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source: trunk/GSASIIIO.py @ 2298

Last change on this file since 2298 was 2298, checked in by vondreele, 7 years ago
Add stubs for BondDialog? & AngleDialog? for adding these to Seq results table Add menu items for above fix a bug in showing seq results revert the occurrence counter for image integrations capture bad pids in OnPageChanged?
Property svn:eol-style set to `native` Property svn:keywords set to `Date Author Revision URL Id`
File size: 103.2 KB

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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2016-05-27 19:48:22 +0000 (Fri, 27 May 2016) $
4	# $Author: vondreele $
5	# $Revision: 2298 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 2298 2016-05-27 19:48:22Z vondreele $
8	########### SVN repository information ###################
9	'''
10	GSASIIIO: Misc I/O routines
11	=============================
12
13	Module with miscellaneous routines for input and output. Many
14	are GUI routines to interact with user.
15
16	Includes support for image reading.
17
18	Also includes base classes for data import routines.
19
20	'''
21	"""GSASIIIO: functions for IO of data
22	Copyright: 2008, Robert B. Von Dreele (Argonne National Laboratory)
23	"""
24	import wx
25	import math
26	import numpy as np
27	import copy
28	import cPickle
29	import sys
30	import re
31	import random as ran
32	import GSASIIpath
33	GSASIIpath.SetVersionNumber("$Revision: 2298 $")
34	import GSASIIgrid as G2gd
35	import GSASIIspc as G2spc
36	import GSASIIobj as G2obj
37	import GSASIIlattice as G2lat
38	import GSASIIpwdGUI as G2pdG
39	import GSASIIimgGUI as G2imG
40	import GSASIIimage as G2img
41	import GSASIIElem as G2el
42	import GSASIIstrIO as G2stIO
43	import GSASIImapvars as G2mv
44	import GSASIIctrls as G2G
45	import os
46	import os.path as ospath
47
48	DEBUG = False #=True for various prints
49	TRANSP = False #=true to transpose images for testing
50	if GSASIIpath.GetConfigValue('Transpose'): TRANSP = True
51	npsind = lambda x: np.sin(x*np.pi/180.)
52
53	def sfloat(S):
54	'Convert a string to float. An empty field or a unconvertable value is treated as zero'
55	if S.strip():
56	try:
57	return float(S)
58	except ValueError:
59	pass
60	return 0.0
61
62	def sint(S):
63	'Convert a string to int. An empty field is treated as zero'
64	if S.strip():
65	return int(S)
66	else:
67	return 0
68
69	def trim(val):
70	'''Simplify a string containing leading and trailing spaces
71	as well as newlines, tabs, repeated spaces etc. into a shorter and
72	more simple string, by replacing all ranges of whitespace
73	characters with a single space.
74
75	:param str val: the string to be simplified
76
77	:returns: the (usually) shortened version of the string
78	'''
79	return re.sub('\s+', ' ', val).strip()
80
81	def makeInstDict(names,data,codes):
82	inst = dict(zip(names,zip(data,data,codes)))
83	for item in inst:
84	inst[item] = list(inst[item])
85	return inst
86
87	def FileDlgFixExt(dlg,file):
88	'this is needed to fix a problem in linux wx.FileDialog'
89	ext = dlg.GetWildcard().split('\|')[2dlg.GetFilterIndex()+1].strip('')
90	if ext not in file:
91	file += ext
92	return file
93
94	def GetPowderPeaks(fileName):
95	'Read powder peaks from a file'
96	sind = lambda x: math.sin(x*math.pi/180.)
97	asind = lambda x: 180.*math.asin(x)/math.pi
98	wave = 1.54052
99	File = open(fileName,'Ur')
100	Comments = []
101	peaks = []
102	S = File.readline()
103	while S:
104	if S[:1] == '#':
105	Comments.append(S[:-1])
106	else:
107	item = S.split()
108	if len(item) == 1:
109	peaks.append([float(item[0]),1.0])
110	elif len(item) > 1:
111	peaks.append([float(item[0]),float(item[0])])
112	S = File.readline()
113	File.close()
114	if Comments:
115	print 'Comments on file:'
116	for Comment in Comments:
117	print Comment
118	if 'wavelength' in Comment:
119	wave = float(Comment.split('=')[1])
120	Peaks = []
121	if peaks[0][0] > peaks[-1][0]: # d-spacings - assume CuKa
122	for peak in peaks:
123	dsp = peak[0]
124	sth = wave/(2.0*dsp)
125	if sth < 1.0:
126	tth = 2.0*asind(sth)
127	else:
128	break
129	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
130	else: #2-thetas - assume Cuka (for now)
131	for peak in peaks:
132	tth = peak[0]
133	dsp = wave/(2.0*sind(tth/2.0))
134	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
135	limits = [1000.,0.]
136	for peak in Peaks:
137	limits[0] = min(limits[0],peak[0])
138	limits[1] = max(limits[1],peak[0])
139	limits[0] = max(1.,(int(limits[0]-1.)/5)*5.)
140	limits[1] = min(170.,(int(limits[1]+1.)/5)*5.)
141	return Comments,Peaks,limits,wave
142
143	def CheckImageFile(G2frame,imagefile):
144	'''Try to locate an image file if the project and image have been moved
145	together. If the image file cannot be found, request the location from
146	the user.
147
148	:param wx.Frame G2frame: main GSAS-II Frame and data object
149	:param str imagefile: name of image file
150	:returns: imagefile, if it exists, or the name of a file
151	that does exist or False if the user presses Cancel
152
153	'''
154	if not os.path.exists(imagefile):
155	print 'Image file '+imagefile+' not found'
156	fil = imagefile.replace('\\','/') # windows?!
157	# see if we can find a file with same name or in a similarly named sub-dir
158	pth,fil = os.path.split(fil)
159	prevpth = None
160	while pth and pth != prevpth:
161	prevpth = pth
162	if os.path.exists(os.path.join(G2frame.dirname,fil)):
163	print 'found image file '+os.path.join(G2frame.dirname,fil)
164	return os.path.join(G2frame.dirname,fil)
165	pth,enddir = os.path.split(pth)
166	fil = os.path.join(enddir,fil)
167	# not found as a subdirectory, drop common parts of path for last saved & image file names
168	# if image was .../A/B/C/imgs/ima.ge
169	# & GPX was .../A/B/C/refs/fil.gpx but is now .../NEW/TEST/TEST1
170	# will look for .../NEW/TEST/TEST1/imgs/ima.ge, .../NEW/TEST/imgs/ima.ge, .../NEW/imgs/ima.ge and so on
171	Controls = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
172	gpxPath = Controls.get('LastSavedAs','').replace('\\','/').split('/') # blank in older .GPX files
173	imgPath = imagefile.replace('\\','/').split('/')
174	for p1,p2 in zip(gpxPath,imgPath):
175	if p1 == p2:
176	gpxPath.pop(0),imgPath.pop(0)
177	else:
178	break
179	fil = os.path.join(*imgPath) # file with non-common prefix elements
180	prevpth = None
181	pth = os.path.abspath(G2frame.dirname)
182	while pth and pth != prevpth:
183	prevpth = pth
184	if os.path.exists(os.path.join(pth,fil)):
185	print 'found image file '+os.path.join(pth,fil)
186	return os.path.join(pth,fil)
187	pth,enddir = os.path.split(pth)
188	#GSASIIpath.IPyBreak()
189
190	if not os.path.exists(imagefile):
191	prevnam = os.path.split(imagefile)[1]
192	prevext = os.path.splitext(imagefile)[1]
193	wildcard = 'Image format ('+prevext+')\|'+prevext
194	dlg = wx.FileDialog(G2frame, 'Previous image file ('+prevnam+') not found; open here', '.', prevnam,
195	wildcard,wx.OPEN)
196	try:
197	dlg.SetFilename(''+ospath.split(imagefile)[1])
198	if dlg.ShowModal() == wx.ID_OK:
199	imagefile = dlg.GetPath()
200	else:
201	imagefile = False
202	finally:
203	dlg.Destroy()
204	return imagefile
205
206	def EditImageParms(parent,Data,Comments,Image,filename):
207	dlg = wx.Dialog(parent, wx.ID_ANY, 'Edit image parameters',
208	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
209	def onClose(event):
210	dlg.EndModal(wx.ID_OK)
211	mainsizer = wx.BoxSizer(wx.VERTICAL)
212	h,w = Image.shape[:2]
213	mainsizer.Add(wx.StaticText(dlg,wx.ID_ANY,
214	'File '+str(filename)+'\nImage size: '+str(h)+' x '+str(w)),
215	0,wx.ALIGN_LEFT\|wx.ALL, 2)
216
217	vsizer = wx.BoxSizer(wx.HORIZONTAL)
218	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Wavelength (\xC5) '),
219	0,wx.ALIGN_LEFT\|wx.ALL, 2)
220	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'wavelength')
221	vsizer.Add(wdgt)
222	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
223
224	vsizer = wx.BoxSizer(wx.HORIZONTAL)
225	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Pixel size (\xb5m). Width '),
226	0,wx.ALIGN_LEFT\|wx.ALL, 2)
227	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],0,
228	size=(50,-1))
229	vsizer.Add(wdgt)
230	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Height '),
231	wx.ALIGN_LEFT\|wx.ALL, 2)
232	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],1,
233	size=(50,-1))
234	vsizer.Add(wdgt)
235	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
236
237	vsizer = wx.BoxSizer(wx.HORIZONTAL)
238	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Sample to detector (mm) '),
239	0,wx.ALIGN_LEFT\|wx.ALL, 2)
240	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'distance')
241	vsizer.Add(wdgt)
242	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
243
244	vsizer = wx.BoxSizer(wx.HORIZONTAL)
245	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Beam center (pixels). X = '),
246	0,wx.ALIGN_LEFT\|wx.ALL, 2)
247	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],0,
248	size=(75,-1))
249	vsizer.Add(wdgt)
250	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Y = '),
251	wx.ALIGN_LEFT\|wx.ALL, 2)
252	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],1,
253	size=(75,-1))
254	vsizer.Add(wdgt)
255	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
256
257	vsizer = wx.BoxSizer(wx.HORIZONTAL)
258	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Comments '),
259	0,wx.ALIGN_LEFT\|wx.ALL, 2)
260	wdgt = G2G.ValidatedTxtCtrl(dlg,Comments,0,size=(250,-1))
261	vsizer.Add(wdgt)
262	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
263
264	btnsizer = wx.StdDialogButtonSizer()
265	OKbtn = wx.Button(dlg, wx.ID_OK, 'Continue')
266	OKbtn.SetDefault()
267	OKbtn.Bind(wx.EVT_BUTTON,onClose)
268	btnsizer.AddButton(OKbtn) # not sure why this is needed
269	btnsizer.Realize()
270	mainsizer.Add(btnsizer, 1, wx.ALIGN_CENTER\|wx.ALL\|wx.EXPAND, 5)
271	dlg.SetSizer(mainsizer)
272	dlg.CenterOnParent()
273	dlg.ShowModal()
274
275	def LoadImage2Tree(imagefile,G2frame,Comments,Data,Npix,Image):
276	'''Load an image into the tree. Saves the location of the image, as well as the
277	ImageTag (where there is more than one image in the file), if defined.
278	'''
279	ImgNames = G2gd.GetPatternTreeDataNames(G2frame,['IMG ',])
280	TreeLbl = 'IMG '+os.path.basename(imagefile)
281	ImageTag = Data.get('ImageTag')
282	if ImageTag:
283	TreeLbl += ' #'+'%04d'%(ImageTag)
284	imageInfo = (imagefile,ImageTag)
285	else:
286	imageInfo = imagefile
287	TreeName = G2obj.MakeUniqueLabel(TreeLbl,ImgNames)
288	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=TreeName)
289	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
290	Imax = np.amax(Image)
291	Imin = max(0.0,np.amin(Image)) #force positive
292	if G2frame.imageDefault:
293	Data = copy.copy(G2frame.imageDefault)
294	Data['showLines'] = True
295	Data['ring'] = []
296	Data['rings'] = []
297	Data['cutoff'] = 10
298	Data['pixLimit'] = 20
299	Data['edgemin'] = 100000000
300	Data['calibdmin'] = 0.5
301	Data['calibskip'] = 0
302	Data['ellipses'] = []
303	Data['calibrant'] = ''
304	Data['GonioAngles'] = [0.,0.,0.]
305	Data['DetDepthRef'] = False
306	else:
307	Data['type'] = 'PWDR'
308	Data['color'] = 'Paired'
309	Data['tilt'] = 0.0
310	Data['rotation'] = 0.0
311	Data['showLines'] = False
312	Data['ring'] = []
313	Data['rings'] = []
314	Data['cutoff'] = 10
315	Data['pixLimit'] = 20
316	Data['calibdmin'] = 0.5
317	Data['calibskip'] = 0
318	Data['edgemin'] = 100000000
319	Data['ellipses'] = []
320	Data['GonioAngles'] = [0.,0.,0.]
321	Data['DetDepth'] = 0.
322	Data['DetDepthRef'] = False
323	Data['calibrant'] = ''
324	Data['IOtth'] = [2.0,5.0]
325	Data['LRazimuth'] = [135,225]
326	Data['azmthOff'] = 0.0
327	Data['outChannels'] = 2500
328	Data['outAzimuths'] = 1
329	Data['centerAzm'] = False
330	Data['fullIntegrate'] = False
331	Data['setRings'] = False
332	Data['background image'] = ['',-1.0]
333	Data['dark image'] = ['',-1.0]
334	Data['Flat Bkg'] = 0.0
335	Data['setDefault'] = False
336	Data['range'] = [(0,Imax),[0,Imax]]
337	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Image Controls'),Data)
338	Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],'Thresholds':[(0,Imax),[0,Imax]]}
339	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Masks'),Masks)
340	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Stress/Strain'),
341	{'Type':'True','d-zero':[],'Sample phi':0.0,'Sample z':0.0,'Sample load':0.0})
342	G2frame.PatternTree.SetItemPyData(Id,[Npix,imageInfo])
343	G2frame.PickId = Id
344	G2frame.PickIdText = G2frame.GetTreeItemsList(G2frame.PickId)
345	G2frame.Image = Id
346
347	def GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None,FormatName=''):
348	'''Read a single image with an image importer.
349
350	:param wx.Frame G2frame: main GSAS-II Frame and data object.
351	:param str imagefile: name of image file
352	:param bool imageOnly: If True return only the image,
353	otherwise (default) return more (see below)
354	:param int/str ImageTag: specifies a particular image to be read from a file.
355	First image is read if None (default).
356	:param str formatName: the image reader formatName
357
358	:returns: an image as a numpy array or a list of four items:
359	Comments, Data, Npix and the Image, as selected by imageOnly
360
361	'''
362	# determine which formats are compatible with this file
363	primaryReaders = []
364	secondaryReaders = []
365	for rd in G2frame.ImportImageReaderlist:
366	flag = rd.ExtensionValidator(imagefile)
367	if flag is None:
368	secondaryReaders.append(rd)
369	elif flag:
370	if not FormatName:
371	primaryReaders.append(rd)
372	elif FormatName == rd.formatName:
373	primaryReaders.append(rd)
374	if len(secondaryReaders) + len(primaryReaders) == 0:
375	print('Error: No matching format for file '+filename)
376	raise Exception('No image read')
377	fp = None
378	errorReport = ''
379	fp = open(imagefile,'Ur')
380	for rd in primaryReaders+secondaryReaders:
381	rd.ReInitialize() # purge anything from a previous read
382	fp.seek(0) # rewind
383	rd.errors = "" # clear out any old errors
384	if not rd.ContentsValidator(fp): # rejected on cursory check
385	errorReport += "\n "+rd.formatName + ' validator error'
386	if rd.errors:
387	errorReport += ': '+rd.errors
388	continue
389	rdbuffer = {} # create temporary storage for file reader
390	if imageOnly:
391	ParentFrame = None # prevent GUI access on reread
392	else:
393	ParentFrame = G2frame
394	if GSASIIpath.GetConfigValue('debug'):
395	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=ImageTag)
396	else:
397	flag = False
398	try:
399	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=ImageTag)
400	except rd.ImportException as detail:
401	rd.errors += "\n Read exception: "+str(detail)
402	except Exception as detail:
403	import traceback
404	rd.errors += "\n Unhandled read exception: "+str(detail)
405	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
406	if flag: # this read succeeded
407	if rd.Image is None:
408	raise Exception('No image read. Strange!')
409	if GSASIIpath.GetConfigValue('Transpose'):
410	print 'Transposing Image!'
411	rd.Image = rd.Image.T
412	#rd.readfilename = imagefile
413	if imageOnly:
414	return rd.Image
415	else:
416	return rd.Comments,rd.Data,rd.Npix,rd.Image
417	else:
418	print('Error reading file '+filename)
419	print('Error messages(s)\n'+errorReport)
420	raise Exception('No image read')
421
422	def ReadImages(G2frame,imagefile):
423	'''Read one or more images from a file and put them into the Tree
424	using image importers. Called only in :meth:`AutoIntFrame.OnTimerLoop`.
425
426	:param wx.Frame G2frame: main GSAS-II Frame and data object.
427	:param str imagefile: name of image file
428
429	:returns: a list of the id's of the IMG tree items created
430	'''
431	# determine which formats are compatible with this file
432	primaryReaders = []
433	secondaryReaders = []
434	for rd in G2frame.ImportImageReaderlist:
435	flag = rd.ExtensionValidator(imagefile)
436	if flag is None:
437	secondaryReaders.append(rd)
438	elif flag:
439	primaryReaders.append(rd)
440	if len(secondaryReaders) + len(primaryReaders) == 0:
441	print('Error: No matching format for file '+filename)
442	raise Exception('No image read')
443	errorReport = ''
444	fp = open(imagefile,'Ur')
445	rdbuffer = {} # create temporary storage for file reader
446	for rd in primaryReaders+secondaryReaders:
447	rd.ReInitialize() # purge anything from a previous read
448	fp.seek(0) # rewind
449	rd.errors = "" # clear out any old errors
450	if not rd.ContentsValidator(fp): # rejected on cursory check
451	errorReport += "\n "+rd.formatName + ' validator error'
452	if rd.errors:
453	errorReport += ': '+rd.errors
454	continue
455	ParentFrame = G2frame
456	block = 0
457	repeat = True
458	CreatedIMGitems = []
459	while repeat: # loop if the reader asks for another pass on the file
460	block += 1
461	repeat = False
462	if GSASIIpath.GetConfigValue('debug'):
463	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=block,Buffer=rdbuffer)
464	else:
465	flag = False
466	try:
467	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=block,Buffer=rdbuffer)
468	except rd.ImportException as detail:
469	rd.errors += "\n Read exception: "+str(detail)
470	except Exception as detail:
471	import traceback
472	rd.errors += "\n Unhandled read exception: "+str(detail)
473	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
474	if flag: # this read succeeded
475	if rd.Image is None:
476	raise Exception('No image read. Strange!')
477	if GSASIIpath.GetConfigValue('Transpose'):
478	print 'Transposing Image!'
479	rd.Image = rd.Image.T
480	rd.Data['ImageTag'] = rd.repeatcount
481	LoadImage2Tree(imagefile,G2frame,rd.Comments,rd.Data,rd.Npix,rd.Image)
482	repeat = rd.repeat
483	CreatedIMGitems.append(G2frame.Image)
484	if CreatedIMGitems: return CreatedIMGitems
485	else:
486	print('Error reading file '+filename)
487	print('Error messages(s)\n'+errorReport)
488	return []
489	#raise Exception('No image read')
490
491	def SaveMultipleImg(G2frame):
492	if not G2frame.PatternTree.GetCount():
493	print 'no images!'
494	return
495	choices = G2gd.GetPatternTreeDataNames(G2frame,['IMG ',])
496	if len(choices) == 1:
497	names = choices
498	else:
499	dlg = G2G.G2MultiChoiceDialog(G2frame,'Stress/Strain fitting','Select images to fit:',choices)
500	dlg.SetSelections([])
501	names = []
502	if dlg.ShowModal() == wx.ID_OK:
503	names = [choices[sel] for sel in dlg.GetSelections()]
504	dlg.Destroy()
505	if not names: return
506	for name in names:
507	Id = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, name)
508	Npix,imagefile,imagetag = G2frame.PatternTree.GetImageLoc(Id)
509	imroot = os.path.splitext(imagefile)[0]
510	if imagetag:
511	imroot += '_' + str(imagetag)
512	Data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Image Controls'))
513	print('Writing '+imroot+'.imctrl')
514	File = open(imroot+'.imctrl','w')
515	keys = ['type','wavelength','calibrant','distance','center',
516	'tilt','rotation','azmthOff','fullIntegrate','LRazimuth',
517	'IOtth','outChannels','outAzimuths','invert_x','invert_y','DetDepth',
518	'calibskip','pixLimit','cutoff','calibdmin','chisq','Flat Bkg',
519	'binType','SampleShape','PolaVal','SampleAbs','dark image','background image']
520	for key in keys:
521	if key not in Data: continue #uncalibrated!
522	File.write(key+':'+str(Data[key])+'\n')
523	File.close()
524	mask = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Masks'))
525	G2imG.CleanupMasks(mask)
526	print('Writing '+imroot+'.immask')
527	File = open(imroot+'.immask','w')
528	for key in ['Points','Rings','Arcs','Polygons','Frames','Thresholds']:
529	File.write(key+':'+str(mask[key])+'\n')
530	File.close()
531
532	def PutG2Image(filename,Comments,Data,Npix,image):
533	'Write an image as a python pickle - might be better as an .edf file?'
534	File = open(filename,'wb')
535	cPickle.dump([Comments,Data,Npix,image],File,1)
536	File.close()
537	return
538
539	# should get moved to importer when ready to test
540	def GetEdfData(filename,imageOnly=False):
541	'Read European detector data edf file'
542	import struct as st
543	import array as ar
544	if not imageOnly:
545	print 'Read European detector data edf file: ',filename
546	File = open(filename,'rb')
547	fileSize = os.stat(filename).st_size
548	head = File.read(3072)
549	lines = head.split('\n')
550	sizexy = [0,0]
551	pixSize = [154,154] #Pixium4700?
552	cent = [0,0]
553	wave = 1.54187 #default <CuKa>
554	dist = 1000.
555	head = ['European detector data',]
556	for line in lines:
557	line = line.replace(';',' ').strip()
558	fields = line.split()
559	if 'Dim_1' in line:
560	sizexy[0] = int(fields[2])
561	elif 'Dim_2' in line:
562	sizexy[1] = int(fields[2])
563	elif 'DataType' in line:
564	dType = fields[2]
565	elif 'wavelength' in line:
566	wave = float(fields[2])
567	elif 'Size' in line:
568	imSize = int(fields[2])
569	# elif 'DataType' in lines:
570	# dType = fields[2]
571	elif 'pixel_size_x' in line:
572	pixSize[0] = float(fields[2])
573	elif 'pixel_size_y' in line:
574	pixSize[1] = float(fields[2])
575	elif 'beam_center_x' in line:
576	cent[0] = float(fields[2])
577	elif 'beam_center_y' in line:
578	cent[1] = float(fields[2])
579	elif 'refined_distance' in line:
580	dist = float(fields[2])
581	if line:
582	head.append(line)
583	else: #blank line at end of header
584	break
585	File.seek(fileSize-imSize)
586	if dType == 'UnsignedShort':
587	image = np.array(ar.array('H',File.read(imSize)),dtype=np.int32)
588	elif dType == 'UnsignedInt':
589	image = np.array(ar.array('L',File.read(imSize)),dtype=np.int32)
590	elif dType == 'UnsignedLong':
591	image = np.array(ar.array('L',File.read(imSize)),dtype=np.int32)
592	elif dType == 'SignedInteger':
593	image = np.array(ar.array('l',File.read(imSize)),dtype=np.int32)
594	image = np.reshape(image,(sizexy[1],sizexy[0]))
595	data = {'pixelSize':pixSize,'wavelength':wave,'distance':dist,'center':cent,'size':sizexy}
596	Npix = sizexy[0]*sizexy[1]
597	File.close()
598	if imageOnly:
599	return image
600	else:
601	return head,data,Npix,image
602
603	# should get moved to importer when ready to test
604	def GetRigaku(filename,imageOnly=False):
605	'Read Rigaku R-Axis IV image file'
606	import struct as st
607	import array as ar
608	if not imageOnly:
609	print 'Read Rigaku R-Axis IV file: ',filename
610	File = open(filename,'rb')
611	fileSize = os.stat(filename).st_size
612	Npix = (fileSize-6000)/2
613	Head = File.read(6000)
614	head = ['Rigaku R-Axis IV detector data',]
615	image = np.array(ar.array('H',File.read(fileSize-6000)),dtype=np.int32)
616	print fileSize,image.shape
617	print head
618	if Npix == 9000000:
619	sizexy = [3000,3000]
620	pixSize = [100.,100.]
621	elif Npix == 2250000:
622	sizexy = [1500,1500]
623	pixSize = [200.,200.]
624	else:
625	sizexy = [6000,6000]
626	pixSize = [50.,50.]
627	image = np.reshape(image,(sizexy[1],sizexy[0]))
628	data = {'pixelSize':pixSize,'wavelength':1.5428,'distance':250.0,'center':[150.,150.],'size':sizexy}
629	File.close()
630	if imageOnly:
631	return image
632	else:
633	return head,data,Npix,image
634
635	# should get moved to importer when ready to test
636	def GetImgData(filename,imageOnly=False):
637	'Read an ADSC image file'
638	import struct as st
639	import array as ar
640	if not imageOnly:
641	print 'Read ADSC img file: ',filename
642	File = open(filename,'rb')
643	head = File.read(511)
644	lines = head.split('\n')
645	head = []
646	center = [0,0]
647	for line in lines[1:-2]:
648	line = line.strip()[:-1]
649	if line:
650	if 'SIZE1' in line:
651	size = int(line.split('=')[1])
652	Npix = size*size
653	elif 'WAVELENGTH' in line:
654	wave = float(line.split('=')[1])
655	elif 'BIN' in line:
656	if line.split('=')[1] == '2x2':
657	pixel=(102,102)
658	else:
659	pixel = (51,51)
660	elif 'DISTANCE' in line:
661	distance = float(line.split('=')[1])
662	elif 'CENTER_X' in line:
663	center[0] = float(line.split('=')[1])
664	elif 'CENTER_Y' in line:
665	center[1] = float(line.split('=')[1])
666	head.append(line)
667	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center,'size':[size,size]}
668	image = []
669	row = 0
670	pos = 512
671	File.seek(pos)
672	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
673	image = np.reshape(image,(sizexy[1],sizexy[0]))
674	# image = np.zeros(shape=(size,size),dtype=np.int32)
675	# while row < size:
676	# File.seek(pos)
677	# line = ar.array('H',File.read(2*size))
678	# image[row] = np.asarray(line)
679	# row += 1
680	# pos += 2*size
681	File.close()
682	if imageOnly:
683	return image
684	else:
685	return lines[1:-2],data,Npix,image
686
687	# should get moved to importer when ready to test
688	def GetMAR345Data(filename,imageOnly=False):
689	'Read a MAR-345 image plate image'
690	import array as ar
691	import struct as st
692	try:
693	import pack_f as pf
694	except:
695	msg = wx.MessageDialog(None, message="Unable to load the GSAS MAR image decompression, pack_f",
696	caption="Import Error",
697	style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
698	msg.ShowModal()
699	return None,None,None,None
700
701	if not imageOnly:
702	print 'Read Mar345 file: ',filename
703	File = open(filename,'rb')
704	head = File.read(4095)
705	numbers = st.unpack('<iiiiiiiiii',head[:40])
706	lines = head[128:].split('\n')
707	head = []
708	for line in lines:
709	line = line.strip()
710	if 'PIXEL' in line:
711	values = line.split()
712	pixel = (int(values[2]),int(values[4])) #in microns
713	elif 'WAVELENGTH' in line:
714	wave = float(line.split()[1])
715	elif 'DISTANCE' in line:
716	distance = float(line.split()[1]) #in mm
717	if not distance:
718	distance = 500.
719	elif 'CENTER' in line:
720	values = line.split()
721	center = [float(values[2])/10.,float(values[4])/10.] #make in mm from pixels
722	if line:
723	head.append(line)
724	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center}
725	for line in head:
726	if 'FORMAT' in line[0:6]:
727	items = line.split()
728	sizex = int(items[1])
729	Npix = int(items[3])
730	sizey = int(Npix/sizex)
731	pos = 4096
732	data['size'] = [sizex,sizey]
733	File.seek(pos)
734	line = File.read(8)
735	while 'CCP4' not in line: #get past overflow list for now
736	line = File.read(8)
737	pos += 8
738	pos += 37
739	File.seek(pos)
740	raw = File.read()
741	File.close()
742	image = np.zeros(shape=(sizex,sizey),dtype=np.int32)
743
744	image = np.flipud(pf.pack_f(len(raw),raw,sizex,sizey,image).T) #transpose to get it right way around & flip
745	if imageOnly:
746	return image
747	else:
748	return head,data,Npix,image
749
750	def ProjFileOpen(G2frame,showProvenance=True):
751	'Read a GSAS-II project file and load into the G2 data tree'
752	if not os.path.exists(G2frame.GSASprojectfile):
753	print ('\n*** Error attempt to open project file that does not exist:\n '+
754	str(G2frame.GSASprojectfile))
755	return
756	LastSavedUsing = None
757	file = open(G2frame.GSASprojectfile,'rb')
758	if showProvenance: print 'loading from file: ',G2frame.GSASprojectfile
759	G2frame.SetTitle("GSAS-II data tree: "+
760	os.path.split(G2frame.GSASprojectfile)[1])
761	wx.BeginBusyCursor()
762	try:
763	while True:
764	try:
765	data = cPickle.load(file)
766	except EOFError:
767	break
768	datum = data[0]
769
770	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=datum[0])
771	if 'PWDR' in datum[0]:
772	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
773	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
774	G2frame.PatternTree.SetItemPyData(Id,datum[1][:3]) #temp. trim off junk (patch?)
775	elif datum[0].startswith('HKLF'):
776	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
777	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
778	G2frame.PatternTree.SetItemPyData(Id,datum[1])
779	else:
780	G2frame.PatternTree.SetItemPyData(Id,datum[1])
781	if datum[0] == 'Controls' and 'LastSavedUsing' in datum[1]:
782	LastSavedUsing = datum[1]['LastSavedUsing']
783	if datum[0] == 'Controls' and 'PythonVersions' in datum[1] and GSASIIpath.GetConfigValue('debug') and showProvenance:
784	print('Packages used to create .GPX file:')
785	if 'dict' in str(type(datum[1]['PythonVersions'])): #patch
786	for p in sorted(datum[1]['PythonVersions'],key=lambda s: s.lower()):
787	print("{:>14s}: {:s}".format(p[0],p[1]))
788	else:
789	for p in datum[1]['PythonVersions']:
790	print("{:<12s} {:s}".format(p[0]+':',p[1]))
791	for datus in data[1:]:
792	sub = G2frame.PatternTree.AppendItem(Id,datus[0])
793	#patch
794	if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
795	if 'PWDR' in datum[0]:
796	datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
797	else:
798	datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
799	for item in datus[1][0]: #zip makes tuples - now make lists!
800	datus[1][0][item] = list(datus[1][0][item])
801	#end patch
802	G2frame.PatternTree.SetItemPyData(sub,datus[1])
803	if 'IMG' in datum[0]: #retrieve image default flag & data if set
804	Data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Image Controls'))
805	if Data['setDefault']:
806	G2frame.imageDefault = Data
807	file.close()
808	if LastSavedUsing:
809	print('GPX load successful. Last saved with GSAS-II version '+LastSavedUsing)
810	else:
811	print('project load successful')
812	G2frame.NewPlot = True
813	except:
814	msg = wx.MessageDialog(G2frame,message="Error reading file "+
815	str(G2frame.GSASprojectfile)+". This is not a GSAS-II .gpx file",
816	caption="Load Error",style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
817	msg.ShowModal()
818	finally:
819	wx.EndBusyCursor()
820	G2frame.Status.SetStatusText('To reorder tree items, use mouse RB to drag/drop them')
821
822	def ProjFileSave(G2frame):
823	'Save a GSAS-II project file'
824	if not G2frame.PatternTree.IsEmpty():
825	file = open(G2frame.GSASprojectfile,'wb')
826	print 'save to file: ',G2frame.GSASprojectfile
827	# stick the file name into the tree and version info into tree so they are saved.
828	# (Controls should always be created at this point)
829	try:
830	Controls = G2frame.PatternTree.GetItemPyData(
831	G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
832	Controls['LastSavedAs'] = os.path.abspath(G2frame.GSASprojectfile)
833	Controls['LastSavedUsing'] = str(GSASIIpath.GetVersionNumber())
834	Controls['PythonVersions'] = G2frame.PackageVersions
835	except:
836	pass
837	wx.BeginBusyCursor()
838	try:
839	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
840	while item:
841	data = []
842	name = G2frame.PatternTree.GetItemText(item)
843	data.append([name,G2frame.PatternTree.GetItemPyData(item)])
844	item2, cookie2 = G2frame.PatternTree.GetFirstChild(item)
845	while item2:
846	name = G2frame.PatternTree.GetItemText(item2)
847	data.append([name,G2frame.PatternTree.GetItemPyData(item2)])
848	item2, cookie2 = G2frame.PatternTree.GetNextChild(item, cookie2)
849	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
850	cPickle.dump(data,file,1)
851	file.close()
852	pth = os.path.split(os.path.abspath(G2frame.GSASprojectfile))[0]
853	if GSASIIpath.GetConfigValue('Save_paths'): G2G.SaveGPXdirectory(pth)
854	G2frame.LastGPXdir = pth
855	finally:
856	wx.EndBusyCursor()
857	print('project save successful')
858
859	def SaveIntegration(G2frame,PickId,data,Overwrite=False):
860	'Save image integration results as powder pattern(s)'
861	azms = G2frame.Integrate[1]
862	X = G2frame.Integrate[2][:-1]
863	N = len(X)
864	Id = G2frame.PatternTree.GetItemParent(PickId)
865	name = G2frame.PatternTree.GetItemText(Id)
866	name = name.replace('IMG ',data['type']+' ')
867	Comments = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Comments'))
868	if 'PWDR' in name:
869	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','SH/L','Azimuth']
870	codes = [0 for i in range(11)]
871	elif 'SASD' in name:
872	names = ['Type','Lam','Zero','Azimuth']
873	codes = [0 for i in range(4)]
874	X = 4.np.pinpsind(X/2.)/data['wavelength'] #convert to q
875	Xminmax = [X[0],X[-1]]
876	LRazm = data['LRazimuth']
877	Azms = []
878	dazm = 0.
879	if data['fullIntegrate'] and data['outAzimuths'] == 1:
880	Azms = [45.0,] #a poor man's average?
881	else:
882	for i,azm in enumerate(azms[:-1]):
883	if azm > 360. and azms[i+1] > 360.:
884	Azms.append(G2img.meanAzm(azm%360.,azms[i+1]%360.))
885	else:
886	Azms.append(G2img.meanAzm(azm,azms[i+1]))
887	dazm = np.min(np.abs(np.diff(azms)))/2.
888	G2frame.IntgOutList = []
889	for i,azm in enumerate(azms[:-1]):
890	Aname = name+" Azm= %.2f"%((azm+dazm)%360.)
891	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
892	# if Overwrite delete any duplicate
893	if Overwrite and G2gd.GetPatternTreeItemId(G2frame,G2frame.root,Aname):
894	print('Replacing '+Aname)
895	item = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,Aname)
896	G2frame.PatternTree.Delete(item)
897	else:
898	nOcc = 0
899	while item:
900	Name = G2frame.PatternTree.GetItemText(item)
901	if Aname in Name:
902	nOcc += 1
903	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
904	if nOcc:
905	Aname += '(%d)'%(nOcc)
906	Sample = G2pdG.SetDefaultSample()
907	Sample['Gonio. radius'] = data['distance']
908	Sample['Omega'] = data['GonioAngles'][0]
909	Sample['Chi'] = data['GonioAngles'][1]
910	Sample['Phi'] = data['GonioAngles'][2]
911	Sample['Azimuth'] = (azm+dazm)%360. #put here as bin center
912	if 'PWDR' in Aname:
913	parms = ['PXC',data['wavelength'],0.0,0.99,1.0,-0.10,0.4,0.30,1.0,0.0001,Azms[i]] #set polarization for synchrotron radiation!
914	elif 'SASD' in Aname:
915	Sample['Trans'] = data['SampleAbs'][0]
916	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
917	Y = G2frame.Integrate[0][i]
918	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
919	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=Aname)
920	G2frame.IntgOutList.append(Id)
921	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
922	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Limits'),[tuple(Xminmax),Xminmax])
923	if 'PWDR' in Aname:
924	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Background'),[['chebyschev',1,3,1.0,0.0,0.0],
925	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
926	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
927	for item in inst[0]:
928	inst[0][item] = list(inst[0][item])
929	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Instrument Parameters'),inst)
930	if 'PWDR' in Aname:
931	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
932	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
933	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Index Peak List'),[[],[]])
934	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Unit Cells List'),[])
935	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Reflection Lists'),{})
936	elif 'SASD' in Aname:
937	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
938	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
939	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
940	valuesdict = {
941	'wtFactor':1.0,
942	'Dummy':False,
943	'ranId':ran.randint(0,sys.maxint),
944	'Offset':[0.0,0.0],'delOffset':0.02,'refOffset':-1.0,'refDelt':0.01,
945	'qPlot':False,'dPlot':False,'sqrtPlot':False
946	}
947	G2frame.PatternTree.SetItemPyData(
948	Id,[valuesdict,
949	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
950	return Id #last powder pattern generated
951
952	def PDFSave(G2frame,exports):
953	'Save a PDF G(r) and S(Q) in column formats'
954	for export in exports:
955	PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
956	SQname = 'S(Q)'+export[4:]
957	GRname = 'G(R)'+export[4:]
958	sqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.sq')
959	grfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.gr')
960	sqId = G2gd.GetPatternTreeItemId(G2frame, PickId, SQname)
961	grId = G2gd.GetPatternTreeItemId(G2frame, PickId, GRname)
962	sqdata = np.array(G2frame.PatternTree.GetItemPyData(sqId)[1][:2]).T
963	grdata = np.array(G2frame.PatternTree.GetItemPyData(grId)[1][:2]).T
964	sqfile = open(sqfilename,'w')
965	grfile = open(grfilename,'w')
966	sqfile.write('#T S(Q) %s\n'%(export))
967	grfile.write('#T G(R) %s\n'%(export))
968	sqfile.write('#L Q S(Q)\n')
969	grfile.write('#L R G(R)\n')
970	for q,sq in sqdata:
971	sqfile.write("%15.6g %15.6g\n" % (q,sq))
972	sqfile.close()
973	for r,gr in grdata:
974	grfile.write("%15.6g %15.6g\n" % (r,gr))
975	grfile.close()
976
977	def PeakListSave(G2frame,file,peaks):
978	'Save powder peaks to a data file'
979	print 'save peak list to file: ',G2frame.peaklistfile
980	if not peaks:
981	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
982	try:
983	result = dlg.ShowModal()
984	finally:
985	dlg.Destroy()
986	return
987	for peak in peaks:
988	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
989	(peak[0],peak[2],peak[4],peak[6]))
990	print 'peak list saved'
991
992	def IndexPeakListSave(G2frame,peaks):
993	'Save powder peaks from the indexing list'
994	file = open(G2frame.peaklistfile,'wa')
995	print 'save index peak list to file: ',G2frame.peaklistfile
996	wx.BeginBusyCursor()
997	try:
998	if not peaks:
999	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1000	try:
1001	result = dlg.ShowModal()
1002	finally:
1003	dlg.Destroy()
1004	return
1005	for peak in peaks:
1006	file.write("%12.6f\n" % (peak[7]))
1007	file.close()
1008	finally:
1009	wx.EndBusyCursor()
1010	print 'index peak list saved'
1011
1012	def SetNewPhase(Name='New Phase',SGData=None,cell=None,Super=None):
1013	'''Create a new phase dict with default values for various parameters
1014
1015	:param str Name: Name for new Phase
1016
1017	:param dict SGData: space group data from :func:`GSASIIspc:SpcGroup`;
1018	defaults to data for P 1
1019
1020	:param list cell: unit cell parameter list; defaults to
1021	[1.0,1.0,1.0,90.,90,90.,1.]
1022
1023	'''
1024	if SGData is None: SGData = G2spc.SpcGroup('P 1')[1]
1025	if cell is None: cell=[1.0,1.0,1.0,90.,90,90.,1.]
1026	phaseData = {
1027	'ranId':ran.randint(0,sys.maxint),
1028	'General':{
1029	'Name':Name,
1030	'Type':'nuclear',
1031	'AtomPtrs':[3,1,7,9],
1032	'SGData':SGData,
1033	'Cell':[False,]+cell,
1034	'Pawley dmin':1.0,
1035	'Data plot type':'None',
1036	'SH Texture':{
1037	'Order':0,
1038	'Model':'cylindrical',
1039	'Sample omega':[False,0.0],
1040	'Sample chi':[False,0.0],
1041	'Sample phi':[False,0.0],
1042	'SH Coeff':[False,{}],
1043	'SHShow':False,
1044	'PFhkl':[0,0,1],
1045	'PFxyz':[0,0,1],
1046	'PlotType':'Pole figure',
1047	'Penalty':[['',],0.1,False,1.0]}},
1048	'Atoms':[],
1049	'Drawing':{},
1050	'Histograms':{},
1051	'Pawley ref':[],
1052	'RBModels':{},
1053	}
1054	if Super and Super.get('Use',False):
1055	phaseData['General'].update({'Type':'modulated','Super':True,'SuperSg':Super['ssSymb']})
1056	phaseData['General']['SSGData'] = G2spc.SSpcGroup(SGData,Super['ssSymb'])
1057	phaseData['General']['SuperVec'] = [Super['ModVec'],False,Super['maxH']]
1058
1059	return phaseData
1060
1061	class MultipleChoicesDialog(wx.Dialog):
1062	'''A dialog that offers a series of choices, each with a
1063	title and a wx.Choice widget. Intended to be used Modally.
1064	typical input:
1065
1066	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1067	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1068
1069	selections are placed in self.chosen when OK is pressed
1070	'''
1071	def __init__(self,choicelist,headinglist,
1072	head='Select options',
1073	title='Please select from options below',
1074	parent=None):
1075	self.chosen = []
1076	wx.Dialog.__init__(
1077	self,parent,wx.ID_ANY,head,
1078	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
1079	panel = wx.Panel(self)
1080	mainSizer = wx.BoxSizer(wx.VERTICAL)
1081	mainSizer.Add((10,10),1)
1082	topLabl = wx.StaticText(panel,wx.ID_ANY,title)
1083	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.CENTER,10)
1084	self.ChItems = []
1085	for choice,lbl in zip(choicelist,headinglist):
1086	mainSizer.Add((10,10),1)
1087	self.chosen.append(0)
1088	topLabl = wx.StaticText(panel,wx.ID_ANY,' '+lbl)
1089	mainSizer.Add(topLabl,0,wx.ALIGN_LEFT,10)
1090	self.ChItems.append(wx.Choice(self, wx.ID_ANY, (100, 50), choices = choice))
1091	mainSizer.Add(self.ChItems[-1],0,wx.ALIGN_CENTER,10)
1092
1093	OkBtn = wx.Button(panel,-1,"Ok")
1094	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
1095	cancelBtn = wx.Button(panel,-1,"Cancel")
1096	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
1097	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1098	btnSizer.Add((20,20),1)
1099	btnSizer.Add(OkBtn)
1100	btnSizer.Add((20,20),1)
1101	btnSizer.Add(cancelBtn)
1102	btnSizer.Add((20,20),1)
1103	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1104	panel.SetSizer(mainSizer)
1105	panel.Fit()
1106	self.Fit()
1107
1108	def OnOk(self,event):
1109	parent = self.GetParent()
1110	if parent is not None: parent.Raise()
1111	# save the results from the choice widgets
1112	self.chosen = []
1113	for w in self.ChItems:
1114	self.chosen.append(w.GetSelection())
1115	self.EndModal(wx.ID_OK)
1116
1117	def OnCancel(self,event):
1118	parent = self.GetParent()
1119	if parent is not None: parent.Raise()
1120	self.chosen = []
1121	self.EndModal(wx.ID_CANCEL)
1122
1123	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1124	confirmoverwrite=True, parent=None,
1125	multipleselect=False):
1126	'''If the filename is a zip file, extract a file from that
1127	archive.
1128
1129	:param list Selection: used to predefine the name of the file
1130	to be extracted. Filename case and zip directory name are
1131	ignored in selection; the first matching file is used.
1132
1133	:param bool confirmread: if True asks the user to confirm before expanding
1134	the only file in a zip
1135
1136	:param bool confirmoverwrite: if True asks the user to confirm
1137	before overwriting if the extracted file already exists
1138
1139	:param bool multipleselect: if True allows more than one zip
1140	file to be extracted, a list of file(s) is returned.
1141	If only one file is present, do not ask which one, otherwise
1142	offer a list of choices (unless selection is used).
1143
1144	:returns: the name of the file that has been created or a
1145	list of files (see multipleselect)
1146
1147	If the file is not a zipfile, return the name of the input file.
1148	If the zipfile is empty or no file has been selected, return None
1149	'''
1150	import zipfile # do this now, since we can save startup time by doing this only on need
1151	import shutil
1152	zloc = os.path.split(filename)[0]
1153	if not zipfile.is_zipfile(filename):
1154	#print("not zip")
1155	return filename
1156
1157	z = zipfile.ZipFile(filename,'r')
1158	zinfo = z.infolist()
1159
1160	if len(zinfo) == 0:
1161	#print('Zip has no files!')
1162	zlist = [-1]
1163	if selection:
1164	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1165	if selection.lower() in choices:
1166	zlist = [choices.index(selection.lower())]
1167	else:
1168	print('debug: file '+str(selection)+' was not found in '+str(filename))
1169	zlist = [-1]
1170	elif len(zinfo) == 1 and confirmread:
1171	result = wx.ID_NO
1172	dlg = wx.MessageDialog(
1173	parent,
1174	'Is file '+str(zinfo[0].filename)+
1175	' what you want to extract from '+
1176	str(os.path.split(filename)[1])+'?',
1177	'Confirm file',
1178	wx.YES_NO \| wx.ICON_QUESTION)
1179	try:
1180	result = dlg.ShowModal()
1181	finally:
1182	dlg.Destroy()
1183	if result == wx.ID_NO:
1184	zlist = [-1]
1185	else:
1186	zlist = [0]
1187	elif len(zinfo) == 1:
1188	zlist = [0]
1189	elif multipleselect:
1190	# select one or more from a from list
1191	choices = [i.filename for i in zinfo]
1192	dlg = G2G.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1193	'Choose file(s)',choices)
1194	if dlg.ShowModal() == wx.ID_OK:
1195	zlist = dlg.GetSelections()
1196	else:
1197	zlist = []
1198	dlg.Destroy()
1199	else:
1200	# select one from a from list
1201	choices = [i.filename for i in zinfo]
1202	dlg = wx.SingleChoiceDialog(parent,
1203	'Select file to extract from zip file'+str(filename),'Choose file',
1204	choices,)
1205	if dlg.ShowModal() == wx.ID_OK:
1206	zlist = [dlg.GetSelection()]
1207	else:
1208	zlist = [-1]
1209	dlg.Destroy()
1210
1211	outlist = []
1212	for zindex in zlist:
1213	if zindex >= 0:
1214	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1215	if os.path.exists(efil) and confirmoverwrite:
1216	result = wx.ID_NO
1217	dlg = wx.MessageDialog(parent,
1218	'File '+str(efil)+' already exists. OK to overwrite it?',
1219	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1220	try:
1221	result = dlg.ShowModal()
1222	finally:
1223	dlg.Destroy()
1224	if result == wx.ID_NO:
1225	zindex = -1
1226	if zindex >= 0:
1227	# extract the file to the current directory, regardless of it's original path
1228	#z.extract(zinfo[zindex],zloc)
1229	eloc,efil = os.path.split(zinfo[zindex].filename)
1230	outfile = os.path.join(zloc, efil)
1231	fpin = z.open(zinfo[zindex])
1232	fpout = file(outfile, "wb")
1233	shutil.copyfileobj(fpin, fpout)
1234	fpin.close()
1235	fpout.close()
1236	outlist.append(outfile)
1237	z.close()
1238	if multipleselect and len(outlist) >= 1:
1239	return outlist
1240	elif len(outlist) == 1:
1241	return outlist[0]
1242	else:
1243	return None
1244
1245	######################################################################
1246	# base classes for reading various types of data files
1247	# not used directly, only by subclassing
1248	######################################################################
1249	try:
1250	E,SGData = G2spc.SpcGroup('P 1') # data structure for default space group
1251	except: # errors on doc build
1252	SGData = None
1253	P1SGData = SGData
1254	######################################################################
1255	class ImportBaseclass(object):
1256	'''Defines a base class for the reading of input files (diffraction
1257	data, coordinates,...). See :ref:`Writing a Import Routine<Import_routines>`
1258	for an explanation on how to use a subclass of this class.
1259	'''
1260	class ImportException(Exception):
1261	'''Defines an Exception that is used when an import routine hits an expected error,
1262	usually in .Reader.
1263
1264	Good practice is that the Reader should define a value in self.errors that
1265	tells the user some information about what is wrong with their file.
1266	'''
1267	pass
1268
1269	UseReader = True # in __init__ set value of self.UseReader to False to skip use of current importer
1270	def __init__(self,formatName,longFormatName=None,
1271	extensionlist=[],strictExtension=False,):
1272	self.formatName = formatName # short string naming file type
1273	if longFormatName: # longer string naming file type
1274	self.longFormatName = longFormatName
1275	else:
1276	self.longFormatName = formatName
1277	# define extensions that are allowed for the file type
1278	# for windows, remove any extensions that are duplicate, as case is ignored
1279	if sys.platform == 'windows' and extensionlist:
1280	extensionlist = list(set([s.lower() for s in extensionlist]))
1281	self.extensionlist = extensionlist
1282	# If strictExtension is True, the file will not be read, unless
1283	# the extension matches one in the extensionlist
1284	self.strictExtension = strictExtension
1285	self.errors = ''
1286	self.warnings = ''
1287	# used for readers that will use multiple passes to read
1288	# more than one data block
1289	self.repeat = False
1290	self.selections = []
1291	self.repeatcount = 0
1292	self.readfilename = '?'
1293	#print 'created',self.__class__
1294
1295	def ReInitialize(self):
1296	'Reinitialize the Reader to initial settings'
1297	self.errors = ''
1298	self.warnings = ''
1299	self.repeat = False
1300	self.repeatcount = 0
1301	self.readfilename = '?'
1302
1303	def BlockSelector(self, ChoiceList, ParentFrame=None,title='Select a block',
1304	size=None, header='Block Selector',useCancel=True):
1305	''' Provide a wx dialog to select a block if the file contains more
1306	than one set of data and one must be selected
1307	'''
1308	if useCancel:
1309	dlg = wx.SingleChoiceDialog(
1310	ParentFrame,title, header,ChoiceList)
1311	else:
1312	dlg = wx.SingleChoiceDialog(
1313	ParentFrame,title, header,ChoiceList,
1314	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.OK\|wx.CENTRE)
1315	if size: dlg.SetSize(size)
1316	dlg.CenterOnParent()
1317	if dlg.ShowModal() == wx.ID_OK:
1318	sel = dlg.GetSelection()
1319	return sel
1320	else:
1321	return None
1322	dlg.Destroy()
1323
1324	def MultipleBlockSelector(self, ChoiceList, ParentFrame=None,
1325	title='Select a block',size=None, header='Block Selector'):
1326	'''Provide a wx dialog to select a block of data if the
1327	file contains more than one set of data and one must be
1328	selected.
1329
1330	:returns: a list of the selected blocks
1331	'''
1332	dlg = wx.MultiChoiceDialog(ParentFrame,title, header,ChoiceList+['Select all'],
1333	wx.CHOICEDLG_STYLE)
1334	dlg.CenterOnScreen()
1335	if size: dlg.SetSize(size)
1336	if dlg.ShowModal() == wx.ID_OK:
1337	sel = dlg.GetSelections()
1338	else:
1339	return []
1340	dlg.Destroy()
1341	selected = []
1342	if len(ChoiceList) in sel:
1343	return range(len(ChoiceList))
1344	else:
1345	return sel
1346	return selected
1347
1348	def MultipleChoicesDialog(self, choicelist, headinglist, ParentFrame=None, **kwargs):
1349	'''A modal dialog that offers a series of choices, each with a title and a wx.Choice
1350	widget. Typical input:
1351
1352	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1353
1354	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1355
1356	optional keyword parameters are: head (window title) and title
1357	returns a list of selected indicies for each choice (or None)
1358	'''
1359	result = None
1360	dlg = MultipleChoicesDialog(choicelist,headinglist,
1361	parent=ParentFrame, **kwargs)
1362	dlg.CenterOnParent()
1363	if dlg.ShowModal() == wx.ID_OK:
1364	result = dlg.chosen
1365	dlg.Destroy()
1366	return result
1367
1368	def ShowBusy(self):
1369	wx.BeginBusyCursor()
1370	# wx.Yield() # make it happen now!
1371
1372	def DoneBusy(self):
1373	wx.EndBusyCursor()
1374	wx.Yield() # make it happen now!
1375
1376	# def Reader(self, filename, filepointer, ParentFrame=None, **unused):
1377	# '''This method must be supplied in the child class to read the file.
1378	# if the read fails either return False or raise an Exception
1379	# preferably of type ImportException.
1380	# '''
1381	# #start reading
1382	# raise ImportException("Error occurred while...")
1383	# self.errors += "Hint for user on why the error occur
1384	# return False # if an error occurs
1385	# return True # if read OK
1386
1387	def ExtensionValidator(self, filename):
1388	'''This methods checks if the file has the correct extension
1389	Return False if this filename will not be supported by this reader
1390	Return True if the extension matches the list supplied by the reader
1391	Return None if the reader allows un-registered extensions
1392	'''
1393	if filename:
1394	ext = os.path.splitext(filename)[1]
1395	if sys.platform == 'windows': ext = ext.lower()
1396	if ext in self.extensionlist: return True
1397	if self.strictExtension: return False
1398	return None
1399
1400	def ContentsValidator(self, filepointer):
1401	'''This routine will attempt to determine if the file can be read
1402	with the current format.
1403	This will typically be overridden with a method that
1404	takes a quick scan of [some of]
1405	the file contents to do a "sanity" check if the file
1406	appears to match the selected format.
1407	Expected to be called via self.Validator()
1408	'''
1409	#filepointer.seek(0) # rewind the file pointer
1410	return True
1411
1412	def CIFValidator(self, filepointer):
1413	'''A :meth:`ContentsValidator` for use to validate CIF files.
1414	'''
1415	for i,l in enumerate(filepointer):
1416	if i >= 1000: return True
1417	'''Encountered only blank lines or comments in first 1000
1418	lines. This is unlikely, but assume it is CIF anyway, since we are
1419	even less likely to find a file with nothing but hashes and
1420	blank lines'''
1421	line = l.strip()
1422	if len(line) == 0: # ignore blank lines
1423	continue
1424	elif line.startswith('#'): # ignore comments
1425	continue
1426	elif line.startswith('data_'): # on the right track, accept this file
1427	return True
1428	else: # found something invalid
1429	self.errors = 'line '+str(i+1)+' contains unexpected data:\n'
1430	self.errors += ' '+str(l)
1431	self.errors += ' Note: a CIF should only have blank lines or comments before'
1432	self.errors += ' a data_ statement begins a block.'
1433	return False
1434
1435	######################################################################
1436	class ImportPhase(ImportBaseclass):
1437	'''Defines a base class for the reading of files with coordinates
1438
1439	Objects constructed that subclass this (in import/G2phase_*.py etc.) will be used
1440	in :meth:`GSASII.GSASII.OnImportPhase`.
1441	See :ref:`Writing a Import Routine<Import_Routines>`
1442	for an explanation on how to use this class.
1443
1444	'''
1445	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1446	strictExtension=False,):
1447	# call parent __init__
1448	ImportBaseclass.__init__(self,formatName,longFormatName,
1449	extensionlist,strictExtension)
1450	self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
1451	self.Constraints = None
1452
1453	def PhaseSelector(self, ChoiceList, ParentFrame=None,
1454	title='Select a phase', size=None,header='Phase Selector'):
1455	''' Provide a wx dialog to select a phase if the file contains more
1456	than one phase
1457	'''
1458	return self.BlockSelector(ChoiceList,ParentFrame,title,
1459	size,header)
1460
1461	######################################################################
1462	class ImportStructFactor(ImportBaseclass):
1463	'''Defines a base class for the reading of files with tables
1464	of structure factors.
1465
1466	Structure factors are read with a call to :meth:`GSASII.GSASII.OnImportSfact`
1467	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`, which calls
1468	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1469	:meth:`Reader`.
1470
1471	See :ref:`Writing a Import Routine<Import_Routines>`
1472	for an explanation on how to use import classes in general. The specifics
1473	for reading a structure factor histogram require that
1474	the ``Reader()`` routine in the import
1475	class need to do only a few things: It
1476	should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
1477	and set :attr:`Parameters` with the instrument parameters
1478	(initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
1479	'''
1480	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1481	strictExtension=False,):
1482	ImportBaseclass.__init__(self,formatName,longFormatName,
1483	extensionlist,strictExtension)
1484
1485	# define contents of Structure Factor entry
1486	self.Parameters = []
1487	'self.Parameters is a list with two dicts for data parameter settings'
1488	self.InitParameters()
1489	self.RefDict = {'RefList':[],'FF':{},'Super':0}
1490	self.Banks = [] #for multi bank data (usually TOF)
1491	'''self.RefDict is a dict containing the reflection information, as read from the file.
1492	Item 'RefList' contains the reflection information. See the
1493	:ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
1494	for the contents of each row. Dict element 'FF'
1495	contains the form factor values for each element type; if this entry
1496	is left as initialized (an empty list) it will be initialized as needed later.
1497	'''
1498	def ReInitialize(self):
1499	'Reinitialize the Reader to initial settings'
1500	ImportBaseclass.ReInitialize(self)
1501	self.InitParameters()
1502	self.Banks = [] #for multi bank data (usually TOF)
1503	self.RefDict = {'RefList':[],'FF':{},'Super':0}
1504
1505	def InitParameters(self):
1506	'initialize the instrument parameters structure'
1507	Lambda = 0.70926
1508	HistType = 'SXC'
1509	self.Parameters = [{'Type':[HistType,HistType], # create the structure
1510	'Lam':[Lambda,Lambda]
1511	}, {}]
1512	'Parameters is a list with two dicts for data parameter settings'
1513
1514	def UpdateParameters(self,Type=None,Wave=None):
1515	'Revise the instrument parameters'
1516	if Type is not None:
1517	self.Parameters[0]['Type'] = [Type,Type]
1518	if Wave is not None:
1519	self.Parameters[0]['Lam'] = [Wave,Wave]
1520
1521	######################################################################
1522	class ImportPowderData(ImportBaseclass):
1523	'''Defines a base class for the reading of files with powder data.
1524
1525	Objects constructed that subclass this (in import/G2pwd_*.py etc.) will be used
1526	in :meth:`GSASII.GSASII.OnImportPowder`.
1527	See :ref:`Writing a Import Routine<Import_Routines>`
1528	for an explanation on how to use this class.
1529	'''
1530	def __init__(self,formatName,longFormatName=None,
1531	extensionlist=[],strictExtension=False,):
1532	ImportBaseclass.__init__(self,formatName,longFormatName,
1533	extensionlist,strictExtension)
1534	self.clockWd = None # used in TOF
1535	self.ReInitialize()
1536
1537	def ReInitialize(self):
1538	'Reinitialize the Reader to initial settings'
1539	ImportBaseclass.ReInitialize(self)
1540	self.powderentry = ['',None,None] # (filename,Pos,Bank)
1541	self.powderdata = [] # Powder dataset
1542	'''A powder data set is a list with items [x,y,w,yc,yb,yd]:
1543	np.array(x), # x-axis values
1544	np.array(y), # powder pattern intensities
1545	np.array(w), # 1/sig(intensity)^2 values (weights)
1546	np.array(yc), # calc. intensities (zero)
1547	np.array(yb), # calc. background (zero)
1548	np.array(yd), # obs-calc profiles
1549	'''
1550	self.comments = []
1551	self.idstring = ''
1552	self.Sample = G2pdG.SetDefaultSample() # default sample parameters
1553	self.Controls = {} # items to be placed in top-level Controls
1554	self.GSAS = None # used in TOF
1555	self.repeat_instparm = True # Should a parm file be
1556	# used for multiple histograms?
1557	self.instparm = None # name hint from file of instparm to use
1558	self.instfile = '' # full path name to instrument parameter file
1559	self.instbank = '' # inst parm bank number
1560	self.instmsg = '' # a label that gets printed to show
1561	# where instrument parameters are from
1562	self.numbanks = 1
1563	self.instdict = {} # place items here that will be transferred to the instrument parameters
1564	self.pwdparms = {} # place parameters that are transferred directly to the tree
1565	# here (typically from an existing GPX file)
1566	######################################################################
1567	class ImportSmallAngleData(ImportBaseclass):
1568	'''Defines a base class for the reading of files with small angle data.
1569	See :ref:`Writing a Import Routine<Import_Routines>`
1570	for an explanation on how to use this class.
1571	'''
1572	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1573	strictExtension=False,):
1574
1575	ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
1576	strictExtension)
1577	self.ReInitialize()
1578
1579	def ReInitialize(self):
1580	'Reinitialize the Reader to initial settings'
1581	ImportBaseclass.ReInitialize(self)
1582	self.smallangleentry = ['',None,None] # (filename,Pos,Bank)
1583	self.smallangledata = [] # SASD dataset
1584	'''A small angle data set is a list with items [x,y,w,yc,yd]:
1585	np.array(x), # x-axis values
1586	np.array(y), # powder pattern intensities
1587	np.array(w), # 1/sig(intensity)^2 values (weights)
1588	np.array(yc), # calc. intensities (zero)
1589	np.array(yd), # obs-calc profiles
1590	np.array(yb), # preset bkg
1591	'''
1592	self.comments = []
1593	self.idstring = ''
1594	self.Sample = G2pdG.SetDefaultSample()
1595	self.GSAS = None # used in TOF
1596	self.clockWd = None # used in TOF
1597	self.numbanks = 1
1598	self.instdict = {} # place items here that will be transferred to the instrument parameters
1599
1600	######################################################################
1601	class ImportImage(ImportBaseclass):
1602	'''Defines a base class for the reading of images
1603
1604	Images are read in only these places:
1605
1606	* Initial reading is typically done from a menu item
1607	with a call to :meth:`GSASII.GSASII.OnImportImage`
1608	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`. That calls
1609	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1610	:meth:`Reader`. This returns a list of reader objects for each read image.
1611
1612	* Images are read alternatively in :func:`GSASIIIO.ReadImages`, which puts image info
1613	directly into the data tree.
1614
1615	* Images are reloaded with :func:`GSASIIIO.GetImageData`.
1616
1617	.. _Image_import_routines:
1618
1619	When reading an image, the ``Reader()`` routine in the ImportImage class
1620	should set:
1621
1622	* :attr:`Comments`: a list of strings (str),
1623	* :attr:`Npix`: the number of pixels in the image (int),
1624	* :attr:`Image`: the actual image as a numpy array (np.array)
1625	* :attr:`Data`: a dict defining image parameters (dict). Within this dict the following
1626	data items are needed:
1627
1628	* 'pixelSize': size of each pixel in microns (such as ``[200,200]``.
1629	* 'wavelength': wavelength in Angstoms.
1630	* 'distance': distance of detector from sample in cm.
1631	* 'center': uncalibrated center of beam on detector (such as ``[204.8,204.8]``.
1632	* 'size': size of image (such as ``[2048,2048]``).
1633	* 'ImageTag': image number or other keyword used to retrieve image from
1634	a multi-image data file (defaults to ``1`` if not specified).
1635	* 'sumfile': holds sum image file name if a sum was produced from a multi image file
1636
1637	optional data items:
1638
1639	* :attr:`repeat`: set to True if there are additional images to
1640	read in the file, False otherwise
1641	* :attr:`repeatcount`: set to the number of the image.
1642
1643	Note that the above is initialized with :meth:`InitParameters`.
1644	(Also see :ref:`Writing a Import Routine<Import_Routines>`
1645	for an explanation on how to use import classes in general.)
1646	'''
1647	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1648	strictExtension=False,):
1649	ImportBaseclass.__init__(self,formatName,longFormatName,
1650	extensionlist,strictExtension)
1651	self.InitParameters()
1652
1653	def ReInitialize(self):
1654	'Reinitialize the Reader to initial settings -- not used at present'
1655	ImportBaseclass.ReInitialize(self)
1656	self.InitParameters()
1657
1658	def InitParameters(self):
1659	'initialize the instrument parameters structure'
1660	self.Comments = ['No comments']
1661	self.Data = {}
1662	self.Npix = 0
1663	self.Image = None
1664	self.repeat = False
1665	self.repeatcount = 1
1666	self.sumfile = ''
1667
1668	def LoadImage(self,ParentFrame,imagefile,imagetag=None):
1669	'''Optionally, call this after reading in an image to load it into the tree.
1670	This saves time by preventing a reread of the same information.
1671	'''
1672	if ParentFrame:
1673	ParentFrame.ImageZ = self.Image # store the image for plotting
1674	ParentFrame.oldImagefile = imagefile # save the name of the last image file read
1675	ParentFrame.oldImageTag = imagetag # save the tag of the last image file read
1676
1677	######################################################################
1678	class ExportBaseclass(object):
1679	'''Defines a base class for the exporting of GSAS-II results.
1680
1681	This class is subclassed in the various exports/G2export_*.py files. Those files
1682	are imported in :meth:`GSASII.GSASII._init_Exports` which defines the
1683	appropriate menu items for each one and the .Exporter method is called
1684	directly from the menu item.
1685
1686	Routines may also define a .Writer method, which is used to write a single
1687	file without invoking any GUI objects.
1688	'''
1689	def __init__(self,G2frame,formatName,extension,longFormatName=None,):
1690	self.G2frame = G2frame
1691	self.formatName = formatName # short string naming file type
1692	self.extension = extension
1693	if longFormatName: # longer string naming file type
1694	self.longFormatName = longFormatName
1695	else:
1696	self.longFormatName = formatName
1697	self.OverallParms = {}
1698	self.Phases = {}
1699	self.Histograms = {}
1700	self.powderDict = {}
1701	self.xtalDict = {}
1702	self.parmDict = {}
1703	self.sigDict = {}
1704	# updated in InitExport:
1705	self.currentExportType = None # type of export that has been requested
1706	# updated in ExportSelect (when used):
1707	self.phasenam = None # a list of selected phases
1708	self.histnam = None # a list of selected histograms
1709	self.filename = None # name of file to be written (single export) or template (multiple files)
1710	self.dirname = '' # name of directory where file(s) will be written
1711	self.fullpath = '' # name of file being written -- full path
1712
1713	# items that should be defined in a subclass of this class
1714	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1715	# The following types are defined: 'project', "phase", "powder", "single"
1716	self.multiple = False # set as True if the class can export multiple phases or histograms
1717	# self.multiple is ignored for "project" exports
1718
1719	def InitExport(self,event):
1720	'''Determines the type of menu that called the Exporter and
1721	misc initialization.
1722	'''
1723	self.filename = None # name of file to be written (single export)
1724	self.dirname = '' # name of file to be written (multiple export)
1725	if event:
1726	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1727
1728	def MakePWDRfilename(self,hist):
1729	'''Make a filename root (no extension) from a PWDR histogram name
1730
1731	:param str hist: the histogram name in data tree (starts with "PWDR ")
1732	'''
1733	file0 = ''
1734	file1 = hist[5:]
1735	# replace repeated blanks
1736	while file1 != file0:
1737	file0 = file1
1738	file1 = file0.replace(' ',' ').strip()
1739	file0 = file1.replace('Azm= ','A')
1740	# if angle has unneeded decimal places on aziumuth, remove them
1741	if file0[-3:] == '.00': file0 = file0[:-3]
1742	file0 = file0.replace('.','_')
1743	file0 = file0.replace(' ','_')
1744	return file0
1745
1746	def ExportSelect(self,AskFile='ask'):
1747	'''Selects histograms or phases when needed. Sets a default file name when
1748	requested in self.filename; always sets a default directory in self.dirname.
1749
1750	:param bool AskFile: Determines how this routine processes getting a
1751	location to store the current export(s).
1752
1753	* if AskFile is 'ask' (default option), get the name of the file to be written;
1754	self.filename and self.dirname are always set. In the case where
1755	multiple files must be generated, the export routine should do this
1756	based on self.filename as a template.
1757	* if AskFile is 'dir', get the name of the directory to be used;
1758	self.filename is not used, but self.dirname is always set. The export routine
1759	will always generate the file name.
1760	* if AskFile is 'single', get only the name of the directory to be used when
1761	multiple items will be written (as multiple files) are used
1762	or a complete file name is requested when a single file
1763	name is selected. self.dirname is always set and self.filename used
1764	only when a single file is selected.
1765	* if AskFile is 'default', creates a name of the file to be used from
1766	the name of the project (.gpx) file. If the project has not been saved,
1767	then the name of file is requested.
1768	self.filename and self.dirname are always set. In the case where
1769	multiple file names must be generated, the export routine should do this
1770	based on self.filename.
1771	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1772	file. If the project has not been saved, then a directory is requested.
1773	self.filename is not used.
1774
1775	:returns: True in case of an error
1776	'''
1777
1778	numselected = 1
1779	if self.currentExportType == 'phase':
1780	if len(self.Phases) == 0:
1781	self.G2frame.ErrorDialog(
1782	'Empty project',
1783	'Project does not contain any phases.')
1784	return True
1785	elif len(self.Phases) == 1:
1786	self.phasenam = self.Phases.keys()
1787	elif self.multiple:
1788	choices = sorted(self.Phases.keys())
1789	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1790	if phasenum is None: return True
1791	self.phasenam = [choices[i] for i in phasenum]
1792	if not self.phasenam: return True
1793	numselected = len(self.phasenam)
1794	else:
1795	choices = sorted(self.Phases.keys())
1796	phasenum = G2G.ItemSelector(choices,self.G2frame)
1797	if phasenum is None: return True
1798	self.phasenam = [choices[phasenum]]
1799	numselected = len(self.phasenam)
1800	elif self.currentExportType == 'single':
1801	if len(self.xtalDict) == 0:
1802	self.G2frame.ErrorDialog(
1803	'Empty project',
1804	'Project does not contain any single crystal data.')
1805	return True
1806	elif len(self.xtalDict) == 1:
1807	self.histnam = self.xtalDict.values()
1808	elif self.multiple:
1809	choices = sorted(self.xtalDict.values())
1810	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1811	if not hnum: return True
1812	self.histnam = [choices[i] for i in hnum]
1813	numselected = len(self.histnam)
1814	else:
1815	choices = sorted(self.xtalDict.values())
1816	hnum = G2G.ItemSelector(choices,self.G2frame)
1817	if hnum is None: return True
1818	self.histnam = [choices[hnum]]
1819	numselected = len(self.histnam)
1820	elif self.currentExportType == 'powder':
1821	if len(self.powderDict) == 0:
1822	self.G2frame.ErrorDialog(
1823	'Empty project',
1824	'Project does not contain any powder data.')
1825	return True
1826	elif len(self.powderDict) == 1:
1827	self.histnam = self.powderDict.values()
1828	elif self.multiple:
1829	choices = sorted(self.powderDict.values())
1830	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1831	if not hnum: return True
1832	self.histnam = [choices[i] for i in hnum]
1833	numselected = len(self.histnam)
1834	else:
1835	choices = sorted(self.powderDict.values())
1836	hnum = G2G.ItemSelector(choices,self.G2frame)
1837	if hnum is None: return True
1838	self.histnam = [choices[hnum]]
1839	numselected = len(self.histnam)
1840	elif self.currentExportType == 'image':
1841	if len(self.Histograms) == 0:
1842	self.G2frame.ErrorDialog(
1843	'Empty project',
1844	'Project does not contain any images.')
1845	return True
1846	elif len(self.Histograms) == 1:
1847	self.histnam = self.Histograms.keys()
1848	else:
1849	choices = sorted(self.Histograms.keys())
1850	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1851	if self.multiple:
1852	if not hnum: return True
1853	self.histnam = [choices[i] for i in hnum]
1854	else:
1855	if hnum is None: return True
1856	self.histnam = [choices[hnum]]
1857	numselected = len(self.histnam)
1858	if self.currentExportType == 'map':
1859	# search for phases with maps
1860	mapPhases = []
1861	choices = []
1862	for phasenam in sorted(self.Phases):
1863	phasedict = self.Phases[phasenam] # pointer to current phase info
1864	if len(phasedict['General']['Map'].get('rho',[])):
1865	mapPhases.append(phasenam)
1866	if phasedict['General']['Map'].get('Flip'):
1867	choices.append('Charge flip map: '+str(phasenam))
1868	elif phasedict['General']['Map'].get('MapType'):
1869	choices.append(
1870	str(phasedict['General']['Map'].get('MapType'))
1871	+ ' map: ' + str(phasenam))
1872	else:
1873	choices.append('unknown map: '+str(phasenam))
1874	# select a map if needed
1875	if len(mapPhases) == 0:
1876	self.G2frame.ErrorDialog(
1877	'Empty project',
1878	'Project does not contain any maps.')
1879	return True
1880	elif len(mapPhases) == 1:
1881	self.phasenam = mapPhases
1882	else:
1883	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1884	if self.multiple:
1885	if not phasenum: return True
1886	self.phasenam = [mapPhases[i] for i in phasenum]
1887	else:
1888	if phasenum is None: return True
1889	self.phasenam = [mapPhases[phasenum]]
1890	numselected = len(self.phasenam)
1891
1892	# items selected, now set self.dirname and usually self.filename
1893	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
1894	AskFile == 'default' and not self.G2frame.GSASprojectfile
1895	):
1896	filename = self.askSaveFile()
1897	if not filename: return True
1898	self.dirname,self.filename = os.path.split(filename)
1899	elif AskFile == 'dir' or AskFile == 'single' or (
1900	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
1901	):
1902	self.dirname = self.askSaveDirectory()
1903	if not self.dirname: return True
1904	elif AskFile == 'default-dir' or AskFile == 'default':
1905	self.dirname,self.filename = os.path.split(
1906	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
1907	)
1908	else:
1909	raise Exception('This should not happen!')
1910
1911	def loadParmDict(self):
1912	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
1913	refined values to those from the last cycle and set the uncertainties for the
1914	refined parameters in another dict (self.sigDict).
1915
1916	Expands the parm & sig dicts to include values derived from constraints.
1917	'''
1918	self.parmDict = {}
1919	self.sigDict = {}
1920	rigidbodyDict = {}
1921	covDict = {}
1922	consDict = {}
1923	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1924	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
1925	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
1926	while item:
1927	name = self.G2frame.PatternTree.GetItemText(item)
1928	if name == 'Rigid bodies':
1929	rigidbodyDict = self.G2frame.PatternTree.GetItemPyData(item)
1930	elif name == 'Covariance':
1931	covDict = self.G2frame.PatternTree.GetItemPyData(item)
1932	elif name == 'Constraints':
1933	consDict = self.G2frame.PatternTree.GetItemPyData(item)
1934	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
1935	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1936	self.parmDict.update(rbDict)
1937	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1938	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,maxSSwave = G2stIO.GetPhaseData(
1939	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
1940	self.parmDict.update(phaseDict)
1941	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
1942	Phases,Histograms,Print=False,resetRefList=False)
1943	self.parmDict.update(hapDict)
1944	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
1945	self.parmDict.update(histDict)
1946	self.parmDict.update(zip(
1947	covDict.get('varyList',[]),
1948	covDict.get('variables',[])))
1949	self.sigDict = dict(zip(
1950	covDict.get('varyList',[]),
1951	covDict.get('sig',[])))
1952	# expand to include constraints: first compile a list of constraints
1953	constList = []
1954	for item in consDict:
1955	if item.startswith('_'): continue
1956	constList += consDict[item]
1957	# now process the constraints
1958	G2mv.InitVars()
1959	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
1960	varyList = covDict.get('varyListStart')
1961	if varyList is None and len(constDict) == 0:
1962	# no constraints can use varyList
1963	varyList = covDict.get('varyList')
1964	elif varyList is None:
1965	# old GPX file from before pre-constraint varyList is saved
1966	print ' * Old refinement: Please use Calculate/Refine to redo *'
1967	raise Exception(' * Export aborted *')
1968	else:
1969	varyList = list(varyList)
1970	try:
1971	groups,parmlist = G2mv.GroupConstraints(constDict)
1972	G2mv.GenerateConstraints(groups,parmlist,varyList,constDict,fixedList,self.parmDict)
1973	except:
1974	# this really should not happen
1975	print ' * ERROR - constraints are internally inconsistent *'
1976	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
1977	print 'Errors',errmsg
1978	if warnmsg: print 'Warnings',warnmsg
1979	raise Exception(' * CIF creation aborted *')
1980	# add the constrained values to the parameter dictionary
1981	G2mv.Dict2Map(self.parmDict,varyList)
1982	# and add their uncertainties into the esd dictionary (sigDict)
1983	if covDict.get('covMatrix') is not None:
1984	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
1985
1986	def loadTree(self):
1987	'''Load the contents of the data tree into a set of dicts
1988	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
1989	& self.xtalDict)
1990
1991	* The childrenless data tree items are overall parameters/controls for the
1992	entire project and are placed in self.OverallParms
1993	* Phase items are placed in self.Phases
1994	* Data items are placed in self.Histogram. The key for these data items
1995	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
1996	'''
1997	self.OverallParms = {}
1998	self.powderDict = {}
1999	self.xtalDict = {}
2000	self.Phases = {}
2001	self.Histograms = {}
2002	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2003	histType = None
2004	if self.currentExportType == 'phase':
2005	# if exporting phases load them here
2006	sub = G2gd.GetPatternTreeItemId(self.G2frame,self.G2frame.root,'Phases')
2007	if not sub:
2008	print 'no phases found'
2009	return True
2010	item, cookie = self.G2frame.PatternTree.GetFirstChild(sub)
2011	while item:
2012	phaseName = self.G2frame.PatternTree.GetItemText(item)
2013	self.Phases[phaseName] = self.G2frame.PatternTree.GetItemPyData(item)
2014	item, cookie = self.G2frame.PatternTree.GetNextChild(sub, cookie)
2015	return
2016	elif self.currentExportType == 'single':
2017	histType = 'HKLF'
2018	elif self.currentExportType == 'powder':
2019	histType = 'PWDR'
2020	elif self.currentExportType == 'image':
2021	histType = 'IMG'
2022
2023	if histType: # Loading just one kind of tree entry
2024	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2025	while item:
2026	name = self.G2frame.PatternTree.GetItemText(item)
2027	if name.startswith(histType):
2028	if self.Histograms.get(name): # there is already an item with this name
2029	print('Histogram name '+str(name)+' is repeated. Renaming')
2030	if name[-1] == '9':
2031	name = name[:-1] + '10'
2032	elif name[-1] in '012345678':
2033	name = name[:-1] + str(int(name[-1])+1)
2034	else:
2035	name += '-1'
2036	self.Histograms[name] = {}
2037	# the main info goes into Data, but the 0th
2038	# element contains refinement results, carry
2039	# that over too now.
2040	self.Histograms[name]['Data'] = self.G2frame.PatternTree.GetItemPyData(item)[1]
2041	self.Histograms[name][0] = self.G2frame.PatternTree.GetItemPyData(item)[0]
2042	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2043	while item2:
2044	child = self.G2frame.PatternTree.GetItemText(item2)
2045	self.Histograms[name][child] = self.G2frame.PatternTree.GetItemPyData(item2)
2046	item2, cookie2 = self.G2frame.PatternTree.GetNextChild(item, cookie2)
2047	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2048	# index powder and single crystal histograms by number
2049	for hist in self.Histograms:
2050	if hist.startswith("PWDR"):
2051	d = self.powderDict
2052	elif hist.startswith("HKLF"):
2053	d = self.xtalDict
2054	else:
2055	return
2056	i = self.Histograms[hist].get('hId')
2057	if i is None and not d.keys():
2058	i = 0
2059	elif i is None or i in d.keys():
2060	i = max(d.keys())+1
2061	d[i] = hist
2062	return
2063	# else standard load: using all interlinked phases and histograms
2064	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2065	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2066	while item:
2067	name = self.G2frame.PatternTree.GetItemText(item)
2068	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2069	if not item2:
2070	self.OverallParms[name] = self.G2frame.PatternTree.GetItemPyData(item)
2071	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2072	# index powder and single crystal histograms
2073	for hist in self.Histograms:
2074	i = self.Histograms[hist]['hId']
2075	if hist.startswith("PWDR"):
2076	self.powderDict[i] = hist
2077	elif hist.startswith("HKLF"):
2078	self.xtalDict[i] = hist
2079
2080	def dumpTree(self,mode='type'):
2081	'''Print out information on the data tree dicts loaded in loadTree
2082	'''
2083	print '\nOverall'
2084	if mode == 'type':
2085	def Show(arg): return type(arg)
2086	else:
2087	def Show(arg): return arg
2088	for key in self.OverallParms:
2089	print ' ',key,Show(self.OverallParms[key])
2090	print 'Phases'
2091	for key1 in self.Phases:
2092	print ' ',key1,Show(self.Phases[key1])
2093	print 'Histogram'
2094	for key1 in self.Histograms:
2095	print ' ',key1,Show(self.Histograms[key1])
2096	for key2 in self.Histograms[key1]:
2097	print ' ',key2,Show(self.Histograms[key1][key2])
2098
2099	def defaultSaveFile(self):
2100	return os.path.abspath(
2101	os.path.splitext(self.G2frame.GSASprojectfile
2102	)[0]+self.extension)
2103
2104	def askSaveFile(self):
2105	'''Ask the user to supply a file name
2106
2107	:returns: a file name (str) or None if Cancel is pressed
2108	'''
2109
2110	pth = G2G.GetExportPath(self.G2frame)
2111	defnam = os.path.splitext(
2112	os.path.split(self.G2frame.GSASprojectfile)[1]
2113	)[0]+self.extension
2114	dlg = wx.FileDialog(
2115	self.G2frame, 'Input name for file to write', pth, defnam,
2116	self.longFormatName+' ('+self.extension+')\|'+self.extension,
2117	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
2118	dlg.CenterOnParent()
2119	try:
2120	if dlg.ShowModal() == wx.ID_OK:
2121	filename = dlg.GetPath()
2122	self.G2frame.LastExportDir = os.path.split(filename)[0]
2123	filename = os.path.splitext(filename)[0]+self.extension # make sure extension is correct
2124	else:
2125	filename = None
2126	finally:
2127	dlg.Destroy()
2128	return filename
2129
2130	def askSaveDirectory(self):
2131	'''Ask the user to supply a directory name. Path name is used as the
2132	starting point for the next export path search.
2133
2134	:returns: a directory name (str) or None if Cancel is pressed
2135	'''
2136	pth = G2G.GetExportPath(self.G2frame)
2137	dlg = wx.DirDialog(
2138	self.G2frame, 'Input directory where file(s) will be written', pth,
2139	wx.DD_DEFAULT_STYLE)
2140	dlg.CenterOnParent()
2141	try:
2142	if dlg.ShowModal() == wx.ID_OK:
2143	filename = dlg.GetPath()
2144	self.G2frame.LastExportDir = filename
2145	else:
2146	filename = None
2147	finally:
2148	dlg.Destroy()
2149	return filename
2150
2151	# Tools for file writing.
2152	def OpenFile(self,fil=None,mode='w'):
2153	'''Open the output file
2154
2155	:param str fil: The name of the file to open. If None (default)
2156	the name defaults to self.dirname + self.filename.
2157	If an extension is supplied, it is not overridded,
2158	but if not, the default extension is used.
2159	:returns: the file object opened by the routine which is also
2160	saved as self.fp
2161	'''
2162	if not fil:
2163	if not os.path.splitext(self.filename)[1]:
2164	self.filename += self.extension
2165	fil = os.path.join(self.dirname,self.filename)
2166	self.fullpath = os.path.abspath(fil)
2167	self.fp = open(self.fullpath,mode)
2168	return self.fp
2169
2170	def Write(self,line):
2171	'''write a line of output, attaching a line-end character
2172
2173	:param str line: the text to be written.
2174	'''
2175	self.fp.write(line+'\n')
2176	def CloseFile(self,fp=None):
2177	'''Close a file opened in OpenFile
2178
2179	:param file fp: the file object to be closed. If None (default)
2180	file object self.fp is closed.
2181	'''
2182	if fp is None:
2183	fp = self.fp
2184	self.fp = None
2185	fp.close()
2186	# Tools to pull information out of the data arrays
2187	def GetCell(self,phasenam):
2188	"""Gets the unit cell parameters and their s.u.'s for a selected phase
2189
2190	:param str phasenam: the name for the selected phase
2191	:returns: `cellList,cellSig` where each is a 7 element list corresponding
2192	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
2193	cell values and `cellSig` has their uncertainties.
2194	"""
2195	phasedict = self.Phases[phasenam] # pointer to current phase info
2196	try:
2197	pfx = str(phasedict['pId'])+'::'
2198	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
2199	cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A,
2200	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
2201	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
2202	return cellList,cellSig
2203	except KeyError:
2204	cell = phasedict['General']['Cell'][1:]
2205	return cell,7*[0]
2206
2207	def GetAtoms(self,phasenam):
2208	"""Gets the atoms associated with a phase. Can be used with standard
2209	or macromolecular phases
2210
2211	:param str phasenam: the name for the selected phase
2212	:returns: a list of items for eac atom where each item is a list containing:
2213	label, typ, mult, xyz, and td, where
2214
2215	* label and typ are the atom label and the scattering factor type (str)
2216	* mult is the site multiplicity (int)
2217	* xyz is contains a list with four pairs of numbers:
2218	x, y, z and fractional occupancy and
2219	their standard uncertainty (or a negative value)
2220	* td is contains a list with either one or six pairs of numbers:
2221	if one number it is U\ :sub:`iso` and with six numbers it is
2222	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
2223	paired with their standard uncertainty (or a negative value)
2224	"""
2225	phasedict = self.Phases[phasenam] # pointer to current phase info
2226	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
2227	cfrac = cx+3
2228	fpfx = str(phasedict['pId'])+'::Afrac:'
2229	atomslist = []
2230	for i,at in enumerate(phasedict['Atoms']):
2231	if phasedict['General']['Type'] == 'macromolecular':
2232	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
2233	else:
2234	label = at[ct-1]
2235	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
2236	fsig = self.sigDict.get(fpfx+str(i),-0.009)
2237	mult = at[cs+1]
2238	typ = at[ct]
2239	xyz = []
2240	for j,v in enumerate(('x','y','z')):
2241	val = at[cx+j]
2242	pfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
2243	sig = self.sigDict.get(pfx,-0.000009)
2244	xyz.append((val,sig))
2245	xyz.append((fval,fsig))
2246	td = []
2247	if at[cia] == 'I':
2248	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
2249	val = self.parmDict.get(pfx,at[cia+1])
2250	sig = self.sigDict.get(pfx,-0.0009)
2251	td.append((val,sig))
2252	else:
2253	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
2254	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
2255	val = self.parmDict.get(pfx,at[cia+2+i])
2256	sig = self.sigDict.get(pfx,-0.0009)
2257	td.append((val,sig))
2258	atomslist.append((label,typ,mult,xyz,td))
2259	return atomslist
2260	######################################################################
2261	def ExportPowderList(G2frame):
2262	'''Returns a list of extensions supported by :func:`GSASIIIO:ExportPowder`
2263
2264	:param wx.Frame G2frame: the GSAS-II main data tree window
2265	'''
2266	extList = []
2267	for obj in G2frame.exporterlist:
2268	if 'powder' in obj.exporttype:
2269	try:
2270	obj.Writer
2271	extList.append(obj.extension)
2272	except AttributeError:
2273	pass
2274	return extList
2275
2276	def ExportPowder(G2frame,TreeName,fileroot,extension):
2277	'''Writes a single powder histogram using the Export routines
2278
2279	:param wx.Frame G2frame: the GSAS-II main data tree window
2280	:param str TreeName: the name of the histogram (PWDR ...) in the data tree
2281	:param str fileroot: name for file to be written, extension ignored
2282	:param str extension: extension for file to be written (start with '.'). Must
2283	match a powder export routine that has a Writer object.
2284	'''
2285	filename = os.path.abspath(os.path.splitext(fileroot)[0]+extension)
2286	for obj in G2frame.exporterlist:
2287	if obj.extension == extension and 'powder' in obj.exporttype:
2288	obj.currentExportType = 'powder'
2289	obj.InitExport(None)
2290	obj.loadTree() # load all histograms in tree into dicts
2291	if TreeName not in obj.Histograms:
2292	raise Exception('Histogram not found: '+str(TreeName))
2293	try:
2294	obj.Writer
2295	except AttributeError:
2296	continue
2297	try:
2298	obj.Writer(TreeName,filename)
2299	return
2300	except Exception,err:
2301	print('Export Routine for '+extension+' failed.')
2302	print err
2303	else:
2304	print('No Export routine supports extension '+extension)
2305
2306	def ReadDIFFaX(DIFFaXfile):
2307	print 'read ',DIFFaXfile
2308	Layer = {'Laue':'-1','Cell':[False,1.,1.,1.,90.,90.,90,1.],'Width':[[10.,10.],[False,False]],
2309	'Layers':[],'Stacking':[],'Transitions':[],'Toler':0.01,'AtInfo':{}}
2310	df = open(DIFFaXfile,'r')
2311	lines = df.readlines()
2312	df.close()
2313	struct = False
2314	Struct = []
2315	stack = False
2316	Stack = []
2317	trans = False
2318	Trans = []
2319	instr = False
2320	for diff in lines:
2321	diff = diff[:-1].lower()
2322	if '!' in diff:
2323	continue
2324	while '}' in diff: #strip comments
2325	iB = diff.index('{')
2326	iF = diff.index('}')+1
2327	if iB:
2328	diff = diff[:iB]
2329	else:
2330	diff = diff[iF:]
2331	if not diff:
2332	continue
2333	if diff.strip() == 'instrumental':
2334	instr = True
2335	continue
2336	if diff.strip() == 'structural':
2337	instr = False
2338	struct = True
2339	continue
2340	elif diff.strip() == 'stacking':
2341	struct = False
2342	stack = True
2343	continue
2344	elif diff.strip() == 'transitions':
2345	stack = False
2346	trans = True
2347	continue
2348	diff = diff.strip()
2349	if struct:
2350	if diff:
2351	Struct.append(diff)
2352	elif stack:
2353	if diff:
2354	Stack.append(diff)
2355	elif trans:
2356	if diff:
2357	Trans.append(diff)
2358
2359	#STRUCTURE records
2360	laueRec = Struct[1].split()
2361	Layer['Laue'] = laueRec[0]
2362	if Layer['Laue'] == 'unknown' and len(laueRec) > 1:
2363	Layer['Toler'] = float(laueRec[1]) #tolerance for 'unknown'?
2364	if Layer['Laue'] == '2/m(1)': Layer['Laue'] = '2/m(c)'
2365	if Layer['Laue'] == '2/m(2)': Layer['Laue'] = '2/m(ab)'
2366	cell = Struct[0].split()
2367	Layer['Cell'] = [False,float(cell[0]),float(cell[1]),float(cell[2]),90.,90.,float(cell[3]),1.0]
2368	nLayers = int(Struct[2])
2369	N = 3
2370	if 'layer' not in Struct[3]:
2371	N = 4
2372	if Struct[3] != 'infinite':
2373	width = Struct[3].split()
2374	Layer['Width'][0] = [float(width[0]),float(width[1])]
2375	for nL in range(nLayers):
2376	if '=' in Struct[N]:
2377	name = Struct[N].split('=')
2378	sameas = int(name[1])-1
2379	Layer['Layers'].append({'Name':name[0],'SameAs':Layer['Layers'][sameas]['Name'],'Symm':'None','Atoms':[]})
2380	N += 1
2381	continue
2382	Symm = 'None'
2383	if 'centro' in Struct[N+1]: Symm = '-1'
2384	Layer['Layers'].append({'Name':Struct[N],'SameAs':'','Symm':Symm,'Atoms':[]})
2385	N += 2
2386	iatm = 0
2387	while 'layer' not in Struct[N]:
2388	atom = Struct[N][4:].split()
2389	atomType = G2el.FixValence(Struct[N][:4].replace(' ','').strip().capitalize())
2390	if atomType not in Layer['AtInfo']:
2391	Layer['AtInfo'][atomType] = G2el.GetAtomInfo(atomType)
2392	atomName = '%s(%s)'%(atomType,atom[0])
2393	newVals = []
2394	for val in atom[1:6]:
2395	if '/' in val:
2396	newVals.append(eval(val+'.'))
2397	else:
2398	newVals.append(float(val))
2399	atomRec = [atomName,atomType,newVals[0],newVals[1],newVals[2],newVals[4],newVals[3]/78.9568]
2400	Layer['Layers'][-1]['Atoms'].append(atomRec)
2401	N += 1
2402	if N > len(Struct)-1:
2403	break
2404	#TRANSITIONS records
2405	transArray = []
2406	N = 0
2407	for i in range(nLayers):
2408	transArray.append([])
2409	for j in range(nLayers):
2410	vals = Trans[N].split()
2411	newVals = []
2412	for val in vals[:4]:
2413	if '/' in val:
2414	newVals.append(eval(val+'.'))
2415	else:
2416	newVals.append(float(val))
2417	transArray[-1].append(newVals+['',False])
2418	N += 1
2419	Layer['Transitions'] = transArray
2420	#STACKING records
2421	Layer['Stacking'] = [Stack[0],'']
2422	if Stack[0] == 'recursive':
2423	Layer['Stacking'][1] = Stack[1]
2424	elif Stack[0] == 'explicit':
2425	if Stack[1] == 'random':
2426	Layer['Stacking'][1] = Stack[1]
2427	else:
2428	Layer['Stacking'][1] = 'list'
2429	Layer['Stacking'].append('')
2430	for stack in Stack[2:]:
2431	Layer['Stacking'][2] += ' '+stack
2432	return Layer
2433
2434	def ReadCIF(URLorFile):
2435	'''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
2436	(from James Hester).
2437	The open routine gets confused with DOS names that begin with a letter and colon
2438	"C:\dir\" so this routine will try to open the passed name as a file and if that
2439	fails, try it as a URL
2440
2441	:param str URLorFile: string containing a URL or a file name. Code will try first
2442	to open it as a file and then as a URL.
2443
2444	:returns: a PyCifRW CIF object.
2445	'''
2446	import CifFile as cif # PyCifRW from James Hester
2447
2448	# alternate approach:
2449	#import urllib
2450	#ciffile = 'file:'+urllib.pathname2url(filename)
2451
2452	try:
2453	fp = open(URLorFile,'r')
2454	cf = cif.ReadCif(fp)
2455	fp.close()
2456	return cf
2457	except IOError:
2458	return cif.ReadCif(URLorFile)
2459
2460	if __name__ == '__main__':
2461	import GSASII
2462	application = GSASII.GSASIImain(0)
2463	G2frame = application.main
2464	#app = wx.PySimpleApp()
2465	#G2frame = wx.Frame(None) # create a frame
2466	#frm.Show(True)
2467	#filename = '/tmp/notzip.zip'
2468	#filename = '/tmp/all.zip'
2469	#filename = '/tmp/11bmb_7652.zip'
2470
2471	#selection=None, confirmoverwrite=True, parent=None
2472	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2473	#print ExtractFileFromZip(filename,multipleselect=True)
2474	# #confirmread=False, confirmoverwrite=False)
2475
2476	# choicelist=[ ('a','b','c'),
2477	# ('test1','test2'),('no choice',)]
2478	# titles = [ 'a, b or c', 'tests', 'No option here']
2479	# dlg = MultipleChoicesDialog(
2480	# choicelist,titles,
2481	# parent=frm)
2482	# if dlg.ShowModal() == wx.ID_OK:
2483	# print 'Got OK'
2484	imagefile = '/tmp/NDC5_00237_3.ge3'
2485	Comments, Data, Npix, Image = GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None)
2486
2487	print("\n\nResults loaded to Comments, Data, Npix and Image\n\n")
2488
2489	GSASIIpath.IPyBreak_base()

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