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source: trunk/GSASIIIO.py @ 2710

Last change on this file since 2710 was 2710, checked in by vondreele, 7 years ago
improve ExportPDF with G2file selector & allow selection of I(Q), S(Q), F(Q) & G(R)
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: 2017-02-16 22:31:20 +0000 (Thu, 16 Feb 2017) $
4	# $Author: vondreele $
5	# $Revision: 2710 $
6	# $URL: trunk/GSASIIIO.py $
7	# $Id: GSASIIIO.py 2710 2017-02-16 22:31:20Z 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: 2710 $")
34	import GSASIIgrid as G2gd
35	import GSASIIspc as G2spc
36	import GSASIIobj as G2obj
37	import GSASIIlattice as G2lat
38	import GSASIIpwdGUI as G2pdG
39	import GSASIIimgGUI as G2imG
40	import GSASIIimage as G2img
41	import GSASIIElem as G2el
42	import GSASIIstrIO as G2stIO
43	import GSASIImapvars as G2mv
44	import GSASIIctrls as G2G
45	import os
46	import os.path as ospath
47
48	DEBUG = False #=True for various prints
49	TRANSP = False #=true to transpose images for testing
50	if GSASIIpath.GetConfigValue('Transpose'): TRANSP = True
51	npsind = lambda x: np.sin(x*np.pi/180.)
52
53	def sfloat(S):
54	'Convert a string to float. An empty field or a unconvertable value is treated as zero'
55	if S.strip():
56	try:
57	return float(S)
58	except ValueError:
59	pass
60	return 0.0
61
62	def sint(S):
63	'Convert a string to int. An empty field is treated as zero'
64	if S.strip():
65	return int(S)
66	else:
67	return 0
68
69	def trim(val):
70	'''Simplify a string containing leading and trailing spaces
71	as well as newlines, tabs, repeated spaces etc. into a shorter and
72	more simple string, by replacing all ranges of whitespace
73	characters with a single space.
74
75	:param str val: the string to be simplified
76
77	:returns: the (usually) shortened version of the string
78	'''
79	return re.sub('\s+', ' ', val).strip()
80
81	def makeInstDict(names,data,codes):
82	inst = dict(zip(names,zip(data,data,codes)))
83	for item in inst:
84	inst[item] = list(inst[item])
85	return inst
86
87	def FileDlgFixExt(dlg,file):
88	'this is needed to fix a problem in linux wx.FileDialog'
89	ext = dlg.GetWildcard().split('\|')[2dlg.GetFilterIndex()+1].strip('')
90	if ext not in file:
91	file += ext
92	return file
93
94	def GetPowderPeaks(fileName):
95	'Read powder peaks from a file'
96	sind = lambda x: math.sin(x*math.pi/180.)
97	asind = lambda x: 180.*math.asin(x)/math.pi
98	wave = 1.54052
99	File = open(fileName,'Ur')
100	Comments = []
101	peaks = []
102	S = File.readline()
103	while S:
104	if S[:1] == '#':
105	Comments.append(S[:-1])
106	else:
107	item = S.split()
108	if len(item) == 1:
109	peaks.append([float(item[0]),1.0])
110	elif len(item) > 1:
111	peaks.append([float(item[0]),float(item[0])])
112	S = File.readline()
113	File.close()
114	if Comments:
115	print 'Comments on file:'
116	for Comment in Comments:
117	print Comment
118	if 'wavelength' in Comment:
119	wave = float(Comment.split('=')[1])
120	Peaks = []
121	if peaks[0][0] > peaks[-1][0]: # d-spacings - assume CuKa
122	for peak in peaks:
123	dsp = peak[0]
124	sth = wave/(2.0*dsp)
125	if sth < 1.0:
126	tth = 2.0*asind(sth)
127	else:
128	break
129	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
130	else: #2-thetas - assume Cuka (for now)
131	for peak in peaks:
132	tth = peak[0]
133	dsp = wave/(2.0*sind(tth/2.0))
134	Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
135	limits = [1000.,0.]
136	for peak in Peaks:
137	limits[0] = min(limits[0],peak[0])
138	limits[1] = max(limits[1],peak[0])
139	limits[0] = max(1.,(int(limits[0]-1.)/5)*5.)
140	limits[1] = min(170.,(int(limits[1]+1.)/5)*5.)
141	return Comments,Peaks,limits,wave
142
143	def GetCheckImageFile(G2frame,treeId):
144	'''Try to locate an image file if the project and image have been moved
145	together. If the image file cannot be found, request the location from
146	the user.
147
148	:param wx.Frame G2frame: main GSAS-II Frame and data object
149	:param wx.Id treeId: Id for the main tree item for the image
150	:returns: Npix,imagefile,imagetag with (Npix) number of pixels,
151	imagefile, if it exists, or the name of a file that does exist or False if the user presses Cancel
152	and (imagetag) an optional image number
153
154	'''
155	Npix,imagefile,imagetag = G2frame.PatternTree.GetImageLoc(treeId)
156	if not os.path.exists(imagefile):
157	print 'Image file '+imagefile+' not found'
158	fil = imagefile.replace('\\','/') # windows?!
159	# see if we can find a file with same name or in a similarly named sub-dir
160	pth,fil = os.path.split(fil)
161	prevpth = None
162	while pth and pth != prevpth:
163	prevpth = pth
164	if os.path.exists(os.path.join(G2frame.dirname,fil)):
165	print 'found image file '+os.path.join(G2frame.dirname,fil)
166	imagefile = os.path.join(G2frame.dirname,fil)
167	G2frame.PatternTree.UpdateImageLoc(treeId,imagefile)
168	return Npix,imagefile,imagetag
169	pth,enddir = os.path.split(pth)
170	fil = os.path.join(enddir,fil)
171	# not found as a subdirectory, drop common parts of path for last saved & image file names
172	# if image was .../A/B/C/imgs/ima.ge
173	# & GPX was .../A/B/C/refs/fil.gpx but is now .../NEW/TEST/TEST1
174	# will look for .../NEW/TEST/TEST1/imgs/ima.ge, .../NEW/TEST/imgs/ima.ge, .../NEW/imgs/ima.ge and so on
175	Controls = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
176	gpxPath = Controls.get('LastSavedAs','').replace('\\','/').split('/') # blank in older .GPX files
177	imgPath = imagefile.replace('\\','/').split('/')
178	for p1,p2 in zip(gpxPath,imgPath):
179	if p1 == p2:
180	gpxPath.pop(0),imgPath.pop(0)
181	else:
182	break
183	fil = os.path.join(*imgPath) # file with non-common prefix elements
184	prevpth = None
185	pth = os.path.abspath(G2frame.dirname)
186	while pth and pth != prevpth:
187	prevpth = pth
188	if os.path.exists(os.path.join(pth,fil)):
189	print 'found image file '+os.path.join(pth,fil)
190	imagefile = os.path.join(pth,fil)
191	G2frame.PatternTree.UpdateImageLoc(treeId,imagefile)
192	return Npix,imagefile,imagetag
193	pth,enddir = os.path.split(pth)
194	#GSASIIpath.IPyBreak()
195
196	if not os.path.exists(imagefile):
197	prevnam = os.path.split(imagefile)[1]
198	prevext = os.path.splitext(imagefile)[1]
199	wildcard = 'Image format ('+prevext+')\|'+prevext
200	dlg = wx.FileDialog(G2frame, 'Previous image file ('+prevnam+') not found; open here', '.', prevnam,
201	wildcard,wx.OPEN)
202	try:
203	dlg.SetFilename(''+ospath.split(imagefile)[1])
204	if dlg.ShowModal() == wx.ID_OK:
205	imagefile = dlg.GetPath()
206	G2frame.PatternTree.UpdateImageLoc(treeId,imagefile)
207	else:
208	imagefile = False
209	finally:
210	dlg.Destroy()
211	return Npix,imagefile,imagetag
212
213	def EditImageParms(parent,Data,Comments,Image,filename):
214	dlg = wx.Dialog(parent, wx.ID_ANY, 'Edit image parameters',
215	style=wx.DEFAULT_DIALOG_STYLE \| wx.RESIZE_BORDER)
216	def onClose(event):
217	dlg.EndModal(wx.ID_OK)
218	mainsizer = wx.BoxSizer(wx.VERTICAL)
219	h,w = Image.shape[:2]
220	mainsizer.Add(wx.StaticText(dlg,wx.ID_ANY,
221	'File '+str(filename)+'\nImage size: '+str(h)+' x '+str(w)),
222	0,wx.ALIGN_LEFT\|wx.ALL, 2)
223
224	vsizer = wx.BoxSizer(wx.HORIZONTAL)
225	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Wavelength (\xC5) '),
226	0,wx.ALIGN_LEFT\|wx.ALL, 2)
227	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'wavelength')
228	vsizer.Add(wdgt)
229	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
230
231	vsizer = wx.BoxSizer(wx.HORIZONTAL)
232	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Pixel size (\xb5m). Width '),
233	0,wx.ALIGN_LEFT\|wx.ALL, 2)
234	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],0,
235	size=(50,-1))
236	vsizer.Add(wdgt)
237	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Height '),
238	wx.ALIGN_LEFT\|wx.ALL, 2)
239	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],1,
240	size=(50,-1))
241	vsizer.Add(wdgt)
242	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
243
244	vsizer = wx.BoxSizer(wx.HORIZONTAL)
245	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Sample to detector (mm) '),
246	0,wx.ALIGN_LEFT\|wx.ALL, 2)
247	wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'distance')
248	vsizer.Add(wdgt)
249	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
250
251	vsizer = wx.BoxSizer(wx.HORIZONTAL)
252	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Beam center (pixels). X = '),
253	0,wx.ALIGN_LEFT\|wx.ALL, 2)
254	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],0,
255	size=(75,-1))
256	vsizer.Add(wdgt)
257	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u' Y = '),
258	wx.ALIGN_LEFT\|wx.ALL, 2)
259	wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],1,
260	size=(75,-1))
261	vsizer.Add(wdgt)
262	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
263
264	vsizer = wx.BoxSizer(wx.HORIZONTAL)
265	vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Comments '),
266	0,wx.ALIGN_LEFT\|wx.ALL, 2)
267	wdgt = G2G.ValidatedTxtCtrl(dlg,Comments,0,size=(250,-1))
268	vsizer.Add(wdgt)
269	mainsizer.Add(vsizer,0,wx.ALIGN_LEFT\|wx.ALL, 2)
270
271	btnsizer = wx.StdDialogButtonSizer()
272	OKbtn = wx.Button(dlg, wx.ID_OK, 'Continue')
273	OKbtn.SetDefault()
274	OKbtn.Bind(wx.EVT_BUTTON,onClose)
275	btnsizer.AddButton(OKbtn) # not sure why this is needed
276	btnsizer.Realize()
277	mainsizer.Add(btnsizer, 1, wx.ALIGN_CENTER\|wx.ALL\|wx.EXPAND, 5)
278	dlg.SetSizer(mainsizer)
279	dlg.CenterOnParent()
280	dlg.ShowModal()
281
282	def LoadImage2Tree(imagefile,G2frame,Comments,Data,Npix,Image):
283	'''Load an image into the tree. Saves the location of the image, as well as the
284	ImageTag (where there is more than one image in the file), if defined.
285	'''
286	ImgNames = G2gd.GetPatternTreeDataNames(G2frame,['IMG ',])
287	TreeLbl = 'IMG '+os.path.basename(imagefile)
288	ImageTag = Data.get('ImageTag')
289	if ImageTag:
290	TreeLbl += ' #'+'%04d'%(ImageTag)
291	imageInfo = (imagefile,ImageTag)
292	else:
293	imageInfo = imagefile
294	TreeName = G2obj.MakeUniqueLabel(TreeLbl,ImgNames)
295	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=TreeName)
296	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
297	Imax = np.amax(Image)
298	if G2frame.imageDefault:
299	Data = copy.copy(G2frame.imageDefault)
300	Data['showLines'] = True
301	Data['ring'] = []
302	Data['rings'] = []
303	Data['cutoff'] = 10
304	Data['pixLimit'] = 20
305	Data['edgemin'] = 100000000
306	Data['calibdmin'] = 0.5
307	Data['calibskip'] = 0
308	Data['ellipses'] = []
309	Data['calibrant'] = ''
310	Data['GonioAngles'] = [0.,0.,0.]
311	Data['DetDepthRef'] = False
312	else:
313	Data['type'] = 'PWDR'
314	Data['color'] = 'Paired'
315	Data['tilt'] = 0.0
316	Data['rotation'] = 0.0
317	Data['showLines'] = False
318	Data['ring'] = []
319	Data['rings'] = []
320	Data['cutoff'] = 10
321	Data['pixLimit'] = 20
322	Data['calibdmin'] = 0.5
323	Data['calibskip'] = 0
324	Data['edgemin'] = 100000000
325	Data['ellipses'] = []
326	Data['GonioAngles'] = [0.,0.,0.]
327	Data['DetDepth'] = 0.
328	Data['DetDepthRef'] = False
329	Data['calibrant'] = ''
330	Data['IOtth'] = [2.0,5.0]
331	Data['LRazimuth'] = [0.,180.]
332	Data['azmthOff'] = 0.0
333	Data['outChannels'] = 2500
334	Data['outAzimuths'] = 1
335	Data['centerAzm'] = False
336	Data['fullIntegrate'] = False
337	Data['setRings'] = False
338	Data['background image'] = ['',-1.0]
339	Data['dark image'] = ['',-1.0]
340	Data['Flat Bkg'] = 0.0
341	Data['setDefault'] = False
342	Data['range'] = [(0,Imax),[0,Imax]]
343	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Image Controls'),Data)
344	Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],'Thresholds':[(0,Imax),[0,Imax]]}
345	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Masks'),Masks)
346	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Stress/Strain'),
347	{'Type':'True','d-zero':[],'Sample phi':0.0,'Sample z':0.0,'Sample load':0.0})
348	G2frame.PatternTree.SetItemPyData(Id,[Npix,imageInfo])
349	G2frame.PickId = Id
350	G2frame.PickIdText = G2frame.GetTreeItemsList(G2frame.PickId)
351	G2frame.Image = Id
352
353	def GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None,FormatName=''):
354	'''Read a single image with an image importer.
355
356	:param wx.Frame G2frame: main GSAS-II Frame and data object.
357	:param str imagefile: name of image file
358	:param bool imageOnly: If True return only the image,
359	otherwise (default) return more (see below)
360	:param int/str ImageTag: specifies a particular image to be read from a file.
361	First image is read if None (default).
362	:param str formatName: the image reader formatName
363
364	:returns: an image as a numpy array or a list of four items:
365	Comments, Data, Npix and the Image, as selected by imageOnly
366
367	'''
368	# determine which formats are compatible with this file
369	primaryReaders = []
370	secondaryReaders = []
371	for rd in G2frame.ImportImageReaderlist:
372	flag = rd.ExtensionValidator(imagefile)
373	if flag is None:
374	secondaryReaders.append(rd)
375	elif flag:
376	if not FormatName:
377	primaryReaders.append(rd)
378	elif FormatName == rd.formatName:
379	primaryReaders.append(rd)
380	if len(secondaryReaders) + len(primaryReaders) == 0:
381	print('Error: No matching format for file '+imagefile)
382	raise Exception('No image read')
383	fp = None
384	errorReport = ''
385	if not imagefile:
386	return
387	fp = open(imagefile,'Ur')
388	for rd in primaryReaders+secondaryReaders:
389	rd.ReInitialize() # purge anything from a previous read
390	fp.seek(0) # rewind
391	rd.errors = "" # clear out any old errors
392	if not rd.ContentsValidator(fp): # rejected on cursory check
393	errorReport += "\n "+rd.formatName + ' validator error'
394	if rd.errors:
395	errorReport += ': '+rd.errors
396	continue
397	if imageOnly:
398	ParentFrame = None # prevent GUI access on reread
399	else:
400	ParentFrame = G2frame
401	if GSASIIpath.GetConfigValue('debug'):
402	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=ImageTag)
403	else:
404	flag = False
405	try:
406	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=ImageTag)
407	except rd.ImportException as detail:
408	rd.errors += "\n Read exception: "+str(detail)
409	except Exception as detail:
410	import traceback
411	rd.errors += "\n Unhandled read exception: "+str(detail)
412	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
413	if flag: # this read succeeded
414	if rd.Image is None:
415	raise Exception('No image read. Strange!')
416	if GSASIIpath.GetConfigValue('Transpose'):
417	print 'Transposing Image!'
418	rd.Image = rd.Image.T
419	#rd.readfilename = imagefile
420	if imageOnly:
421	return rd.Image
422	else:
423	return rd.Comments,rd.Data,rd.Npix,rd.Image
424	else:
425	print('Error reading file '+imagefile)
426	print('Error messages(s)\n'+errorReport)
427	raise Exception('No image read')
428
429	def ReadImages(G2frame,imagefile):
430	'''Read one or more images from a file and put them into the Tree
431	using image importers. Called only in :meth:`AutoIntFrame.OnTimerLoop`.
432
433	:param wx.Frame G2frame: main GSAS-II Frame and data object.
434	:param str imagefile: name of image file
435
436	:returns: a list of the id's of the IMG tree items created
437	'''
438	# determine which formats are compatible with this file
439	primaryReaders = []
440	secondaryReaders = []
441	for rd in G2frame.ImportImageReaderlist:
442	flag = rd.ExtensionValidator(imagefile)
443	if flag is None:
444	secondaryReaders.append(rd)
445	elif flag:
446	primaryReaders.append(rd)
447	if len(secondaryReaders) + len(primaryReaders) == 0:
448	print('Error: No matching format for file '+imagefile)
449	raise Exception('No image read')
450	errorReport = ''
451	fp = open(imagefile,'Ur')
452	rdbuffer = {} # create temporary storage for file reader
453	for rd in primaryReaders+secondaryReaders:
454	rd.ReInitialize() # purge anything from a previous read
455	fp.seek(0) # rewind
456	rd.errors = "" # clear out any old errors
457	if not rd.ContentsValidator(fp): # rejected on cursory check
458	errorReport += "\n "+rd.formatName + ' validator error'
459	if rd.errors:
460	errorReport += ': '+rd.errors
461	continue
462	ParentFrame = G2frame
463	block = 0
464	repeat = True
465	CreatedIMGitems = []
466	while repeat: # loop if the reader asks for another pass on the file
467	block += 1
468	repeat = False
469	if GSASIIpath.GetConfigValue('debug'):
470	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=block,Buffer=rdbuffer)
471	else:
472	flag = False
473	try:
474	flag = rd.Reader(imagefile,fp,ParentFrame,blocknum=block,Buffer=rdbuffer)
475	except rd.ImportException as detail:
476	rd.errors += "\n Read exception: "+str(detail)
477	except Exception as detail:
478	import traceback
479	rd.errors += "\n Unhandled read exception: "+str(detail)
480	rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
481	if flag: # this read succeeded
482	if rd.Image is None:
483	raise Exception('No image read. Strange!')
484	if GSASIIpath.GetConfigValue('Transpose'):
485	print 'Transposing Image!'
486	rd.Image = rd.Image.T
487	rd.Data['ImageTag'] = rd.repeatcount
488	LoadImage2Tree(imagefile,G2frame,rd.Comments,rd.Data,rd.Npix,rd.Image)
489	repeat = rd.repeat
490	CreatedIMGitems.append(G2frame.Image)
491	if CreatedIMGitems: return CreatedIMGitems
492	else:
493	print('Error reading file '+imagefile)
494	print('Error messages(s)\n'+errorReport)
495	return []
496	#raise Exception('No image read')
497
498	def SaveMultipleImg(G2frame):
499	if not G2frame.PatternTree.GetCount():
500	print 'no images!'
501	return
502	choices = G2gd.GetPatternTreeDataNames(G2frame,['IMG ',])
503	if len(choices) == 1:
504	names = choices
505	else:
506	dlg = G2G.G2MultiChoiceDialog(G2frame,'Stress/Strain fitting','Select images to fit:',choices)
507	dlg.SetSelections([])
508	names = []
509	if dlg.ShowModal() == wx.ID_OK:
510	names = [choices[sel] for sel in dlg.GetSelections()]
511	dlg.Destroy()
512	if not names: return
513	for name in names:
514	Id = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, name)
515	Npix,imagefile,imagetag = G2frame.PatternTree.GetImageLoc(Id)
516	imroot = os.path.splitext(imagefile)[0]
517	if imagetag:
518	imroot += '_' + str(imagetag)
519	Data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Image Controls'))
520	print('Writing '+imroot+'.imctrl')
521	File = open(imroot+'.imctrl','w')
522	keys = ['type','wavelength','calibrant','distance','center',
523	'tilt','rotation','azmthOff','fullIntegrate','LRazimuth',
524	'IOtth','outChannels','outAzimuths','invert_x','invert_y','DetDepth',
525	'calibskip','pixLimit','cutoff','calibdmin','chisq','Flat Bkg',
526	'binType','SampleShape','PolaVal','SampleAbs','dark image','background image']
527	for key in keys:
528	if key not in Data: continue #uncalibrated!
529	File.write(key+':'+str(Data[key])+'\n')
530	File.close()
531	mask = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Masks'))
532	G2imG.CleanupMasks(mask)
533	print('Writing '+imroot+'.immask')
534	File = open(imroot+'.immask','w')
535	for key in ['Points','Rings','Arcs','Polygons','Frames','Thresholds']:
536	File.write(key+':'+str(mask[key])+'\n')
537	File.close()
538
539	def PutG2Image(filename,Comments,Data,Npix,image):
540	'Write an image as a python pickle - might be better as an .edf file?'
541	File = open(filename,'wb')
542	cPickle.dump([Comments,Data,Npix,image],File,1)
543	File.close()
544	return
545
546	# should get moved to importer when ready to test
547	def GetEdfData(filename,imageOnly=False):
548	'Read European detector data edf file'
549	if not imageOnly:
550	print 'Read European detector data edf file: ',filename
551	File = open(filename,'rb')
552	fileSize = os.stat(filename).st_size
553	head = File.read(3072)
554	lines = head.split('\n')
555	sizexy = [0,0]
556	pixSize = [154,154] #Pixium4700?
557	cent = [0,0]
558	wave = 1.54187 #default <CuKa>
559	dist = 1000.
560	head = ['European detector data',]
561	for line in lines:
562	line = line.replace(';',' ').strip()
563	fields = line.split()
564	if 'Dim_1' in line:
565	sizexy[0] = int(fields[2])
566	elif 'Dim_2' in line:
567	sizexy[1] = int(fields[2])
568	elif 'DataType' in line:
569	dType = fields[2]
570	elif 'wavelength' in line:
571	wave = float(fields[2])
572	elif 'Size' in line:
573	imSize = int(fields[2])
574	# elif 'DataType' in lines:
575	# dType = fields[2]
576	elif 'pixel_size_x' in line:
577	pixSize[0] = float(fields[2])
578	elif 'pixel_size_y' in line:
579	pixSize[1] = float(fields[2])
580	elif 'beam_center_x' in line:
581	cent[0] = float(fields[2])
582	elif 'beam_center_y' in line:
583	cent[1] = float(fields[2])
584	elif 'refined_distance' in line:
585	dist = float(fields[2])
586	if line:
587	head.append(line)
588	else: #blank line at end of header
589	break
590	File.seek(fileSize-imSize)
591	if dType == 'UnsignedShort':
592	image = np.array(np.frombuffer(File.read(imSize),dtype=np.int16),dtype=np.int32)
593	else:
594	image = np.array(np.frombuffer(File.read(imSize),dtype=np.int32),dtype=np.int32)
595	image = np.reshape(image,(sizexy[1],sizexy[0]))
596	data = {'pixelSize':pixSize,'wavelength':wave,'distance':dist,'center':cent,'size':sizexy}
597	Npix = sizexy[0]*sizexy[1]
598	File.close()
599	if imageOnly:
600	return image
601	else:
602	return head,data,Npix,image
603
604	# should get moved to importer when ready to test
605	def GetRigaku(filename,imageOnly=False):
606	'Read Rigaku R-Axis IV image file'
607	import array as ar
608	if not imageOnly:
609	print 'Read Rigaku R-Axis IV file: ',filename
610	File = open(filename,'rb')
611	fileSize = os.stat(filename).st_size
612	Npix = (fileSize-6000)/2
613	File.read(6000)
614	head = ['Rigaku R-Axis IV detector data',]
615	image = np.array(ar.array('H',File.read(fileSize-6000)),dtype=np.int32)
616	print fileSize,image.shape
617	print head
618	if Npix == 9000000:
619	sizexy = [3000,3000]
620	pixSize = [100.,100.]
621	elif Npix == 2250000:
622	sizexy = [1500,1500]
623	pixSize = [200.,200.]
624	else:
625	sizexy = [6000,6000]
626	pixSize = [50.,50.]
627	image = np.reshape(image,(sizexy[1],sizexy[0]))
628	data = {'pixelSize':pixSize,'wavelength':1.5428,'distance':250.0,'center':[150.,150.],'size':sizexy}
629	File.close()
630	if imageOnly:
631	return image
632	else:
633	return head,data,Npix,image
634
635	# should get moved to importer when ready to test
636	def GetImgData(filename,imageOnly=False):
637	'Read an ADSC image file'
638	import array as ar
639	if not imageOnly:
640	print 'Read ADSC img file: ',filename
641	File = open(filename,'rb')
642	head = File.read(511)
643	lines = head.split('\n')
644	head = []
645	center = [0,0]
646	for line in lines[1:-2]:
647	line = line.strip()[:-1]
648	if line:
649	if 'SIZE1' in line:
650	size = int(line.split('=')[1])
651	Npix = size*size
652	elif 'WAVELENGTH' in line:
653	wave = float(line.split('=')[1])
654	elif 'BIN' in line:
655	if line.split('=')[1] == '2x2':
656	pixel=(102,102)
657	else:
658	pixel = (51,51)
659	elif 'DISTANCE' in line:
660	distance = float(line.split('=')[1])
661	elif 'CENTER_X' in line:
662	center[0] = float(line.split('=')[1])
663	elif 'CENTER_Y' in line:
664	center[1] = float(line.split('=')[1])
665	head.append(line)
666	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center,'size':[size,size]}
667	image = []
668	pos = 512
669	File.seek(pos)
670	image = np.array(ar.array('H',File.read(2*Npix)),dtype=np.int32)
671	image = np.reshape(image,(size,size))
672	# image = np.zeros(shape=(size,size),dtype=np.int32)
673	# while row < size:
674	# File.seek(pos)
675	# line = ar.array('H',File.read(2*size))
676	# image[row] = np.asarray(line)
677	# row += 1
678	# pos += 2*size
679	File.close()
680	if imageOnly:
681	return image
682	else:
683	return lines[1:-2],data,Npix,image
684
685	# should get moved to importer when ready to test
686	def GetMAR345Data(filename,imageOnly=False):
687	'Read a MAR-345 image plate image'
688	try:
689	import pack_f as pf
690	except:
691	msg = wx.MessageDialog(None, message="Unable to load the GSAS MAR image decompression, pack_f",
692	caption="Import Error",
693	style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
694	msg.ShowModal()
695	return None,None,None,None
696
697	if not imageOnly:
698	print 'Read Mar345 file: ',filename
699	File = open(filename,'rb')
700	head = File.read(4095)
701	lines = head[128:].split('\n')
702	head = []
703	for line in lines:
704	line = line.strip()
705	if 'PIXEL' in line:
706	values = line.split()
707	pixel = (int(values[2]),int(values[4])) #in microns
708	elif 'WAVELENGTH' in line:
709	wave = float(line.split()[1])
710	elif 'DISTANCE' in line:
711	distance = float(line.split()[1]) #in mm
712	if not distance:
713	distance = 500.
714	elif 'CENTER' in line:
715	values = line.split()
716	center = [float(values[2])/10.,float(values[4])/10.] #make in mm from pixels
717	if line:
718	head.append(line)
719	data = {'pixelSize':pixel,'wavelength':wave,'distance':distance,'center':center}
720	for line in head:
721	if 'FORMAT' in line[0:6]:
722	items = line.split()
723	sizex = int(items[1])
724	Npix = int(items[3])
725	sizey = int(Npix/sizex)
726	pos = 4096
727	data['size'] = [sizex,sizey]
728	File.seek(pos)
729	line = File.read(8)
730	while 'CCP4' not in line: #get past overflow list for now
731	line = File.read(8)
732	pos += 8
733	pos += 37
734	File.seek(pos)
735	raw = File.read()
736	File.close()
737	image = np.zeros(shape=(sizex,sizey),dtype=np.int32)
738
739	image = np.flipud(pf.pack_f(len(raw),raw,sizex,sizey,image).T) #transpose to get it right way around & flip
740	if imageOnly:
741	return image
742	else:
743	return head,data,Npix,image
744
745	def ProjFileOpen(G2frame,showProvenance=True):
746	'Read a GSAS-II project file and load into the G2 data tree'
747	if not os.path.exists(G2frame.GSASprojectfile):
748	print ('\n*** Error attempt to open project file that does not exist:\n '+
749	str(G2frame.GSASprojectfile))
750	return
751	LastSavedUsing = None
752	file = open(G2frame.GSASprojectfile,'rb')
753	if showProvenance: print 'loading from file: ',G2frame.GSASprojectfile
754	G2frame.SetTitle("GSAS-II data tree: "+
755	os.path.split(G2frame.GSASprojectfile)[1])
756	wx.BeginBusyCursor()
757	try:
758	while True:
759	try:
760	data = cPickle.load(file)
761	except EOFError:
762	break
763	datum = data[0]
764
765	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=datum[0])
766	if datum[0].startswith('PWDR'):
767	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
768	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
769	G2frame.PatternTree.SetItemPyData(Id,datum[1][:3]) #temp. trim off junk (patch?)
770	elif datum[0].startswith('HKLF'):
771	if 'ranId' not in datum[1][0]: # patch: add random Id if not present
772	datum[1][0]['ranId'] = ran.randint(0,sys.maxint)
773	G2frame.PatternTree.SetItemPyData(Id,datum[1])
774	else:
775	G2frame.PatternTree.SetItemPyData(Id,datum[1])
776	if datum[0] == 'Controls' and 'LastSavedUsing' in datum[1]:
777	LastSavedUsing = datum[1]['LastSavedUsing']
778	if datum[0] == 'Controls' and 'PythonVersions' in datum[1] and GSASIIpath.GetConfigValue('debug') and showProvenance:
779	print('Packages used to create .GPX file:')
780	if 'dict' in str(type(datum[1]['PythonVersions'])): #patch
781	for p in sorted(datum[1]['PythonVersions'],key=lambda s: s.lower()):
782	print(" {:<14s}: {:s}".format(p[0],p[1]))
783	else:
784	for p in datum[1]['PythonVersions']:
785	print(" {:<12s} {:s}".format(p[0]+':',p[1]))
786	oldPDF = False
787	for datus in data[1:]:
788	#patch - 1/23/17 PDF cleanup
789	if datus[0][:4] in ['I(Q)','S(Q)','F(Q)','G(R)']:
790	oldPDF = True
791	data[1][1][datus[0][:4]] = copy.deepcopy(datus[1][:2])
792	continue
793	#end PDF cleanup
794	sub = G2frame.PatternTree.AppendItem(Id,datus[0])
795	#patch
796	if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
797	if datum[0].startswith('PWDR'):
798	datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
799	else:
800	datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
801	for item in datus[1][0]: #zip makes tuples - now make lists!
802	datus[1][0][item] = list(datus[1][0][item])
803	#end patch
804	G2frame.PatternTree.SetItemPyData(sub,datus[1])
805	if 'PDF ' in datum[0][:4] and oldPDF:
806	sub = G2frame.PatternTree.AppendItem(Id,'PDF Peaks')
807	G2frame.PatternTree.SetItemPyData(sub,{'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]})
808	if datum[0].startswith('IMG'): #retrieve image default flag & data if set
809	Data = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id,'Image Controls'))
810	if Data['setDefault']:
811	G2frame.imageDefault = Data
812	file.close()
813	if LastSavedUsing:
814	print('GPX load successful. Last saved with GSAS-II revision '+LastSavedUsing)
815	else:
816	print('project load successful')
817	G2frame.NewPlot = True
818	except:
819	msg = wx.MessageDialog(G2frame,message="Error reading file "+
820	str(G2frame.GSASprojectfile)+". This is not a GSAS-II .gpx file",
821	caption="Load Error",style=wx.ICON_ERROR \| wx.OK \| wx.STAY_ON_TOP)
822	msg.ShowModal()
823	finally:
824	wx.EndBusyCursor()
825	G2frame.Status.SetStatusText('Mouse RB click item to refresh/raise; RB drag/drop to reorder')
826
827	def ProjFileSave(G2frame):
828	'Save a GSAS-II project file'
829	if not G2frame.PatternTree.IsEmpty():
830	file = open(G2frame.GSASprojectfile,'wb')
831	print 'save to file: ',G2frame.GSASprojectfile
832	# stick the file name into the tree and version info into tree so they are saved.
833	# (Controls should always be created at this point)
834	try:
835	Controls = G2frame.PatternTree.GetItemPyData(
836	G2gd.GetPatternTreeItemId(G2frame,G2frame.root, 'Controls'))
837	Controls['LastSavedAs'] = os.path.abspath(G2frame.GSASprojectfile)
838	Controls['LastSavedUsing'] = str(GSASIIpath.GetVersionNumber())
839	Controls['PythonVersions'] = G2frame.PackageVersions
840	except:
841	pass
842	wx.BeginBusyCursor()
843	try:
844	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
845	while item:
846	data = []
847	name = G2frame.PatternTree.GetItemText(item)
848	data.append([name,G2frame.PatternTree.GetItemPyData(item)])
849	item2, cookie2 = G2frame.PatternTree.GetFirstChild(item)
850	while item2:
851	name = G2frame.PatternTree.GetItemText(item2)
852	data.append([name,G2frame.PatternTree.GetItemPyData(item2)])
853	item2, cookie2 = G2frame.PatternTree.GetNextChild(item, cookie2)
854	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
855	cPickle.dump(data,file,1)
856	file.close()
857	pth = os.path.split(os.path.abspath(G2frame.GSASprojectfile))[0]
858	if GSASIIpath.GetConfigValue('Save_paths'): G2G.SaveGPXdirectory(pth)
859	G2frame.LastGPXdir = pth
860	finally:
861	wx.EndBusyCursor()
862	print('project save successful')
863
864	def SaveIntegration(G2frame,PickId,data,Overwrite=False):
865	'Save image integration results as powder pattern(s)'
866	azms = G2frame.Integrate[1]
867	X = G2frame.Integrate[2][:-1]
868	N = len(X)
869	Id = G2frame.PatternTree.GetItemParent(PickId)
870	name = G2frame.PatternTree.GetItemText(Id)
871	name = name.replace('IMG ',data['type']+' ')
872	Comments = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame,Id, 'Comments'))
873	if 'PWDR' in name:
874	names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','SH/L','Azimuth']
875	codes = [0 for i in range(11)]
876	elif 'SASD' in name:
877	names = ['Type','Lam','Zero','Azimuth']
878	codes = [0 for i in range(4)]
879	X = 4.np.pinpsind(X/2.)/data['wavelength'] #convert to q
880	Xminmax = [X[0],X[-1]]
881	Azms = []
882	dazm = 0.
883	if data['fullIntegrate'] and data['outAzimuths'] == 1:
884	Azms = [45.0,] #a poor man's average?
885	else:
886	for i,azm in enumerate(azms[:-1]):
887	if azm > 360. and azms[i+1] > 360.:
888	Azms.append(G2img.meanAzm(azm%360.,azms[i+1]%360.))
889	else:
890	Azms.append(G2img.meanAzm(azm,azms[i+1]))
891	dazm = np.min(np.abs(np.diff(azms)))/2.
892	G2frame.IntgOutList = []
893	for i,azm in enumerate(azms[:-1]):
894	Aname = name+" Azm= %.2f"%((azm+dazm)%360.)
895	item, cookie = G2frame.PatternTree.GetFirstChild(G2frame.root)
896	# if Overwrite delete any duplicate
897	if Overwrite and G2gd.GetPatternTreeItemId(G2frame,G2frame.root,Aname):
898	print('Replacing '+Aname)
899	item = G2gd.GetPatternTreeItemId(G2frame,G2frame.root,Aname)
900	G2frame.PatternTree.Delete(item)
901	else:
902	nOcc = 0
903	while item:
904	Name = G2frame.PatternTree.GetItemText(item)
905	if Aname in Name:
906	nOcc += 1
907	item, cookie = G2frame.PatternTree.GetNextChild(G2frame.root, cookie)
908	if nOcc:
909	Aname += '(%d)'%(nOcc)
910	Sample = G2pdG.SetDefaultSample() #set as Debye-Scherrer
911	Sample['Gonio. radius'] = data['distance']
912	Sample['Omega'] = data['GonioAngles'][0]
913	Sample['Chi'] = data['GonioAngles'][1]
914	Sample['Phi'] = data['GonioAngles'][2]
915	Sample['Azimuth'] = (azm+dazm)%360. #put here as bin center
916	polariz = 0.99 #set default polarization for synchrotron radiation!
917	for item in Comments:
918	if 'polariz' in item:
919	try:
920	polariz = float(item.split('=')[1])
921	except:
922	polariz = 0.99
923	if 'PWDR' in Aname:
924	parms = ['PXC',data['wavelength'],0.0,polariz,1.0,-0.10,0.4,0.30,1.0,0.0001,Azms[i]]
925	elif 'SASD' in Aname:
926	Sample['Trans'] = data['SampleAbs'][0]
927	parms = ['LXC',data['wavelength'],0.0,Azms[i]]
928	Y = G2frame.Integrate[0][i]
929	Ymin = np.min(Y)
930	Ymax = np.max(Y)
931	W = np.where(Y>0.,1./Y,1.e-6) #probably not true
932	Id = G2frame.PatternTree.AppendItem(parent=G2frame.root,text=Aname)
933	G2frame.IntgOutList.append(Id)
934	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Comments'),Comments)
935	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Limits'),[tuple(Xminmax),Xminmax])
936	if 'PWDR' in Aname:
937	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Background'),[['chebyschev',1,3,1.0,0.0,0.0],
938	{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
939	inst = [dict(zip(names,zip(parms,parms,codes))),{}]
940	for item in inst[0]:
941	inst[0][item] = list(inst[0][item])
942	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Instrument Parameters'),inst)
943	if 'PWDR' in Aname:
944	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
945	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
946	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Index Peak List'),[[],[]])
947	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Unit Cells List'),[])
948	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Reflection Lists'),{})
949	elif 'SASD' in Aname:
950	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
951	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Sample Parameters'),Sample)
952	G2frame.PatternTree.SetItemPyData(G2frame.PatternTree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
953	valuesdict = {
954	'wtFactor':1.0,
955	'Dummy':False,
956	'ranId':ran.randint(0,sys.maxint),
957	'Offset':[0.0,0.0],'delOffset':0.02Ymax,'refOffset':-0.1Ymax,'refDelt':0.1*Ymax,
958	'qPlot':False,'dPlot':False,'sqrtPlot':False,'Yminmax':[Ymin,Ymax]
959	}
960	G2frame.PatternTree.SetItemPyData(
961	Id,[valuesdict,
962	[np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
963	return Id #last powder pattern generated
964
965	def XYsave(G2frame,XY,labelX='X',labelY='Y',names=None):
966	'Save XY table data'
967	pth = G2G.GetExportPath(G2frame)
968	dlg = wx.FileDialog(
969	G2frame, 'Enter csv filename for XY table', pth, '',
970	'XY table file (.csv)\|.csv',wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
971	try:
972	if dlg.ShowModal() == wx.ID_OK:
973	filename = dlg.GetPath()
974	filename = os.path.splitext(filename)[0]+'.csv'
975	File = open(filename,'w')
976	else:
977	filename = None
978	finally:
979	dlg.Destroy()
980	if not filename:
981	return
982	for i in range(len(XY)):
983	if names != None:
984	header = '%s,%s(%s)\n'%(labelX,labelY,names[i])
985	else:
986	header = '%s,%s(%d)\n'%(labelX,labelY,i)
987	File.write(header)
988	for x,y in XY[i].T:
989	File.write('%.3f,%.3f\n'%(x,y))
990	File.close()
991	print ' XY data saved to: ',filename
992
993	def PDFSave(G2frame,exports,PDFsaves):
994	'Save a PDF I(Q), S(Q), F(Q) and G(r) in column formats'
995	import scipy.interpolate as scintp
996	for export in exports:
997	PickId = G2gd.GetPatternTreeItemId(G2frame, G2frame.root, export)
998	PDFControls = G2frame.PatternTree.GetItemPyData(G2gd.GetPatternTreeItemId(G2frame, PickId,'PDF Controls'))
999	if PDFsaves[0]: #I(Q)
1000	iqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.iq')
1001	iqdata = PDFControls['I(Q)'][0]
1002	iqfxn = scintp.interp1d(iqdata[0],iqdata[1],kind='linear')
1003	iqfile = open(iqfilename,'w')
1004	iqfile.write('#T I(Q) %s\n'%(export))
1005	iqfile.write('#L Q I(Q)\n')
1006	qnew = np.arange(iqdata[0][0],iqdata[0][-1],0.005)
1007	iqnew = zip(qnew,iqfxn(qnew))
1008	for q,iq in iqnew:
1009	iqfile.write("%15.6g %15.6g\n" % (q,iq))
1010	iqfile.close()
1011	print ' I(Q) saved to: ',iqfilename
1012
1013	if PDFsaves[1]: #S(Q)
1014	sqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.sq')
1015	sqdata = PDFControls['S(Q)'][1]
1016	sqfxn = scintp.interp1d(sqdata[0],sqdata[1],kind='linear')
1017	sqfile = open(sqfilename,'w')
1018	sqfile.write('#T S(Q) %s\n'%(export))
1019	sqfile.write('#L Q S(Q)\n')
1020	qnew = np.arange(sqdata[0][0],sqdata[0][-1],0.005)
1021	sqnew = zip(qnew,sqfxn(qnew))
1022	for q,sq in sqnew:
1023	sqfile.write("%15.6g %15.6g\n" % (q,sq))
1024	sqfile.close()
1025	print ' S(Q) saved to: ',sqfilename
1026
1027
1028	if PDFsaves[2]: #F(Q)
1029	fqfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.fq')
1030	fqdata = PDFControls['F(Q)'][1]
1031	fqfxn = scintp.interp1d(fqdata[0],fqdata[1],kind='linear')
1032	fqfile = open(sqfilename,'w')
1033	fqfile.write('#T F(Q) %s\n'%(export))
1034	fqfile.write('#L Q F(Q)\n')
1035	qnew = np.arange(sqdata[0][0],sqdata[0][-1],0.005)
1036	fqnew = zip(qnew,fqfxn(qnew))
1037	for q,fq in fqnew:
1038	fqfile.write("%15.6g %15.6g\n" % (q,fq))
1039	fqfile.close()
1040	print ' F(Q) saved to: ',fqfilename
1041
1042
1043	if PDFsaves[3]: #G(R)
1044	grfilename = ospath.join(G2frame.dirname,export.replace(' ','_')[5:]+'.gr')
1045	grdata = PDFControls['G(R)'][1]
1046	grfxn = scintp.interp1d(grdata[0],grdata[1],kind='linear')
1047	grfile = open(grfilename,'w')
1048	grfile.write('#T G(R) %s\n'%(export))
1049	grfile.write('#L R G(R)\n')
1050	rnew = np.arange(grdata[0][0],grdata[0][-1],0.010)
1051	grnew = zip(rnew,grfxn(rnew))
1052	for r,gr in grnew:
1053	grfile.write("%15.6g %15.6g\n" % (r,gr))
1054	grfile.close()
1055	print ' G)R) saved to: ',grfilename
1056
1057	def PeakListSave(G2frame,file,peaks):
1058	'Save powder peaks to a data file'
1059	print 'save peak list to file: ',G2frame.peaklistfile
1060	if not peaks:
1061	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1062	try:
1063	dlg.ShowModal()
1064	finally:
1065	dlg.Destroy()
1066	return
1067	for peak in peaks:
1068	file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
1069	(peak[0],peak[2],peak[4],peak[6]))
1070	print 'peak list saved'
1071
1072	def IndexPeakListSave(G2frame,peaks):
1073	'Save powder peaks from the indexing list'
1074	file = open(G2frame.peaklistfile,'wa')
1075	print 'save index peak list to file: ',G2frame.peaklistfile
1076	wx.BeginBusyCursor()
1077	try:
1078	if not peaks:
1079	dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1080	try:
1081	dlg.ShowModal()
1082	finally:
1083	dlg.Destroy()
1084	return
1085	for peak in peaks:
1086	file.write("%12.6f\n" % (peak[7]))
1087	file.close()
1088	finally:
1089	wx.EndBusyCursor()
1090	print 'index peak list saved'
1091
1092	def SetNewPhase(Name='New Phase',SGData=None,cell=None,Super=None):
1093	'''Create a new phase dict with default values for various parameters
1094
1095	:param str Name: Name for new Phase
1096
1097	:param dict SGData: space group data from :func:`GSASIIspc:SpcGroup`;
1098	defaults to data for P 1
1099
1100	:param list cell: unit cell parameter list; defaults to
1101	[1.0,1.0,1.0,90.,90,90.,1.]
1102
1103	'''
1104	if SGData is None: SGData = G2spc.SpcGroup('P 1')[1]
1105	if cell is None: cell=[1.0,1.0,1.0,90.,90,90.,1.]
1106	phaseData = {
1107	'ranId':ran.randint(0,sys.maxint),
1108	'General':{
1109	'Name':Name,
1110	'Type':'nuclear',
1111	'Modulated':False,
1112	'AtomPtrs':[3,1,7,9],
1113	'SGData':SGData,
1114	'Cell':[False,]+cell,
1115	'Pawley dmin':1.0,
1116	'Data plot type':'None',
1117	'SH Texture':{
1118	'Order':0,
1119	'Model':'cylindrical',
1120	'Sample omega':[False,0.0],
1121	'Sample chi':[False,0.0],
1122	'Sample phi':[False,0.0],
1123	'SH Coeff':[False,{}],
1124	'SHShow':False,
1125	'PFhkl':[0,0,1],
1126	'PFxyz':[0,0,1],
1127	'PlotType':'Pole figure',
1128	'Penalty':[['',],0.1,False,1.0]}},
1129	'Atoms':[],
1130	'Drawing':{},
1131	'Histograms':{},
1132	'Pawley ref':[],
1133	'RBModels':{},
1134	}
1135	if Super and Super.get('Use',False):
1136	phaseData['General'].update({'Modulated':True,'Super':True,'SuperSg':Super['ssSymb']})
1137	phaseData['General']['SSGData'] = G2spc.SSpcGroup(SGData,Super['ssSymb'])
1138	phaseData['General']['SuperVec'] = [Super['ModVec'],False,Super['maxH']]
1139
1140	return phaseData
1141
1142	class MultipleChoicesDialog(wx.Dialog):
1143	'''A dialog that offers a series of choices, each with a
1144	title and a wx.Choice widget. Intended to be used Modally.
1145	typical input:
1146
1147	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1148	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1149
1150	selections are placed in self.chosen when OK is pressed
1151
1152	Also see GSASIIctrls
1153	'''
1154	def __init__(self,choicelist,headinglist,
1155	head='Select options',
1156	title='Please select from options below',
1157	parent=None):
1158	self.chosen = []
1159	wx.Dialog.__init__(
1160	self,parent,wx.ID_ANY,head,
1161	pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
1162	panel = wx.Panel(self)
1163	mainSizer = wx.BoxSizer(wx.VERTICAL)
1164	mainSizer.Add((10,10),1)
1165	topLabl = wx.StaticText(panel,wx.ID_ANY,title)
1166	mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL\|wx.CENTER,10)
1167	self.ChItems = []
1168	for choice,lbl in zip(choicelist,headinglist):
1169	mainSizer.Add((10,10),1)
1170	self.chosen.append(0)
1171	topLabl = wx.StaticText(panel,wx.ID_ANY,' '+lbl)
1172	mainSizer.Add(topLabl,0,wx.ALIGN_LEFT,10)
1173	self.ChItems.append(wx.Choice(self, wx.ID_ANY, (100, 50), choices = choice))
1174	mainSizer.Add(self.ChItems[-1],0,wx.ALIGN_CENTER,10)
1175
1176	OkBtn = wx.Button(panel,-1,"Ok")
1177	OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
1178	cancelBtn = wx.Button(panel,-1,"Cancel")
1179	cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
1180	btnSizer = wx.BoxSizer(wx.HORIZONTAL)
1181	btnSizer.Add((20,20),1)
1182	btnSizer.Add(OkBtn)
1183	btnSizer.Add((20,20),1)
1184	btnSizer.Add(cancelBtn)
1185	btnSizer.Add((20,20),1)
1186	mainSizer.Add(btnSizer,0,wx.EXPAND\|wx.BOTTOM\|wx.TOP, 10)
1187	panel.SetSizer(mainSizer)
1188	panel.Fit()
1189	self.Fit()
1190
1191	def OnOk(self,event):
1192	parent = self.GetParent()
1193	if parent is not None: parent.Raise()
1194	# save the results from the choice widgets
1195	self.chosen = []
1196	for w in self.ChItems:
1197	self.chosen.append(w.GetSelection())
1198	self.EndModal(wx.ID_OK)
1199
1200	def OnCancel(self,event):
1201	parent = self.GetParent()
1202	if parent is not None: parent.Raise()
1203	self.chosen = []
1204	self.EndModal(wx.ID_CANCEL)
1205
1206	def ExtractFileFromZip(filename, selection=None, confirmread=True,
1207	confirmoverwrite=True, parent=None,
1208	multipleselect=False):
1209	'''If the filename is a zip file, extract a file from that
1210	archive.
1211
1212	:param list Selection: used to predefine the name of the file
1213	to be extracted. Filename case and zip directory name are
1214	ignored in selection; the first matching file is used.
1215
1216	:param bool confirmread: if True asks the user to confirm before expanding
1217	the only file in a zip
1218
1219	:param bool confirmoverwrite: if True asks the user to confirm
1220	before overwriting if the extracted file already exists
1221
1222	:param bool multipleselect: if True allows more than one zip
1223	file to be extracted, a list of file(s) is returned.
1224	If only one file is present, do not ask which one, otherwise
1225	offer a list of choices (unless selection is used).
1226
1227	:returns: the name of the file that has been created or a
1228	list of files (see multipleselect)
1229
1230	If the file is not a zipfile, return the name of the input file.
1231	If the zipfile is empty or no file has been selected, return None
1232	'''
1233	import zipfile # do this now, since we can save startup time by doing this only on need
1234	import shutil
1235	zloc = os.path.split(filename)[0]
1236	if not zipfile.is_zipfile(filename):
1237	#print("not zip")
1238	return filename
1239
1240	z = zipfile.ZipFile(filename,'r')
1241	zinfo = z.infolist()
1242
1243	if len(zinfo) == 0:
1244	#print('Zip has no files!')
1245	zlist = [-1]
1246	if selection:
1247	choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1248	if selection.lower() in choices:
1249	zlist = [choices.index(selection.lower())]
1250	else:
1251	print('debug: file '+str(selection)+' was not found in '+str(filename))
1252	zlist = [-1]
1253	elif len(zinfo) == 1 and confirmread:
1254	result = wx.ID_NO
1255	dlg = wx.MessageDialog(
1256	parent,
1257	'Is file '+str(zinfo[0].filename)+
1258	' what you want to extract from '+
1259	str(os.path.split(filename)[1])+'?',
1260	'Confirm file',
1261	wx.YES_NO \| wx.ICON_QUESTION)
1262	try:
1263	result = dlg.ShowModal()
1264	finally:
1265	dlg.Destroy()
1266	if result == wx.ID_NO:
1267	zlist = [-1]
1268	else:
1269	zlist = [0]
1270	elif len(zinfo) == 1:
1271	zlist = [0]
1272	elif multipleselect:
1273	# select one or more from a from list
1274	choices = [i.filename for i in zinfo]
1275	dlg = G2G.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1276	'Choose file(s)',choices)
1277	if dlg.ShowModal() == wx.ID_OK:
1278	zlist = dlg.GetSelections()
1279	else:
1280	zlist = []
1281	dlg.Destroy()
1282	else:
1283	# select one from a from list
1284	choices = [i.filename for i in zinfo]
1285	dlg = wx.SingleChoiceDialog(parent,
1286	'Select file to extract from zip file'+str(filename),'Choose file',
1287	choices,)
1288	if dlg.ShowModal() == wx.ID_OK:
1289	zlist = [dlg.GetSelection()]
1290	else:
1291	zlist = [-1]
1292	dlg.Destroy()
1293
1294	outlist = []
1295	for zindex in zlist:
1296	if zindex >= 0:
1297	efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1298	if os.path.exists(efil) and confirmoverwrite:
1299	result = wx.ID_NO
1300	dlg = wx.MessageDialog(parent,
1301	'File '+str(efil)+' already exists. OK to overwrite it?',
1302	'Confirm overwrite',wx.YES_NO \| wx.ICON_QUESTION)
1303	try:
1304	result = dlg.ShowModal()
1305	finally:
1306	dlg.Destroy()
1307	if result == wx.ID_NO:
1308	zindex = -1
1309	if zindex >= 0:
1310	# extract the file to the current directory, regardless of it's original path
1311	#z.extract(zinfo[zindex],zloc)
1312	eloc,efil = os.path.split(zinfo[zindex].filename)
1313	outfile = os.path.join(zloc, efil)
1314	fpin = z.open(zinfo[zindex])
1315	fpout = file(outfile, "wb")
1316	shutil.copyfileobj(fpin, fpout)
1317	fpin.close()
1318	fpout.close()
1319	outlist.append(outfile)
1320	z.close()
1321	if multipleselect and len(outlist) >= 1:
1322	return outlist
1323	elif len(outlist) == 1:
1324	return outlist[0]
1325	else:
1326	return None
1327
1328	######################################################################
1329	# base classes for reading various types of data files
1330	# not used directly, only by subclassing
1331	######################################################################
1332	try:
1333	E,SGData = G2spc.SpcGroup('P 1') # data structure for default space group
1334	except: # errors on doc build
1335	SGData = None
1336	P1SGData = SGData
1337	######################################################################
1338	class ImportBaseclass(object):
1339	'''Defines a base class for the reading of input files (diffraction
1340	data, coordinates,...). See :ref:`Writing a Import Routine<Import_routines>`
1341	for an explanation on how to use a subclass of this class.
1342	'''
1343	class ImportException(Exception):
1344	'''Defines an Exception that is used when an import routine hits an expected error,
1345	usually in .Reader.
1346
1347	Good practice is that the Reader should define a value in self.errors that
1348	tells the user some information about what is wrong with their file.
1349	'''
1350	pass
1351
1352	UseReader = True # in __init__ set value of self.UseReader to False to skip use of current importer
1353	def __init__(self,formatName,longFormatName=None,
1354	extensionlist=[],strictExtension=False,):
1355	self.formatName = formatName # short string naming file type
1356	if longFormatName: # longer string naming file type
1357	self.longFormatName = longFormatName
1358	else:
1359	self.longFormatName = formatName
1360	# define extensions that are allowed for the file type
1361	# for windows, remove any extensions that are duplicate, as case is ignored
1362	if sys.platform == 'windows' and extensionlist:
1363	extensionlist = list(set([s.lower() for s in extensionlist]))
1364	self.extensionlist = extensionlist
1365	# If strictExtension is True, the file will not be read, unless
1366	# the extension matches one in the extensionlist
1367	self.strictExtension = strictExtension
1368	self.errors = ''
1369	self.warnings = ''
1370	# used for readers that will use multiple passes to read
1371	# more than one data block
1372	self.repeat = False
1373	self.selections = []
1374	self.repeatcount = 0
1375	self.readfilename = '?'
1376	#print 'created',self.__class__
1377
1378	def ReInitialize(self):
1379	'Reinitialize the Reader to initial settings'
1380	self.errors = ''
1381	self.warnings = ''
1382	self.repeat = False
1383	self.repeatcount = 0
1384	self.readfilename = '?'
1385
1386	def BlockSelector(self, ChoiceList, ParentFrame=None,title='Select a block',
1387	size=None, header='Block Selector',useCancel=True):
1388	''' Provide a wx dialog to select a block if the file contains more
1389	than one set of data and one must be selected
1390	'''
1391	if useCancel:
1392	dlg = wx.SingleChoiceDialog(
1393	ParentFrame,title, header,ChoiceList)
1394	else:
1395	dlg = wx.SingleChoiceDialog(
1396	ParentFrame,title, header,ChoiceList,
1397	style=wx.DEFAULT_DIALOG_STYLE\|wx.RESIZE_BORDER\|wx.OK\|wx.CENTRE)
1398	if size: dlg.SetSize(size)
1399	dlg.CenterOnParent()
1400	if dlg.ShowModal() == wx.ID_OK:
1401	sel = dlg.GetSelection()
1402	return sel
1403	else:
1404	return None
1405	dlg.Destroy()
1406
1407	def MultipleBlockSelector(self, ChoiceList, ParentFrame=None,
1408	title='Select a block',size=None, header='Block Selector'):
1409	'''Provide a wx dialog to select a block of data if the
1410	file contains more than one set of data and one must be
1411	selected.
1412
1413	:returns: a list of the selected blocks
1414	'''
1415	dlg = wx.MultiChoiceDialog(ParentFrame,title, header,ChoiceList+['Select all'],
1416	wx.CHOICEDLG_STYLE)
1417	dlg.CenterOnScreen()
1418	if size: dlg.SetSize(size)
1419	if dlg.ShowModal() == wx.ID_OK:
1420	sel = dlg.GetSelections()
1421	else:
1422	return []
1423	dlg.Destroy()
1424	selected = []
1425	if len(ChoiceList) in sel:
1426	return range(len(ChoiceList))
1427	else:
1428	return sel
1429	return selected
1430
1431	def MultipleChoicesDialog(self, choicelist, headinglist, ParentFrame=None, **kwargs):
1432	'''A modal dialog that offers a series of choices, each with a title and a wx.Choice
1433	widget. Typical input:
1434
1435	* choicelist=[ ('a','b','c'), ('test1','test2'),('no choice',)]
1436
1437	* headinglist = [ 'select a, b or c', 'select 1 of 2', 'No option here']
1438
1439	optional keyword parameters are: head (window title) and title
1440	returns a list of selected indicies for each choice (or None)
1441	'''
1442	result = None
1443	dlg = MultipleChoicesDialog(choicelist,headinglist,
1444	parent=ParentFrame, **kwargs)
1445	dlg.CenterOnParent()
1446	if dlg.ShowModal() == wx.ID_OK:
1447	result = dlg.chosen
1448	dlg.Destroy()
1449	return result
1450
1451	def ShowBusy(self):
1452	wx.BeginBusyCursor()
1453	# wx.Yield() # make it happen now!
1454
1455	def DoneBusy(self):
1456	wx.EndBusyCursor()
1457	wx.Yield() # make it happen now!
1458
1459	# def Reader(self, filename, filepointer, ParentFrame=None, **unused):
1460	# '''This method must be supplied in the child class to read the file.
1461	# if the read fails either return False or raise an Exception
1462	# preferably of type ImportException.
1463	# '''
1464	# #start reading
1465	# raise ImportException("Error occurred while...")
1466	# self.errors += "Hint for user on why the error occur
1467	# return False # if an error occurs
1468	# return True # if read OK
1469
1470	def ExtensionValidator(self, filename):
1471	'''This methods checks if the file has the correct extension
1472	Return False if this filename will not be supported by this reader
1473	Return True if the extension matches the list supplied by the reader
1474	Return None if the reader allows un-registered extensions
1475	'''
1476	if filename:
1477	ext = os.path.splitext(filename)[1]
1478	if sys.platform == 'windows': ext = ext.lower()
1479	if ext in self.extensionlist: return True
1480	if self.strictExtension: return False
1481	return None
1482
1483	def ContentsValidator(self, filepointer):
1484	'''This routine will attempt to determine if the file can be read
1485	with the current format.
1486	This will typically be overridden with a method that
1487	takes a quick scan of [some of]
1488	the file contents to do a "sanity" check if the file
1489	appears to match the selected format.
1490	Expected to be called via self.Validator()
1491	'''
1492	#filepointer.seek(0) # rewind the file pointer
1493	return True
1494
1495	def CIFValidator(self, filepointer):
1496	'''A :meth:`ContentsValidator` for use to validate CIF files.
1497	'''
1498	for i,l in enumerate(filepointer):
1499	if i >= 1000: return True
1500	'''Encountered only blank lines or comments in first 1000
1501	lines. This is unlikely, but assume it is CIF anyway, since we are
1502	even less likely to find a file with nothing but hashes and
1503	blank lines'''
1504	line = l.strip()
1505	if len(line) == 0: # ignore blank lines
1506	continue
1507	elif line.startswith('#'): # ignore comments
1508	continue
1509	elif line.startswith('data_'): # on the right track, accept this file
1510	return True
1511	else: # found something invalid
1512	self.errors = 'line '+str(i+1)+' contains unexpected data:\n'
1513	if all([ord(c) < 128 and ord(c) != 0 for c in str(l)]): # show only if ASCII
1514	self.errors += ' '+str(l)
1515	else:
1516	self.errors += ' (binary)'
1517	self.errors += '\n Note: a CIF should only have blank lines or comments before'
1518	self.errors += '\n a data_ statement begins a block.'
1519	return False
1520
1521	######################################################################
1522	class ImportPhase(ImportBaseclass):
1523	'''Defines a base class for the reading of files with coordinates
1524
1525	Objects constructed that subclass this (in import/G2phase_*.py etc.) will be used
1526	in :meth:`GSASII.GSASII.OnImportPhase`.
1527	See :ref:`Writing a Import Routine<Import_Routines>`
1528	for an explanation on how to use this class.
1529
1530	'''
1531	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1532	strictExtension=False,):
1533	# call parent __init__
1534	ImportBaseclass.__init__(self,formatName,longFormatName,
1535	extensionlist,strictExtension)
1536	self.Phase = None # a phase must be created with G2IO.SetNewPhase in the Reader
1537	self.Constraints = None
1538
1539	def PhaseSelector(self, ChoiceList, ParentFrame=None,
1540	title='Select a phase', size=None,header='Phase Selector'):
1541	''' Provide a wx dialog to select a phase if the file contains more
1542	than one phase
1543	'''
1544	return self.BlockSelector(ChoiceList,ParentFrame,title,
1545	size,header)
1546
1547	######################################################################
1548	class ImportStructFactor(ImportBaseclass):
1549	'''Defines a base class for the reading of files with tables
1550	of structure factors.
1551
1552	Structure factors are read with a call to :meth:`GSASII.GSASII.OnImportSfact`
1553	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`, which calls
1554	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1555	:meth:`Reader`.
1556
1557	See :ref:`Writing a Import Routine<Import_Routines>`
1558	for an explanation on how to use import classes in general. The specifics
1559	for reading a structure factor histogram require that
1560	the ``Reader()`` routine in the import
1561	class need to do only a few things: It
1562	should load :attr:`RefDict` item ``'RefList'`` with the reflection list,
1563	and set :attr:`Parameters` with the instrument parameters
1564	(initialized with :meth:`InitParameters` and set with :meth:`UpdateParameters`).
1565	'''
1566	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1567	strictExtension=False,):
1568	ImportBaseclass.__init__(self,formatName,longFormatName,
1569	extensionlist,strictExtension)
1570
1571	# define contents of Structure Factor entry
1572	self.Parameters = []
1573	'self.Parameters is a list with two dicts for data parameter settings'
1574	self.InitParameters()
1575	self.RefDict = {'RefList':[],'FF':{},'Super':0}
1576	self.Banks = [] #for multi bank data (usually TOF)
1577	'''self.RefDict is a dict containing the reflection information, as read from the file.
1578	Item 'RefList' contains the reflection information. See the
1579	:ref:`Single Crystal Reflection Data Structure<XtalRefl_table>`
1580	for the contents of each row. Dict element 'FF'
1581	contains the form factor values for each element type; if this entry
1582	is left as initialized (an empty list) it will be initialized as needed later.
1583	'''
1584	def ReInitialize(self):
1585	'Reinitialize the Reader to initial settings'
1586	ImportBaseclass.ReInitialize(self)
1587	self.InitParameters()
1588	self.Banks = [] #for multi bank data (usually TOF)
1589	self.RefDict = {'RefList':[],'FF':{},'Super':0}
1590
1591	def InitParameters(self):
1592	'initialize the instrument parameters structure'
1593	Lambda = 0.70926
1594	HistType = 'SXC'
1595	self.Parameters = [{'Type':[HistType,HistType], # create the structure
1596	'Lam':[Lambda,Lambda]
1597	}, {}]
1598	'Parameters is a list with two dicts for data parameter settings'
1599
1600	def UpdateParameters(self,Type=None,Wave=None):
1601	'Revise the instrument parameters'
1602	if Type is not None:
1603	self.Parameters[0]['Type'] = [Type,Type]
1604	if Wave is not None:
1605	self.Parameters[0]['Lam'] = [Wave,Wave]
1606
1607	######################################################################
1608	class ImportPowderData(ImportBaseclass):
1609	'''Defines a base class for the reading of files with powder data.
1610
1611	Objects constructed that subclass this (in import/G2pwd_*.py etc.) will be used
1612	in :meth:`GSASII.GSASII.OnImportPowder`.
1613	See :ref:`Writing a Import Routine<Import_Routines>`
1614	for an explanation on how to use this class.
1615	'''
1616	def __init__(self,formatName,longFormatName=None,
1617	extensionlist=[],strictExtension=False,):
1618	ImportBaseclass.__init__(self,formatName,longFormatName,
1619	extensionlist,strictExtension)
1620	self.clockWd = None # used in TOF
1621	self.ReInitialize()
1622
1623	def ReInitialize(self):
1624	'Reinitialize the Reader to initial settings'
1625	ImportBaseclass.ReInitialize(self)
1626	self.powderentry = ['',None,None] # (filename,Pos,Bank)
1627	self.powderdata = [] # Powder dataset
1628	'''A powder data set is a list with items [x,y,w,yc,yb,yd]:
1629	np.array(x), # x-axis values
1630	np.array(y), # powder pattern intensities
1631	np.array(w), # 1/sig(intensity)^2 values (weights)
1632	np.array(yc), # calc. intensities (zero)
1633	np.array(yb), # calc. background (zero)
1634	np.array(yd), # obs-calc profiles
1635	'''
1636	self.comments = []
1637	self.idstring = ''
1638	self.Sample = G2pdG.SetDefaultSample() # default sample parameters
1639	self.Controls = {} # items to be placed in top-level Controls
1640	self.GSAS = None # used in TOF
1641	self.repeat_instparm = True # Should a parm file be
1642	# used for multiple histograms?
1643	self.instparm = None # name hint from file of instparm to use
1644	self.instfile = '' # full path name to instrument parameter file
1645	self.instbank = '' # inst parm bank number
1646	self.instmsg = '' # a label that gets printed to show
1647	# where instrument parameters are from
1648	self.numbanks = 1
1649	self.instdict = {} # place items here that will be transferred to the instrument parameters
1650	self.pwdparms = {} # place parameters that are transferred directly to the tree
1651	# here (typically from an existing GPX file)
1652	######################################################################
1653	class ImportSmallAngleData(ImportBaseclass):
1654	'''Defines a base class for the reading of files with small angle data.
1655	See :ref:`Writing a Import Routine<Import_Routines>`
1656	for an explanation on how to use this class.
1657	'''
1658	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1659	strictExtension=False,):
1660
1661	ImportBaseclass.__init__(self,formatName,longFormatName,extensionlist,
1662	strictExtension)
1663	self.ReInitialize()
1664
1665	def ReInitialize(self):
1666	'Reinitialize the Reader to initial settings'
1667	ImportBaseclass.ReInitialize(self)
1668	self.smallangleentry = ['',None,None] # (filename,Pos,Bank)
1669	self.smallangledata = [] # SASD dataset
1670	'''A small angle data set is a list with items [x,y,w,yc,yd]:
1671	np.array(x), # x-axis values
1672	np.array(y), # powder pattern intensities
1673	np.array(w), # 1/sig(intensity)^2 values (weights)
1674	np.array(yc), # calc. intensities (zero)
1675	np.array(yd), # obs-calc profiles
1676	np.array(yb), # preset bkg
1677	'''
1678	self.comments = []
1679	self.idstring = ''
1680	self.Sample = G2pdG.SetDefaultSample()
1681	self.GSAS = None # used in TOF
1682	self.clockWd = None # used in TOF
1683	self.numbanks = 1
1684	self.instdict = {} # place items here that will be transferred to the instrument parameters
1685
1686	######################################################################
1687	class ImportImage(ImportBaseclass):
1688	'''Defines a base class for the reading of images
1689
1690	Images are read in only these places:
1691
1692	* Initial reading is typically done from a menu item
1693	with a call to :meth:`GSASII.GSASII.OnImportImage`
1694	which in turn calls :meth:`GSASII.GSASII.OnImportGeneric`. That calls
1695	methods :meth:`ExtensionValidator`, :meth:`ContentsValidator` and
1696	:meth:`Reader`. This returns a list of reader objects for each read image.
1697
1698	* Images are read alternatively in :func:`GSASIIIO.ReadImages`, which puts image info
1699	directly into the data tree.
1700
1701	* Images are reloaded with :func:`GSASIIIO.GetImageData`.
1702
1703	.. _Image_import_routines:
1704
1705	When reading an image, the ``Reader()`` routine in the ImportImage class
1706	should set:
1707
1708	* :attr:`Comments`: a list of strings (str),
1709	* :attr:`Npix`: the number of pixels in the image (int),
1710	* :attr:`Image`: the actual image as a numpy array (np.array)
1711	* :attr:`Data`: a dict defining image parameters (dict). Within this dict the following
1712	data items are needed:
1713
1714	* 'pixelSize': size of each pixel in microns (such as ``[200,200]``.
1715	* 'wavelength': wavelength in Angstoms.
1716	* 'distance': distance of detector from sample in cm.
1717	* 'center': uncalibrated center of beam on detector (such as ``[204.8,204.8]``.
1718	* 'size': size of image (such as ``[2048,2048]``).
1719	* 'ImageTag': image number or other keyword used to retrieve image from
1720	a multi-image data file (defaults to ``1`` if not specified).
1721	* 'sumfile': holds sum image file name if a sum was produced from a multi image file
1722
1723	optional data items:
1724
1725	* :attr:`repeat`: set to True if there are additional images to
1726	read in the file, False otherwise
1727	* :attr:`repeatcount`: set to the number of the image.
1728
1729	Note that the above is initialized with :meth:`InitParameters`.
1730	(Also see :ref:`Writing a Import Routine<Import_Routines>`
1731	for an explanation on how to use import classes in general.)
1732	'''
1733	def __init__(self,formatName,longFormatName=None,extensionlist=[],
1734	strictExtension=False,):
1735	ImportBaseclass.__init__(self,formatName,longFormatName,
1736	extensionlist,strictExtension)
1737	self.InitParameters()
1738
1739	def ReInitialize(self):
1740	'Reinitialize the Reader to initial settings -- not used at present'
1741	ImportBaseclass.ReInitialize(self)
1742	self.InitParameters()
1743
1744	def InitParameters(self):
1745	'initialize the instrument parameters structure'
1746	self.Comments = ['No comments']
1747	self.Data = {}
1748	self.Npix = 0
1749	self.Image = None
1750	self.repeat = False
1751	self.repeatcount = 1
1752	self.sumfile = ''
1753
1754	def LoadImage(self,ParentFrame,imagefile,imagetag=None):
1755	'''Optionally, call this after reading in an image to load it into the tree.
1756	This saves time by preventing a reread of the same information.
1757	'''
1758	if ParentFrame:
1759	ParentFrame.ImageZ = self.Image # store the image for plotting
1760	ParentFrame.oldImagefile = imagefile # save the name of the last image file read
1761	ParentFrame.oldImageTag = imagetag # save the tag of the last image file read
1762
1763	######################################################################
1764	def striphist(var,insChar=''):
1765	'strip a histogram number from a var name'
1766	sv = var.split(':')
1767	if len(sv) <= 1: return var
1768	if sv[1]:
1769	sv[1] = insChar
1770	return ':'.join(sv)
1771	class ExportBaseclass(object):
1772	'''Defines a base class for the exporting of GSAS-II results.
1773
1774	This class is subclassed in the various exports/G2export_*.py files. Those files
1775	are imported in :meth:`GSASII.GSASII._init_Exports` which defines the
1776	appropriate menu items for each one and the .Exporter method is called
1777	directly from the menu item.
1778
1779	Routines may also define a .Writer method, which is used to write a single
1780	file without invoking any GUI objects.
1781	'''
1782	def __init__(self,G2frame,formatName,extension,longFormatName=None,):
1783	self.G2frame = G2frame
1784	self.formatName = formatName # short string naming file type
1785	self.extension = extension
1786	if longFormatName: # longer string naming file type
1787	self.longFormatName = longFormatName
1788	else:
1789	self.longFormatName = formatName
1790	self.OverallParms = {}
1791	self.Phases = {}
1792	self.Histograms = {}
1793	self.powderDict = {}
1794	self.xtalDict = {}
1795	self.parmDict = {}
1796	self.sigDict = {}
1797	# updated in InitExport:
1798	self.currentExportType = None # type of export that has been requested
1799	# updated in ExportSelect (when used):
1800	self.phasenam = None # a list of selected phases
1801	self.histnam = None # a list of selected histograms
1802	self.filename = None # name of file to be written (single export) or template (multiple files)
1803	self.dirname = '' # name of directory where file(s) will be written
1804	self.fullpath = '' # name of file being written -- full path
1805
1806	# items that should be defined in a subclass of this class
1807	self.exporttype = [] # defines the type(s) of exports that the class can handle.
1808	# The following types are defined: 'project', "phase", "powder", "single"
1809	self.multiple = False # set as True if the class can export multiple phases or histograms
1810	# self.multiple is ignored for "project" exports
1811
1812	def InitExport(self,event):
1813	'''Determines the type of menu that called the Exporter and
1814	misc initialization.
1815	'''
1816	self.filename = None # name of file to be written (single export)
1817	self.dirname = '' # name of file to be written (multiple export)
1818	if event:
1819	self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1820
1821	def MakePWDRfilename(self,hist):
1822	'''Make a filename root (no extension) from a PWDR histogram name
1823
1824	:param str hist: the histogram name in data tree (starts with "PWDR ")
1825	'''
1826	file0 = ''
1827	file1 = hist[5:]
1828	# replace repeated blanks
1829	while file1 != file0:
1830	file0 = file1
1831	file1 = file0.replace(' ',' ').strip()
1832	file0 = file1.replace('Azm= ','A')
1833	# if angle has unneeded decimal places on aziumuth, remove them
1834	if file0[-3:] == '.00': file0 = file0[:-3]
1835	file0 = file0.replace('.','_')
1836	file0 = file0.replace(' ','_')
1837	return file0
1838
1839	def ExportSelect(self,AskFile='ask'):
1840	'''Selects histograms or phases when needed. Sets a default file name when
1841	requested into self.filename; always sets a default directory in self.dirname.
1842
1843	:param bool AskFile: Determines how this routine processes getting a
1844	location to store the current export(s).
1845
1846	* if AskFile is 'ask' (default option), get the name of the file to be written;
1847	self.filename and self.dirname are always set. In the case where
1848	multiple files must be generated, the export routine should do this
1849	based on self.filename as a template.
1850	* if AskFile is 'dir', get the name of the directory to be used;
1851	self.filename is not used, but self.dirname is always set. The export routine
1852	will always generate the file name.
1853	* if AskFile is 'single', get only the name of the directory to be used when
1854	multiple items will be written (as multiple files) are used
1855	or a complete file name is requested when a single file
1856	name is selected. self.dirname is always set and self.filename used
1857	only when a single file is selected.
1858	* if AskFile is 'default', creates a name of the file to be used from
1859	the name of the project (.gpx) file. If the project has not been saved,
1860	then the name of file is requested.
1861	self.filename and self.dirname are always set. In the case where
1862	multiple file names must be generated, the export routine should do this
1863	based on self.filename.
1864	* if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1865	file. If the project has not been saved, then a directory is requested.
1866	self.filename is not used.
1867
1868	:returns: True in case of an error
1869	'''
1870
1871	numselected = 1
1872	if self.currentExportType == 'phase':
1873	if len(self.Phases) == 0:
1874	self.G2frame.ErrorDialog(
1875	'Empty project',
1876	'Project does not contain any phases.')
1877	return True
1878	elif len(self.Phases) == 1:
1879	self.phasenam = self.Phases.keys()
1880	elif self.multiple:
1881	choices = sorted(self.Phases.keys())
1882	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1883	if phasenum is None: return True
1884	self.phasenam = [choices[i] for i in phasenum]
1885	if not self.phasenam: return True
1886	numselected = len(self.phasenam)
1887	else:
1888	choices = sorted(self.Phases.keys())
1889	phasenum = G2G.ItemSelector(choices,self.G2frame)
1890	if phasenum is None: return True
1891	self.phasenam = [choices[phasenum]]
1892	numselected = len(self.phasenam)
1893	elif self.currentExportType == 'single':
1894	if len(self.xtalDict) == 0:
1895	self.G2frame.ErrorDialog(
1896	'Empty project',
1897	'Project does not contain any single crystal data.')
1898	return True
1899	elif len(self.xtalDict) == 1:
1900	self.histnam = self.xtalDict.values()
1901	elif self.multiple:
1902	choices = sorted(self.xtalDict.values())
1903	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1904	if not hnum: return True
1905	self.histnam = [choices[i] for i in hnum]
1906	numselected = len(self.histnam)
1907	else:
1908	choices = sorted(self.xtalDict.values())
1909	hnum = G2G.ItemSelector(choices,self.G2frame)
1910	if hnum is None: return True
1911	self.histnam = [choices[hnum]]
1912	numselected = len(self.histnam)
1913	elif self.currentExportType == 'powder':
1914	if len(self.powderDict) == 0:
1915	self.G2frame.ErrorDialog(
1916	'Empty project',
1917	'Project does not contain any powder data.')
1918	return True
1919	elif len(self.powderDict) == 1:
1920	self.histnam = self.powderDict.values()
1921	elif self.multiple:
1922	choices = sorted(self.powderDict.values())
1923	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1924	if not hnum: return True
1925	self.histnam = [choices[i] for i in hnum]
1926	numselected = len(self.histnam)
1927	else:
1928	choices = sorted(self.powderDict.values())
1929	hnum = G2G.ItemSelector(choices,self.G2frame)
1930	if hnum is None: return True
1931	self.histnam = [choices[hnum]]
1932	numselected = len(self.histnam)
1933	elif self.currentExportType == 'image':
1934	if len(self.Histograms) == 0:
1935	self.G2frame.ErrorDialog(
1936	'Empty project',
1937	'Project does not contain any images.')
1938	return True
1939	elif len(self.Histograms) == 1:
1940	self.histnam = self.Histograms.keys()
1941	else:
1942	choices = sorted(self.Histograms.keys())
1943	hnum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1944	if self.multiple:
1945	if not hnum: return True
1946	self.histnam = [choices[i] for i in hnum]
1947	else:
1948	if hnum is None: return True
1949	self.histnam = [choices[hnum]]
1950	numselected = len(self.histnam)
1951	if self.currentExportType == 'map':
1952	# search for phases with maps
1953	mapPhases = []
1954	choices = []
1955	for phasenam in sorted(self.Phases):
1956	phasedict = self.Phases[phasenam] # pointer to current phase info
1957	if len(phasedict['General']['Map'].get('rho',[])):
1958	mapPhases.append(phasenam)
1959	if phasedict['General']['Map'].get('Flip'):
1960	choices.append('Charge flip map: '+str(phasenam))
1961	elif phasedict['General']['Map'].get('MapType'):
1962	choices.append(
1963	str(phasedict['General']['Map'].get('MapType'))
1964	+ ' map: ' + str(phasenam))
1965	else:
1966	choices.append('unknown map: '+str(phasenam))
1967	# select a map if needed
1968	if len(mapPhases) == 0:
1969	self.G2frame.ErrorDialog(
1970	'Empty project',
1971	'Project does not contain any maps.')
1972	return True
1973	elif len(mapPhases) == 1:
1974	self.phasenam = mapPhases
1975	else:
1976	phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1977	if self.multiple:
1978	if not phasenum: return True
1979	self.phasenam = [mapPhases[i] for i in phasenum]
1980	else:
1981	if phasenum is None: return True
1982	self.phasenam = [mapPhases[phasenum]]
1983	numselected = len(self.phasenam)
1984
1985	# items selected, now set self.dirname and usually self.filename
1986	if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
1987	AskFile == 'default' and not self.G2frame.GSASprojectfile
1988	):
1989	filename = self.askSaveFile()
1990	if not filename: return True
1991	self.dirname,self.filename = os.path.split(filename)
1992	elif AskFile == 'dir' or AskFile == 'single' or (
1993	AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
1994	):
1995	self.dirname = self.askSaveDirectory()
1996	if not self.dirname: return True
1997	elif AskFile == 'default-dir' or AskFile == 'default':
1998	self.dirname,self.filename = os.path.split(
1999	os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
2000	)
2001	else:
2002	raise Exception('This should not happen!')
2003
2004	def loadParmDict(self):
2005	'''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
2006	refined values to those from the last cycle and set the uncertainties for the
2007	refined parameters in another dict (self.sigDict).
2008
2009	Expands the parm & sig dicts to include values derived from constraints.
2010	'''
2011	self.parmDict = {}
2012	self.sigDict = {}
2013	rigidbodyDict = {}
2014	covDict = {}
2015	consDict = {}
2016	Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2017	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2018	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2019	while item:
2020	name = self.G2frame.PatternTree.GetItemText(item)
2021	if name == 'Rigid bodies':
2022	rigidbodyDict = self.G2frame.PatternTree.GetItemPyData(item)
2023	elif name == 'Covariance':
2024	covDict = self.G2frame.PatternTree.GetItemPyData(item)
2025	elif name == 'Constraints':
2026	consDict = self.G2frame.PatternTree.GetItemPyData(item)
2027	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2028	rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
2029	self.parmDict.update(rbDict)
2030	rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
2031	Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData(
2032	Phases,RestraintDict=None,rbIds=rbIds,Print=False)
2033	self.parmDict.update(phaseDict)
2034	hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(
2035	Phases,Histograms,Print=False,resetRefList=False)
2036	self.parmDict.update(hapDict)
2037	histVary,histDict,controlDict = G2stIO.GetHistogramData(Histograms,Print=False)
2038	self.parmDict.update(histDict)
2039	self.parmDict.update(zip(
2040	covDict.get('varyList',[]),
2041	covDict.get('variables',[])))
2042	self.sigDict = dict(zip(
2043	covDict.get('varyList',[]),
2044	covDict.get('sig',[])))
2045	# expand to include constraints: first compile a list of constraints
2046	constList = []
2047	for item in consDict:
2048	if item.startswith('_'): continue
2049	constList += consDict[item]
2050	# now process the constraints
2051	G2mv.InitVars()
2052	constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
2053	varyList = covDict.get('varyListStart')
2054	if varyList is None and len(constDict) == 0:
2055	# no constraints can use varyList
2056	varyList = covDict.get('varyList')
2057	elif varyList is None:
2058	# old GPX file from before pre-constraint varyList is saved
2059	print ' * Old refinement: Please use Calculate/Refine to redo *'
2060	raise Exception(' * Export aborted *')
2061	else:
2062	varyList = list(varyList)
2063	try:
2064	groups,parmlist = G2mv.GroupConstraints(constDict)
2065	G2mv.GenerateConstraints(groups,parmlist,varyList,constDict,fixedList,self.parmDict)
2066	except:
2067	# this really should not happen
2068	print ' * ERROR - constraints are internally inconsistent *'
2069	errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
2070	print 'Errors',errmsg
2071	if warnmsg: print 'Warnings',warnmsg
2072	raise Exception(' * CIF creation aborted *')
2073	# add the constrained values to the parameter dictionary
2074	G2mv.Dict2Map(self.parmDict,varyList)
2075	# and add their uncertainties into the esd dictionary (sigDict)
2076	if covDict.get('covMatrix') is not None:
2077	self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
2078
2079	def loadTree(self):
2080	'''Load the contents of the data tree into a set of dicts
2081	(self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
2082	& self.xtalDict)
2083
2084	* The childrenless data tree items are overall parameters/controls for the
2085	entire project and are placed in self.OverallParms
2086	* Phase items are placed in self.Phases
2087	* Data items are placed in self.Histogram. The key for these data items
2088	begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
2089	'''
2090	self.OverallParms = {}
2091	self.powderDict = {}
2092	self.xtalDict = {}
2093	self.Phases = {}
2094	self.Histograms = {}
2095	self.SeqRefdata = None
2096	self.SeqRefhist = None
2097	if self.G2frame.PatternTree.IsEmpty(): return # nothing to do
2098	histType = None
2099	if self.currentExportType == 'phase':
2100	# if exporting phases load them here
2101	sub = G2gd.GetPatternTreeItemId(self.G2frame,self.G2frame.root,'Phases')
2102	if not sub:
2103	print 'no phases found'
2104	return True
2105	item, cookie = self.G2frame.PatternTree.GetFirstChild(sub)
2106	while item:
2107	phaseName = self.G2frame.PatternTree.GetItemText(item)
2108	self.Phases[phaseName] = self.G2frame.PatternTree.GetItemPyData(item)
2109	item, cookie = self.G2frame.PatternTree.GetNextChild(sub, cookie)
2110	return
2111	elif self.currentExportType == 'single':
2112	histType = 'HKLF'
2113	elif self.currentExportType == 'powder':
2114	histType = 'PWDR'
2115	elif self.currentExportType == 'image':
2116	histType = 'IMG'
2117
2118	if histType: # Loading just one kind of tree entry
2119	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2120	while item:
2121	name = self.G2frame.PatternTree.GetItemText(item)
2122	if name.startswith(histType):
2123	if self.Histograms.get(name): # there is already an item with this name
2124	print('Histogram name '+str(name)+' is repeated. Renaming')
2125	if name[-1] == '9':
2126	name = name[:-1] + '10'
2127	elif name[-1] in '012345678':
2128	name = name[:-1] + str(int(name[-1])+1)
2129	else:
2130	name += '-1'
2131	self.Histograms[name] = {}
2132	# the main info goes into Data, but the 0th
2133	# element contains refinement results, carry
2134	# that over too now.
2135	self.Histograms[name]['Data'] = self.G2frame.PatternTree.GetItemPyData(item)[1]
2136	self.Histograms[name][0] = self.G2frame.PatternTree.GetItemPyData(item)[0]
2137	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2138	while item2:
2139	child = self.G2frame.PatternTree.GetItemText(item2)
2140	self.Histograms[name][child] = self.G2frame.PatternTree.GetItemPyData(item2)
2141	item2, cookie2 = self.G2frame.PatternTree.GetNextChild(item, cookie2)
2142	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2143	# index powder and single crystal histograms by number
2144	for hist in self.Histograms:
2145	if hist.startswith("PWDR"):
2146	d = self.powderDict
2147	elif hist.startswith("HKLF"):
2148	d = self.xtalDict
2149	else:
2150	return
2151	i = self.Histograms[hist].get('hId')
2152	if i is None and not d.keys():
2153	i = 0
2154	elif i is None or i in d.keys():
2155	i = max(d.keys())+1
2156	d[i] = hist
2157	return
2158	# else standard load: using all interlinked phases and histograms
2159	self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
2160	item, cookie = self.G2frame.PatternTree.GetFirstChild(self.G2frame.root)
2161	while item:
2162	name = self.G2frame.PatternTree.GetItemText(item)
2163	item2, cookie2 = self.G2frame.PatternTree.GetFirstChild(item)
2164	if not item2:
2165	self.OverallParms[name] = self.G2frame.PatternTree.GetItemPyData(item)
2166	item, cookie = self.G2frame.PatternTree.GetNextChild(self.G2frame.root, cookie)
2167	# index powder and single crystal histograms
2168	for hist in self.Histograms:
2169	i = self.Histograms[hist]['hId']
2170	if hist.startswith("PWDR"):
2171	self.powderDict[i] = hist
2172	elif hist.startswith("HKLF"):
2173	self.xtalDict[i] = hist
2174
2175	def dumpTree(self,mode='type'):
2176	'''Print out information on the data tree dicts loaded in loadTree.
2177	Used for testing only.
2178	'''
2179	if self.SeqRefdata and self.SeqRefhist:
2180	print('Note that dumpTree does not show sequential results')
2181	print '\nOverall'
2182	if mode == 'type':
2183	def Show(arg): return type(arg)
2184	else:
2185	def Show(arg): return arg
2186	for key in self.OverallParms:
2187	print ' ',key,Show(self.OverallParms[key])
2188	print 'Phases'
2189	for key1 in self.Phases:
2190	print ' ',key1,Show(self.Phases[key1])
2191	print 'Histogram'
2192	for key1 in self.Histograms:
2193	print ' ',key1,Show(self.Histograms[key1])
2194	for key2 in self.Histograms[key1]:
2195	print ' ',key2,Show(self.Histograms[key1][key2])
2196
2197	def defaultSaveFile(self):
2198	return os.path.abspath(
2199	os.path.splitext(self.G2frame.GSASprojectfile
2200	)[0]+self.extension)
2201
2202	def askSaveFile(self):
2203	'''Ask the user to supply a file name
2204
2205	:returns: a file name (str) or None if Cancel is pressed
2206	'''
2207
2208	pth = G2G.GetExportPath(self.G2frame)
2209	defnam = os.path.splitext(
2210	os.path.split(self.G2frame.GSASprojectfile)[1]
2211	)[0]+self.extension
2212	dlg = wx.FileDialog(
2213	self.G2frame, 'Input name for file to write', pth, defnam,
2214	self.longFormatName+' ('+self.extension+')\|'+self.extension,
2215	wx.FD_SAVE\|wx.FD_OVERWRITE_PROMPT)
2216	dlg.CenterOnParent()
2217	try:
2218	if dlg.ShowModal() == wx.ID_OK:
2219	filename = dlg.GetPath()
2220	self.G2frame.LastExportDir = os.path.split(filename)[0]
2221	filename = os.path.splitext(filename)[0]+self.extension # make sure extension is correct
2222	else:
2223	filename = None
2224	finally:
2225	dlg.Destroy()
2226	return filename
2227
2228	def askSaveDirectory(self):
2229	'''Ask the user to supply a directory name. Path name is used as the
2230	starting point for the next export path search.
2231
2232	:returns: a directory name (str) or None if Cancel is pressed
2233	'''
2234	pth = G2G.GetExportPath(self.G2frame)
2235	dlg = wx.DirDialog(
2236	self.G2frame, 'Input directory where file(s) will be written', pth,
2237	wx.DD_DEFAULT_STYLE)
2238	dlg.CenterOnParent()
2239	try:
2240	if dlg.ShowModal() == wx.ID_OK:
2241	filename = dlg.GetPath()
2242	self.G2frame.LastExportDir = filename
2243	else:
2244	filename = None
2245	finally:
2246	dlg.Destroy()
2247	return filename
2248
2249	# Tools for file writing.
2250	def OpenFile(self,fil=None,mode='w'):
2251	'''Open the output file
2252
2253	:param str fil: The name of the file to open. If None (default)
2254	the name defaults to self.dirname + self.filename.
2255	If an extension is supplied, it is not overridded,
2256	but if not, the default extension is used.
2257	:returns: the file object opened by the routine which is also
2258	saved as self.fp
2259	'''
2260	if mode == 'd': # debug mode
2261	self.fullpath = '(stdout)'
2262	self.fp = sys.stdout
2263	return
2264	if not fil:
2265	if not os.path.splitext(self.filename)[1]:
2266	self.filename += self.extension
2267	fil = os.path.join(self.dirname,self.filename)
2268	self.fullpath = os.path.abspath(fil)
2269	self.fp = open(self.fullpath,mode)
2270	return self.fp
2271
2272	def Write(self,line):
2273	'''write a line of output, attaching a line-end character
2274
2275	:param str line: the text to be written.
2276	'''
2277	self.fp.write(line+'\n')
2278
2279	def CloseFile(self,fp=None):
2280	'''Close a file opened in OpenFile
2281
2282	:param file fp: the file object to be closed. If None (default)
2283	file object self.fp is closed.
2284	'''
2285	if self.fp == sys.stdout: return # debug mode
2286	if fp is None:
2287	fp = self.fp
2288	self.fp = None
2289	fp.close()
2290
2291	def SetSeqRef(self,data,hist):
2292	'''Set the exporter to retrieve results from a sequential refinement
2293	rather than the main tree
2294	'''
2295	self.SeqRefdata = data
2296	self.SeqRefhist = hist
2297	data_name = data[hist]
2298	for i,val in zip(data_name['varyList'],data_name['sig']):
2299	self.sigDict[i] = val
2300	self.sigDict[striphist(i)] = val
2301	for i in data_name['parmDict']:
2302	self.parmDict[striphist(i)] = data_name['parmDict'][i]
2303	self.parmDict[i] = data_name['parmDict'][i]
2304	# zero out the dA[xyz] terms, they would only bring confusion
2305	key = i.split(':')
2306	if len(key) < 3: continue
2307	if key[2].startswith('dA'):
2308	self.parmDict[i] = 0.0
2309	for i,(val,sig) in data_name.get('depParmDict',{}).iteritems():
2310	self.parmDict[i] = val
2311	self.sigDict[i] = sig
2312	#GSASIIpath.IPyBreak()
2313
2314	# Tools to pull information out of the data arrays
2315	def GetCell(self,phasenam):
2316	"""Gets the unit cell parameters and their s.u.'s for a selected phase
2317
2318	:param str phasenam: the name for the selected phase
2319	:returns: `cellList,cellSig` where each is a 7 element list corresponding
2320	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
2321	cell values and `cellSig` has their uncertainties.
2322	"""
2323	if self.SeqRefdata and self.SeqRefhist:
2324	return self.GetSeqCell(phasenam,self.SeqRefdata[self.SeqRefhist])
2325	phasedict = self.Phases[phasenam] # pointer to current phase info
2326	try:
2327	pfx = str(phasedict['pId'])+'::'
2328	A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
2329	cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A,
2330	self.OverallParms['Covariance']) # returns 7 vals, includes sigVol
2331	cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
2332	return cellList,cellSig
2333	except KeyError:
2334	cell = phasedict['General']['Cell'][1:]
2335	return cell,7*[0]
2336
2337	def GetSeqCell(self,phasenam,data_name):
2338	"""Gets the unit cell parameters and their s.u.'s for a selected phase
2339	and histogram in a sequential fit
2340
2341	:param str phasenam: the name for the selected phase
2342	:param dict data_name: the sequential refinement parameters for the selected histogram
2343	:returns: `cellList,cellSig` where each is a 7 element list corresponding
2344	to a, b, c, alpha, beta, gamma, volume where `cellList` has the
2345	cell values and `cellSig` has their uncertainties.
2346	"""
2347	phasedict = self.Phases[phasenam]
2348	SGdata = phasedict['General']['SGData']
2349	pId = phasedict['pId']
2350	RecpCellTerms = G2lat.cell2A(phasedict['General']['Cell'][1:7])
2351	ESDlookup = {}
2352	Dlookup = {}
2353	varied = [striphist(i) for i in data_name['varyList']]
2354	for item,val in data_name['newCellDict'].iteritems():
2355	if item in varied:
2356	ESDlookup[val[0]] = item
2357	Dlookup[item] = val[0]
2358	A = RecpCellTerms[:]
2359	for i in range(6):
2360	var = str(pId)+'::A'+str(i)
2361	if var in ESDlookup:
2362	A[i] = data_name['newCellDict'][ESDlookup[var]][1] # override with refined value
2363	cellDict = dict(zip([str(pId)+'::A'+str(i) for i in range(6)],A))
2364	zeroDict = {i:0.0 for i in cellDict}
2365	A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata,cellDict,zeroDict)
2366	covData = {
2367	'varyList': [Dlookup.get(striphist(v),v) for v in data_name['varyList']],
2368	'covMatrix': data_name['covMatrix']
2369	}
2370	return list(G2lat.A2cell(A)) + [G2lat.calc_V(A)], G2stIO.getCellEsd(str(pId)+'::',SGdata,A,covData)
2371
2372	def GetAtoms(self,phasenam):
2373	"""Gets the atoms associated with a phase. Can be used with standard
2374	or macromolecular phases
2375
2376	:param str phasenam: the name for the selected phase
2377	:returns: a list of items for eac atom where each item is a list containing:
2378	label, typ, mult, xyz, and td, where
2379
2380	* label and typ are the atom label and the scattering factor type (str)
2381	* mult is the site multiplicity (int)
2382	* xyz is contains a list with four pairs of numbers:
2383	x, y, z and fractional occupancy and
2384	their standard uncertainty (or a negative value)
2385	* td is contains a list with either one or six pairs of numbers:
2386	if one number it is U\ :sub:`iso` and with six numbers it is
2387	U\ :sub:`11`, U\ :sub:`22`, U\ :sub:`33`, U\ :sub:`12`, U\ :sub:`13` & U\ :sub:`23`
2388	paired with their standard uncertainty (or a negative value)
2389	"""
2390	phasedict = self.Phases[phasenam] # pointer to current phase info
2391	cx,ct,cs,cia = phasedict['General']['AtomPtrs']
2392	cfrac = cx+3
2393	fpfx = str(phasedict['pId'])+'::Afrac:'
2394	atomslist = []
2395	for i,at in enumerate(phasedict['Atoms']):
2396	if phasedict['General']['Type'] == 'macromolecular':
2397	label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
2398	else:
2399	label = at[ct-1]
2400	fval = self.parmDict.get(fpfx+str(i),at[cfrac])
2401	fsig = self.sigDict.get(fpfx+str(i),-0.009)
2402	mult = at[cs+1]
2403	typ = at[ct]
2404	xyz = []
2405	for j,v in enumerate(('x','y','z')):
2406	val = at[cx+j]
2407	pfx = str(phasedict['pId']) + '::A' + v + ':' + str(i)
2408	val = self.parmDict.get(pfx, val)
2409	dpfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
2410	sig = self.sigDict.get(dpfx,-0.000009)
2411	xyz.append((val,sig))
2412	xyz.append((fval,fsig))
2413	td = []
2414	if at[cia] == 'I':
2415	pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
2416	val = self.parmDict.get(pfx,at[cia+1])
2417	sig = self.sigDict.get(pfx,-0.0009)
2418	td.append((val,sig))
2419	else:
2420	for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
2421	pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
2422	val = self.parmDict.get(pfx,at[cia+2+i])
2423	sig = self.sigDict.get(pfx,-0.0009)
2424	td.append((val,sig))
2425	atomslist.append((label,typ,mult,xyz,td))
2426	return atomslist
2427	######################################################################
2428	def ExportPowderList(G2frame):
2429	'''Returns a list of extensions supported by :func:`GSASIIIO:ExportPowder`
2430	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
2431
2432	:param wx.Frame G2frame: the GSAS-II main data tree window
2433	'''
2434	extList = []
2435	for obj in G2frame.exporterlist:
2436	if 'powder' in obj.exporttype:
2437	try:
2438	obj.Writer
2439	extList.append(obj.extension)
2440	except AttributeError:
2441	pass
2442	return extList
2443
2444	def ExportPowder(G2frame,TreeName,fileroot,extension):
2445	'''Writes a single powder histogram using the Export routines.
2446	This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
2447
2448	:param wx.Frame G2frame: the GSAS-II main data tree window
2449	:param str TreeName: the name of the histogram (PWDR ...) in the data tree
2450	:param str fileroot: name for file to be written, extension ignored
2451	:param str extension: extension for file to be written (start with '.'). Must
2452	match a powder export routine that has a Writer object.
2453	'''
2454	filename = os.path.abspath(os.path.splitext(fileroot)[0]+extension)
2455	for obj in G2frame.exporterlist:
2456	if obj.extension == extension and 'powder' in obj.exporttype:
2457	obj.currentExportType = 'powder'
2458	obj.InitExport(None)
2459	obj.loadTree() # load all histograms in tree into dicts
2460	if TreeName not in obj.Histograms:
2461	raise Exception('Histogram not found: '+str(TreeName))
2462	try:
2463	obj.Writer
2464	except AttributeError:
2465	continue
2466	try:
2467	obj.Writer(TreeName,filename)
2468	return
2469	except Exception,err:
2470	print('Export Routine for '+extension+' failed.')
2471	print err
2472	else:
2473	print('No Export routine supports extension '+extension)
2474
2475	def ExportSequential(G2frame,data,obj,exporttype):
2476	'''
2477	Used to export from every phase/dataset in a sequential refinement using
2478	a .Writer method for either projects or phases. Prompts to select histograms
2479	and for phase exports, which phase(s).
2480
2481	:param wx.Frame G2frame: the GSAS-II main data tree window
2482	:param dict data: the sequential refinement data object
2483	:param str exporttype: indicates the type of export ('project' or 'phase')
2484	'''
2485	if len(data['histNames']) == 0:
2486	G2G.G2MessageBox(G2frame,'There are no sequential histograms','Warning')
2487	obj.InitExport(None)
2488	obj.loadTree()
2489	obj.loadParmDict()
2490	if len(data['histNames']) == 1:
2491	histlist = data['histNames']
2492	else:
2493	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select histograms to export from list',
2494	'Select histograms',data['histNames'])
2495	if dlg.ShowModal() == wx.ID_OK:
2496	histlist = [data['histNames'][l] for l in dlg.GetSelections()]
2497	dlg.Destroy()
2498	else:
2499	dlg.Destroy()
2500	return
2501	if exporttype == 'Phase':
2502	phaselist = obj.Phases.keys()
2503	if len(obj.Phases) == 0:
2504	G2G.G2MessageBox(G2frame,'There are no phases in sequential ref.','Warning')
2505	return
2506	elif len(obj.Phases) > 1:
2507	dlg = G2G.G2MultiChoiceDialog(G2frame,'Select phases to export from list',
2508	'Select phases', phaselist)
2509	if dlg.ShowModal() == wx.ID_OK:
2510	phaselist = [phaselist[l] for l in dlg.GetSelections()]
2511	dlg.Destroy()
2512	else:
2513	dlg.Destroy()
2514	return
2515	filename = obj.askSaveFile()
2516	if not filename: return True
2517	obj.dirname,obj.filename = os.path.split(filename)
2518	print('Writing output to file '+str(obj.filename)+"...")
2519	mode = 'w'
2520	for p in phaselist:
2521	for h in histlist:
2522	obj.SetSeqRef(data,h)
2523	#GSASIIpath.IPyBreak()
2524	obj.Writer(h,phasenam=p,mode=mode)
2525	mode = 'a'
2526	print('...done')
2527	elif exporttype == 'Project':
2528	filename = obj.askSaveFile()
2529	if not filename: return True
2530	obj.dirname,obj.filename = os.path.split(filename)
2531	print('Writing output to file '+str(obj.filename)+"...")
2532	mode = 'w'
2533	for h in histlist:
2534	obj.SetSeqRef(data,h)
2535	obj.Writer(h,mode=mode)
2536	print('\t'+str(h)+' written')
2537	mode = 'a'
2538	print('...done')
2539
2540	def ReadDIFFaX(DIFFaXfile):
2541	print 'read ',DIFFaXfile
2542	Layer = {'Laue':'-1','Cell':[False,1.,1.,1.,90.,90.,90,1.],'Width':[[10.,10.],[False,False]],
2543	'Layers':[],'Stacking':[],'Transitions':[],'Toler':0.01,'AtInfo':{}}
2544	df = open(DIFFaXfile,'r')
2545	lines = df.readlines()
2546	df.close()
2547	struct = False
2548	Struct = []
2549	stack = False
2550	Stack = []
2551	trans = False
2552	Trans = []
2553	for diff in lines:
2554	diff = diff[:-1].lower()
2555	if '!' in diff:
2556	continue
2557	while '}' in diff: #strip comments
2558	iB = diff.index('{')
2559	iF = diff.index('}')+1
2560	if iB:
2561	diff = diff[:iB]
2562	else:
2563	diff = diff[iF:]
2564	if not diff:
2565	continue
2566	if diff.strip() == 'instrumental':
2567	continue
2568	if diff.strip() == 'structural':
2569	struct = True
2570	continue
2571	elif diff.strip() == 'stacking':
2572	struct = False
2573	stack = True
2574	continue
2575	elif diff.strip() == 'transitions':
2576	stack = False
2577	trans = True
2578	continue
2579	diff = diff.strip()
2580	if struct:
2581	if diff:
2582	Struct.append(diff)
2583	elif stack:
2584	if diff:
2585	Stack.append(diff)
2586	elif trans:
2587	if diff:
2588	Trans.append(diff)
2589
2590	#STRUCTURE records
2591	laueRec = Struct[1].split()
2592	Layer['Laue'] = laueRec[0]
2593	if Layer['Laue'] == 'unknown' and len(laueRec) > 1:
2594	Layer['Toler'] = float(laueRec[1]) #tolerance for 'unknown'?
2595	if Layer['Laue'] == '2/m(1)': Layer['Laue'] = '2/m(c)'
2596	if Layer['Laue'] == '2/m(2)': Layer['Laue'] = '2/m(ab)'
2597	cell = Struct[0].split()
2598	Layer['Cell'] = [False,float(cell[0]),float(cell[1]),float(cell[2]),90.,90.,float(cell[3]),1.0]
2599	nLayers = int(Struct[2])
2600	N = 3
2601	if 'layer' not in Struct[3]:
2602	N = 4
2603	if Struct[3] != 'infinite':
2604	width = Struct[3].split()
2605	Layer['Width'][0] = [float(width[0]),float(width[1])]
2606	for nL in range(nLayers):
2607	if '=' in Struct[N]:
2608	name = Struct[N].split('=')
2609	sameas = int(name[1])-1
2610	Layer['Layers'].append({'Name':name[0],'SameAs':Layer['Layers'][sameas]['Name'],'Symm':'None','Atoms':[]})
2611	N += 1
2612	continue
2613	Symm = 'None'
2614	if 'centro' in Struct[N+1]: Symm = '-1'
2615	Layer['Layers'].append({'Name':Struct[N],'SameAs':'','Symm':Symm,'Atoms':[]})
2616	N += 2
2617	while 'layer' not in Struct[N]:
2618	atom = Struct[N][4:].split()
2619	atomType = G2el.FixValence(Struct[N][:4].replace(' ','').strip().capitalize())
2620	if atomType not in Layer['AtInfo']:
2621	Layer['AtInfo'][atomType] = G2el.GetAtomInfo(atomType)
2622	atomName = '%s(%s)'%(atomType,atom[0])
2623	newVals = []
2624	for val in atom[1:6]:
2625	if '/' in val:
2626	newVals.append(eval(val+'.'))
2627	else:
2628	newVals.append(float(val))
2629	atomRec = [atomName,atomType,newVals[0],newVals[1],newVals[2],newVals[4],newVals[3]/78.9568]
2630	Layer['Layers'][-1]['Atoms'].append(atomRec)
2631	N += 1
2632	if N > len(Struct)-1:
2633	break
2634	#TRANSITIONS records
2635	transArray = []
2636	N = 0
2637	for i in range(nLayers):
2638	transArray.append([])
2639	for j in range(nLayers):
2640	vals = Trans[N].split()
2641	newVals = []
2642	for val in vals[:4]:
2643	if '/' in val:
2644	newVals.append(eval(val+'.'))
2645	else:
2646	newVals.append(float(val))
2647	transArray[-1].append(newVals+['',False])
2648	N += 1
2649	Layer['Transitions'] = transArray
2650	#STACKING records
2651	Layer['Stacking'] = [Stack[0],'']
2652	if Stack[0] == 'recursive':
2653	Layer['Stacking'][1] = Stack[1]
2654	elif Stack[0] == 'explicit':
2655	if Stack[1] == 'random':
2656	Layer['Stacking'][1] = Stack[1]
2657	else:
2658	Layer['Stacking'][1] = 'list'
2659	Layer['Stacking'].append('')
2660	for stack in Stack[2:]:
2661	Layer['Stacking'][2] += ' '+stack
2662	return Layer
2663
2664	def ReadCIF(URLorFile):
2665	'''Open a CIF, which may be specified as a file name or as a URL using PyCifRW
2666	(from James Hester).
2667	The open routine gets confused with DOS names that begin with a letter and colon
2668	"C:\dir\" so this routine will try to open the passed name as a file and if that
2669	fails, try it as a URL
2670
2671	:param str URLorFile: string containing a URL or a file name. Code will try first
2672	to open it as a file and then as a URL.
2673
2674	:returns: a PyCifRW CIF object.
2675	'''
2676	import CifFile as cif # PyCifRW from James Hester
2677
2678	# alternate approach:
2679	#import urllib
2680	#ciffile = 'file:'+urllib.pathname2url(filename)
2681
2682	try:
2683	fp = open(URLorFile,'r')
2684	cf = cif.ReadCif(fp)
2685	fp.close()
2686	return cf
2687	except IOError:
2688	return cif.ReadCif(URLorFile)
2689
2690	if __name__ == '__main__':
2691	import GSASII
2692	application = GSASII.GSASIImain(0)
2693	G2frame = application.main
2694	#app = wx.PySimpleApp()
2695	#G2frame = wx.Frame(None) # create a frame
2696	#frm.Show(True)
2697	#filename = '/tmp/notzip.zip'
2698	#filename = '/tmp/all.zip'
2699	#filename = '/tmp/11bmb_7652.zip'
2700
2701	#selection=None, confirmoverwrite=True, parent=None
2702	#print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2703	#print ExtractFileFromZip(filename,multipleselect=True)
2704	# #confirmread=False, confirmoverwrite=False)
2705
2706	# choicelist=[ ('a','b','c'),
2707	# ('test1','test2'),('no choice',)]
2708	# titles = [ 'a, b or c', 'tests', 'No option here']
2709	# dlg = MultipleChoicesDialog(
2710	# choicelist,titles,
2711	# parent=frm)
2712	# if dlg.ShowModal() == wx.ID_OK:
2713	# print 'Got OK'
2714	imagefile = '/tmp/NDC5_00237_3.ge3'
2715	Comments, Data, Npix, Image = GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None)
2716
2717	print("\n\nResults loaded to Comments, Data, Npix and Image\n\n")
2718
2719	GSASIIpath.IPyBreak_base()

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