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source: trunk/GSASIIIO.py @ 2083

Last change on this file since 2083 was 2083, checked in by toby, 7 years ago
Export multiple masks/controls
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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2015-12-05 19:49:31 +0000 (Sat, 05 Dec 2015) $
4	# $Author: toby $
5	# $Revision: 2083 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 2083 2015-12-05 19:49:31Z 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: 2083 $")
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	dlg = wx.FileDialog(G2frame, 'Previous image file not found; open here', '.', '',\
191	'Any image file (.edf;.tif;.tiff;.mar;.ge;.avg;.sum;.img;.cor;.stl)\
192	\|.edf;.tif;.tiff;.mar;.ge;.avg;.sum;.img;.cor;.stl\|\
193	European detector file (.edf)\|.edf\|\
194	Any detector tif (.tif;.tiff)\|.tif;.tiff\|\
195	MAR file (.mar)\|.mar\|\
196	GE Image (.ge;.avg;.sum;.cor)\|.ge;.avg;.sum;.cor\|\
197	ADSC Image (.img)\|.img\|\
198	Rigaku-Axis4 (.stl)\|.stl\|\
199	All files (.)\|.',wx.OPEN\|wx.CHANGE_DIR)
200	try:
201	dlg.SetFilename(''+ospath.split(imagefile)[1])
202	if dlg.ShowModal() == wx.ID_OK:
203	imagefile = dlg.GetPath()
204	else:
205	imagefile = False
206	finally:
207	dlg.Destroy()
208	return imagefile
209
210	def EditImageParms(parent,Data,Comments,Image,filename):
211	dlg = wx.Dialog(parent, wx.ID_ANY, 'Edit image parameters',
212	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
213	def onClose(event):
214	dlg.EndModal(wx.ID_OK)
215	mainsizer = wx.BoxSizer(wx.VERTICAL)
216	h,w = Image.shape[:2]
217	mainsizer.Add(wx.StaticText(dlg,wx.ID_ANY,
218	'File '+str(filename)+'\nImage size: '+str(h)+' x '+str(w)),
219	0,wx.ALIGN_LEFT\|wx.ALL, 2)
220
221	vsizer = wx.BoxSizer(wx.HORIZONTAL)
222	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Wavelength (\xC5) '),
223	0,wx.ALIGN_LEFT\|wx.ALL, 2)
224	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'wavelength')
225	vsizer.Add(wdgt)
226	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
227
228	vsizer = wx.BoxSizer(wx.HORIZONTAL)
229	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Pixel size (\xb5m). Width '),
230	0,wx.ALIGN_LEFT\|wx.ALL, 2)
231	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],0,
232	size=(50,-1))
233	vsizer.Add(wdgt)
234	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Height '),
235	wx.ALIGN_LEFT\|wx.ALL, 2)
236	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],1,
237	size=(50,-1))
238	vsizer.Add(wdgt)
239	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
240
241	vsizer = wx.BoxSizer(wx.HORIZONTAL)
242	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Sample to detector (mm) '),
243	0,wx.ALIGN_LEFT\|wx.ALL, 2)
244	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'distance')
245	vsizer.Add(wdgt)
246	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
247
248	vsizer = wx.BoxSizer(wx.HORIZONTAL)
249	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Beam center (pixels). X = '),
250	0,wx.ALIGN_LEFT\|wx.ALL, 2)
251	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],0,
252	size=(75,-1))
253	vsizer.Add(wdgt)
254	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Y = '),
255	wx.ALIGN_LEFT\|wx.ALL, 2)
256	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],1,
257	size=(75,-1))
258	vsizer.Add(wdgt)
259	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
260
261	vsizer = wx.BoxSizer(wx.HORIZONTAL)
262	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Comments '),
263	0,wx.ALIGN_LEFT\|wx.ALL, 2)
264	wdgt = G2G.ValidatedTxtCtrl(dlg,Comments,0,size=(250,-1))
265	vsizer.Add(wdgt)
266	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
267
268	btnsizer = wx.StdDialogButtonSizer()
269	OKbtn = wx.Button(dlg, wx.ID_OK, 'Continue')
270	OKbtn.SetDefault()
271	OKbtn.Bind(wx.EVT_BUTTON,onClose)
272	btnsizer.AddButton(OKbtn) # not sure why this is needed
273	btnsizer.Realize()
274	mainsizer.Add(btnsizer, 1, wx.ALIGN_CENTER\|wx.ALL\|wx.EXPAND, 5)
275	dlg.SetSizer(mainsizer)
276	dlg.CenterOnParent()
277	dlg.ShowModal()
278
279	def ReadLoadImage(imagefile,G2frame):
280	'''Read a GSAS-II image file and load it into the data tree
281	Called only from GSASII.OnImageRead (depreciated).
282	'''
283	# if a zip file, open and extract
284	if os.path.splitext(imagefile)[1].lower() == '.zip':
285	extractedfile = ExtractFileFromZip(imagefile,parent=G2frame)
286	if extractedfile is not None and extractedfile != imagefile:
287	imagefile = extractedfile
288	Comments,Data,Npix,Image = GetImageData(G2frame,imagefile) # can only read 1st image
289	if Comments:
290	LoadImage2Tree(imagefile,G2frame,Comments,Data,Npix,Image)
291
292	def LoadImage2Tree(imagefile,G2frame,Comments,Data,Npix,Image):
293	'''Load an image into the tree. Saves the location of the image, as well as the
294	ImageTag (where there is more than one image in the file), if defined.
295	'''
296	ImgNames = []
297	if G2frame.PatternTree.GetCount(): # get a list of existing Image entries
298	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
299	while item:
300	name = G2frame.PatternTree.GetItemText(item)
301	if name.startswith('IMG'): ImgNames.append(name)
302	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
303	TreeLbl = 'IMG '+os.path.basename(imagefile)
304	ImageTag = Data.get('ImageTag')
305	if ImageTag:
306	TreeLbl += ' #'+str(ImageTag)
307	imageInfo = (imagefile,ImageTag)
308	else:
309	imageInfo = imagefile
310	TreeName = G2obj.MakeUniqueLabel(TreeLbl,ImgNames)
311	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=TreeName)
312	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
313	Imax = np.amax(Image)
314	Imin = max(0.0,np.amin(Image)) #force positive
315	if G2frame.imageDefault:
316	Data = copy.copy(G2frame.imageDefault)
317	Data['showLines'] = True
318	Data['ring'] = []
319	Data['rings'] = []
320	Data['cutoff'] = 10
321	Data['pixLimit'] = 20
322	Data['edgemin'] = 100000000
323	Data['calibdmin'] = 0.5
324	Data['calibskip'] = 0
325	Data['ellipses'] = []
326	Data['calibrant'] = ''
327	Data['GonioAngles'] = [0.,0.,0.]
328	Data['DetDepthRef'] = False
329	else:
330	Data['type'] = 'PWDR'
331	Data['color'] = 'Paired'
332	Data['tilt'] = 0.0
333	Data['rotation'] = 0.0
334	Data['showLines'] = False
335	Data['ring'] = []
336	Data['rings'] = []
337	Data['cutoff'] = 10
338	Data['pixLimit'] = 20
339	Data['calibdmin'] = 0.5
340	Data['calibskip'] = 0
341	Data['edgemin'] = 100000000
342	Data['ellipses'] = []
343	Data['GonioAngles'] = [0.,0.,0.]
344	Data['DetDepth'] = 0.
345	Data['DetDepthRef'] = False
346	Data['calibrant'] = ''
347	Data['IOtth'] = [2.0,5.0]
348	Data['LRazimuth'] = [135,225]
349	Data['azmthOff'] = 0.0
350	Data['outChannels'] = 2500
351	Data['outAzimuths'] = 1
352	Data['centerAzm'] = False
353	Data['fullIntegrate'] = False
354	Data['setRings'] = False
355	Data['background image'] = ['',-1.0]
356	Data['dark image'] = ['',-1.0]
357	Data['Flat Bkg'] = 0.0
358	Data['setDefault'] = False
359	Data['range'] = [(Imin,Imax),[Imin,Imax]]
360	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Image Controls'),Data)
361	Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],'Thresholds':[(Imin,Imax),[Imin,Imax]]}
362	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Masks'),Masks)
363	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Stress/Strain'),
364	{'Type':'True','d-zero':[],'Sample phi':0.0,'Sample z':0.0,'Sample load':0.0})
365	G2frame.PatternTree.SetItemPyData(Id,[Npix,imageInfo])
366	G2frame.PickId = Id
367	G2frame.PickIdText = G2frame.GetTreeItemsList(G2frame.PickId)
368	G2frame.Image = Id
369
370	def GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None):
371	'''Read a single image with an image importer.
372
373	:param wx.Frame G2frame: main GSAS-II Frame and data object.
374	:param str imagefile: name of image file
375	:param bool imageOnly: If True return only the image,
376	otherwise (default) return more (see below)
377	:param int/str ImageTag: specifies a particular image to be read from a file.
378	First image is read if None (default).
379
380	:returns: an image as a numpy array or a list of four items:
381	Comments, Data, Npix and the Image, as selected by imageOnly
382
383	'''
384	# determine which formats are compatible with this file
385	primaryReaders = []
386	secondaryReaders = []
387	for rd in G2frame.ImportImageReaderlist:
388	flag = rd.ExtensionValidator(imagefile)
389	if flag is None:
390	secondaryReaders.append(rd)
391	elif flag:
392	primaryReaders.append(rd)
393	if len(secondaryReaders) + len(primaryReaders) == 0:
394	print('Error: No matching format for file '+filename)
395	raise Exception('No image read')
396	fp = None
397	errorReport = ''
398	fp = open(imagefile,'Ur')
399	for rd in primaryReaders+secondaryReaders:
400	rd.ReInitialize() # purge anything from a previous read
401	fp.seek(0) # rewind
402	rd.errors = "" # clear out any old errors
403	if not rd.ContentsValidator(fp): # rejected on cursory check
404	errorReport += "\n "+rd.formatName + ' validator error'
405	if rd.errors:
406	errorReport += ': '+rd.errors
407	continue
408	rdbuffer = {} # create temporary storage for file reader
409	if imageOnly:
410	ParentFrame = None # prevent GUI access on reread
411	else:
412	ParentFrame = G2frame
413	if GSASIIpath.GetConfigValue('debug'):
414	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=ImageTag)
415	else:
416	flag = False
417	try:
418	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=ImageTag)
419	except rd.ImportException as detail:
420	rd.errors += "\n Read exception: "+str(detail)
421	except Exception as detail:
422	import traceback
423	rd.errors += "\n Unhandled read exception: "+str(detail)
424	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
425	if flag: # this read succeeded
426	if rd.Image is None:
427	raise Exception('No image read. Strange!')
428	if GSASIIpath.GetConfigValue('Transpose'):
429	print 'Transposing Image!'
430	rd.Image = rd.Image.T
431	#rd.readfilename = imagefile
432	if imageOnly:
433	return rd.Image
434	else:
435	return rd.Comments,rd.Data,rd.Npix,rd.Image
436	else:
437	print('Error reading file '+filename)
438	print('Error messages(s)\n'+errorReport)
439	raise Exception('No image read')
440
441	def ReadImages(G2frame,imagefile):
442	'''Read one or more images from a file and put them into the Tree
443	using image importers. Called only in :meth:`AutoIntFrame.OnTimerLoop`.
444
445	:param wx.Frame G2frame: main GSAS-II Frame and data object.
446	:param str imagefile: name of image file
447
448	:returns: a list of the id's of the IMG tree items created
449	'''
450	# determine which formats are compatible with this file
451	primaryReaders = []
452	secondaryReaders = []
453	for rd in G2frame.ImportImageReaderlist:
454	flag = rd.ExtensionValidator(imagefile)
455	if flag is None:
456	secondaryReaders.append(rd)
457	elif flag:
458	primaryReaders.append(rd)
459	if len(secondaryReaders) + len(primaryReaders) == 0:
460	print('Error: No matching format for file '+filename)
461	raise Exception('No image read')
462	errorReport = ''
463	fp = open(imagefile,'Ur')
464	rdbuffer = {} # create temporary storage for file reader
465	for rd in primaryReaders+secondaryReaders:
466	rd.ReInitialize() # purge anything from a previous read
467	fp.seek(0) # rewind
468	rd.errors = "" # clear out any old errors
469	if not rd.ContentsValidator(fp): # rejected on cursory check
470	errorReport += "\n "+rd.formatName + ' validator error'
471	if rd.errors:
472	errorReport += ': '+rd.errors
473	continue
474	ParentFrame = G2frame
475	block = 0
476	repeat = True
477	CreatedIMGitems = []
478	while repeat: # loop if the reader asks for another pass on the file
479	block += 1
480	repeat = False
481	if GSASIIpath.GetConfigValue('debug'):
482	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=block,Buffer=rdbuffer)
483	else:
484	flag = False
485	try:
486	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=block,Buffer=rdbuffer)
487	except rd.ImportException as detail:
488	rd.errors += "\n Read exception: "+str(detail)
489	except Exception as detail:
490	import traceback
491	rd.errors += "\n Unhandled read exception: "+str(detail)
492	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
493	if flag: # this read succeeded
494	if rd.Image is None:
495	raise Exception('No image read. Strange!')
496	if GSASIIpath.GetConfigValue('Transpose'):
497	print 'Transposing Image!'
498	rd.Image = rd.Image.T
499	rd.Data['ImageTag'] = rd.repeatcount
500	LoadImage2Tree(imagefile,G2frame,rd.Comments,rd.Data,rd.Npix,rd.Image)
501	repeat = rd.repeat
502	CreatedIMGitems.append(G2frame.Image)
503	if CreatedIMGitems: return CreatedIMGitems
504	else:
505	print('Error reading file '+filename)
506	print('Error messages(s)\n'+errorReport)
507	return []
508	#raise Exception('No image read')
509
510	def SaveMultipleImg(G2frame):
511	if not G2frame.PatternTree.GetCount():
512	print 'no images!'
513	return
514	choices = G2gd.GetPatternTreeDataNames(G2frame,['IMG ',])
515	if len(choices) == 1:
516	names = choices
517	else:
518	dlg = G2G.G2MultiChoiceDialog(G2frame,'Stress/Strain fitting','Select images to fit:',choices)
519	dlg.SetSelections([])
520	names = []
521	if dlg.ShowModal() == wx.ID_OK:
522	names = [choices[sel] for sel in dlg.GetSelections()]
523	dlg.Destroy()
524	if not names: return
525	for name in names:
526	Id = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, name)
527	Npix,imagefile,imagetag = G2frame.PatternTree.GetImageLoc(Id)
528	imroot = os.path.splitext(imagefile)[0]
529	if imagetag:
530	imroot += '_' + str(imagetag)
531	Data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Image Controls'))
532	print('Writing '+imroot+'.imctrl')
533	File = open(imroot+'.imctrl','w')
534	keys = ['type','wavelength','calibrant','distance','center',
535	'tilt','rotation','azmthOff','fullIntegrate','LRazimuth',
536	'IOtth','outChannels','outAzimuths','invert_x','invert_y','DetDepth',
537	'calibskip','pixLimit','cutoff','calibdmin','chisq','Flat Bkg',
538	'binType','SampleShape','PolaVal','SampleAbs','dark image','background image']
539	for key in keys:
540	if key not in Data: continue #uncalibrated!
541	File.write(key+':'+str(Data[key])+'\n')
542	File.close()
543	mask = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Masks'))
544	G2imG.CleanupMasks(mask)
545	print('Writing '+imroot+'.immask')
546	File = open(imroot+'.immask','w')
547	for key in ['Points','Rings','Arcs','Polygons','Frames','Thresholds']:
548	File.write(key+':'+str(mask[key])+'\n')
549	File.close()
550
551	def PutG2Image(filename,Comments,Data,Npix,image):
552	'Write an image as a python pickle - might be better as an .edf file?'
553	File = open(filename,'wb')
554	cPickle.dump([Comments,Data,Npix,image],File,1)
555	File.close()
556	return
557
558	# should get moved to importer when ready to test
559	def GetEdfData(filename,imageOnly=False):
560	'Read European detector data edf file'
561	import struct as st
562	import array as ar
563	if not imageOnly:
564	print 'Read European detector data edf file: ',filename
565	File = open(filename,'rb')
566	fileSize = os.stat(filename).st_size
567	head = File.read(3072)
568	lines = head.split('\n')
569	sizexy = [0,0]
570	pixSize = [154,154] #Pixium4700?
571	cent = [0,0]
572	wave = 1.54187 #default <CuKa>
573	dist = 1000.
574	head = ['European detector data',]
575	for line in lines:
576	line = line.replace(';',' ').strip()
577	fields = line.split()
578	if 'Dim_1' in line:
579	sizexy[0] = int(fields[2])
580	elif 'Dim_2' in line:
581	sizexy[1] = int(fields[2])
582	elif 'DataType' in line:
583	dType = fields[2]
584	elif 'wavelength' in line:
585	wave = float(fields[2])
586	elif 'Size' in line:
587	imSize = int(fields[2])
588	# elif 'DataType' in lines:
589	# dType = fields[2]
590	elif 'pixel_size_x' in line:
591	pixSize[0] = float(fields[2])
592	elif 'pixel_size_y' in line:
593	pixSize[1] = float(fields[2])
594	elif 'beam_center_x' in line:
595	cent[0] = float(fields[2])
596	elif 'beam_center_y' in line:
597	cent[1] = float(fields[2])
598	elif 'refined_distance' in line:
599	dist = float(fields[2])
600	if line:
601	head.append(line)
602	else: #blank line at end of header
603	break
604	File.seek(fileSize-imSize)
605	if dType == 'UnsignedShort':
606	image = np.array(ar.array('H',File.read(imSize)),dtype=np.int32)
607	elif dType == 'UnsignedInt':
608	image = np.array(ar.array('L',File.read(imSize)),dtype=np.int32)
609	elif dType == 'UnsignedLong':
610	image = np.array(ar.array('L',File.read(imSize)),dtype=np.int32)
611	elif dType == 'SignedInteger':
612	image = np.array(ar.array('l',File.read(imSize)),dtype=np.int32)
613	image = np.reshape(image,(sizexy[1],sizexy[0]))
614	data = {'pixelSize':pixSize,'wavelength':wave,'distance':dist,'center':cent,'size':sizexy}
615	Npix = sizexy[0]*sizexy[1]
616	File.close()
617	if imageOnly:
618	return image
619	else:
620	return head,data,Npix,image
621
622	# should get moved to importer when ready to test
623	def GetRigaku(filename,imageOnly=False):
624	'Read Rigaku R-Axis IV image file'
625	import struct as st
626	import array as ar
627	if not imageOnly:
628	print 'Read Rigaku R-Axis IV file: ',filename
629	File = open(filename,'rb')
630	fileSize = os.stat(filename).st_size
631	Npix = (fileSize-6000)/2
632	Head = File.read(6000)
633	head = ['Rigaku R-Axis IV detector data',]
634	image = np.array(ar.array('H',File.read(fileSize-6000)),dtype=np.int32)
635	print fileSize,image.shape
636	print head
637	if Npix == 9000000:
638	sizexy = [3000,3000]
639	pixSize = [100.,100.]
640	elif Npix == 2250000:
641	sizexy = [1500,1500]
642	pixSize = [200.,200.]
643	else:
644	sizexy = [6000,6000]
645	pixSize = [50.,50.]
646	image = np.reshape(image,(sizexy[1],sizexy[0]))
647	data = {'pixelSize':pixSize,'wavelength':1.5428,'distance':250.0,'center':[150.,150.],'size':sizexy}
648	File.close()
649	if imageOnly:
650	return image
651	else:
652	return head,data,Npix,image
653
654	# should get moved to importer when ready to test
655	def GetImgData(filename,imageOnly=False):
656	'Read an ADSC image file'
657	import struct as st
658	import array as ar
659	if not imageOnly:
660	print 'Read ADSC img file: ',filename
661	File = open(filename,'rb')
662	head = File.read(511)
663	lines = head.split('\n')
664	head = []
665	center = [0,0]
666	for line in lines[1:-2]:
667	line = line.strip()[:-1]
668	if line:
669	if 'SIZE1' in line:
670	size = int(line.split('=')[1])
671	Npix = size*size
672	elif 'WAVELENGTH' in line:
673	wave = float(line.split('=')[1])
674	elif 'BIN' in line:
675	if line.split('=')[1] == '2x2':
676	pixel=(102,102)
677	else:
678	pixel = (51,51)
679	elif 'DISTANCE' in line:
680	distance = float(line.split('=')[1])
681	elif 'CENTER_X' in line:
682	center[0] = float(line.split('=')[1])
683	elif 'CENTER_Y' in line:
684	center[1] = float(line.split('=')[1])
685	head.append(line)
686	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center,'size':[size,size]}
687	image = []
688	row = 0
689	pos = 512
690	File.seek(pos)
691	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
692	image = np.reshape(image,(sizexy[1],sizexy[0]))
693	# image = np.zeros(shape=(size,size),dtype=np.int32)
694	# while row < size:
695	# File.seek(pos)
696	# line = ar.array('H',File.read(2*size))
697	# image[row] = np.asarray(line)
698	# row += 1
699	# pos += 2*size
700	File.close()
701	if imageOnly:
702	return image
703	else:
704	return lines[1:-2],data,Npix,image
705
706	# should get moved to importer when ready to test
707	def GetMAR345Data(filename,imageOnly=False):
708	'Read a MAR-345 image plate image'
709	import array as ar
710	import struct as st
711	try:
712	import pack_f as pf
713	except:
714	msg = wx.MessageDialog(None, message="Unable to load the GSAS MAR image decompression, pack_f",
715	caption="Import Error",
716	style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
717	msg.ShowModal()
718	return None,None,None,None
719
720	if not imageOnly:
721	print 'Read Mar345 file: ',filename
722	File = open(filename,'rb')
723	head = File.read(4095)
724	numbers = st.unpack('<iiiiiiiiii',head[:40])
725	lines = head[128:].split('\n')
726	head = []
727	for line in lines:
728	line = line.strip()
729	if 'PIXEL' in line:
730	values = line.split()
731	pixel = (int(values[2]),int(values[4])) #in microns
732	elif 'WAVELENGTH' in line:
733	wave = float(line.split()[1])
734	elif 'DISTANCE' in line:
735	distance = float(line.split()[1]) #in mm
736	elif 'CENTER' in line:
737	values = line.split()
738	center = [float(values[2])/10.,float(values[4])/10.] #make in mm from pixels
739	if line:
740	head.append(line)
741	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center}
742	for line in head:
743	if 'FORMAT' in line[0:6]:
744	items = line.split()
745	sizex = int(items[1])
746	Npix = int(items[3])
747	sizey = int(Npix/sizex)
748	pos = 4096
749	data['size'] = [sizex,sizey]
750	File.seek(pos)
751	line = File.read(8)
752	while 'CCP4' not in line: #get past overflow list for now
753	line = File.read(8)
754	pos += 8
755	pos += 37
756	File.seek(pos)
757	raw = File.read()
758	File.close()
759	image = np.zeros(shape=(sizex,sizey),dtype=np.int32)
760
761	image = np.flipud(pf.pack_f(len(raw),raw,sizex,sizey,image).T) #transpose to get it right way around & flip
762	if imageOnly:
763	return image
764	else:
765	return head,data,Npix,image
766
767	def ProjFileOpen(G2frame):
768	'Read a GSAS-II project file and load into the G2 data tree'
769	if not os.path.exists(G2frame.GSASprojectfile):
770	print ('\n*** Error attempt to open project file that does not exist:\n '+
771	str(G2frame.GSASprojectfile))
772	return
773	LastSavedUsing = None
774	file = open(G2frame.GSASprojectfile,'rb')
775	print 'load from file: ',G2frame.GSASprojectfile
776	G2frame.SetTitle("GSAS-II data tree: "+
777	os.path.split(G2frame.GSASprojectfile)[1])
778	wx.BeginBusyCursor()
779	try:
780	while True:
781	try:
782	data = cPickle.load(file)
783	except EOFError:
784	break
785	datum = data[0]
786
787	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=datum[0])
788	if 'PWDR' in datum[0]:
789	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
790	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
791	G2frame.PatternTree.SetItemPyData(Id,datum[1][:3]) #temp. trim off junk (patch?)
792	elif datum[0].startswith('HKLF'):
793	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
794	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
795	G2frame.PatternTree.SetItemPyData(Id,datum[1])
796	else:
797	G2frame.PatternTree.SetItemPyData(Id,datum[1])
798	if datum[0] == 'Controls' and 'LastSavedUsing' in datum[1]:
799	LastSavedUsing = datum[1]['LastSavedUsing']
800	if datum[0] == 'Controls' and 'PythonVersions' in datum[1] and GSASIIpath.GetConfigValue('debug'):
801	print('Packages used to create .GPX file:')
802	if 'dict' in str(type(datum[1]['PythonVersions'])): #patch
803	for p in sorted(datum[1]['PythonVersions'],key=lambda s: s.lower()):
804	print("{:>14s}: {:s}".format(p[0],p[1]))
805	else:
806	for p in datum[1]['PythonVersions']:
807	print("{:<12s} {:s}".format(p[0]+':',p[1]))
808	for datus in data[1:]:
809	sub = G2frame.PatternTree.AppendItem(Id,datus[0])
810	#patch
811	if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
812	if 'PWDR' in datum[0]:
813	datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
814	else:
815	datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
816	for item in datus[1][0]: #zip makes tuples - now make lists!
817	datus[1][0][item] = list(datus[1][0][item])
818	#end patch
819	G2frame.PatternTree.SetItemPyData(sub,datus[1])
820	if 'IMG' in datum[0]: #retrieve image default flag & data if set
821	Data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Image Controls'))
822	if Data['setDefault']:
823	G2frame.imageDefault = Data
824	file.close()
825	if LastSavedUsing:
826	print('GPX load successful. Last saved with GSAS-II version '+LastSavedUsing)
827	else:
828	print('project load successful')
829	G2frame.NewPlot = True
830	except:
831	msg = wx.MessageDialog(G2frame,message="Error reading file "+
832	str(G2frame.GSASprojectfile)+". This is not a GSAS-II .gpx file",
833	caption="Load Error",style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
834	msg.ShowModal()
835	finally:
836	wx.EndBusyCursor()
837	G2frame.Status.SetStatusText('To reorder tree items, use mouse RB to drag/drop them')
838
839	def ProjFileSave(G2frame):
840	'Save a GSAS-II project file'
841	if not G2frame.PatternTree.IsEmpty():
842	file = open(G2frame.GSASprojectfile,'wb')
843	print 'save to file: ',G2frame.GSASprojectfile
844	# stick the file name into the tree and version info into tree so they are saved.
845	# (Controls should always be created at this point)
846	try:
847	Controls = G2frame.PatternTree.GetItemPyData(
848	G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
849	Controls['LastSavedAs'] = os.path.abspath(G2frame.GSASprojectfile)
850	Controls['LastSavedUsing'] = str(GSASIIpath.GetVersionNumber())
851	Controls['PythonVersions'] = G2frame.PackageVersions
852	except:
853	pass
854	wx.BeginBusyCursor()
855	try:
856	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
857	while item:
858	data = []
859	name = G2frame.PatternTree.GetItemText(item)
860	data.append([name,G2frame.PatternTree.GetItemPyData(item)])
861	item2, cookie2 = G2frame.PatternTree.GetFirstChild(item)
862	while item2:
863	name = G2frame.PatternTree.GetItemText(item2)
864	data.append([name,G2frame.PatternTree.GetItemPyData(item2)])
865	item2, cookie2 = G2frame.PatternTree.GetNextChild(item, cookie2)
866	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
867	cPickle.dump(data,file,1)
868	file.close()
869	finally:
870	wx.EndBusyCursor()
871	print('project save successful')
872
873	def SaveIntegration(G2frame,PickId,data):
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	nOcc = 0
907	while item:
908	Name = G2frame.PatternTree.GetItemText(item)
909	if Aname in Name:
910	nOcc += 1
911	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
912	if nOcc:
913	Aname += '(%d)'%(nOcc)
914	Sample = G2pdG.SetDefaultSample()
915	Sample['Gonio. radius'] = data['distance']
916	Sample['Omega'] = data['GonioAngles'][0]
917	Sample['Chi'] = data['GonioAngles'][1]
918	Sample['Phi'] = data['GonioAngles'][2]
919	Sample['Azimuth'] = (azm+dazm)%360. #put here as bin center
920	if 'PWDR' in Aname:
921	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!
922	elif 'SASD' in Aname:
923	Sample['Trans'] = data['SampleAbs'][0]
924	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
925	Y = G2frame.Integrate[0][i]
926	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
927	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=Aname)
928	G2frame.IntgOutList.append(Id)
929	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
930	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Limits'),[tuple(Xminmax),Xminmax])
931	if 'PWDR' in Aname:
932	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Background'),[['chebyschev',1,3,1.0,0.0,0.0],
933	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
934	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
935	for item in inst[0]:
936	inst[0][item] = list(inst[0][item])
937	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Instrument Parameters'),inst)
938	if 'PWDR' in Aname:
939	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
940	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
941	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Index Peak List'),[[],[]])
942	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Unit Cells List'),[])
943	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Reflection Lists'),{})
944	elif 'SASD' in Aname:
945	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
946	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
947	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
948	valuesdict = {
949	'wtFactor':1.0,
950	'Dummy':False,
951	'ranId':ran.randint(0,sys.maxint),
952	'Offset':[0.0,0.0],'delOffset':0.02,'refOffset':-1.0,'refDelt':0.01,
953	'qPlot':False,'dPlot':False,'sqrtPlot':False
954	}
955	G2frame.PatternTree.SetItemPyData(
956	Id,[valuesdict,
957	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
958	return Id #last powder pattern generated
959
960	# def powderFxyeSave(G2frame,exports,powderfile):
961	# 'Save a powder histogram as a GSAS FXYE file'
962	# head,tail = ospath.split(powderfile)
963	# name,ext = tail.split('.')
964	# for i,export in enumerate(exports):
965	# filename = ospath.join(head,name+'-%03d.'%(i)+ext)
966	# prmname = filename.strip(ext)+'prm'
967	# prm = open(prmname,'w') #old style GSAS parm file
968	# PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
969	# Inst = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame, \
970	# PickId, 'Instrument Parameters'))[0]
971	# prm.write( ' 123456789012345678901234567890123456789012345678901234567890 '+'\n')
972	# prm.write( 'INS BANK 1 '+'\n')
973	# prm.write(('INS HTYPE %sR '+'\n')%(Inst['Type'][0]))
974	# if 'Lam1' in Inst: #Ka1 & Ka2
975	# prm.write(('INS 1 ICONS%10.7f%10.7f 0.0000 0.990 0 0.500 '+'\n')%(Inst['Lam1'][0],Inst['Lam2'][0]))
976	# elif 'Lam' in Inst: #single wavelength
977	# prm.write(('INS 1 ICONS%10.7f%10.7f 0.0000 0.990 0 0.500 '+'\n')%(Inst['Lam'][1],0.0))
978	# prm.write( 'INS 1 IRAD 0 '+'\n')
979	# prm.write( 'INS 1I HEAD '+'\n')
980	# prm.write( 'INS 1I ITYP 0 0.0000 180.0000 1 '+'\n')
981	# prm.write(('INS 1DETAZM%10.3f '+'\n')%(Inst['Azimuth'][0]))
982	# prm.write( 'INS 1PRCF1 3 8 0.00100 '+'\n')
983	# prm.write(('INS 1PRCF11 %15.6g%15.6g%15.6g%15.6g '+'\n')%(Inst['U'][1],Inst['V'][1],Inst['W'][1],0.0))
984	# prm.write(('INS 1PRCF12 %15.6g%15.6g%15.6g%15.6g '+'\n')%(Inst['X'][1],Inst['Y'][1],Inst['SH/L'][1]/2.,Inst['SH/L'][1]/2.))
985	# prm.close()
986	# file = open(filename,'w')
987	# print 'save powder pattern to file: ',filename
988	# x,y,w,yc,yb,yd = G2frame.PatternTree.GetItemPyData(PickId)[1]
989	# file.write(powderfile+'\n')
990	# file.write('Instrument parameter file:'+ospath.split(prmname)[1]+'\n')
991	# file.write('BANK 1 %d %d CONS %.2f %.2f 0 0 FXYE\n'%(len(x),len(x),\
992	# 100.x[0],100.(x[1]-x[0])))
993	# s = list(np.sqrt(1./np.array(w)))
994	# XYW = zip(x,y,s)
995	# for X,Y,S in XYW:
996	# file.write("%15.6g %15.6g %15.6g\n" % (100.*X,Y,max(S,1.0)))
997	# file.close()
998	# print 'powder pattern file '+filename+' written'
999
1000	# def powderXyeSave(G2frame,exports,powderfile):
1001	# 'Save a powder histogram as a Topas XYE file'
1002	# head,tail = ospath.split(powderfile)
1003	# name,ext = tail.split('.')
1004	# for i,export in enumerate(exports):
1005	# filename = ospath.join(head,name+'-%03d.'%(i)+ext)
1006	# PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1007	# file = open(filename,'w')
1008	# file.write('#%s\n'%(export))
1009	# print 'save powder pattern to file: ',filename
1010	# x,y,w,yc,yb,yd = G2frame.PatternTree.GetItemPyData(PickId)[1]
1011	# s = list(np.sqrt(1./np.array(w)))
1012	# XYW = zip(x,y,s)
1013	# for X,Y,W in XYW:
1014	# file.write("%15.6g %15.6g %15.6g\n" % (X,Y,W))
1015	# file.close()
1016	# print 'powder pattern file '+filename+' written'
1017
1018	def PDFSave(G2frame,exports):
1019	'Save a PDF G(r) and S(Q) in column formats'
1020	for export in exports:
1021	PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
1022	SQname = 'S(Q)'+export[4:]
1023	GRname = 'G(R)'+export[4:]
1024	sqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.sq')
1025	grfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.gr')
1026	sqId = G2gd.GetPatternTreeItemId(G2frame, PickId, SQname)
1027	grId = G2gd.GetPatternTreeItemId(G2frame, PickId, GRname)
1028	sqdata = np.array(G2frame.PatternTree.GetItemPyData(sqId)[1][:2]).T
1029	grdata = np.array(G2frame.PatternTree.GetItemPyData(grId)[1][:2]).T
1030	sqfile = open(sqfilename,'w')
1031	grfile = open(grfilename,'w')
1032	sqfile.write('#T S(Q) %s\n'%(export))
1033	grfile.write('#T G(R) %s\n'%(export))
1034	sqfile.write('#L Q S(Q)\n')
1035	grfile.write('#L R G(R)\n')
1036	for q,sq in sqdata:
1037	sqfile.write("%15.6g %15.6g\n" % (q,sq))
1038	sqfile.close()
1039	for r,gr in grdata:
1040	grfile.write("%15.6g %15.6g\n" % (r,gr))
1041	grfile.close()
1042
1043	def PeakListSave(G2frame,file,peaks):
1044	'Save powder peaks to a data file'
1045	print 'save peak list to file: ',G2frame.peaklistfile
1046	if not peaks:
1047	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1048	try:
1049	result = dlg.ShowModal()
1050	finally:
1051	dlg.Destroy()
1052	return
1053	for peak in peaks:
1054	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
1055	(peak[0],peak[2],peak[4],peak[6]))
1056	print 'peak list saved'
1057
1058	def IndexPeakListSave(G2frame,peaks):
1059	'Save powder peaks from the indexing list'
1060	file = open(G2frame.peaklistfile,'wa')
1061	print 'save index peak list to file: ',G2frame.peaklistfile
1062	wx.BeginBusyCursor()
1063	try:
1064	if not peaks:
1065	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1066	try:
1067	result = dlg.ShowModal()
1068	finally:
1069	dlg.Destroy()
1070	return
1071	for peak in peaks:
1072	file.write("%12.6f\n" % (peak[7]))
1073	file.close()
1074	finally:
1075	wx.EndBusyCursor()
1076	print 'index peak list saved'
1077
1078	def SetNewPhase(Name='New Phase',SGData=None,cell=None,Super=None):
1079	'''Create a new phase dict with default values for various parameters
1080
1081	:param str Name: Name for new Phase
1082
1083	:param dict SGData: space group data from :func:`GSASIIspc:SpcGroup`;
1084	defaults to data for P 1
1085
1086	:param list cell: unit cell parameter list; defaults to
1087	[1.0,1.0,1.0,90.,90,90.,1.]
1088
1089	'''
1090	if SGData is None: SGData = G2spc.SpcGroup('P 1')[1]
1091	if cell is None: cell=[1.0,1.0,1.0,90.,90,90.,1.]
1092	phaseData = {
1093	'ranId':ran.randint(0,sys.maxint),
1094	'General':{
1095	'Name':Name,
1096	'Type':'nuclear',
1097	'AtomPtrs':[3,1,7,9],
1098	'SGData':SGData,
1099	'Cell':[False,]+cell,
1100	'Pawley dmin':1.0,
1101	'Data plot type':'None',
1102	'SH Texture':{
1103	'Order':0,
1104	'Model':'cylindrical',
1105	'Sample omega':[False,0.0],
1106	'Sample chi':[False,0.0],
1107	'Sample phi':[False,0.0],
1108	'SH Coeff':[False,{}],
1109	'SHShow':False,
1110	'PFhkl':[0,0,1],
1111	'PFxyz':[0,0,1],
1112	'PlotType':'Pole figure',
1113	'Penalty':[['',],0.1,False,1.0]}},
1114	'Atoms':[],
1115	'Drawing':{},
1116	'Histograms':{},
1117	'Pawley ref':[],
1118	'RBModels':{},
1119	}
1120	if Super and Super.get('Use',False):
1121	phaseData['General'].update({'Type':'modulated','Super':True,'SuperSg':Super['ssSymb']})
1122	phaseData['General']['SSGData'] = G2spc.SSpcGroup(SGData,Super['ssSymb'])
1123	phaseData['General']['SuperVec'] = [Super['ModVec'],False,Super['maxH']]
1124
1125	return phaseData
1126
1127	class MultipleChoicesDialog(wx.Dialog):
1128	'''A dialog that offers a series of choices, each with a
1129	title and a wx.Choice widget. Intended to be used Modally.
1130	typical input:
1131
1132	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1133	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1134
1135	selections are placed in self.chosen when OK is pressed
1136	'''
1137	def __init__(self,choicelist,headinglist,
1138	head='Select options',
1139	title='Please select from options below',
1140	parent=None):
1141	self.chosen = []
1142	wx.Dialog.__init__(
1143	self,parent,wx.ID_ANY,head,
1144	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
1145	panel = wx.Panel(self)
1146	mainSizer = wx.BoxSizer(wx.VERTICAL)
1147	mainSizer.Add((10,10),1)
1148	topLabl = wx.StaticText(panel,wx.ID_ANY,title)
1149	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.CENTER,10)
1150	self.ChItems = []
1151	for choice,lbl in zip(choicelist,headinglist):
1152	mainSizer.Add((10,10),1)
1153	self.chosen.append(0)
1154	topLabl = wx.StaticText(panel,wx.ID_ANY,' '+lbl)
1155	mainSizer.Add(topLabl,0,wx.ALIGN_LEFT,10)
1156	self.ChItems.append(wx.Choice(self, wx.ID_ANY, (100, 50), choices = choice))
1157	mainSizer.Add(self.ChItems[-1],0,wx.ALIGN_CENTER,10)
1158
1159	OkBtn = wx.Button(panel,-1,"Ok")
1160	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
1161	cancelBtn = wx.Button(panel,-1,"Cancel")
1162	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
1163	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1164	btnSizer.Add((20,20),1)
1165	btnSizer.Add(OkBtn)
1166	btnSizer.Add((20,20),1)
1167	btnSizer.Add(cancelBtn)
1168	btnSizer.Add((20,20),1)
1169	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1170	panel.SetSizer(mainSizer)
1171	panel.Fit()
1172	self.Fit()
1173
1174	def OnOk(self,event):
1175	parent = self.GetParent()
1176	if parent is not None: parent.Raise()
1177	# save the results from the choice widgets
1178	self.chosen = []
1179	for w in self.ChItems:
1180	self.chosen.append(w.GetSelection())
1181	self.EndModal(wx.ID_OK)
1182
1183	def OnCancel(self,event):
1184	parent = self.GetParent()
1185	if parent is not None: parent.Raise()
1186	self.chosen = []
1187	self.EndModal(wx.ID_CANCEL)
1188
1189	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1190	confirmoverwrite=True, parent=None,
1191	multipleselect=False):
1192	'''If the filename is a zip file, extract a file from that
1193	archive.
1194
1195	:param list Selection: used to predefine the name of the file
1196	to be extracted. Filename case and zip directory name are
1197	ignored in selection; the first matching file is used.
1198
1199	:param bool confirmread: if True asks the user to confirm before expanding
1200	the only file in a zip
1201
1202	:param bool confirmoverwrite: if True asks the user to confirm
1203	before overwriting if the extracted file already exists
1204
1205	:param bool multipleselect: if True allows more than one zip
1206	file to be extracted, a list of file(s) is returned.
1207	If only one file is present, do not ask which one, otherwise
1208	offer a list of choices (unless selection is used).
1209
1210	:returns: the name of the file that has been created or a
1211	list of files (see multipleselect)
1212
1213	If the file is not a zipfile, return the name of the input file.
1214	If the zipfile is empty or no file has been selected, return None
1215	'''
1216	import zipfile # do this now, since we can save startup time by doing this only on need
1217	import shutil
1218	zloc = os.path.split(filename)[0]
1219	if not zipfile.is_zipfile(filename):
1220	#print("not zip")
1221	return filename
1222
1223	z = zipfile.ZipFile(filename,'r')
1224	zinfo = z.infolist()
1225
1226	if len(zinfo) == 0:
1227	#print('Zip has no files!')
1228	zlist = [-1]
1229	if selection:
1230	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1231	if selection.lower() in choices:
1232	zlist = [choices.index(selection.lower())]
1233	else:
1234	print('debug: file '+str(selection)+' was not found in '+str(filename))
1235	zlist = [-1]
1236	elif len(zinfo) == 1 and confirmread:
1237	result = wx.ID_NO
1238	dlg = wx.MessageDialog(
1239	parent,
1240	'Is file '+str(zinfo[0].filename)+
1241	' what you want to extract from '+
1242	str(os.path.split(filename)[1])+'?',
1243	'Confirm file',
1244	wx.YES_NO \| wx.ICON_QUESTION)
1245	try:
1246	result = dlg.ShowModal()
1247	finally:
1248	dlg.Destroy()
1249	if result == wx.ID_NO:
1250	zlist = [-1]
1251	else:
1252	zlist = [0]
1253	elif len(zinfo) == 1:
1254	zlist = [0]
1255	elif multipleselect:
1256	# select one or more from a from list
1257	choices = [i.filename for i in zinfo]
1258	dlg = G2G.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1259	'Choose file(s)',choices)
1260	if dlg.ShowModal() == wx.ID_OK:
1261	zlist = dlg.GetSelections()
1262	else:
1263	zlist = []
1264	dlg.Destroy()
1265	else:
1266	# select one from a from list
1267	choices = [i.filename for i in zinfo]
1268	dlg = wx.SingleChoiceDialog(parent,
1269	'Select file to extract from zip file'+str(filename),'Choose file',
1270	choices,)
1271	if dlg.ShowModal() == wx.ID_OK:
1272	zlist = [dlg.GetSelection()]
1273	else:
1274	zlist = [-1]
1275	dlg.Destroy()
1276
1277	outlist = []
1278	for zindex in zlist:
1279	if zindex >= 0:
1280	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1281	if os.path.exists(efil) and confirmoverwrite:
1282	result = wx.ID_NO
1283	dlg = wx.MessageDialog(parent,
1284	'File '+str(efil)+' already exists. OK to overwrite it?',
1285	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1286	try:
1287	result = dlg.ShowModal()
1288	finally:
1289	dlg.Destroy()
1290	if result == wx.ID_NO:
1291	zindex = -1
1292	if zindex >= 0:
1293	# extract the file to the current directory, regardless of it's original path
1294	#z.extract(zinfo[zindex],zloc)
1295	eloc,efil = os.path.split(zinfo[zindex].filename)
1296	outfile = os.path.join(zloc, efil)
1297	fpin = z.open(zinfo[zindex])
1298	fpout = file(outfile, "wb")
1299	shutil.copyfileobj(fpin, fpout)
1300	fpin.close()
1301	fpout.close()
1302	outlist.append(outfile)
1303	z.close()
1304	if multipleselect and len(outlist) >= 1:
1305	return outlist
1306	elif len(outlist) == 1:
1307	return outlist[0]
1308	else:
1309	return None
1310
1311	######################################################################
1312	# base classes for reading various types of data files
1313	# not used directly, only by subclassing
1314	######################################################################
1315	try:
1316	E,SGData = G2spc.SpcGroup('P 1') # data structure for default space group
1317	except: # errors on doc build
1318	SGData = None
1319	P1SGData = SGData
1320	class ImportBaseclass(object):
1321	'''Defines a base class for the reading of input files (diffraction
1322	data, coordinates,...). See :ref:`Writing a Import Routine<Import_routines>`
1323	for an explanation on how to use a subclass of this class.
1324	'''
1325	class ImportException(Exception):
1326	'''Defines an Exception that is used when an import routine hits an expected error,
1327	usually in .Reader.
1328
1329	Good practice is that the Reader should define a value in self.errors that
1330	tells the user some information about what is wrong with their file.
1331	'''
1332	pass
1333
1334	def __init__(self,
1335	formatName,
1336	longFormatName=None,
1337	extensionlist=[],
1338	strictExtension=False,
1339	):
1340	self.formatName = formatName # short string naming file type
1341	if longFormatName: # longer string naming file type
1342	self.longFormatName = longFormatName
1343	else:
1344	self.longFormatName = formatName
1345	# define extensions that are allowed for the file type
1346	# for windows, remove any extensions that are duplicate, as case is ignored
1347	if sys.platform == 'windows' and extensionlist:
1348	extensionlist = list(set([s.lower() for s in extensionlist]))
1349	self.extensionlist = extensionlist
1350	# If strictExtension is True, the file will not be read, unless
1351	# the extension matches one in the extensionlist
1352	self.strictExtension = strictExtension
1353	self.errors = ''
1354	self.warnings = ''
1355	# used for readers that will use multiple passes to read
1356	# more than one data block
1357	self.repeat = False
1358	self.selections = []
1359	self.repeatcount = 0
1360	self.readfilename = '?'
1361	#print 'created',self.__class__
1362
1363	def ReInitialize(self):
1364	'Reinitialize the Reader to initial settings'
1365	self.errors = ''
1366	self.warnings = ''
1367	self.repeat = False
1368	self.repeatcount = 0
1369	self.readfilename = '?'
1370
1371	def BlockSelector(self, ChoiceList, ParentFrame=None,
1372	title='Select a block',
1373	size=None, header='Block Selector',
1374	useCancel=True):
1375	''' Provide a wx dialog to select a block if the file contains more
1376	than one set of data and one must be selected
1377	'''
1378	if useCancel:
1379	dlg = wx.SingleChoiceDialog(
1380	ParentFrame,title, header,ChoiceList)
1381	else:
1382	dlg = wx.SingleChoiceDialog(
1383	ParentFrame,title, header,ChoiceList,
1384	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.OK\|wx.CENTRE)
1385	if size: dlg.SetSize(size)
1386	dlg.CenterOnParent()
1387	if dlg.ShowModal() == wx.ID_OK:
1388	sel = dlg.GetSelection()
1389	return sel
1390	else:
1391	return None
1392	dlg.Destroy()
1393
1394	def MultipleBlockSelector(self, ChoiceList, ParentFrame=None,
1395	title='Select a block',size=None, header='Block Selector'):
1396	'''Provide a wx dialog to select a block of data if the
1397	file contains more than one set of data and one must be
1398	selected.
1399
1400	:returns: a list of the selected blocks
1401	'''
1402	dlg = wx.MultiChoiceDialog(ParentFrame,title, header,ChoiceList+['Select all'],
1403	wx.CHOICEDLG_STYLE)
1404	dlg.CenterOnParent()
1405	if size: dlg.SetSize(size)
1406	if dlg.ShowModal() == wx.ID_OK:
1407	sel = dlg.GetSelections()
1408	else:
1409	return []
1410	dlg.Destroy()
1411	selected = []
1412	if len(ChoiceList) in sel:
1413	return range(len(ChoiceList))
1414	else:
1415	return sel
1416	return selected
1417
1418	def MultipleChoicesDialog(self, choicelist, headinglist, ParentFrame=None, **kwargs):
1419	'''A modal dialog that offers a series of choices, each with a title and a wx.Choice
1420	widget. Typical input:
1421
1422	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1423
1424	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1425
1426	optional keyword parameters are: head (window title) and title
1427	returns a list of selected indicies for each choice (or None)
1428	'''
1429	result = None
1430	dlg = MultipleChoicesDialog(choicelist,headinglist,
1431	parent=ParentFrame, **kwargs)
1432	dlg.CenterOnParent()
1433	if dlg.ShowModal() == wx.ID_OK:
1434	result = dlg.chosen
1435	dlg.Destroy()
1436	return result
1437
1438	def ShowBusy(self):
1439	wx.BeginBusyCursor()
1440	# wx.Yield() # make it happen now!
1441
1442	def DoneBusy(self):
1443	wx.EndBusyCursor()
1444	wx.Yield() # make it happen now!
1445
1446	# def Reader(self, filename, filepointer, ParentFrame=None, **unused):
1447	# '''This method must be supplied in the child class to read the file.
1448	# if the read fails either return False or raise an Exception
1449	# preferably of type ImportException.
1450	# '''
1451	# #start reading
1452	# raise ImportException("Error occurred while...")
1453	# self.errors += "Hint for user on why the error occur
1454	# return False # if an error occurs
1455	# return True # if read OK
1456
1457	def ExtensionValidator(self, filename):
1458	'''This methods checks if the file has the correct extension
1459	Return False if this filename will not be supported by this reader
1460	Return True if the extension matches the list supplied by the reader
1461	Return None if the reader allows un-registered extensions
1462	'''
1463	if filename:
1464	ext = os.path.splitext(filename)[1]
1465	if sys.platform == 'windows': ext = ext.lower()
1466	if ext in self.extensionlist: return True
1467	if self.strictExtension: return False
1468	return None
1469
1470	def ContentsValidator(self, filepointer):
1471	'''This routine will attempt to determine if the file can be read
1472	with the current format.
1473	This will typically be overridden with a method that
1474	takes a quick scan of [some of]
1475	the file contents to do a "sanity" check if the file
1476	appears to match the selected format.
1477	Expected to be called via self.Validator()
1478	'''
1479	#filepointer.seek(0) # rewind the file pointer
1480	return True
1481
1482	def CIFValidator(self, filepointer):
1483	'''A :meth:`ContentsValidator` for use to validate CIF files.
1484	'''
1485	for i,l in enumerate(filepointer):
1486	if i >= 1000: return True
1487	'''Encountered only blank lines or comments in first 1000
1488	lines. This is unlikely, but assume it is CIF anyway, since we are
1489	even less likely to find a file with nothing but hashes and
1490	blank lines'''
1491	line = l.strip()
1492	if len(line) == 0: # ignore blank lines
1493	continue
1494	elif line.startswith('#'): # ignore comments
1495	continue
1496	elif line.startswith('data_'): # on the right track, accept this file
1497	return True
1498	else: # found something invalid
1499	self.errors = 'line '+str(i+1)+' contains unexpected data:\n'
1500	self.errors += ' '+str(l)
1501	self.errors += ' Note: a CIF should only have blank lines or comments before'
1502	self.errors += ' a data_ statement begins a block.'
1503	return False
1504
1505	class ImportPhase(ImportBaseclass):
1506	'''Defines a base class for the reading of files with coordinates
1507
1508	Objects constructed that subclass this (in import/G2phase_*.py etc.) will be used
1509	in :meth:`GSASII.GSASII.OnImportPhase`.
1510	See :ref:`Writing a Import Routine<Import_Routines>`
1511	for an explanation on how to use this class.
1512
1513	'''
1514	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1515	strictExtension=False,):
1516	# call parent __init__
1517	ImportBaseclass.__init__(self,formatName,longFormatName,
1518	extensionlist,strictExtension)
1519	self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
1520	self.Constraints = None
1521
1522	def PhaseSelector(self, ChoiceList, ParentFrame=None,
1523	title='Select a phase', size=None,header='Phase Selector'):
1524	''' Provide a wx dialog to select a phase if the file contains more
1525	than one phase
1526	'''
1527	return self.BlockSelector(ChoiceList,ParentFrame,title,
1528	size,header)
1529
1530	class ImportStructFactor(ImportBaseclass):
1531	'''Defines a base class for the reading of files with tables
1532	of structure factors.
1533
1534	Structure factors are read with a call to :meth:`GSASII.GSASII.OnImportSfact`
1535	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`, which calls
1536	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1537	:meth:`Reader`.
1538
1539	See :ref:`Writing a Import Routine<Import_Routines>`
1540	for an explanation on how to use import classes in general. The specifics
1541	for reading a structure factor histogram require that
1542	the ``Reader()`` routine in the import
1543	class need to do only a few things: It
1544	should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
1545	and set :attr:`Parameters` with the instrument parameters
1546	(initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
1547	'''
1548	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1549	strictExtension=False,):
1550	ImportBaseclass.__init__(self,formatName,longFormatName,
1551	extensionlist,strictExtension)
1552
1553	# define contents of Structure Factor entry
1554	self.Parameters = []
1555	'self.Parameters is a list with two dicts for data parameter settings'
1556	self.InitParameters()
1557	self.RefDict = {'RefList':[],'FF':{},'Super':0}
1558	self.Banks = [] #for multi bank data (usually TOF)
1559	'''self.RefDict is a dict containing the reflection information, as read from the file.
1560	Item 'RefList' contains the reflection information. See the
1561	:ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
1562	for the contents of each row. Dict element 'FF'
1563	contains the form factor values for each element type; if this entry
1564	is left as initialized (an empty list) it will be initialized as needed later.
1565	'''
1566	def ReInitialize(self):
1567	'Reinitialize the Reader to initial settings'
1568	ImportBaseclass.ReInitialize(self)
1569	self.InitParameters()
1570	self.Banks = [] #for multi bank data (usually TOF)
1571	self.RefDict = {'RefList':[],'FF':{},'Super':0}
1572
1573	def InitParameters(self):
1574	'initialize the instrument parameters structure'
1575	Lambda = 0.70926
1576	HistType = 'SXC'
1577	self.Parameters = [{'Type':[HistType,HistType], # create the structure
1578	'Lam':[Lambda,Lambda]
1579	}, {}]
1580	'Parameters is a list with two dicts for data parameter settings'
1581
1582	def UpdateParameters(self,Type=None,Wave=None):
1583	'Revise the instrument parameters'
1584	if Type is not None:
1585	self.Parameters[0]['Type'] = [Type,Type]
1586	if Wave is not None:
1587	self.Parameters[0]['Lam'] = [Wave,Wave]
1588
1589	######################################################################
1590	class ImportPowderData(ImportBaseclass):
1591	'''Defines a base class for the reading of files with powder data.
1592
1593	Objects constructed that subclass this (in import/G2pwd_*.py etc.) will be used
1594	in :meth:`GSASII.GSASII.OnImportPowder`.
1595	See :ref:`Writing a Import Routine<Import_Routines>`
1596	for an explanation on how to use this class.
1597	'''
1598	def __init__(self,
1599	formatName,
1600	longFormatName=None,
1601	extensionlist=[],
1602	strictExtension=False,
1603	):
1604	ImportBaseclass.__init__(self,formatName,
1605	longFormatName,
1606	extensionlist,
1607	strictExtension)
1608	self.clockWd = None # used in TOF
1609	self.ReInitialize()
1610
1611	def ReInitialize(self):
1612	'Reinitialize the Reader to initial settings'
1613	ImportBaseclass.ReInitialize(self)
1614	self.powderentry = ['',None,None] # (filename,Pos,Bank)
1615	self.powderdata = [] # Powder dataset
1616	'''A powder data set is a list with items [x,y,w,yc,yb,yd]:
1617	np.array(x), # x-axis values
1618	np.array(y), # powder pattern intensities
1619	np.array(w), # 1/sig(intensity)^2 values (weights)
1620	np.array(yc), # calc. intensities (zero)
1621	np.array(yb), # calc. background (zero)
1622	np.array(yd), # obs-calc profiles
1623	'''
1624	self.comments = []
1625	self.idstring = ''
1626	self.Sample = G2pdG.SetDefaultSample() # default sample parameters
1627	self.Controls = {} # items to be placed in top-level Controls
1628	self.GSAS = None # used in TOF
1629	self.repeat_instparm = True # Should a parm file be
1630	# used for multiple histograms?
1631	self.instparm = None # name hint from file of instparm to use
1632	self.instfile = '' # full path name to instrument parameter file
1633	self.instbank = '' # inst parm bank number
1634	self.instmsg = '' # a label that gets printed to show
1635	# where instrument parameters are from
1636	self.numbanks = 1
1637	self.instdict = {} # place items here that will be transferred to the instrument parameters
1638	self.pwdparms = {} # place parameters that are transferred directly to the tree
1639	# here (typically from an existing GPX file)
1640	######################################################################
1641	class ImportSmallAngleData(ImportBaseclass):
1642	'''Defines a base class for the reading of files with small angle data.
1643	See :ref:`Writing a Import Routine<Import_Routines>`
1644	for an explanation on how to use this class.
1645	'''
1646	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1647	strictExtension=False,):
1648
1649	ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
1650	strictExtension)
1651	self.ReInitialize()
1652
1653	def ReInitialize(self):
1654	'Reinitialize the Reader to initial settings'
1655	ImportBaseclass.ReInitialize(self)
1656	self.smallangleentry = ['',None,None] # (filename,Pos,Bank)
1657	self.smallangledata = [] # SASD dataset
1658	'''A small angle data set is a list with items [x,y,w,yc,yd]:
1659	np.array(x), # x-axis values
1660	np.array(y), # powder pattern intensities
1661	np.array(w), # 1/sig(intensity)^2 values (weights)
1662	np.array(yc), # calc. intensities (zero)
1663	np.array(yd), # obs-calc profiles
1664	np.array(yb), # preset bkg
1665	'''
1666	self.comments = []
1667	self.idstring = ''
1668	self.Sample = G2pdG.SetDefaultSample()
1669	self.GSAS = None # used in TOF
1670	self.clockWd = None # used in TOF
1671	self.numbanks = 1
1672	self.instdict = {} # place items here that will be transferred to the instrument parameters
1673
1674	######################################################################
1675	class ImportImage(ImportBaseclass):
1676	'''Defines a base class for the reading of images
1677
1678	Images are read in only these places:
1679
1680	* Initial reading is typically done from a menu item
1681	with a call to :meth:`GSASII.GSASII.OnImportImage`
1682	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`. That calls
1683	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1684	:meth:`Reader`. This returns a list of reader objects for each read image.
1685
1686	* Images are read alternatively in :func:`GSASIIIO.ReadImages`, which puts image info
1687	directly into the data tree.
1688
1689	* Images are reloaded with :func:`GSASIIIO.GetImageData`.
1690
1691	.. _Image_import_routines:
1692
1693	When reading an image, the ``Reader()`` routine in the ImportImage class
1694	should set:
1695
1696	* :attr:`Comments`: a list of strings (str),
1697	* :attr:`Npix`: the number of pixels in the image (int),
1698	* :attr:`Image`: the actual image as a numpy array (np.array)
1699	* :attr:`Data`: a dict defining image parameters (dict). Within this dict the following
1700	data items are needed:
1701
1702	* 'pixelSize': size of each pixel in microns (such as ``[200,200]``.
1703	* 'wavelength': wavelength in Angstoms.
1704	* 'distance': distance of detector from sample in cm.
1705	* 'center': uncalibrated center of beam on detector (such as ``[204.8,204.8]``.
1706	* 'size': size of image (such as ``[2048,2048]``).
1707	* 'ImageTag': image number or other keyword used to retrieve image from
1708	a multi-image data file (defaults to ``1`` if not specified).
1709
1710	optional data items:
1711
1712	* :attr:`repeat`: set to True if there are additional images to
1713	read in the file, False otherwise
1714	* :attr:`repeatcount`: set to the number of the image.
1715
1716	Note that the above is initialized with :meth:`InitParameters`.
1717	(Also see :ref:`Writing a Import Routine<Import_Routines>`
1718	for an explanation on how to use import classes in general.)
1719	'''
1720	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1721	strictExtension=False,):
1722	ImportBaseclass.__init__(self,formatName,longFormatName,
1723	extensionlist,strictExtension)
1724	self.InitParameters()
1725
1726	def ReInitialize(self):
1727	'Reinitialize the Reader to initial settings -- not used at present'
1728	ImportBaseclass.ReInitialize(self)
1729	self.InitParameters()
1730
1731	def InitParameters(self):
1732	'initialize the instrument parameters structure'
1733	self.Comments = ['No comments']
1734	self.Data = {}
1735	self.Npix = 0
1736	self.Image = None
1737	self.repeat = False
1738	self.repeatcount = 1
1739
1740	def LoadImage(self,ParentFrame,imagefile,imagetag=None):
1741	'''Optionally, call this after reading in an image to load it into the tree.
1742	This saves time by preventing a reread of the same information.
1743	'''
1744	if ParentFrame:
1745	ParentFrame.ImageZ = self.Image # store the image for plotting
1746	ParentFrame.oldImagefile = imagefile # save the name of the last image file read
1747	ParentFrame.oldImageTag = imagetag # save the tag of the last image file read
1748
1749	######################################################################
1750	class ExportBaseclass(object):
1751	'''Defines a base class for the exporting of GSAS-II results.
1752
1753	This class is subclassed in the various exports/G2export_*.py files. Those files
1754	are imported in :meth:`GSASII.GSASII._init_Exports` which defines the
1755	appropriate menu items for each one and the .Exporter method is called
1756	directly from the menu item.
1757
1758	Routines may also define a .Writer method, which is used to write a single
1759	file without invoking any GUI objects.
1760	'''
1761	def __init__(self,
1762	G2frame,
1763	formatName,
1764	extension,
1765	longFormatName=None,
1766	):
1767	self.G2frame = G2frame
1768	self.formatName = formatName # short string naming file type
1769	self.extension = extension
1770	if longFormatName: # longer string naming file type
1771	self.longFormatName = longFormatName
1772	else:
1773	self.longFormatName = formatName
1774	self.OverallParms = {}
1775	self.Phases = {}
1776	self.Histograms = {}
1777	self.powderDict = {}
1778	self.xtalDict = {}
1779	self.parmDict = {}
1780	self.sigDict = {}
1781	# updated in InitExport:
1782	self.currentExportType = None # type of export that has been requested
1783	# updated in ExportSelect (when used):
1784	self.phasenam = None # a list of selected phases
1785	self.histnam = None # a list of selected histograms
1786	self.filename = None # name of file to be written (single export) or template (multiple files)
1787	self.dirname = '' # name of directory where file(s) will be written
1788	self.fullpath = '' # name of file being written -- full path
1789
1790	# items that should be defined in a subclass of this class
1791	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1792	# The following types are defined: 'project', "phase", "powder", "single"
1793	self.multiple = False # set as True if the class can export multiple phases or histograms
1794	# self.multiple is ignored for "project" exports
1795
1796	def InitExport(self,event):
1797	'''Determines the type of menu that called the Exporter and
1798	misc initialization.
1799	'''
1800	self.filename = None # name of file to be written (single export)
1801	self.dirname = '' # name of file to be written (multiple export)
1802	if event:
1803	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1804
1805	def MakePWDRfilename(self,hist):
1806	'''Make a filename root (no extension) from a PWDR histogram name
1807
1808	:param str hist: the histogram name in data tree (starts with "PWDR ")
1809	'''
1810	file0 = ''
1811	file1 = hist[5:]
1812	# replace repeated blanks
1813	while file1 != file0:
1814	file0 = file1
1815	file1 = file0.replace(' ',' ').strip()
1816	file0 = file1.replace('Azm= ','A')
1817	# if angle has unneeded decimal places on aziumuth, remove them
1818	if file0[-3:] == '.00': file0 = file0[:-3]
1819	file0 = file0.replace('.','_')
1820	file0 = file0.replace(' ','_')
1821	return file0
1822
1823	def ExportSelect(self,AskFile='ask'):
1824	'''Selects histograms or phases when needed. Sets a default file name when
1825	requested in self.filename; always sets a default directory in self.dirname.
1826
1827	:param bool AskFile: Determines how this routine processes getting a
1828	location to store the current export(s).
1829
1830	* if AskFile is 'ask' (default option), get the name of the file to be written;
1831	self.filename and self.dirname are always set. In the case where
1832	multiple files must be generated, the export routine should do this
1833	based on self.filename as a template.
1834	* if AskFile is 'dir', get the name of the directory to be used;
1835	self.filename is not used, but self.dirname is always set. The export routine
1836	will always generate the file name.
1837	* if AskFile is 'single', get only the name of the directory to be used when
1838	multiple items will be written (as multiple files) are used
1839	or a complete file name is requested when a single file
1840	name is selected. self.dirname is always set and self.filename used
1841	only when a single file is selected.
1842	* if AskFile is 'default', creates a name of the file to be used from
1843	the name of the project (.gpx) file. If the project has not been saved,
1844	then the name of file is requested.
1845	self.filename and self.dirname are always set. In the case where
1846	multiple file names must be generated, the export routine should do this
1847	based on self.filename.
1848	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1849	file. If the project has not been saved, then a directory is requested.
1850	self.filename is not used.
1851
1852	:returns: True in case of an error
1853	'''
1854
1855	numselected = 1
1856	if self.currentExportType == 'phase':
1857	if len(self.Phases) == 0:
1858	self.G2frame.ErrorDialog(
1859	'Empty project',
1860	'Project does not contain any phases.')
1861	return True
1862	elif len(self.Phases) == 1:
1863	self.phasenam = self.Phases.keys()
1864	elif self.multiple:
1865	choices = sorted(self.Phases.keys())
1866	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1867	if phasenum is None: return True
1868	self.phasenam = [choices[i] for i in phasenum]
1869	if not self.phasenam: return True
1870	numselected = len(self.phasenam)
1871	else:
1872	choices = sorted(self.Phases.keys())
1873	phasenum = G2G.ItemSelector(choices,self.G2frame)
1874	if phasenum is None: return True
1875	self.phasenam = [choices[phasenum]]
1876	numselected = len(self.phasenam)
1877	elif self.currentExportType == 'single':
1878	if len(self.xtalDict) == 0:
1879	self.G2frame.ErrorDialog(
1880	'Empty project',
1881	'Project does not contain any single crystal data.')
1882	return True
1883	elif len(self.xtalDict) == 1:
1884	self.histnam = self.xtalDict.values()
1885	elif self.multiple:
1886	choices = sorted(self.xtalDict.values())
1887	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1888	if not hnum: return True
1889	self.histnam = [choices[i] for i in hnum]
1890	numselected = len(self.histnam)
1891	else:
1892	choices = sorted(self.xtalDict.values())
1893	hnum = G2G.ItemSelector(choices,self.G2frame)
1894	if hnum is None: return True
1895	self.histnam = [choices[hnum]]
1896	numselected = len(self.histnam)
1897	elif self.currentExportType == 'powder':
1898	if len(self.powderDict) == 0:
1899	self.G2frame.ErrorDialog(
1900	'Empty project',
1901	'Project does not contain any powder data.')
1902	return True
1903	elif len(self.powderDict) == 1:
1904	self.histnam = self.powderDict.values()
1905	elif self.multiple:
1906	choices = sorted(self.powderDict.values())
1907	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1908	if not hnum: return True
1909	self.histnam = [choices[i] for i in hnum]
1910	numselected = len(self.histnam)
1911	else:
1912	choices = sorted(self.powderDict.values())
1913	hnum = G2G.ItemSelector(choices,self.G2frame)
1914	if hnum is None: return True
1915	self.histnam = [choices[hnum]]
1916	numselected = len(self.histnam)
1917	elif self.currentExportType == 'image':
1918	if len(self.Histograms) == 0:
1919	self.G2frame.ErrorDialog(
1920	'Empty project',
1921	'Project does not contain any images.')
1922	return True
1923	elif len(self.Histograms) == 1:
1924	self.histnam = self.Histograms.keys()
1925	else:
1926	choices = sorted(self.Histograms.keys())
1927	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1928	if self.multiple:
1929	if not hnum: return True
1930	self.histnam = [choices[i] for i in hnum]
1931	else:
1932	if hnum is None: return True
1933	self.histnam = [choices[hnum]]
1934	numselected = len(self.histnam)
1935	if self.currentExportType == 'map':
1936	# search for phases with maps
1937	mapPhases = []
1938	choices = []
1939	for phasenam in sorted(self.Phases):
1940	phasedict = self.Phases[phasenam] # pointer to current phase info
1941	if len(phasedict['General']['Map'].get('rho',[])):
1942	mapPhases.append(phasenam)
1943	if phasedict['General']['Map'].get('Flip'):
1944	choices.append('Charge flip map: '+str(phasenam))
1945	elif phasedict['General']['Map'].get('MapType'):
1946	choices.append(
1947	str(phasedict['General']['Map'].get('MapType'))
1948	+ ' map: ' + str(phasenam))
1949	else:
1950	choices.append('unknown map: '+str(phasenam))
1951	# select a map if needed
1952	if len(mapPhases) == 0:
1953	self.G2frame.ErrorDialog(
1954	'Empty project',
1955	'Project does not contain any maps.')
1956	return True
1957	elif len(mapPhases) == 1:
1958	self.phasenam = mapPhases
1959	else:
1960	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1961	if self.multiple:
1962	if not phasenum: return True
1963	self.phasenam = [mapPhases[i] for i in phasenum]
1964	else:
1965	if phasenum is None: return True
1966	self.phasenam = [mapPhases[phasenum]]
1967	numselected = len(self.phasenam)
1968
1969	# items selected, now set self.dirname and usually self.filename
1970	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
1971	AskFile == 'default' and not self.G2frame.GSASprojectfile
1972	):
1973	filename = self.askSaveFile()
1974	if not filename: return True
1975	self.dirname,self.filename = os.path.split(filename)
1976	elif AskFile == 'dir' or AskFile == 'single' or (
1977	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
1978	):
1979	self.dirname = self.askSaveDirectory()
1980	if not self.dirname: return True
1981	elif AskFile == 'default-dir' or AskFile == 'default':
1982	self.dirname,self.filename = os.path.split(
1983	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
1984	)
1985	else:
1986	raise Exception('This should not happen!')
1987
1988	def loadParmDict(self):
1989	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
1990	refined values to those from the last cycle and set the uncertainties for the
1991	refined parameters in another dict (self.sigDict).
1992
1993	Expands the parm & sig dicts to include values derived from constraints.
1994	'''
1995	self.parmDict = {}
1996	self.sigDict = {}
1997	rigidbodyDict = {}
1998	covDict = {}
1999	consDict = {}
2000	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2001	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2002	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2003	while item:
2004	name = self.G2frame.PatternTree.GetItemText(item)
2005	if name == 'Rigid bodies':
2006	rigidbodyDict = self.G2frame.PatternTree.GetItemPyData(item)
2007	elif name == 'Covariance':
2008	covDict = self.G2frame.PatternTree.GetItemPyData(item)
2009	elif name == 'Constraints':
2010	consDict = self.G2frame.PatternTree.GetItemPyData(item)
2011	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2012	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
2013	self.parmDict.update(rbDict)
2014	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
2015	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,maxSSwave = G2stIO.GetPhaseData(
2016	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
2017	self.parmDict.update(phaseDict)
2018	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
2019	Phases,Histograms,Print=False,resetRefList=False)
2020	self.parmDict.update(hapDict)
2021	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
2022	self.parmDict.update(histDict)
2023	self.parmDict.update(zip(
2024	covDict.get('varyList',[]),
2025	covDict.get('variables',[])))
2026	self.sigDict = dict(zip(
2027	covDict.get('varyList',[]),
2028	covDict.get('sig',[])))
2029	# expand to include constraints: first compile a list of constraints
2030	constList = []
2031	for item in consDict:
2032	if item.startswith('_'): continue
2033	constList += consDict[item]
2034	# now process the constraints
2035	G2mv.InitVars()
2036	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
2037	varyList = covDict.get('varyListStart')
2038	if varyList is None and len(constDict) == 0:
2039	# no constraints can use varyList
2040	varyList = covDict.get('varyList')
2041	elif varyList is None:
2042	# old GPX file from before pre-constraint varyList is saved
2043	print ' * Old refinement: Please use Calculate/Refine to redo *'
2044	raise Exception(' * Export aborted *')
2045	else:
2046	varyList = list(varyList)
2047	try:
2048	groups,parmlist = G2mv.GroupConstraints(constDict)
2049	G2mv.GenerateConstraints(groups,parmlist,varyList,constDict,fixedList,self.parmDict)
2050	except:
2051	# this really should not happen
2052	print ' * ERROR - constraints are internally inconsistent *'
2053	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
2054	print 'Errors',errmsg
2055	if warnmsg: print 'Warnings',warnmsg
2056	raise Exception(' * CIF creation aborted *')
2057	# add the constrained values to the parameter dictionary
2058	G2mv.Dict2Map(self.parmDict,varyList)
2059	# and add their uncertainties into the esd dictionary (sigDict)
2060	if covDict.get('covMatrix') is not None:
2061	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
2062
2063	def loadTree(self):
2064	'''Load the contents of the data tree into a set of dicts
2065	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
2066	& self.xtalDict)
2067
2068	* The childrenless data tree items are overall parameters/controls for the
2069	entire project and are placed in self.OverallParms
2070	* Phase items are placed in self.Phases
2071	* Data items are placed in self.Histogram. The key for these data items
2072	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
2073	'''
2074	self.OverallParms = {}
2075	self.powderDict = {}
2076	self.xtalDict = {}
2077	self.Phases = {}
2078	self.Histograms = {}
2079	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2080	histType = None
2081	if self.currentExportType == 'phase':
2082	# if exporting phases load them here
2083	sub = G2gd.GetPatternTreeItemId(self.G2frame,self.G2frame.root,'Phases')
2084	if not sub:
2085	print 'no phases found'
2086	return True
2087	item, cookie = self.G2frame.PatternTree.GetFirstChild(sub)
2088	while item:
2089	phaseName = self.G2frame.PatternTree.GetItemText(item)
2090	self.Phases[phaseName] = self.G2frame.PatternTree.GetItemPyData(item)
2091	item, cookie = self.G2frame.PatternTree.GetNextChild(sub, cookie)
2092	return
2093	elif self.currentExportType == 'single':
2094	histType = 'HKLF'
2095	elif self.currentExportType == 'powder':
2096	histType = 'PWDR'
2097	elif self.currentExportType == 'image':
2098	histType = 'IMG'
2099
2100	if histType: # Loading just one kind of tree entry
2101	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2102	while item:
2103	name = self.G2frame.PatternTree.GetItemText(item)
2104	if name.startswith(histType):
2105	if self.Histograms.get(name): # there is already an item with this name
2106	print('Histogram name '+str(name)+' is repeated. Renaming')
2107	if name[-1] == '9':
2108	name = name[:-1] + '10'
2109	elif name[-1] in '012345678':
2110	name = name[:-1] + str(int(name[-1])+1)
2111	else:
2112	name += '-1'
2113	self.Histograms[name] = {}
2114	# the main info goes into Data, but the 0th
2115	# element contains refinement results, carry
2116	# that over too now.
2117	self.Histograms[name]['Data'] = self.G2frame.PatternTree.GetItemPyData(item)[1]
2118	self.Histograms[name][0] = self.G2frame.PatternTree.GetItemPyData(item)[0]
2119	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2120	while item2:
2121	child = self.G2frame.PatternTree.GetItemText(item2)
2122	self.Histograms[name][child] = self.G2frame.PatternTree.GetItemPyData(item2)
2123	item2, cookie2 = self.G2frame.PatternTree.GetNextChild(item, cookie2)
2124	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2125	# index powder and single crystal histograms by number
2126	for hist in self.Histograms:
2127	if hist.startswith("PWDR"):
2128	d = self.powderDict
2129	elif hist.startswith("HKLF"):
2130	d = self.xtalDict
2131	else:
2132	return
2133	i = self.Histograms[hist].get('hId')
2134	if i is None and not d.keys():
2135	i = 0
2136	elif i is None or i in d.keys():
2137	i = max(d.keys())+1
2138	d[i] = hist
2139	return
2140	# else standard load: using all interlinked phases and histograms
2141	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2142	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2143	while item:
2144	name = self.G2frame.PatternTree.GetItemText(item)
2145	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2146	if not item2:
2147	self.OverallParms[name] = self.G2frame.PatternTree.GetItemPyData(item)
2148	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2149	# index powder and single crystal histograms
2150	for hist in self.Histograms:
2151	i = self.Histograms[hist]['hId']
2152	if hist.startswith("PWDR"):
2153	self.powderDict[i] = hist
2154	elif hist.startswith("HKLF"):
2155	self.xtalDict[i] = hist
2156
2157	def dumpTree(self,mode='type'):
2158	'''Print out information on the data tree dicts loaded in loadTree
2159	'''
2160	print '\nOverall'
2161	if mode == 'type':
2162	def Show(arg): return type(arg)
2163	else:
2164	def Show(arg): return arg
2165	for key in self.OverallParms:
2166	print ' ',key,Show(self.OverallParms[key])
2167	print 'Phases'
2168	for key1 in self.Phases:
2169	print ' ',key1,Show(self.Phases[key1])
2170	print 'Histogram'
2171	for key1 in self.Histograms:
2172	print ' ',key1,Show(self.Histograms[key1])
2173	for key2 in self.Histograms[key1]:
2174	print ' ',key2,Show(self.Histograms[key1][key2])
2175
2176	def defaultSaveFile(self):
2177	return os.path.abspath(
2178	os.path.splitext(self.G2frame.GSASprojectfile
2179	)[0]+self.extension)
2180
2181	def askSaveFile(self):
2182	'''Ask the user to supply a file name
2183
2184	:returns: a file name (str) or None if Cancel is pressed
2185	'''
2186	defnam = os.path.splitext(
2187	os.path.split(self.G2frame.GSASprojectfile)[1]
2188	)[0]+self.extension
2189	dlg = wx.FileDialog(
2190	self.G2frame, 'Input name for file to write', '.', defnam,
2191	self.longFormatName+' ('+self.extension+')\|'+self.extension,
2192	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT\|wx.CHANGE_DIR)
2193	dlg.CenterOnParent()
2194	try:
2195	if dlg.ShowModal() == wx.ID_OK:
2196	filename = dlg.GetPath()
2197	# make sure extension is correct
2198	filename = os.path.splitext(filename)[0]+self.extension
2199	else:
2200	filename = None
2201	finally:
2202	dlg.Destroy()
2203	return filename
2204
2205	def askSaveDirectory(self):
2206	'''Ask the user to supply a directory name. Path name is used as the
2207	starting point for the next export path search.
2208
2209	:returns: a directory name (str) or None if Cancel is pressed
2210	'''
2211	if self.G2frame.exportDir:
2212	startdir = self.G2frame.exportDir
2213	elif self.G2frame.GSASprojectfile:
2214	startdir = os.path.split(self.G2frame.GSASprojectfile)[0]
2215	elif self.G2frame.dirname:
2216	startdir = self.G2frame.dirname
2217	else:
2218	startdir = ''
2219	dlg = wx.DirDialog(
2220	self.G2frame, 'Input directory where file(s) will be written', startdir,
2221	wx.DD_DEFAULT_STYLE)
2222	dlg.CenterOnParent()
2223	try:
2224	if dlg.ShowModal() == wx.ID_OK:
2225	filename = dlg.GetPath()
2226	self.G2frame.exportDir = filename
2227	else:
2228	filename = None
2229	finally:
2230	dlg.Destroy()
2231	return filename
2232
2233	# Tools for file writing.
2234	def OpenFile(self,fil=None,mode='w'):
2235	'''Open the output file
2236
2237	:param str fil: The name of the file to open. If None (default)
2238	the name defaults to self.dirname + self.filename.
2239	If an extension is supplied, it is not overridded,
2240	but if not, the default extension is used.
2241	:returns: the file object opened by the routine which is also
2242	saved as self.fp
2243	'''
2244	if not fil:
2245	if not os.path.splitext(self.filename)[1]:
2246	self.filename += self.extension
2247	fil = os.path.join(self.dirname,self.filename)
2248	self.fullpath = os.path.abspath(fil)
2249	self.fp = open(self.fullpath,mode)
2250	return self.fp
2251
2252	def Write(self,line):
2253	'''write a line of output, attaching a line-end character
2254
2255	:param str line: the text to be written.
2256	'''
2257	self.fp.write(line+'\n')
2258	def CloseFile(self,fp=None):
2259	'''Close a file opened in OpenFile
2260
2261	:param file fp: the file object to be closed. If None (default)
2262	file object self.fp is closed.
2263	'''
2264	if fp is None:
2265	fp = self.fp
2266	self.fp = None
2267	fp.close()
2268	# Tools to pull information out of the data arrays
2269	def GetCell(self,phasenam):
2270	"""Gets the unit cell parameters and their s.u.'s for a selected phase
2271
2272	:param str phasenam: the name for the selected phase
2273	:returns: `cellList,cellSig` where each is a 7 element list corresponding
2274	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
2275	cell values and `cellSig` has their uncertainties.
2276	"""
2277	phasedict = self.Phases[phasenam] # pointer to current phase info
2278	try:
2279	pfx = str(phasedict['pId'])+'::'
2280	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
2281	cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A,
2282	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
2283	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
2284	return cellList,cellSig
2285	except KeyError:
2286	cell = phasedict['General']['Cell'][1:]
2287	return cell,7*[0]
2288
2289	def GetAtoms(self,phasenam):
2290	"""Gets the atoms associated with a phase. Can be used with standard
2291	or macromolecular phases
2292
2293	:param str phasenam: the name for the selected phase
2294	:returns: a list of items for eac atom where each item is a list containing:
2295	label, typ, mult, xyz, and td, where
2296
2297	* label and typ are the atom label and the scattering factor type (str)
2298	* mult is the site multiplicity (int)
2299	* xyz is contains a list with four pairs of numbers:
2300	x, y, z and fractional occupancy and
2301	their standard uncertainty (or a negative value)
2302	* td is contains a list with either one or six pairs of numbers:
2303	if one number it is U\ :sub:`iso` and with six numbers it is
2304	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
2305	paired with their standard uncertainty (or a negative value)
2306	"""
2307	phasedict = self.Phases[phasenam] # pointer to current phase info
2308	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
2309	cfrac = cx+3
2310	fpfx = str(phasedict['pId'])+'::Afrac:'
2311	atomslist = []
2312	for i,at in enumerate(phasedict['Atoms']):
2313	if phasedict['General']['Type'] == 'macromolecular':
2314	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
2315	else:
2316	label = at[ct-1]
2317	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
2318	fsig = self.sigDict.get(fpfx+str(i),-0.009)
2319	mult = at[cs+1]
2320	typ = at[ct]
2321	xyz = []
2322	for j,v in enumerate(('x','y','z')):
2323	val = at[cx+j]
2324	pfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
2325	sig = self.sigDict.get(pfx,-0.000009)
2326	xyz.append((val,sig))
2327	xyz.append((fval,fsig))
2328	td = []
2329	if at[cia] == 'I':
2330	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
2331	val = self.parmDict.get(pfx,at[cia+1])
2332	sig = self.sigDict.get(pfx,-0.0009)
2333	td.append((val,sig))
2334	else:
2335	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
2336	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
2337	val = self.parmDict.get(pfx,at[cia+2+i])
2338	sig = self.sigDict.get(pfx,-0.0009)
2339	td.append((val,sig))
2340	atomslist.append((label,typ,mult,xyz,td))
2341	return atomslist
2342	######################################################################
2343	def ExportPowderList(G2frame):
2344	'''Returns a list of extensions supported by :func:`GSASIIIO:ExportPowder`
2345
2346	:param wx.Frame G2frame: the GSAS-II main data tree window
2347	'''
2348	extList = []
2349	for obj in G2frame.exporterlist:
2350	if 'powder' in obj.exporttype:
2351	try:
2352	obj.Writer
2353	extList.append(obj.extension)
2354	except AttributeError:
2355	pass
2356	return extList
2357
2358	def ExportPowder(G2frame,TreeName,fileroot,extension):
2359	'''Writes a single powder histogram using the Export routines
2360
2361	:param wx.Frame G2frame: the GSAS-II main data tree window
2362	:param str TreeName: the name of the histogram (PWDR ...) in the data tree
2363	:param str fileroot: name for file to be written, extension ignored
2364	:param str extension: extension for file to be written (start with '.'). Must
2365	match a powder export routine that has a Writer object.
2366	'''
2367	filename = os.path.abspath(os.path.splitext(fileroot)[0]+extension)
2368	for obj in G2frame.exporterlist:
2369	if obj.extension == extension and 'powder' in obj.exporttype:
2370	obj.currentExportType = 'powder'
2371	obj.InitExport(None)
2372	obj.loadTree() # load all histograms in tree into dicts
2373	if TreeName not in obj.Histograms:
2374	raise Exception('Histogram not found: '+str(TreeName))
2375	try:
2376	obj.Writer
2377	except AttributeError:
2378	continue
2379	try:
2380	obj.Writer(TreeName,filename)
2381	return
2382	except Exception,err:
2383	print('Export Routine for '+extension+' failed.')
2384	print err
2385	else:
2386	print('No Export routine supports extension '+extension)
2387
2388	def ReadCIF(URLorFile):
2389	'''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
2390	(from James Hester).
2391	The open routine gets confused with DOS names that begin with a letter and colon
2392	"C:\dir\" so this routine will try to open the passed name as a file and if that
2393	fails, try it as a URL
2394
2395	:param str URLorFile: string containing a URL or a file name. Code will try first
2396	to open it as a file and then as a URL.
2397
2398	:returns: a PyCifRW CIF object.
2399	'''
2400	import CifFile as cif # PyCifRW from James Hester
2401
2402	# alternate approach:
2403	#import urllib
2404	#ciffile = 'file:'+urllib.pathname2url(filename)
2405
2406	try:
2407	fp = open(URLorFile,'r')
2408	cf = cif.ReadCif(fp)
2409	fp.close()
2410	return cf
2411	except IOError:
2412	return cif.ReadCif(URLorFile)
2413
2414	if __name__ == '__main__':
2415	import GSASII
2416	application = GSASII.GSASIImain(0)
2417	G2frame = application.main
2418	#app = wx.PySimpleApp()
2419	#G2frame = wx.Frame(None) # create a frame
2420	#frm.Show(True)
2421	#filename = '/tmp/notzip.zip'
2422	#filename = '/tmp/all.zip'
2423	#filename = '/tmp/11bmb_7652.zip'
2424
2425	#selection=None, confirmoverwrite=True, parent=None
2426	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2427	#print ExtractFileFromZip(filename,multipleselect=True)
2428	# #confirmread=False, confirmoverwrite=False)
2429
2430	# choicelist=[ ('a','b','c'),
2431	# ('test1','test2'),('no choice',)]
2432	# titles = [ 'a, b or c', 'tests', 'No option here']
2433	# dlg = MultipleChoicesDialog(
2434	# choicelist,titles,
2435	# parent=frm)
2436	# if dlg.ShowModal() == wx.ID_OK:
2437	# print 'Got OK'
2438	imagefile = '/tmp/NDC5_00237_3.ge3'
2439	Comments, Data, Npix, Image = GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None)
2440
2441	print("\n\nResults loaded to Comments, Data, Npix and Image\n\n")
2442
2443	GSASIIpath.IPyBreak_base()

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