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source: trunk/GSASIIIO.py @ 2341

Last change on this file since 2341 was 2341, checked in by toby, 7 years ago
improve powder imports: suppress printing of binary data; improve validation of old GSAS binary files
Property svn:eol-style set to `native` Property svn:keywords set to `Date Author Revision URL Id`
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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2016-06-24 02:25:06 +0000 (Fri, 24 Jun 2016) $
4	# $Author: toby $
5	# $Revision: 2341 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 2341 2016-06-24 02:25:06Z toby $
8	########### SVN repository information ###################
9	'''
10	GSASIIIO: Misc I/O routines
11	=============================
12
13	Module with miscellaneous routines for input and output. Many
14	are GUI routines to interact with user.
15
16	Includes support for image reading.
17
18	Also includes base classes for data import routines.
19
20	'''
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: 2341 $")
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	if all([ord(c) < 128 and ord(c) != 0 for c in str(l)]): # show only if ASCII
1431	self.errors += ' '+str(l)
1432	else:
1433	self.errors += ' (binary)'
1434	self.errors += '\n Note: a CIF should only have blank lines or comments before'
1435	self.errors += '\n a data_ statement begins a block.'
1436	return False
1437
1438	######################################################################
1439	class ImportPhase(ImportBaseclass):
1440	'''Defines a base class for the reading of files with coordinates
1441
1442	Objects constructed that subclass this (in import/G2phase_*.py etc.) will be used
1443	in :meth:`GSASII.GSASII.OnImportPhase`.
1444	See :ref:`Writing a Import Routine<Import_Routines>`
1445	for an explanation on how to use this class.
1446
1447	'''
1448	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1449	strictExtension=False,):
1450	# call parent __init__
1451	ImportBaseclass.__init__(self,formatName,longFormatName,
1452	extensionlist,strictExtension)
1453	self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
1454	self.Constraints = None
1455
1456	def PhaseSelector(self, ChoiceList, ParentFrame=None,
1457	title='Select a phase', size=None,header='Phase Selector'):
1458	''' Provide a wx dialog to select a phase if the file contains more
1459	than one phase
1460	'''
1461	return self.BlockSelector(ChoiceList,ParentFrame,title,
1462	size,header)
1463
1464	######################################################################
1465	class ImportStructFactor(ImportBaseclass):
1466	'''Defines a base class for the reading of files with tables
1467	of structure factors.
1468
1469	Structure factors are read with a call to :meth:`GSASII.GSASII.OnImportSfact`
1470	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`, which calls
1471	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1472	:meth:`Reader`.
1473
1474	See :ref:`Writing a Import Routine<Import_Routines>`
1475	for an explanation on how to use import classes in general. The specifics
1476	for reading a structure factor histogram require that
1477	the ``Reader()`` routine in the import
1478	class need to do only a few things: It
1479	should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
1480	and set :attr:`Parameters` with the instrument parameters
1481	(initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
1482	'''
1483	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1484	strictExtension=False,):
1485	ImportBaseclass.__init__(self,formatName,longFormatName,
1486	extensionlist,strictExtension)
1487
1488	# define contents of Structure Factor entry
1489	self.Parameters = []
1490	'self.Parameters is a list with two dicts for data parameter settings'
1491	self.InitParameters()
1492	self.RefDict = {'RefList':[],'FF':{},'Super':0}
1493	self.Banks = [] #for multi bank data (usually TOF)
1494	'''self.RefDict is a dict containing the reflection information, as read from the file.
1495	Item 'RefList' contains the reflection information. See the
1496	:ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
1497	for the contents of each row. Dict element 'FF'
1498	contains the form factor values for each element type; if this entry
1499	is left as initialized (an empty list) it will be initialized as needed later.
1500	'''
1501	def ReInitialize(self):
1502	'Reinitialize the Reader to initial settings'
1503	ImportBaseclass.ReInitialize(self)
1504	self.InitParameters()
1505	self.Banks = [] #for multi bank data (usually TOF)
1506	self.RefDict = {'RefList':[],'FF':{},'Super':0}
1507
1508	def InitParameters(self):
1509	'initialize the instrument parameters structure'
1510	Lambda = 0.70926
1511	HistType = 'SXC'
1512	self.Parameters = [{'Type':[HistType,HistType], # create the structure
1513	'Lam':[Lambda,Lambda]
1514	}, {}]
1515	'Parameters is a list with two dicts for data parameter settings'
1516
1517	def UpdateParameters(self,Type=None,Wave=None):
1518	'Revise the instrument parameters'
1519	if Type is not None:
1520	self.Parameters[0]['Type'] = [Type,Type]
1521	if Wave is not None:
1522	self.Parameters[0]['Lam'] = [Wave,Wave]
1523
1524	######################################################################
1525	class ImportPowderData(ImportBaseclass):
1526	'''Defines a base class for the reading of files with powder data.
1527
1528	Objects constructed that subclass this (in import/G2pwd_*.py etc.) will be used
1529	in :meth:`GSASII.GSASII.OnImportPowder`.
1530	See :ref:`Writing a Import Routine<Import_Routines>`
1531	for an explanation on how to use this class.
1532	'''
1533	def __init__(self,formatName,longFormatName=None,
1534	extensionlist=[],strictExtension=False,):
1535	ImportBaseclass.__init__(self,formatName,longFormatName,
1536	extensionlist,strictExtension)
1537	self.clockWd = None # used in TOF
1538	self.ReInitialize()
1539
1540	def ReInitialize(self):
1541	'Reinitialize the Reader to initial settings'
1542	ImportBaseclass.ReInitialize(self)
1543	self.powderentry = ['',None,None] # (filename,Pos,Bank)
1544	self.powderdata = [] # Powder dataset
1545	'''A powder data set is a list with items [x,y,w,yc,yb,yd]:
1546	np.array(x), # x-axis values
1547	np.array(y), # powder pattern intensities
1548	np.array(w), # 1/sig(intensity)^2 values (weights)
1549	np.array(yc), # calc. intensities (zero)
1550	np.array(yb), # calc. background (zero)
1551	np.array(yd), # obs-calc profiles
1552	'''
1553	self.comments = []
1554	self.idstring = ''
1555	self.Sample = G2pdG.SetDefaultSample() # default sample parameters
1556	self.Controls = {} # items to be placed in top-level Controls
1557	self.GSAS = None # used in TOF
1558	self.repeat_instparm = True # Should a parm file be
1559	# used for multiple histograms?
1560	self.instparm = None # name hint from file of instparm to use
1561	self.instfile = '' # full path name to instrument parameter file
1562	self.instbank = '' # inst parm bank number
1563	self.instmsg = '' # a label that gets printed to show
1564	# where instrument parameters are from
1565	self.numbanks = 1
1566	self.instdict = {} # place items here that will be transferred to the instrument parameters
1567	self.pwdparms = {} # place parameters that are transferred directly to the tree
1568	# here (typically from an existing GPX file)
1569	######################################################################
1570	class ImportSmallAngleData(ImportBaseclass):
1571	'''Defines a base class for the reading of files with small angle data.
1572	See :ref:`Writing a Import Routine<Import_Routines>`
1573	for an explanation on how to use this class.
1574	'''
1575	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1576	strictExtension=False,):
1577
1578	ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
1579	strictExtension)
1580	self.ReInitialize()
1581
1582	def ReInitialize(self):
1583	'Reinitialize the Reader to initial settings'
1584	ImportBaseclass.ReInitialize(self)
1585	self.smallangleentry = ['',None,None] # (filename,Pos,Bank)
1586	self.smallangledata = [] # SASD dataset
1587	'''A small angle data set is a list with items [x,y,w,yc,yd]:
1588	np.array(x), # x-axis values
1589	np.array(y), # powder pattern intensities
1590	np.array(w), # 1/sig(intensity)^2 values (weights)
1591	np.array(yc), # calc. intensities (zero)
1592	np.array(yd), # obs-calc profiles
1593	np.array(yb), # preset bkg
1594	'''
1595	self.comments = []
1596	self.idstring = ''
1597	self.Sample = G2pdG.SetDefaultSample()
1598	self.GSAS = None # used in TOF
1599	self.clockWd = None # used in TOF
1600	self.numbanks = 1
1601	self.instdict = {} # place items here that will be transferred to the instrument parameters
1602
1603	######################################################################
1604	class ImportImage(ImportBaseclass):
1605	'''Defines a base class for the reading of images
1606
1607	Images are read in only these places:
1608
1609	* Initial reading is typically done from a menu item
1610	with a call to :meth:`GSASII.GSASII.OnImportImage`
1611	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`. That calls
1612	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1613	:meth:`Reader`. This returns a list of reader objects for each read image.
1614
1615	* Images are read alternatively in :func:`GSASIIIO.ReadImages`, which puts image info
1616	directly into the data tree.
1617
1618	* Images are reloaded with :func:`GSASIIIO.GetImageData`.
1619
1620	.. _Image_import_routines:
1621
1622	When reading an image, the ``Reader()`` routine in the ImportImage class
1623	should set:
1624
1625	* :attr:`Comments`: a list of strings (str),
1626	* :attr:`Npix`: the number of pixels in the image (int),
1627	* :attr:`Image`: the actual image as a numpy array (np.array)
1628	* :attr:`Data`: a dict defining image parameters (dict). Within this dict the following
1629	data items are needed:
1630
1631	* 'pixelSize': size of each pixel in microns (such as ``[200,200]``.
1632	* 'wavelength': wavelength in Angstoms.
1633	* 'distance': distance of detector from sample in cm.
1634	* 'center': uncalibrated center of beam on detector (such as ``[204.8,204.8]``.
1635	* 'size': size of image (such as ``[2048,2048]``).
1636	* 'ImageTag': image number or other keyword used to retrieve image from
1637	a multi-image data file (defaults to ``1`` if not specified).
1638	* 'sumfile': holds sum image file name if a sum was produced from a multi image file
1639
1640	optional data items:
1641
1642	* :attr:`repeat`: set to True if there are additional images to
1643	read in the file, False otherwise
1644	* :attr:`repeatcount`: set to the number of the image.
1645
1646	Note that the above is initialized with :meth:`InitParameters`.
1647	(Also see :ref:`Writing a Import Routine<Import_Routines>`
1648	for an explanation on how to use import classes in general.)
1649	'''
1650	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1651	strictExtension=False,):
1652	ImportBaseclass.__init__(self,formatName,longFormatName,
1653	extensionlist,strictExtension)
1654	self.InitParameters()
1655
1656	def ReInitialize(self):
1657	'Reinitialize the Reader to initial settings -- not used at present'
1658	ImportBaseclass.ReInitialize(self)
1659	self.InitParameters()
1660
1661	def InitParameters(self):
1662	'initialize the instrument parameters structure'
1663	self.Comments = ['No comments']
1664	self.Data = {}
1665	self.Npix = 0
1666	self.Image = None
1667	self.repeat = False
1668	self.repeatcount = 1
1669	self.sumfile = ''
1670
1671	def LoadImage(self,ParentFrame,imagefile,imagetag=None):
1672	'''Optionally, call this after reading in an image to load it into the tree.
1673	This saves time by preventing a reread of the same information.
1674	'''
1675	if ParentFrame:
1676	ParentFrame.ImageZ = self.Image # store the image for plotting
1677	ParentFrame.oldImagefile = imagefile # save the name of the last image file read
1678	ParentFrame.oldImageTag = imagetag # save the tag of the last image file read
1679
1680	######################################################################
1681	class ExportBaseclass(object):
1682	'''Defines a base class for the exporting of GSAS-II results.
1683
1684	This class is subclassed in the various exports/G2export_*.py files. Those files
1685	are imported in :meth:`GSASII.GSASII._init_Exports` which defines the
1686	appropriate menu items for each one and the .Exporter method is called
1687	directly from the menu item.
1688
1689	Routines may also define a .Writer method, which is used to write a single
1690	file without invoking any GUI objects.
1691	'''
1692	def __init__(self,G2frame,formatName,extension,longFormatName=None,):
1693	self.G2frame = G2frame
1694	self.formatName = formatName # short string naming file type
1695	self.extension = extension
1696	if longFormatName: # longer string naming file type
1697	self.longFormatName = longFormatName
1698	else:
1699	self.longFormatName = formatName
1700	self.OverallParms = {}
1701	self.Phases = {}
1702	self.Histograms = {}
1703	self.powderDict = {}
1704	self.xtalDict = {}
1705	self.parmDict = {}
1706	self.sigDict = {}
1707	# updated in InitExport:
1708	self.currentExportType = None # type of export that has been requested
1709	# updated in ExportSelect (when used):
1710	self.phasenam = None # a list of selected phases
1711	self.histnam = None # a list of selected histograms
1712	self.filename = None # name of file to be written (single export) or template (multiple files)
1713	self.dirname = '' # name of directory where file(s) will be written
1714	self.fullpath = '' # name of file being written -- full path
1715
1716	# items that should be defined in a subclass of this class
1717	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1718	# The following types are defined: 'project', "phase", "powder", "single"
1719	self.multiple = False # set as True if the class can export multiple phases or histograms
1720	# self.multiple is ignored for "project" exports
1721
1722	def InitExport(self,event):
1723	'''Determines the type of menu that called the Exporter and
1724	misc initialization.
1725	'''
1726	self.filename = None # name of file to be written (single export)
1727	self.dirname = '' # name of file to be written (multiple export)
1728	if event:
1729	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1730
1731	def MakePWDRfilename(self,hist):
1732	'''Make a filename root (no extension) from a PWDR histogram name
1733
1734	:param str hist: the histogram name in data tree (starts with "PWDR ")
1735	'''
1736	file0 = ''
1737	file1 = hist[5:]
1738	# replace repeated blanks
1739	while file1 != file0:
1740	file0 = file1
1741	file1 = file0.replace(' ',' ').strip()
1742	file0 = file1.replace('Azm= ','A')
1743	# if angle has unneeded decimal places on aziumuth, remove them
1744	if file0[-3:] == '.00': file0 = file0[:-3]
1745	file0 = file0.replace('.','_')
1746	file0 = file0.replace(' ','_')
1747	return file0
1748
1749	def ExportSelect(self,AskFile='ask'):
1750	'''Selects histograms or phases when needed. Sets a default file name when
1751	requested in self.filename; always sets a default directory in self.dirname.
1752
1753	:param bool AskFile: Determines how this routine processes getting a
1754	location to store the current export(s).
1755
1756	* if AskFile is 'ask' (default option), get the name of the file to be written;
1757	self.filename and self.dirname are always set. In the case where
1758	multiple files must be generated, the export routine should do this
1759	based on self.filename as a template.
1760	* if AskFile is 'dir', get the name of the directory to be used;
1761	self.filename is not used, but self.dirname is always set. The export routine
1762	will always generate the file name.
1763	* if AskFile is 'single', get only the name of the directory to be used when
1764	multiple items will be written (as multiple files) are used
1765	or a complete file name is requested when a single file
1766	name is selected. self.dirname is always set and self.filename used
1767	only when a single file is selected.
1768	* if AskFile is 'default', creates a name of the file to be used from
1769	the name of the project (.gpx) file. If the project has not been saved,
1770	then the name of file is requested.
1771	self.filename and self.dirname are always set. In the case where
1772	multiple file names must be generated, the export routine should do this
1773	based on self.filename.
1774	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1775	file. If the project has not been saved, then a directory is requested.
1776	self.filename is not used.
1777
1778	:returns: True in case of an error
1779	'''
1780
1781	numselected = 1
1782	if self.currentExportType == 'phase':
1783	if len(self.Phases) == 0:
1784	self.G2frame.ErrorDialog(
1785	'Empty project',
1786	'Project does not contain any phases.')
1787	return True
1788	elif len(self.Phases) == 1:
1789	self.phasenam = self.Phases.keys()
1790	elif self.multiple:
1791	choices = sorted(self.Phases.keys())
1792	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1793	if phasenum is None: return True
1794	self.phasenam = [choices[i] for i in phasenum]
1795	if not self.phasenam: return True
1796	numselected = len(self.phasenam)
1797	else:
1798	choices = sorted(self.Phases.keys())
1799	phasenum = G2G.ItemSelector(choices,self.G2frame)
1800	if phasenum is None: return True
1801	self.phasenam = [choices[phasenum]]
1802	numselected = len(self.phasenam)
1803	elif self.currentExportType == 'single':
1804	if len(self.xtalDict) == 0:
1805	self.G2frame.ErrorDialog(
1806	'Empty project',
1807	'Project does not contain any single crystal data.')
1808	return True
1809	elif len(self.xtalDict) == 1:
1810	self.histnam = self.xtalDict.values()
1811	elif self.multiple:
1812	choices = sorted(self.xtalDict.values())
1813	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1814	if not hnum: return True
1815	self.histnam = [choices[i] for i in hnum]
1816	numselected = len(self.histnam)
1817	else:
1818	choices = sorted(self.xtalDict.values())
1819	hnum = G2G.ItemSelector(choices,self.G2frame)
1820	if hnum is None: return True
1821	self.histnam = [choices[hnum]]
1822	numselected = len(self.histnam)
1823	elif self.currentExportType == 'powder':
1824	if len(self.powderDict) == 0:
1825	self.G2frame.ErrorDialog(
1826	'Empty project',
1827	'Project does not contain any powder data.')
1828	return True
1829	elif len(self.powderDict) == 1:
1830	self.histnam = self.powderDict.values()
1831	elif self.multiple:
1832	choices = sorted(self.powderDict.values())
1833	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1834	if not hnum: return True
1835	self.histnam = [choices[i] for i in hnum]
1836	numselected = len(self.histnam)
1837	else:
1838	choices = sorted(self.powderDict.values())
1839	hnum = G2G.ItemSelector(choices,self.G2frame)
1840	if hnum is None: return True
1841	self.histnam = [choices[hnum]]
1842	numselected = len(self.histnam)
1843	elif self.currentExportType == 'image':
1844	if len(self.Histograms) == 0:
1845	self.G2frame.ErrorDialog(
1846	'Empty project',
1847	'Project does not contain any images.')
1848	return True
1849	elif len(self.Histograms) == 1:
1850	self.histnam = self.Histograms.keys()
1851	else:
1852	choices = sorted(self.Histograms.keys())
1853	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1854	if self.multiple:
1855	if not hnum: return True
1856	self.histnam = [choices[i] for i in hnum]
1857	else:
1858	if hnum is None: return True
1859	self.histnam = [choices[hnum]]
1860	numselected = len(self.histnam)
1861	if self.currentExportType == 'map':
1862	# search for phases with maps
1863	mapPhases = []
1864	choices = []
1865	for phasenam in sorted(self.Phases):
1866	phasedict = self.Phases[phasenam] # pointer to current phase info
1867	if len(phasedict['General']['Map'].get('rho',[])):
1868	mapPhases.append(phasenam)
1869	if phasedict['General']['Map'].get('Flip'):
1870	choices.append('Charge flip map: '+str(phasenam))
1871	elif phasedict['General']['Map'].get('MapType'):
1872	choices.append(
1873	str(phasedict['General']['Map'].get('MapType'))
1874	+ ' map: ' + str(phasenam))
1875	else:
1876	choices.append('unknown map: '+str(phasenam))
1877	# select a map if needed
1878	if len(mapPhases) == 0:
1879	self.G2frame.ErrorDialog(
1880	'Empty project',
1881	'Project does not contain any maps.')
1882	return True
1883	elif len(mapPhases) == 1:
1884	self.phasenam = mapPhases
1885	else:
1886	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1887	if self.multiple:
1888	if not phasenum: return True
1889	self.phasenam = [mapPhases[i] for i in phasenum]
1890	else:
1891	if phasenum is None: return True
1892	self.phasenam = [mapPhases[phasenum]]
1893	numselected = len(self.phasenam)
1894
1895	# items selected, now set self.dirname and usually self.filename
1896	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
1897	AskFile == 'default' and not self.G2frame.GSASprojectfile
1898	):
1899	filename = self.askSaveFile()
1900	if not filename: return True
1901	self.dirname,self.filename = os.path.split(filename)
1902	elif AskFile == 'dir' or AskFile == 'single' or (
1903	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
1904	):
1905	self.dirname = self.askSaveDirectory()
1906	if not self.dirname: return True
1907	elif AskFile == 'default-dir' or AskFile == 'default':
1908	self.dirname,self.filename = os.path.split(
1909	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
1910	)
1911	else:
1912	raise Exception('This should not happen!')
1913
1914	def loadParmDict(self):
1915	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
1916	refined values to those from the last cycle and set the uncertainties for the
1917	refined parameters in another dict (self.sigDict).
1918
1919	Expands the parm & sig dicts to include values derived from constraints.
1920	'''
1921	self.parmDict = {}
1922	self.sigDict = {}
1923	rigidbodyDict = {}
1924	covDict = {}
1925	consDict = {}
1926	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1927	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
1928	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
1929	while item:
1930	name = self.G2frame.PatternTree.GetItemText(item)
1931	if name == 'Rigid bodies':
1932	rigidbodyDict = self.G2frame.PatternTree.GetItemPyData(item)
1933	elif name == 'Covariance':
1934	covDict = self.G2frame.PatternTree.GetItemPyData(item)
1935	elif name == 'Constraints':
1936	consDict = self.G2frame.PatternTree.GetItemPyData(item)
1937	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
1938	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1939	self.parmDict.update(rbDict)
1940	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1941	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,maxSSwave = G2stIO.GetPhaseData(
1942	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
1943	self.parmDict.update(phaseDict)
1944	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
1945	Phases,Histograms,Print=False,resetRefList=False)
1946	self.parmDict.update(hapDict)
1947	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
1948	self.parmDict.update(histDict)
1949	self.parmDict.update(zip(
1950	covDict.get('varyList',[]),
1951	covDict.get('variables',[])))
1952	self.sigDict = dict(zip(
1953	covDict.get('varyList',[]),
1954	covDict.get('sig',[])))
1955	# expand to include constraints: first compile a list of constraints
1956	constList = []
1957	for item in consDict:
1958	if item.startswith('_'): continue
1959	constList += consDict[item]
1960	# now process the constraints
1961	G2mv.InitVars()
1962	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
1963	varyList = covDict.get('varyListStart')
1964	if varyList is None and len(constDict) == 0:
1965	# no constraints can use varyList
1966	varyList = covDict.get('varyList')
1967	elif varyList is None:
1968	# old GPX file from before pre-constraint varyList is saved
1969	print ' * Old refinement: Please use Calculate/Refine to redo *'
1970	raise Exception(' * Export aborted *')
1971	else:
1972	varyList = list(varyList)
1973	try:
1974	groups,parmlist = G2mv.GroupConstraints(constDict)
1975	G2mv.GenerateConstraints(groups,parmlist,varyList,constDict,fixedList,self.parmDict)
1976	except:
1977	# this really should not happen
1978	print ' * ERROR - constraints are internally inconsistent *'
1979	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
1980	print 'Errors',errmsg
1981	if warnmsg: print 'Warnings',warnmsg
1982	raise Exception(' * CIF creation aborted *')
1983	# add the constrained values to the parameter dictionary
1984	G2mv.Dict2Map(self.parmDict,varyList)
1985	# and add their uncertainties into the esd dictionary (sigDict)
1986	if covDict.get('covMatrix') is not None:
1987	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
1988
1989	def loadTree(self):
1990	'''Load the contents of the data tree into a set of dicts
1991	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
1992	& self.xtalDict)
1993
1994	* The childrenless data tree items are overall parameters/controls for the
1995	entire project and are placed in self.OverallParms
1996	* Phase items are placed in self.Phases
1997	* Data items are placed in self.Histogram. The key for these data items
1998	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
1999	'''
2000	self.OverallParms = {}
2001	self.powderDict = {}
2002	self.xtalDict = {}
2003	self.Phases = {}
2004	self.Histograms = {}
2005	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2006	histType = None
2007	if self.currentExportType == 'phase':
2008	# if exporting phases load them here
2009	sub = G2gd.GetPatternTreeItemId(self.G2frame,self.G2frame.root,'Phases')
2010	if not sub:
2011	print 'no phases found'
2012	return True
2013	item, cookie = self.G2frame.PatternTree.GetFirstChild(sub)
2014	while item:
2015	phaseName = self.G2frame.PatternTree.GetItemText(item)
2016	self.Phases[phaseName] = self.G2frame.PatternTree.GetItemPyData(item)
2017	item, cookie = self.G2frame.PatternTree.GetNextChild(sub, cookie)
2018	return
2019	elif self.currentExportType == 'single':
2020	histType = 'HKLF'
2021	elif self.currentExportType == 'powder':
2022	histType = 'PWDR'
2023	elif self.currentExportType == 'image':
2024	histType = 'IMG'
2025
2026	if histType: # Loading just one kind of tree entry
2027	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2028	while item:
2029	name = self.G2frame.PatternTree.GetItemText(item)
2030	if name.startswith(histType):
2031	if self.Histograms.get(name): # there is already an item with this name
2032	print('Histogram name '+str(name)+' is repeated. Renaming')
2033	if name[-1] == '9':
2034	name = name[:-1] + '10'
2035	elif name[-1] in '012345678':
2036	name = name[:-1] + str(int(name[-1])+1)
2037	else:
2038	name += '-1'
2039	self.Histograms[name] = {}
2040	# the main info goes into Data, but the 0th
2041	# element contains refinement results, carry
2042	# that over too now.
2043	self.Histograms[name]['Data'] = self.G2frame.PatternTree.GetItemPyData(item)[1]
2044	self.Histograms[name][0] = self.G2frame.PatternTree.GetItemPyData(item)[0]
2045	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2046	while item2:
2047	child = self.G2frame.PatternTree.GetItemText(item2)
2048	self.Histograms[name][child] = self.G2frame.PatternTree.GetItemPyData(item2)
2049	item2, cookie2 = self.G2frame.PatternTree.GetNextChild(item, cookie2)
2050	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2051	# index powder and single crystal histograms by number
2052	for hist in self.Histograms:
2053	if hist.startswith("PWDR"):
2054	d = self.powderDict
2055	elif hist.startswith("HKLF"):
2056	d = self.xtalDict
2057	else:
2058	return
2059	i = self.Histograms[hist].get('hId')
2060	if i is None and not d.keys():
2061	i = 0
2062	elif i is None or i in d.keys():
2063	i = max(d.keys())+1
2064	d[i] = hist
2065	return
2066	# else standard load: using all interlinked phases and histograms
2067	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2068	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2069	while item:
2070	name = self.G2frame.PatternTree.GetItemText(item)
2071	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2072	if not item2:
2073	self.OverallParms[name] = self.G2frame.PatternTree.GetItemPyData(item)
2074	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2075	# index powder and single crystal histograms
2076	for hist in self.Histograms:
2077	i = self.Histograms[hist]['hId']
2078	if hist.startswith("PWDR"):
2079	self.powderDict[i] = hist
2080	elif hist.startswith("HKLF"):
2081	self.xtalDict[i] = hist
2082
2083	def dumpTree(self,mode='type'):
2084	'''Print out information on the data tree dicts loaded in loadTree
2085	'''
2086	print '\nOverall'
2087	if mode == 'type':
2088	def Show(arg): return type(arg)
2089	else:
2090	def Show(arg): return arg
2091	for key in self.OverallParms:
2092	print ' ',key,Show(self.OverallParms[key])
2093	print 'Phases'
2094	for key1 in self.Phases:
2095	print ' ',key1,Show(self.Phases[key1])
2096	print 'Histogram'
2097	for key1 in self.Histograms:
2098	print ' ',key1,Show(self.Histograms[key1])
2099	for key2 in self.Histograms[key1]:
2100	print ' ',key2,Show(self.Histograms[key1][key2])
2101
2102	def defaultSaveFile(self):
2103	return os.path.abspath(
2104	os.path.splitext(self.G2frame.GSASprojectfile
2105	)[0]+self.extension)
2106
2107	def askSaveFile(self):
2108	'''Ask the user to supply a file name
2109
2110	:returns: a file name (str) or None if Cancel is pressed
2111	'''
2112
2113	pth = G2G.GetExportPath(self.G2frame)
2114	defnam = os.path.splitext(
2115	os.path.split(self.G2frame.GSASprojectfile)[1]
2116	)[0]+self.extension
2117	dlg = wx.FileDialog(
2118	self.G2frame, 'Input name for file to write', pth, defnam,
2119	self.longFormatName+' ('+self.extension+')\|'+self.extension,
2120	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
2121	dlg.CenterOnParent()
2122	try:
2123	if dlg.ShowModal() == wx.ID_OK:
2124	filename = dlg.GetPath()
2125	self.G2frame.LastExportDir = os.path.split(filename)[0]
2126	filename = os.path.splitext(filename)[0]+self.extension # make sure extension is correct
2127	else:
2128	filename = None
2129	finally:
2130	dlg.Destroy()
2131	return filename
2132
2133	def askSaveDirectory(self):
2134	'''Ask the user to supply a directory name. Path name is used as the
2135	starting point for the next export path search.
2136
2137	:returns: a directory name (str) or None if Cancel is pressed
2138	'''
2139	pth = G2G.GetExportPath(self.G2frame)
2140	dlg = wx.DirDialog(
2141	self.G2frame, 'Input directory where file(s) will be written', pth,
2142	wx.DD_DEFAULT_STYLE)
2143	dlg.CenterOnParent()
2144	try:
2145	if dlg.ShowModal() == wx.ID_OK:
2146	filename = dlg.GetPath()
2147	self.G2frame.LastExportDir = filename
2148	else:
2149	filename = None
2150	finally:
2151	dlg.Destroy()
2152	return filename
2153
2154	# Tools for file writing.
2155	def OpenFile(self,fil=None,mode='w'):
2156	'''Open the output file
2157
2158	:param str fil: The name of the file to open. If None (default)
2159	the name defaults to self.dirname + self.filename.
2160	If an extension is supplied, it is not overridded,
2161	but if not, the default extension is used.
2162	:returns: the file object opened by the routine which is also
2163	saved as self.fp
2164	'''
2165	if not fil:
2166	if not os.path.splitext(self.filename)[1]:
2167	self.filename += self.extension
2168	fil = os.path.join(self.dirname,self.filename)
2169	self.fullpath = os.path.abspath(fil)
2170	self.fp = open(self.fullpath,mode)
2171	return self.fp
2172
2173	def Write(self,line):
2174	'''write a line of output, attaching a line-end character
2175
2176	:param str line: the text to be written.
2177	'''
2178	self.fp.write(line+'\n')
2179	def CloseFile(self,fp=None):
2180	'''Close a file opened in OpenFile
2181
2182	:param file fp: the file object to be closed. If None (default)
2183	file object self.fp is closed.
2184	'''
2185	if fp is None:
2186	fp = self.fp
2187	self.fp = None
2188	fp.close()
2189	# Tools to pull information out of the data arrays
2190	def GetCell(self,phasenam):
2191	"""Gets the unit cell parameters and their s.u.'s for a selected phase
2192
2193	:param str phasenam: the name for the selected phase
2194	:returns: `cellList,cellSig` where each is a 7 element list corresponding
2195	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
2196	cell values and `cellSig` has their uncertainties.
2197	"""
2198	phasedict = self.Phases[phasenam] # pointer to current phase info
2199	try:
2200	pfx = str(phasedict['pId'])+'::'
2201	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
2202	cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A,
2203	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
2204	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
2205	return cellList,cellSig
2206	except KeyError:
2207	cell = phasedict['General']['Cell'][1:]
2208	return cell,7*[0]
2209
2210	def GetAtoms(self,phasenam):
2211	"""Gets the atoms associated with a phase. Can be used with standard
2212	or macromolecular phases
2213
2214	:param str phasenam: the name for the selected phase
2215	:returns: a list of items for eac atom where each item is a list containing:
2216	label, typ, mult, xyz, and td, where
2217
2218	* label and typ are the atom label and the scattering factor type (str)
2219	* mult is the site multiplicity (int)
2220	* xyz is contains a list with four pairs of numbers:
2221	x, y, z and fractional occupancy and
2222	their standard uncertainty (or a negative value)
2223	* td is contains a list with either one or six pairs of numbers:
2224	if one number it is U\ :sub:`iso` and with six numbers it is
2225	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
2226	paired with their standard uncertainty (or a negative value)
2227	"""
2228	phasedict = self.Phases[phasenam] # pointer to current phase info
2229	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
2230	cfrac = cx+3
2231	fpfx = str(phasedict['pId'])+'::Afrac:'
2232	atomslist = []
2233	for i,at in enumerate(phasedict['Atoms']):
2234	if phasedict['General']['Type'] == 'macromolecular':
2235	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
2236	else:
2237	label = at[ct-1]
2238	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
2239	fsig = self.sigDict.get(fpfx+str(i),-0.009)
2240	mult = at[cs+1]
2241	typ = at[ct]
2242	xyz = []
2243	for j,v in enumerate(('x','y','z')):
2244	val = at[cx+j]
2245	pfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
2246	sig = self.sigDict.get(pfx,-0.000009)
2247	xyz.append((val,sig))
2248	xyz.append((fval,fsig))
2249	td = []
2250	if at[cia] == 'I':
2251	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
2252	val = self.parmDict.get(pfx,at[cia+1])
2253	sig = self.sigDict.get(pfx,-0.0009)
2254	td.append((val,sig))
2255	else:
2256	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
2257	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
2258	val = self.parmDict.get(pfx,at[cia+2+i])
2259	sig = self.sigDict.get(pfx,-0.0009)
2260	td.append((val,sig))
2261	atomslist.append((label,typ,mult,xyz,td))
2262	return atomslist
2263	######################################################################
2264	def ExportPowderList(G2frame):
2265	'''Returns a list of extensions supported by :func:`GSASIIIO:ExportPowder`
2266
2267	:param wx.Frame G2frame: the GSAS-II main data tree window
2268	'''
2269	extList = []
2270	for obj in G2frame.exporterlist:
2271	if 'powder' in obj.exporttype:
2272	try:
2273	obj.Writer
2274	extList.append(obj.extension)
2275	except AttributeError:
2276	pass
2277	return extList
2278
2279	def ExportPowder(G2frame,TreeName,fileroot,extension):
2280	'''Writes a single powder histogram using the Export routines
2281
2282	:param wx.Frame G2frame: the GSAS-II main data tree window
2283	:param str TreeName: the name of the histogram (PWDR ...) in the data tree
2284	:param str fileroot: name for file to be written, extension ignored
2285	:param str extension: extension for file to be written (start with '.'). Must
2286	match a powder export routine that has a Writer object.
2287	'''
2288	filename = os.path.abspath(os.path.splitext(fileroot)[0]+extension)
2289	for obj in G2frame.exporterlist:
2290	if obj.extension == extension and 'powder' in obj.exporttype:
2291	obj.currentExportType = 'powder'
2292	obj.InitExport(None)
2293	obj.loadTree() # load all histograms in tree into dicts
2294	if TreeName not in obj.Histograms:
2295	raise Exception('Histogram not found: '+str(TreeName))
2296	try:
2297	obj.Writer
2298	except AttributeError:
2299	continue
2300	try:
2301	obj.Writer(TreeName,filename)
2302	return
2303	except Exception,err:
2304	print('Export Routine for '+extension+' failed.')
2305	print err
2306	else:
2307	print('No Export routine supports extension '+extension)
2308
2309	def ReadDIFFaX(DIFFaXfile):
2310	print 'read ',DIFFaXfile
2311	Layer = {'Laue':'-1','Cell':[False,1.,1.,1.,90.,90.,90,1.],'Width':[[10.,10.],[False,False]],
2312	'Layers':[],'Stacking':[],'Transitions':[],'Toler':0.01,'AtInfo':{}}
2313	df = open(DIFFaXfile,'r')
2314	lines = df.readlines()
2315	df.close()
2316	struct = False
2317	Struct = []
2318	stack = False
2319	Stack = []
2320	trans = False
2321	Trans = []
2322	instr = False
2323	for diff in lines:
2324	diff = diff[:-1].lower()
2325	if '!' in diff:
2326	continue
2327	while '}' in diff: #strip comments
2328	iB = diff.index('{')
2329	iF = diff.index('}')+1
2330	if iB:
2331	diff = diff[:iB]
2332	else:
2333	diff = diff[iF:]
2334	if not diff:
2335	continue
2336	if diff.strip() == 'instrumental':
2337	instr = True
2338	continue
2339	if diff.strip() == 'structural':
2340	instr = False
2341	struct = True
2342	continue
2343	elif diff.strip() == 'stacking':
2344	struct = False
2345	stack = True
2346	continue
2347	elif diff.strip() == 'transitions':
2348	stack = False
2349	trans = True
2350	continue
2351	diff = diff.strip()
2352	if struct:
2353	if diff:
2354	Struct.append(diff)
2355	elif stack:
2356	if diff:
2357	Stack.append(diff)
2358	elif trans:
2359	if diff:
2360	Trans.append(diff)
2361
2362	#STRUCTURE records
2363	laueRec = Struct[1].split()
2364	Layer['Laue'] = laueRec[0]
2365	if Layer['Laue'] == 'unknown' and len(laueRec) > 1:
2366	Layer['Toler'] = float(laueRec[1]) #tolerance for 'unknown'?
2367	if Layer['Laue'] == '2/m(1)': Layer['Laue'] = '2/m(c)'
2368	if Layer['Laue'] == '2/m(2)': Layer['Laue'] = '2/m(ab)'
2369	cell = Struct[0].split()
2370	Layer['Cell'] = [False,float(cell[0]),float(cell[1]),float(cell[2]),90.,90.,float(cell[3]),1.0]
2371	nLayers = int(Struct[2])
2372	N = 3
2373	if 'layer' not in Struct[3]:
2374	N = 4
2375	if Struct[3] != 'infinite':
2376	width = Struct[3].split()
2377	Layer['Width'][0] = [float(width[0]),float(width[1])]
2378	for nL in range(nLayers):
2379	if '=' in Struct[N]:
2380	name = Struct[N].split('=')
2381	sameas = int(name[1])-1
2382	Layer['Layers'].append({'Name':name[0],'SameAs':Layer['Layers'][sameas]['Name'],'Symm':'None','Atoms':[]})
2383	N += 1
2384	continue
2385	Symm = 'None'
2386	if 'centro' in Struct[N+1]: Symm = '-1'
2387	Layer['Layers'].append({'Name':Struct[N],'SameAs':'','Symm':Symm,'Atoms':[]})
2388	N += 2
2389	iatm = 0
2390	while 'layer' not in Struct[N]:
2391	atom = Struct[N][4:].split()
2392	atomType = G2el.FixValence(Struct[N][:4].replace(' ','').strip().capitalize())
2393	if atomType not in Layer['AtInfo']:
2394	Layer['AtInfo'][atomType] = G2el.GetAtomInfo(atomType)
2395	atomName = '%s(%s)'%(atomType,atom[0])
2396	newVals = []
2397	for val in atom[1:6]:
2398	if '/' in val:
2399	newVals.append(eval(val+'.'))
2400	else:
2401	newVals.append(float(val))
2402	atomRec = [atomName,atomType,newVals[0],newVals[1],newVals[2],newVals[4],newVals[3]/78.9568]
2403	Layer['Layers'][-1]['Atoms'].append(atomRec)
2404	N += 1
2405	if N > len(Struct)-1:
2406	break
2407	#TRANSITIONS records
2408	transArray = []
2409	N = 0
2410	for i in range(nLayers):
2411	transArray.append([])
2412	for j in range(nLayers):
2413	vals = Trans[N].split()
2414	newVals = []
2415	for val in vals[:4]:
2416	if '/' in val:
2417	newVals.append(eval(val+'.'))
2418	else:
2419	newVals.append(float(val))
2420	transArray[-1].append(newVals+['',False])
2421	N += 1
2422	Layer['Transitions'] = transArray
2423	#STACKING records
2424	Layer['Stacking'] = [Stack[0],'']
2425	if Stack[0] == 'recursive':
2426	Layer['Stacking'][1] = Stack[1]
2427	elif Stack[0] == 'explicit':
2428	if Stack[1] == 'random':
2429	Layer['Stacking'][1] = Stack[1]
2430	else:
2431	Layer['Stacking'][1] = 'list'
2432	Layer['Stacking'].append('')
2433	for stack in Stack[2:]:
2434	Layer['Stacking'][2] += ' '+stack
2435	return Layer
2436
2437	def ReadCIF(URLorFile):
2438	'''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
2439	(from James Hester).
2440	The open routine gets confused with DOS names that begin with a letter and colon
2441	"C:\dir\" so this routine will try to open the passed name as a file and if that
2442	fails, try it as a URL
2443
2444	:param str URLorFile: string containing a URL or a file name. Code will try first
2445	to open it as a file and then as a URL.
2446
2447	:returns: a PyCifRW CIF object.
2448	'''
2449	import CifFile as cif # PyCifRW from James Hester
2450
2451	# alternate approach:
2452	#import urllib
2453	#ciffile = 'file:'+urllib.pathname2url(filename)
2454
2455	try:
2456	fp = open(URLorFile,'r')
2457	cf = cif.ReadCif(fp)
2458	fp.close()
2459	return cf
2460	except IOError:
2461	return cif.ReadCif(URLorFile)
2462
2463	if __name__ == '__main__':
2464	import GSASII
2465	application = GSASII.GSASIImain(0)
2466	G2frame = application.main
2467	#app = wx.PySimpleApp()
2468	#G2frame = wx.Frame(None) # create a frame
2469	#frm.Show(True)
2470	#filename = '/tmp/notzip.zip'
2471	#filename = '/tmp/all.zip'
2472	#filename = '/tmp/11bmb_7652.zip'
2473
2474	#selection=None, confirmoverwrite=True, parent=None
2475	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2476	#print ExtractFileFromZip(filename,multipleselect=True)
2477	# #confirmread=False, confirmoverwrite=False)
2478
2479	# choicelist=[ ('a','b','c'),
2480	# ('test1','test2'),('no choice',)]
2481	# titles = [ 'a, b or c', 'tests', 'No option here']
2482	# dlg = MultipleChoicesDialog(
2483	# choicelist,titles,
2484	# parent=frm)
2485	# if dlg.ShowModal() == wx.ID_OK:
2486	# print 'Got OK'
2487	imagefile = '/tmp/NDC5_00237_3.ge3'
2488	Comments, Data, Npix, Image = GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None)
2489
2490	print("\n\nResults loaded to Comments, Data, Npix and Image\n\n")
2491
2492	GSASIIpath.IPyBreak_base()

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