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source: trunk/GSASIIIO.py @ 2196

Last change on this file since 2196 was 2196, checked in by toby, 7 years ago
redo plot window graphics to redraw after refinement (need to update more plotting routines & save plot zoom stack, etc.)
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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2016-04-05 22:24:38 +0000 (Tue, 05 Apr 2016) $
4	# $Author: toby $
5	# $Revision: 2196 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 2196 2016-04-05 22:24:38Z 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 cPickle
28	import sys
29	import re
30	import random as ran
31	import GSASIIpath
32	GSASIIpath.SetVersionNumber("$Revision: 2196 $")
33	import GSASIIgrid as G2gd
34	import GSASIIspc as G2spc
35	import GSASIIobj as G2obj
36	import GSASIIlattice as G2lat
37	import GSASIIpwdGUI as G2pdG
38	import GSASIIimgGUI as G2imG
39	import GSASIIimage as G2img
40	import GSASIIElem as G2el
41	import GSASIIstrIO as G2stIO
42	import GSASIImapvars as G2mv
43	import GSASIIctrls as G2G
44	import os
45	import os.path as ospath
46
47	DEBUG = False #=True for various prints
48	TRANSP = False #=true to transpose images for testing
49	if GSASIIpath.GetConfigValue('Transpose'): TRANSP = True
50	npsind = lambda x: np.sin(x*np.pi/180.)
51
52	def sfloat(S):
53	'Convert a string to float. An empty field or a unconvertable value is treated as zero'
54	if S.strip():
55	try:
56	return float(S)
57	except ValueError:
58	pass
59	return 0.0
60
61	def sint(S):
62	'Convert a string to int. An empty field is treated as zero'
63	if S.strip():
64	return int(S)
65	else:
66	return 0
67
68	def trim(val):
69	'''Simplify a string containing leading and trailing spaces
70	as well as newlines, tabs, repeated spaces etc. into a shorter and
71	more simple string, by replacing all ranges of whitespace
72	characters with a single space.
73
74	:param str val: the string to be simplified
75
76	:returns: the (usually) shortened version of the string
77	'''
78	return re.sub('\s+', ' ', val).strip()
79
80	def makeInstDict(names,data,codes):
81	inst = dict(zip(names,zip(data,data,codes)))
82	for item in inst:
83	inst[item] = list(inst[item])
84	return inst
85
86	def FileDlgFixExt(dlg,file):
87	'this is needed to fix a problem in linux wx.FileDialog'
88	ext = dlg.GetWildcard().split('\|')[2dlg.GetFilterIndex()+1].strip('')
89	if ext not in file:
90	file += ext
91	return file
92
93	def GetPowderPeaks(fileName):
94	'Read powder peaks from a file'
95	sind = lambda x: math.sin(x*math.pi/180.)
96	asind = lambda x: 180.*math.asin(x)/math.pi
97	wave = 1.54052
98	File = open(fileName,'Ur')
99	Comments = []
100	peaks = []
101	S = File.readline()
102	while S:
103	if S[:1] == '#':
104	Comments.append(S[:-1])
105	else:
106	item = S.split()
107	if len(item) == 1:
108	peaks.append([float(item[0]),1.0])
109	elif len(item) > 1:
110	peaks.append([float(item[0]),float(item[0])])
111	S = File.readline()
112	File.close()
113	if Comments:
114	print 'Comments on file:'
115	for Comment in Comments:
116	print Comment
117	if 'wavelength' in Comment:
118	wave = float(Comment.split('=')[1])
119	Peaks = []
120	if peaks[0][0] > peaks[-1][0]: # d-spacings - assume CuKa
121	for peak in peaks:
122	dsp = peak[0]
123	sth = wave/(2.0*dsp)
124	if sth < 1.0:
125	tth = 2.0*asind(sth)
126	else:
127	break
128	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
129	else: #2-thetas - assume Cuka (for now)
130	for peak in peaks:
131	tth = peak[0]
132	dsp = wave/(2.0*sind(tth/2.0))
133	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
134	limits = [1000.,0.]
135	for peak in Peaks:
136	limits[0] = min(limits[0],peak[0])
137	limits[1] = max(limits[1],peak[0])
138	limits[0] = max(1.,(int(limits[0]-1.)/5)*5.)
139	limits[1] = min(170.,(int(limits[1]+1.)/5)*5.)
140	return Comments,Peaks,limits,wave
141
142	def CheckImageFile(G2frame,imagefile):
143	'''Try to locate an image file if the project and image have been moved
144	together. If the image file cannot be found, request the location from
145	the user.
146
147	:param wx.Frame G2frame: main GSAS-II Frame and data object
148	:param str imagefile: name of image file
149	:returns: imagefile, if it exists, or the name of a file
150	that does exist or False if the user presses Cancel
151
152	'''
153	if not os.path.exists(imagefile):
154	print 'Image file '+imagefile+' not found'
155	fil = imagefile.replace('\\','/') # windows?!
156	# see if we can find a file with same name or in a similarly named sub-dir
157	pth,fil = os.path.split(fil)
158	prevpth = None
159	while pth and pth != prevpth:
160	prevpth = pth
161	if os.path.exists(os.path.join(G2frame.dirname,fil)):
162	print 'found image file '+os.path.join(G2frame.dirname,fil)
163	return os.path.join(G2frame.dirname,fil)
164	pth,enddir = os.path.split(pth)
165	fil = os.path.join(enddir,fil)
166	# not found as a subdirectory, drop common parts of path for last saved & image file names
167	# if image was .../A/B/C/imgs/ima.ge
168	# & GPX was .../A/B/C/refs/fil.gpx but is now .../NEW/TEST/TEST1
169	# will look for .../NEW/TEST/TEST1/imgs/ima.ge, .../NEW/TEST/imgs/ima.ge, .../NEW/imgs/ima.ge and so on
170	Controls = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
171	gpxPath = Controls.get('LastSavedAs','').replace('\\','/').split('/') # blank in older .GPX files
172	imgPath = imagefile.replace('\\','/').split('/')
173	for p1,p2 in zip(gpxPath,imgPath):
174	if p1 == p2:
175	gpxPath.pop(0),imgPath.pop(0)
176	else:
177	break
178	fil = os.path.join(*imgPath) # file with non-common prefix elements
179	prevpth = None
180	pth = os.path.abspath(G2frame.dirname)
181	while pth and pth != prevpth:
182	prevpth = pth
183	if os.path.exists(os.path.join(pth,fil)):
184	print 'found image file '+os.path.join(pth,fil)
185	return os.path.join(pth,fil)
186	pth,enddir = os.path.split(pth)
187	#GSASIIpath.IPyBreak()
188
189	if not os.path.exists(imagefile):
190	prevnam = os.path.split(imagefile)[1]
191	prevext = os.path.splitext(imagefile)[1]
192	wildcard = 'Image format ('+prevext+')\|'+prevext
193	dlg = wx.FileDialog(G2frame, 'Previous image file ('+prevnam+') not found; open here', '.', prevnam,
194	wildcard,wx.OPEN)
195	try:
196	dlg.SetFilename(''+ospath.split(imagefile)[1])
197	if dlg.ShowModal() == wx.ID_OK:
198	imagefile = dlg.GetPath()
199	else:
200	imagefile = False
201	finally:
202	dlg.Destroy()
203	return imagefile
204
205	def EditImageParms(parent,Data,Comments,Image,filename):
206	dlg = wx.Dialog(parent, wx.ID_ANY, 'Edit image parameters',
207	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
208	def onClose(event):
209	dlg.EndModal(wx.ID_OK)
210	mainsizer = wx.BoxSizer(wx.VERTICAL)
211	h,w = Image.shape[:2]
212	mainsizer.Add(wx.StaticText(dlg,wx.ID_ANY,
213	'File '+str(filename)+'\nImage size: '+str(h)+' x '+str(w)),
214	0,wx.ALIGN_LEFT\|wx.ALL, 2)
215
216	vsizer = wx.BoxSizer(wx.HORIZONTAL)
217	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Wavelength (\xC5) '),
218	0,wx.ALIGN_LEFT\|wx.ALL, 2)
219	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'wavelength')
220	vsizer.Add(wdgt)
221	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
222
223	vsizer = wx.BoxSizer(wx.HORIZONTAL)
224	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Pixel size (\xb5m). Width '),
225	0,wx.ALIGN_LEFT\|wx.ALL, 2)
226	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],0,
227	size=(50,-1))
228	vsizer.Add(wdgt)
229	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Height '),
230	wx.ALIGN_LEFT\|wx.ALL, 2)
231	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],1,
232	size=(50,-1))
233	vsizer.Add(wdgt)
234	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
235
236	vsizer = wx.BoxSizer(wx.HORIZONTAL)
237	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Sample to detector (mm) '),
238	0,wx.ALIGN_LEFT\|wx.ALL, 2)
239	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'distance')
240	vsizer.Add(wdgt)
241	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
242
243	vsizer = wx.BoxSizer(wx.HORIZONTAL)
244	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Beam center (pixels). X = '),
245	0,wx.ALIGN_LEFT\|wx.ALL, 2)
246	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],0,
247	size=(75,-1))
248	vsizer.Add(wdgt)
249	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Y = '),
250	wx.ALIGN_LEFT\|wx.ALL, 2)
251	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],1,
252	size=(75,-1))
253	vsizer.Add(wdgt)
254	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
255
256	vsizer = wx.BoxSizer(wx.HORIZONTAL)
257	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Comments '),
258	0,wx.ALIGN_LEFT\|wx.ALL, 2)
259	wdgt = G2G.ValidatedTxtCtrl(dlg,Comments,0,size=(250,-1))
260	vsizer.Add(wdgt)
261	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
262
263	btnsizer = wx.StdDialogButtonSizer()
264	OKbtn = wx.Button(dlg, wx.ID_OK, 'Continue')
265	OKbtn.SetDefault()
266	OKbtn.Bind(wx.EVT_BUTTON,onClose)
267	btnsizer.AddButton(OKbtn) # not sure why this is needed
268	btnsizer.Realize()
269	mainsizer.Add(btnsizer, 1, wx.ALIGN_CENTER\|wx.ALL\|wx.EXPAND, 5)
270	dlg.SetSizer(mainsizer)
271	dlg.CenterOnParent()
272	dlg.ShowModal()
273
274	def ReadLoadImage(imagefile,G2frame):
275	'''Read a GSAS-II image file and load it into the data tree
276	Called only from GSASII.OnImageRead (depreciated).
277	'''
278	# if a zip file, open and extract
279	if os.path.splitext(imagefile)[1].lower() == '.zip':
280	extractedfile = ExtractFileFromZip(imagefile,parent=G2frame)
281	if extractedfile is not None and extractedfile != imagefile:
282	imagefile = extractedfile
283	Comments,Data,Npix,Image = GetImageData(G2frame,imagefile) # can only read 1st image
284	if Comments:
285	LoadImage2Tree(imagefile,G2frame,Comments,Data,Npix,Image)
286
287	def LoadImage2Tree(imagefile,G2frame,Comments,Data,Npix,Image):
288	'''Load an image into the tree. Saves the location of the image, as well as the
289	ImageTag (where there is more than one image in the file), if defined.
290	'''
291	ImgNames = []
292	if G2frame.PatternTree.GetCount(): # get a list of existing Image entries
293	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
294	while item:
295	name = G2frame.PatternTree.GetItemText(item)
296	if name.startswith('IMG'): ImgNames.append(name)
297	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
298	TreeLbl = 'IMG '+os.path.basename(imagefile)
299	ImageTag = Data.get('ImageTag')
300	if ImageTag:
301	TreeLbl += ' #'+str(ImageTag)
302	imageInfo = (imagefile,ImageTag)
303	else:
304	imageInfo = imagefile
305	TreeName = G2obj.MakeUniqueLabel(TreeLbl,ImgNames)
306	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=TreeName)
307	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
308	Imax = np.amax(Image)
309	Imin = max(0.0,np.amin(Image)) #force positive
310	if G2frame.imageDefault:
311	Data = copy.copy(G2frame.imageDefault)
312	Data['showLines'] = True
313	Data['ring'] = []
314	Data['rings'] = []
315	Data['cutoff'] = 10
316	Data['pixLimit'] = 20
317	Data['edgemin'] = 100000000
318	Data['calibdmin'] = 0.5
319	Data['calibskip'] = 0
320	Data['ellipses'] = []
321	Data['calibrant'] = ''
322	Data['GonioAngles'] = [0.,0.,0.]
323	Data['DetDepthRef'] = False
324	else:
325	Data['type'] = 'PWDR'
326	Data['color'] = 'Paired'
327	Data['tilt'] = 0.0
328	Data['rotation'] = 0.0
329	Data['showLines'] = False
330	Data['ring'] = []
331	Data['rings'] = []
332	Data['cutoff'] = 10
333	Data['pixLimit'] = 20
334	Data['calibdmin'] = 0.5
335	Data['calibskip'] = 0
336	Data['edgemin'] = 100000000
337	Data['ellipses'] = []
338	Data['GonioAngles'] = [0.,0.,0.]
339	Data['DetDepth'] = 0.
340	Data['DetDepthRef'] = False
341	Data['calibrant'] = ''
342	Data['IOtth'] = [2.0,5.0]
343	Data['LRazimuth'] = [135,225]
344	Data['azmthOff'] = 0.0
345	Data['outChannels'] = 2500
346	Data['outAzimuths'] = 1
347	Data['centerAzm'] = False
348	Data['fullIntegrate'] = False
349	Data['setRings'] = False
350	Data['background image'] = ['',-1.0]
351	Data['dark image'] = ['',-1.0]
352	Data['Flat Bkg'] = 0.0
353	Data['setDefault'] = False
354	Data['range'] = [(Imin,Imax),[Imin,Imax]]
355	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Image Controls'),Data)
356	Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],'Thresholds':[(Imin,Imax),[Imin,Imax]]}
357	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Masks'),Masks)
358	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Stress/Strain'),
359	{'Type':'True','d-zero':[],'Sample phi':0.0,'Sample z':0.0,'Sample load':0.0})
360	G2frame.PatternTree.SetItemPyData(Id,[Npix,imageInfo])
361	G2frame.PickId = Id
362	G2frame.PickIdText = G2frame.GetTreeItemsList(G2frame.PickId)
363	G2frame.Image = Id
364
365	def GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None):
366	'''Read a single image with an image importer.
367
368	:param wx.Frame G2frame: main GSAS-II Frame and data object.
369	:param str imagefile: name of image file
370	:param bool imageOnly: If True return only the image,
371	otherwise (default) return more (see below)
372	:param int/str ImageTag: specifies a particular image to be read from a file.
373	First image is read if None (default).
374
375	:returns: an image as a numpy array or a list of four items:
376	Comments, Data, Npix and the Image, as selected by imageOnly
377
378	'''
379	# determine which formats are compatible with this file
380	primaryReaders = []
381	secondaryReaders = []
382	for rd in G2frame.ImportImageReaderlist:
383	flag = rd.ExtensionValidator(imagefile)
384	if flag is None:
385	secondaryReaders.append(rd)
386	elif flag:
387	primaryReaders.append(rd)
388	if len(secondaryReaders) + len(primaryReaders) == 0:
389	print('Error: No matching format for file '+filename)
390	raise Exception('No image read')
391	fp = None
392	errorReport = ''
393	fp = open(imagefile,'Ur')
394	for rd in primaryReaders+secondaryReaders:
395	rd.ReInitialize() # purge anything from a previous read
396	fp.seek(0) # rewind
397	rd.errors = "" # clear out any old errors
398	if not rd.ContentsValidator(fp): # rejected on cursory check
399	errorReport += "\n "+rd.formatName + ' validator error'
400	if rd.errors:
401	errorReport += ': '+rd.errors
402	continue
403	rdbuffer = {} # create temporary storage for file reader
404	if imageOnly:
405	ParentFrame = None # prevent GUI access on reread
406	else:
407	ParentFrame = G2frame
408	if GSASIIpath.GetConfigValue('debug'):
409	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=ImageTag)
410	else:
411	flag = False
412	try:
413	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=ImageTag)
414	except rd.ImportException as detail:
415	rd.errors += "\n Read exception: "+str(detail)
416	except Exception as detail:
417	import traceback
418	rd.errors += "\n Unhandled read exception: "+str(detail)
419	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
420	if flag: # this read succeeded
421	if rd.Image is None:
422	raise Exception('No image read. Strange!')
423	if GSASIIpath.GetConfigValue('Transpose'):
424	print 'Transposing Image!'
425	rd.Image = rd.Image.T
426	#rd.readfilename = imagefile
427	if imageOnly:
428	return rd.Image
429	else:
430	return rd.Comments,rd.Data,rd.Npix,rd.Image
431	else:
432	print('Error reading file '+filename)
433	print('Error messages(s)\n'+errorReport)
434	raise Exception('No image read')
435
436	def ReadImages(G2frame,imagefile):
437	'''Read one or more images from a file and put them into the Tree
438	using image importers. Called only in :meth:`AutoIntFrame.OnTimerLoop`.
439
440	:param wx.Frame G2frame: main GSAS-II Frame and data object.
441	:param str imagefile: name of image file
442
443	:returns: a list of the id's of the IMG tree items created
444	'''
445	# determine which formats are compatible with this file
446	primaryReaders = []
447	secondaryReaders = []
448	for rd in G2frame.ImportImageReaderlist:
449	flag = rd.ExtensionValidator(imagefile)
450	if flag is None:
451	secondaryReaders.append(rd)
452	elif flag:
453	primaryReaders.append(rd)
454	if len(secondaryReaders) + len(primaryReaders) == 0:
455	print('Error: No matching format for file '+filename)
456	raise Exception('No image read')
457	errorReport = ''
458	fp = open(imagefile,'Ur')
459	rdbuffer = {} # create temporary storage for file reader
460	for rd in primaryReaders+secondaryReaders:
461	rd.ReInitialize() # purge anything from a previous read
462	fp.seek(0) # rewind
463	rd.errors = "" # clear out any old errors
464	if not rd.ContentsValidator(fp): # rejected on cursory check
465	errorReport += "\n "+rd.formatName + ' validator error'
466	if rd.errors:
467	errorReport += ': '+rd.errors
468	continue
469	ParentFrame = G2frame
470	block = 0
471	repeat = True
472	CreatedIMGitems = []
473	while repeat: # loop if the reader asks for another pass on the file
474	block += 1
475	repeat = False
476	if GSASIIpath.GetConfigValue('debug'):
477	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=block,Buffer=rdbuffer)
478	else:
479	flag = False
480	try:
481	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=block,Buffer=rdbuffer)
482	except rd.ImportException as detail:
483	rd.errors += "\n Read exception: "+str(detail)
484	except Exception as detail:
485	import traceback
486	rd.errors += "\n Unhandled read exception: "+str(detail)
487	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
488	if flag: # this read succeeded
489	if rd.Image is None:
490	raise Exception('No image read. Strange!')
491	if GSASIIpath.GetConfigValue('Transpose'):
492	print 'Transposing Image!'
493	rd.Image = rd.Image.T
494	rd.Data['ImageTag'] = rd.repeatcount
495	LoadImage2Tree(imagefile,G2frame,rd.Comments,rd.Data,rd.Npix,rd.Image)
496	repeat = rd.repeat
497	CreatedIMGitems.append(G2frame.Image)
498	if CreatedIMGitems: return CreatedIMGitems
499	else:
500	print('Error reading file '+filename)
501	print('Error messages(s)\n'+errorReport)
502	return []
503	#raise Exception('No image read')
504
505	def SaveMultipleImg(G2frame):
506	if not G2frame.PatternTree.GetCount():
507	print 'no images!'
508	return
509	choices = G2gd.GetPatternTreeDataNames(G2frame,['IMG ',])
510	if len(choices) == 1:
511	names = choices
512	else:
513	dlg = G2G.G2MultiChoiceDialog(G2frame,'Stress/Strain fitting','Select images to fit:',choices)
514	dlg.SetSelections([])
515	names = []
516	if dlg.ShowModal() == wx.ID_OK:
517	names = [choices[sel] for sel in dlg.GetSelections()]
518	dlg.Destroy()
519	if not names: return
520	for name in names:
521	Id = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, name)
522	Npix,imagefile,imagetag = G2frame.PatternTree.GetImageLoc(Id)
523	imroot = os.path.splitext(imagefile)[0]
524	if imagetag:
525	imroot += '_' + str(imagetag)
526	Data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Image Controls'))
527	print('Writing '+imroot+'.imctrl')
528	File = open(imroot+'.imctrl','w')
529	keys = ['type','wavelength','calibrant','distance','center',
530	'tilt','rotation','azmthOff','fullIntegrate','LRazimuth',
531	'IOtth','outChannels','outAzimuths','invert_x','invert_y','DetDepth',
532	'calibskip','pixLimit','cutoff','calibdmin','chisq','Flat Bkg',
533	'binType','SampleShape','PolaVal','SampleAbs','dark image','background image']
534	for key in keys:
535	if key not in Data: continue #uncalibrated!
536	File.write(key+':'+str(Data[key])+'\n')
537	File.close()
538	mask = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Masks'))
539	G2imG.CleanupMasks(mask)
540	print('Writing '+imroot+'.immask')
541	File = open(imroot+'.immask','w')
542	for key in ['Points','Rings','Arcs','Polygons','Frames','Thresholds']:
543	File.write(key+':'+str(mask[key])+'\n')
544	File.close()
545
546	def PutG2Image(filename,Comments,Data,Npix,image):
547	'Write an image as a python pickle - might be better as an .edf file?'
548	File = open(filename,'wb')
549	cPickle.dump([Comments,Data,Npix,image],File,1)
550	File.close()
551	return
552
553	# should get moved to importer when ready to test
554	def GetEdfData(filename,imageOnly=False):
555	'Read European detector data edf file'
556	import struct as st
557	import array as ar
558	if not imageOnly:
559	print 'Read European detector data edf file: ',filename
560	File = open(filename,'rb')
561	fileSize = os.stat(filename).st_size
562	head = File.read(3072)
563	lines = head.split('\n')
564	sizexy = [0,0]
565	pixSize = [154,154] #Pixium4700?
566	cent = [0,0]
567	wave = 1.54187 #default <CuKa>
568	dist = 1000.
569	head = ['European detector data',]
570	for line in lines:
571	line = line.replace(';',' ').strip()
572	fields = line.split()
573	if 'Dim_1' in line:
574	sizexy[0] = int(fields[2])
575	elif 'Dim_2' in line:
576	sizexy[1] = int(fields[2])
577	elif 'DataType' in line:
578	dType = fields[2]
579	elif 'wavelength' in line:
580	wave = float(fields[2])
581	elif 'Size' in line:
582	imSize = int(fields[2])
583	# elif 'DataType' in lines:
584	# dType = fields[2]
585	elif 'pixel_size_x' in line:
586	pixSize[0] = float(fields[2])
587	elif 'pixel_size_y' in line:
588	pixSize[1] = float(fields[2])
589	elif 'beam_center_x' in line:
590	cent[0] = float(fields[2])
591	elif 'beam_center_y' in line:
592	cent[1] = float(fields[2])
593	elif 'refined_distance' in line:
594	dist = float(fields[2])
595	if line:
596	head.append(line)
597	else: #blank line at end of header
598	break
599	File.seek(fileSize-imSize)
600	if dType == 'UnsignedShort':
601	image = np.array(ar.array('H',File.read(imSize)),dtype=np.int32)
602	elif dType == 'UnsignedInt':
603	image = np.array(ar.array('L',File.read(imSize)),dtype=np.int32)
604	elif dType == 'UnsignedLong':
605	image = np.array(ar.array('L',File.read(imSize)),dtype=np.int32)
606	elif dType == 'SignedInteger':
607	image = np.array(ar.array('l',File.read(imSize)),dtype=np.int32)
608	image = np.reshape(image,(sizexy[1],sizexy[0]))
609	data = {'pixelSize':pixSize,'wavelength':wave,'distance':dist,'center':cent,'size':sizexy}
610	Npix = sizexy[0]*sizexy[1]
611	File.close()
612	if imageOnly:
613	return image
614	else:
615	return head,data,Npix,image
616
617	# should get moved to importer when ready to test
618	def GetRigaku(filename,imageOnly=False):
619	'Read Rigaku R-Axis IV image file'
620	import struct as st
621	import array as ar
622	if not imageOnly:
623	print 'Read Rigaku R-Axis IV file: ',filename
624	File = open(filename,'rb')
625	fileSize = os.stat(filename).st_size
626	Npix = (fileSize-6000)/2
627	Head = File.read(6000)
628	head = ['Rigaku R-Axis IV detector data',]
629	image = np.array(ar.array('H',File.read(fileSize-6000)),dtype=np.int32)
630	print fileSize,image.shape
631	print head
632	if Npix == 9000000:
633	sizexy = [3000,3000]
634	pixSize = [100.,100.]
635	elif Npix == 2250000:
636	sizexy = [1500,1500]
637	pixSize = [200.,200.]
638	else:
639	sizexy = [6000,6000]
640	pixSize = [50.,50.]
641	image = np.reshape(image,(sizexy[1],sizexy[0]))
642	data = {'pixelSize':pixSize,'wavelength':1.5428,'distance':250.0,'center':[150.,150.],'size':sizexy}
643	File.close()
644	if imageOnly:
645	return image
646	else:
647	return head,data,Npix,image
648
649	# should get moved to importer when ready to test
650	def GetImgData(filename,imageOnly=False):
651	'Read an ADSC image file'
652	import struct as st
653	import array as ar
654	if not imageOnly:
655	print 'Read ADSC img file: ',filename
656	File = open(filename,'rb')
657	head = File.read(511)
658	lines = head.split('\n')
659	head = []
660	center = [0,0]
661	for line in lines[1:-2]:
662	line = line.strip()[:-1]
663	if line:
664	if 'SIZE1' in line:
665	size = int(line.split('=')[1])
666	Npix = size*size
667	elif 'WAVELENGTH' in line:
668	wave = float(line.split('=')[1])
669	elif 'BIN' in line:
670	if line.split('=')[1] == '2x2':
671	pixel=(102,102)
672	else:
673	pixel = (51,51)
674	elif 'DISTANCE' in line:
675	distance = float(line.split('=')[1])
676	elif 'CENTER_X' in line:
677	center[0] = float(line.split('=')[1])
678	elif 'CENTER_Y' in line:
679	center[1] = float(line.split('=')[1])
680	head.append(line)
681	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center,'size':[size,size]}
682	image = []
683	row = 0
684	pos = 512
685	File.seek(pos)
686	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
687	image = np.reshape(image,(sizexy[1],sizexy[0]))
688	# image = np.zeros(shape=(size,size),dtype=np.int32)
689	# while row < size:
690	# File.seek(pos)
691	# line = ar.array('H',File.read(2*size))
692	# image[row] = np.asarray(line)
693	# row += 1
694	# pos += 2*size
695	File.close()
696	if imageOnly:
697	return image
698	else:
699	return lines[1:-2],data,Npix,image
700
701	# should get moved to importer when ready to test
702	def GetMAR345Data(filename,imageOnly=False):
703	'Read a MAR-345 image plate image'
704	import array as ar
705	import struct as st
706	try:
707	import pack_f as pf
708	except:
709	msg = wx.MessageDialog(None, message="Unable to load the GSAS MAR image decompression, pack_f",
710	caption="Import Error",
711	style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
712	msg.ShowModal()
713	return None,None,None,None
714
715	if not imageOnly:
716	print 'Read Mar345 file: ',filename
717	File = open(filename,'rb')
718	head = File.read(4095)
719	numbers = st.unpack('<iiiiiiiiii',head[:40])
720	lines = head[128:].split('\n')
721	head = []
722	for line in lines:
723	line = line.strip()
724	if 'PIXEL' in line:
725	values = line.split()
726	pixel = (int(values[2]),int(values[4])) #in microns
727	elif 'WAVELENGTH' in line:
728	wave = float(line.split()[1])
729	elif 'DISTANCE' in line:
730	distance = float(line.split()[1]) #in mm
731	if not distance:
732	distance = 500.
733	elif 'CENTER' in line:
734	values = line.split()
735	center = [float(values[2])/10.,float(values[4])/10.] #make in mm from pixels
736	if line:
737	head.append(line)
738	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center}
739	for line in head:
740	if 'FORMAT' in line[0:6]:
741	items = line.split()
742	sizex = int(items[1])
743	Npix = int(items[3])
744	sizey = int(Npix/sizex)
745	pos = 4096
746	data['size'] = [sizex,sizey]
747	File.seek(pos)
748	line = File.read(8)
749	while 'CCP4' not in line: #get past overflow list for now
750	line = File.read(8)
751	pos += 8
752	pos += 37
753	File.seek(pos)
754	raw = File.read()
755	File.close()
756	image = np.zeros(shape=(sizex,sizey),dtype=np.int32)
757
758	image = np.flipud(pf.pack_f(len(raw),raw,sizex,sizey,image).T) #transpose to get it right way around & flip
759	if imageOnly:
760	return image
761	else:
762	return head,data,Npix,image
763
764	def ProjFileOpen(G2frame,showProvenance=True):
765	'Read a GSAS-II project file and load into the G2 data tree'
766	if not os.path.exists(G2frame.GSASprojectfile):
767	print ('\n*** Error attempt to open project file that does not exist:\n '+
768	str(G2frame.GSASprojectfile))
769	return
770	LastSavedUsing = None
771	file = open(G2frame.GSASprojectfile,'rb')
772	if showProvenance: print 'loading from file: ',G2frame.GSASprojectfile
773	G2frame.SetTitle("GSAS-II data tree: "+
774	os.path.split(G2frame.GSASprojectfile)[1])
775	wx.BeginBusyCursor()
776	try:
777	while True:
778	try:
779	data = cPickle.load(file)
780	except EOFError:
781	break
782	datum = data[0]
783
784	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=datum[0])
785	if 'PWDR' in datum[0]:
786	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
787	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
788	G2frame.PatternTree.SetItemPyData(Id,datum[1][:3]) #temp. trim off junk (patch?)
789	elif datum[0].startswith('HKLF'):
790	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
791	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
792	G2frame.PatternTree.SetItemPyData(Id,datum[1])
793	else:
794	G2frame.PatternTree.SetItemPyData(Id,datum[1])
795	if datum[0] == 'Controls' and 'LastSavedUsing' in datum[1]:
796	LastSavedUsing = datum[1]['LastSavedUsing']
797	if datum[0] == 'Controls' and 'PythonVersions' in datum[1] and GSASIIpath.GetConfigValue('debug') and showProvenance:
798	print('Packages used to create .GPX file:')
799	if 'dict' in str(type(datum[1]['PythonVersions'])): #patch
800	for p in sorted(datum[1]['PythonVersions'],key=lambda s: s.lower()):
801	print("{:>14s}: {:s}".format(p[0],p[1]))
802	else:
803	for p in datum[1]['PythonVersions']:
804	print("{:<12s} {:s}".format(p[0]+':',p[1]))
805	for datus in data[1:]:
806	sub = G2frame.PatternTree.AppendItem(Id,datus[0])
807	#patch
808	if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
809	if 'PWDR' in datum[0]:
810	datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
811	else:
812	datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
813	for item in datus[1][0]: #zip makes tuples - now make lists!
814	datus[1][0][item] = list(datus[1][0][item])
815	#end patch
816	G2frame.PatternTree.SetItemPyData(sub,datus[1])
817	if 'IMG' in datum[0]: #retrieve image default flag & data if set
818	Data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Image Controls'))
819	if Data['setDefault']:
820	G2frame.imageDefault = Data
821	file.close()
822	if LastSavedUsing:
823	print('GPX load successful. Last saved with GSAS-II version '+LastSavedUsing)
824	else:
825	print('project load successful')
826	G2frame.NewPlot = True
827	except:
828	msg = wx.MessageDialog(G2frame,message="Error reading file "+
829	str(G2frame.GSASprojectfile)+". This is not a GSAS-II .gpx file",
830	caption="Load Error",style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
831	msg.ShowModal()
832	finally:
833	wx.EndBusyCursor()
834	G2frame.Status.SetStatusText('To reorder tree items, use mouse RB to drag/drop them')
835
836	def ProjFileSave(G2frame):
837	'Save a GSAS-II project file'
838	if not G2frame.PatternTree.IsEmpty():
839	file = open(G2frame.GSASprojectfile,'wb')
840	print 'save to file: ',G2frame.GSASprojectfile
841	# stick the file name into the tree and version info into tree so they are saved.
842	# (Controls should always be created at this point)
843	try:
844	Controls = G2frame.PatternTree.GetItemPyData(
845	G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
846	Controls['LastSavedAs'] = os.path.abspath(G2frame.GSASprojectfile)
847	Controls['LastSavedUsing'] = str(GSASIIpath.GetVersionNumber())
848	Controls['PythonVersions'] = G2frame.PackageVersions
849	except:
850	pass
851	wx.BeginBusyCursor()
852	try:
853	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
854	while item:
855	data = []
856	name = G2frame.PatternTree.GetItemText(item)
857	data.append([name,G2frame.PatternTree.GetItemPyData(item)])
858	item2, cookie2 = G2frame.PatternTree.GetFirstChild(item)
859	while item2:
860	name = G2frame.PatternTree.GetItemText(item2)
861	data.append([name,G2frame.PatternTree.GetItemPyData(item2)])
862	item2, cookie2 = G2frame.PatternTree.GetNextChild(item, cookie2)
863	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
864	cPickle.dump(data,file,1)
865	file.close()
866	pth = os.path.split(os.path.abspath(G2frame.GSASprojectfile))[0]
867	if GSASIIpath.GetConfigValue('Save_paths'): G2G.SaveGPXdirectory(pth)
868	G2frame.LastGPXdir = pth
869	finally:
870	wx.EndBusyCursor()
871	print('project save successful')
872
873	def SaveIntegration(G2frame,PickId,data,Overwrite=False):
874	'Save image integration results as powder pattern(s)'
875	azms = G2frame.Integrate[1]
876	X = G2frame.Integrate[2][:-1]
877	N = len(X)
878	Id = G2frame.PatternTree.GetItemParent(PickId)
879	name = G2frame.PatternTree.GetItemText(Id)
880	name = name.replace('IMG ',data['type']+' ')
881	Comments = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Comments'))
882	if 'PWDR' in name:
883	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','SH/L','Azimuth']
884	codes = [0 for i in range(11)]
885	elif 'SASD' in name:
886	names = ['Type','Lam','Zero','Azimuth']
887	codes = [0 for i in range(4)]
888	X = 4.np.pinpsind(X/2.)/data['wavelength'] #convert to q
889	Xminmax = [X[0],X[-1]]
890	LRazm = data['LRazimuth']
891	Azms = []
892	dazm = 0.
893	if data['fullIntegrate'] and data['outAzimuths'] == 1:
894	Azms = [45.0,] #a poor man's average?
895	else:
896	for i,azm in enumerate(azms[:-1]):
897	if azm > 360. and azms[i+1] > 360.:
898	Azms.append(G2img.meanAzm(azm%360.,azms[i+1]%360.))
899	else:
900	Azms.append(G2img.meanAzm(azm,azms[i+1]))
901	dazm = np.min(np.abs(np.diff(azms)))/2.
902	G2frame.IntgOutList = []
903	for i,azm in enumerate(azms[:-1]):
904	Aname = name+" Azm= %.2f"%((azm+dazm)%360.)
905	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
906	# if Overwrite delete any duplicate
907	if Overwrite and G2gd.GetPatternTreeItemId(G2frame,G2frame.root,Aname):
908	print('Replacing '+Aname)
909	item = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,Aname)
910	G2frame.PatternTree.Delete(item)
911	else:
912	nOcc = 0
913	while item:
914	Name = G2frame.PatternTree.GetItemText(item)
915	if Aname in Name:
916	nOcc += 1
917	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
918	if nOcc:
919	Aname += '(%d)'%(nOcc)
920	Sample = G2pdG.SetDefaultSample()
921	Sample['Gonio. radius'] = data['distance']
922	Sample['Omega'] = data['GonioAngles'][0]
923	Sample['Chi'] = data['GonioAngles'][1]
924	Sample['Phi'] = data['GonioAngles'][2]
925	Sample['Azimuth'] = (azm+dazm)%360. #put here as bin center
926	if 'PWDR' in Aname:
927	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!
928	elif 'SASD' in Aname:
929	Sample['Trans'] = data['SampleAbs'][0]
930	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
931	Y = G2frame.Integrate[0][i]
932	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
933	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=Aname)
934	G2frame.IntgOutList.append(Id)
935	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
936	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Limits'),[tuple(Xminmax),Xminmax])
937	if 'PWDR' in Aname:
938	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Background'),[['chebyschev',1,3,1.0,0.0,0.0],
939	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
940	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
941	for item in inst[0]:
942	inst[0][item] = list(inst[0][item])
943	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Instrument Parameters'),inst)
944	if 'PWDR' in Aname:
945	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
946	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
947	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Index Peak List'),[[],[]])
948	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Unit Cells List'),[])
949	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Reflection Lists'),{})
950	elif 'SASD' in Aname:
951	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
952	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
953	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
954	valuesdict = {
955	'wtFactor':1.0,
956	'Dummy':False,
957	'ranId':ran.randint(0,sys.maxint),
958	'Offset':[0.0,0.0],'delOffset':0.02,'refOffset':-1.0,'refDelt':0.01,
959	'qPlot':False,'dPlot':False,'sqrtPlot':False
960	}
961	G2frame.PatternTree.SetItemPyData(
962	Id,[valuesdict,
963	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
964	return Id #last powder pattern generated
965
966	def PDFSave(G2frame,exports):
967	'Save a PDF G(r) and S(Q) in column formats'
968	for export in exports:
969	PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
970	SQname = 'S(Q)'+export[4:]
971	GRname = 'G(R)'+export[4:]
972	sqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.sq')
973	grfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.gr')
974	sqId = G2gd.GetPatternTreeItemId(G2frame, PickId, SQname)
975	grId = G2gd.GetPatternTreeItemId(G2frame, PickId, GRname)
976	sqdata = np.array(G2frame.PatternTree.GetItemPyData(sqId)[1][:2]).T
977	grdata = np.array(G2frame.PatternTree.GetItemPyData(grId)[1][:2]).T
978	sqfile = open(sqfilename,'w')
979	grfile = open(grfilename,'w')
980	sqfile.write('#T S(Q) %s\n'%(export))
981	grfile.write('#T G(R) %s\n'%(export))
982	sqfile.write('#L Q S(Q)\n')
983	grfile.write('#L R G(R)\n')
984	for q,sq in sqdata:
985	sqfile.write("%15.6g %15.6g\n" % (q,sq))
986	sqfile.close()
987	for r,gr in grdata:
988	grfile.write("%15.6g %15.6g\n" % (r,gr))
989	grfile.close()
990
991	def PeakListSave(G2frame,file,peaks):
992	'Save powder peaks to a data file'
993	print 'save peak list to file: ',G2frame.peaklistfile
994	if not peaks:
995	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
996	try:
997	result = dlg.ShowModal()
998	finally:
999	dlg.Destroy()
1000	return
1001	for peak in peaks:
1002	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
1003	(peak[0],peak[2],peak[4],peak[6]))
1004	print 'peak list saved'
1005
1006	def IndexPeakListSave(G2frame,peaks):
1007	'Save powder peaks from the indexing list'
1008	file = open(G2frame.peaklistfile,'wa')
1009	print 'save index peak list to file: ',G2frame.peaklistfile
1010	wx.BeginBusyCursor()
1011	try:
1012	if not peaks:
1013	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1014	try:
1015	result = dlg.ShowModal()
1016	finally:
1017	dlg.Destroy()
1018	return
1019	for peak in peaks:
1020	file.write("%12.6f\n" % (peak[7]))
1021	file.close()
1022	finally:
1023	wx.EndBusyCursor()
1024	print 'index peak list saved'
1025
1026	def SetNewPhase(Name='New Phase',SGData=None,cell=None,Super=None):
1027	'''Create a new phase dict with default values for various parameters
1028
1029	:param str Name: Name for new Phase
1030
1031	:param dict SGData: space group data from :func:`GSASIIspc:SpcGroup`;
1032	defaults to data for P 1
1033
1034	:param list cell: unit cell parameter list; defaults to
1035	[1.0,1.0,1.0,90.,90,90.,1.]
1036
1037	'''
1038	if SGData is None: SGData = G2spc.SpcGroup('P 1')[1]
1039	if cell is None: cell=[1.0,1.0,1.0,90.,90,90.,1.]
1040	phaseData = {
1041	'ranId':ran.randint(0,sys.maxint),
1042	'General':{
1043	'Name':Name,
1044	'Type':'nuclear',
1045	'AtomPtrs':[3,1,7,9],
1046	'SGData':SGData,
1047	'Cell':[False,]+cell,
1048	'Pawley dmin':1.0,
1049	'Data plot type':'None',
1050	'SH Texture':{
1051	'Order':0,
1052	'Model':'cylindrical',
1053	'Sample omega':[False,0.0],
1054	'Sample chi':[False,0.0],
1055	'Sample phi':[False,0.0],
1056	'SH Coeff':[False,{}],
1057	'SHShow':False,
1058	'PFhkl':[0,0,1],
1059	'PFxyz':[0,0,1],
1060	'PlotType':'Pole figure',
1061	'Penalty':[['',],0.1,False,1.0]}},
1062	'Atoms':[],
1063	'Drawing':{},
1064	'Histograms':{},
1065	'Pawley ref':[],
1066	'RBModels':{},
1067	}
1068	if Super and Super.get('Use',False):
1069	phaseData['General'].update({'Type':'modulated','Super':True,'SuperSg':Super['ssSymb']})
1070	phaseData['General']['SSGData'] = G2spc.SSpcGroup(SGData,Super['ssSymb'])
1071	phaseData['General']['SuperVec'] = [Super['ModVec'],False,Super['maxH']]
1072
1073	return phaseData
1074
1075	class MultipleChoicesDialog(wx.Dialog):
1076	'''A dialog that offers a series of choices, each with a
1077	title and a wx.Choice widget. Intended to be used Modally.
1078	typical input:
1079
1080	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1081	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1082
1083	selections are placed in self.chosen when OK is pressed
1084	'''
1085	def __init__(self,choicelist,headinglist,
1086	head='Select options',
1087	title='Please select from options below',
1088	parent=None):
1089	self.chosen = []
1090	wx.Dialog.__init__(
1091	self,parent,wx.ID_ANY,head,
1092	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
1093	panel = wx.Panel(self)
1094	mainSizer = wx.BoxSizer(wx.VERTICAL)
1095	mainSizer.Add((10,10),1)
1096	topLabl = wx.StaticText(panel,wx.ID_ANY,title)
1097	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.CENTER,10)
1098	self.ChItems = []
1099	for choice,lbl in zip(choicelist,headinglist):
1100	mainSizer.Add((10,10),1)
1101	self.chosen.append(0)
1102	topLabl = wx.StaticText(panel,wx.ID_ANY,' '+lbl)
1103	mainSizer.Add(topLabl,0,wx.ALIGN_LEFT,10)
1104	self.ChItems.append(wx.Choice(self, wx.ID_ANY, (100, 50), choices = choice))
1105	mainSizer.Add(self.ChItems[-1],0,wx.ALIGN_CENTER,10)
1106
1107	OkBtn = wx.Button(panel,-1,"Ok")
1108	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
1109	cancelBtn = wx.Button(panel,-1,"Cancel")
1110	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
1111	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1112	btnSizer.Add((20,20),1)
1113	btnSizer.Add(OkBtn)
1114	btnSizer.Add((20,20),1)
1115	btnSizer.Add(cancelBtn)
1116	btnSizer.Add((20,20),1)
1117	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1118	panel.SetSizer(mainSizer)
1119	panel.Fit()
1120	self.Fit()
1121
1122	def OnOk(self,event):
1123	parent = self.GetParent()
1124	if parent is not None: parent.Raise()
1125	# save the results from the choice widgets
1126	self.chosen = []
1127	for w in self.ChItems:
1128	self.chosen.append(w.GetSelection())
1129	self.EndModal(wx.ID_OK)
1130
1131	def OnCancel(self,event):
1132	parent = self.GetParent()
1133	if parent is not None: parent.Raise()
1134	self.chosen = []
1135	self.EndModal(wx.ID_CANCEL)
1136
1137	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1138	confirmoverwrite=True, parent=None,
1139	multipleselect=False):
1140	'''If the filename is a zip file, extract a file from that
1141	archive.
1142
1143	:param list Selection: used to predefine the name of the file
1144	to be extracted. Filename case and zip directory name are
1145	ignored in selection; the first matching file is used.
1146
1147	:param bool confirmread: if True asks the user to confirm before expanding
1148	the only file in a zip
1149
1150	:param bool confirmoverwrite: if True asks the user to confirm
1151	before overwriting if the extracted file already exists
1152
1153	:param bool multipleselect: if True allows more than one zip
1154	file to be extracted, a list of file(s) is returned.
1155	If only one file is present, do not ask which one, otherwise
1156	offer a list of choices (unless selection is used).
1157
1158	:returns: the name of the file that has been created or a
1159	list of files (see multipleselect)
1160
1161	If the file is not a zipfile, return the name of the input file.
1162	If the zipfile is empty or no file has been selected, return None
1163	'''
1164	import zipfile # do this now, since we can save startup time by doing this only on need
1165	import shutil
1166	zloc = os.path.split(filename)[0]
1167	if not zipfile.is_zipfile(filename):
1168	#print("not zip")
1169	return filename
1170
1171	z = zipfile.ZipFile(filename,'r')
1172	zinfo = z.infolist()
1173
1174	if len(zinfo) == 0:
1175	#print('Zip has no files!')
1176	zlist = [-1]
1177	if selection:
1178	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1179	if selection.lower() in choices:
1180	zlist = [choices.index(selection.lower())]
1181	else:
1182	print('debug: file '+str(selection)+' was not found in '+str(filename))
1183	zlist = [-1]
1184	elif len(zinfo) == 1 and confirmread:
1185	result = wx.ID_NO
1186	dlg = wx.MessageDialog(
1187	parent,
1188	'Is file '+str(zinfo[0].filename)+
1189	' what you want to extract from '+
1190	str(os.path.split(filename)[1])+'?',
1191	'Confirm file',
1192	wx.YES_NO \| wx.ICON_QUESTION)
1193	try:
1194	result = dlg.ShowModal()
1195	finally:
1196	dlg.Destroy()
1197	if result == wx.ID_NO:
1198	zlist = [-1]
1199	else:
1200	zlist = [0]
1201	elif len(zinfo) == 1:
1202	zlist = [0]
1203	elif multipleselect:
1204	# select one or more from a from list
1205	choices = [i.filename for i in zinfo]
1206	dlg = G2G.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1207	'Choose file(s)',choices)
1208	if dlg.ShowModal() == wx.ID_OK:
1209	zlist = dlg.GetSelections()
1210	else:
1211	zlist = []
1212	dlg.Destroy()
1213	else:
1214	# select one from a from list
1215	choices = [i.filename for i in zinfo]
1216	dlg = wx.SingleChoiceDialog(parent,
1217	'Select file to extract from zip file'+str(filename),'Choose file',
1218	choices,)
1219	if dlg.ShowModal() == wx.ID_OK:
1220	zlist = [dlg.GetSelection()]
1221	else:
1222	zlist = [-1]
1223	dlg.Destroy()
1224
1225	outlist = []
1226	for zindex in zlist:
1227	if zindex >= 0:
1228	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1229	if os.path.exists(efil) and confirmoverwrite:
1230	result = wx.ID_NO
1231	dlg = wx.MessageDialog(parent,
1232	'File '+str(efil)+' already exists. OK to overwrite it?',
1233	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1234	try:
1235	result = dlg.ShowModal()
1236	finally:
1237	dlg.Destroy()
1238	if result == wx.ID_NO:
1239	zindex = -1
1240	if zindex >= 0:
1241	# extract the file to the current directory, regardless of it's original path
1242	#z.extract(zinfo[zindex],zloc)
1243	eloc,efil = os.path.split(zinfo[zindex].filename)
1244	outfile = os.path.join(zloc, efil)
1245	fpin = z.open(zinfo[zindex])
1246	fpout = file(outfile, "wb")
1247	shutil.copyfileobj(fpin, fpout)
1248	fpin.close()
1249	fpout.close()
1250	outlist.append(outfile)
1251	z.close()
1252	if multipleselect and len(outlist) >= 1:
1253	return outlist
1254	elif len(outlist) == 1:
1255	return outlist[0]
1256	else:
1257	return None
1258
1259	######################################################################
1260	# base classes for reading various types of data files
1261	# not used directly, only by subclassing
1262	######################################################################
1263	try:
1264	E,SGData = G2spc.SpcGroup('P 1') # data structure for default space group
1265	except: # errors on doc build
1266	SGData = None
1267	P1SGData = SGData
1268	######################################################################
1269	class ImportBaseclass(object):
1270	'''Defines a base class for the reading of input files (diffraction
1271	data, coordinates,...). See :ref:`Writing a Import Routine<Import_routines>`
1272	for an explanation on how to use a subclass of this class.
1273	'''
1274	class ImportException(Exception):
1275	'''Defines an Exception that is used when an import routine hits an expected error,
1276	usually in .Reader.
1277
1278	Good practice is that the Reader should define a value in self.errors that
1279	tells the user some information about what is wrong with their file.
1280	'''
1281	pass
1282
1283	UseReader = True # in __init__ set value of self.UseReader to False to skip use of current importer
1284	def __init__(self,formatName,longFormatName=None,
1285	extensionlist=[],strictExtension=False,):
1286	self.formatName = formatName # short string naming file type
1287	if longFormatName: # longer string naming file type
1288	self.longFormatName = longFormatName
1289	else:
1290	self.longFormatName = formatName
1291	# define extensions that are allowed for the file type
1292	# for windows, remove any extensions that are duplicate, as case is ignored
1293	if sys.platform == 'windows' and extensionlist:
1294	extensionlist = list(set([s.lower() for s in extensionlist]))
1295	self.extensionlist = extensionlist
1296	# If strictExtension is True, the file will not be read, unless
1297	# the extension matches one in the extensionlist
1298	self.strictExtension = strictExtension
1299	self.errors = ''
1300	self.warnings = ''
1301	# used for readers that will use multiple passes to read
1302	# more than one data block
1303	self.repeat = False
1304	self.selections = []
1305	self.repeatcount = 0
1306	self.readfilename = '?'
1307	#print 'created',self.__class__
1308
1309	def ReInitialize(self):
1310	'Reinitialize the Reader to initial settings'
1311	self.errors = ''
1312	self.warnings = ''
1313	self.repeat = False
1314	self.repeatcount = 0
1315	self.readfilename = '?'
1316
1317	def BlockSelector(self, ChoiceList, ParentFrame=None,title='Select a block',
1318	size=None, header='Block Selector',useCancel=True):
1319	''' Provide a wx dialog to select a block if the file contains more
1320	than one set of data and one must be selected
1321	'''
1322	if useCancel:
1323	dlg = wx.SingleChoiceDialog(
1324	ParentFrame,title, header,ChoiceList)
1325	else:
1326	dlg = wx.SingleChoiceDialog(
1327	ParentFrame,title, header,ChoiceList,
1328	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.OK\|wx.CENTRE)
1329	if size: dlg.SetSize(size)
1330	dlg.CenterOnParent()
1331	if dlg.ShowModal() == wx.ID_OK:
1332	sel = dlg.GetSelection()
1333	return sel
1334	else:
1335	return None
1336	dlg.Destroy()
1337
1338	def MultipleBlockSelector(self, ChoiceList, ParentFrame=None,
1339	title='Select a block',size=None, header='Block Selector'):
1340	'''Provide a wx dialog to select a block of data if the
1341	file contains more than one set of data and one must be
1342	selected.
1343
1344	:returns: a list of the selected blocks
1345	'''
1346	dlg = wx.MultiChoiceDialog(ParentFrame,title, header,ChoiceList+['Select all'],
1347	wx.CHOICEDLG_STYLE)
1348	dlg.CenterOnScreen()
1349	if size: dlg.SetSize(size)
1350	if dlg.ShowModal() == wx.ID_OK:
1351	sel = dlg.GetSelections()
1352	else:
1353	return []
1354	dlg.Destroy()
1355	selected = []
1356	if len(ChoiceList) in sel:
1357	return range(len(ChoiceList))
1358	else:
1359	return sel
1360	return selected
1361
1362	def MultipleChoicesDialog(self, choicelist, headinglist, ParentFrame=None, **kwargs):
1363	'''A modal dialog that offers a series of choices, each with a title and a wx.Choice
1364	widget. Typical input:
1365
1366	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1367
1368	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1369
1370	optional keyword parameters are: head (window title) and title
1371	returns a list of selected indicies for each choice (or None)
1372	'''
1373	result = None
1374	dlg = MultipleChoicesDialog(choicelist,headinglist,
1375	parent=ParentFrame, **kwargs)
1376	dlg.CenterOnParent()
1377	if dlg.ShowModal() == wx.ID_OK:
1378	result = dlg.chosen
1379	dlg.Destroy()
1380	return result
1381
1382	def ShowBusy(self):
1383	wx.BeginBusyCursor()
1384	# wx.Yield() # make it happen now!
1385
1386	def DoneBusy(self):
1387	wx.EndBusyCursor()
1388	wx.Yield() # make it happen now!
1389
1390	# def Reader(self, filename, filepointer, ParentFrame=None, **unused):
1391	# '''This method must be supplied in the child class to read the file.
1392	# if the read fails either return False or raise an Exception
1393	# preferably of type ImportException.
1394	# '''
1395	# #start reading
1396	# raise ImportException("Error occurred while...")
1397	# self.errors += "Hint for user on why the error occur
1398	# return False # if an error occurs
1399	# return True # if read OK
1400
1401	def ExtensionValidator(self, filename):
1402	'''This methods checks if the file has the correct extension
1403	Return False if this filename will not be supported by this reader
1404	Return True if the extension matches the list supplied by the reader
1405	Return None if the reader allows un-registered extensions
1406	'''
1407	if filename:
1408	ext = os.path.splitext(filename)[1]
1409	if sys.platform == 'windows': ext = ext.lower()
1410	if ext in self.extensionlist: return True
1411	if self.strictExtension: return False
1412	return None
1413
1414	def ContentsValidator(self, filepointer):
1415	'''This routine will attempt to determine if the file can be read
1416	with the current format.
1417	This will typically be overridden with a method that
1418	takes a quick scan of [some of]
1419	the file contents to do a "sanity" check if the file
1420	appears to match the selected format.
1421	Expected to be called via self.Validator()
1422	'''
1423	#filepointer.seek(0) # rewind the file pointer
1424	return True
1425
1426	def CIFValidator(self, filepointer):
1427	'''A :meth:`ContentsValidator` for use to validate CIF files.
1428	'''
1429	for i,l in enumerate(filepointer):
1430	if i >= 1000: return True
1431	'''Encountered only blank lines or comments in first 1000
1432	lines. This is unlikely, but assume it is CIF anyway, since we are
1433	even less likely to find a file with nothing but hashes and
1434	blank lines'''
1435	line = l.strip()
1436	if len(line) == 0: # ignore blank lines
1437	continue
1438	elif line.startswith('#'): # ignore comments
1439	continue
1440	elif line.startswith('data_'): # on the right track, accept this file
1441	return True
1442	else: # found something invalid
1443	self.errors = 'line '+str(i+1)+' contains unexpected data:\n'
1444	self.errors += ' '+str(l)
1445	self.errors += ' Note: a CIF should only have blank lines or comments before'
1446	self.errors += ' a data_ statement begins a block.'
1447	return False
1448
1449	######################################################################
1450	class ImportPhase(ImportBaseclass):
1451	'''Defines a base class for the reading of files with coordinates
1452
1453	Objects constructed that subclass this (in import/G2phase_*.py etc.) will be used
1454	in :meth:`GSASII.GSASII.OnImportPhase`.
1455	See :ref:`Writing a Import Routine<Import_Routines>`
1456	for an explanation on how to use this class.
1457
1458	'''
1459	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1460	strictExtension=False,):
1461	# call parent __init__
1462	ImportBaseclass.__init__(self,formatName,longFormatName,
1463	extensionlist,strictExtension)
1464	self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
1465	self.Constraints = None
1466
1467	def PhaseSelector(self, ChoiceList, ParentFrame=None,
1468	title='Select a phase', size=None,header='Phase Selector'):
1469	''' Provide a wx dialog to select a phase if the file contains more
1470	than one phase
1471	'''
1472	return self.BlockSelector(ChoiceList,ParentFrame,title,
1473	size,header)
1474
1475	######################################################################
1476	class ImportStructFactor(ImportBaseclass):
1477	'''Defines a base class for the reading of files with tables
1478	of structure factors.
1479
1480	Structure factors are read with a call to :meth:`GSASII.GSASII.OnImportSfact`
1481	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`, which calls
1482	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1483	:meth:`Reader`.
1484
1485	See :ref:`Writing a Import Routine<Import_Routines>`
1486	for an explanation on how to use import classes in general. The specifics
1487	for reading a structure factor histogram require that
1488	the ``Reader()`` routine in the import
1489	class need to do only a few things: It
1490	should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
1491	and set :attr:`Parameters` with the instrument parameters
1492	(initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
1493	'''
1494	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1495	strictExtension=False,):
1496	ImportBaseclass.__init__(self,formatName,longFormatName,
1497	extensionlist,strictExtension)
1498
1499	# define contents of Structure Factor entry
1500	self.Parameters = []
1501	'self.Parameters is a list with two dicts for data parameter settings'
1502	self.InitParameters()
1503	self.RefDict = {'RefList':[],'FF':{},'Super':0}
1504	self.Banks = [] #for multi bank data (usually TOF)
1505	'''self.RefDict is a dict containing the reflection information, as read from the file.
1506	Item 'RefList' contains the reflection information. See the
1507	:ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
1508	for the contents of each row. Dict element 'FF'
1509	contains the form factor values for each element type; if this entry
1510	is left as initialized (an empty list) it will be initialized as needed later.
1511	'''
1512	def ReInitialize(self):
1513	'Reinitialize the Reader to initial settings'
1514	ImportBaseclass.ReInitialize(self)
1515	self.InitParameters()
1516	self.Banks = [] #for multi bank data (usually TOF)
1517	self.RefDict = {'RefList':[],'FF':{},'Super':0}
1518
1519	def InitParameters(self):
1520	'initialize the instrument parameters structure'
1521	Lambda = 0.70926
1522	HistType = 'SXC'
1523	self.Parameters = [{'Type':[HistType,HistType], # create the structure
1524	'Lam':[Lambda,Lambda]
1525	}, {}]
1526	'Parameters is a list with two dicts for data parameter settings'
1527
1528	def UpdateParameters(self,Type=None,Wave=None):
1529	'Revise the instrument parameters'
1530	if Type is not None:
1531	self.Parameters[0]['Type'] = [Type,Type]
1532	if Wave is not None:
1533	self.Parameters[0]['Lam'] = [Wave,Wave]
1534
1535	######################################################################
1536	class ImportPowderData(ImportBaseclass):
1537	'''Defines a base class for the reading of files with powder data.
1538
1539	Objects constructed that subclass this (in import/G2pwd_*.py etc.) will be used
1540	in :meth:`GSASII.GSASII.OnImportPowder`.
1541	See :ref:`Writing a Import Routine<Import_Routines>`
1542	for an explanation on how to use this class.
1543	'''
1544	def __init__(self,formatName,longFormatName=None,
1545	extensionlist=[],strictExtension=False,):
1546	ImportBaseclass.__init__(self,formatName,longFormatName,
1547	extensionlist,strictExtension)
1548	self.clockWd = None # used in TOF
1549	self.ReInitialize()
1550
1551	def ReInitialize(self):
1552	'Reinitialize the Reader to initial settings'
1553	ImportBaseclass.ReInitialize(self)
1554	self.powderentry = ['',None,None] # (filename,Pos,Bank)
1555	self.powderdata = [] # Powder dataset
1556	'''A powder data set is a list with items [x,y,w,yc,yb,yd]:
1557	np.array(x), # x-axis values
1558	np.array(y), # powder pattern intensities
1559	np.array(w), # 1/sig(intensity)^2 values (weights)
1560	np.array(yc), # calc. intensities (zero)
1561	np.array(yb), # calc. background (zero)
1562	np.array(yd), # obs-calc profiles
1563	'''
1564	self.comments = []
1565	self.idstring = ''
1566	self.Sample = G2pdG.SetDefaultSample() # default sample parameters
1567	self.Controls = {} # items to be placed in top-level Controls
1568	self.GSAS = None # used in TOF
1569	self.repeat_instparm = True # Should a parm file be
1570	# used for multiple histograms?
1571	self.instparm = None # name hint from file of instparm to use
1572	self.instfile = '' # full path name to instrument parameter file
1573	self.instbank = '' # inst parm bank number
1574	self.instmsg = '' # a label that gets printed to show
1575	# where instrument parameters are from
1576	self.numbanks = 1
1577	self.instdict = {} # place items here that will be transferred to the instrument parameters
1578	self.pwdparms = {} # place parameters that are transferred directly to the tree
1579	# here (typically from an existing GPX file)
1580	######################################################################
1581	class ImportSmallAngleData(ImportBaseclass):
1582	'''Defines a base class for the reading of files with small angle data.
1583	See :ref:`Writing a Import Routine<Import_Routines>`
1584	for an explanation on how to use this class.
1585	'''
1586	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1587	strictExtension=False,):
1588
1589	ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
1590	strictExtension)
1591	self.ReInitialize()
1592
1593	def ReInitialize(self):
1594	'Reinitialize the Reader to initial settings'
1595	ImportBaseclass.ReInitialize(self)
1596	self.smallangleentry = ['',None,None] # (filename,Pos,Bank)
1597	self.smallangledata = [] # SASD dataset
1598	'''A small angle data set is a list with items [x,y,w,yc,yd]:
1599	np.array(x), # x-axis values
1600	np.array(y), # powder pattern intensities
1601	np.array(w), # 1/sig(intensity)^2 values (weights)
1602	np.array(yc), # calc. intensities (zero)
1603	np.array(yd), # obs-calc profiles
1604	np.array(yb), # preset bkg
1605	'''
1606	self.comments = []
1607	self.idstring = ''
1608	self.Sample = G2pdG.SetDefaultSample()
1609	self.GSAS = None # used in TOF
1610	self.clockWd = None # used in TOF
1611	self.numbanks = 1
1612	self.instdict = {} # place items here that will be transferred to the instrument parameters
1613
1614	######################################################################
1615	class ImportImage(ImportBaseclass):
1616	'''Defines a base class for the reading of images
1617
1618	Images are read in only these places:
1619
1620	* Initial reading is typically done from a menu item
1621	with a call to :meth:`GSASII.GSASII.OnImportImage`
1622	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`. That calls
1623	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1624	:meth:`Reader`. This returns a list of reader objects for each read image.
1625
1626	* Images are read alternatively in :func:`GSASIIIO.ReadImages`, which puts image info
1627	directly into the data tree.
1628
1629	* Images are reloaded with :func:`GSASIIIO.GetImageData`.
1630
1631	.. _Image_import_routines:
1632
1633	When reading an image, the ``Reader()`` routine in the ImportImage class
1634	should set:
1635
1636	* :attr:`Comments`: a list of strings (str),
1637	* :attr:`Npix`: the number of pixels in the image (int),
1638	* :attr:`Image`: the actual image as a numpy array (np.array)
1639	* :attr:`Data`: a dict defining image parameters (dict). Within this dict the following
1640	data items are needed:
1641
1642	* 'pixelSize': size of each pixel in microns (such as ``[200,200]``.
1643	* 'wavelength': wavelength in Angstoms.
1644	* 'distance': distance of detector from sample in cm.
1645	* 'center': uncalibrated center of beam on detector (such as ``[204.8,204.8]``.
1646	* 'size': size of image (such as ``[2048,2048]``).
1647	* 'ImageTag': image number or other keyword used to retrieve image from
1648	a multi-image data file (defaults to ``1`` if not specified).
1649
1650	optional data items:
1651
1652	* :attr:`repeat`: set to True if there are additional images to
1653	read in the file, False otherwise
1654	* :attr:`repeatcount`: set to the number of the image.
1655
1656	Note that the above is initialized with :meth:`InitParameters`.
1657	(Also see :ref:`Writing a Import Routine<Import_Routines>`
1658	for an explanation on how to use import classes in general.)
1659	'''
1660	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1661	strictExtension=False,):
1662	ImportBaseclass.__init__(self,formatName,longFormatName,
1663	extensionlist,strictExtension)
1664	self.InitParameters()
1665
1666	def ReInitialize(self):
1667	'Reinitialize the Reader to initial settings -- not used at present'
1668	ImportBaseclass.ReInitialize(self)
1669	self.InitParameters()
1670
1671	def InitParameters(self):
1672	'initialize the instrument parameters structure'
1673	self.Comments = ['No comments']
1674	self.Data = {}
1675	self.Npix = 0
1676	self.Image = None
1677	self.repeat = False
1678	self.repeatcount = 1
1679
1680	def LoadImage(self,ParentFrame,imagefile,imagetag=None):
1681	'''Optionally, call this after reading in an image to load it into the tree.
1682	This saves time by preventing a reread of the same information.
1683	'''
1684	if ParentFrame:
1685	ParentFrame.ImageZ = self.Image # store the image for plotting
1686	ParentFrame.oldImagefile = imagefile # save the name of the last image file read
1687	ParentFrame.oldImageTag = imagetag # save the tag of the last image file read
1688
1689	######################################################################
1690	class ExportBaseclass(object):
1691	'''Defines a base class for the exporting of GSAS-II results.
1692
1693	This class is subclassed in the various exports/G2export_*.py files. Those files
1694	are imported in :meth:`GSASII.GSASII._init_Exports` which defines the
1695	appropriate menu items for each one and the .Exporter method is called
1696	directly from the menu item.
1697
1698	Routines may also define a .Writer method, which is used to write a single
1699	file without invoking any GUI objects.
1700	'''
1701	def __init__(self,G2frame,formatName,extension,longFormatName=None,):
1702	self.G2frame = G2frame
1703	self.formatName = formatName # short string naming file type
1704	self.extension = extension
1705	if longFormatName: # longer string naming file type
1706	self.longFormatName = longFormatName
1707	else:
1708	self.longFormatName = formatName
1709	self.OverallParms = {}
1710	self.Phases = {}
1711	self.Histograms = {}
1712	self.powderDict = {}
1713	self.xtalDict = {}
1714	self.parmDict = {}
1715	self.sigDict = {}
1716	# updated in InitExport:
1717	self.currentExportType = None # type of export that has been requested
1718	# updated in ExportSelect (when used):
1719	self.phasenam = None # a list of selected phases
1720	self.histnam = None # a list of selected histograms
1721	self.filename = None # name of file to be written (single export) or template (multiple files)
1722	self.dirname = '' # name of directory where file(s) will be written
1723	self.fullpath = '' # name of file being written -- full path
1724
1725	# items that should be defined in a subclass of this class
1726	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1727	# The following types are defined: 'project', "phase", "powder", "single"
1728	self.multiple = False # set as True if the class can export multiple phases or histograms
1729	# self.multiple is ignored for "project" exports
1730
1731	def InitExport(self,event):
1732	'''Determines the type of menu that called the Exporter and
1733	misc initialization.
1734	'''
1735	self.filename = None # name of file to be written (single export)
1736	self.dirname = '' # name of file to be written (multiple export)
1737	if event:
1738	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1739
1740	def MakePWDRfilename(self,hist):
1741	'''Make a filename root (no extension) from a PWDR histogram name
1742
1743	:param str hist: the histogram name in data tree (starts with "PWDR ")
1744	'''
1745	file0 = ''
1746	file1 = hist[5:]
1747	# replace repeated blanks
1748	while file1 != file0:
1749	file0 = file1
1750	file1 = file0.replace(' ',' ').strip()
1751	file0 = file1.replace('Azm= ','A')
1752	# if angle has unneeded decimal places on aziumuth, remove them
1753	if file0[-3:] == '.00': file0 = file0[:-3]
1754	file0 = file0.replace('.','_')
1755	file0 = file0.replace(' ','_')
1756	return file0
1757
1758	def ExportSelect(self,AskFile='ask'):
1759	'''Selects histograms or phases when needed. Sets a default file name when
1760	requested in self.filename; always sets a default directory in self.dirname.
1761
1762	:param bool AskFile: Determines how this routine processes getting a
1763	location to store the current export(s).
1764
1765	* if AskFile is 'ask' (default option), get the name of the file to be written;
1766	self.filename and self.dirname are always set. In the case where
1767	multiple files must be generated, the export routine should do this
1768	based on self.filename as a template.
1769	* if AskFile is 'dir', get the name of the directory to be used;
1770	self.filename is not used, but self.dirname is always set. The export routine
1771	will always generate the file name.
1772	* if AskFile is 'single', get only the name of the directory to be used when
1773	multiple items will be written (as multiple files) are used
1774	or a complete file name is requested when a single file
1775	name is selected. self.dirname is always set and self.filename used
1776	only when a single file is selected.
1777	* if AskFile is 'default', creates a name of the file to be used from
1778	the name of the project (.gpx) file. If the project has not been saved,
1779	then the name of file is requested.
1780	self.filename and self.dirname are always set. In the case where
1781	multiple file names must be generated, the export routine should do this
1782	based on self.filename.
1783	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1784	file. If the project has not been saved, then a directory is requested.
1785	self.filename is not used.
1786
1787	:returns: True in case of an error
1788	'''
1789
1790	numselected = 1
1791	if self.currentExportType == 'phase':
1792	if len(self.Phases) == 0:
1793	self.G2frame.ErrorDialog(
1794	'Empty project',
1795	'Project does not contain any phases.')
1796	return True
1797	elif len(self.Phases) == 1:
1798	self.phasenam = self.Phases.keys()
1799	elif self.multiple:
1800	choices = sorted(self.Phases.keys())
1801	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1802	if phasenum is None: return True
1803	self.phasenam = [choices[i] for i in phasenum]
1804	if not self.phasenam: return True
1805	numselected = len(self.phasenam)
1806	else:
1807	choices = sorted(self.Phases.keys())
1808	phasenum = G2G.ItemSelector(choices,self.G2frame)
1809	if phasenum is None: return True
1810	self.phasenam = [choices[phasenum]]
1811	numselected = len(self.phasenam)
1812	elif self.currentExportType == 'single':
1813	if len(self.xtalDict) == 0:
1814	self.G2frame.ErrorDialog(
1815	'Empty project',
1816	'Project does not contain any single crystal data.')
1817	return True
1818	elif len(self.xtalDict) == 1:
1819	self.histnam = self.xtalDict.values()
1820	elif self.multiple:
1821	choices = sorted(self.xtalDict.values())
1822	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1823	if not hnum: return True
1824	self.histnam = [choices[i] for i in hnum]
1825	numselected = len(self.histnam)
1826	else:
1827	choices = sorted(self.xtalDict.values())
1828	hnum = G2G.ItemSelector(choices,self.G2frame)
1829	if hnum is None: return True
1830	self.histnam = [choices[hnum]]
1831	numselected = len(self.histnam)
1832	elif self.currentExportType == 'powder':
1833	if len(self.powderDict) == 0:
1834	self.G2frame.ErrorDialog(
1835	'Empty project',
1836	'Project does not contain any powder data.')
1837	return True
1838	elif len(self.powderDict) == 1:
1839	self.histnam = self.powderDict.values()
1840	elif self.multiple:
1841	choices = sorted(self.powderDict.values())
1842	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1843	if not hnum: return True
1844	self.histnam = [choices[i] for i in hnum]
1845	numselected = len(self.histnam)
1846	else:
1847	choices = sorted(self.powderDict.values())
1848	hnum = G2G.ItemSelector(choices,self.G2frame)
1849	if hnum is None: return True
1850	self.histnam = [choices[hnum]]
1851	numselected = len(self.histnam)
1852	elif self.currentExportType == 'image':
1853	if len(self.Histograms) == 0:
1854	self.G2frame.ErrorDialog(
1855	'Empty project',
1856	'Project does not contain any images.')
1857	return True
1858	elif len(self.Histograms) == 1:
1859	self.histnam = self.Histograms.keys()
1860	else:
1861	choices = sorted(self.Histograms.keys())
1862	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1863	if self.multiple:
1864	if not hnum: return True
1865	self.histnam = [choices[i] for i in hnum]
1866	else:
1867	if hnum is None: return True
1868	self.histnam = [choices[hnum]]
1869	numselected = len(self.histnam)
1870	if self.currentExportType == 'map':
1871	# search for phases with maps
1872	mapPhases = []
1873	choices = []
1874	for phasenam in sorted(self.Phases):
1875	phasedict = self.Phases[phasenam] # pointer to current phase info
1876	if len(phasedict['General']['Map'].get('rho',[])):
1877	mapPhases.append(phasenam)
1878	if phasedict['General']['Map'].get('Flip'):
1879	choices.append('Charge flip map: '+str(phasenam))
1880	elif phasedict['General']['Map'].get('MapType'):
1881	choices.append(
1882	str(phasedict['General']['Map'].get('MapType'))
1883	+ ' map: ' + str(phasenam))
1884	else:
1885	choices.append('unknown map: '+str(phasenam))
1886	# select a map if needed
1887	if len(mapPhases) == 0:
1888	self.G2frame.ErrorDialog(
1889	'Empty project',
1890	'Project does not contain any maps.')
1891	return True
1892	elif len(mapPhases) == 1:
1893	self.phasenam = mapPhases
1894	else:
1895	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1896	if self.multiple:
1897	if not phasenum: return True
1898	self.phasenam = [mapPhases[i] for i in phasenum]
1899	else:
1900	if phasenum is None: return True
1901	self.phasenam = [mapPhases[phasenum]]
1902	numselected = len(self.phasenam)
1903
1904	# items selected, now set self.dirname and usually self.filename
1905	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
1906	AskFile == 'default' and not self.G2frame.GSASprojectfile
1907	):
1908	filename = self.askSaveFile()
1909	if not filename: return True
1910	self.dirname,self.filename = os.path.split(filename)
1911	elif AskFile == 'dir' or AskFile == 'single' or (
1912	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
1913	):
1914	self.dirname = self.askSaveDirectory()
1915	if not self.dirname: return True
1916	elif AskFile == 'default-dir' or AskFile == 'default':
1917	self.dirname,self.filename = os.path.split(
1918	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
1919	)
1920	else:
1921	raise Exception('This should not happen!')
1922
1923	def loadParmDict(self):
1924	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
1925	refined values to those from the last cycle and set the uncertainties for the
1926	refined parameters in another dict (self.sigDict).
1927
1928	Expands the parm & sig dicts to include values derived from constraints.
1929	'''
1930	self.parmDict = {}
1931	self.sigDict = {}
1932	rigidbodyDict = {}
1933	covDict = {}
1934	consDict = {}
1935	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1936	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
1937	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
1938	while item:
1939	name = self.G2frame.PatternTree.GetItemText(item)
1940	if name == 'Rigid bodies':
1941	rigidbodyDict = self.G2frame.PatternTree.GetItemPyData(item)
1942	elif name == 'Covariance':
1943	covDict = self.G2frame.PatternTree.GetItemPyData(item)
1944	elif name == 'Constraints':
1945	consDict = self.G2frame.PatternTree.GetItemPyData(item)
1946	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
1947	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1948	self.parmDict.update(rbDict)
1949	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1950	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,maxSSwave = G2stIO.GetPhaseData(
1951	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
1952	self.parmDict.update(phaseDict)
1953	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
1954	Phases,Histograms,Print=False,resetRefList=False)
1955	self.parmDict.update(hapDict)
1956	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
1957	self.parmDict.update(histDict)
1958	self.parmDict.update(zip(
1959	covDict.get('varyList',[]),
1960	covDict.get('variables',[])))
1961	self.sigDict = dict(zip(
1962	covDict.get('varyList',[]),
1963	covDict.get('sig',[])))
1964	# expand to include constraints: first compile a list of constraints
1965	constList = []
1966	for item in consDict:
1967	if item.startswith('_'): continue
1968	constList += consDict[item]
1969	# now process the constraints
1970	G2mv.InitVars()
1971	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
1972	varyList = covDict.get('varyListStart')
1973	if varyList is None and len(constDict) == 0:
1974	# no constraints can use varyList
1975	varyList = covDict.get('varyList')
1976	elif varyList is None:
1977	# old GPX file from before pre-constraint varyList is saved
1978	print ' * Old refinement: Please use Calculate/Refine to redo *'
1979	raise Exception(' * Export aborted *')
1980	else:
1981	varyList = list(varyList)
1982	try:
1983	groups,parmlist = G2mv.GroupConstraints(constDict)
1984	G2mv.GenerateConstraints(groups,parmlist,varyList,constDict,fixedList,self.parmDict)
1985	except:
1986	# this really should not happen
1987	print ' * ERROR - constraints are internally inconsistent *'
1988	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
1989	print 'Errors',errmsg
1990	if warnmsg: print 'Warnings',warnmsg
1991	raise Exception(' * CIF creation aborted *')
1992	# add the constrained values to the parameter dictionary
1993	G2mv.Dict2Map(self.parmDict,varyList)
1994	# and add their uncertainties into the esd dictionary (sigDict)
1995	if covDict.get('covMatrix') is not None:
1996	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
1997
1998	def loadTree(self):
1999	'''Load the contents of the data tree into a set of dicts
2000	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
2001	& self.xtalDict)
2002
2003	* The childrenless data tree items are overall parameters/controls for the
2004	entire project and are placed in self.OverallParms
2005	* Phase items are placed in self.Phases
2006	* Data items are placed in self.Histogram. The key for these data items
2007	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
2008	'''
2009	self.OverallParms = {}
2010	self.powderDict = {}
2011	self.xtalDict = {}
2012	self.Phases = {}
2013	self.Histograms = {}
2014	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2015	histType = None
2016	if self.currentExportType == 'phase':
2017	# if exporting phases load them here
2018	sub = G2gd.GetPatternTreeItemId(self.G2frame,self.G2frame.root,'Phases')
2019	if not sub:
2020	print 'no phases found'
2021	return True
2022	item, cookie = self.G2frame.PatternTree.GetFirstChild(sub)
2023	while item:
2024	phaseName = self.G2frame.PatternTree.GetItemText(item)
2025	self.Phases[phaseName] = self.G2frame.PatternTree.GetItemPyData(item)
2026	item, cookie = self.G2frame.PatternTree.GetNextChild(sub, cookie)
2027	return
2028	elif self.currentExportType == 'single':
2029	histType = 'HKLF'
2030	elif self.currentExportType == 'powder':
2031	histType = 'PWDR'
2032	elif self.currentExportType == 'image':
2033	histType = 'IMG'
2034
2035	if histType: # Loading just one kind of tree entry
2036	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2037	while item:
2038	name = self.G2frame.PatternTree.GetItemText(item)
2039	if name.startswith(histType):
2040	if self.Histograms.get(name): # there is already an item with this name
2041	print('Histogram name '+str(name)+' is repeated. Renaming')
2042	if name[-1] == '9':
2043	name = name[:-1] + '10'
2044	elif name[-1] in '012345678':
2045	name = name[:-1] + str(int(name[-1])+1)
2046	else:
2047	name += '-1'
2048	self.Histograms[name] = {}
2049	# the main info goes into Data, but the 0th
2050	# element contains refinement results, carry
2051	# that over too now.
2052	self.Histograms[name]['Data'] = self.G2frame.PatternTree.GetItemPyData(item)[1]
2053	self.Histograms[name][0] = self.G2frame.PatternTree.GetItemPyData(item)[0]
2054	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2055	while item2:
2056	child = self.G2frame.PatternTree.GetItemText(item2)
2057	self.Histograms[name][child] = self.G2frame.PatternTree.GetItemPyData(item2)
2058	item2, cookie2 = self.G2frame.PatternTree.GetNextChild(item, cookie2)
2059	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2060	# index powder and single crystal histograms by number
2061	for hist in self.Histograms:
2062	if hist.startswith("PWDR"):
2063	d = self.powderDict
2064	elif hist.startswith("HKLF"):
2065	d = self.xtalDict
2066	else:
2067	return
2068	i = self.Histograms[hist].get('hId')
2069	if i is None and not d.keys():
2070	i = 0
2071	elif i is None or i in d.keys():
2072	i = max(d.keys())+1
2073	d[i] = hist
2074	return
2075	# else standard load: using all interlinked phases and histograms
2076	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2077	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2078	while item:
2079	name = self.G2frame.PatternTree.GetItemText(item)
2080	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2081	if not item2:
2082	self.OverallParms[name] = self.G2frame.PatternTree.GetItemPyData(item)
2083	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2084	# index powder and single crystal histograms
2085	for hist in self.Histograms:
2086	i = self.Histograms[hist]['hId']
2087	if hist.startswith("PWDR"):
2088	self.powderDict[i] = hist
2089	elif hist.startswith("HKLF"):
2090	self.xtalDict[i] = hist
2091
2092	def dumpTree(self,mode='type'):
2093	'''Print out information on the data tree dicts loaded in loadTree
2094	'''
2095	print '\nOverall'
2096	if mode == 'type':
2097	def Show(arg): return type(arg)
2098	else:
2099	def Show(arg): return arg
2100	for key in self.OverallParms:
2101	print ' ',key,Show(self.OverallParms[key])
2102	print 'Phases'
2103	for key1 in self.Phases:
2104	print ' ',key1,Show(self.Phases[key1])
2105	print 'Histogram'
2106	for key1 in self.Histograms:
2107	print ' ',key1,Show(self.Histograms[key1])
2108	for key2 in self.Histograms[key1]:
2109	print ' ',key2,Show(self.Histograms[key1][key2])
2110
2111	def defaultSaveFile(self):
2112	return os.path.abspath(
2113	os.path.splitext(self.G2frame.GSASprojectfile
2114	)[0]+self.extension)
2115
2116	def askSaveFile(self):
2117	'''Ask the user to supply a file name
2118
2119	:returns: a file name (str) or None if Cancel is pressed
2120	'''
2121
2122	pth = G2G.GetExportPath(self.G2frame)
2123	defnam = os.path.splitext(
2124	os.path.split(self.G2frame.GSASprojectfile)[1]
2125	)[0]+self.extension
2126	dlg = wx.FileDialog(
2127	self.G2frame, 'Input name for file to write', pth, defnam,
2128	self.longFormatName+' ('+self.extension+')\|'+self.extension,
2129	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
2130	dlg.CenterOnParent()
2131	try:
2132	if dlg.ShowModal() == wx.ID_OK:
2133	filename = dlg.GetPath()
2134	self.G2frame.LastExportDir = os.path.split(filename)[0]
2135	filename = os.path.splitext(filename)[0]+self.extension # make sure extension is correct
2136	else:
2137	filename = None
2138	finally:
2139	dlg.Destroy()
2140	return filename
2141
2142	def askSaveDirectory(self):
2143	'''Ask the user to supply a directory name. Path name is used as the
2144	starting point for the next export path search.
2145
2146	:returns: a directory name (str) or None if Cancel is pressed
2147	'''
2148	pth = G2G.GetExportPath(self.G2frame)
2149	dlg = wx.DirDialog(
2150	self.G2frame, 'Input directory where file(s) will be written', pth,
2151	wx.DD_DEFAULT_STYLE)
2152	dlg.CenterOnParent()
2153	try:
2154	if dlg.ShowModal() == wx.ID_OK:
2155	filename = dlg.GetPath()
2156	self.G2frame.LastExportDir = filename
2157	else:
2158	filename = None
2159	finally:
2160	dlg.Destroy()
2161	return filename
2162
2163	# Tools for file writing.
2164	def OpenFile(self,fil=None,mode='w'):
2165	'''Open the output file
2166
2167	:param str fil: The name of the file to open. If None (default)
2168	the name defaults to self.dirname + self.filename.
2169	If an extension is supplied, it is not overridded,
2170	but if not, the default extension is used.
2171	:returns: the file object opened by the routine which is also
2172	saved as self.fp
2173	'''
2174	if not fil:
2175	if not os.path.splitext(self.filename)[1]:
2176	self.filename += self.extension
2177	fil = os.path.join(self.dirname,self.filename)
2178	self.fullpath = os.path.abspath(fil)
2179	self.fp = open(self.fullpath,mode)
2180	return self.fp
2181
2182	def Write(self,line):
2183	'''write a line of output, attaching a line-end character
2184
2185	:param str line: the text to be written.
2186	'''
2187	self.fp.write(line+'\n')
2188	def CloseFile(self,fp=None):
2189	'''Close a file opened in OpenFile
2190
2191	:param file fp: the file object to be closed. If None (default)
2192	file object self.fp is closed.
2193	'''
2194	if fp is None:
2195	fp = self.fp
2196	self.fp = None
2197	fp.close()
2198	# Tools to pull information out of the data arrays
2199	def GetCell(self,phasenam):
2200	"""Gets the unit cell parameters and their s.u.'s for a selected phase
2201
2202	:param str phasenam: the name for the selected phase
2203	:returns: `cellList,cellSig` where each is a 7 element list corresponding
2204	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
2205	cell values and `cellSig` has their uncertainties.
2206	"""
2207	phasedict = self.Phases[phasenam] # pointer to current phase info
2208	try:
2209	pfx = str(phasedict['pId'])+'::'
2210	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
2211	cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A,
2212	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
2213	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
2214	return cellList,cellSig
2215	except KeyError:
2216	cell = phasedict['General']['Cell'][1:]
2217	return cell,7*[0]
2218
2219	def GetAtoms(self,phasenam):
2220	"""Gets the atoms associated with a phase. Can be used with standard
2221	or macromolecular phases
2222
2223	:param str phasenam: the name for the selected phase
2224	:returns: a list of items for eac atom where each item is a list containing:
2225	label, typ, mult, xyz, and td, where
2226
2227	* label and typ are the atom label and the scattering factor type (str)
2228	* mult is the site multiplicity (int)
2229	* xyz is contains a list with four pairs of numbers:
2230	x, y, z and fractional occupancy and
2231	their standard uncertainty (or a negative value)
2232	* td is contains a list with either one or six pairs of numbers:
2233	if one number it is U\ :sub:`iso` and with six numbers it is
2234	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
2235	paired with their standard uncertainty (or a negative value)
2236	"""
2237	phasedict = self.Phases[phasenam] # pointer to current phase info
2238	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
2239	cfrac = cx+3
2240	fpfx = str(phasedict['pId'])+'::Afrac:'
2241	atomslist = []
2242	for i,at in enumerate(phasedict['Atoms']):
2243	if phasedict['General']['Type'] == 'macromolecular':
2244	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
2245	else:
2246	label = at[ct-1]
2247	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
2248	fsig = self.sigDict.get(fpfx+str(i),-0.009)
2249	mult = at[cs+1]
2250	typ = at[ct]
2251	xyz = []
2252	for j,v in enumerate(('x','y','z')):
2253	val = at[cx+j]
2254	pfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
2255	sig = self.sigDict.get(pfx,-0.000009)
2256	xyz.append((val,sig))
2257	xyz.append((fval,fsig))
2258	td = []
2259	if at[cia] == 'I':
2260	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
2261	val = self.parmDict.get(pfx,at[cia+1])
2262	sig = self.sigDict.get(pfx,-0.0009)
2263	td.append((val,sig))
2264	else:
2265	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
2266	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
2267	val = self.parmDict.get(pfx,at[cia+2+i])
2268	sig = self.sigDict.get(pfx,-0.0009)
2269	td.append((val,sig))
2270	atomslist.append((label,typ,mult,xyz,td))
2271	return atomslist
2272	######################################################################
2273	def ExportPowderList(G2frame):
2274	'''Returns a list of extensions supported by :func:`GSASIIIO:ExportPowder`
2275
2276	:param wx.Frame G2frame: the GSAS-II main data tree window
2277	'''
2278	extList = []
2279	for obj in G2frame.exporterlist:
2280	if 'powder' in obj.exporttype:
2281	try:
2282	obj.Writer
2283	extList.append(obj.extension)
2284	except AttributeError:
2285	pass
2286	return extList
2287
2288	def ExportPowder(G2frame,TreeName,fileroot,extension):
2289	'''Writes a single powder histogram using the Export routines
2290
2291	:param wx.Frame G2frame: the GSAS-II main data tree window
2292	:param str TreeName: the name of the histogram (PWDR ...) in the data tree
2293	:param str fileroot: name for file to be written, extension ignored
2294	:param str extension: extension for file to be written (start with '.'). Must
2295	match a powder export routine that has a Writer object.
2296	'''
2297	filename = os.path.abspath(os.path.splitext(fileroot)[0]+extension)
2298	for obj in G2frame.exporterlist:
2299	if obj.extension == extension and 'powder' in obj.exporttype:
2300	obj.currentExportType = 'powder'
2301	obj.InitExport(None)
2302	obj.loadTree() # load all histograms in tree into dicts
2303	if TreeName not in obj.Histograms:
2304	raise Exception('Histogram not found: '+str(TreeName))
2305	try:
2306	obj.Writer
2307	except AttributeError:
2308	continue
2309	try:
2310	obj.Writer(TreeName,filename)
2311	return
2312	except Exception,err:
2313	print('Export Routine for '+extension+' failed.')
2314	print err
2315	else:
2316	print('No Export routine supports extension '+extension)
2317
2318	def ReadDIFFaX(DIFFaXfile):
2319	print 'read ',DIFFaXfile
2320	Layer = {'Laue':'-1','Cell':[False,1.,1.,1.,90.,90.,90,1.],'Width':[[10.,10.],[False,False]],
2321	'Layers':[],'Stacking':[],'Transitions':[],'Toler':0.01,'AtInfo':{}}
2322	df = open(DIFFaXfile,'r')
2323	lines = df.readlines()
2324	df.close()
2325	struct = False
2326	Struct = []
2327	stack = False
2328	Stack = []
2329	trans = False
2330	Trans = []
2331	instr = False
2332	for diff in lines:
2333	diff = diff[:-1].lower()
2334	if '!' in diff:
2335	continue
2336	while '}' in diff: #strip comments
2337	iB = diff.index('{')
2338	iF = diff.index('}')+1
2339	if iB:
2340	diff = diff[:iB]
2341	else:
2342	diff = diff[iF:]
2343	if not diff:
2344	continue
2345	if diff.strip() == 'instrumental':
2346	instr = True
2347	continue
2348	if diff.strip() == 'structural':
2349	instr = False
2350	struct = True
2351	continue
2352	elif diff.strip() == 'stacking':
2353	struct = False
2354	stack = True
2355	continue
2356	elif diff.strip() == 'transitions':
2357	stack = False
2358	trans = True
2359	continue
2360	diff = diff.strip()
2361	if struct:
2362	if diff:
2363	Struct.append(diff)
2364	elif stack:
2365	if diff:
2366	Stack.append(diff)
2367	elif trans:
2368	if diff:
2369	Trans.append(diff)
2370
2371	#STRUCTURE records
2372	laueRec = Struct[1].split()
2373	Layer['Laue'] = laueRec[0]
2374	if Layer['Laue'] == 'unknown' and len(laueRec) > 1:
2375	Layer['Toler'] = float(laueRec[1]) #tolerance for 'unknown'?
2376	if Layer['Laue'] == '2/m(1)': Layer['Laue'] = '2/m(c)'
2377	if Layer['Laue'] == '2/m(2)': Layer['Laue'] = '2/m(ab)'
2378	cell = Struct[0].split()
2379	Layer['Cell'] = [False,float(cell[0]),float(cell[1]),float(cell[2]),90.,90.,float(cell[3]),1.0]
2380	nLayers = int(Struct[2])
2381	N = 3
2382	if 'layer' not in Struct[3]:
2383	N = 4
2384	if Struct[3] != 'infinite':
2385	width = Struct[3].split()
2386	Layer['Width'][0] = [float(width[0]),float(width[1])]
2387	for nL in range(nLayers):
2388	if '=' in Struct[N]:
2389	name = Struct[N].split('=')
2390	sameas = int(name[1])-1
2391	Layer['Layers'].append({'Name':name[0],'SameAs':Layer['Layers'][sameas]['Name'],'Symm':'None','Atoms':[]})
2392	N += 1
2393	continue
2394	Symm = 'None'
2395	if 'centro' in Struct[N+1]: Symm = '-1'
2396	Layer['Layers'].append({'Name':Struct[N],'SameAs':'','Symm':Symm,'Atoms':[]})
2397	N += 2
2398	iatm = 0
2399	while 'layer' not in Struct[N]:
2400	atom = Struct[N][4:].split()
2401	atomType = G2el.FixValence(Struct[N][:4].replace(' ','').strip().capitalize())
2402	if atomType not in Layer['AtInfo']:
2403	Layer['AtInfo'][atomType] = G2el.GetAtomInfo(atomType)
2404	atomName = '%s(%s)'%(atomType,atom[0])
2405	newVals = []
2406	for val in atom[1:6]:
2407	if '/' in val:
2408	newVals.append(eval(val+'.'))
2409	else:
2410	newVals.append(float(val))
2411	atomRec = [atomName,atomType,newVals[0],newVals[1],newVals[2],newVals[4],newVals[3]/78.9568]
2412	Layer['Layers'][-1]['Atoms'].append(atomRec)
2413	N += 1
2414	if N > len(Struct)-1:
2415	break
2416	#TRANSITIONS records
2417	transArray = []
2418	N = 0
2419	for i in range(nLayers):
2420	transArray.append([])
2421	for j in range(nLayers):
2422	vals = Trans[N].split()
2423	newVals = []
2424	for val in vals[:4]:
2425	if '/' in val:
2426	newVals.append(eval(val+'.'))
2427	else:
2428	newVals.append(float(val))
2429	transArray[-1].append(newVals+['',False])
2430	N += 1
2431	Layer['Transitions'] = transArray
2432	#STACKING records
2433	Layer['Stacking'] = [Stack[0],'']
2434	if Stack[0] == 'recursive':
2435	Layer['Stacking'][1] = Stack[1]
2436	elif Stack[0] == 'explicit':
2437	if Stack[1] == 'random':
2438	Layer['Stacking'][1] = Stack[1]
2439	else:
2440	Layer['Stacking'][1] = 'list'
2441	Layer['Stacking'].append('')
2442	for stack in Stack[2:]:
2443	Layer['Stacking'][2] += ' '+stack
2444	return Layer
2445
2446	def ReadCIF(URLorFile):
2447	'''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
2448	(from James Hester).
2449	The open routine gets confused with DOS names that begin with a letter and colon
2450	"C:\dir\" so this routine will try to open the passed name as a file and if that
2451	fails, try it as a URL
2452
2453	:param str URLorFile: string containing a URL or a file name. Code will try first
2454	to open it as a file and then as a URL.
2455
2456	:returns: a PyCifRW CIF object.
2457	'''
2458	import CifFile as cif # PyCifRW from James Hester
2459
2460	# alternate approach:
2461	#import urllib
2462	#ciffile = 'file:'+urllib.pathname2url(filename)
2463
2464	try:
2465	fp = open(URLorFile,'r')
2466	cf = cif.ReadCif(fp)
2467	fp.close()
2468	return cf
2469	except IOError:
2470	return cif.ReadCif(URLorFile)
2471
2472	if __name__ == '__main__':
2473	import GSASII
2474	application = GSASII.GSASIImain(0)
2475	G2frame = application.main
2476	#app = wx.PySimpleApp()
2477	#G2frame = wx.Frame(None) # create a frame
2478	#frm.Show(True)
2479	#filename = '/tmp/notzip.zip'
2480	#filename = '/tmp/all.zip'
2481	#filename = '/tmp/11bmb_7652.zip'
2482
2483	#selection=None, confirmoverwrite=True, parent=None
2484	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2485	#print ExtractFileFromZip(filename,multipleselect=True)
2486	# #confirmread=False, confirmoverwrite=False)
2487
2488	# choicelist=[ ('a','b','c'),
2489	# ('test1','test2'),('no choice',)]
2490	# titles = [ 'a, b or c', 'tests', 'No option here']
2491	# dlg = MultipleChoicesDialog(
2492	# choicelist,titles,
2493	# parent=frm)
2494	# if dlg.ShowModal() == wx.ID_OK:
2495	# print 'Got OK'
2496	imagefile = '/tmp/NDC5_00237_3.ge3'
2497	Comments, Data, Npix, Image = GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None)
2498
2499	print("\n\nResults loaded to Comments, Data, Npix and Image\n\n")
2500
2501	GSASIIpath.IPyBreak_base()

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