]: #F(Q)
851	fqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.fq')
852	fqdata = PDFControls['F(Q)'][1]
853	fqfxn = scintp.interp1d(fqdata[0],fqdata[1],kind='linear')
854	fqfile = open(sqfilename,'w')
855	fqfile.write('#T F(Q) %s\n'%(export))
856	fqfile.write('#L Q F(Q)\n')
857	qnew = np.arange(sqdata[0][0],sqdata[0][-1],0.005)
858	fqnew = zip(qnew,fqfxn(qnew))
859	for q,fq in fqnew:
860	fqfile.write("%15.6g %15.6g\n" % (q,fq))
861	fqfile.close()
862	print (' F(Q) saved to: '+fqfilename)
863
864	if PDFsaves[3]: #G(R)
865	grfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.gr')
866	grdata = PDFControls['G(R)'][1]
867	grfxn = scintp.interp1d(grdata[0],grdata[1],kind='linear')
868	grfile = open(grfilename,'w')
869	grfile.write('#T G(R) %s\n'%(export))
870	grfile.write('#L R G(R)\n')
871	rnew = np.arange(grdata[0][0],grdata[0][-1],0.010)
872	grnew = zip(rnew,grfxn(rnew))
873	for r,gr in grnew:
874	grfile.write("%15.6g %15.6g\n" % (r,gr))
875	grfile.close()
876	print (' G(R) saved to: '+grfilename)
877
878	if PDFsaves[4]: #pdfGUI file for G(R)
879	pId = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, 'PWDR'+export[4:])
880	Inst = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame, pId,'Instrument Parameters'))[0]
881	Limits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame, pId,'Limits'))
882	grfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.gr')
883	grdata = PDFControls['G(R)'][1]
884	qdata = PDFControls['I(Q)'][1][0]
885	grfxn = scintp.interp1d(grdata[0],grdata[1],kind='linear')
886	grfile = open(grfilename,'w')
887	rnew = np.arange(grdata[0][0],grdata[0][-1],0.010)
888	grnew = zip(rnew,grfxn(rnew))
889
890	grfile.write('[DEFAULT]\n')
891	grfile.write('\n')
892	grfile.write('version = GSAS-II-v'+str(GSASIIpath.GetVersionNumber())+'\n')
893	grfile.write('\n')
894	grfile.write('# input and output specifications\n')
895	grfile.write('dataformat = Qnm\n')
896	grfile.write('inputfile = %s\n'%(PDFControls['Sample']['Name']))
897	grfile.write('backgroundfile = %s\n'%(PDFControls['Sample Bkg.']['Name']))
898	grfile.write('outputtype = gr\n')
899	grfile.write('\n')
900	grfile.write('# PDF calculation setup\n')
901	if 'x' in Inst['Type']:
902	grfile.write('mode = %s\n'%('xray'))
903	elif 'N' in Inst['Type']:
904	grfile.write('mode = %s\n'%('neutron'))
905	wave = G2mth.getMeanWave(Inst)
906	grfile.write('wavelength = %.5f\n'%(wave))
907	formula = ''
908	for el in PDFControls['ElList']:
909	formula += el
910	num = PDFControls['ElList'][el]['FormulaNo']
911	if num == round(num):
912	formula += '%d'%(int(num))
913	else:
914	formula += '%.2f'%(num)
915	grfile.write('composition = %s\n'%(formula))
916	grfile.write('bgscale = %.3f\n'%(-PDFControls['Sample Bkg.']['Mult']))
917	highQ = 2.*np.pi/G2lat.Pos2dsp(Inst,Limits[1][1])
918	grfile.write('qmaxinst = %.2f\n'%(highQ))
919	grfile.write('qmin = %.5f\n'%(qdata[0]))
920	grfile.write('qmax = %.4f\n'%(qdata[-1]))
921	grfile.write('rmin = %.2f\n'%(PDFControls['Rmin']))
922	grfile.write('rmax = %.2f\n'%(PDFControls['Rmax']))
923	grfile.write('rstep = 0.01\n')
924
925
926	grfile.write('\n')
927	grfile.write('# End of config '+63*'-')
928	grfile.write('\n')
929	grfile.write('#### start data\n')
930	grfile.write('#S 1\n')
931	grfile.write('#L r($\AA$) G($\AA^{-2}$)\n')
932	for r,gr in grnew:
933	grfile.write("%15.2F %15.6F\n" % (r,gr))
934	grfile.close()
935	print (' G(R) saved to: '+grfilename)
936
937	def PeakListSave(G2frame,file,peaks):
938	'Save powder peaks to a data file'
939	print ('save peak list to file: '+G2frame.peaklistfile)
940	if not peaks:
941	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
942	try:
943	dlg.ShowModal()
944	finally:
945	dlg.Destroy()
946	return
947	for peak in peaks:
948	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
949	(peak[0],peak[2],peak[4],peak[6]))
950	print ('peak list saved')
951
952	def IndexPeakListSave(G2frame,peaks):
953	'Save powder peaks from the indexing list'
954	file = open(G2frame.peaklistfile,'wa')
955	print ('save index peak list to file: '+G2frame.peaklistfile)
956	wx.BeginBusyCursor()
957	try:
958	if not peaks:
959	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
960	try:
961	dlg.ShowModal()
962	finally:
963	dlg.Destroy()
964	return
965	for peak in peaks:
966	file.write("%12.6f\n" % (peak[7]))
967	file.close()
968	finally:
969	wx.EndBusyCursor()
970	print ('index peak list saved')
971
972	class MultipleChoicesDialog(wx.Dialog):
973	'''A dialog that offers a series of choices, each with a
974	title and a wx.Choice widget. Intended to be used Modally.
975	typical input:
976
977	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
978	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
979
980	selections are placed in self.chosen when OK is pressed
981
982	Also see GSASIIctrlGUI
983	'''
984	def __init__(self,choicelist,headinglist,
985	head='Select options',
986	title='Please select from options below',
987	parent=None):
988	self.chosen = []
989	wx.Dialog.__init__(
990	self,parent,wx.ID_ANY,head,
991	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
992	panel = wx.Panel(self)
993	mainSizer = wx.BoxSizer(wx.VERTICAL)
994	mainSizer.Add((10,10),1)
995	topLabl = wx.StaticText(panel,wx.ID_ANY,title)
996	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.CENTER,10)
997	self.ChItems = []
998	for choice,lbl in zip(choicelist,headinglist):
999	mainSizer.Add((10,10),1)
1000	self.chosen.append(0)
1001	topLabl = wx.StaticText(panel,wx.ID_ANY,' '+lbl)
1002	mainSizer.Add(topLabl,0,wx.ALIGN_LEFT,10)
1003	self.ChItems.append(wx.Choice(self, wx.ID_ANY, (100, 50), choices = choice))
1004	mainSizer.Add(self.ChItems[-1],0,wx.ALIGN_CENTER,10)
1005
1006	OkBtn = wx.Button(panel,-1,"Ok")
1007	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
1008	cancelBtn = wx.Button(panel,-1,"Cancel")
1009	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
1010	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1011	btnSizer.Add((20,20),1)
1012	btnSizer.Add(OkBtn)
1013	btnSizer.Add((20,20),1)
1014	btnSizer.Add(cancelBtn)
1015	btnSizer.Add((20,20),1)
1016	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1017	panel.SetSizer(mainSizer)
1018	panel.Fit()
1019	self.Fit()
1020
1021	def OnOk(self,event):
1022	parent = self.GetParent()
1023	if parent is not None: parent.Raise()
1024	# save the results from the choice widgets
1025	self.chosen = []
1026	for w in self.ChItems:
1027	self.chosen.append(w.GetSelection())
1028	self.EndModal(wx.ID_OK)
1029
1030	def OnCancel(self,event):
1031	parent = self.GetParent()
1032	if parent is not None: parent.Raise()
1033	self.chosen = []
1034	self.EndModal(wx.ID_CANCEL)
1035
1036	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1037	confirmoverwrite=True, parent=None,
1038	multipleselect=False):
1039	'''If the filename is a zip file, extract a file from that
1040	archive.
1041
1042	:param list Selection: used to predefine the name of the file
1043	to be extracted. Filename case and zip directory name are
1044	ignored in selection; the first matching file is used.
1045
1046	:param bool confirmread: if True asks the user to confirm before expanding
1047	the only file in a zip
1048
1049	:param bool confirmoverwrite: if True asks the user to confirm
1050	before overwriting if the extracted file already exists
1051
1052	:param bool multipleselect: if True allows more than one zip
1053	file to be extracted, a list of file(s) is returned.
1054	If only one file is present, do not ask which one, otherwise
1055	offer a list of choices (unless selection is used).
1056
1057	:returns: the name of the file that has been created or a
1058	list of files (see multipleselect)
1059
1060	If the file is not a zipfile, return the name of the input file.
1061	If the zipfile is empty or no file has been selected, return None
1062	'''
1063	import zipfile # do this now, since we can save startup time by doing this only on need
1064	import shutil
1065	zloc = os.path.split(filename)[0]
1066	if not zipfile.is_zipfile(filename):
1067	#print("not zip")
1068	return filename
1069
1070	z = zipfile.ZipFile(filename,'r')
1071	zinfo = z.infolist()
1072
1073	if len(zinfo) == 0:
1074	#print('Zip has no files!')
1075	zlist = [-1]
1076	if selection:
1077	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1078	if selection.lower() in choices:
1079	zlist = [choices.index(selection.lower())]
1080	else:
1081	print('debug: file '+str(selection)+' was not found in '+str(filename))
1082	zlist = [-1]
1083	elif len(zinfo) == 1 and confirmread:
1084	result = wx.ID_NO
1085	dlg = wx.MessageDialog(
1086	parent,
1087	'Is file '+str(zinfo[0].filename)+
1088	' what you want to extract from '+
1089	str(os.path.split(filename)[1])+'?',
1090	'Confirm file',
1091	wx.YES_NO \| wx.ICON_QUESTION)
1092	try:
1093	result = dlg.ShowModal()
1094	finally:
1095	dlg.Destroy()
1096	if result == wx.ID_NO:
1097	zlist = [-1]
1098	else:
1099	zlist = [0]
1100	elif len(zinfo) == 1:
1101	zlist = [0]
1102	elif multipleselect:
1103	# select one or more from a from list
1104	choices = [i.filename for i in zinfo]
1105	dlg = G2G.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1106	'Choose file(s)',choices)
1107	if dlg.ShowModal() == wx.ID_OK:
1108	zlist = dlg.GetSelections()
1109	else:
1110	zlist = []
1111	dlg.Destroy()
1112	else:
1113	# select one from a from list
1114	choices = [i.filename for i in zinfo]
1115	dlg = wx.SingleChoiceDialog(parent,
1116	'Select file to extract from zip file'+str(filename),'Choose file',
1117	choices,)
1118	if dlg.ShowModal() == wx.ID_OK:
1119	zlist = [dlg.GetSelection()]
1120	else:
1121	zlist = [-1]
1122	dlg.Destroy()
1123
1124	outlist = []
1125	for zindex in zlist:
1126	if zindex >= 0:
1127	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1128	if os.path.exists(efil) and confirmoverwrite:
1129	result = wx.ID_NO
1130	dlg = wx.MessageDialog(parent,
1131	'File '+str(efil)+' already exists. OK to overwrite it?',
1132	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1133	try:
1134	result = dlg.ShowModal()
1135	finally:
1136	dlg.Destroy()
1137	if result == wx.ID_NO:
1138	zindex = -1
1139	if zindex >= 0:
1140	# extract the file to the current directory, regardless of it's original path
1141	#z.extract(zinfo[zindex],zloc)
1142	eloc,efil = os.path.split(zinfo[zindex].filename)
1143	outfile = os.path.join(zloc, efil)
1144	fpin = z.open(zinfo[zindex])
1145	fpout = file(outfile, "wb")
1146	shutil.copyfileobj(fpin, fpout)
1147	fpin.close()
1148	fpout.close()
1149	outlist.append(outfile)
1150	z.close()
1151	if multipleselect and len(outlist) >= 1:
1152	return outlist
1153	elif len(outlist) == 1:
1154	return outlist[0]
1155	else:
1156	return None
1157
1158	######################################################################
1159	# base classes for reading various types of data files
1160	# not used directly, only by subclassing
1161	######################################################################
1162	def BlockSelector(ChoiceList, ParentFrame=None,title='Select a block',
1163	size=None, header='Block Selector',useCancel=True):
1164	''' Provide a wx dialog to select a block if the file contains more
1165	than one set of data and one must be selected
1166	'''
1167	if useCancel:
1168	dlg = wx.SingleChoiceDialog(
1169	ParentFrame,title, header,ChoiceList)
1170	else:
1171	dlg = wx.SingleChoiceDialog(
1172	ParentFrame,title, header,ChoiceList,
1173	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.OK\|wx.CENTRE)
1174	if size: dlg.SetSize(size)
1175	dlg.CenterOnParent()
1176	if dlg.ShowModal() == wx.ID_OK:
1177	sel = dlg.GetSelection()
1178	return sel
1179	else:
1180	return None
1181	dlg.Destroy()
1182
1183	def MultipleBlockSelector(ChoiceList, ParentFrame=None,
1184	title='Select a block',size=None, header='Block Selector'):
1185	'''Provide a wx dialog to select a block of data if the
1186	file contains more than one set of data and one must be
1187	selected.
1188
1189	:returns: a list of the selected blocks
1190	'''
1191	dlg = wx.MultiChoiceDialog(ParentFrame,title, header,ChoiceList+['Select all'],
1192	wx.CHOICEDLG_STYLE)
1193	dlg.CenterOnScreen()
1194	if size: dlg.SetSize(size)
1195	if dlg.ShowModal() == wx.ID_OK:
1196	sel = dlg.GetSelections()
1197	else:
1198	return []
1199	dlg.Destroy()
1200	selected = []
1201	if len(ChoiceList) in sel:
1202	return range(len(ChoiceList))
1203	else:
1204	return sel
1205	return selected
1206
1207	def MultipleChoicesSelector(choicelist, headinglist, ParentFrame=None, **kwargs):
1208	'''A modal dialog that offers a series of choices, each with a title and a wx.Choice
1209	widget. Typical input:
1210
1211	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1212
1213	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1214
1215	optional keyword parameters are: head (window title) and title
1216	returns a list of selected indicies for each choice (or None)
1217	'''
1218	result = None
1219	dlg = MultipleChoicesDialog(choicelist,headinglist,
1220	parent=ParentFrame, **kwargs)
1221	dlg.CenterOnParent()
1222	if dlg.ShowModal() == wx.ID_OK:
1223	result = dlg.chosen
1224	dlg.Destroy()
1225	return result
1226
1227	def PhaseSelector(ChoiceList, ParentFrame=None,
1228	title='Select a phase', size=None,header='Phase Selector'):
1229	''' Provide a wx dialog to select a phase if the file contains more
1230	than one phase
1231	'''
1232	return BlockSelector(ChoiceList,ParentFrame,title,
1233	size,header)
1234
1235	######################################################################
1236	def striphist(var,insChar=''):
1237	'strip a histogram number from a var name'
1238	sv = var.split(':')
1239	if len(sv) <= 1: return var
1240	if sv[1]:
1241	sv[1] = insChar
1242	return ':'.join(sv)
1243	class ExportBaseclass(object):
1244	'''Defines a base class for the exporting of GSAS-II results.
1245
1246	This class is subclassed in the various exports/G2export_*.py files. Those files
1247	are imported in :meth:`GSASIIdataGUI.GSASII._init_Exports` which defines the
1248	appropriate menu items for each one and the .Exporter method is called
1249	directly from the menu item.
1250
1251	Routines may also define a .Writer method, which is used to write a single
1252	file without invoking any GUI objects.
1253	'''
1254	def __init__(self,G2frame,formatName,extension,longFormatName=None,):
1255	self.G2frame = G2frame
1256	self.formatName = formatName # short string naming file type
1257	self.extension = extension
1258	if longFormatName: # longer string naming file type
1259	self.longFormatName = longFormatName
1260	else:
1261	self.longFormatName = formatName
1262	self.OverallParms = {}
1263	self.Phases = {}
1264	self.Histograms = {}
1265	self.powderDict = {}
1266	self.xtalDict = {}
1267	self.parmDict = {}
1268	self.sigDict = {}
1269	# updated in InitExport:
1270	self.currentExportType = None # type of export that has been requested
1271	# updated in ExportSelect (when used):
1272	self.phasenam = None # a list of selected phases
1273	self.histnam = None # a list of selected histograms
1274	self.filename = None # name of file to be written (single export) or template (multiple files)
1275	self.dirname = '' # name of directory where file(s) will be written
1276	self.fullpath = '' # name of file being written -- full path
1277
1278	# items that should be defined in a subclass of this class
1279	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1280	# The following types are defined: 'project', "phase", "powder", "single"
1281	self.multiple = False # set as True if the class can export multiple phases or histograms
1282	# self.multiple is ignored for "project" exports
1283
1284	def InitExport(self,event):
1285	'''Determines the type of menu that called the Exporter and
1286	misc initialization.
1287	'''
1288	self.filename = None # name of file to be written (single export)
1289	self.dirname = '' # name of file to be written (multiple export)
1290	if event:
1291	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1292
1293	def MakePWDRfilename(self,hist):
1294	'''Make a filename root (no extension) from a PWDR histogram name
1295
1296	:param str hist: the histogram name in data tree (starts with "PWDR ")
1297	'''
1298	file0 = ''
1299	file1 = hist[5:]
1300	# replace repeated blanks
1301	while file1 != file0:
1302	file0 = file1
1303	file1 = file0.replace(' ',' ').strip()
1304	file0 = file1.replace('Azm= ','A')
1305	# if angle has unneeded decimal places on aziumuth, remove them
1306	if file0[-3:] == '.00': file0 = file0[:-3]
1307	file0 = file0.replace('.','_')
1308	file0 = file0.replace(' ','_')
1309	return file0
1310
1311	def ExportSelect(self,AskFile='ask'):
1312	'''Selects histograms or phases when needed. Sets a default file name when
1313	requested into self.filename; always sets a default directory in self.dirname.
1314
1315	:param bool AskFile: Determines how this routine processes getting a
1316	location to store the current export(s).
1317
1318	* if AskFile is 'ask' (default option), get the name of the file to be written;
1319	self.filename and self.dirname are always set. In the case where
1320	multiple files must be generated, the export routine should do this
1321	based on self.filename as a template.
1322	* if AskFile is 'dir', get the name of the directory to be used;
1323	self.filename is not used, but self.dirname is always set. The export routine
1324	will always generate the file name.
1325	* if AskFile is 'single', get only the name of the directory to be used when
1326	multiple items will be written (as multiple files) are used
1327	or a complete file name is requested when a single file
1328	name is selected. self.dirname is always set and self.filename used
1329	only when a single file is selected.
1330	* if AskFile is 'default', creates a name of the file to be used from
1331	the name of the project (.gpx) file. If the project has not been saved,
1332	then the name of file is requested.
1333	self.filename and self.dirname are always set. In the case where
1334	multiple file names must be generated, the export routine should do this
1335	based on self.filename.
1336	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1337	file. If the project has not been saved, then a directory is requested.
1338	self.filename is not used.
1339
1340	:returns: True in case of an error
1341	'''
1342
1343	numselected = 1
1344	if self.currentExportType == 'phase':
1345	if len(self.Phases) == 0:
1346	self.G2frame.ErrorDialog(
1347	'Empty project',
1348	'Project does not contain any phases.')
1349	return True
1350	elif len(self.Phases) == 1:
1351	self.phasenam = self.Phases.keys()
1352	elif self.multiple:
1353	choices = sorted(self.Phases.keys())
1354	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1355	if phasenum is None: return True
1356	self.phasenam = [choices[i] for i in phasenum]
1357	if not self.phasenam: return True
1358	numselected = len(self.phasenam)
1359	else:
1360	choices = sorted(self.Phases.keys())
1361	phasenum = G2G.ItemSelector(choices,self.G2frame)
1362	if phasenum is None: return True
1363	self.phasenam = [choices[phasenum]]
1364	numselected = len(self.phasenam)
1365	elif self.currentExportType == 'single':
1366	if len(self.xtalDict) == 0:
1367	self.G2frame.ErrorDialog(
1368	'Empty project',
1369	'Project does not contain any single crystal data.')
1370	return True
1371	elif len(self.xtalDict) == 1:
1372	self.histnam = self.xtalDict.values()
1373	elif self.multiple:
1374	choices = sorted(self.xtalDict.values())
1375	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1376	if not hnum: return True
1377	self.histnam = [choices[i] for i in hnum]
1378	numselected = len(self.histnam)
1379	else:
1380	choices = sorted(self.xtalDict.values())
1381	hnum = G2G.ItemSelector(choices,self.G2frame)
1382	if hnum is None: return True
1383	self.histnam = [choices[hnum]]
1384	numselected = len(self.histnam)
1385	elif self.currentExportType == 'powder':
1386	if len(self.powderDict) == 0:
1387	self.G2frame.ErrorDialog(
1388	'Empty project',
1389	'Project does not contain any powder data.')
1390	return True
1391	elif len(self.powderDict) == 1:
1392	self.histnam = self.powderDict.values()
1393	elif self.multiple:
1394	choices = sorted(self.powderDict.values())
1395	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1396	if not hnum: return True
1397	self.histnam = [choices[i] for i in hnum]
1398	numselected = len(self.histnam)
1399	else:
1400	choices = sorted(self.powderDict.values())
1401	hnum = G2G.ItemSelector(choices,self.G2frame)
1402	if hnum is None: return True
1403	self.histnam = [choices[hnum]]
1404	numselected = len(self.histnam)
1405	elif self.currentExportType == 'image':
1406	if len(self.Histograms) == 0:
1407	self.G2frame.ErrorDialog(
1408	'Empty project',
1409	'Project does not contain any images.')
1410	return True
1411	elif len(self.Histograms) == 1:
1412	self.histnam = self.Histograms.keys()
1413	else:
1414	choices = sorted(self.Histograms.keys())
1415	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1416	if self.multiple:
1417	if not hnum: return True
1418	self.histnam = [choices[i] for i in hnum]
1419	else:
1420	if hnum is None: return True
1421	self.histnam = [choices[hnum]]
1422	numselected = len(self.histnam)
1423	if self.currentExportType == 'map':
1424	# search for phases with maps
1425	mapPhases = []
1426	choices = []
1427	for phasenam in sorted(self.Phases):
1428	phasedict = self.Phases[phasenam] # pointer to current phase info
1429	if len(phasedict['General']['Map'].get('rho',[])):
1430	mapPhases.append(phasenam)
1431	if phasedict['General']['Map'].get('Flip'):
1432	choices.append('Charge flip map: '+str(phasenam))
1433	elif phasedict['General']['Map'].get('MapType'):
1434	choices.append(
1435	str(phasedict['General']['Map'].get('MapType'))
1436	+ ' map: ' + str(phasenam))
1437	else:
1438	choices.append('unknown map: '+str(phasenam))
1439	# select a map if needed
1440	if len(mapPhases) == 0:
1441	self.G2frame.ErrorDialog(
1442	'Empty project',
1443	'Project does not contain any maps.')
1444	return True
1445	elif len(mapPhases) == 1:
1446	self.phasenam = mapPhases
1447	else:
1448	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1449	if self.multiple:
1450	if not phasenum: return True
1451	self.phasenam = [mapPhases[i] for i in phasenum]
1452	else:
1453	if phasenum is None: return True
1454	self.phasenam = [mapPhases[phasenum]]
1455	numselected = len(self.phasenam)
1456
1457	# items selected, now set self.dirname and usually self.filename
1458	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
1459	AskFile == 'default' and not self.G2frame.GSASprojectfile
1460	):
1461	filename = self.askSaveFile()
1462	if not filename: return True
1463	self.dirname,self.filename = os.path.split(filename)
1464	elif AskFile == 'dir' or AskFile == 'single' or (
1465	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
1466	):
1467	self.dirname = self.askSaveDirectory()
1468	if not self.dirname: return True
1469	elif AskFile == 'default-dir' or AskFile == 'default':
1470	self.dirname,self.filename = os.path.split(
1471	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
1472	)
1473	else:
1474	raise Exception('This should not happen!')
1475
1476	def loadParmDict(self):
1477	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
1478	refined values to those from the last cycle and set the uncertainties for the
1479	refined parameters in another dict (self.sigDict).
1480
1481	Expands the parm & sig dicts to include values derived from constraints.
1482	'''
1483	self.parmDict = {}
1484	self.sigDict = {}
1485	rigidbodyDict = {}
1486	covDict = {}
1487	consDict = {}
1488	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1489	if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1490	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1491	while item:
1492	name = self.G2frame.GPXtree.GetItemText(item)
1493	if name == 'Rigid bodies':
1494	rigidbodyDict = self.G2frame.GPXtree.GetItemPyData(item)
1495	elif name == 'Covariance':
1496	covDict = self.G2frame.GPXtree.GetItemPyData(item)
1497	elif name == 'Constraints':
1498	consDict = self.G2frame.GPXtree.GetItemPyData(item)
1499	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1500	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1501	self.parmDict.update(rbDict)
1502	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1503	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData(
1504	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
1505	self.parmDict.update(phaseDict)
1506	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
1507	Phases,Histograms,Print=False,resetRefList=False)
1508	self.parmDict.update(hapDict)
1509	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
1510	self.parmDict.update(histDict)
1511	self.parmDict.update(zip(
1512	covDict.get('varyList',[]),
1513	covDict.get('variables',[])))
1514	self.sigDict = dict(zip(
1515	covDict.get('varyList',[]),
1516	covDict.get('sig',[])))
1517	# expand to include constraints: first compile a list of constraints
1518	constList = []
1519	for item in consDict:
1520	if item.startswith('_'): continue
1521	constList += consDict[item]
1522	# now process the constraints
1523	G2mv.InitVars()
1524	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
1525	varyList = covDict.get('varyListStart')
1526	if varyList is None and len(constDict) == 0:
1527	# no constraints can use varyList
1528	varyList = covDict.get('varyList')
1529	elif varyList is None:
1530	# old GPX file from before pre-constraint varyList is saved
1531	print (' * Old refinement: Please use Calculate/Refine to redo *')
1532	raise Exception(' * Export aborted *')
1533	else:
1534	varyList = list(varyList)
1535	try:
1536	groups,parmlist = G2mv.GroupConstraints(constDict)
1537	G2mv.GenerateConstraints(groups,parmlist,varyList,constDict,fixedList,self.parmDict)
1538	except:
1539	# this really should not happen
1540	print (' * ERROR - constraints are internally inconsistent *')
1541	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
1542	print ('Errors'+errmsg)
1543	if warnmsg: print ('Warnings'+warnmsg)
1544	raise Exception(' * CIF creation aborted *')
1545	# add the constrained values to the parameter dictionary
1546	G2mv.Dict2Map(self.parmDict,varyList)
1547	# and add their uncertainties into the esd dictionary (sigDict)
1548	if covDict.get('covMatrix') is not None:
1549	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
1550
1551	def loadTree(self):
1552	'''Load the contents of the data tree into a set of dicts
1553	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
1554	& self.xtalDict)
1555
1556	* The childrenless data tree items are overall parameters/controls for the
1557	entire project and are placed in self.OverallParms
1558	* Phase items are placed in self.Phases
1559	* Data items are placed in self.Histogram. The key for these data items
1560	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
1561	'''
1562	self.OverallParms = {}
1563	self.powderDict = {}
1564	self.xtalDict = {}
1565	self.Phases = {}
1566	self.Histograms = {}
1567	self.SeqRefdata = None
1568	self.SeqRefhist = None
1569	if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1570	histType = None
1571	if self.currentExportType == 'phase':
1572	# if exporting phases load them here
1573	sub = G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,'Phases')
1574	if not sub:
1575	print ('no phases found')
1576	return True
1577	item, cookie = self.G2frame.GPXtree.GetFirstChild(sub)
1578	while item:
1579	phaseName = self.G2frame.GPXtree.GetItemText(item)
1580	self.Phases[phaseName] = self.G2frame.GPXtree.GetItemPyData(item)
1581	item, cookie = self.G2frame.GPXtree.GetNextChild(sub, cookie)
1582	return
1583	elif self.currentExportType == 'single':
1584	histType = 'HKLF'
1585	elif self.currentExportType == 'powder':
1586	histType = 'PWDR'
1587	elif self.currentExportType == 'image':
1588	histType = 'IMG'
1589
1590	if histType: # Loading just one kind of tree entry
1591	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1592	while item:
1593	name = self.G2frame.GPXtree.GetItemText(item)
1594	if name.startswith(histType):
1595	if self.Histograms.get(name): # there is already an item with this name
1596	print('Histogram name '+str(name)+' is repeated. Renaming')
1597	if name[-1] == '9':
1598	name = name[:-1] + '10'
1599	elif name[-1] in '012345678':
1600	name = name[:-1] + str(int(name[-1])+1)
1601	else:
1602	name += '-1'
1603	self.Histograms[name] = {}
1604	# the main info goes into Data, but the 0th
1605	# element contains refinement results, carry
1606	# that over too now.
1607	self.Histograms[name]['Data'] = self.G2frame.GPXtree.GetItemPyData(item)[1]
1608	self.Histograms[name][0] = self.G2frame.GPXtree.GetItemPyData(item)[0]
1609	item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1610	while item2:
1611	child = self.G2frame.GPXtree.GetItemText(item2)
1612	self.Histograms[name][child] = self.G2frame.GPXtree.GetItemPyData(item2)
1613	item2, cookie2 = self.G2frame.GPXtree.GetNextChild(item, cookie2)
1614	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1615	# index powder and single crystal histograms by number
1616	for hist in self.Histograms:
1617	if hist.startswith("PWDR"):
1618	d = self.powderDict
1619	elif hist.startswith("HKLF"):
1620	d = self.xtalDict
1621	else:
1622	return
1623	i = self.Histograms[hist].get('hId')
1624	if i is None and not d.keys():
1625	i = 0
1626	elif i is None or i in d.keys():
1627	i = max(d.keys())+1
1628	d[i] = hist
1629	return
1630	# else standard load: using all interlinked phases and histograms
1631	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1632	item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1633	while item:
1634	name = self.G2frame.GPXtree.GetItemText(item)
1635	item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1636	if not item2:
1637	self.OverallParms[name] = self.G2frame.GPXtree.GetItemPyData(item)
1638	item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1639	# index powder and single crystal histograms
1640	for hist in self.Histograms:
1641	i = self.Histograms[hist]['hId']
1642	if hist.startswith("PWDR"):
1643	self.powderDict[i] = hist
1644	elif hist.startswith("HKLF"):
1645	self.xtalDict[i] = hist
1646
1647	def dumpTree(self,mode='type'):
1648	'''Print out information on the data tree dicts loaded in loadTree.
1649	Used for testing only.
1650	'''
1651	if self.SeqRefdata and self.SeqRefhist:
1652	print('Note that dumpTree does not show sequential results')
1653	print ('\nOverall')
1654	if mode == 'type':
1655	def Show(arg): return type(arg)
1656	else:
1657	def Show(arg): return arg
1658	for key in self.OverallParms:
1659	print (' '+key+Show(self.OverallParms[key]))
1660	print ('Phases')
1661	for key1 in self.Phases:
1662	print (' '+key1+Show(self.Phases[key1]))
1663	print ('Histogram')
1664	for key1 in self.Histograms:
1665	print (' '+key1+Show(self.Histograms[key1]))
1666	for key2 in self.Histograms[key1]:
1667	print (' '+key2+Show(self.Histograms[key1][key2]))
1668
1669	def defaultSaveFile(self):
1670	return os.path.abspath(
1671	os.path.splitext(self.G2frame.GSASprojectfile
1672	)[0]+self.extension)
1673
1674	def askSaveFile(self):
1675	'''Ask the user to supply a file name
1676
1677	:returns: a file name (str) or None if Cancel is pressed
1678	'''
1679
1680	pth = G2G.GetExportPath(self.G2frame)
1681	defnam = os.path.splitext(
1682	os.path.split(self.G2frame.GSASprojectfile)[1]
1683	)[0]+self.extension
1684	dlg = wx.FileDialog(
1685	self.G2frame, 'Input name for file to write', pth, defnam,
1686	self.longFormatName+' ('+self.extension+')\|'+self.extension,
1687	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
1688	dlg.CenterOnParent()
1689	try:
1690	if dlg.ShowModal() == wx.ID_OK:
1691	filename = dlg.GetPath()
1692	self.G2frame.LastExportDir = os.path.split(filename)[0]
1693	filename = os.path.splitext(filename)[0]+self.extension # make sure extension is correct
1694	else:
1695	filename = None
1696	finally:
1697	dlg.Destroy()
1698	return filename
1699
1700	def askSaveDirectory(self):
1701	'''Ask the user to supply a directory name. Path name is used as the
1702	starting point for the next export path search.
1703
1704	:returns: a directory name (str) or None if Cancel is pressed
1705	'''
1706	pth = G2G.GetExportPath(self.G2frame)
1707	dlg = wx.DirDialog(
1708	self.G2frame, 'Input directory where file(s) will be written', pth,
1709	wx.DD_DEFAULT_STYLE)
1710	dlg.CenterOnParent()
1711	try:
1712	if dlg.ShowModal() == wx.ID_OK:
1713	filename = dlg.GetPath()
1714	self.G2frame.LastExportDir = filename
1715	else:
1716	filename = None
1717	finally:
1718	dlg.Destroy()
1719	return filename
1720
1721	# Tools for file writing.
1722	def OpenFile(self,fil=None,mode='w'):
1723	'''Open the output file
1724
1725	:param str fil: The name of the file to open. If None (default)
1726	the name defaults to self.dirname + self.filename.
1727	If an extension is supplied, it is not overridded,
1728	but if not, the default extension is used.
1729	:returns: the file object opened by the routine which is also
1730	saved as self.fp
1731	'''
1732	if mode == 'd': # debug mode
1733	self.fullpath = '(stdout)'
1734	self.fp = sys.stdout
1735	return
1736	if not fil:
1737	if not os.path.splitext(self.filename)[1]:
1738	self.filename += self.extension
1739	fil = os.path.join(self.dirname,self.filename)
1740	self.fullpath = os.path.abspath(fil)
1741	self.fp = open(self.fullpath,mode)
1742	return self.fp
1743
1744	def Write(self,line):
1745	'''write a line of output, attaching a line-end character
1746
1747	:param str line: the text to be written.
1748	'''
1749	self.fp.write(line+'\n')
1750
1751	def CloseFile(self,fp=None):
1752	'''Close a file opened in OpenFile
1753
1754	:param file fp: the file object to be closed. If None (default)
1755	file object self.fp is closed.
1756	'''
1757	if self.fp == sys.stdout: return # debug mode
1758	if fp is None:
1759	fp = self.fp
1760	self.fp = None
1761	if fp is not None: fp.close()
1762
1763	def SetSeqRef(self,data,hist):
1764	'''Set the exporter to retrieve results from a sequential refinement
1765	rather than the main tree
1766	'''
1767	self.SeqRefdata = data
1768	self.SeqRefhist = hist
1769	data_name = data[hist]
1770	for i,val in zip(data_name['varyList'],data_name['sig']):
1771	self.sigDict[i] = val
1772	self.sigDict[striphist(i)] = val
1773	for i in data_name['parmDict']:
1774	self.parmDict[striphist(i)] = data_name['parmDict'][i]
1775	self.parmDict[i] = data_name['parmDict'][i]
1776	# zero out the dA[xyz] terms, they would only bring confusion
1777	key = i.split(':')
1778	if len(key) < 3: continue
1779	if key[2].startswith('dA'):
1780	self.parmDict[i] = 0.0
1781	for i,(val,sig) in data_name.get('depParmDict',{}).iteritems():
1782	self.parmDict[i] = val
1783	self.sigDict[i] = sig
1784	#GSASIIpath.IPyBreak()
1785
1786	# Tools to pull information out of the data arrays
1787	def GetCell(self,phasenam):
1788	"""Gets the unit cell parameters and their s.u.'s for a selected phase
1789
1790	:param str phasenam: the name for the selected phase
1791	:returns: `cellList,cellSig` where each is a 7 element list corresponding
1792	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1793	cell values and `cellSig` has their uncertainties.
1794	"""
1795	if self.SeqRefdata and self.SeqRefhist:
1796	return self.GetSeqCell(phasenam,self.SeqRefdata[self.SeqRefhist])
1797	phasedict = self.Phases[phasenam] # pointer to current phase info
1798	try:
1799	pfx = str(phasedict['pId'])+'::'
1800	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
1801	cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A,
1802	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
1803	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
1804	return cellList,cellSig
1805	except KeyError:
1806	cell = phasedict['General']['Cell'][1:]
1807	return cell,7*[0]
1808
1809	def GetSeqCell(self,phasenam,data_name):
1810	"""Gets the unit cell parameters and their s.u.'s for a selected phase
1811	and histogram in a sequential fit
1812
1813	:param str phasenam: the name for the selected phase
1814	:param dict data_name: the sequential refinement parameters for the selected histogram
1815	:returns: `cellList,cellSig` where each is a 7 element list corresponding
1816	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1817	cell values and `cellSig` has their uncertainties.
1818	"""
1819	phasedict = self.Phases[phasenam]
1820	SGdata = phasedict['General']['SGData']
1821	pId = phasedict['pId']
1822	RecpCellTerms = G2lat.cell2A(phasedict['General']['Cell'][1:7])
1823	ESDlookup = {}
1824	Dlookup = {}
1825	varied = [striphist(i) for i in data_name['varyList']]
1826	for item,val in data_name['newCellDict'].iteritems():
1827	if item in varied:
1828	ESDlookup[val[0]] = item
1829	Dlookup[item] = val[0]
1830	A = RecpCellTerms[:]
1831	for i in range(6):
1832	var = str(pId)+'::A'+str(i)
1833	if var in ESDlookup:
1834	A[i] = data_name['newCellDict'][ESDlookup[var]][1] # override with refined value
1835	cellDict = dict(zip([str(pId)+'::A'+str(i) for i in range(6)],A))
1836	zeroDict = {i:0.0 for i in cellDict}
1837	A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata,cellDict,zeroDict)
1838	covData = {
1839	'varyList': [Dlookup.get(striphist(v),v) for v in data_name['varyList']],
1840	'covMatrix': data_name['covMatrix']
1841	}
1842	return list(G2lat.A2cell(A)) + [G2lat.calc_V(A)], G2stIO.getCellEsd(str(pId)+'::',SGdata,A,covData)
1843
1844	def GetAtoms(self,phasenam):
1845	"""Gets the atoms associated with a phase. Can be used with standard
1846	or macromolecular phases
1847
1848	:param str phasenam: the name for the selected phase
1849	:returns: a list of items for eac atom where each item is a list containing:
1850	label, typ, mult, xyz, and td, where
1851
1852	* label and typ are the atom label and the scattering factor type (str)
1853	* mult is the site multiplicity (int)
1854	* xyz is contains a list with four pairs of numbers:
1855	x, y, z and fractional occupancy and
1856	their standard uncertainty (or a negative value)
1857	* td is contains a list with either one or six pairs of numbers:
1858	if one number it is U\ :sub:`iso` and with six numbers it is
1859	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
1860	paired with their standard uncertainty (or a negative value)
1861	"""
1862	phasedict = self.Phases[phasenam] # pointer to current phase info
1863	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
1864	cfrac = cx+3
1865	fpfx = str(phasedict['pId'])+'::Afrac:'
1866	atomslist = []
1867	for i,at in enumerate(phasedict['Atoms']):
1868	if phasedict['General']['Type'] == 'macromolecular':
1869	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
1870	else:
1871	label = at[ct-1]
1872	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
1873	fsig = self.sigDict.get(fpfx+str(i),-0.009)
1874	mult = at[cs+1]
1875	typ = at[ct]
1876	xyz = []
1877	for j,v in enumerate(('x','y','z')):
1878	val = at[cx+j]
1879	pfx = str(phasedict['pId']) + '::A' + v + ':' + str(i)
1880	val = self.parmDict.get(pfx, val)
1881	dpfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
1882	sig = self.sigDict.get(dpfx,-0.000009)
1883	xyz.append((val,sig))
1884	xyz.append((fval,fsig))
1885	td = []
1886	if at[cia] == 'I':
1887	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
1888	val = self.parmDict.get(pfx,at[cia+1])
1889	sig = self.sigDict.get(pfx,-0.0009)
1890	td.append((val,sig))
1891	else:
1892	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
1893	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
1894	val = self.parmDict.get(pfx,at[cia+2+i])
1895	sig = self.sigDict.get(pfx,-0.0009)
1896	td.append((val,sig))
1897	atomslist.append((label,typ,mult,xyz,td))
1898	return atomslist
1899	######################################################################
1900	def ExportPowderList(G2frame):
1901	'''Returns a list of extensions supported by :func:`GSASIIIO:ExportPowder`
1902	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
1903
1904	:param wx.Frame G2frame: the GSAS-II main data tree window
1905	'''
1906	extList = []
1907	for obj in G2frame.exporterlist:
1908	if 'powder' in obj.exporttype:
1909	try:
1910	obj.Writer
1911	extList.append(obj.extension)
1912	except AttributeError:
1913	pass
1914	return extList
1915
1916	def ExportPowder(G2frame,TreeName,fileroot,extension):
1917	'''Writes a single powder histogram using the Export routines.
1918	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
1919
1920	:param wx.Frame G2frame: the GSAS-II main data tree window
1921	:param str TreeName: the name of the histogram (PWDR ...) in the data tree
1922	:param str fileroot: name for file to be written, extension ignored
1923	:param str extension: extension for file to be written (start with '.'). Must
1924	match a powder export routine that has a Writer object.
1925	'''
1926	filename = os.path.abspath(os.path.splitext(fileroot)[0]+extension)
1927	for obj in G2frame.exporterlist:
1928	if obj.extension == extension and 'powder' in obj.exporttype:
1929	obj.currentExportType = 'powder'
1930	obj.InitExport(None)
1931	obj.loadTree() # load all histograms in tree into dicts
1932	if TreeName not in obj.Histograms:
1933	raise Exception('Histogram not found: '+str(TreeName))
1934	try:
1935	obj.Writer
1936	except AttributeError:
1937	continue
1938	try:
1939	obj.Writer(TreeName,filename)
1940	print('wrote file '+filename)
1941	return
1942	except Exception:
1943	print('Export Routine for '+extension+' failed.')
1944	else:
1945	print('No Export routine supports extension '+extension)
1946
1947	def ExportSequential(G2frame,data,obj,exporttype):
1948	'''
1949	Used to export from every phase/dataset in a sequential refinement using
1950	a .Writer method for either projects or phases. Prompts to select histograms
1951	and for phase exports, which phase(s).
1952
1953	:param wx.Frame G2frame: the GSAS-II main data tree window
1954	:param dict data: the sequential refinement data object
1955	:param str exporttype: indicates the type of export ('project' or 'phase')
1956	'''
1957	if len(data['histNames']) == 0:
1958	G2G.G2MessageBox(G2frame,'There are no sequential histograms','Warning')
1959	obj.InitExport(None)
1960	obj.loadTree()
1961	obj.loadParmDict()
1962	if len(data['histNames']) == 1:
1963	histlist = data['histNames']
1964	else:
1965	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select histograms to export from list',
1966	'Select histograms',data['histNames'])
1967	if dlg.ShowModal() == wx.ID_OK:
1968	histlist = [data['histNames'][l] for l in dlg.GetSelections()]
1969	dlg.Destroy()
1970	else:
1971	dlg.Destroy()
1972	return
1973	if exporttype == 'Phase':
1974	phaselist = list(obj.Phases.keys())
1975	if len(obj.Phases) == 0:
1976	G2G.G2MessageBox(G2frame,'There are no phases in sequential ref.','Warning')
1977	return
1978	elif len(obj.Phases) > 1:
1979	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select phases to export from list',
1980	'Select phases', phaselist)
1981	if dlg.ShowModal() == wx.ID_OK:
1982	phaselist = [phaselist[l] for l in dlg.GetSelections()]
1983	dlg.Destroy()
1984	else:
1985	dlg.Destroy()
1986	return
1987	filename = obj.askSaveFile()
1988	if not filename: return True
1989	obj.dirname,obj.filename = os.path.split(filename)
1990	print('Writing output to file '+str(obj.filename)+"...")
1991	mode = 'w'
1992	for p in phaselist:
1993	for h in histlist:
1994	obj.SetSeqRef(data,h)
1995	#GSASIIpath.IPyBreak()
1996	obj.Writer(h,phasenam=p,mode=mode)
1997	mode = 'a'
1998	print('...done')
1999	elif exporttype == 'Project': # note that the CIF exporter is not yet ready for this
2000	filename = obj.askSaveFile()
2001	if not filename: return True
2002	obj.dirname,obj.filename = os.path.split(filename)
2003	print('Writing output to file '+str(obj.filename)+"...")
2004	mode = 'w'
2005	for h in histlist:
2006	obj.SetSeqRef(data,h)
2007	obj.Writer(h,mode=mode)
2008	print('\t'+str(h)+' written')
2009	mode = 'a'
2010	print('...done')
2011	elif exporttype == 'Powder':
2012	filename = obj.askSaveFile()
2013	if not filename: return True
2014	obj.dirname,obj.filename = os.path.split(filename)
2015	print('Writing output to file '+str(obj.filename)+"...")
2016	mode = 'w'
2017	for h in histlist:
2018	obj.SetSeqRef(data,h)
2019	obj.Writer(h,mode=mode)
2020	print('\t'+str(h)+' written')
2021	mode = 'a'
2022	print('...done')
2023
2024	def ReadDIFFaX(DIFFaXfile):
2025	print ('read '+DIFFaXfile)
2026	Layer = {'Laue':'-1','Cell':[False,1.,1.,1.,90.,90.,90,1.],'Width':[[10.,10.],[False,False]],
2027	'Layers':[],'Stacking':[],'Transitions':[],'Toler':0.01,'AtInfo':{}}
2028	df = open(DIFFaXfile,'r')
2029	lines = df.readlines()
2030	df.close()
2031	struct = False
2032	Struct = []
2033	stack = False
2034	Stack = []
2035	trans = False
2036	Trans = []
2037	for diff in lines:
2038	diff = diff[:-1].lower()
2039	if '!' in diff:
2040	continue
2041	while '}' in diff: #strip comments
2042	iB = diff.index('{')
2043	iF = diff.index('}')+1
2044	if iB:
2045	diff = diff[:iB]
2046	else:
2047	diff = diff[iF:]
2048	if not diff:
2049	continue
2050	if diff.strip() == 'instrumental':
2051	continue
2052	if diff.strip() == 'structural':
2053	struct = True
2054	continue
2055	elif diff.strip() == 'stacking':
2056	struct = False
2057	stack = True
2058	continue
2059	elif diff.strip() == 'transitions':
2060	stack = False
2061	trans = True
2062	continue
2063	diff = diff.strip()
2064	if struct:
2065	if diff:
2066	Struct.append(diff)
2067	elif stack:
2068	if diff:
2069	Stack.append(diff)
2070	elif trans:
2071	if diff:
2072	Trans.append(diff)
2073
2074	#STRUCTURE records
2075	laueRec = Struct[1].split()
2076	Layer['Laue'] = laueRec[0]
2077	if Layer['Laue'] == 'unknown' and len(laueRec) > 1:
2078	Layer['Toler'] = float(laueRec[1]) #tolerance for 'unknown'?
2079	if Layer['Laue'] == '2/m(1)': Layer['Laue'] = '2/m(c)'
2080	if Layer['Laue'] == '2/m(2)': Layer['Laue'] = '2/m(ab)'
2081	cell = Struct[0].split()
2082	Layer['Cell'] = [False,float(cell[0]),float(cell[1]),float(cell[2]),90.,90.,float(cell[3]),1.0]
2083	nLayers = int(Struct[2])
2084	N = 3
2085	if 'layer' not in Struct[3]:
2086	N = 4
2087	if Struct[3] != 'infinite':
2088	width = Struct[3].split()
2089	Layer['Width'][0] = [float(width[0]),float(width[1])]
2090	for nL in range(nLayers):
2091	if '=' in Struct[N]:
2092	name = Struct[N].split('=')
2093	sameas = int(name[1])-1
2094	Layer['Layers'].append({'Name':name[0],'SameAs':Layer['Layers'][sameas]['Name'],'Symm':'None','Atoms':[]})
2095	N += 1
2096	continue
2097	Symm = 'None'
2098	if 'centro' in Struct[N+1]: Symm = '-1'
2099	Layer['Layers'].append({'Name':Struct[N],'SameAs':'','Symm':Symm,'Atoms':[]})
2100	N += 2
2101	while 'layer' not in Struct[N]:
2102	atom = Struct[N][4:].split()
2103	atomType = G2el.FixValence(Struct[N][:4].replace(' ','').strip().capitalize())
2104	if atomType not in Layer['AtInfo']:
2105	Layer['AtInfo'][atomType] = G2el.GetAtomInfo(atomType)
2106	atomName = '%s(%s)'%(atomType,atom[0])
2107	newVals = []
2108	for val in atom[1:6]:
2109	if '/' in val:
2110	newVals.append(eval(val+'.'))
2111	else:
2112	newVals.append(float(val))
2113	atomRec = [atomName,atomType,newVals[0],newVals[1],newVals[2],newVals[4],newVals[3]/78.9568]
2114	Layer['Layers'][-1]['Atoms'].append(atomRec)
2115	N += 1
2116	if N > len(Struct)-1:
2117	break
2118	#TRANSITIONS records
2119	transArray = []
2120	N = 0
2121	for i in range(nLayers):
2122	transArray.append([])
2123	for j in range(nLayers):
2124	vals = Trans[N].split()
2125	newVals = []
2126	for val in vals[:4]:
2127	if '/' in val:
2128	newVals.append(eval(val+'.'))
2129	else:
2130	newVals.append(float(val))
2131	transArray[-1].append(newVals+['',False])
2132	N += 1
2133	Layer['Transitions'] = transArray
2134	#STACKING records
2135	Layer['Stacking'] = [Stack[0],'']
2136	if Stack[0] == 'recursive':
2137	Layer['Stacking'][1] = Stack[1]
2138	elif Stack[0] == 'explicit':
2139	if Stack[1] == 'random':
2140	Layer['Stacking'][1] = Stack[1]
2141	else:
2142	Layer['Stacking'][1] = 'list'
2143	Layer['Stacking'].append('')
2144	for stack in Stack[2:]:
2145	Layer['Stacking'][2] += ' '+stack
2146	return Layer
2147
2148	def Read1IDpar(imagefile):
2149	'''Reads image metadata from a 1-ID style .par file from the same directory
2150	as the image. The .par file has any number of columns separated by spaces.
2151	As an index to the .par file a second label file must be specified with the
2152	same file name as the .par file but the extension must be .XXX_lbls (where
2153	.XXX is the extension of the image) or if that is not present extension
2154	.lbls. Called by :func:`Get1IDMetadata`
2155
2156	:param str imagefile: the full name of the image file (with directory and extension)
2157
2158	:returns: a dict with parameter values. Named parameters will have the type based on
2159	the specified Python function, named columns will be character strings
2160
2161	The contents of the label file will look like this::
2162
2163	# define keywords
2164	filename:lambda x,y: "{}_{:0>6}".format(x,y)\|33,34
2165	distance: float \| 75
2166	wavelength:lambda keV: 12.398425/float(keV)\|9
2167	pixelSize:lambda x: [74.8, 74.8]\|0
2168	ISOlikeDate: lambda dow,m,d,t,y:"{}-{}-{}T{} ({})".format(y,m,d,t,dow)\|0,1,2,3,4
2169	# define other variables
2170	0:day
2171	1:month
2172	2:date
2173	3:time
2174	4:year
2175	7:I_ring
2176
2177	This file contains three types of lines in any order.
2178	* Named parameters are evaluated with user-supplied Python code (see
2179	subsequent information). Specific named parameters are used
2180	to determine values that are used for image interpretation (see table,
2181	below). Any others are copied to the Comments subsection of the Image
2182	tree item.
2183	* Column labels are defined with a column number (integer) followed by
2184	a colon (:) and a label to be assigned to that column. All labeled
2185	columns are copied to the Image's Comments subsection.
2186	* Comments are any line that does not contain a colon.
2187
2188	Note that columns are numbered starting at zero.
2189
2190	Any named parameter may be defined provided it is not a valid integer,
2191	but the named parameters in the table have special meanings, as descibed.
2192	The parameter name is followed by a colon. After the colon, specify
2193	Python code that defines or specifies a function that will be called to
2194	generate a value for that parameter. After that code, supply a vertical
2195	bar (\|) and then a list of one more more columns that will be supplied
2196	as arguments to that function. The examples above are discussed below:
2197
2198	``filename:lambda x,y: "{}_{:0>6}".format(x,y)\|33,34``
2199	Here the function to be used is defined with a lambda statement:
2200
2201	lambda x,y: "{}_{:0>6}".format(x,y)
2202
2203	This function will use the format function to create a file name from the
2204	contents of columns 33 and 34. The first parameter (x, col. 33) is inserted directly into
2205	the file name, followed by a underscore (_), followed by the second parameter (y, col. 34),
2206	which will be left-padded with zeros to six characters (format directive ``:0>6``).
2207
2208	``distance: float \| 75``
2209	Here the contents of column 75 will be converted to a floating point number
2210	by calling float on it. Note that the spaces here are ignored.
2211
2212	``wavelength:lambda keV: 12.398425/float(keV)\|9``
2213	Here we define an algebraic expression to convert an energy in keV to a
2214	wavelength and pass the contents of column 9 as that input energy
2215
2216	``pixelSize:lambda x: [74.8, 74.8]\|0``
2217	In this case the pixel size is a constant (a list of two numbers). The first
2218	column is passed as an argument as at least one argument is required, but that
2219	value is not used in the expression.
2220
2221	``ISOlikeDate: lambda dow,m,d,t,y:"{}-{}-{}T{} ({})".format(y,m,d,t,dow)\|0,1,2,3,4``
2222	This example defines a parameter that takes items in the first five columns
2223	and formats them in a different way. This parameter is not one of the pre-defined
2224	parameter names below. Some external code could be used to change the month string
2225	(argument ``m``) to a integer from 1 to 12.
2226
2227	Pre-defined parameter names
2228
2229	============= ========= ======== ====================================================
2230	keyword required type Description
2231	============= ========= ======== ====================================================
2232	filename yes str generates the file name prefix for the matching image
2233	file (MyImage001 for file /tmp/MyImage001.tif).
2234	polarization no float generates the polarization expected based on the
2235	monochromator angle, defaults to 0.99.
2236	center no list of generates the approximate beam center on the detector
2237	2 floats in mm, such as [204.8, 204.8].
2238	distance yes float generates the distance from the sample to the detector
2239	in mm
2240	pixelSize no list of generates the size of the pixels in microns such as
2241	2 floats [200.0, 200.0].
2242	wavelength yes float generates the wavelength in Angstroms
2243	============= ========= ======== ====================================================
2244
2245
2246	'''
2247	dir,fil = os.path.split(os.path.abspath(imagefile))
2248	imageName,ext = os.path.splitext(fil)
2249	parfiles = glob.glob(os.path.join(dir,'*.par'))
2250	if len(parfiles) == 0:
2251	print('Sorry, No 1-ID .par file found in '+dir)
2252	return {}
2253	for parFil in parfiles: # loop over all .par files (hope just 1) in image dir until image is found
2254	parRoot = os.path.splitext(parFil)[0]
2255	for e in (ext+'_lbls','.lbls'):
2256	if os.path.exists(parRoot+e):
2257	lblFil = parRoot+e
2258	break
2259	else:
2260	print('Warning: No labels definitions found for '+parFil)
2261	return {}
2262	fp = open(lblFil,'Ur') # read column labels
2263	lbldict = {}
2264	fmt = ""
2265	keyExp = {}
2266	keyCols = {}
2267	for line in fp: # read label definitions
2268	items = line.strip().split(':')
2269	if len(items) < 2: continue # no colon, line is a comment
2270	# is this line a definition for a named parameter?
2271	key = items[0]
2272	try:
2273	int(key)
2274	except ValueError: # named parameters are not valid numbers
2275	items = line.split(':',1)[1].split('\|')
2276	try:
2277	keyExp[key] = eval(items[0]) # compile the expression
2278	if not callable(keyExp[key]):
2279	raise Exception("Expression not a function")
2280	except Exception as msg:
2281	print('Warning: Expression "{}" is not valid for key {}'.format(items[0],key))
2282	print(msg)
2283	keyCols[key] = [int(i) for i in items[1].strip().split(',')]
2284	continue
2285	if len(items) == 2: # simple column definition
2286	lbldict[int(items[0])] = items[1]
2287	fp.close()
2288	if 'filename' not in keyExp:
2289	print("Warning: No valid filename expression in {} file, skipping .par".format(lblFil))
2290	continue
2291	# read the .par, looking for the matching image rootname
2292	fp = open(parFil,'Ur')
2293	for i,line in enumerate(fp):
2294	items = line.strip().split(' ')
2295	name = keyExp['filename'](*[items[j] for j in keyCols['filename']])
2296	if name == imageName: # got our match, parse the line and finish
2297	metadata = {lbldict[i]:items[i] for i in lbldict}
2298	metadata.update(
2299	{key:keyExp[key](*[items[j] for j in keyCols[key]]) for key in keyExp})
2300	metadata['par file'] = parFil
2301	metadata['lbls file'] = lblFil
2302	print("Metadata read from {}".format(parFil))
2303	return metadata
2304	else:
2305	print("Image {} not found in {}".format(imageName,parFil))
2306	fp.close()
2307	continue
2308	fp.close()
2309	else:
2310	print("Warning: No 1-ID metadata for image {}".format(imageName))
2311	return {}
2312
2313	def Get1IDMetadata(reader):
2314	'''Add 1-ID metadata to an image using a 1-ID .par file using :func:`Read1IDpar`
2315
2316	:param reader: a reader object from reading an image
2317
2318	'''
2319	parParms = Read1IDpar(reader.readfilename)
2320	if not parParms: return # check for read failure
2321	specialKeys = ('filename',"polarization", "center", "distance", "pixelSize", "wavelength",)
2322	reader.Comments = ['Metadata from {} assigned by {}'.format(parParms['par file'],parParms['lbls file'])]
2323	for key in parParms:
2324	if key in specialKeys+('par file','lbls file'): continue
2325	reader.Comments += ["{} = {}".format(key,parParms[key])]
2326	if "polarization" in parParms:
2327	reader.Data['PolaVal'][0] = parParms["polarization"]
2328	else:
2329	reader.Data['PolaVal'][0] = 0.99
2330	if "center" in parParms:
2331	reader.Data['center'] = parParms["center"]
2332	if "pixelSize" in parParms:
2333	reader.Data['pixelSize'] = parParms["pixelSize"]
2334	if "wavelength" in parParms:
2335	reader.Data['wavelength'] = parParms['wavelength']
2336	else:
2337	print('Error: wavelength not defined in {}'.format(parParms['lbls file']))
2338	if "distance" in parParms:
2339	reader.Data['distance'] = parParms['distance']
2340	reader.Data['setdist'] = parParms['distance']
2341	else:
2342	print('Error: distance not defined in {}'.format(parParms['lbls file']))
2343
2344	if __name__ == '__main__':
2345	import GSASIIdataGUI
2346	application = GSASIIdataGUI.GSASIImain(0)
2347	G2frame = application.main
2348	#app = wx.PySimpleApp()
2349	#G2frame = wx.Frame(None) # create a frame
2350	#frm.Show(True)
2351	#filename = '/tmp/notzip.zip'
2352	#filename = '/tmp/all.zip'
2353	#filename = '/tmp/11bmb_7652.zip'
2354
2355	#selection=None, confirmoverwrite=True, parent=None
2356	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2357	#print ExtractFileFromZip(filename,multipleselect=True)
2358	# #confirmread=False, confirmoverwrite=False)
2359
2360	# choicelist=[ ('a','b','c'),
2361	# ('test1','test2'),('no choice',)]
2362	# titles = [ 'a, b or c', 'tests', 'No option here']
2363	# dlg = MultipleChoicesDialog(
2364	# choicelist,titles,
2365	# parent=frm)
2366	# if dlg.ShowModal() == wx.ID_OK:
2367	# print 'Got OK'
2368	imagefile = '/tmp/NDC5_00237_3.ge3'
2369	Comments, Data, Npix, Image = GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None)
2370
2371	print("\n\nResults loaded to Comments, Data, Npix and Image\n\n")
2372
2373	GSASIIpath.IPyBreak_base()

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