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source: trunk/GSASIIIO.py @ 2625

Last change on this file since 2625 was 2625, checked in by vondreele, 6 years ago
fix problem with using dark/background images - GetCheckImageFile? needed to refer to treeId rather than G2frame.Image fix Progress bar problem in integration should be destroyed after each use
Property svn:eol-style set to `native` Property svn:keywords set to `Date Author Revision URL Id`
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1	# -- coding: utf-8 --
2	########### SVN repository information ###################
3	# $Date: 2017-01-12 17:01:40 +0000 (Thu, 12 Jan 2017) $
4	# $Author: vondreele $
5	# $Revision: 2625 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 2625 2017-01-12 17:01:40Z 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: 2625 $")
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	for datus in data[1:]:
787	sub = G2frame.PatternTree.AppendItem(Id,datus[0])
788	#patch
789	if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
790	if datum[0].startswith('PWDR'):
791	datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
792	else:
793	datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
794	for item in datus[1][0]: #zip makes tuples - now make lists!
795	datus[1][0][item] = list(datus[1][0][item])
796	#end patch
797	G2frame.PatternTree.SetItemPyData(sub,datus[1])
798	if datum[0].startswith('IMG'): #retrieve image default flag & data if set
799	Data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Image Controls'))
800	if Data['setDefault']:
801	G2frame.imageDefault = Data
802	file.close()
803	if LastSavedUsing:
804	print('GPX load successful. Last saved with GSAS-II revision '+LastSavedUsing)
805	else:
806	print('project load successful')
807	G2frame.NewPlot = True
808	except:
809	msg = wx.MessageDialog(G2frame,message="Error reading file "+
810	str(G2frame.GSASprojectfile)+". This is not a GSAS-II .gpx file",
811	caption="Load Error",style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
812	msg.ShowModal()
813	finally:
814	wx.EndBusyCursor()
815	G2frame.Status.SetStatusText('Mouse RB click item to refresh/raise; RB drag/drop to reorder')
816
817	def ProjFileSave(G2frame):
818	'Save a GSAS-II project file'
819	if not G2frame.PatternTree.IsEmpty():
820	file = open(G2frame.GSASprojectfile,'wb')
821	print 'save to file: ',G2frame.GSASprojectfile
822	# stick the file name into the tree and version info into tree so they are saved.
823	# (Controls should always be created at this point)
824	try:
825	Controls = G2frame.PatternTree.GetItemPyData(
826	G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
827	Controls['LastSavedAs'] = os.path.abspath(G2frame.GSASprojectfile)
828	Controls['LastSavedUsing'] = str(GSASIIpath.GetVersionNumber())
829	Controls['PythonVersions'] = G2frame.PackageVersions
830	except:
831	pass
832	wx.BeginBusyCursor()
833	try:
834	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
835	while item:
836	data = []
837	name = G2frame.PatternTree.GetItemText(item)
838	data.append([name,G2frame.PatternTree.GetItemPyData(item)])
839	item2, cookie2 = G2frame.PatternTree.GetFirstChild(item)
840	while item2:
841	name = G2frame.PatternTree.GetItemText(item2)
842	data.append([name,G2frame.PatternTree.GetItemPyData(item2)])
843	item2, cookie2 = G2frame.PatternTree.GetNextChild(item, cookie2)
844	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
845	cPickle.dump(data,file,1)
846	file.close()
847	pth = os.path.split(os.path.abspath(G2frame.GSASprojectfile))[0]
848	if GSASIIpath.GetConfigValue('Save_paths'): G2G.SaveGPXdirectory(pth)
849	G2frame.LastGPXdir = pth
850	finally:
851	wx.EndBusyCursor()
852	print('project save successful')
853
854	def SaveIntegration(G2frame,PickId,data,Overwrite=False):
855	'Save image integration results as powder pattern(s)'
856	azms = G2frame.Integrate[1]
857	X = G2frame.Integrate[2][:-1]
858	N = len(X)
859	Id = G2frame.PatternTree.GetItemParent(PickId)
860	name = G2frame.PatternTree.GetItemText(Id)
861	name = name.replace('IMG ',data['type']+' ')
862	Comments = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Comments'))
863	if 'PWDR' in name:
864	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','SH/L','Azimuth']
865	codes = [0 for i in range(11)]
866	elif 'SASD' in name:
867	names = ['Type','Lam','Zero','Azimuth']
868	codes = [0 for i in range(4)]
869	X = 4.np.pinpsind(X/2.)/data['wavelength'] #convert to q
870	Xminmax = [X[0],X[-1]]
871	Azms = []
872	dazm = 0.
873	if data['fullIntegrate'] and data['outAzimuths'] == 1:
874	Azms = [45.0,] #a poor man's average?
875	else:
876	for i,azm in enumerate(azms[:-1]):
877	if azm > 360. and azms[i+1] > 360.:
878	Azms.append(G2img.meanAzm(azm%360.,azms[i+1]%360.))
879	else:
880	Azms.append(G2img.meanAzm(azm,azms[i+1]))
881	dazm = np.min(np.abs(np.diff(azms)))/2.
882	G2frame.IntgOutList = []
883	for i,azm in enumerate(azms[:-1]):
884	Aname = name+" Azm= %.2f"%((azm+dazm)%360.)
885	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
886	# if Overwrite delete any duplicate
887	if Overwrite and G2gd.GetPatternTreeItemId(G2frame,G2frame.root,Aname):
888	print('Replacing '+Aname)
889	item = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,Aname)
890	G2frame.PatternTree.Delete(item)
891	else:
892	nOcc = 0
893	while item:
894	Name = G2frame.PatternTree.GetItemText(item)
895	if Aname in Name:
896	nOcc += 1
897	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
898	if nOcc:
899	Aname += '(%d)'%(nOcc)
900	Sample = G2pdG.SetDefaultSample()
901	Sample['Gonio. radius'] = data['distance']
902	Sample['Omega'] = data['GonioAngles'][0]
903	Sample['Chi'] = data['GonioAngles'][1]
904	Sample['Phi'] = data['GonioAngles'][2]
905	Sample['Azimuth'] = (azm+dazm)%360. #put here as bin center
906	polariz = 0.99 #set default polarization for synchrotron radiation!
907	for item in Comments:
908	if 'polariz' in item:
909	try:
910	polariz = float(item.split('=')[1])
911	except:
912	polariz = 0.99
913	if 'PWDR' in Aname:
914	parms = ['PXC',data['wavelength'],0.0,polariz,1.0,-0.10,0.4,0.30,1.0,0.0001,Azms[i]]
915	elif 'SASD' in Aname:
916	Sample['Trans'] = data['SampleAbs'][0]
917	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
918	Y = G2frame.Integrate[0][i]
919	Ymax = np.max(Y)
920	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
921	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=Aname)
922	G2frame.IntgOutList.append(Id)
923	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
924	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Limits'),[tuple(Xminmax),Xminmax])
925	if 'PWDR' in Aname:
926	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Background'),[['chebyschev',1,3,1.0,0.0,0.0],
927	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
928	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
929	for item in inst[0]:
930	inst[0][item] = list(inst[0][item])
931	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Instrument Parameters'),inst)
932	if 'PWDR' in Aname:
933	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
934	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
935	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Index Peak List'),[[],[]])
936	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Unit Cells List'),[])
937	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Reflection Lists'),{})
938	elif 'SASD' in Aname:
939	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
940	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
941	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
942	valuesdict = {
943	'wtFactor':1.0,
944	'Dummy':False,
945	'ranId':ran.randint(0,sys.maxint),
946	'Offset':[0.0,0.0],'delOffset':0.02Ymax,'refOffset':-0.1Ymax,'refDelt':0.1*Ymax,
947	'qPlot':False,'dPlot':False,'sqrtPlot':False
948	}
949	G2frame.PatternTree.SetItemPyData(
950	Id,[valuesdict,
951	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
952	return Id #last powder pattern generated
953
954	def XYsave(G2frame,XY,labelX='X',labelY='Y',names=None):
955	'Save XY table data'
956	pth = G2G.GetExportPath(G2frame)
957	dlg = wx.FileDialog(
958	G2frame, 'Enter csv filename for XY table', pth, '',
959	'XY table file (.csv)\|.csv',wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
960	try:
961	if dlg.ShowModal() == wx.ID_OK:
962	filename = dlg.GetPath()
963	filename = os.path.splitext(filename)[0]+'.csv'
964	File = open(filename,'w')
965	else:
966	filename = None
967	finally:
968	dlg.Destroy()
969	if not filename:
970	return
971	for i in range(len(XY)):
972	if names != None:
973	header = '%s,%s(%s)\n'%(labelX,labelY,names[i])
974	else:
975	header = '%s,%s(%d)\n'%(labelX,labelY,i)
976	File.write(header)
977	for x,y in XY[i].T:
978	File.write('%.3f,%.3f\n'%(x,y))
979	File.close()
980	print ' XY data saved to: ',filename
981
982	def PDFSave(G2frame,exports):
983	'Save a PDF G(r) and F(Q), S(Q) in column formats'
984	import scipy.interpolate as scintp
985	for export in exports:
986	PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
987	SQname = 'S(Q)'+export[4:]
988	FQname = 'F(Q)'+export[4:]
989	GRname = 'G(R)'+export[4:]
990	sqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.sq')
991	fqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.fq')
992	grfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.gr')
993	sqId = G2gd.GetPatternTreeItemId(G2frame, PickId, SQname)
994	fqId = G2gd.GetPatternTreeItemId(G2frame, PickId, FQname)
995	grId = G2gd.GetPatternTreeItemId(G2frame, PickId, GRname)
996	sqdata = np.array(G2frame.PatternTree.GetItemPyData(sqId)[1][:2])
997	sqfxn = scintp.interp1d(sqdata[0],sqdata[1],kind='linear')
998	fqdata = np.array(G2frame.PatternTree.GetItemPyData(fqId)[1][:2])
999	fqfxn = scintp.interp1d(fqdata[0],fqdata[1],kind='linear')
1000	grdata = np.array(G2frame.PatternTree.GetItemPyData(grId)[1][:2])
1001	grfxn = scintp.interp1d(grdata[0],grdata[1],kind='linear')
1002	sqfile = open(sqfilename,'w')
1003	fqfile = open(sqfilename,'w')
1004	grfile = open(grfilename,'w')
1005	sqfile.write('#T S(Q) %s\n'%(export))
1006	fqfile.write('#T F(Q) %s\n'%(export))
1007	grfile.write('#T G(R) %s\n'%(export))
1008	sqfile.write('#L Q S(Q)\n')
1009	fqfile.write('#L Q F(Q)\n')
1010	grfile.write('#L R G(R)\n')
1011	qnew = np.arange(sqdata[0][0],sqdata[0][-1],0.005)
1012	rnew = np.arange(grdata[0][0],grdata[0][-1],0.010)
1013	sqnew = zip(qnew,sqfxn(qnew))
1014	for q,sq in sqnew:
1015	sqfile.write("%15.6g %15.6g\n" % (q,sq))
1016	sqfile.close()
1017	print ' S(Q) saved to: ',sqfilename
1018	fqnew = zip(qnew,fqfxn(qnew))
1019	for q,fq in fqnew:
1020	fqfile.write("%15.6g %15.6g\n" % (q,fq))
1021	fqfile.close()
1022	print ' F(Q) saved to: ',fqfilename
1023	grnew = zip(rnew,grfxn(rnew))
1024	for r,gr in grnew:
1025	grfile.write("%15.6g %15.6g\n" % (r,gr))
1026	grfile.close()
1027	print ' G)R) saved to: ',grfilename
1028
1029	def PeakListSave(G2frame,file,peaks):
1030	'Save powder peaks to a data file'
1031	print 'save peak list to file: ',G2frame.peaklistfile
1032	if not peaks:
1033	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1034	try:
1035	dlg.ShowModal()
1036	finally:
1037	dlg.Destroy()
1038	return
1039	for peak in peaks:
1040	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
1041	(peak[0],peak[2],peak[4],peak[6]))
1042	print 'peak list saved'
1043
1044	def IndexPeakListSave(G2frame,peaks):
1045	'Save powder peaks from the indexing list'
1046	file = open(G2frame.peaklistfile,'wa')
1047	print 'save index peak list to file: ',G2frame.peaklistfile
1048	wx.BeginBusyCursor()
1049	try:
1050	if not peaks:
1051	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1052	try:
1053	dlg.ShowModal()
1054	finally:
1055	dlg.Destroy()
1056	return
1057	for peak in peaks:
1058	file.write("%12.6f\n" % (peak[7]))
1059	file.close()
1060	finally:
1061	wx.EndBusyCursor()
1062	print 'index peak list saved'
1063
1064	def SetNewPhase(Name='New Phase',SGData=None,cell=None,Super=None):
1065	'''Create a new phase dict with default values for various parameters
1066
1067	:param str Name: Name for new Phase
1068
1069	:param dict SGData: space group data from :func:`GSASIIspc:SpcGroup`;
1070	defaults to data for P 1
1071
1072	:param list cell: unit cell parameter list; defaults to
1073	[1.0,1.0,1.0,90.,90,90.,1.]
1074
1075	'''
1076	if SGData is None: SGData = G2spc.SpcGroup('P 1')[1]
1077	if cell is None: cell=[1.0,1.0,1.0,90.,90,90.,1.]
1078	phaseData = {
1079	'ranId':ran.randint(0,sys.maxint),
1080	'General':{
1081	'Name':Name,
1082	'Type':'nuclear',
1083	'Modulated':False,
1084	'AtomPtrs':[3,1,7,9],
1085	'SGData':SGData,
1086	'Cell':[False,]+cell,
1087	'Pawley dmin':1.0,
1088	'Data plot type':'None',
1089	'SH Texture':{
1090	'Order':0,
1091	'Model':'cylindrical',
1092	'Sample omega':[False,0.0],
1093	'Sample chi':[False,0.0],
1094	'Sample phi':[False,0.0],
1095	'SH Coeff':[False,{}],
1096	'SHShow':False,
1097	'PFhkl':[0,0,1],
1098	'PFxyz':[0,0,1],
1099	'PlotType':'Pole figure',
1100	'Penalty':[['',],0.1,False,1.0]}},
1101	'Atoms':[],
1102	'Drawing':{},
1103	'Histograms':{},
1104	'Pawley ref':[],
1105	'RBModels':{},
1106	}
1107	if Super and Super.get('Use',False):
1108	phaseData['General'].update({'Modulated':True,'Super':True,'SuperSg':Super['ssSymb']})
1109	phaseData['General']['SSGData'] = G2spc.SSpcGroup(SGData,Super['ssSymb'])
1110	phaseData['General']['SuperVec'] = [Super['ModVec'],False,Super['maxH']]
1111
1112	return phaseData
1113
1114	class MultipleChoicesDialog(wx.Dialog):
1115	'''A dialog that offers a series of choices, each with a
1116	title and a wx.Choice widget. Intended to be used Modally.
1117	typical input:
1118
1119	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1120	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1121
1122	selections are placed in self.chosen when OK is pressed
1123
1124	Also see GSASIIctrls
1125	'''
1126	def __init__(self,choicelist,headinglist,
1127	head='Select options',
1128	title='Please select from options below',
1129	parent=None):
1130	self.chosen = []
1131	wx.Dialog.__init__(
1132	self,parent,wx.ID_ANY,head,
1133	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
1134	panel = wx.Panel(self)
1135	mainSizer = wx.BoxSizer(wx.VERTICAL)
1136	mainSizer.Add((10,10),1)
1137	topLabl = wx.StaticText(panel,wx.ID_ANY,title)
1138	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.CENTER,10)
1139	self.ChItems = []
1140	for choice,lbl in zip(choicelist,headinglist):
1141	mainSizer.Add((10,10),1)
1142	self.chosen.append(0)
1143	topLabl = wx.StaticText(panel,wx.ID_ANY,' '+lbl)
1144	mainSizer.Add(topLabl,0,wx.ALIGN_LEFT,10)
1145	self.ChItems.append(wx.Choice(self, wx.ID_ANY, (100, 50), choices = choice))
1146	mainSizer.Add(self.ChItems[-1],0,wx.ALIGN_CENTER,10)
1147
1148	OkBtn = wx.Button(panel,-1,"Ok")
1149	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
1150	cancelBtn = wx.Button(panel,-1,"Cancel")
1151	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
1152	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1153	btnSizer.Add((20,20),1)
1154	btnSizer.Add(OkBtn)
1155	btnSizer.Add((20,20),1)
1156	btnSizer.Add(cancelBtn)
1157	btnSizer.Add((20,20),1)
1158	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1159	panel.SetSizer(mainSizer)
1160	panel.Fit()
1161	self.Fit()
1162
1163	def OnOk(self,event):
1164	parent = self.GetParent()
1165	if parent is not None: parent.Raise()
1166	# save the results from the choice widgets
1167	self.chosen = []
1168	for w in self.ChItems:
1169	self.chosen.append(w.GetSelection())
1170	self.EndModal(wx.ID_OK)
1171
1172	def OnCancel(self,event):
1173	parent = self.GetParent()
1174	if parent is not None: parent.Raise()
1175	self.chosen = []
1176	self.EndModal(wx.ID_CANCEL)
1177
1178	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1179	confirmoverwrite=True, parent=None,
1180	multipleselect=False):
1181	'''If the filename is a zip file, extract a file from that
1182	archive.
1183
1184	:param list Selection: used to predefine the name of the file
1185	to be extracted. Filename case and zip directory name are
1186	ignored in selection; the first matching file is used.
1187
1188	:param bool confirmread: if True asks the user to confirm before expanding
1189	the only file in a zip
1190
1191	:param bool confirmoverwrite: if True asks the user to confirm
1192	before overwriting if the extracted file already exists
1193
1194	:param bool multipleselect: if True allows more than one zip
1195	file to be extracted, a list of file(s) is returned.
1196	If only one file is present, do not ask which one, otherwise
1197	offer a list of choices (unless selection is used).
1198
1199	:returns: the name of the file that has been created or a
1200	list of files (see multipleselect)
1201
1202	If the file is not a zipfile, return the name of the input file.
1203	If the zipfile is empty or no file has been selected, return None
1204	'''
1205	import zipfile # do this now, since we can save startup time by doing this only on need
1206	import shutil
1207	zloc = os.path.split(filename)[0]
1208	if not zipfile.is_zipfile(filename):
1209	#print("not zip")
1210	return filename
1211
1212	z = zipfile.ZipFile(filename,'r')
1213	zinfo = z.infolist()
1214
1215	if len(zinfo) == 0:
1216	#print('Zip has no files!')
1217	zlist = [-1]
1218	if selection:
1219	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1220	if selection.lower() in choices:
1221	zlist = [choices.index(selection.lower())]
1222	else:
1223	print('debug: file '+str(selection)+' was not found in '+str(filename))
1224	zlist = [-1]
1225	elif len(zinfo) == 1 and confirmread:
1226	result = wx.ID_NO
1227	dlg = wx.MessageDialog(
1228	parent,
1229	'Is file '+str(zinfo[0].filename)+
1230	' what you want to extract from '+
1231	str(os.path.split(filename)[1])+'?',
1232	'Confirm file',
1233	wx.YES_NO \| wx.ICON_QUESTION)
1234	try:
1235	result = dlg.ShowModal()
1236	finally:
1237	dlg.Destroy()
1238	if result == wx.ID_NO:
1239	zlist = [-1]
1240	else:
1241	zlist = [0]
1242	elif len(zinfo) == 1:
1243	zlist = [0]
1244	elif multipleselect:
1245	# select one or more from a from list
1246	choices = [i.filename for i in zinfo]
1247	dlg = G2G.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1248	'Choose file(s)',choices)
1249	if dlg.ShowModal() == wx.ID_OK:
1250	zlist = dlg.GetSelections()
1251	else:
1252	zlist = []
1253	dlg.Destroy()
1254	else:
1255	# select one from a from list
1256	choices = [i.filename for i in zinfo]
1257	dlg = wx.SingleChoiceDialog(parent,
1258	'Select file to extract from zip file'+str(filename),'Choose file',
1259	choices,)
1260	if dlg.ShowModal() == wx.ID_OK:
1261	zlist = [dlg.GetSelection()]
1262	else:
1263	zlist = [-1]
1264	dlg.Destroy()
1265
1266	outlist = []
1267	for zindex in zlist:
1268	if zindex >= 0:
1269	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1270	if os.path.exists(efil) and confirmoverwrite:
1271	result = wx.ID_NO
1272	dlg = wx.MessageDialog(parent,
1273	'File '+str(efil)+' already exists. OK to overwrite it?',
1274	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1275	try:
1276	result = dlg.ShowModal()
1277	finally:
1278	dlg.Destroy()
1279	if result == wx.ID_NO:
1280	zindex = -1
1281	if zindex >= 0:
1282	# extract the file to the current directory, regardless of it's original path
1283	#z.extract(zinfo[zindex],zloc)
1284	eloc,efil = os.path.split(zinfo[zindex].filename)
1285	outfile = os.path.join(zloc, efil)
1286	fpin = z.open(zinfo[zindex])
1287	fpout = file(outfile, "wb")
1288	shutil.copyfileobj(fpin, fpout)
1289	fpin.close()
1290	fpout.close()
1291	outlist.append(outfile)
1292	z.close()
1293	if multipleselect and len(outlist) >= 1:
1294	return outlist
1295	elif len(outlist) == 1:
1296	return outlist[0]
1297	else:
1298	return None
1299
1300	######################################################################
1301	# base classes for reading various types of data files
1302	# not used directly, only by subclassing
1303	######################################################################
1304	try:
1305	E,SGData = G2spc.SpcGroup('P 1') # data structure for default space group
1306	except: # errors on doc build
1307	SGData = None
1308	P1SGData = SGData
1309	######################################################################
1310	class ImportBaseclass(object):
1311	'''Defines a base class for the reading of input files (diffraction
1312	data, coordinates,...). See :ref:`Writing a Import Routine<Import_routines>`
1313	for an explanation on how to use a subclass of this class.
1314	'''
1315	class ImportException(Exception):
1316	'''Defines an Exception that is used when an import routine hits an expected error,
1317	usually in .Reader.
1318
1319	Good practice is that the Reader should define a value in self.errors that
1320	tells the user some information about what is wrong with their file.
1321	'''
1322	pass
1323
1324	UseReader = True # in __init__ set value of self.UseReader to False to skip use of current importer
1325	def __init__(self,formatName,longFormatName=None,
1326	extensionlist=[],strictExtension=False,):
1327	self.formatName = formatName # short string naming file type
1328	if longFormatName: # longer string naming file type
1329	self.longFormatName = longFormatName
1330	else:
1331	self.longFormatName = formatName
1332	# define extensions that are allowed for the file type
1333	# for windows, remove any extensions that are duplicate, as case is ignored
1334	if sys.platform == 'windows' and extensionlist:
1335	extensionlist = list(set([s.lower() for s in extensionlist]))
1336	self.extensionlist = extensionlist
1337	# If strictExtension is True, the file will not be read, unless
1338	# the extension matches one in the extensionlist
1339	self.strictExtension = strictExtension
1340	self.errors = ''
1341	self.warnings = ''
1342	# used for readers that will use multiple passes to read
1343	# more than one data block
1344	self.repeat = False
1345	self.selections = []
1346	self.repeatcount = 0
1347	self.readfilename = '?'
1348	#print 'created',self.__class__
1349
1350	def ReInitialize(self):
1351	'Reinitialize the Reader to initial settings'
1352	self.errors = ''
1353	self.warnings = ''
1354	self.repeat = False
1355	self.repeatcount = 0
1356	self.readfilename = '?'
1357
1358	def BlockSelector(self, ChoiceList, ParentFrame=None,title='Select a block',
1359	size=None, header='Block Selector',useCancel=True):
1360	''' Provide a wx dialog to select a block if the file contains more
1361	than one set of data and one must be selected
1362	'''
1363	if useCancel:
1364	dlg = wx.SingleChoiceDialog(
1365	ParentFrame,title, header,ChoiceList)
1366	else:
1367	dlg = wx.SingleChoiceDialog(
1368	ParentFrame,title, header,ChoiceList,
1369	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.OK\|wx.CENTRE)
1370	if size: dlg.SetSize(size)
1371	dlg.CenterOnParent()
1372	if dlg.ShowModal() == wx.ID_OK:
1373	sel = dlg.GetSelection()
1374	return sel
1375	else:
1376	return None
1377	dlg.Destroy()
1378
1379	def MultipleBlockSelector(self, ChoiceList, ParentFrame=None,
1380	title='Select a block',size=None, header='Block Selector'):
1381	'''Provide a wx dialog to select a block of data if the
1382	file contains more than one set of data and one must be
1383	selected.
1384
1385	:returns: a list of the selected blocks
1386	'''
1387	dlg = wx.MultiChoiceDialog(ParentFrame,title, header,ChoiceList+['Select all'],
1388	wx.CHOICEDLG_STYLE)
1389	dlg.CenterOnScreen()
1390	if size: dlg.SetSize(size)
1391	if dlg.ShowModal() == wx.ID_OK:
1392	sel = dlg.GetSelections()
1393	else:
1394	return []
1395	dlg.Destroy()
1396	selected = []
1397	if len(ChoiceList) in sel:
1398	return range(len(ChoiceList))
1399	else:
1400	return sel
1401	return selected
1402
1403	def MultipleChoicesDialog(self, choicelist, headinglist, ParentFrame=None, **kwargs):
1404	'''A modal dialog that offers a series of choices, each with a title and a wx.Choice
1405	widget. Typical input:
1406
1407	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1408
1409	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1410
1411	optional keyword parameters are: head (window title) and title
1412	returns a list of selected indicies for each choice (or None)
1413	'''
1414	result = None
1415	dlg = MultipleChoicesDialog(choicelist,headinglist,
1416	parent=ParentFrame, **kwargs)
1417	dlg.CenterOnParent()
1418	if dlg.ShowModal() == wx.ID_OK:
1419	result = dlg.chosen
1420	dlg.Destroy()
1421	return result
1422
1423	def ShowBusy(self):
1424	wx.BeginBusyCursor()
1425	# wx.Yield() # make it happen now!
1426
1427	def DoneBusy(self):
1428	wx.EndBusyCursor()
1429	wx.Yield() # make it happen now!
1430
1431	# def Reader(self, filename, filepointer, ParentFrame=None, **unused):
1432	# '''This method must be supplied in the child class to read the file.
1433	# if the read fails either return False or raise an Exception
1434	# preferably of type ImportException.
1435	# '''
1436	# #start reading
1437	# raise ImportException("Error occurred while...")
1438	# self.errors += "Hint for user on why the error occur
1439	# return False # if an error occurs
1440	# return True # if read OK
1441
1442	def ExtensionValidator(self, filename):
1443	'''This methods checks if the file has the correct extension
1444	Return False if this filename will not be supported by this reader
1445	Return True if the extension matches the list supplied by the reader
1446	Return None if the reader allows un-registered extensions
1447	'''
1448	if filename:
1449	ext = os.path.splitext(filename)[1]
1450	if sys.platform == 'windows': ext = ext.lower()
1451	if ext in self.extensionlist: return True
1452	if self.strictExtension: return False
1453	return None
1454
1455	def ContentsValidator(self, filepointer):
1456	'''This routine will attempt to determine if the file can be read
1457	with the current format.
1458	This will typically be overridden with a method that
1459	takes a quick scan of [some of]
1460	the file contents to do a "sanity" check if the file
1461	appears to match the selected format.
1462	Expected to be called via self.Validator()
1463	'''
1464	#filepointer.seek(0) # rewind the file pointer
1465	return True
1466
1467	def CIFValidator(self, filepointer):
1468	'''A :meth:`ContentsValidator` for use to validate CIF files.
1469	'''
1470	for i,l in enumerate(filepointer):
1471	if i >= 1000: return True
1472	'''Encountered only blank lines or comments in first 1000
1473	lines. This is unlikely, but assume it is CIF anyway, since we are
1474	even less likely to find a file with nothing but hashes and
1475	blank lines'''
1476	line = l.strip()
1477	if len(line) == 0: # ignore blank lines
1478	continue
1479	elif line.startswith('#'): # ignore comments
1480	continue
1481	elif line.startswith('data_'): # on the right track, accept this file
1482	return True
1483	else: # found something invalid
1484	self.errors = 'line '+str(i+1)+' contains unexpected data:\n'
1485	if all([ord(c) < 128 and ord(c) != 0 for c in str(l)]): # show only if ASCII
1486	self.errors += ' '+str(l)
1487	else:
1488	self.errors += ' (binary)'
1489	self.errors += '\n Note: a CIF should only have blank lines or comments before'
1490	self.errors += '\n a data_ statement begins a block.'
1491	return False
1492
1493	######################################################################
1494	class ImportPhase(ImportBaseclass):
1495	'''Defines a base class for the reading of files with coordinates
1496
1497	Objects constructed that subclass this (in import/G2phase_*.py etc.) will be used
1498	in :meth:`GSASII.GSASII.OnImportPhase`.
1499	See :ref:`Writing a Import Routine<Import_Routines>`
1500	for an explanation on how to use this class.
1501
1502	'''
1503	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1504	strictExtension=False,):
1505	# call parent __init__
1506	ImportBaseclass.__init__(self,formatName,longFormatName,
1507	extensionlist,strictExtension)
1508	self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
1509	self.Constraints = None
1510
1511	def PhaseSelector(self, ChoiceList, ParentFrame=None,
1512	title='Select a phase', size=None,header='Phase Selector'):
1513	''' Provide a wx dialog to select a phase if the file contains more
1514	than one phase
1515	'''
1516	return self.BlockSelector(ChoiceList,ParentFrame,title,
1517	size,header)
1518
1519	######################################################################
1520	class ImportStructFactor(ImportBaseclass):
1521	'''Defines a base class for the reading of files with tables
1522	of structure factors.
1523
1524	Structure factors are read with a call to :meth:`GSASII.GSASII.OnImportSfact`
1525	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`, which calls
1526	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1527	:meth:`Reader`.
1528
1529	See :ref:`Writing a Import Routine<Import_Routines>`
1530	for an explanation on how to use import classes in general. The specifics
1531	for reading a structure factor histogram require that
1532	the ``Reader()`` routine in the import
1533	class need to do only a few things: It
1534	should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
1535	and set :attr:`Parameters` with the instrument parameters
1536	(initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
1537	'''
1538	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1539	strictExtension=False,):
1540	ImportBaseclass.__init__(self,formatName,longFormatName,
1541	extensionlist,strictExtension)
1542
1543	# define contents of Structure Factor entry
1544	self.Parameters = []
1545	'self.Parameters is a list with two dicts for data parameter settings'
1546	self.InitParameters()
1547	self.RefDict = {'RefList':[],'FF':{},'Super':0}
1548	self.Banks = [] #for multi bank data (usually TOF)
1549	'''self.RefDict is a dict containing the reflection information, as read from the file.
1550	Item 'RefList' contains the reflection information. See the
1551	:ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
1552	for the contents of each row. Dict element 'FF'
1553	contains the form factor values for each element type; if this entry
1554	is left as initialized (an empty list) it will be initialized as needed later.
1555	'''
1556	def ReInitialize(self):
1557	'Reinitialize the Reader to initial settings'
1558	ImportBaseclass.ReInitialize(self)
1559	self.InitParameters()
1560	self.Banks = [] #for multi bank data (usually TOF)
1561	self.RefDict = {'RefList':[],'FF':{},'Super':0}
1562
1563	def InitParameters(self):
1564	'initialize the instrument parameters structure'
1565	Lambda = 0.70926
1566	HistType = 'SXC'
1567	self.Parameters = [{'Type':[HistType,HistType], # create the structure
1568	'Lam':[Lambda,Lambda]
1569	}, {}]
1570	'Parameters is a list with two dicts for data parameter settings'
1571
1572	def UpdateParameters(self,Type=None,Wave=None):
1573	'Revise the instrument parameters'
1574	if Type is not None:
1575	self.Parameters[0]['Type'] = [Type,Type]
1576	if Wave is not None:
1577	self.Parameters[0]['Lam'] = [Wave,Wave]
1578
1579	######################################################################
1580	class ImportPowderData(ImportBaseclass):
1581	'''Defines a base class for the reading of files with powder data.
1582
1583	Objects constructed that subclass this (in import/G2pwd_*.py etc.) will be used
1584	in :meth:`GSASII.GSASII.OnImportPowder`.
1585	See :ref:`Writing a Import Routine<Import_Routines>`
1586	for an explanation on how to use this class.
1587	'''
1588	def __init__(self,formatName,longFormatName=None,
1589	extensionlist=[],strictExtension=False,):
1590	ImportBaseclass.__init__(self,formatName,longFormatName,
1591	extensionlist,strictExtension)
1592	self.clockWd = None # used in TOF
1593	self.ReInitialize()
1594
1595	def ReInitialize(self):
1596	'Reinitialize the Reader to initial settings'
1597	ImportBaseclass.ReInitialize(self)
1598	self.powderentry = ['',None,None] # (filename,Pos,Bank)
1599	self.powderdata = [] # Powder dataset
1600	'''A powder data set is a list with items [x,y,w,yc,yb,yd]:
1601	np.array(x), # x-axis values
1602	np.array(y), # powder pattern intensities
1603	np.array(w), # 1/sig(intensity)^2 values (weights)
1604	np.array(yc), # calc. intensities (zero)
1605	np.array(yb), # calc. background (zero)
1606	np.array(yd), # obs-calc profiles
1607	'''
1608	self.comments = []
1609	self.idstring = ''
1610	self.Sample = G2pdG.SetDefaultSample() # default sample parameters
1611	self.Controls = {} # items to be placed in top-level Controls
1612	self.GSAS = None # used in TOF
1613	self.repeat_instparm = True # Should a parm file be
1614	# used for multiple histograms?
1615	self.instparm = None # name hint from file of instparm to use
1616	self.instfile = '' # full path name to instrument parameter file
1617	self.instbank = '' # inst parm bank number
1618	self.instmsg = '' # a label that gets printed to show
1619	# where instrument parameters are from
1620	self.numbanks = 1
1621	self.instdict = {} # place items here that will be transferred to the instrument parameters
1622	self.pwdparms = {} # place parameters that are transferred directly to the tree
1623	# here (typically from an existing GPX file)
1624	######################################################################
1625	class ImportSmallAngleData(ImportBaseclass):
1626	'''Defines a base class for the reading of files with small angle data.
1627	See :ref:`Writing a Import Routine<Import_Routines>`
1628	for an explanation on how to use this class.
1629	'''
1630	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1631	strictExtension=False,):
1632
1633	ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
1634	strictExtension)
1635	self.ReInitialize()
1636
1637	def ReInitialize(self):
1638	'Reinitialize the Reader to initial settings'
1639	ImportBaseclass.ReInitialize(self)
1640	self.smallangleentry = ['',None,None] # (filename,Pos,Bank)
1641	self.smallangledata = [] # SASD dataset
1642	'''A small angle data set is a list with items [x,y,w,yc,yd]:
1643	np.array(x), # x-axis values
1644	np.array(y), # powder pattern intensities
1645	np.array(w), # 1/sig(intensity)^2 values (weights)
1646	np.array(yc), # calc. intensities (zero)
1647	np.array(yd), # obs-calc profiles
1648	np.array(yb), # preset bkg
1649	'''
1650	self.comments = []
1651	self.idstring = ''
1652	self.Sample = G2pdG.SetDefaultSample()
1653	self.GSAS = None # used in TOF
1654	self.clockWd = None # used in TOF
1655	self.numbanks = 1
1656	self.instdict = {} # place items here that will be transferred to the instrument parameters
1657
1658	######################################################################
1659	class ImportImage(ImportBaseclass):
1660	'''Defines a base class for the reading of images
1661
1662	Images are read in only these places:
1663
1664	* Initial reading is typically done from a menu item
1665	with a call to :meth:`GSASII.GSASII.OnImportImage`
1666	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`. That calls
1667	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1668	:meth:`Reader`. This returns a list of reader objects for each read image.
1669
1670	* Images are read alternatively in :func:`GSASIIIO.ReadImages`, which puts image info
1671	directly into the data tree.
1672
1673	* Images are reloaded with :func:`GSASIIIO.GetImageData`.
1674
1675	.. _Image_import_routines:
1676
1677	When reading an image, the ``Reader()`` routine in the ImportImage class
1678	should set:
1679
1680	* :attr:`Comments`: a list of strings (str),
1681	* :attr:`Npix`: the number of pixels in the image (int),
1682	* :attr:`Image`: the actual image as a numpy array (np.array)
1683	* :attr:`Data`: a dict defining image parameters (dict). Within this dict the following
1684	data items are needed:
1685
1686	* 'pixelSize': size of each pixel in microns (such as ``[200,200]``.
1687	* 'wavelength': wavelength in Angstoms.
1688	* 'distance': distance of detector from sample in cm.
1689	* 'center': uncalibrated center of beam on detector (such as ``[204.8,204.8]``.
1690	* 'size': size of image (such as ``[2048,2048]``).
1691	* 'ImageTag': image number or other keyword used to retrieve image from
1692	a multi-image data file (defaults to ``1`` if not specified).
1693	* 'sumfile': holds sum image file name if a sum was produced from a multi image file
1694
1695	optional data items:
1696
1697	* :attr:`repeat`: set to True if there are additional images to
1698	read in the file, False otherwise
1699	* :attr:`repeatcount`: set to the number of the image.
1700
1701	Note that the above is initialized with :meth:`InitParameters`.
1702	(Also see :ref:`Writing a Import Routine<Import_Routines>`
1703	for an explanation on how to use import classes in general.)
1704	'''
1705	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1706	strictExtension=False,):
1707	ImportBaseclass.__init__(self,formatName,longFormatName,
1708	extensionlist,strictExtension)
1709	self.InitParameters()
1710
1711	def ReInitialize(self):
1712	'Reinitialize the Reader to initial settings -- not used at present'
1713	ImportBaseclass.ReInitialize(self)
1714	self.InitParameters()
1715
1716	def InitParameters(self):
1717	'initialize the instrument parameters structure'
1718	self.Comments = ['No comments']
1719	self.Data = {}
1720	self.Npix = 0
1721	self.Image = None
1722	self.repeat = False
1723	self.repeatcount = 1
1724	self.sumfile = ''
1725
1726	def LoadImage(self,ParentFrame,imagefile,imagetag=None):
1727	'''Optionally, call this after reading in an image to load it into the tree.
1728	This saves time by preventing a reread of the same information.
1729	'''
1730	if ParentFrame:
1731	ParentFrame.ImageZ = self.Image # store the image for plotting
1732	ParentFrame.oldImagefile = imagefile # save the name of the last image file read
1733	ParentFrame.oldImageTag = imagetag # save the tag of the last image file read
1734
1735	######################################################################
1736	def striphist(var,insChar=''):
1737	'strip a histogram number from a var name'
1738	sv = var.split(':')
1739	if len(sv) <= 1: return var
1740	if sv[1]:
1741	sv[1] = insChar
1742	return ':'.join(sv)
1743	class ExportBaseclass(object):
1744	'''Defines a base class for the exporting of GSAS-II results.
1745
1746	This class is subclassed in the various exports/G2export_*.py files. Those files
1747	are imported in :meth:`GSASII.GSASII._init_Exports` which defines the
1748	appropriate menu items for each one and the .Exporter method is called
1749	directly from the menu item.
1750
1751	Routines may also define a .Writer method, which is used to write a single
1752	file without invoking any GUI objects.
1753	'''
1754	def __init__(self,G2frame,formatName,extension,longFormatName=None,):
1755	self.G2frame = G2frame
1756	self.formatName = formatName # short string naming file type
1757	self.extension = extension
1758	if longFormatName: # longer string naming file type
1759	self.longFormatName = longFormatName
1760	else:
1761	self.longFormatName = formatName
1762	self.OverallParms = {}
1763	self.Phases = {}
1764	self.Histograms = {}
1765	self.powderDict = {}
1766	self.xtalDict = {}
1767	self.parmDict = {}
1768	self.sigDict = {}
1769	# updated in InitExport:
1770	self.currentExportType = None # type of export that has been requested
1771	# updated in ExportSelect (when used):
1772	self.phasenam = None # a list of selected phases
1773	self.histnam = None # a list of selected histograms
1774	self.filename = None # name of file to be written (single export) or template (multiple files)
1775	self.dirname = '' # name of directory where file(s) will be written
1776	self.fullpath = '' # name of file being written -- full path
1777
1778	# items that should be defined in a subclass of this class
1779	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1780	# The following types are defined: 'project', "phase", "powder", "single"
1781	self.multiple = False # set as True if the class can export multiple phases or histograms
1782	# self.multiple is ignored for "project" exports
1783
1784	def InitExport(self,event):
1785	'''Determines the type of menu that called the Exporter and
1786	misc initialization.
1787	'''
1788	self.filename = None # name of file to be written (single export)
1789	self.dirname = '' # name of file to be written (multiple export)
1790	if event:
1791	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1792
1793	def MakePWDRfilename(self,hist):
1794	'''Make a filename root (no extension) from a PWDR histogram name
1795
1796	:param str hist: the histogram name in data tree (starts with "PWDR ")
1797	'''
1798	file0 = ''
1799	file1 = hist[5:]
1800	# replace repeated blanks
1801	while file1 != file0:
1802	file0 = file1
1803	file1 = file0.replace(' ',' ').strip()
1804	file0 = file1.replace('Azm= ','A')
1805	# if angle has unneeded decimal places on aziumuth, remove them
1806	if file0[-3:] == '.00': file0 = file0[:-3]
1807	file0 = file0.replace('.','_')
1808	file0 = file0.replace(' ','_')
1809	return file0
1810
1811	def ExportSelect(self,AskFile='ask'):
1812	'''Selects histograms or phases when needed. Sets a default file name when
1813	requested into self.filename; always sets a default directory in self.dirname.
1814
1815	:param bool AskFile: Determines how this routine processes getting a
1816	location to store the current export(s).
1817
1818	* if AskFile is 'ask' (default option), get the name of the file to be written;
1819	self.filename and self.dirname are always set. In the case where
1820	multiple files must be generated, the export routine should do this
1821	based on self.filename as a template.
1822	* if AskFile is 'dir', get the name of the directory to be used;
1823	self.filename is not used, but self.dirname is always set. The export routine
1824	will always generate the file name.
1825	* if AskFile is 'single', get only the name of the directory to be used when
1826	multiple items will be written (as multiple files) are used
1827	or a complete file name is requested when a single file
1828	name is selected. self.dirname is always set and self.filename used
1829	only when a single file is selected.
1830	* if AskFile is 'default', creates a name of the file to be used from
1831	the name of the project (.gpx) file. If the project has not been saved,
1832	then the name of file is requested.
1833	self.filename and self.dirname are always set. In the case where
1834	multiple file names must be generated, the export routine should do this
1835	based on self.filename.
1836	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1837	file. If the project has not been saved, then a directory is requested.
1838	self.filename is not used.
1839
1840	:returns: True in case of an error
1841	'''
1842
1843	numselected = 1
1844	if self.currentExportType == 'phase':
1845	if len(self.Phases) == 0:
1846	self.G2frame.ErrorDialog(
1847	'Empty project',
1848	'Project does not contain any phases.')
1849	return True
1850	elif len(self.Phases) == 1:
1851	self.phasenam = self.Phases.keys()
1852	elif self.multiple:
1853	choices = sorted(self.Phases.keys())
1854	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1855	if phasenum is None: return True
1856	self.phasenam = [choices[i] for i in phasenum]
1857	if not self.phasenam: return True
1858	numselected = len(self.phasenam)
1859	else:
1860	choices = sorted(self.Phases.keys())
1861	phasenum = G2G.ItemSelector(choices,self.G2frame)
1862	if phasenum is None: return True
1863	self.phasenam = [choices[phasenum]]
1864	numselected = len(self.phasenam)
1865	elif self.currentExportType == 'single':
1866	if len(self.xtalDict) == 0:
1867	self.G2frame.ErrorDialog(
1868	'Empty project',
1869	'Project does not contain any single crystal data.')
1870	return True
1871	elif len(self.xtalDict) == 1:
1872	self.histnam = self.xtalDict.values()
1873	elif self.multiple:
1874	choices = sorted(self.xtalDict.values())
1875	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1876	if not hnum: return True
1877	self.histnam = [choices[i] for i in hnum]
1878	numselected = len(self.histnam)
1879	else:
1880	choices = sorted(self.xtalDict.values())
1881	hnum = G2G.ItemSelector(choices,self.G2frame)
1882	if hnum is None: return True
1883	self.histnam = [choices[hnum]]
1884	numselected = len(self.histnam)
1885	elif self.currentExportType == 'powder':
1886	if len(self.powderDict) == 0:
1887	self.G2frame.ErrorDialog(
1888	'Empty project',
1889	'Project does not contain any powder data.')
1890	return True
1891	elif len(self.powderDict) == 1:
1892	self.histnam = self.powderDict.values()
1893	elif self.multiple:
1894	choices = sorted(self.powderDict.values())
1895	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1896	if not hnum: return True
1897	self.histnam = [choices[i] for i in hnum]
1898	numselected = len(self.histnam)
1899	else:
1900	choices = sorted(self.powderDict.values())
1901	hnum = G2G.ItemSelector(choices,self.G2frame)
1902	if hnum is None: return True
1903	self.histnam = [choices[hnum]]
1904	numselected = len(self.histnam)
1905	elif self.currentExportType == 'image':
1906	if len(self.Histograms) == 0:
1907	self.G2frame.ErrorDialog(
1908	'Empty project',
1909	'Project does not contain any images.')
1910	return True
1911	elif len(self.Histograms) == 1:
1912	self.histnam = self.Histograms.keys()
1913	else:
1914	choices = sorted(self.Histograms.keys())
1915	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1916	if self.multiple:
1917	if not hnum: return True
1918	self.histnam = [choices[i] for i in hnum]
1919	else:
1920	if hnum is None: return True
1921	self.histnam = [choices[hnum]]
1922	numselected = len(self.histnam)
1923	if self.currentExportType == 'map':
1924	# search for phases with maps
1925	mapPhases = []
1926	choices = []
1927	for phasenam in sorted(self.Phases):
1928	phasedict = self.Phases[phasenam] # pointer to current phase info
1929	if len(phasedict['General']['Map'].get('rho',[])):
1930	mapPhases.append(phasenam)
1931	if phasedict['General']['Map'].get('Flip'):
1932	choices.append('Charge flip map: '+str(phasenam))
1933	elif phasedict['General']['Map'].get('MapType'):
1934	choices.append(
1935	str(phasedict['General']['Map'].get('MapType'))
1936	+ ' map: ' + str(phasenam))
1937	else:
1938	choices.append('unknown map: '+str(phasenam))
1939	# select a map if needed
1940	if len(mapPhases) == 0:
1941	self.G2frame.ErrorDialog(
1942	'Empty project',
1943	'Project does not contain any maps.')
1944	return True
1945	elif len(mapPhases) == 1:
1946	self.phasenam = mapPhases
1947	else:
1948	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1949	if self.multiple:
1950	if not phasenum: return True
1951	self.phasenam = [mapPhases[i] for i in phasenum]
1952	else:
1953	if phasenum is None: return True
1954	self.phasenam = [mapPhases[phasenum]]
1955	numselected = len(self.phasenam)
1956
1957	# items selected, now set self.dirname and usually self.filename
1958	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
1959	AskFile == 'default' and not self.G2frame.GSASprojectfile
1960	):
1961	filename = self.askSaveFile()
1962	if not filename: return True
1963	self.dirname,self.filename = os.path.split(filename)
1964	elif AskFile == 'dir' or AskFile == 'single' or (
1965	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
1966	):
1967	self.dirname = self.askSaveDirectory()
1968	if not self.dirname: return True
1969	elif AskFile == 'default-dir' or AskFile == 'default':
1970	self.dirname,self.filename = os.path.split(
1971	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
1972	)
1973	else:
1974	raise Exception('This should not happen!')
1975
1976	def loadParmDict(self):
1977	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
1978	refined values to those from the last cycle and set the uncertainties for the
1979	refined parameters in another dict (self.sigDict).
1980
1981	Expands the parm & sig dicts to include values derived from constraints.
1982	'''
1983	self.parmDict = {}
1984	self.sigDict = {}
1985	rigidbodyDict = {}
1986	covDict = {}
1987	consDict = {}
1988	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1989	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
1990	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
1991	while item:
1992	name = self.G2frame.PatternTree.GetItemText(item)
1993	if name == 'Rigid bodies':
1994	rigidbodyDict = self.G2frame.PatternTree.GetItemPyData(item)
1995	elif name == 'Covariance':
1996	covDict = self.G2frame.PatternTree.GetItemPyData(item)
1997	elif name == 'Constraints':
1998	consDict = self.G2frame.PatternTree.GetItemPyData(item)
1999	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2000	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
2001	self.parmDict.update(rbDict)
2002	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
2003	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData(
2004	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
2005	self.parmDict.update(phaseDict)
2006	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
2007	Phases,Histograms,Print=False,resetRefList=False)
2008	self.parmDict.update(hapDict)
2009	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
2010	self.parmDict.update(histDict)
2011	self.parmDict.update(zip(
2012	covDict.get('varyList',[]),
2013	covDict.get('variables',[])))
2014	self.sigDict = dict(zip(
2015	covDict.get('varyList',[]),
2016	covDict.get('sig',[])))
2017	# expand to include constraints: first compile a list of constraints
2018	constList = []
2019	for item in consDict:
2020	if item.startswith('_'): continue
2021	constList += consDict[item]
2022	# now process the constraints
2023	G2mv.InitVars()
2024	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
2025	varyList = covDict.get('varyListStart')
2026	if varyList is None and len(constDict) == 0:
2027	# no constraints can use varyList
2028	varyList = covDict.get('varyList')
2029	elif varyList is None:
2030	# old GPX file from before pre-constraint varyList is saved
2031	print ' * Old refinement: Please use Calculate/Refine to redo *'
2032	raise Exception(' * Export aborted *')
2033	else:
2034	varyList = list(varyList)
2035	try:
2036	groups,parmlist = G2mv.GroupConstraints(constDict)
2037	G2mv.GenerateConstraints(groups,parmlist,varyList,constDict,fixedList,self.parmDict)
2038	except:
2039	# this really should not happen
2040	print ' * ERROR - constraints are internally inconsistent *'
2041	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
2042	print 'Errors',errmsg
2043	if warnmsg: print 'Warnings',warnmsg
2044	raise Exception(' * CIF creation aborted *')
2045	# add the constrained values to the parameter dictionary
2046	G2mv.Dict2Map(self.parmDict,varyList)
2047	# and add their uncertainties into the esd dictionary (sigDict)
2048	if covDict.get('covMatrix') is not None:
2049	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
2050
2051	def loadTree(self):
2052	'''Load the contents of the data tree into a set of dicts
2053	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
2054	& self.xtalDict)
2055
2056	* The childrenless data tree items are overall parameters/controls for the
2057	entire project and are placed in self.OverallParms
2058	* Phase items are placed in self.Phases
2059	* Data items are placed in self.Histogram. The key for these data items
2060	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
2061	'''
2062	self.OverallParms = {}
2063	self.powderDict = {}
2064	self.xtalDict = {}
2065	self.Phases = {}
2066	self.Histograms = {}
2067	self.SeqRefdata = None
2068	self.SeqRefhist = None
2069	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2070	histType = None
2071	if self.currentExportType == 'phase':
2072	# if exporting phases load them here
2073	sub = G2gd.GetPatternTreeItemId(self.G2frame,self.G2frame.root,'Phases')
2074	if not sub:
2075	print 'no phases found'
2076	return True
2077	item, cookie = self.G2frame.PatternTree.GetFirstChild(sub)
2078	while item:
2079	phaseName = self.G2frame.PatternTree.GetItemText(item)
2080	self.Phases[phaseName] = self.G2frame.PatternTree.GetItemPyData(item)
2081	item, cookie = self.G2frame.PatternTree.GetNextChild(sub, cookie)
2082	return
2083	elif self.currentExportType == 'single':
2084	histType = 'HKLF'
2085	elif self.currentExportType == 'powder':
2086	histType = 'PWDR'
2087	elif self.currentExportType == 'image':
2088	histType = 'IMG'
2089
2090	if histType: # Loading just one kind of tree entry
2091	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2092	while item:
2093	name = self.G2frame.PatternTree.GetItemText(item)
2094	if name.startswith(histType):
2095	if self.Histograms.get(name): # there is already an item with this name
2096	print('Histogram name '+str(name)+' is repeated. Renaming')
2097	if name[-1] == '9':
2098	name = name[:-1] + '10'
2099	elif name[-1] in '012345678':
2100	name = name[:-1] + str(int(name[-1])+1)
2101	else:
2102	name += '-1'
2103	self.Histograms[name] = {}
2104	# the main info goes into Data, but the 0th
2105	# element contains refinement results, carry
2106	# that over too now.
2107	self.Histograms[name]['Data'] = self.G2frame.PatternTree.GetItemPyData(item)[1]
2108	self.Histograms[name][0] = self.G2frame.PatternTree.GetItemPyData(item)[0]
2109	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2110	while item2:
2111	child = self.G2frame.PatternTree.GetItemText(item2)
2112	self.Histograms[name][child] = self.G2frame.PatternTree.GetItemPyData(item2)
2113	item2, cookie2 = self.G2frame.PatternTree.GetNextChild(item, cookie2)
2114	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2115	# index powder and single crystal histograms by number
2116	for hist in self.Histograms:
2117	if hist.startswith("PWDR"):
2118	d = self.powderDict
2119	elif hist.startswith("HKLF"):
2120	d = self.xtalDict
2121	else:
2122	return
2123	i = self.Histograms[hist].get('hId')
2124	if i is None and not d.keys():
2125	i = 0
2126	elif i is None or i in d.keys():
2127	i = max(d.keys())+1
2128	d[i] = hist
2129	return
2130	# else standard load: using all interlinked phases and histograms
2131	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2132	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2133	while item:
2134	name = self.G2frame.PatternTree.GetItemText(item)
2135	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2136	if not item2:
2137	self.OverallParms[name] = self.G2frame.PatternTree.GetItemPyData(item)
2138	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2139	# index powder and single crystal histograms
2140	for hist in self.Histograms:
2141	i = self.Histograms[hist]['hId']
2142	if hist.startswith("PWDR"):
2143	self.powderDict[i] = hist
2144	elif hist.startswith("HKLF"):
2145	self.xtalDict[i] = hist
2146
2147	def dumpTree(self,mode='type'):
2148	'''Print out information on the data tree dicts loaded in loadTree.
2149	Used for testing only.
2150	'''
2151	if self.SeqRefdata and self.SeqRefhist:
2152	print('Note that dumpTree does not show sequential results')
2153	print '\nOverall'
2154	if mode == 'type':
2155	def Show(arg): return type(arg)
2156	else:
2157	def Show(arg): return arg
2158	for key in self.OverallParms:
2159	print ' ',key,Show(self.OverallParms[key])
2160	print 'Phases'
2161	for key1 in self.Phases:
2162	print ' ',key1,Show(self.Phases[key1])
2163	print 'Histogram'
2164	for key1 in self.Histograms:
2165	print ' ',key1,Show(self.Histograms[key1])
2166	for key2 in self.Histograms[key1]:
2167	print ' ',key2,Show(self.Histograms[key1][key2])
2168
2169	def defaultSaveFile(self):
2170	return os.path.abspath(
2171	os.path.splitext(self.G2frame.GSASprojectfile
2172	)[0]+self.extension)
2173
2174	def askSaveFile(self):
2175	'''Ask the user to supply a file name
2176
2177	:returns: a file name (str) or None if Cancel is pressed
2178	'''
2179
2180	pth = G2G.GetExportPath(self.G2frame)
2181	defnam = os.path.splitext(
2182	os.path.split(self.G2frame.GSASprojectfile)[1]
2183	)[0]+self.extension
2184	dlg = wx.FileDialog(
2185	self.G2frame, 'Input name for file to write', pth, defnam,
2186	self.longFormatName+' ('+self.extension+')\|'+self.extension,
2187	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
2188	dlg.CenterOnParent()
2189	try:
2190	if dlg.ShowModal() == wx.ID_OK:
2191	filename = dlg.GetPath()
2192	self.G2frame.LastExportDir = os.path.split(filename)[0]
2193	filename = os.path.splitext(filename)[0]+self.extension # make sure extension is correct
2194	else:
2195	filename = None
2196	finally:
2197	dlg.Destroy()
2198	return filename
2199
2200	def askSaveDirectory(self):
2201	'''Ask the user to supply a directory name. Path name is used as the
2202	starting point for the next export path search.
2203
2204	:returns: a directory name (str) or None if Cancel is pressed
2205	'''
2206	pth = G2G.GetExportPath(self.G2frame)
2207	dlg = wx.DirDialog(
2208	self.G2frame, 'Input directory where file(s) will be written', pth,
2209	wx.DD_DEFAULT_STYLE)
2210	dlg.CenterOnParent()
2211	try:
2212	if dlg.ShowModal() == wx.ID_OK:
2213	filename = dlg.GetPath()
2214	self.G2frame.LastExportDir = filename
2215	else:
2216	filename = None
2217	finally:
2218	dlg.Destroy()
2219	return filename
2220
2221	# Tools for file writing.
2222	def OpenFile(self,fil=None,mode='w'):
2223	'''Open the output file
2224
2225	:param str fil: The name of the file to open. If None (default)
2226	the name defaults to self.dirname + self.filename.
2227	If an extension is supplied, it is not overridded,
2228	but if not, the default extension is used.
2229	:returns: the file object opened by the routine which is also
2230	saved as self.fp
2231	'''
2232	if mode == 'd': # debug mode
2233	self.fullpath = '(stdout)'
2234	self.fp = sys.stdout
2235	return
2236	if not fil:
2237	if not os.path.splitext(self.filename)[1]:
2238	self.filename += self.extension
2239	fil = os.path.join(self.dirname,self.filename)
2240	self.fullpath = os.path.abspath(fil)
2241	self.fp = open(self.fullpath,mode)
2242	return self.fp
2243
2244	def Write(self,line):
2245	'''write a line of output, attaching a line-end character
2246
2247	:param str line: the text to be written.
2248	'''
2249	self.fp.write(line+'\n')
2250
2251	def CloseFile(self,fp=None):
2252	'''Close a file opened in OpenFile
2253
2254	:param file fp: the file object to be closed. If None (default)
2255	file object self.fp is closed.
2256	'''
2257	if self.fp == sys.stdout: return # debug mode
2258	if fp is None:
2259	fp = self.fp
2260	self.fp = None
2261	fp.close()
2262
2263	def SetSeqRef(self,data,hist):
2264	'''Set the exporter to retrieve results from a sequential refinement
2265	rather than the main tree
2266	'''
2267	self.SeqRefdata = data
2268	self.SeqRefhist = hist
2269	data_name = data[hist]
2270	for i,val in zip(data_name['varyList'],data_name['sig']):
2271	self.sigDict[i] = val
2272	self.sigDict[striphist(i)] = val
2273	for i in data_name['parmDict']:
2274	self.parmDict[striphist(i)] = data_name['parmDict'][i]
2275	self.parmDict[i] = data_name['parmDict'][i]
2276	# zero out the dA[xyz] terms, they would only bring confusion
2277	key = i.split(':')
2278	if len(key) < 3: continue
2279	if key[2].startswith('dA'):
2280	self.parmDict[i] = 0.0
2281	for i,(val,sig) in data_name.get('depParmDict',{}).iteritems():
2282	self.parmDict[i] = val
2283	self.sigDict[i] = sig
2284	#GSASIIpath.IPyBreak()
2285
2286	# Tools to pull information out of the data arrays
2287	def GetCell(self,phasenam):
2288	"""Gets the unit cell parameters and their s.u.'s for a selected phase
2289
2290	:param str phasenam: the name for the selected phase
2291	:returns: `cellList,cellSig` where each is a 7 element list corresponding
2292	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
2293	cell values and `cellSig` has their uncertainties.
2294	"""
2295	if self.SeqRefdata and self.SeqRefhist:
2296	return self.GetSeqCell(phasenam,self.SeqRefdata[self.SeqRefhist])
2297	phasedict = self.Phases[phasenam] # pointer to current phase info
2298	try:
2299	pfx = str(phasedict['pId'])+'::'
2300	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
2301	cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A,
2302	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
2303	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
2304	return cellList,cellSig
2305	except KeyError:
2306	cell = phasedict['General']['Cell'][1:]
2307	return cell,7*[0]
2308
2309	def GetSeqCell(self,phasenam,data_name):
2310	"""Gets the unit cell parameters and their s.u.'s for a selected phase
2311	and histogram in a sequential fit
2312
2313	:param str phasenam: the name for the selected phase
2314	:param dict data_name: the sequential refinement parameters for the selected histogram
2315	:returns: `cellList,cellSig` where each is a 7 element list corresponding
2316	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
2317	cell values and `cellSig` has their uncertainties.
2318	"""
2319	phasedict = self.Phases[phasenam]
2320	SGdata = phasedict['General']['SGData']
2321	pId = phasedict['pId']
2322	RecpCellTerms = G2lat.cell2A(phasedict['General']['Cell'][1:7])
2323	ESDlookup = {}
2324	Dlookup = {}
2325	varied = [striphist(i) for i in data_name['varyList']]
2326	for item,val in data_name['newCellDict'].iteritems():
2327	if item in varied:
2328	ESDlookup[val[0]] = item
2329	Dlookup[item] = val[0]
2330	A = RecpCellTerms[:]
2331	for i in range(6):
2332	var = str(pId)+'::A'+str(i)
2333	if var in ESDlookup:
2334	A[i] = data_name['newCellDict'][ESDlookup[var]][1] # override with refined value
2335	cellDict = dict(zip([str(pId)+'::A'+str(i) for i in range(6)],A))
2336	zeroDict = {i:0.0 for i in cellDict}
2337	A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata,cellDict,zeroDict)
2338	covData = {
2339	'varyList': [Dlookup.get(striphist(v),v) for v in data_name['varyList']],
2340	'covMatrix': data_name['covMatrix']
2341	}
2342	return list(G2lat.A2cell(A)) + [G2lat.calc_V(A)], G2stIO.getCellEsd(str(pId)+'::',SGdata,A,covData)
2343
2344	def GetAtoms(self,phasenam):
2345	"""Gets the atoms associated with a phase. Can be used with standard
2346	or macromolecular phases
2347
2348	:param str phasenam: the name for the selected phase
2349	:returns: a list of items for eac atom where each item is a list containing:
2350	label, typ, mult, xyz, and td, where
2351
2352	* label and typ are the atom label and the scattering factor type (str)
2353	* mult is the site multiplicity (int)
2354	* xyz is contains a list with four pairs of numbers:
2355	x, y, z and fractional occupancy and
2356	their standard uncertainty (or a negative value)
2357	* td is contains a list with either one or six pairs of numbers:
2358	if one number it is U\ :sub:`iso` and with six numbers it is
2359	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
2360	paired with their standard uncertainty (or a negative value)
2361	"""
2362	phasedict = self.Phases[phasenam] # pointer to current phase info
2363	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
2364	cfrac = cx+3
2365	fpfx = str(phasedict['pId'])+'::Afrac:'
2366	atomslist = []
2367	for i,at in enumerate(phasedict['Atoms']):
2368	if phasedict['General']['Type'] == 'macromolecular':
2369	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
2370	else:
2371	label = at[ct-1]
2372	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
2373	fsig = self.sigDict.get(fpfx+str(i),-0.009)
2374	mult = at[cs+1]
2375	typ = at[ct]
2376	xyz = []
2377	for j,v in enumerate(('x','y','z')):
2378	val = at[cx+j]
2379	pfx = str(phasedict['pId']) + '::A' + v + ':' + str(i)
2380	val = self.parmDict.get(pfx, val)
2381	dpfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
2382	sig = self.sigDict.get(dpfx,-0.000009)
2383	xyz.append((val,sig))
2384	xyz.append((fval,fsig))
2385	td = []
2386	if at[cia] == 'I':
2387	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
2388	val = self.parmDict.get(pfx,at[cia+1])
2389	sig = self.sigDict.get(pfx,-0.0009)
2390	td.append((val,sig))
2391	else:
2392	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
2393	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
2394	val = self.parmDict.get(pfx,at[cia+2+i])
2395	sig = self.sigDict.get(pfx,-0.0009)
2396	td.append((val,sig))
2397	atomslist.append((label,typ,mult,xyz,td))
2398	return atomslist
2399	######################################################################
2400	def ExportPowderList(G2frame):
2401	'''Returns a list of extensions supported by :func:`GSASIIIO:ExportPowder`
2402	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
2403
2404	:param wx.Frame G2frame: the GSAS-II main data tree window
2405	'''
2406	extList = []
2407	for obj in G2frame.exporterlist:
2408	if 'powder' in obj.exporttype:
2409	try:
2410	obj.Writer
2411	extList.append(obj.extension)
2412	except AttributeError:
2413	pass
2414	return extList
2415
2416	def ExportPowder(G2frame,TreeName,fileroot,extension):
2417	'''Writes a single powder histogram using the Export routines.
2418	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
2419
2420	:param wx.Frame G2frame: the GSAS-II main data tree window
2421	:param str TreeName: the name of the histogram (PWDR ...) in the data tree
2422	:param str fileroot: name for file to be written, extension ignored
2423	:param str extension: extension for file to be written (start with '.'). Must
2424	match a powder export routine that has a Writer object.
2425	'''
2426	filename = os.path.abspath(os.path.splitext(fileroot)[0]+extension)
2427	for obj in G2frame.exporterlist:
2428	if obj.extension == extension and 'powder' in obj.exporttype:
2429	obj.currentExportType = 'powder'
2430	obj.InitExport(None)
2431	obj.loadTree() # load all histograms in tree into dicts
2432	if TreeName not in obj.Histograms:
2433	raise Exception('Histogram not found: '+str(TreeName))
2434	try:
2435	obj.Writer
2436	except AttributeError:
2437	continue
2438	try:
2439	obj.Writer(TreeName,filename)
2440	return
2441	except Exception,err:
2442	print('Export Routine for '+extension+' failed.')
2443	print err
2444	else:
2445	print('No Export routine supports extension '+extension)
2446
2447	def ExportSequential(G2frame,data,obj,exporttype):
2448	'''
2449	Used to export from every phase/dataset in a sequential refinement using
2450	a .Writer method for either projects or phases. Prompts to select histograms
2451	and for phase exports, which phase(s).
2452
2453	:param wx.Frame G2frame: the GSAS-II main data tree window
2454	:param dict data: the sequential refinement data object
2455	:param str exporttype: indicates the type of export ('project' or 'phase')
2456	'''
2457	if len(data['histNames']) == 0:
2458	G2G.G2MessageBox(G2frame,'There are no sequential histograms','Warning')
2459	obj.InitExport(None)
2460	obj.loadTree()
2461	obj.loadParmDict()
2462	if len(data['histNames']) == 1:
2463	histlist = data['histNames']
2464	else:
2465	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select histograms to export from list',
2466	'Select histograms',data['histNames'])
2467	if dlg.ShowModal() == wx.ID_OK:
2468	histlist = [data['histNames'][l] for l in dlg.GetSelections()]
2469	dlg.Destroy()
2470	else:
2471	dlg.Destroy()
2472	return
2473	if exporttype == 'Phase':
2474	phaselist = obj.Phases.keys()
2475	if len(obj.Phases) == 0:
2476	G2G.G2MessageBox(G2frame,'There are no phases in sequential ref.','Warning')
2477	return
2478	elif len(obj.Phases) > 1:
2479	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select phases to export from list',
2480	'Select phases', phaselist)
2481	if dlg.ShowModal() == wx.ID_OK:
2482	phaselist = [phaselist[l] for l in dlg.GetSelections()]
2483	dlg.Destroy()
2484	else:
2485	dlg.Destroy()
2486	return
2487	filename = obj.askSaveFile()
2488	if not filename: return True
2489	obj.dirname,obj.filename = os.path.split(filename)
2490	print('Writing output to file '+str(obj.filename)+"...")
2491	mode = 'w'
2492	for p in phaselist:
2493	for h in histlist:
2494	obj.SetSeqRef(data,h)
2495	#GSASIIpath.IPyBreak()
2496	obj.Writer(h,phasenam=p,mode=mode)
2497	mode = 'a'
2498	print('...done')
2499	elif exporttype == 'Project':
2500	filename = obj.askSaveFile()
2501	if not filename: return True
2502	obj.dirname,obj.filename = os.path.split(filename)
2503	print('Writing output to file '+str(obj.filename)+"...")
2504	mode = 'w'
2505	for h in histlist:
2506	obj.SetSeqRef(data,h)
2507	obj.Writer(h,mode=mode)
2508	print('\t'+str(h)+' written')
2509	mode = 'a'
2510	print('...done')
2511
2512	def ReadDIFFaX(DIFFaXfile):
2513	print 'read ',DIFFaXfile
2514	Layer = {'Laue':'-1','Cell':[False,1.,1.,1.,90.,90.,90,1.],'Width':[[10.,10.],[False,False]],
2515	'Layers':[],'Stacking':[],'Transitions':[],'Toler':0.01,'AtInfo':{}}
2516	df = open(DIFFaXfile,'r')
2517	lines = df.readlines()
2518	df.close()
2519	struct = False
2520	Struct = []
2521	stack = False
2522	Stack = []
2523	trans = False
2524	Trans = []
2525	for diff in lines:
2526	diff = diff[:-1].lower()
2527	if '!' in diff:
2528	continue
2529	while '}' in diff: #strip comments
2530	iB = diff.index('{')
2531	iF = diff.index('}')+1
2532	if iB:
2533	diff = diff[:iB]
2534	else:
2535	diff = diff[iF:]
2536	if not diff:
2537	continue
2538	if diff.strip() == 'instrumental':
2539	continue
2540	if diff.strip() == 'structural':
2541	struct = True
2542	continue
2543	elif diff.strip() == 'stacking':
2544	struct = False
2545	stack = True
2546	continue
2547	elif diff.strip() == 'transitions':
2548	stack = False
2549	trans = True
2550	continue
2551	diff = diff.strip()
2552	if struct:
2553	if diff:
2554	Struct.append(diff)
2555	elif stack:
2556	if diff:
2557	Stack.append(diff)
2558	elif trans:
2559	if diff:
2560	Trans.append(diff)
2561
2562	#STRUCTURE records
2563	laueRec = Struct[1].split()
2564	Layer['Laue'] = laueRec[0]
2565	if Layer['Laue'] == 'unknown' and len(laueRec) > 1:
2566	Layer['Toler'] = float(laueRec[1]) #tolerance for 'unknown'?
2567	if Layer['Laue'] == '2/m(1)': Layer['Laue'] = '2/m(c)'
2568	if Layer['Laue'] == '2/m(2)': Layer['Laue'] = '2/m(ab)'
2569	cell = Struct[0].split()
2570	Layer['Cell'] = [False,float(cell[0]),float(cell[1]),float(cell[2]),90.,90.,float(cell[3]),1.0]
2571	nLayers = int(Struct[2])
2572	N = 3
2573	if 'layer' not in Struct[3]:
2574	N = 4
2575	if Struct[3] != 'infinite':
2576	width = Struct[3].split()
2577	Layer['Width'][0] = [float(width[0]),float(width[1])]
2578	for nL in range(nLayers):
2579	if '=' in Struct[N]:
2580	name = Struct[N].split('=')
2581	sameas = int(name[1])-1
2582	Layer['Layers'].append({'Name':name[0],'SameAs':Layer['Layers'][sameas]['Name'],'Symm':'None','Atoms':[]})
2583	N += 1
2584	continue
2585	Symm = 'None'
2586	if 'centro' in Struct[N+1]: Symm = '-1'
2587	Layer['Layers'].append({'Name':Struct[N],'SameAs':'','Symm':Symm,'Atoms':[]})
2588	N += 2
2589	while 'layer' not in Struct[N]:
2590	atom = Struct[N][4:].split()
2591	atomType = G2el.FixValence(Struct[N][:4].replace(' ','').strip().capitalize())
2592	if atomType not in Layer['AtInfo']:
2593	Layer['AtInfo'][atomType] = G2el.GetAtomInfo(atomType)
2594	atomName = '%s(%s)'%(atomType,atom[0])
2595	newVals = []
2596	for val in atom[1:6]:
2597	if '/' in val:
2598	newVals.append(eval(val+'.'))
2599	else:
2600	newVals.append(float(val))
2601	atomRec = [atomName,atomType,newVals[0],newVals[1],newVals[2],newVals[4],newVals[3]/78.9568]
2602	Layer['Layers'][-1]['Atoms'].append(atomRec)
2603	N += 1
2604	if N > len(Struct)-1:
2605	break
2606	#TRANSITIONS records
2607	transArray = []
2608	N = 0
2609	for i in range(nLayers):
2610	transArray.append([])
2611	for j in range(nLayers):
2612	vals = Trans[N].split()
2613	newVals = []
2614	for val in vals[:4]:
2615	if '/' in val:
2616	newVals.append(eval(val+'.'))
2617	else:
2618	newVals.append(float(val))
2619	transArray[-1].append(newVals+['',False])
2620	N += 1
2621	Layer['Transitions'] = transArray
2622	#STACKING records
2623	Layer['Stacking'] = [Stack[0],'']
2624	if Stack[0] == 'recursive':
2625	Layer['Stacking'][1] = Stack[1]
2626	elif Stack[0] == 'explicit':
2627	if Stack[1] == 'random':
2628	Layer['Stacking'][1] = Stack[1]
2629	else:
2630	Layer['Stacking'][1] = 'list'
2631	Layer['Stacking'].append('')
2632	for stack in Stack[2:]:
2633	Layer['Stacking'][2] += ' '+stack
2634	return Layer
2635
2636	def ReadCIF(URLorFile):
2637	'''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
2638	(from James Hester).
2639	The open routine gets confused with DOS names that begin with a letter and colon
2640	"C:\dir\" so this routine will try to open the passed name as a file and if that
2641	fails, try it as a URL
2642
2643	:param str URLorFile: string containing a URL or a file name. Code will try first
2644	to open it as a file and then as a URL.
2645
2646	:returns: a PyCifRW CIF object.
2647	'''
2648	import CifFile as cif # PyCifRW from James Hester
2649
2650	# alternate approach:
2651	#import urllib
2652	#ciffile = 'file:'+urllib.pathname2url(filename)
2653
2654	try:
2655	fp = open(URLorFile,'r')
2656	cf = cif.ReadCif(fp)
2657	fp.close()
2658	return cf
2659	except IOError:
2660	return cif.ReadCif(URLorFile)
2661
2662	if __name__ == '__main__':
2663	import GSASII
2664	application = GSASII.GSASIImain(0)
2665	G2frame = application.main
2666	#app = wx.PySimpleApp()
2667	#G2frame = wx.Frame(None) # create a frame
2668	#frm.Show(True)
2669	#filename = '/tmp/notzip.zip'
2670	#filename = '/tmp/all.zip'
2671	#filename = '/tmp/11bmb_7652.zip'
2672
2673	#selection=None, confirmoverwrite=True, parent=None
2674	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2675	#print ExtractFileFromZip(filename,multipleselect=True)
2676	# #confirmread=False, confirmoverwrite=False)
2677
2678	# choicelist=[ ('a','b','c'),
2679	# ('test1','test2'),('no choice',)]
2680	# titles = [ 'a, b or c', 'tests', 'No option here']
2681	# dlg = MultipleChoicesDialog(
2682	# choicelist,titles,
2683	# parent=frm)
2684	# if dlg.ShowModal() == wx.ID_OK:
2685	# print 'Got OK'
2686	imagefile = '/tmp/NDC5_00237_3.ge3'
2687	Comments, Data, Npix, Image = GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None)
2688
2689	print("\n\nResults loaded to Comments, Data, Npix and Image\n\n")
2690
2691	GSASIIpath.IPyBreak_base()

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