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source: trunk/GSASIIIO.py @ 2703

Last change on this file since 2703 was 2703, checked in by vondreele, 7 years ago
fix problem with default Sample parms for lab data default selection
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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2017-02-14 15:52:37 +0000 (Tue, 14 Feb 2017) $
4	# $Author: vondreele $
5	# $Revision: 2703 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 2703 2017-02-14 15:52:37Z vondreele $
8	########### SVN repository information ###################
9	'''
10	GSASIIIO: Misc I/O routines
11	=============================
12
13	Module with miscellaneous routines for input and output. Many
14	are GUI routines to interact with user.
15
16	Includes support for image reading.
17
18	Also includes base classes for data import routines.
19
20	'''
21	"""GSASIIIO: functions for IO of data
22	Copyright: 2008, Robert B. Von Dreele (Argonne National Laboratory)
23	"""
24	import wx
25	import math
26	import numpy as np
27	import copy
28	import cPickle
29	import sys
30	import re
31	import random as ran
32	import GSASIIpath
33	GSASIIpath.SetVersionNumber("$Revision: 2703 $")
34	import GSASIIgrid as G2gd
35	import GSASIIspc as G2spc
36	import GSASIIobj as G2obj
37	import GSASIIlattice as G2lat
38	import GSASIIpwdGUI as G2pdG
39	import GSASIIimgGUI as G2imG
40	import GSASIIimage as G2img
41	import GSASIIElem as G2el
42	import GSASIIstrIO as G2stIO
43	import GSASIImapvars as G2mv
44	import GSASIIctrls as G2G
45	import os
46	import os.path as ospath
47
48	DEBUG = False #=True for various prints
49	TRANSP = False #=true to transpose images for testing
50	if GSASIIpath.GetConfigValue('Transpose'): TRANSP = True
51	npsind = lambda x: np.sin(x*np.pi/180.)
52
53	def sfloat(S):
54	'Convert a string to float. An empty field or a unconvertable value is treated as zero'
55	if S.strip():
56	try:
57	return float(S)
58	except ValueError:
59	pass
60	return 0.0
61
62	def sint(S):
63	'Convert a string to int. An empty field is treated as zero'
64	if S.strip():
65	return int(S)
66	else:
67	return 0
68
69	def trim(val):
70	'''Simplify a string containing leading and trailing spaces
71	as well as newlines, tabs, repeated spaces etc. into a shorter and
72	more simple string, by replacing all ranges of whitespace
73	characters with a single space.
74
75	:param str val: the string to be simplified
76
77	:returns: the (usually) shortened version of the string
78	'''
79	return re.sub('\s+', ' ', val).strip()
80
81	def makeInstDict(names,data,codes):
82	inst = dict(zip(names,zip(data,data,codes)))
83	for item in inst:
84	inst[item] = list(inst[item])
85	return inst
86
87	def FileDlgFixExt(dlg,file):
88	'this is needed to fix a problem in linux wx.FileDialog'
89	ext = dlg.GetWildcard().split('\|')[2dlg.GetFilterIndex()+1].strip('')
90	if ext not in file:
91	file += ext
92	return file
93
94	def GetPowderPeaks(fileName):
95	'Read powder peaks from a file'
96	sind = lambda x: math.sin(x*math.pi/180.)
97	asind = lambda x: 180.*math.asin(x)/math.pi
98	wave = 1.54052
99	File = open(fileName,'Ur')
100	Comments = []
101	peaks = []
102	S = File.readline()
103	while S:
104	if S[:1] == '#':
105	Comments.append(S[:-1])
106	else:
107	item = S.split()
108	if len(item) == 1:
109	peaks.append([float(item[0]),1.0])
110	elif len(item) > 1:
111	peaks.append([float(item[0]),float(item[0])])
112	S = File.readline()
113	File.close()
114	if Comments:
115	print 'Comments on file:'
116	for Comment in Comments:
117	print Comment
118	if 'wavelength' in Comment:
119	wave = float(Comment.split('=')[1])
120	Peaks = []
121	if peaks[0][0] > peaks[-1][0]: # d-spacings - assume CuKa
122	for peak in peaks:
123	dsp = peak[0]
124	sth = wave/(2.0*dsp)
125	if sth < 1.0:
126	tth = 2.0*asind(sth)
127	else:
128	break
129	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
130	else: #2-thetas - assume Cuka (for now)
131	for peak in peaks:
132	tth = peak[0]
133	dsp = wave/(2.0*sind(tth/2.0))
134	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
135	limits = [1000.,0.]
136	for peak in Peaks:
137	limits[0] = min(limits[0],peak[0])
138	limits[1] = max(limits[1],peak[0])
139	limits[0] = max(1.,(int(limits[0]-1.)/5)*5.)
140	limits[1] = min(170.,(int(limits[1]+1.)/5)*5.)
141	return Comments,Peaks,limits,wave
142
143	def GetCheckImageFile(G2frame,treeId):
144	'''Try to locate an image file if the project and image have been moved
145	together. If the image file cannot be found, request the location from
146	the user.
147
148	:param wx.Frame G2frame: main GSAS-II Frame and data object
149	:param wx.Id treeId: Id for the main tree item for the image
150	:returns: Npix,imagefile,imagetag with (Npix) number of pixels,
151	imagefile, if it exists, or the name of a file that does exist or False if the user presses Cancel
152	and (imagetag) an optional image number
153
154	'''
155	Npix,imagefile,imagetag = G2frame.PatternTree.GetImageLoc(treeId)
156	if not os.path.exists(imagefile):
157	print 'Image file '+imagefile+' not found'
158	fil = imagefile.replace('\\','/') # windows?!
159	# see if we can find a file with same name or in a similarly named sub-dir
160	pth,fil = os.path.split(fil)
161	prevpth = None
162	while pth and pth != prevpth:
163	prevpth = pth
164	if os.path.exists(os.path.join(G2frame.dirname,fil)):
165	print 'found image file '+os.path.join(G2frame.dirname,fil)
166	imagefile = os.path.join(G2frame.dirname,fil)
167	G2frame.PatternTree.UpdateImageLoc(treeId,imagefile)
168	return Npix,imagefile,imagetag
169	pth,enddir = os.path.split(pth)
170	fil = os.path.join(enddir,fil)
171	# not found as a subdirectory, drop common parts of path for last saved & image file names
172	# if image was .../A/B/C/imgs/ima.ge
173	# & GPX was .../A/B/C/refs/fil.gpx but is now .../NEW/TEST/TEST1
174	# will look for .../NEW/TEST/TEST1/imgs/ima.ge, .../NEW/TEST/imgs/ima.ge, .../NEW/imgs/ima.ge and so on
175	Controls = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
176	gpxPath = Controls.get('LastSavedAs','').replace('\\','/').split('/') # blank in older .GPX files
177	imgPath = imagefile.replace('\\','/').split('/')
178	for p1,p2 in zip(gpxPath,imgPath):
179	if p1 == p2:
180	gpxPath.pop(0),imgPath.pop(0)
181	else:
182	break
183	fil = os.path.join(*imgPath) # file with non-common prefix elements
184	prevpth = None
185	pth = os.path.abspath(G2frame.dirname)
186	while pth and pth != prevpth:
187	prevpth = pth
188	if os.path.exists(os.path.join(pth,fil)):
189	print 'found image file '+os.path.join(pth,fil)
190	imagefile = os.path.join(pth,fil)
191	G2frame.PatternTree.UpdateImageLoc(treeId,imagefile)
192	return Npix,imagefile,imagetag
193	pth,enddir = os.path.split(pth)
194	#GSASIIpath.IPyBreak()
195
196	if not os.path.exists(imagefile):
197	prevnam = os.path.split(imagefile)[1]
198	prevext = os.path.splitext(imagefile)[1]
199	wildcard = 'Image format ('+prevext+')\|'+prevext
200	dlg = wx.FileDialog(G2frame, 'Previous image file ('+prevnam+') not found; open here', '.', prevnam,
201	wildcard,wx.OPEN)
202	try:
203	dlg.SetFilename(''+ospath.split(imagefile)[1])
204	if dlg.ShowModal() == wx.ID_OK:
205	imagefile = dlg.GetPath()
206	G2frame.PatternTree.UpdateImageLoc(treeId,imagefile)
207	else:
208	imagefile = False
209	finally:
210	dlg.Destroy()
211	return Npix,imagefile,imagetag
212
213	def EditImageParms(parent,Data,Comments,Image,filename):
214	dlg = wx.Dialog(parent, wx.ID_ANY, 'Edit image parameters',
215	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
216	def onClose(event):
217	dlg.EndModal(wx.ID_OK)
218	mainsizer = wx.BoxSizer(wx.VERTICAL)
219	h,w = Image.shape[:2]
220	mainsizer.Add(wx.StaticText(dlg,wx.ID_ANY,
221	'File '+str(filename)+'\nImage size: '+str(h)+' x '+str(w)),
222	0,wx.ALIGN_LEFT\|wx.ALL, 2)
223
224	vsizer = wx.BoxSizer(wx.HORIZONTAL)
225	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Wavelength (\xC5) '),
226	0,wx.ALIGN_LEFT\|wx.ALL, 2)
227	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'wavelength')
228	vsizer.Add(wdgt)
229	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
230
231	vsizer = wx.BoxSizer(wx.HORIZONTAL)
232	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Pixel size (\xb5m). Width '),
233	0,wx.ALIGN_LEFT\|wx.ALL, 2)
234	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],0,
235	size=(50,-1))
236	vsizer.Add(wdgt)
237	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Height '),
238	wx.ALIGN_LEFT\|wx.ALL, 2)
239	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],1,
240	size=(50,-1))
241	vsizer.Add(wdgt)
242	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
243
244	vsizer = wx.BoxSizer(wx.HORIZONTAL)
245	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Sample to detector (mm) '),
246	0,wx.ALIGN_LEFT\|wx.ALL, 2)
247	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'distance')
248	vsizer.Add(wdgt)
249	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
250
251	vsizer = wx.BoxSizer(wx.HORIZONTAL)
252	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Beam center (pixels). X = '),
253	0,wx.ALIGN_LEFT\|wx.ALL, 2)
254	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],0,
255	size=(75,-1))
256	vsizer.Add(wdgt)
257	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Y = '),
258	wx.ALIGN_LEFT\|wx.ALL, 2)
259	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],1,
260	size=(75,-1))
261	vsizer.Add(wdgt)
262	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
263
264	vsizer = wx.BoxSizer(wx.HORIZONTAL)
265	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Comments '),
266	0,wx.ALIGN_LEFT\|wx.ALL, 2)
267	wdgt = G2G.ValidatedTxtCtrl(dlg,Comments,0,size=(250,-1))
268	vsizer.Add(wdgt)
269	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
270
271	btnsizer = wx.StdDialogButtonSizer()
272	OKbtn = wx.Button(dlg, wx.ID_OK, 'Continue')
273	OKbtn.SetDefault()
274	OKbtn.Bind(wx.EVT_BUTTON,onClose)
275	btnsizer.AddButton(OKbtn) # not sure why this is needed
276	btnsizer.Realize()
277	mainsizer.Add(btnsizer, 1, wx.ALIGN_CENTER\|wx.ALL\|wx.EXPAND, 5)
278	dlg.SetSizer(mainsizer)
279	dlg.CenterOnParent()
280	dlg.ShowModal()
281
282	def LoadImage2Tree(imagefile,G2frame,Comments,Data,Npix,Image):
283	'''Load an image into the tree. Saves the location of the image, as well as the
284	ImageTag (where there is more than one image in the file), if defined.
285	'''
286	ImgNames = G2gd.GetPatternTreeDataNames(G2frame,['IMG ',])
287	TreeLbl = 'IMG '+os.path.basename(imagefile)
288	ImageTag = Data.get('ImageTag')
289	if ImageTag:
290	TreeLbl += ' #'+'%04d'%(ImageTag)
291	imageInfo = (imagefile,ImageTag)
292	else:
293	imageInfo = imagefile
294	TreeName = G2obj.MakeUniqueLabel(TreeLbl,ImgNames)
295	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=TreeName)
296	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
297	Imax = np.amax(Image)
298	if G2frame.imageDefault:
299	Data = copy.copy(G2frame.imageDefault)
300	Data['showLines'] = True
301	Data['ring'] = []
302	Data['rings'] = []
303	Data['cutoff'] = 10
304	Data['pixLimit'] = 20
305	Data['edgemin'] = 100000000
306	Data['calibdmin'] = 0.5
307	Data['calibskip'] = 0
308	Data['ellipses'] = []
309	Data['calibrant'] = ''
310	Data['GonioAngles'] = [0.,0.,0.]
311	Data['DetDepthRef'] = False
312	else:
313	Data['type'] = 'PWDR'
314	Data['color'] = 'Paired'
315	Data['tilt'] = 0.0
316	Data['rotation'] = 0.0
317	Data['showLines'] = False
318	Data['ring'] = []
319	Data['rings'] = []
320	Data['cutoff'] = 10
321	Data['pixLimit'] = 20
322	Data['calibdmin'] = 0.5
323	Data['calibskip'] = 0
324	Data['edgemin'] = 100000000
325	Data['ellipses'] = []
326	Data['GonioAngles'] = [0.,0.,0.]
327	Data['DetDepth'] = 0.
328	Data['DetDepthRef'] = False
329	Data['calibrant'] = ''
330	Data['IOtth'] = [2.0,5.0]
331	Data['LRazimuth'] = [0.,180.]
332	Data['azmthOff'] = 0.0
333	Data['outChannels'] = 2500
334	Data['outAzimuths'] = 1
335	Data['centerAzm'] = False
336	Data['fullIntegrate'] = False
337	Data['setRings'] = False
338	Data['background image'] = ['',-1.0]
339	Data['dark image'] = ['',-1.0]
340	Data['Flat Bkg'] = 0.0
341	Data['setDefault'] = False
342	Data['range'] = [(0,Imax),[0,Imax]]
343	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Image Controls'),Data)
344	Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],'Thresholds':[(0,Imax),[0,Imax]]}
345	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Masks'),Masks)
346	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Stress/Strain'),
347	{'Type':'True','d-zero':[],'Sample phi':0.0,'Sample z':0.0,'Sample load':0.0})
348	G2frame.PatternTree.SetItemPyData(Id,[Npix,imageInfo])
349	G2frame.PickId = Id
350	G2frame.PickIdText = G2frame.GetTreeItemsList(G2frame.PickId)
351	G2frame.Image = Id
352
353	def GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None,FormatName=''):
354	'''Read a single image with an image importer.
355
356	:param wx.Frame G2frame: main GSAS-II Frame and data object.
357	:param str imagefile: name of image file
358	:param bool imageOnly: If True return only the image,
359	otherwise (default) return more (see below)
360	:param int/str ImageTag: specifies a particular image to be read from a file.
361	First image is read if None (default).
362	:param str formatName: the image reader formatName
363
364	:returns: an image as a numpy array or a list of four items:
365	Comments, Data, Npix and the Image, as selected by imageOnly
366
367	'''
368	# determine which formats are compatible with this file
369	primaryReaders = []
370	secondaryReaders = []
371	for rd in G2frame.ImportImageReaderlist:
372	flag = rd.ExtensionValidator(imagefile)
373	if flag is None:
374	secondaryReaders.append(rd)
375	elif flag:
376	if not FormatName:
377	primaryReaders.append(rd)
378	elif FormatName == rd.formatName:
379	primaryReaders.append(rd)
380	if len(secondaryReaders) + len(primaryReaders) == 0:
381	print('Error: No matching format for file '+imagefile)
382	raise Exception('No image read')
383	fp = None
384	errorReport = ''
385	if not imagefile:
386	return
387	fp = open(imagefile,'Ur')
388	for rd in primaryReaders+secondaryReaders:
389	rd.ReInitialize() # purge anything from a previous read
390	fp.seek(0) # rewind
391	rd.errors = "" # clear out any old errors
392	if not rd.ContentsValidator(fp): # rejected on cursory check
393	errorReport += "\n "+rd.formatName + ' validator error'
394	if rd.errors:
395	errorReport += ': '+rd.errors
396	continue
397	if imageOnly:
398	ParentFrame = None # prevent GUI access on reread
399	else:
400	ParentFrame = G2frame
401	if GSASIIpath.GetConfigValue('debug'):
402	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=ImageTag)
403	else:
404	flag = False
405	try:
406	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=ImageTag)
407	except rd.ImportException as detail:
408	rd.errors += "\n Read exception: "+str(detail)
409	except Exception as detail:
410	import traceback
411	rd.errors += "\n Unhandled read exception: "+str(detail)
412	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
413	if flag: # this read succeeded
414	if rd.Image is None:
415	raise Exception('No image read. Strange!')
416	if GSASIIpath.GetConfigValue('Transpose'):
417	print 'Transposing Image!'
418	rd.Image = rd.Image.T
419	#rd.readfilename = imagefile
420	if imageOnly:
421	return rd.Image
422	else:
423	return rd.Comments,rd.Data,rd.Npix,rd.Image
424	else:
425	print('Error reading file '+imagefile)
426	print('Error messages(s)\n'+errorReport)
427	raise Exception('No image read')
428
429	def ReadImages(G2frame,imagefile):
430	'''Read one or more images from a file and put them into the Tree
431	using image importers. Called only in :meth:`AutoIntFrame.OnTimerLoop`.
432
433	:param wx.Frame G2frame: main GSAS-II Frame and data object.
434	:param str imagefile: name of image file
435
436	:returns: a list of the id's of the IMG tree items created
437	'''
438	# determine which formats are compatible with this file
439	primaryReaders = []
440	secondaryReaders = []
441	for rd in G2frame.ImportImageReaderlist:
442	flag = rd.ExtensionValidator(imagefile)
443	if flag is None:
444	secondaryReaders.append(rd)
445	elif flag:
446	primaryReaders.append(rd)
447	if len(secondaryReaders) + len(primaryReaders) == 0:
448	print('Error: No matching format for file '+imagefile)
449	raise Exception('No image read')
450	errorReport = ''
451	fp = open(imagefile,'Ur')
452	rdbuffer = {} # create temporary storage for file reader
453	for rd in primaryReaders+secondaryReaders:
454	rd.ReInitialize() # purge anything from a previous read
455	fp.seek(0) # rewind
456	rd.errors = "" # clear out any old errors
457	if not rd.ContentsValidator(fp): # rejected on cursory check
458	errorReport += "\n "+rd.formatName + ' validator error'
459	if rd.errors:
460	errorReport += ': '+rd.errors
461	continue
462	ParentFrame = G2frame
463	block = 0
464	repeat = True
465	CreatedIMGitems = []
466	while repeat: # loop if the reader asks for another pass on the file
467	block += 1
468	repeat = False
469	if GSASIIpath.GetConfigValue('debug'):
470	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=block,Buffer=rdbuffer)
471	else:
472	flag = False
473	try:
474	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=block,Buffer=rdbuffer)
475	except rd.ImportException as detail:
476	rd.errors += "\n Read exception: "+str(detail)
477	except Exception as detail:
478	import traceback
479	rd.errors += "\n Unhandled read exception: "+str(detail)
480	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
481	if flag: # this read succeeded
482	if rd.Image is None:
483	raise Exception('No image read. Strange!')
484	if GSASIIpath.GetConfigValue('Transpose'):
485	print 'Transposing Image!'
486	rd.Image = rd.Image.T
487	rd.Data['ImageTag'] = rd.repeatcount
488	LoadImage2Tree(imagefile,G2frame,rd.Comments,rd.Data,rd.Npix,rd.Image)
489	repeat = rd.repeat
490	CreatedIMGitems.append(G2frame.Image)
491	if CreatedIMGitems: return CreatedIMGitems
492	else:
493	print('Error reading file '+imagefile)
494	print('Error messages(s)\n'+errorReport)
495	return []
496	#raise Exception('No image read')
497
498	def SaveMultipleImg(G2frame):
499	if not G2frame.PatternTree.GetCount():
500	print 'no images!'
501	return
502	choices = G2gd.GetPatternTreeDataNames(G2frame,['IMG ',])
503	if len(choices) == 1:
504	names = choices
505	else:
506	dlg = G2G.G2MultiChoiceDialog(G2frame,'Stress/Strain fitting','Select images to fit:',choices)
507	dlg.SetSelections([])
508	names = []
509	if dlg.ShowModal() == wx.ID_OK:
510	names = [choices[sel] for sel in dlg.GetSelections()]
511	dlg.Destroy()
512	if not names: return
513	for name in names:
514	Id = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, name)
515	Npix,imagefile,imagetag = G2frame.PatternTree.GetImageLoc(Id)
516	imroot = os.path.splitext(imagefile)[0]
517	if imagetag:
518	imroot += '_' + str(imagetag)
519	Data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Image Controls'))
520	print('Writing '+imroot+'.imctrl')
521	File = open(imroot+'.imctrl','w')
522	keys = ['type','wavelength','calibrant','distance','center',
523	'tilt','rotation','azmthOff','fullIntegrate','LRazimuth',
524	'IOtth','outChannels','outAzimuths','invert_x','invert_y','DetDepth',
525	'calibskip','pixLimit','cutoff','calibdmin','chisq','Flat Bkg',
526	'binType','SampleShape','PolaVal','SampleAbs','dark image','background image']
527	for key in keys:
528	if key not in Data: continue #uncalibrated!
529	File.write(key+':'+str(Data[key])+'\n')
530	File.close()
531	mask = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Masks'))
532	G2imG.CleanupMasks(mask)
533	print('Writing '+imroot+'.immask')
534	File = open(imroot+'.immask','w')
535	for key in ['Points','Rings','Arcs','Polygons','Frames','Thresholds']:
536	File.write(key+':'+str(mask[key])+'\n')
537	File.close()
538
539	def PutG2Image(filename,Comments,Data,Npix,image):
540	'Write an image as a python pickle - might be better as an .edf file?'
541	File = open(filename,'wb')
542	cPickle.dump([Comments,Data,Npix,image],File,1)
543	File.close()
544	return
545
546	# should get moved to importer when ready to test
547	def GetEdfData(filename,imageOnly=False):
548	'Read European detector data edf file'
549	if not imageOnly:
550	print 'Read European detector data edf file: ',filename
551	File = open(filename,'rb')
552	fileSize = os.stat(filename).st_size
553	head = File.read(3072)
554	lines = head.split('\n')
555	sizexy = [0,0]
556	pixSize = [154,154] #Pixium4700?
557	cent = [0,0]
558	wave = 1.54187 #default <CuKa>
559	dist = 1000.
560	head = ['European detector data',]
561	for line in lines:
562	line = line.replace(';',' ').strip()
563	fields = line.split()
564	if 'Dim_1' in line:
565	sizexy[0] = int(fields[2])
566	elif 'Dim_2' in line:
567	sizexy[1] = int(fields[2])
568	elif 'DataType' in line:
569	dType = fields[2]
570	elif 'wavelength' in line:
571	wave = float(fields[2])
572	elif 'Size' in line:
573	imSize = int(fields[2])
574	# elif 'DataType' in lines:
575	# dType = fields[2]
576	elif 'pixel_size_x' in line:
577	pixSize[0] = float(fields[2])
578	elif 'pixel_size_y' in line:
579	pixSize[1] = float(fields[2])
580	elif 'beam_center_x' in line:
581	cent[0] = float(fields[2])
582	elif 'beam_center_y' in line:
583	cent[1] = float(fields[2])
584	elif 'refined_distance' in line:
585	dist = float(fields[2])
586	if line:
587	head.append(line)
588	else: #blank line at end of header
589	break
590	File.seek(fileSize-imSize)
591	if dType == 'UnsignedShort':
592	image = np.array(np.frombuffer(File.read(imSize),dtype=np.int16),dtype=np.int32)
593	else:
594	image = np.array(np.frombuffer(File.read(imSize),dtype=np.int32),dtype=np.int32)
595	image = np.reshape(image,(sizexy[1],sizexy[0]))
596	data = {'pixelSize':pixSize,'wavelength':wave,'distance':dist,'center':cent,'size':sizexy}
597	Npix = sizexy[0]*sizexy[1]
598	File.close()
599	if imageOnly:
600	return image
601	else:
602	return head,data,Npix,image
603
604	# should get moved to importer when ready to test
605	def GetRigaku(filename,imageOnly=False):
606	'Read Rigaku R-Axis IV image file'
607	import array as ar
608	if not imageOnly:
609	print 'Read Rigaku R-Axis IV file: ',filename
610	File = open(filename,'rb')
611	fileSize = os.stat(filename).st_size
612	Npix = (fileSize-6000)/2
613	File.read(6000)
614	head = ['Rigaku R-Axis IV detector data',]
615	image = np.array(ar.array('H',File.read(fileSize-6000)),dtype=np.int32)
616	print fileSize,image.shape
617	print head
618	if Npix == 9000000:
619	sizexy = [3000,3000]
620	pixSize = [100.,100.]
621	elif Npix == 2250000:
622	sizexy = [1500,1500]
623	pixSize = [200.,200.]
624	else:
625	sizexy = [6000,6000]
626	pixSize = [50.,50.]
627	image = np.reshape(image,(sizexy[1],sizexy[0]))
628	data = {'pixelSize':pixSize,'wavelength':1.5428,'distance':250.0,'center':[150.,150.],'size':sizexy}
629	File.close()
630	if imageOnly:
631	return image
632	else:
633	return head,data,Npix,image
634
635	# should get moved to importer when ready to test
636	def GetImgData(filename,imageOnly=False):
637	'Read an ADSC image file'
638	import array as ar
639	if not imageOnly:
640	print 'Read ADSC img file: ',filename
641	File = open(filename,'rb')
642	head = File.read(511)
643	lines = head.split('\n')
644	head = []
645	center = [0,0]
646	for line in lines[1:-2]:
647	line = line.strip()[:-1]
648	if line:
649	if 'SIZE1' in line:
650	size = int(line.split('=')[1])
651	Npix = size*size
652	elif 'WAVELENGTH' in line:
653	wave = float(line.split('=')[1])
654	elif 'BIN' in line:
655	if line.split('=')[1] == '2x2':
656	pixel=(102,102)
657	else:
658	pixel = (51,51)
659	elif 'DISTANCE' in line:
660	distance = float(line.split('=')[1])
661	elif 'CENTER_X' in line:
662	center[0] = float(line.split('=')[1])
663	elif 'CENTER_Y' in line:
664	center[1] = float(line.split('=')[1])
665	head.append(line)
666	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center,'size':[size,size]}
667	image = []
668	pos = 512
669	File.seek(pos)
670	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
671	image = np.reshape(image,(size,size))
672	# image = np.zeros(shape=(size,size),dtype=np.int32)
673	# while row < size:
674	# File.seek(pos)
675	# line = ar.array('H',File.read(2*size))
676	# image[row] = np.asarray(line)
677	# row += 1
678	# pos += 2*size
679	File.close()
680	if imageOnly:
681	return image
682	else:
683	return lines[1:-2],data,Npix,image
684
685	# should get moved to importer when ready to test
686	def GetMAR345Data(filename,imageOnly=False):
687	'Read a MAR-345 image plate image'
688	try:
689	import pack_f as pf
690	except:
691	msg = wx.MessageDialog(None, message="Unable to load the GSAS MAR image decompression, pack_f",
692	caption="Import Error",
693	style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
694	msg.ShowModal()
695	return None,None,None,None
696
697	if not imageOnly:
698	print 'Read Mar345 file: ',filename
699	File = open(filename,'rb')
700	head = File.read(4095)
701	lines = head[128:].split('\n')
702	head = []
703	for line in lines:
704	line = line.strip()
705	if 'PIXEL' in line:
706	values = line.split()
707	pixel = (int(values[2]),int(values[4])) #in microns
708	elif 'WAVELENGTH' in line:
709	wave = float(line.split()[1])
710	elif 'DISTANCE' in line:
711	distance = float(line.split()[1]) #in mm
712	if not distance:
713	distance = 500.
714	elif 'CENTER' in line:
715	values = line.split()
716	center = [float(values[2])/10.,float(values[4])/10.] #make in mm from pixels
717	if line:
718	head.append(line)
719	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center}
720	for line in head:
721	if 'FORMAT' in line[0:6]:
722	items = line.split()
723	sizex = int(items[1])
724	Npix = int(items[3])
725	sizey = int(Npix/sizex)
726	pos = 4096
727	data['size'] = [sizex,sizey]
728	File.seek(pos)
729	line = File.read(8)
730	while 'CCP4' not in line: #get past overflow list for now
731	line = File.read(8)
732	pos += 8
733	pos += 37
734	File.seek(pos)
735	raw = File.read()
736	File.close()
737	image = np.zeros(shape=(sizex,sizey),dtype=np.int32)
738
739	image = np.flipud(pf.pack_f(len(raw),raw,sizex,sizey,image).T) #transpose to get it right way around & flip
740	if imageOnly:
741	return image
742	else:
743	return head,data,Npix,image
744
745	def ProjFileOpen(G2frame,showProvenance=True):
746	'Read a GSAS-II project file and load into the G2 data tree'
747	if not os.path.exists(G2frame.GSASprojectfile):
748	print ('\n*** Error attempt to open project file that does not exist:\n '+
749	str(G2frame.GSASprojectfile))
750	return
751	LastSavedUsing = None
752	file = open(G2frame.GSASprojectfile,'rb')
753	if showProvenance: print 'loading from file: ',G2frame.GSASprojectfile
754	G2frame.SetTitle("GSAS-II data tree: "+
755	os.path.split(G2frame.GSASprojectfile)[1])
756	wx.BeginBusyCursor()
757	try:
758	while True:
759	try:
760	data = cPickle.load(file)
761	except EOFError:
762	break
763	datum = data[0]
764
765	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=datum[0])
766	if datum[0].startswith('PWDR'):
767	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
768	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
769	G2frame.PatternTree.SetItemPyData(Id,datum[1][:3]) #temp. trim off junk (patch?)
770	elif datum[0].startswith('HKLF'):
771	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
772	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
773	G2frame.PatternTree.SetItemPyData(Id,datum[1])
774	else:
775	G2frame.PatternTree.SetItemPyData(Id,datum[1])
776	if datum[0] == 'Controls' and 'LastSavedUsing' in datum[1]:
777	LastSavedUsing = datum[1]['LastSavedUsing']
778	if datum[0] == 'Controls' and 'PythonVersions' in datum[1] and GSASIIpath.GetConfigValue('debug') and showProvenance:
779	print('Packages used to create .GPX file:')
780	if 'dict' in str(type(datum[1]['PythonVersions'])): #patch
781	for p in sorted(datum[1]['PythonVersions'],key=lambda s: s.lower()):
782	print(" {:<14s}: {:s}".format(p[0],p[1]))
783	else:
784	for p in datum[1]['PythonVersions']:
785	print(" {:<12s} {:s}".format(p[0]+':',p[1]))
786	oldPDF = False
787	for datus in data[1:]:
788	#patch - 1/23/17 PDF cleanup
789	if datus[0][:4] in ['I(Q)','S(Q)','F(Q)','G(R)']:
790	oldPDF = True
791	data[1][1][datus[0][:4]] = copy.deepcopy(datus[1][:2])
792	continue
793	#end PDF cleanup
794	sub = G2frame.PatternTree.AppendItem(Id,datus[0])
795	#patch
796	if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
797	if datum[0].startswith('PWDR'):
798	datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
799	else:
800	datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
801	for item in datus[1][0]: #zip makes tuples - now make lists!
802	datus[1][0][item] = list(datus[1][0][item])
803	#end patch
804	G2frame.PatternTree.SetItemPyData(sub,datus[1])
805	if 'PDF ' in datum[0][:4] and oldPDF:
806	sub = G2frame.PatternTree.AppendItem(Id,'PDF Peaks')
807	G2frame.PatternTree.SetItemPyData(sub,{'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]})
808	if datum[0].startswith('IMG'): #retrieve image default flag & data if set
809	Data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Image Controls'))
810	if Data['setDefault']:
811	G2frame.imageDefault = Data
812	file.close()
813	if LastSavedUsing:
814	print('GPX load successful. Last saved with GSAS-II revision '+LastSavedUsing)
815	else:
816	print('project load successful')
817	G2frame.NewPlot = True
818	except:
819	msg = wx.MessageDialog(G2frame,message="Error reading file "+
820	str(G2frame.GSASprojectfile)+". This is not a GSAS-II .gpx file",
821	caption="Load Error",style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
822	msg.ShowModal()
823	finally:
824	wx.EndBusyCursor()
825	G2frame.Status.SetStatusText('Mouse RB click item to refresh/raise; RB drag/drop to reorder')
826
827	def ProjFileSave(G2frame):
828	'Save a GSAS-II project file'
829	if not G2frame.PatternTree.IsEmpty():
830	file = open(G2frame.GSASprojectfile,'wb')
831	print 'save to file: ',G2frame.GSASprojectfile
832	# stick the file name into the tree and version info into tree so they are saved.
833	# (Controls should always be created at this point)
834	try:
835	Controls = G2frame.PatternTree.GetItemPyData(
836	G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
837	Controls['LastSavedAs'] = os.path.abspath(G2frame.GSASprojectfile)
838	Controls['LastSavedUsing'] = str(GSASIIpath.GetVersionNumber())
839	Controls['PythonVersions'] = G2frame.PackageVersions
840	except:
841	pass
842	wx.BeginBusyCursor()
843	try:
844	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
845	while item:
846	data = []
847	name = G2frame.PatternTree.GetItemText(item)
848	data.append([name,G2frame.PatternTree.GetItemPyData(item)])
849	item2, cookie2 = G2frame.PatternTree.GetFirstChild(item)
850	while item2:
851	name = G2frame.PatternTree.GetItemText(item2)
852	data.append([name,G2frame.PatternTree.GetItemPyData(item2)])
853	item2, cookie2 = G2frame.PatternTree.GetNextChild(item, cookie2)
854	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
855	cPickle.dump(data,file,1)
856	file.close()
857	pth = os.path.split(os.path.abspath(G2frame.GSASprojectfile))[0]
858	if GSASIIpath.GetConfigValue('Save_paths'): G2G.SaveGPXdirectory(pth)
859	G2frame.LastGPXdir = pth
860	finally:
861	wx.EndBusyCursor()
862	print('project save successful')
863
864	def SaveIntegration(G2frame,PickId,data,Overwrite=False):
865	'Save image integration results as powder pattern(s)'
866	azms = G2frame.Integrate[1]
867	X = G2frame.Integrate[2][:-1]
868	N = len(X)
869	Id = G2frame.PatternTree.GetItemParent(PickId)
870	name = G2frame.PatternTree.GetItemText(Id)
871	name = name.replace('IMG ',data['type']+' ')
872	Comments = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Comments'))
873	if 'PWDR' in name:
874	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','SH/L','Azimuth']
875	codes = [0 for i in range(11)]
876	elif 'SASD' in name:
877	names = ['Type','Lam','Zero','Azimuth']
878	codes = [0 for i in range(4)]
879	X = 4.np.pinpsind(X/2.)/data['wavelength'] #convert to q
880	Xminmax = [X[0],X[-1]]
881	Azms = []
882	dazm = 0.
883	if data['fullIntegrate'] and data['outAzimuths'] == 1:
884	Azms = [45.0,] #a poor man's average?
885	else:
886	for i,azm in enumerate(azms[:-1]):
887	if azm > 360. and azms[i+1] > 360.:
888	Azms.append(G2img.meanAzm(azm%360.,azms[i+1]%360.))
889	else:
890	Azms.append(G2img.meanAzm(azm,azms[i+1]))
891	dazm = np.min(np.abs(np.diff(azms)))/2.
892	G2frame.IntgOutList = []
893	for i,azm in enumerate(azms[:-1]):
894	Aname = name+" Azm= %.2f"%((azm+dazm)%360.)
895	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
896	# if Overwrite delete any duplicate
897	if Overwrite and G2gd.GetPatternTreeItemId(G2frame,G2frame.root,Aname):
898	print('Replacing '+Aname)
899	item = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,Aname)
900	G2frame.PatternTree.Delete(item)
901	else:
902	nOcc = 0
903	while item:
904	Name = G2frame.PatternTree.GetItemText(item)
905	if Aname in Name:
906	nOcc += 1
907	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
908	if nOcc:
909	Aname += '(%d)'%(nOcc)
910	Sample = G2pdG.SetDefaultSample() #set as Debye-Scherrer
911	Sample['Gonio. radius'] = data['distance']
912	Sample['Omega'] = data['GonioAngles'][0]
913	Sample['Chi'] = data['GonioAngles'][1]
914	Sample['Phi'] = data['GonioAngles'][2]
915	Sample['Azimuth'] = (azm+dazm)%360. #put here as bin center
916	polariz = 0.99 #set default polarization for synchrotron radiation!
917	for item in Comments:
918	if 'polariz' in item:
919	try:
920	polariz = float(item.split('=')[1])
921	except:
922	polariz = 0.99
923	if 'PWDR' in Aname:
924	parms = ['PXC',data['wavelength'],0.0,polariz,1.0,-0.10,0.4,0.30,1.0,0.0001,Azms[i]]
925	elif 'SASD' in Aname:
926	Sample['Trans'] = data['SampleAbs'][0]
927	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
928	Y = G2frame.Integrate[0][i]
929	Ymin = np.min(Y)
930	Ymax = np.max(Y)
931	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
932	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=Aname)
933	G2frame.IntgOutList.append(Id)
934	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
935	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Limits'),[tuple(Xminmax),Xminmax])
936	if 'PWDR' in Aname:
937	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Background'),[['chebyschev',1,3,1.0,0.0,0.0],
938	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
939	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
940	for item in inst[0]:
941	inst[0][item] = list(inst[0][item])
942	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Instrument Parameters'),inst)
943	if 'PWDR' in Aname:
944	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
945	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
946	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Index Peak List'),[[],[]])
947	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Unit Cells List'),[])
948	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Reflection Lists'),{})
949	elif 'SASD' in Aname:
950	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
951	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
952	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
953	valuesdict = {
954	'wtFactor':1.0,
955	'Dummy':False,
956	'ranId':ran.randint(0,sys.maxint),
957	'Offset':[0.0,0.0],'delOffset':0.02Ymax,'refOffset':-0.1Ymax,'refDelt':0.1*Ymax,
958	'qPlot':False,'dPlot':False,'sqrtPlot':False,'Yminmax':[Ymin,Ymax]
959	}
960	G2frame.PatternTree.SetItemPyData(
961	Id,[valuesdict,
962	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
963	return Id #last powder pattern generated
964
965	def XYsave(G2frame,XY,labelX='X',labelY='Y',names=None):
966	'Save XY table data'
967	pth = G2G.GetExportPath(G2frame)
968	dlg = wx.FileDialog(
969	G2frame, 'Enter csv filename for XY table', pth, '',
970	'XY table file (.csv)\|.csv',wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
971	try:
972	if dlg.ShowModal() == wx.ID_OK:
973	filename = dlg.GetPath()
974	filename = os.path.splitext(filename)[0]+'.csv'
975	File = open(filename,'w')
976	else:
977	filename = None
978	finally:
979	dlg.Destroy()
980	if not filename:
981	return
982	for i in range(len(XY)):
983	if names != None:
984	header = '%s,%s(%s)\n'%(labelX,labelY,names[i])
985	else:
986	header = '%s,%s(%d)\n'%(labelX,labelY,i)
987	File.write(header)
988	for x,y in XY[i].T:
989	File.write('%.3f,%.3f\n'%(x,y))
990	File.close()
991	print ' XY data saved to: ',filename
992
993	def PDFSave(G2frame,exports):
994	'Save a PDF G(r) and F(Q), S(Q) in column formats'
995	import scipy.interpolate as scintp
996	for export in exports:
997	PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
998	PDFControls = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame, PickId,'PDF Controls'))
999	sqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.sq')
1000	fqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.fq')
1001	grfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.gr')
1002	sqdata = PDFControls['S(Q)'][1]
1003	sqfxn = scintp.interp1d(sqdata[0],sqdata[1],kind='linear')
1004	fqdata = PDFControls['F(Q)'][1]
1005	fqfxn = scintp.interp1d(fqdata[0],fqdata[1],kind='linear')
1006	grdata = PDFControls['G(R)'][1]
1007	grfxn = scintp.interp1d(grdata[0],grdata[1],kind='linear')
1008	sqfile = open(sqfilename,'w')
1009	fqfile = open(sqfilename,'w')
1010	grfile = open(grfilename,'w')
1011	sqfile.write('#T S(Q) %s\n'%(export))
1012	fqfile.write('#T F(Q) %s\n'%(export))
1013	grfile.write('#T G(R) %s\n'%(export))
1014	sqfile.write('#L Q S(Q)\n')
1015	fqfile.write('#L Q F(Q)\n')
1016	grfile.write('#L R G(R)\n')
1017	qnew = np.arange(sqdata[0][0],sqdata[0][-1],0.005)
1018	rnew = np.arange(grdata[0][0],grdata[0][-1],0.010)
1019	sqnew = zip(qnew,sqfxn(qnew))
1020	for q,sq in sqnew:
1021	sqfile.write("%15.6g %15.6g\n" % (q,sq))
1022	sqfile.close()
1023	print ' S(Q) saved to: ',sqfilename
1024	fqnew = zip(qnew,fqfxn(qnew))
1025	for q,fq in fqnew:
1026	fqfile.write("%15.6g %15.6g\n" % (q,fq))
1027	fqfile.close()
1028	print ' F(Q) saved to: ',fqfilename
1029	grnew = zip(rnew,grfxn(rnew))
1030	for r,gr in grnew:
1031	grfile.write("%15.6g %15.6g\n" % (r,gr))
1032	grfile.close()
1033	print ' G)R) saved to: ',grfilename
1034
1035	def PeakListSave(G2frame,file,peaks):
1036	'Save powder peaks to a data file'
1037	print 'save peak list to file: ',G2frame.peaklistfile
1038	if not peaks:
1039	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1040	try:
1041	dlg.ShowModal()
1042	finally:
1043	dlg.Destroy()
1044	return
1045	for peak in peaks:
1046	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
1047	(peak[0],peak[2],peak[4],peak[6]))
1048	print 'peak list saved'
1049
1050	def IndexPeakListSave(G2frame,peaks):
1051	'Save powder peaks from the indexing list'
1052	file = open(G2frame.peaklistfile,'wa')
1053	print 'save index peak list to file: ',G2frame.peaklistfile
1054	wx.BeginBusyCursor()
1055	try:
1056	if not peaks:
1057	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1058	try:
1059	dlg.ShowModal()
1060	finally:
1061	dlg.Destroy()
1062	return
1063	for peak in peaks:
1064	file.write("%12.6f\n" % (peak[7]))
1065	file.close()
1066	finally:
1067	wx.EndBusyCursor()
1068	print 'index peak list saved'
1069
1070	def SetNewPhase(Name='New Phase',SGData=None,cell=None,Super=None):
1071	'''Create a new phase dict with default values for various parameters
1072
1073	:param str Name: Name for new Phase
1074
1075	:param dict SGData: space group data from :func:`GSASIIspc:SpcGroup`;
1076	defaults to data for P 1
1077
1078	:param list cell: unit cell parameter list; defaults to
1079	[1.0,1.0,1.0,90.,90,90.,1.]
1080
1081	'''
1082	if SGData is None: SGData = G2spc.SpcGroup('P 1')[1]
1083	if cell is None: cell=[1.0,1.0,1.0,90.,90,90.,1.]
1084	phaseData = {
1085	'ranId':ran.randint(0,sys.maxint),
1086	'General':{
1087	'Name':Name,
1088	'Type':'nuclear',
1089	'Modulated':False,
1090	'AtomPtrs':[3,1,7,9],
1091	'SGData':SGData,
1092	'Cell':[False,]+cell,
1093	'Pawley dmin':1.0,
1094	'Data plot type':'None',
1095	'SH Texture':{
1096	'Order':0,
1097	'Model':'cylindrical',
1098	'Sample omega':[False,0.0],
1099	'Sample chi':[False,0.0],
1100	'Sample phi':[False,0.0],
1101	'SH Coeff':[False,{}],
1102	'SHShow':False,
1103	'PFhkl':[0,0,1],
1104	'PFxyz':[0,0,1],
1105	'PlotType':'Pole figure',
1106	'Penalty':[['',],0.1,False,1.0]}},
1107	'Atoms':[],
1108	'Drawing':{},
1109	'Histograms':{},
1110	'Pawley ref':[],
1111	'RBModels':{},
1112	}
1113	if Super and Super.get('Use',False):
1114	phaseData['General'].update({'Modulated':True,'Super':True,'SuperSg':Super['ssSymb']})
1115	phaseData['General']['SSGData'] = G2spc.SSpcGroup(SGData,Super['ssSymb'])
1116	phaseData['General']['SuperVec'] = [Super['ModVec'],False,Super['maxH']]
1117
1118	return phaseData
1119
1120	class MultipleChoicesDialog(wx.Dialog):
1121	'''A dialog that offers a series of choices, each with a
1122	title and a wx.Choice widget. Intended to be used Modally.
1123	typical input:
1124
1125	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1126	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1127
1128	selections are placed in self.chosen when OK is pressed
1129
1130	Also see GSASIIctrls
1131	'''
1132	def __init__(self,choicelist,headinglist,
1133	head='Select options',
1134	title='Please select from options below',
1135	parent=None):
1136	self.chosen = []
1137	wx.Dialog.__init__(
1138	self,parent,wx.ID_ANY,head,
1139	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
1140	panel = wx.Panel(self)
1141	mainSizer = wx.BoxSizer(wx.VERTICAL)
1142	mainSizer.Add((10,10),1)
1143	topLabl = wx.StaticText(panel,wx.ID_ANY,title)
1144	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.CENTER,10)
1145	self.ChItems = []
1146	for choice,lbl in zip(choicelist,headinglist):
1147	mainSizer.Add((10,10),1)
1148	self.chosen.append(0)
1149	topLabl = wx.StaticText(panel,wx.ID_ANY,' '+lbl)
1150	mainSizer.Add(topLabl,0,wx.ALIGN_LEFT,10)
1151	self.ChItems.append(wx.Choice(self, wx.ID_ANY, (100, 50), choices = choice))
1152	mainSizer.Add(self.ChItems[-1],0,wx.ALIGN_CENTER,10)
1153
1154	OkBtn = wx.Button(panel,-1,"Ok")
1155	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
1156	cancelBtn = wx.Button(panel,-1,"Cancel")
1157	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
1158	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1159	btnSizer.Add((20,20),1)
1160	btnSizer.Add(OkBtn)
1161	btnSizer.Add((20,20),1)
1162	btnSizer.Add(cancelBtn)
1163	btnSizer.Add((20,20),1)
1164	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1165	panel.SetSizer(mainSizer)
1166	panel.Fit()
1167	self.Fit()
1168
1169	def OnOk(self,event):
1170	parent = self.GetParent()
1171	if parent is not None: parent.Raise()
1172	# save the results from the choice widgets
1173	self.chosen = []
1174	for w in self.ChItems:
1175	self.chosen.append(w.GetSelection())
1176	self.EndModal(wx.ID_OK)
1177
1178	def OnCancel(self,event):
1179	parent = self.GetParent()
1180	if parent is not None: parent.Raise()
1181	self.chosen = []
1182	self.EndModal(wx.ID_CANCEL)
1183
1184	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1185	confirmoverwrite=True, parent=None,
1186	multipleselect=False):
1187	'''If the filename is a zip file, extract a file from that
1188	archive.
1189
1190	:param list Selection: used to predefine the name of the file
1191	to be extracted. Filename case and zip directory name are
1192	ignored in selection; the first matching file is used.
1193
1194	:param bool confirmread: if True asks the user to confirm before expanding
1195	the only file in a zip
1196
1197	:param bool confirmoverwrite: if True asks the user to confirm
1198	before overwriting if the extracted file already exists
1199
1200	:param bool multipleselect: if True allows more than one zip
1201	file to be extracted, a list of file(s) is returned.
1202	If only one file is present, do not ask which one, otherwise
1203	offer a list of choices (unless selection is used).
1204
1205	:returns: the name of the file that has been created or a
1206	list of files (see multipleselect)
1207
1208	If the file is not a zipfile, return the name of the input file.
1209	If the zipfile is empty or no file has been selected, return None
1210	'''
1211	import zipfile # do this now, since we can save startup time by doing this only on need
1212	import shutil
1213	zloc = os.path.split(filename)[0]
1214	if not zipfile.is_zipfile(filename):
1215	#print("not zip")
1216	return filename
1217
1218	z = zipfile.ZipFile(filename,'r')
1219	zinfo = z.infolist()
1220
1221	if len(zinfo) == 0:
1222	#print('Zip has no files!')
1223	zlist = [-1]
1224	if selection:
1225	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1226	if selection.lower() in choices:
1227	zlist = [choices.index(selection.lower())]
1228	else:
1229	print('debug: file '+str(selection)+' was not found in '+str(filename))
1230	zlist = [-1]
1231	elif len(zinfo) == 1 and confirmread:
1232	result = wx.ID_NO
1233	dlg = wx.MessageDialog(
1234	parent,
1235	'Is file '+str(zinfo[0].filename)+
1236	' what you want to extract from '+
1237	str(os.path.split(filename)[1])+'?',
1238	'Confirm file',
1239	wx.YES_NO \| wx.ICON_QUESTION)
1240	try:
1241	result = dlg.ShowModal()
1242	finally:
1243	dlg.Destroy()
1244	if result == wx.ID_NO:
1245	zlist = [-1]
1246	else:
1247	zlist = [0]
1248	elif len(zinfo) == 1:
1249	zlist = [0]
1250	elif multipleselect:
1251	# select one or more from a from list
1252	choices = [i.filename for i in zinfo]
1253	dlg = G2G.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1254	'Choose file(s)',choices)
1255	if dlg.ShowModal() == wx.ID_OK:
1256	zlist = dlg.GetSelections()
1257	else:
1258	zlist = []
1259	dlg.Destroy()
1260	else:
1261	# select one from a from list
1262	choices = [i.filename for i in zinfo]
1263	dlg = wx.SingleChoiceDialog(parent,
1264	'Select file to extract from zip file'+str(filename),'Choose file',
1265	choices,)
1266	if dlg.ShowModal() == wx.ID_OK:
1267	zlist = [dlg.GetSelection()]
1268	else:
1269	zlist = [-1]
1270	dlg.Destroy()
1271
1272	outlist = []
1273	for zindex in zlist:
1274	if zindex >= 0:
1275	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1276	if os.path.exists(efil) and confirmoverwrite:
1277	result = wx.ID_NO
1278	dlg = wx.MessageDialog(parent,
1279	'File '+str(efil)+' already exists. OK to overwrite it?',
1280	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1281	try:
1282	result = dlg.ShowModal()
1283	finally:
1284	dlg.Destroy()
1285	if result == wx.ID_NO:
1286	zindex = -1
1287	if zindex >= 0:
1288	# extract the file to the current directory, regardless of it's original path
1289	#z.extract(zinfo[zindex],zloc)
1290	eloc,efil = os.path.split(zinfo[zindex].filename)
1291	outfile = os.path.join(zloc, efil)
1292	fpin = z.open(zinfo[zindex])
1293	fpout = file(outfile, "wb")
1294	shutil.copyfileobj(fpin, fpout)
1295	fpin.close()
1296	fpout.close()
1297	outlist.append(outfile)
1298	z.close()
1299	if multipleselect and len(outlist) >= 1:
1300	return outlist
1301	elif len(outlist) == 1:
1302	return outlist[0]
1303	else:
1304	return None
1305
1306	######################################################################
1307	# base classes for reading various types of data files
1308	# not used directly, only by subclassing
1309	######################################################################
1310	try:
1311	E,SGData = G2spc.SpcGroup('P 1') # data structure for default space group
1312	except: # errors on doc build
1313	SGData = None
1314	P1SGData = SGData
1315	######################################################################
1316	class ImportBaseclass(object):
1317	'''Defines a base class for the reading of input files (diffraction
1318	data, coordinates,...). See :ref:`Writing a Import Routine<Import_routines>`
1319	for an explanation on how to use a subclass of this class.
1320	'''
1321	class ImportException(Exception):
1322	'''Defines an Exception that is used when an import routine hits an expected error,
1323	usually in .Reader.
1324
1325	Good practice is that the Reader should define a value in self.errors that
1326	tells the user some information about what is wrong with their file.
1327	'''
1328	pass
1329
1330	UseReader = True # in __init__ set value of self.UseReader to False to skip use of current importer
1331	def __init__(self,formatName,longFormatName=None,
1332	extensionlist=[],strictExtension=False,):
1333	self.formatName = formatName # short string naming file type
1334	if longFormatName: # longer string naming file type
1335	self.longFormatName = longFormatName
1336	else:
1337	self.longFormatName = formatName
1338	# define extensions that are allowed for the file type
1339	# for windows, remove any extensions that are duplicate, as case is ignored
1340	if sys.platform == 'windows' and extensionlist:
1341	extensionlist = list(set([s.lower() for s in extensionlist]))
1342	self.extensionlist = extensionlist
1343	# If strictExtension is True, the file will not be read, unless
1344	# the extension matches one in the extensionlist
1345	self.strictExtension = strictExtension
1346	self.errors = ''
1347	self.warnings = ''
1348	# used for readers that will use multiple passes to read
1349	# more than one data block
1350	self.repeat = False
1351	self.selections = []
1352	self.repeatcount = 0
1353	self.readfilename = '?'
1354	#print 'created',self.__class__
1355
1356	def ReInitialize(self):
1357	'Reinitialize the Reader to initial settings'
1358	self.errors = ''
1359	self.warnings = ''
1360	self.repeat = False
1361	self.repeatcount = 0
1362	self.readfilename = '?'
1363
1364	def BlockSelector(self, ChoiceList, ParentFrame=None,title='Select a block',
1365	size=None, header='Block Selector',useCancel=True):
1366	''' Provide a wx dialog to select a block if the file contains more
1367	than one set of data and one must be selected
1368	'''
1369	if useCancel:
1370	dlg = wx.SingleChoiceDialog(
1371	ParentFrame,title, header,ChoiceList)
1372	else:
1373	dlg = wx.SingleChoiceDialog(
1374	ParentFrame,title, header,ChoiceList,
1375	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.OK\|wx.CENTRE)
1376	if size: dlg.SetSize(size)
1377	dlg.CenterOnParent()
1378	if dlg.ShowModal() == wx.ID_OK:
1379	sel = dlg.GetSelection()
1380	return sel
1381	else:
1382	return None
1383	dlg.Destroy()
1384
1385	def MultipleBlockSelector(self, ChoiceList, ParentFrame=None,
1386	title='Select a block',size=None, header='Block Selector'):
1387	'''Provide a wx dialog to select a block of data if the
1388	file contains more than one set of data and one must be
1389	selected.
1390
1391	:returns: a list of the selected blocks
1392	'''
1393	dlg = wx.MultiChoiceDialog(ParentFrame,title, header,ChoiceList+['Select all'],
1394	wx.CHOICEDLG_STYLE)
1395	dlg.CenterOnScreen()
1396	if size: dlg.SetSize(size)
1397	if dlg.ShowModal() == wx.ID_OK:
1398	sel = dlg.GetSelections()
1399	else:
1400	return []
1401	dlg.Destroy()
1402	selected = []
1403	if len(ChoiceList) in sel:
1404	return range(len(ChoiceList))
1405	else:
1406	return sel
1407	return selected
1408
1409	def MultipleChoicesDialog(self, choicelist, headinglist, ParentFrame=None, **kwargs):
1410	'''A modal dialog that offers a series of choices, each with a title and a wx.Choice
1411	widget. Typical input:
1412
1413	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1414
1415	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1416
1417	optional keyword parameters are: head (window title) and title
1418	returns a list of selected indicies for each choice (or None)
1419	'''
1420	result = None
1421	dlg = MultipleChoicesDialog(choicelist,headinglist,
1422	parent=ParentFrame, **kwargs)
1423	dlg.CenterOnParent()
1424	if dlg.ShowModal() == wx.ID_OK:
1425	result = dlg.chosen
1426	dlg.Destroy()
1427	return result
1428
1429	def ShowBusy(self):
1430	wx.BeginBusyCursor()
1431	# wx.Yield() # make it happen now!
1432
1433	def DoneBusy(self):
1434	wx.EndBusyCursor()
1435	wx.Yield() # make it happen now!
1436
1437	# def Reader(self, filename, filepointer, ParentFrame=None, **unused):
1438	# '''This method must be supplied in the child class to read the file.
1439	# if the read fails either return False or raise an Exception
1440	# preferably of type ImportException.
1441	# '''
1442	# #start reading
1443	# raise ImportException("Error occurred while...")
1444	# self.errors += "Hint for user on why the error occur
1445	# return False # if an error occurs
1446	# return True # if read OK
1447
1448	def ExtensionValidator(self, filename):
1449	'''This methods checks if the file has the correct extension
1450	Return False if this filename will not be supported by this reader
1451	Return True if the extension matches the list supplied by the reader
1452	Return None if the reader allows un-registered extensions
1453	'''
1454	if filename:
1455	ext = os.path.splitext(filename)[1]
1456	if sys.platform == 'windows': ext = ext.lower()
1457	if ext in self.extensionlist: return True
1458	if self.strictExtension: return False
1459	return None
1460
1461	def ContentsValidator(self, filepointer):
1462	'''This routine will attempt to determine if the file can be read
1463	with the current format.
1464	This will typically be overridden with a method that
1465	takes a quick scan of [some of]
1466	the file contents to do a "sanity" check if the file
1467	appears to match the selected format.
1468	Expected to be called via self.Validator()
1469	'''
1470	#filepointer.seek(0) # rewind the file pointer
1471	return True
1472
1473	def CIFValidator(self, filepointer):
1474	'''A :meth:`ContentsValidator` for use to validate CIF files.
1475	'''
1476	for i,l in enumerate(filepointer):
1477	if i >= 1000: return True
1478	'''Encountered only blank lines or comments in first 1000
1479	lines. This is unlikely, but assume it is CIF anyway, since we are
1480	even less likely to find a file with nothing but hashes and
1481	blank lines'''
1482	line = l.strip()
1483	if len(line) == 0: # ignore blank lines
1484	continue
1485	elif line.startswith('#'): # ignore comments
1486	continue
1487	elif line.startswith('data_'): # on the right track, accept this file
1488	return True
1489	else: # found something invalid
1490	self.errors = 'line '+str(i+1)+' contains unexpected data:\n'
1491	if all([ord(c) < 128 and ord(c) != 0 for c in str(l)]): # show only if ASCII
1492	self.errors += ' '+str(l)
1493	else:
1494	self.errors += ' (binary)'
1495	self.errors += '\n Note: a CIF should only have blank lines or comments before'
1496	self.errors += '\n a data_ statement begins a block.'
1497	return False
1498
1499	######################################################################
1500	class ImportPhase(ImportBaseclass):
1501	'''Defines a base class for the reading of files with coordinates
1502
1503	Objects constructed that subclass this (in import/G2phase_*.py etc.) will be used
1504	in :meth:`GSASII.GSASII.OnImportPhase`.
1505	See :ref:`Writing a Import Routine<Import_Routines>`
1506	for an explanation on how to use this class.
1507
1508	'''
1509	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1510	strictExtension=False,):
1511	# call parent __init__
1512	ImportBaseclass.__init__(self,formatName,longFormatName,
1513	extensionlist,strictExtension)
1514	self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
1515	self.Constraints = None
1516
1517	def PhaseSelector(self, ChoiceList, ParentFrame=None,
1518	title='Select a phase', size=None,header='Phase Selector'):
1519	''' Provide a wx dialog to select a phase if the file contains more
1520	than one phase
1521	'''
1522	return self.BlockSelector(ChoiceList,ParentFrame,title,
1523	size,header)
1524
1525	######################################################################
1526	class ImportStructFactor(ImportBaseclass):
1527	'''Defines a base class for the reading of files with tables
1528	of structure factors.
1529
1530	Structure factors are read with a call to :meth:`GSASII.GSASII.OnImportSfact`
1531	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`, which calls
1532	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1533	:meth:`Reader`.
1534
1535	See :ref:`Writing a Import Routine<Import_Routines>`
1536	for an explanation on how to use import classes in general. The specifics
1537	for reading a structure factor histogram require that
1538	the ``Reader()`` routine in the import
1539	class need to do only a few things: It
1540	should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
1541	and set :attr:`Parameters` with the instrument parameters
1542	(initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
1543	'''
1544	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1545	strictExtension=False,):
1546	ImportBaseclass.__init__(self,formatName,longFormatName,
1547	extensionlist,strictExtension)
1548
1549	# define contents of Structure Factor entry
1550	self.Parameters = []
1551	'self.Parameters is a list with two dicts for data parameter settings'
1552	self.InitParameters()
1553	self.RefDict = {'RefList':[],'FF':{},'Super':0}
1554	self.Banks = [] #for multi bank data (usually TOF)
1555	'''self.RefDict is a dict containing the reflection information, as read from the file.
1556	Item 'RefList' contains the reflection information. See the
1557	:ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
1558	for the contents of each row. Dict element 'FF'
1559	contains the form factor values for each element type; if this entry
1560	is left as initialized (an empty list) it will be initialized as needed later.
1561	'''
1562	def ReInitialize(self):
1563	'Reinitialize the Reader to initial settings'
1564	ImportBaseclass.ReInitialize(self)
1565	self.InitParameters()
1566	self.Banks = [] #for multi bank data (usually TOF)
1567	self.RefDict = {'RefList':[],'FF':{},'Super':0}
1568
1569	def InitParameters(self):
1570	'initialize the instrument parameters structure'
1571	Lambda = 0.70926
1572	HistType = 'SXC'
1573	self.Parameters = [{'Type':[HistType,HistType], # create the structure
1574	'Lam':[Lambda,Lambda]
1575	}, {}]
1576	'Parameters is a list with two dicts for data parameter settings'
1577
1578	def UpdateParameters(self,Type=None,Wave=None):
1579	'Revise the instrument parameters'
1580	if Type is not None:
1581	self.Parameters[0]['Type'] = [Type,Type]
1582	if Wave is not None:
1583	self.Parameters[0]['Lam'] = [Wave,Wave]
1584
1585	######################################################################
1586	class ImportPowderData(ImportBaseclass):
1587	'''Defines a base class for the reading of files with powder data.
1588
1589	Objects constructed that subclass this (in import/G2pwd_*.py etc.) will be used
1590	in :meth:`GSASII.GSASII.OnImportPowder`.
1591	See :ref:`Writing a Import Routine<Import_Routines>`
1592	for an explanation on how to use this class.
1593	'''
1594	def __init__(self,formatName,longFormatName=None,
1595	extensionlist=[],strictExtension=False,):
1596	ImportBaseclass.__init__(self,formatName,longFormatName,
1597	extensionlist,strictExtension)
1598	self.clockWd = None # used in TOF
1599	self.ReInitialize()
1600
1601	def ReInitialize(self):
1602	'Reinitialize the Reader to initial settings'
1603	ImportBaseclass.ReInitialize(self)
1604	self.powderentry = ['',None,None] # (filename,Pos,Bank)
1605	self.powderdata = [] # Powder dataset
1606	'''A powder data set is a list with items [x,y,w,yc,yb,yd]:
1607	np.array(x), # x-axis values
1608	np.array(y), # powder pattern intensities
1609	np.array(w), # 1/sig(intensity)^2 values (weights)
1610	np.array(yc), # calc. intensities (zero)
1611	np.array(yb), # calc. background (zero)
1612	np.array(yd), # obs-calc profiles
1613	'''
1614	self.comments = []
1615	self.idstring = ''
1616	self.Sample = G2pdG.SetDefaultSample() # default sample parameters
1617	self.Controls = {} # items to be placed in top-level Controls
1618	self.GSAS = None # used in TOF
1619	self.repeat_instparm = True # Should a parm file be
1620	# used for multiple histograms?
1621	self.instparm = None # name hint from file of instparm to use
1622	self.instfile = '' # full path name to instrument parameter file
1623	self.instbank = '' # inst parm bank number
1624	self.instmsg = '' # a label that gets printed to show
1625	# where instrument parameters are from
1626	self.numbanks = 1
1627	self.instdict = {} # place items here that will be transferred to the instrument parameters
1628	self.pwdparms = {} # place parameters that are transferred directly to the tree
1629	# here (typically from an existing GPX file)
1630	######################################################################
1631	class ImportSmallAngleData(ImportBaseclass):
1632	'''Defines a base class for the reading of files with small angle data.
1633	See :ref:`Writing a Import Routine<Import_Routines>`
1634	for an explanation on how to use this class.
1635	'''
1636	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1637	strictExtension=False,):
1638
1639	ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
1640	strictExtension)
1641	self.ReInitialize()
1642
1643	def ReInitialize(self):
1644	'Reinitialize the Reader to initial settings'
1645	ImportBaseclass.ReInitialize(self)
1646	self.smallangleentry = ['',None,None] # (filename,Pos,Bank)
1647	self.smallangledata = [] # SASD dataset
1648	'''A small angle data set is a list with items [x,y,w,yc,yd]:
1649	np.array(x), # x-axis values
1650	np.array(y), # powder pattern intensities
1651	np.array(w), # 1/sig(intensity)^2 values (weights)
1652	np.array(yc), # calc. intensities (zero)
1653	np.array(yd), # obs-calc profiles
1654	np.array(yb), # preset bkg
1655	'''
1656	self.comments = []
1657	self.idstring = ''
1658	self.Sample = G2pdG.SetDefaultSample()
1659	self.GSAS = None # used in TOF
1660	self.clockWd = None # used in TOF
1661	self.numbanks = 1
1662	self.instdict = {} # place items here that will be transferred to the instrument parameters
1663
1664	######################################################################
1665	class ImportImage(ImportBaseclass):
1666	'''Defines a base class for the reading of images
1667
1668	Images are read in only these places:
1669
1670	* Initial reading is typically done from a menu item
1671	with a call to :meth:`GSASII.GSASII.OnImportImage`
1672	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`. That calls
1673	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1674	:meth:`Reader`. This returns a list of reader objects for each read image.
1675
1676	* Images are read alternatively in :func:`GSASIIIO.ReadImages`, which puts image info
1677	directly into the data tree.
1678
1679	* Images are reloaded with :func:`GSASIIIO.GetImageData`.
1680
1681	.. _Image_import_routines:
1682
1683	When reading an image, the ``Reader()`` routine in the ImportImage class
1684	should set:
1685
1686	* :attr:`Comments`: a list of strings (str),
1687	* :attr:`Npix`: the number of pixels in the image (int),
1688	* :attr:`Image`: the actual image as a numpy array (np.array)
1689	* :attr:`Data`: a dict defining image parameters (dict). Within this dict the following
1690	data items are needed:
1691
1692	* 'pixelSize': size of each pixel in microns (such as ``[200,200]``.
1693	* 'wavelength': wavelength in Angstoms.
1694	* 'distance': distance of detector from sample in cm.
1695	* 'center': uncalibrated center of beam on detector (such as ``[204.8,204.8]``.
1696	* 'size': size of image (such as ``[2048,2048]``).
1697	* 'ImageTag': image number or other keyword used to retrieve image from
1698	a multi-image data file (defaults to ``1`` if not specified).
1699	* 'sumfile': holds sum image file name if a sum was produced from a multi image file
1700
1701	optional data items:
1702
1703	* :attr:`repeat`: set to True if there are additional images to
1704	read in the file, False otherwise
1705	* :attr:`repeatcount`: set to the number of the image.
1706
1707	Note that the above is initialized with :meth:`InitParameters`.
1708	(Also see :ref:`Writing a Import Routine<Import_Routines>`
1709	for an explanation on how to use import classes in general.)
1710	'''
1711	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1712	strictExtension=False,):
1713	ImportBaseclass.__init__(self,formatName,longFormatName,
1714	extensionlist,strictExtension)
1715	self.InitParameters()
1716
1717	def ReInitialize(self):
1718	'Reinitialize the Reader to initial settings -- not used at present'
1719	ImportBaseclass.ReInitialize(self)
1720	self.InitParameters()
1721
1722	def InitParameters(self):
1723	'initialize the instrument parameters structure'
1724	self.Comments = ['No comments']
1725	self.Data = {}
1726	self.Npix = 0
1727	self.Image = None
1728	self.repeat = False
1729	self.repeatcount = 1
1730	self.sumfile = ''
1731
1732	def LoadImage(self,ParentFrame,imagefile,imagetag=None):
1733	'''Optionally, call this after reading in an image to load it into the tree.
1734	This saves time by preventing a reread of the same information.
1735	'''
1736	if ParentFrame:
1737	ParentFrame.ImageZ = self.Image # store the image for plotting
1738	ParentFrame.oldImagefile = imagefile # save the name of the last image file read
1739	ParentFrame.oldImageTag = imagetag # save the tag of the last image file read
1740
1741	######################################################################
1742	def striphist(var,insChar=''):
1743	'strip a histogram number from a var name'
1744	sv = var.split(':')
1745	if len(sv) <= 1: return var
1746	if sv[1]:
1747	sv[1] = insChar
1748	return ':'.join(sv)
1749	class ExportBaseclass(object):
1750	'''Defines a base class for the exporting of GSAS-II results.
1751
1752	This class is subclassed in the various exports/G2export_*.py files. Those files
1753	are imported in :meth:`GSASII.GSASII._init_Exports` which defines the
1754	appropriate menu items for each one and the .Exporter method is called
1755	directly from the menu item.
1756
1757	Routines may also define a .Writer method, which is used to write a single
1758	file without invoking any GUI objects.
1759	'''
1760	def __init__(self,G2frame,formatName,extension,longFormatName=None,):
1761	self.G2frame = G2frame
1762	self.formatName = formatName # short string naming file type
1763	self.extension = extension
1764	if longFormatName: # longer string naming file type
1765	self.longFormatName = longFormatName
1766	else:
1767	self.longFormatName = formatName
1768	self.OverallParms = {}
1769	self.Phases = {}
1770	self.Histograms = {}
1771	self.powderDict = {}
1772	self.xtalDict = {}
1773	self.parmDict = {}
1774	self.sigDict = {}
1775	# updated in InitExport:
1776	self.currentExportType = None # type of export that has been requested
1777	# updated in ExportSelect (when used):
1778	self.phasenam = None # a list of selected phases
1779	self.histnam = None # a list of selected histograms
1780	self.filename = None # name of file to be written (single export) or template (multiple files)
1781	self.dirname = '' # name of directory where file(s) will be written
1782	self.fullpath = '' # name of file being written -- full path
1783
1784	# items that should be defined in a subclass of this class
1785	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1786	# The following types are defined: 'project', "phase", "powder", "single"
1787	self.multiple = False # set as True if the class can export multiple phases or histograms
1788	# self.multiple is ignored for "project" exports
1789
1790	def InitExport(self,event):
1791	'''Determines the type of menu that called the Exporter and
1792	misc initialization.
1793	'''
1794	self.filename = None # name of file to be written (single export)
1795	self.dirname = '' # name of file to be written (multiple export)
1796	if event:
1797	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1798
1799	def MakePWDRfilename(self,hist):
1800	'''Make a filename root (no extension) from a PWDR histogram name
1801
1802	:param str hist: the histogram name in data tree (starts with "PWDR ")
1803	'''
1804	file0 = ''
1805	file1 = hist[5:]
1806	# replace repeated blanks
1807	while file1 != file0:
1808	file0 = file1
1809	file1 = file0.replace(' ',' ').strip()
1810	file0 = file1.replace('Azm= ','A')
1811	# if angle has unneeded decimal places on aziumuth, remove them
1812	if file0[-3:] == '.00': file0 = file0[:-3]
1813	file0 = file0.replace('.','_')
1814	file0 = file0.replace(' ','_')
1815	return file0
1816
1817	def ExportSelect(self,AskFile='ask'):
1818	'''Selects histograms or phases when needed. Sets a default file name when
1819	requested into self.filename; always sets a default directory in self.dirname.
1820
1821	:param bool AskFile: Determines how this routine processes getting a
1822	location to store the current export(s).
1823
1824	* if AskFile is 'ask' (default option), get the name of the file to be written;
1825	self.filename and self.dirname are always set. In the case where
1826	multiple files must be generated, the export routine should do this
1827	based on self.filename as a template.
1828	* if AskFile is 'dir', get the name of the directory to be used;
1829	self.filename is not used, but self.dirname is always set. The export routine
1830	will always generate the file name.
1831	* if AskFile is 'single', get only the name of the directory to be used when
1832	multiple items will be written (as multiple files) are used
1833	or a complete file name is requested when a single file
1834	name is selected. self.dirname is always set and self.filename used
1835	only when a single file is selected.
1836	* if AskFile is 'default', creates a name of the file to be used from
1837	the name of the project (.gpx) file. If the project has not been saved,
1838	then the name of file is requested.
1839	self.filename and self.dirname are always set. In the case where
1840	multiple file names must be generated, the export routine should do this
1841	based on self.filename.
1842	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1843	file. If the project has not been saved, then a directory is requested.
1844	self.filename is not used.
1845
1846	:returns: True in case of an error
1847	'''
1848
1849	numselected = 1
1850	if self.currentExportType == 'phase':
1851	if len(self.Phases) == 0:
1852	self.G2frame.ErrorDialog(
1853	'Empty project',
1854	'Project does not contain any phases.')
1855	return True
1856	elif len(self.Phases) == 1:
1857	self.phasenam = self.Phases.keys()
1858	elif self.multiple:
1859	choices = sorted(self.Phases.keys())
1860	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1861	if phasenum is None: return True
1862	self.phasenam = [choices[i] for i in phasenum]
1863	if not self.phasenam: return True
1864	numselected = len(self.phasenam)
1865	else:
1866	choices = sorted(self.Phases.keys())
1867	phasenum = G2G.ItemSelector(choices,self.G2frame)
1868	if phasenum is None: return True
1869	self.phasenam = [choices[phasenum]]
1870	numselected = len(self.phasenam)
1871	elif self.currentExportType == 'single':
1872	if len(self.xtalDict) == 0:
1873	self.G2frame.ErrorDialog(
1874	'Empty project',
1875	'Project does not contain any single crystal data.')
1876	return True
1877	elif len(self.xtalDict) == 1:
1878	self.histnam = self.xtalDict.values()
1879	elif self.multiple:
1880	choices = sorted(self.xtalDict.values())
1881	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1882	if not hnum: return True
1883	self.histnam = [choices[i] for i in hnum]
1884	numselected = len(self.histnam)
1885	else:
1886	choices = sorted(self.xtalDict.values())
1887	hnum = G2G.ItemSelector(choices,self.G2frame)
1888	if hnum is None: return True
1889	self.histnam = [choices[hnum]]
1890	numselected = len(self.histnam)
1891	elif self.currentExportType == 'powder':
1892	if len(self.powderDict) == 0:
1893	self.G2frame.ErrorDialog(
1894	'Empty project',
1895	'Project does not contain any powder data.')
1896	return True
1897	elif len(self.powderDict) == 1:
1898	self.histnam = self.powderDict.values()
1899	elif self.multiple:
1900	choices = sorted(self.powderDict.values())
1901	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1902	if not hnum: return True
1903	self.histnam = [choices[i] for i in hnum]
1904	numselected = len(self.histnam)
1905	else:
1906	choices = sorted(self.powderDict.values())
1907	hnum = G2G.ItemSelector(choices,self.G2frame)
1908	if hnum is None: return True
1909	self.histnam = [choices[hnum]]
1910	numselected = len(self.histnam)
1911	elif self.currentExportType == 'image':
1912	if len(self.Histograms) == 0:
1913	self.G2frame.ErrorDialog(
1914	'Empty project',
1915	'Project does not contain any images.')
1916	return True
1917	elif len(self.Histograms) == 1:
1918	self.histnam = self.Histograms.keys()
1919	else:
1920	choices = sorted(self.Histograms.keys())
1921	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1922	if self.multiple:
1923	if not hnum: return True
1924	self.histnam = [choices[i] for i in hnum]
1925	else:
1926	if hnum is None: return True
1927	self.histnam = [choices[hnum]]
1928	numselected = len(self.histnam)
1929	if self.currentExportType == 'map':
1930	# search for phases with maps
1931	mapPhases = []
1932	choices = []
1933	for phasenam in sorted(self.Phases):
1934	phasedict = self.Phases[phasenam] # pointer to current phase info
1935	if len(phasedict['General']['Map'].get('rho',[])):
1936	mapPhases.append(phasenam)
1937	if phasedict['General']['Map'].get('Flip'):
1938	choices.append('Charge flip map: '+str(phasenam))
1939	elif phasedict['General']['Map'].get('MapType'):
1940	choices.append(
1941	str(phasedict['General']['Map'].get('MapType'))
1942	+ ' map: ' + str(phasenam))
1943	else:
1944	choices.append('unknown map: '+str(phasenam))
1945	# select a map if needed
1946	if len(mapPhases) == 0:
1947	self.G2frame.ErrorDialog(
1948	'Empty project',
1949	'Project does not contain any maps.')
1950	return True
1951	elif len(mapPhases) == 1:
1952	self.phasenam = mapPhases
1953	else:
1954	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1955	if self.multiple:
1956	if not phasenum: return True
1957	self.phasenam = [mapPhases[i] for i in phasenum]
1958	else:
1959	if phasenum is None: return True
1960	self.phasenam = [mapPhases[phasenum]]
1961	numselected = len(self.phasenam)
1962
1963	# items selected, now set self.dirname and usually self.filename
1964	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
1965	AskFile == 'default' and not self.G2frame.GSASprojectfile
1966	):
1967	filename = self.askSaveFile()
1968	if not filename: return True
1969	self.dirname,self.filename = os.path.split(filename)
1970	elif AskFile == 'dir' or AskFile == 'single' or (
1971	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
1972	):
1973	self.dirname = self.askSaveDirectory()
1974	if not self.dirname: return True
1975	elif AskFile == 'default-dir' or AskFile == 'default':
1976	self.dirname,self.filename = os.path.split(
1977	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
1978	)
1979	else:
1980	raise Exception('This should not happen!')
1981
1982	def loadParmDict(self):
1983	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
1984	refined values to those from the last cycle and set the uncertainties for the
1985	refined parameters in another dict (self.sigDict).
1986
1987	Expands the parm & sig dicts to include values derived from constraints.
1988	'''
1989	self.parmDict = {}
1990	self.sigDict = {}
1991	rigidbodyDict = {}
1992	covDict = {}
1993	consDict = {}
1994	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1995	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
1996	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
1997	while item:
1998	name = self.G2frame.PatternTree.GetItemText(item)
1999	if name == 'Rigid bodies':
2000	rigidbodyDict = self.G2frame.PatternTree.GetItemPyData(item)
2001	elif name == 'Covariance':
2002	covDict = self.G2frame.PatternTree.GetItemPyData(item)
2003	elif name == 'Constraints':
2004	consDict = self.G2frame.PatternTree.GetItemPyData(item)
2005	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2006	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
2007	self.parmDict.update(rbDict)
2008	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
2009	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData(
2010	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
2011	self.parmDict.update(phaseDict)
2012	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
2013	Phases,Histograms,Print=False,resetRefList=False)
2014	self.parmDict.update(hapDict)
2015	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
2016	self.parmDict.update(histDict)
2017	self.parmDict.update(zip(
2018	covDict.get('varyList',[]),
2019	covDict.get('variables',[])))
2020	self.sigDict = dict(zip(
2021	covDict.get('varyList',[]),
2022	covDict.get('sig',[])))
2023	# expand to include constraints: first compile a list of constraints
2024	constList = []
2025	for item in consDict:
2026	if item.startswith('_'): continue
2027	constList += consDict[item]
2028	# now process the constraints
2029	G2mv.InitVars()
2030	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
2031	varyList = covDict.get('varyListStart')
2032	if varyList is None and len(constDict) == 0:
2033	# no constraints can use varyList
2034	varyList = covDict.get('varyList')
2035	elif varyList is None:
2036	# old GPX file from before pre-constraint varyList is saved
2037	print ' * Old refinement: Please use Calculate/Refine to redo *'
2038	raise Exception(' * Export aborted *')
2039	else:
2040	varyList = list(varyList)
2041	try:
2042	groups,parmlist = G2mv.GroupConstraints(constDict)
2043	G2mv.GenerateConstraints(groups,parmlist,varyList,constDict,fixedList,self.parmDict)
2044	except:
2045	# this really should not happen
2046	print ' * ERROR - constraints are internally inconsistent *'
2047	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
2048	print 'Errors',errmsg
2049	if warnmsg: print 'Warnings',warnmsg
2050	raise Exception(' * CIF creation aborted *')
2051	# add the constrained values to the parameter dictionary
2052	G2mv.Dict2Map(self.parmDict,varyList)
2053	# and add their uncertainties into the esd dictionary (sigDict)
2054	if covDict.get('covMatrix') is not None:
2055	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
2056
2057	def loadTree(self):
2058	'''Load the contents of the data tree into a set of dicts
2059	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
2060	& self.xtalDict)
2061
2062	* The childrenless data tree items are overall parameters/controls for the
2063	entire project and are placed in self.OverallParms
2064	* Phase items are placed in self.Phases
2065	* Data items are placed in self.Histogram. The key for these data items
2066	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
2067	'''
2068	self.OverallParms = {}
2069	self.powderDict = {}
2070	self.xtalDict = {}
2071	self.Phases = {}
2072	self.Histograms = {}
2073	self.SeqRefdata = None
2074	self.SeqRefhist = None
2075	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2076	histType = None
2077	if self.currentExportType == 'phase':
2078	# if exporting phases load them here
2079	sub = G2gd.GetPatternTreeItemId(self.G2frame,self.G2frame.root,'Phases')
2080	if not sub:
2081	print 'no phases found'
2082	return True
2083	item, cookie = self.G2frame.PatternTree.GetFirstChild(sub)
2084	while item:
2085	phaseName = self.G2frame.PatternTree.GetItemText(item)
2086	self.Phases[phaseName] = self.G2frame.PatternTree.GetItemPyData(item)
2087	item, cookie = self.G2frame.PatternTree.GetNextChild(sub, cookie)
2088	return
2089	elif self.currentExportType == 'single':
2090	histType = 'HKLF'
2091	elif self.currentExportType == 'powder':
2092	histType = 'PWDR'
2093	elif self.currentExportType == 'image':
2094	histType = 'IMG'
2095
2096	if histType: # Loading just one kind of tree entry
2097	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2098	while item:
2099	name = self.G2frame.PatternTree.GetItemText(item)
2100	if name.startswith(histType):
2101	if self.Histograms.get(name): # there is already an item with this name
2102	print('Histogram name '+str(name)+' is repeated. Renaming')
2103	if name[-1] == '9':
2104	name = name[:-1] + '10'
2105	elif name[-1] in '012345678':
2106	name = name[:-1] + str(int(name[-1])+1)
2107	else:
2108	name += '-1'
2109	self.Histograms[name] = {}
2110	# the main info goes into Data, but the 0th
2111	# element contains refinement results, carry
2112	# that over too now.
2113	self.Histograms[name]['Data'] = self.G2frame.PatternTree.GetItemPyData(item)[1]
2114	self.Histograms[name][0] = self.G2frame.PatternTree.GetItemPyData(item)[0]
2115	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2116	while item2:
2117	child = self.G2frame.PatternTree.GetItemText(item2)
2118	self.Histograms[name][child] = self.G2frame.PatternTree.GetItemPyData(item2)
2119	item2, cookie2 = self.G2frame.PatternTree.GetNextChild(item, cookie2)
2120	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2121	# index powder and single crystal histograms by number
2122	for hist in self.Histograms:
2123	if hist.startswith("PWDR"):
2124	d = self.powderDict
2125	elif hist.startswith("HKLF"):
2126	d = self.xtalDict
2127	else:
2128	return
2129	i = self.Histograms[hist].get('hId')
2130	if i is None and not d.keys():
2131	i = 0
2132	elif i is None or i in d.keys():
2133	i = max(d.keys())+1
2134	d[i] = hist
2135	return
2136	# else standard load: using all interlinked phases and histograms
2137	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2138	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2139	while item:
2140	name = self.G2frame.PatternTree.GetItemText(item)
2141	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2142	if not item2:
2143	self.OverallParms[name] = self.G2frame.PatternTree.GetItemPyData(item)
2144	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2145	# index powder and single crystal histograms
2146	for hist in self.Histograms:
2147	i = self.Histograms[hist]['hId']
2148	if hist.startswith("PWDR"):
2149	self.powderDict[i] = hist
2150	elif hist.startswith("HKLF"):
2151	self.xtalDict[i] = hist
2152
2153	def dumpTree(self,mode='type'):
2154	'''Print out information on the data tree dicts loaded in loadTree.
2155	Used for testing only.
2156	'''
2157	if self.SeqRefdata and self.SeqRefhist:
2158	print('Note that dumpTree does not show sequential results')
2159	print '\nOverall'
2160	if mode == 'type':
2161	def Show(arg): return type(arg)
2162	else:
2163	def Show(arg): return arg
2164	for key in self.OverallParms:
2165	print ' ',key,Show(self.OverallParms[key])
2166	print 'Phases'
2167	for key1 in self.Phases:
2168	print ' ',key1,Show(self.Phases[key1])
2169	print 'Histogram'
2170	for key1 in self.Histograms:
2171	print ' ',key1,Show(self.Histograms[key1])
2172	for key2 in self.Histograms[key1]:
2173	print ' ',key2,Show(self.Histograms[key1][key2])
2174
2175	def defaultSaveFile(self):
2176	return os.path.abspath(
2177	os.path.splitext(self.G2frame.GSASprojectfile
2178	)[0]+self.extension)
2179
2180	def askSaveFile(self):
2181	'''Ask the user to supply a file name
2182
2183	:returns: a file name (str) or None if Cancel is pressed
2184	'''
2185
2186	pth = G2G.GetExportPath(self.G2frame)
2187	defnam = os.path.splitext(
2188	os.path.split(self.G2frame.GSASprojectfile)[1]
2189	)[0]+self.extension
2190	dlg = wx.FileDialog(
2191	self.G2frame, 'Input name for file to write', pth, defnam,
2192	self.longFormatName+' ('+self.extension+')\|'+self.extension,
2193	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
2194	dlg.CenterOnParent()
2195	try:
2196	if dlg.ShowModal() == wx.ID_OK:
2197	filename = dlg.GetPath()
2198	self.G2frame.LastExportDir = os.path.split(filename)[0]
2199	filename = os.path.splitext(filename)[0]+self.extension # make sure extension is correct
2200	else:
2201	filename = None
2202	finally:
2203	dlg.Destroy()
2204	return filename
2205
2206	def askSaveDirectory(self):
2207	'''Ask the user to supply a directory name. Path name is used as the
2208	starting point for the next export path search.
2209
2210	:returns: a directory name (str) or None if Cancel is pressed
2211	'''
2212	pth = G2G.GetExportPath(self.G2frame)
2213	dlg = wx.DirDialog(
2214	self.G2frame, 'Input directory where file(s) will be written', pth,
2215	wx.DD_DEFAULT_STYLE)
2216	dlg.CenterOnParent()
2217	try:
2218	if dlg.ShowModal() == wx.ID_OK:
2219	filename = dlg.GetPath()
2220	self.G2frame.LastExportDir = filename
2221	else:
2222	filename = None
2223	finally:
2224	dlg.Destroy()
2225	return filename
2226
2227	# Tools for file writing.
2228	def OpenFile(self,fil=None,mode='w'):
2229	'''Open the output file
2230
2231	:param str fil: The name of the file to open. If None (default)
2232	the name defaults to self.dirname + self.filename.
2233	If an extension is supplied, it is not overridded,
2234	but if not, the default extension is used.
2235	:returns: the file object opened by the routine which is also
2236	saved as self.fp
2237	'''
2238	if mode == 'd': # debug mode
2239	self.fullpath = '(stdout)'
2240	self.fp = sys.stdout
2241	return
2242	if not fil:
2243	if not os.path.splitext(self.filename)[1]:
2244	self.filename += self.extension
2245	fil = os.path.join(self.dirname,self.filename)
2246	self.fullpath = os.path.abspath(fil)
2247	self.fp = open(self.fullpath,mode)
2248	return self.fp
2249
2250	def Write(self,line):
2251	'''write a line of output, attaching a line-end character
2252
2253	:param str line: the text to be written.
2254	'''
2255	self.fp.write(line+'\n')
2256
2257	def CloseFile(self,fp=None):
2258	'''Close a file opened in OpenFile
2259
2260	:param file fp: the file object to be closed. If None (default)
2261	file object self.fp is closed.
2262	'''
2263	if self.fp == sys.stdout: return # debug mode
2264	if fp is None:
2265	fp = self.fp
2266	self.fp = None
2267	fp.close()
2268
2269	def SetSeqRef(self,data,hist):
2270	'''Set the exporter to retrieve results from a sequential refinement
2271	rather than the main tree
2272	'''
2273	self.SeqRefdata = data
2274	self.SeqRefhist = hist
2275	data_name = data[hist]
2276	for i,val in zip(data_name['varyList'],data_name['sig']):
2277	self.sigDict[i] = val
2278	self.sigDict[striphist(i)] = val
2279	for i in data_name['parmDict']:
2280	self.parmDict[striphist(i)] = data_name['parmDict'][i]
2281	self.parmDict[i] = data_name['parmDict'][i]
2282	# zero out the dA[xyz] terms, they would only bring confusion
2283	key = i.split(':')
2284	if len(key) < 3: continue
2285	if key[2].startswith('dA'):
2286	self.parmDict[i] = 0.0
2287	for i,(val,sig) in data_name.get('depParmDict',{}).iteritems():
2288	self.parmDict[i] = val
2289	self.sigDict[i] = sig
2290	#GSASIIpath.IPyBreak()
2291
2292	# Tools to pull information out of the data arrays
2293	def GetCell(self,phasenam):
2294	"""Gets the unit cell parameters and their s.u.'s for a selected phase
2295
2296	:param str phasenam: the name for the selected phase
2297	:returns: `cellList,cellSig` where each is a 7 element list corresponding
2298	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
2299	cell values and `cellSig` has their uncertainties.
2300	"""
2301	if self.SeqRefdata and self.SeqRefhist:
2302	return self.GetSeqCell(phasenam,self.SeqRefdata[self.SeqRefhist])
2303	phasedict = self.Phases[phasenam] # pointer to current phase info
2304	try:
2305	pfx = str(phasedict['pId'])+'::'
2306	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
2307	cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A,
2308	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
2309	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
2310	return cellList,cellSig
2311	except KeyError:
2312	cell = phasedict['General']['Cell'][1:]
2313	return cell,7*[0]
2314
2315	def GetSeqCell(self,phasenam,data_name):
2316	"""Gets the unit cell parameters and their s.u.'s for a selected phase
2317	and histogram in a sequential fit
2318
2319	:param str phasenam: the name for the selected phase
2320	:param dict data_name: the sequential refinement parameters for the selected histogram
2321	:returns: `cellList,cellSig` where each is a 7 element list corresponding
2322	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
2323	cell values and `cellSig` has their uncertainties.
2324	"""
2325	phasedict = self.Phases[phasenam]
2326	SGdata = phasedict['General']['SGData']
2327	pId = phasedict['pId']
2328	RecpCellTerms = G2lat.cell2A(phasedict['General']['Cell'][1:7])
2329	ESDlookup = {}
2330	Dlookup = {}
2331	varied = [striphist(i) for i in data_name['varyList']]
2332	for item,val in data_name['newCellDict'].iteritems():
2333	if item in varied:
2334	ESDlookup[val[0]] = item
2335	Dlookup[item] = val[0]
2336	A = RecpCellTerms[:]
2337	for i in range(6):
2338	var = str(pId)+'::A'+str(i)
2339	if var in ESDlookup:
2340	A[i] = data_name['newCellDict'][ESDlookup[var]][1] # override with refined value
2341	cellDict = dict(zip([str(pId)+'::A'+str(i) for i in range(6)],A))
2342	zeroDict = {i:0.0 for i in cellDict}
2343	A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata,cellDict,zeroDict)
2344	covData = {
2345	'varyList': [Dlookup.get(striphist(v),v) for v in data_name['varyList']],
2346	'covMatrix': data_name['covMatrix']
2347	}
2348	return list(G2lat.A2cell(A)) + [G2lat.calc_V(A)], G2stIO.getCellEsd(str(pId)+'::',SGdata,A,covData)
2349
2350	def GetAtoms(self,phasenam):
2351	"""Gets the atoms associated with a phase. Can be used with standard
2352	or macromolecular phases
2353
2354	:param str phasenam: the name for the selected phase
2355	:returns: a list of items for eac atom where each item is a list containing:
2356	label, typ, mult, xyz, and td, where
2357
2358	* label and typ are the atom label and the scattering factor type (str)
2359	* mult is the site multiplicity (int)
2360	* xyz is contains a list with four pairs of numbers:
2361	x, y, z and fractional occupancy and
2362	their standard uncertainty (or a negative value)
2363	* td is contains a list with either one or six pairs of numbers:
2364	if one number it is U\ :sub:`iso` and with six numbers it is
2365	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
2366	paired with their standard uncertainty (or a negative value)
2367	"""
2368	phasedict = self.Phases[phasenam] # pointer to current phase info
2369	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
2370	cfrac = cx+3
2371	fpfx = str(phasedict['pId'])+'::Afrac:'
2372	atomslist = []
2373	for i,at in enumerate(phasedict['Atoms']):
2374	if phasedict['General']['Type'] == 'macromolecular':
2375	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
2376	else:
2377	label = at[ct-1]
2378	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
2379	fsig = self.sigDict.get(fpfx+str(i),-0.009)
2380	mult = at[cs+1]
2381	typ = at[ct]
2382	xyz = []
2383	for j,v in enumerate(('x','y','z')):
2384	val = at[cx+j]
2385	pfx = str(phasedict['pId']) + '::A' + v + ':' + str(i)
2386	val = self.parmDict.get(pfx, val)
2387	dpfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
2388	sig = self.sigDict.get(dpfx,-0.000009)
2389	xyz.append((val,sig))
2390	xyz.append((fval,fsig))
2391	td = []
2392	if at[cia] == 'I':
2393	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
2394	val = self.parmDict.get(pfx,at[cia+1])
2395	sig = self.sigDict.get(pfx,-0.0009)
2396	td.append((val,sig))
2397	else:
2398	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
2399	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
2400	val = self.parmDict.get(pfx,at[cia+2+i])
2401	sig = self.sigDict.get(pfx,-0.0009)
2402	td.append((val,sig))
2403	atomslist.append((label,typ,mult,xyz,td))
2404	return atomslist
2405	######################################################################
2406	def ExportPowderList(G2frame):
2407	'''Returns a list of extensions supported by :func:`GSASIIIO:ExportPowder`
2408	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
2409
2410	:param wx.Frame G2frame: the GSAS-II main data tree window
2411	'''
2412	extList = []
2413	for obj in G2frame.exporterlist:
2414	if 'powder' in obj.exporttype:
2415	try:
2416	obj.Writer
2417	extList.append(obj.extension)
2418	except AttributeError:
2419	pass
2420	return extList
2421
2422	def ExportPowder(G2frame,TreeName,fileroot,extension):
2423	'''Writes a single powder histogram using the Export routines.
2424	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
2425
2426	:param wx.Frame G2frame: the GSAS-II main data tree window
2427	:param str TreeName: the name of the histogram (PWDR ...) in the data tree
2428	:param str fileroot: name for file to be written, extension ignored
2429	:param str extension: extension for file to be written (start with '.'). Must
2430	match a powder export routine that has a Writer object.
2431	'''
2432	filename = os.path.abspath(os.path.splitext(fileroot)[0]+extension)
2433	for obj in G2frame.exporterlist:
2434	if obj.extension == extension and 'powder' in obj.exporttype:
2435	obj.currentExportType = 'powder'
2436	obj.InitExport(None)
2437	obj.loadTree() # load all histograms in tree into dicts
2438	if TreeName not in obj.Histograms:
2439	raise Exception('Histogram not found: '+str(TreeName))
2440	try:
2441	obj.Writer
2442	except AttributeError:
2443	continue
2444	try:
2445	obj.Writer(TreeName,filename)
2446	return
2447	except Exception,err:
2448	print('Export Routine for '+extension+' failed.')
2449	print err
2450	else:
2451	print('No Export routine supports extension '+extension)
2452
2453	def ExportSequential(G2frame,data,obj,exporttype):
2454	'''
2455	Used to export from every phase/dataset in a sequential refinement using
2456	a .Writer method for either projects or phases. Prompts to select histograms
2457	and for phase exports, which phase(s).
2458
2459	:param wx.Frame G2frame: the GSAS-II main data tree window
2460	:param dict data: the sequential refinement data object
2461	:param str exporttype: indicates the type of export ('project' or 'phase')
2462	'''
2463	if len(data['histNames']) == 0:
2464	G2G.G2MessageBox(G2frame,'There are no sequential histograms','Warning')
2465	obj.InitExport(None)
2466	obj.loadTree()
2467	obj.loadParmDict()
2468	if len(data['histNames']) == 1:
2469	histlist = data['histNames']
2470	else:
2471	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select histograms to export from list',
2472	'Select histograms',data['histNames'])
2473	if dlg.ShowModal() == wx.ID_OK:
2474	histlist = [data['histNames'][l] for l in dlg.GetSelections()]
2475	dlg.Destroy()
2476	else:
2477	dlg.Destroy()
2478	return
2479	if exporttype == 'Phase':
2480	phaselist = obj.Phases.keys()
2481	if len(obj.Phases) == 0:
2482	G2G.G2MessageBox(G2frame,'There are no phases in sequential ref.','Warning')
2483	return
2484	elif len(obj.Phases) > 1:
2485	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select phases to export from list',
2486	'Select phases', phaselist)
2487	if dlg.ShowModal() == wx.ID_OK:
2488	phaselist = [phaselist[l] for l in dlg.GetSelections()]
2489	dlg.Destroy()
2490	else:
2491	dlg.Destroy()
2492	return
2493	filename = obj.askSaveFile()
2494	if not filename: return True
2495	obj.dirname,obj.filename = os.path.split(filename)
2496	print('Writing output to file '+str(obj.filename)+"...")
2497	mode = 'w'
2498	for p in phaselist:
2499	for h in histlist:
2500	obj.SetSeqRef(data,h)
2501	#GSASIIpath.IPyBreak()
2502	obj.Writer(h,phasenam=p,mode=mode)
2503	mode = 'a'
2504	print('...done')
2505	elif exporttype == 'Project':
2506	filename = obj.askSaveFile()
2507	if not filename: return True
2508	obj.dirname,obj.filename = os.path.split(filename)
2509	print('Writing output to file '+str(obj.filename)+"...")
2510	mode = 'w'
2511	for h in histlist:
2512	obj.SetSeqRef(data,h)
2513	obj.Writer(h,mode=mode)
2514	print('\t'+str(h)+' written')
2515	mode = 'a'
2516	print('...done')
2517
2518	def ReadDIFFaX(DIFFaXfile):
2519	print 'read ',DIFFaXfile
2520	Layer = {'Laue':'-1','Cell':[False,1.,1.,1.,90.,90.,90,1.],'Width':[[10.,10.],[False,False]],
2521	'Layers':[],'Stacking':[],'Transitions':[],'Toler':0.01,'AtInfo':{}}
2522	df = open(DIFFaXfile,'r')
2523	lines = df.readlines()
2524	df.close()
2525	struct = False
2526	Struct = []
2527	stack = False
2528	Stack = []
2529	trans = False
2530	Trans = []
2531	for diff in lines:
2532	diff = diff[:-1].lower()
2533	if '!' in diff:
2534	continue
2535	while '}' in diff: #strip comments
2536	iB = diff.index('{')
2537	iF = diff.index('}')+1
2538	if iB:
2539	diff = diff[:iB]
2540	else:
2541	diff = diff[iF:]
2542	if not diff:
2543	continue
2544	if diff.strip() == 'instrumental':
2545	continue
2546	if diff.strip() == 'structural':
2547	struct = True
2548	continue
2549	elif diff.strip() == 'stacking':
2550	struct = False
2551	stack = True
2552	continue
2553	elif diff.strip() == 'transitions':
2554	stack = False
2555	trans = True
2556	continue
2557	diff = diff.strip()
2558	if struct:
2559	if diff:
2560	Struct.append(diff)
2561	elif stack:
2562	if diff:
2563	Stack.append(diff)
2564	elif trans:
2565	if diff:
2566	Trans.append(diff)
2567
2568	#STRUCTURE records
2569	laueRec = Struct[1].split()
2570	Layer['Laue'] = laueRec[0]
2571	if Layer['Laue'] == 'unknown' and len(laueRec) > 1:
2572	Layer['Toler'] = float(laueRec[1]) #tolerance for 'unknown'?
2573	if Layer['Laue'] == '2/m(1)': Layer['Laue'] = '2/m(c)'
2574	if Layer['Laue'] == '2/m(2)': Layer['Laue'] = '2/m(ab)'
2575	cell = Struct[0].split()
2576	Layer['Cell'] = [False,float(cell[0]),float(cell[1]),float(cell[2]),90.,90.,float(cell[3]),1.0]
2577	nLayers = int(Struct[2])
2578	N = 3
2579	if 'layer' not in Struct[3]:
2580	N = 4
2581	if Struct[3] != 'infinite':
2582	width = Struct[3].split()
2583	Layer['Width'][0] = [float(width[0]),float(width[1])]
2584	for nL in range(nLayers):
2585	if '=' in Struct[N]:
2586	name = Struct[N].split('=')
2587	sameas = int(name[1])-1
2588	Layer['Layers'].append({'Name':name[0],'SameAs':Layer['Layers'][sameas]['Name'],'Symm':'None','Atoms':[]})
2589	N += 1
2590	continue
2591	Symm = 'None'
2592	if 'centro' in Struct[N+1]: Symm = '-1'
2593	Layer['Layers'].append({'Name':Struct[N],'SameAs':'','Symm':Symm,'Atoms':[]})
2594	N += 2
2595	while 'layer' not in Struct[N]:
2596	atom = Struct[N][4:].split()
2597	atomType = G2el.FixValence(Struct[N][:4].replace(' ','').strip().capitalize())
2598	if atomType not in Layer['AtInfo']:
2599	Layer['AtInfo'][atomType] = G2el.GetAtomInfo(atomType)
2600	atomName = '%s(%s)'%(atomType,atom[0])
2601	newVals = []
2602	for val in atom[1:6]:
2603	if '/' in val:
2604	newVals.append(eval(val+'.'))
2605	else:
2606	newVals.append(float(val))
2607	atomRec = [atomName,atomType,newVals[0],newVals[1],newVals[2],newVals[4],newVals[3]/78.9568]
2608	Layer['Layers'][-1]['Atoms'].append(atomRec)
2609	N += 1
2610	if N > len(Struct)-1:
2611	break
2612	#TRANSITIONS records
2613	transArray = []
2614	N = 0
2615	for i in range(nLayers):
2616	transArray.append([])
2617	for j in range(nLayers):
2618	vals = Trans[N].split()
2619	newVals = []
2620	for val in vals[:4]:
2621	if '/' in val:
2622	newVals.append(eval(val+'.'))
2623	else:
2624	newVals.append(float(val))
2625	transArray[-1].append(newVals+['',False])
2626	N += 1
2627	Layer['Transitions'] = transArray
2628	#STACKING records
2629	Layer['Stacking'] = [Stack[0],'']
2630	if Stack[0] == 'recursive':
2631	Layer['Stacking'][1] = Stack[1]
2632	elif Stack[0] == 'explicit':
2633	if Stack[1] == 'random':
2634	Layer['Stacking'][1] = Stack[1]
2635	else:
2636	Layer['Stacking'][1] = 'list'
2637	Layer['Stacking'].append('')
2638	for stack in Stack[2:]:
2639	Layer['Stacking'][2] += ' '+stack
2640	return Layer
2641
2642	def ReadCIF(URLorFile):
2643	'''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
2644	(from James Hester).
2645	The open routine gets confused with DOS names that begin with a letter and colon
2646	"C:\dir\" so this routine will try to open the passed name as a file and if that
2647	fails, try it as a URL
2648
2649	:param str URLorFile: string containing a URL or a file name. Code will try first
2650	to open it as a file and then as a URL.
2651
2652	:returns: a PyCifRW CIF object.
2653	'''
2654	import CifFile as cif # PyCifRW from James Hester
2655
2656	# alternate approach:
2657	#import urllib
2658	#ciffile = 'file:'+urllib.pathname2url(filename)
2659
2660	try:
2661	fp = open(URLorFile,'r')
2662	cf = cif.ReadCif(fp)
2663	fp.close()
2664	return cf
2665	except IOError:
2666	return cif.ReadCif(URLorFile)
2667
2668	if __name__ == '__main__':
2669	import GSASII
2670	application = GSASII.GSASIImain(0)
2671	G2frame = application.main
2672	#app = wx.PySimpleApp()
2673	#G2frame = wx.Frame(None) # create a frame
2674	#frm.Show(True)
2675	#filename = '/tmp/notzip.zip'
2676	#filename = '/tmp/all.zip'
2677	#filename = '/tmp/11bmb_7652.zip'
2678
2679	#selection=None, confirmoverwrite=True, parent=None
2680	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2681	#print ExtractFileFromZip(filename,multipleselect=True)
2682	# #confirmread=False, confirmoverwrite=False)
2683
2684	# choicelist=[ ('a','b','c'),
2685	# ('test1','test2'),('no choice',)]
2686	# titles = [ 'a, b or c', 'tests', 'No option here']
2687	# dlg = MultipleChoicesDialog(
2688	# choicelist,titles,
2689	# parent=frm)
2690	# if dlg.ShowModal() == wx.ID_OK:
2691	# print 'Got OK'
2692	imagefile = '/tmp/NDC5_00237_3.ge3'
2693	Comments, Data, Npix, Image = GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None)
2694
2695	print("\n\nResults loaded to Comments, Data, Npix and Image\n\n")
2696
2697	GSASIIpath.IPyBreak_base()

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